Comparative Genomic and Transcriptomic Analyses of Xanthomonas Citri Subsp. Citri and Related Species Provides Insights ...

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Comparative Genomic and Transcriptomic Analyses of Xanthomonas Citri Subsp. Citri and Related Species Provides Insights into Virulence and Host-Specificity
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Jalan, Neha U
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Degree:
Doctorate ( Ph.D.)
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University of Florida
Degree Disciplines:
Microbiology and Cell Science
Committee Chair:
Wang, Nian
Committee Members:
Lorca, Graciela Liliana
Graham, James H
Romeo, Tony
Jones, Jeffrey B

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genomic -- xanthomonas
Microbiology and Cell Science -- Dissertations, Academic -- UF
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Microbiology and Cell Science thesis, Ph.D.
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theses   ( marcgt )
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Abstract:
Citrus canker caused by Xanthomonas citri subsp. citri (Xcc) has significant impact on citrus production worldwide. X. axonopodis pv. citrumelo (Xacm) is another citrus pathogen causing citrus bacterial spot disease which is geographically restricted within the state of Florida. Xcc is distinguished into different strains primarily by host range. The Asiatic strain (A) has a wide host range and is most virulent, whereas Wellington (Aw) strain has host range restricted to Mexican lime and alemow. We hypothesized that gene expression along with gene content, contributes to the difference in virulence and host range of closely related strains. We conducted comparative genomic analyses to study Xacm, A and Aw strains and transcriptomic analyses for A and Aw strains. Illumina, 454 sequencing and optical mapping were used to obtain complete genome sequences of Xacm strain F1 (4.9 Mb chromosome, no plasmid) and X. citri subsp. citri strain Aw12879 (Xcaw) (5.3 Mb chromosome and two plasmids pXcaw19 and pXcaw58). Comparative genomic analysis of Xacm to A strain showed differences in T3SS effectors, T4SS, LPS and others. In addition to pthA, putative effectors such as xopE3, xopAI and hrpW were absent in Xacm, which might be responsible for reduced virulence of this pathogen compared to XccA. We also identified unique effectors like xopC2 and xopW in Xacm that may be related to the restricted host range. Whole genome comparison of Aw to A strain, disclosed numerous genome rearrangements and insertion/deletion regions indicating genome plasticity. Protein blast revealed multiple unique genes in Aw including type III secretion system effectors xopAF and xopAG. Comparative genomic analysis showed various changes in genes related to LPS and T4SS. Furthermore, RNA-seq was used to compare expression profile of Xcaw and XccA strains in nutrient rich (NB) and plant intercellular space mimicking (XVM2) conditions using Illumina sequencing. Up-regulation of effector genes in Xcaw as compared to XccA might also contribute to its limited host range. The overexpression of genes involved in plant cell wall degradation, attachment, reactive oxygen species scavenging, nutrient transportation in XccA might contribute to its expanding of host range. Our data suggest that both gene content and gene expression contribute to difference in virulence and host-specificities of different strains.
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by Neha U Jalan.
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Thesis (Ph.D.)--University of Florida, 2012.
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Adviser: Wang, Nian.
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1 COMPARATIVE GENOMIC AND TRANSCRIPTOMIC ANALYSES OF Xanthomonas citri subsp. citri AND RELATED SPECIES PROVIDES INSIGHTS INTO VIRULENCE AND HOST SPECIFICITY By NEHA JALAN A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF T HE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2012

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2 2012 Neha Jalan

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3 To my wonderful husband Deepak and our families for the ir unconditional love and support in fulfilling my dreams

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4 ACKNOWLEDGMENTS Though only my name appears on the cover of this dissertation, many people have contributed to it. I owe my gratitude to all those people who have made this dissertation possible and because of whom my graduate experience has been one that I will cherish forever. I would like to express my heartfelt thanks to Dr. Nian Wang, my committee chair for his constant guidance and support. I am grateful to him for the opportunity of doing this research in his lab and for his encouragement throughout the past few years. I would also like to extend my gratitude to the members of my committee, Drs. James Graham, Jeffrey Jones, Graciela Lorca and Tony Romeo for their valuable suggestions and pr actical advice. I would like to thank my current and former lab mates for whom I have great regard and pleasure of working with: Pankaj Trivedi, Yinping Guo, Jeong Soon Kim, Aswathy Sreedharan, Qing Yan, Jinyun Li, Nagaraju Akula, Valentine Aritua, Xiufan g Hu, Hongge Jia, Xioabao Ying, Jihua Wang, Maxuel Andrade, Yunzeng Zhang, Samiksha and Xiaofeng Zhou. I am also thankful to the lab staff of Vladimir Kolbasov, Qiongying Liu, Brian Buzzie and Lin Yang who managed all the everyday work in lab and greenhous e immaculately. I owe my sincere and earnest thanks to Drs. Pankaj Trivedi and Yinping Guo for their friendship, support and help in lab and in life. I am grateful to my friends here in Lake Alfred, Gainesville, Tampa and India for their support and lively company during my graduate years. It is a great pleasure to thank everyone at the Citrus Research and Education Center, Department of Microbiology and Cell Science, Department of Plant Pathology and ICBR at the University of Florida. I would like to than k Dr. Jeffrey Jones for the

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5 opportunity to learn in his lab and for providing us with a mutant strains used in this study and Mr. Gerald Minsavage for teaching me to generate deletion mutants. I am truly indebted and grateful to Drs. Valentine Aritua, Diby endu Kumar and Fahong Yu for their help with closing of the genomes and FgeneSB annotation. I want to thank Dr. K. T. Shanmugam for introducing me to optical mapping technique A special mention to the library staff at CREC who were always helpful with all my last minute requests. Most importantly, none of this would have been possible without the love and patience of my family. My parents Savita and Umashanker Fatehchandka and brother Nikhil have been a constant source of love, concern and strength all the se years. I warmly appreciate the encouragement and understanding of my extended family. Finally, I acknowledge my loving husband, Deepak, who has been there with all his love; encouragement and prodding despite me wanting to give up and throw in the towel at times. He stuck with me through all times, helping me keep sane on the way to achieving my dream. Thank you all for making this possible.

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6 TABLE OF CONTENTS page ACKNOWLEDGMENTS ................................ ................................ ................................ .. 4 LIST OF TABLES ................................ ................................ ................................ ............ 8 LIST OF FIGURES ................................ ................................ ................................ ........ 10 LIST OF ABBREVIATIONS ................................ ................................ ........................... 12 ABSTRACT ................................ ................................ ................................ ................... 13 CHAPTER 1 LITERATURE REVIEW ................................ ................................ .......................... 15 Introduction ................................ ................................ ................................ ............. 15 Citrus Canker ................................ ................................ ................................ .......... 15 Management Strategies ................................ ................................ .......................... 17 Host Range Variation of Citrus Canker causing Xanthomonas spp. ....................... 18 Virulence Related Mech anisms Used by Xcc ................................ ......................... 21 Project Goals and Objectives ................................ ................................ .................. 30 2 COMPARATIVE GENOMIC ANALYSIS OF Xanthomonas axonopodis pv citrumelo F1 CAUSING CITRUS BACTERIAL SPOT AND RELATED STRAINS .. 32 Introduction ................................ ................................ ................................ ............. 32 Materials and Methods ................................ ................................ ............................ 35 Bacterial Strain and DNA Sequencing ................................ .............................. 35 Gap Closure and Assembly Validation ................................ ............................. 36 Annotation and Curat ion ................................ ................................ ................... 36 Phylogenetic Analysis ................................ ................................ ...................... 37 Comparative Analysis ................................ ................................ ....................... 37 Addition al Sequence Analysis ................................ ................................ .......... 38 Pectate Lyase Assay ................................ ................................ ........................ 38 Database Submission ................................ ................................ ...................... 39 Results ................................ ................................ ................................ .................... 39 Sequencing and General Features of the Genome ................................ .......... 39 Phylogenetic Relatedness of Xacm to Other Xanthomonads ........................... 41 Comparison of Chromosome Organization of Xacm To XccA and Xcv ............ 42 Horizontal Gene Transfer (HGT) and Genome Plasticity ................................ 43 Comparison of Proteins Encoded by Xacm to XccA and Xcv ........................... 44 Type Three Secretion Gene (T3SS) Clusters ................................ ................... 45 Repertoire of T3SS Effectors of Xacm in Comparison to XccA and Xcv .......... 46 Other Secretion Systems Associated with Virulence ................................ ........ 51 Type 1 Secretion System (T1SS) ................................ ............................... 51 Type 2 Secretion System (T2SS) ................................ ............................... 52

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7 Type 4 Secretion System (T4SS) ................................ ............................... 53 Type 5 Secretion System (T5SS) ................................ ............................... 54 Type 6 Secretion System (T6SS) ................................ ............................... 54 Bacterial Surface Structures ................................ ................................ ............. 55 Lipopolysaccharides (LPS) ................................ ................................ ........ 55 Extracellular Polysaccharides ................................ ................................ .... 56 Flagella ................................ ................................ ................................ ...... 57 Regulation of Pathogenicity Factors (Rpf) Cluster ................................ ............ 58 Other Strain Specific Genes that Might Contribute to the Distinct Virulence of XccA and Xacm on Citrus ................................ ................................ ......... 59 Conclusion ................................ ................................ ................................ .............. 60 3 GENE CONTENT OR GENE EXPRESSION, WHICH DETERMINES THE DIFFERENCE IN HOST RANGE AND VIRULENCE OF STRAINS OF Xanthomonas citri subsp citri ? ................................ ................................ ............... 82 Introduction ................................ ................................ ................................ ............. 82 Material s And Methods ................................ ................................ ........................... 86 Bacterial Strain and DNA Sequencing ................................ .............................. 86 Data Assembly and Annotation ................................ ................................ ........ 86 Phylogenetic and Comparative Analysis ................................ .......................... 87 Preparation of RNA Samples for Transcriptome Analysis ................................ 88 mRNA E nrichment and Library Construction ................................ .................... 89 Illumina Sequencing and Alignment ................................ ................................ 89 Differential Gene Expression Analysis ................................ ............................. 90 Quantitative Real Time One Step RT PCR ................................ ...................... 90 Pathogenicity Assay ................................ ................................ ......................... 91 Generation of the xopAF Mutant and xopAF, avrGf1 Double Mutant ............... 91 Growth Assay in planta ................................ ................................ .................... 92 Pectate Lyase and Proteinase Assay ................................ ............................... 93 Data Access ................................ ................................ ................................ ..... 93 Results ................................ ................................ ................................ .................... 93 Genome Sequencing of Xcaw ................................ ................................ .......... 93 Chromosome Organization and Genome Plasticity ................................ .......... 95 Pathogenicity and Growth Assays ................................ ................................ .... 97 Transcriptome Analysis of Xcaw and XccA Under Nutrient Rich (NB) and Plant Intercellular Space Mimicing (XVM2) Conditions ................................ 99 Discussion ................................ ................................ ................................ ............ 103 4 SUMMARY AND CONCLUSION ................................ ................................ .......... 188 APPENDIX : MEDIA COMPOSITION ................................ ................................ .......... 191 LIST OF REFERENCES ................................ ................................ ............................. 192 BIOGRAPHICAL SKETCH ................................ ................................ .......................... 211

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8 LIST OF TABLES Table page 2 1 Overview of sequence data for Xanthomonas axonopodis pv. citr umelo str. F1 ................................ ................................ ................................ ....................... 64 2 2 General features of X. axonopodis pv. citrumelo str. F1 genome ....................... 64 2 3 Functional classification of annota ted sequences in genome of Xanthomonas axonopodis pv. citrumelo F1 ................................ ................................ ............... 65 2 4 Coordinates, sizes and G+C contents of the segmented domains of X. axonopodis pv. citrumelo str. F1 genome determined by GC Profile.. ................ 66 2 5 Effector repertoire of X. axonopodis pv. citrumelo str. F1, X. citri subsp. citri str. 306 and X. campestris pv. vesicatoria str. 85 10 ................................ .......... 67 2 6 Putative Type 2 Secretion System Substrates in X. axonopodis pv. citrumelo str. F1, X. citri sbsp. citri str. 306 and X. campestris pv. vesicatoria str. 85 10 ... 70 2 7 Putative Type 6 Secretion System clusters in X. axonopodis pv citrumelo str. F1, X. citri subsp. citri str. 306 and X. campestris pv. vesicatoria str. 85 10 ....... 71 3 1 Overview of sequence data for the genome of Xanthomonas citri subsp. citri A w 12879 ................................ ................................ ................................ .......... 114 3 2 Primers used in this study ................................ ................................ ................ 114 3 3 General features of Xanthomonas citri subsp. citri A w 12879 genome ............. 115 3 4 Effector repertoire of X. citri subsp. citri A w 12879 (Xcaw), X. citri subsp. citri str. 306 (XccA), X. fuscans subsp. auran tifolii str. ICPB 11122 (XauB) and X. fuscans subsp. aurantifolii str. ICPB 10535 (XauC) ................................ .......... 116 3 5 Genes unique to Xcaw clustered in groups ................................ ...................... 119 3 6 Summary of cDNA samples sequenced for RNA Seq ................................ ...... 120 3 7 Degree of agreement between biological replicates for RNA Seq .................... 121 3 8 Genes differentially expressed in X. citri subsp. citri str. 306 (A) in XVM2 medium (hrp inducing) as compared to NB (nutrient rich condition). ................ 122 3 9 Genes differentially expressed in X. citri subsp. citri str. A w 12879 (W) in XVM2 medium (hrp inducing) as compared to NB (nutrient rich condition). ..... 130 3 10 Genes differentially expressed between strains X. citr i subsp. citri str. 306 (A) and X. citri subsp. citri str. A w 12879 (W) in NB (nutrient rich) medium. ........... 141

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9 3 11 Genes differentially expressed between strains X. citri subsp. citri str. 306 (A ) and X. citri subsp. citri str. A w 12879 (W) in XVM2 (hrp inducing) medium. ...... 157 3 12 Differentially expressed genes shared between strains X. citri subsp. citri str. 306 (A) and X. citri sub sp. citri str. A w 12879 (W) in both NB (nutrient rich) medium and XVM2 (hrp inducing) medium. ................................ ..................... 169 3 13 Differential expression of effctor genes shared between strains X. citri subsp. citri st r. 306 (A) and X. citri subsp. citri str. A w 12879 (W) in both NB (nutrient rich) medium and XVM2 (hrp inducing) medium. ................................ .............. 174

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10 LIST OF FIGURES Figure page 2 1 Alignments between the whole genome optical maps and the in silico genome sequence assemblies at various stages of the project.. ........................ 72 2 2 Circular representation of Xanthonomas axo nopodis pv. citrumelo F1. ............ 73 2 3 Maximum likelihood tree of the genome of Xanthonomas axonopodis pv. citrumelo F1 showing the relationship to other fully sequenced Xathomonads and related s pecies.. ................................ ................................ .......................... 74 2 4 MAUVE alignment of the genome sequences of the genome of X. citri subsp. citri str. 306, X. axonopodis pv. citrumelo str. F1 and X. campestris pv. vesicatoria str. 85 10. ................................ ................................ ......................... 75 2 5 GC profile and GC content of XACM genome ................................ .................... 76 2 6 Venn diagram representing the pan genome of X. axonopodis pv. citrumelo F1 (XACM), X. campestris pv. vesicatoria str. 85 10 (XCV) and X. citri subsp. citri str. 306 (XCCA).. ................................ ................................ .......................... 77 2 7 Comparison of the hrp gene cluster in the genomes of X. citri subsp. citri str. 306, X. axonopodis pv. citrumelo str. F1 and X. campestris pv. vesicatoria str. 85 10.. ................................ ................................ ................................ .......... 78 2 8 Comparison of the xps and xcs gene cluster in the genomes of X. citri subsp. citri str. 306, X. axono podis pv. citrumelo str. F1 and X. campestris pv. vesicatoria str. 85 10. ................................ ................................ ......................... 78 2 9 Comparison of the pecate lyase production by X. citri subsp. citri str. 306, X. axonopodis pv. citrumelo str. F1 and X. campestris pv. vesicatoria str. 85 10.. 79 2 10 Comparison of the T4SS gene clusters in the genomes of X. citri subsp. citri str. 306, X. axonopodis pv. citrumelo str. F1 and X. cam pestris pv. vesicatoria str. 85 10.. ................................ ................................ ........................ 79 2 11 Relative organization of the LPS gene cluster in the genomes of X. axonopodis pv. citrumelo str. F1, X. citri subsp. citri str. 306 and X. campest ris pv. vesicatoria str. 85 10.. ................................ ................................ 80 2 12 Comparison of the flagella gene clusters in the genomes of X. citri subsp. citri str. 306, X. axonopodis pv. citrumelo str. F1 and X. campestris pv. v esicatoria str. 85 10. ................................ ................................ ......................... 81 3 1 Alignments between the whole genome optical maps and the in silico genome sequence assemblies at various stages of the project.. ...................... 175

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11 3 2 Circular representation of X. citri subsp. citri str. A w 12879 genome and plasmids pXcaw19 & pXcaw58. ................................ ................................ ........ 176 3 3 Maximum likelihood tree of the genome of Xanthonomas citri subsp. citri A w 12879 showing the relationship to other fully sequenced Xathomonads (except XauB and XauC) and related species. ................................ ................. 177 3 4 MAUVE alignment of the genome sequen ces of X. citri subsp. citri str. 306 and X. citri subsp. citri A w 12879. ................................ ................................ ..... 178 3 5 Comparison of the T4SS gene clusters of X. citri subsp. citri str. 306 (A), and X. citri subsp. citri str. A w ................................ ................................ ................. 178 3 6 Prediction and comparison of the TAL effector codes encoded by pthA genes of X. citri subsp. citri str. 306, and X. citri subsp. citri str. A w ............................ 179 3 7 Inoculation by pressure infiltration of X. citri subsp. citri str. 306, X. citri subsp. citri str. A w and X. citri subsp. citri str. A w avrGf1 deletion mutant on young Grapefruit, Valencia and Hamlin leaves.. ................................ ............... 180 3 8 Neighbor joining tree of XopAF protein sequences.. ................................ ........ 181 3 9 Comparison of the LPS gene clusters of X. citri subsp. citri str. 306, X. citri subsp. citri A w 12879 and X. oryzae pv. oryzicola str. BLS256. ........................ 182 3 10 Growth of X. citri subsp. citri str. 306 (blue), and X. citri subsp. citri str. A w 12879 (red) under NB and X VM2 conditions. ................................ ................... 183 3 11 Principal component analysis of DEG of X. citri subsp. citri str. 306 (A), and X. citri subsp. citri str. A w 12879 (Aw) under NB and XVM2 conditions. ........... 183 3 12 RNA seq validation by qRT PCR. Comparison of gene expression by quantitative reverse transcription polymerase chain reaction (qRT PCR) and RNA seq. ................................ ................................ ................................ .......... 184 3 13 Identification of new genes by RNA seq. Comparison of gene expression by aligning reads for XccA in NB and XVM2 medium to the genome.. .................. 185 3 14 Number of differentiall y expressed genes when comparing expression of common genes in X. citri subsp. citri str. A w 12879 against X. citri subsp. citri str. 306 in NB and XVM2 growth conditions.. ................................ ................... 186 3 1 5 Protease and Pectate lyase activity of X. citri subsp. citri str. 306, and X. citri subsp. citri str. A w 12879. ................................ ................................ ................. 187

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12 LIST OF ABBREVIATIONS CBC Citrus bacterial canker CBS Citrus bacterial spot CDS Protein coding sequences COG C lust ers of orthologous groups CPS Capsular polysaccharide DDW Double distilled water EPS Extracellular polysaccharide HGT Horizontal gene transfer HR Hypersensitive reaction/response IS Insertion sequence LPS Lipopolysaccharide QS Qorum sensing Shared gene s Genes that are orthologous only in the strains compared in this study TCS Two component system T1SS T6SS Type one secretion system Type six secretion system Unique/Singleton Genes that are non orthologous only in the strains compared in this genes s tudy Xacm X anthomonas axonopodis pv. citrumelo Xcaw Xanthomonas citri subsp. citri strain A w Xcc Xanthomonas citri subsp. citri Xcc A Xanthomonas citri subsp. citri strain A (306) Xcv Xanthomonas campestris pv. vesicatoria strain 85 10

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13 Abstract of Disse rtation Presented to the Graduate School of the University of Florida in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy COMPARATIVE GENOMIC AND TRANSCRIPTOMIC ANALYSES OF Xanthomonas citri subsp. citri AND R ELATED SPECIES PROVIDES INSIGHTS INTO VIRULENCE AND HOST SPECIFICITY By Neha Jalan December 2012 Chair: Nian Wang Major: Microbiology and Cell Science Citrus canker caused by Xanthomonas citri subsp. citri (Xcc) has significant impact on citrus product ion worldwide. X. axonopodis pv. citrumelo (Xacm) is another citrus pathogen causing citrus bacterial spot disease which is geographically restricted within the state of Florida. Xcc is distinguished into different strains primarily by host range. The Asia tic strain (A) has a wide host range and is most virulent, whereas Wellington (A w ) strain has host range restricted to Mexican lime and alemow. We hypothesized that gene expression along with gene content, contributes to the difference in virulence and hos t range of closely related strains. We conducted comparative genomic analyses to study Xacm, A and A w strains and transcriptomic analyses for A and A w strains. Illumina, 454 sequencing and optical mapping were used to obtain complete genome sequence s of Xa cm strain F1 (4.9 Mb chromosome, no plasmid) and X citri subsp. citri strain A w 12879 ( Xcaw ) (5.3 Mb chromosome and two plasmids pXcaw19 and pXcaw58). Comparative genomic analysis of Xacm to A strain showed differences in T3SS effectors, T4SS, LPS and othe rs. In addition to pthA putative effectors such as xopE3 xopAI and hrpW were absent in Xacm, which might

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14 be responsible for reduced virulence of this pathogen compared to XccA. We also identified unique effectors like xopC2 and xopW in Xacm that may be r elated to the restricted host range. Whole genome comparison of A w to A strain, disclosed numerous genome rearrangements and insertion/deletion regions indicating genome plasticity. Protein blast revealed multiple unique genes in A w including type III secr etion system effectors xopAF and xopAG Comparative genomic analysis showed various changes in genes related to LPS and T4SS. Furthermore, RNA seq was used to compare expression profile of Xcaw and XccA strains in nutrient rich (NB) and plant intercellular space mimicking (XVM2) conditions using Illumina sequencing. Up regulation of effector genes in Xcaw as compared to XccA might also contri bute to its limited host range. The overexpression of genes involved in plant cell wall degradation, attachment, reac tive oxygen species scavenging, nutrient transportation in XccA might contribute to its expanding of host range. Our data suggest that both gene content and gene expression contribute to difference in virulence and host specificities of different strains.

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15 CHAPTER 1 LITERATURE REVIEW Introduction Xanthomonas spp. belong to a very important genus of pathogenic bacteria causing various plant diseases (Ryan et al. 2011). These pathogens are Gram negative rod shaped bacteria belonging to gamma proteobacteria class and infect over 350 plant species (Chan and Goodwin 1999). Xanthomonas genus consists of 27 phytopathogen species most of them causing critical diseases to ornamental plants and crops (Ryan et al. 2011). The genus Xanthomonas affects 124 monocot and 268 dicot plant species, including nut and fruit trees, cereals, and brassicaceous and solanaceous plants (Bogdavone et al. 2011). Xanthomona d s show characteristic uniformity in their physiological and morphological features. These unique characteristics w ithin the genus present difficulties in establishing a stable phylogenic taxonomy reflective of both evolutionary inter relationships and phenotypic diversity (Bogdavone et al. 2011). Vauterin et al. (1995) proposed a taxonomy that is the basis of current classification of these phytopathogens. The approach received further refinement by Rademaker et al. (2005) to increase its robustness. The closeness in phenotypic features is responsible for the convergent evolutionary pathogenic traits witnessed in Xanth omonas strains within similar species infecting same host(s) or different hosts differently (Rademaker et al. 2005). Citrus Canker Citrus canker is an important disease of most commercial citrus cultivars resulting in significant losses in Florida and othe r major citrus producing areas (Gottwald et al. 2001; Gottwald and Riley 2005) The disease is caused by

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16 Xanthomonas citri subsp. citri (Xcc) (syn. X. citri X. axonopodis pv. citri, X. campestris pv. citri ) (Vauterin et al. 1995; Cubero and Graham 2002) Citrus canker disease is characterized by formation of raised circular, water soaked, necrotic lesions surrounded by a chlorotic halo on leav es, stems and fruits. On severely affected trees, citrus canker causes defoliation, twig dieback, general tree decline, blemished fruit and premature fruit drop. The disease cycle of Xcc is relatively simple where the bacteria colonize the plant apoplast which eventually results in the degradation of the epidermal cells due to hyperplasia. Propagation of the bacteria occurs within lesions and it can tak e about 7 60 days for symptoms to appear ( http://edis.ifas.ufl.edu/ hs382 ) During wet weather when moisture flows freely into these lesions, the bacteria l cells ooze out and are dispersed via windblown rain and enter the new plant hosts directly through stomata or through wounds, and grow in the intercellular spaces of th e spongy mesophyll (Gottwald et al. 2002). Wind at speeds over 18 mp h is enough to spread and aid the bacteria to penetrate plant stomatal openings or wounds inflicted on plants by insect s, thorns, or pruning. The dispersed bacteria have limited lifespan u nder unfavorable conditions. Therefore, their survival in the natural environment is dependent on availability of a host and the ability to colonize it For example, exposure to direct sunlight kills the bacteria, and those falling in the soil survive for few days or months. However, infected plant tissues are kept in dry conditions without exposure to sunlight and free from soil increases survival of the bacteria for years (Verniere et al. 2002). Citrus canker is present in more than 30 citrus producing co untries in Asia, the Pacific and Indian Ocean islands, South America and the Southeastern United States (del Campo et al. 2009). The causal agent is considered a quarantine organism in

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17 citrus producing areas of Europe where canker has not been reported. Ca nker free citrus producing countries impose commercial restrictions on the transport and sale of citrus fruits from citrus canker infected areas. Canker greatly affects fresh citrus fruit, l citrus industry (FCM, 2012). The losses have major socioeconomic impacts in addition to hinderance to trees and losses in quality and quantity of fruit because of the perceptions of possible inoculum transmission on the fresh fruit product (Achor et al. 1996; Gottwald et al. 2001). Management Strategies Eradication was the major method of controlling citrus canker until it becomes endemic in most parts of Florida due to hurricanes. For eradication healthy trees in the radius of 1900 ft from infected trees were destroyed (Gottwald et al. 2002). Copper based bactericides are currently the most effective management approach to control citrus canker especially in preventing infection of fruit. Successful management strategies in Florida still include the use o f copper. However, copper resistance has been reported in Argentina ( Canteros 2002 ). Although copper resistant strains have not yet been reported in Florida, there is potential for horizontal gene transfer of copper resistance genes from other closely and distantly related bacterial strains. Also, over time costs of using copper in the fi eld have increased along with increa sing copper resistance and environmental hazard concerns (Fu et al. 2012). The foreseeable long term measures in containing citrus canke r disease lies in application of biological based practices such as cultivation of disease resistant cultivars in regions where Xcc is endemic. Knowledge of virulence and host range factors is the fundamental step in realizing success of this approach.

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18 Ho st Range Variation of Citrus Canker c ausing Xanthomonas s pp Citrus canker is caused by the bacterial pathogen Xanthomonas citri subsp. citri (Xcc) and Xanthomonas fuscans subsp. aurantifoli i (Xau) Based on the causal pathovar, host range and geographic d istribution, Xau has been divided into two strains, B and C. X. citri subsp. citri induces Asiatic (A type) canker and is the most wide spread and virulent strain. Its origin has been linked to southeastern Asia, Indonesia or India (Civerolo 1984). It aff ects most citrus species with grapefruit ( C. paradisi ), Mexican lime ( C. aurantifolia ) and lemon ( C. limon ) being the most susceptible (Gabriel et al. 1988; Egel et al. 1991; Sc h ubert et al. 2001). Within the A type canker, two variants type A w and A*, hav e been described and are currently geographically limited to Florida and Southwest Asia, respectively (Verniere et al. 1998; Sun et al. 2004 ). The Xcc A* and A W are phylogenetically most closely related to Xcc A strain, h owever both have restricted host ra nge s and cause disease on Mexican lime and few other varities Amongst the A type variants, the first to be isolated was Xcc variant (A*) a close relative of A strains. This variant was isolated in 1998 in south west Asia and it mainly affects Mexican lim e (Verniere et al. 1998). In 2003, researchers working in Southern Florida discovered another Xcc variant named (type A W ) (Sun et al. 2004). Type A W bears similarities to A* but its host range is restricted to Alemow ( Citrus macrophylla) in addition to Me xican lime. Therefore, strain A W slightly differs from A* in terms of host range and disease phenotype. The A w strain causes typical symptoms on Mexican lime but elicits a strong hypersensitive response (HR) in grapefruit. Xcc A* causes typical erumpent ba cterial canker lesions on Mexican lime but shows reduced water soaked and blister like symptoms on grapefruit without causing HR (Das 2003). The other two canker types B and C are caused by two strains of X. fuscans subsp aurantifolii that are

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19 exclusively found in South America (Scubert et al. 2001; Das 2003). The B strain of citrus canker affects lemons in Argentina, Uruguay, an d Paraguay. However, Mexican lime, sour orange, Rangpur lime, sweet lime, citron, and occasionally sweet orange and mandarin oran ge can also be affected. The C strain affects only Mexican lime growing in Brazil (Brunings and Gabriel, 2003). X. axonopodis pv. citrumelo (Xacm) (syn X. campestris pv citrumelo ), a close relative of Xcc, causes Citrus Bacterial Spot disease (earlier kn own as Canker E) which is found only in Florida and is primarily restricted to nurseries (Graham and Gottwald 1990; Schoulties et al. 1987). This indigenous bacterium is restricted in infecting hybrid citrus, Swingle citrumelo and its trifoliate orange par ent Poncirus trifoliate, under nurseries conditions, but shows very reduced bacterial populations in the grove (Stall and Civerolo 1991) Unlike strains of Xcc X. axonopodis pv. citrumelo (Xacm) produces flat or sunken necrotic spots on leaf surfaces, wit h more prominent water soaked margins surrounding the necrotic areas, yellow halos on leaves and twigs (Stall and Civerolo 1991). These symptoms rarely appear on fruit and defoliation or dieback does not occur either (Stall and Civerolo 1991; Gottwald et a l. 1991). Significant progress has been made in understanding the infection and epidemiology of the citrus canker disease in the past decade (Burnings and Gabriel 2003; da Silva et al. 2002; Gottwald et al. 2001). The complete genome of Xcc A strain 306 wa s sequenced and compared with X. campestris pv. campestris (da Silva et al. 2002) It showed that the two bacteria share more than 80% of the genes and their chromosomal gene order is conserved. Xcc A has one circul ar chromosome consisting of 5,175,554 base pairs (bp), and two plasmids: pXAC33 (33,699 bp) and pXAC64

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20 (64 ,920 bp). Genomic analyses showed that Xcc has an extensive repertoire of genes associated with pathogenicity and virulence which include effector enc oding genes, genes coding cell wall degrading enzymes and secretion systems, ge nes for quorum sensing and Pathogen Associated Molecular Patterns (PAMPs) amongst others. It has been widely accepted that host range is not determined by attachment and the Typ e Three Secretion System (T3SS) but by the effector proteins that are delivered into plant cells. The effectors can be either avr (avirulence) or pth (pathogenicity) proteins and it is the effectors that result in limitation or ex tension of host range (Bur nings and Gabriel 2003 ) Previous studies have reported virulence factors such as both pthA and avr proteins to be critical for th e infection of citrus by Xac (B r u nings and Gabriel 2003; Moreira et al. 2010). It has previously been proposed that genetic m akeup or genetic background of plant pathogen could influence the function of avirulence genes and the host specificity (Wang et al. 2006) A previous screening attempted to increase host range of Xcc A* strain by transferring the genomic library of Xcc A strain to Xcc A* strain by triparental mating. The conjugants were inoculated on grapefruit, which is not a host for Xcc A* The study however did not result in any findings of host determinants (Al Saadi 2005) In another screening the genomic library of X citri subsp. citri strain A w (X caw ) was transferred to X. perforans and selected the transco n jugants that can cause HR in grapefruit (Rybak e t al. 2009) They found one avirulence gene, named avrGf1 which is present in Xcaw but not in Xcc A strain. The Xcaw avrGf1 strain causes less severe symptoms in grapefruit than a typical XccA strain (Rybak et al. 2009) Thu s they suggest presence of other avirulence genes that may affect the host range and

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21 virulence of Xcaw The host range and pathogenicity can also be affected by other factors such as composition of lipopolysaccharide, as has been shown previously by Kingsl ey et al. where Xacm with mutation in opsX locus encoding for LPS core assembly, lost its pathogenicity on citrus host plants but not on bean plan ts (Kingsley et al. 1993). Virulence Related Mechanisms U sed by Xcc The finished genome of X. citri subsp citri strain 306 (A) has been sequenced giving greater insights on how the pathogen uses key genes and genetic clusters in virulence and strategic invasion mechanisms (da Silva et al. 2002). Genes implicated in Xcc pathogenesis include those coding for bac terial surface structure and adhesion elements, toxins, type III secretion system (T3SS) and effectors, cell wall degradation enzymes and rpf (regulation of pathogenicity factors) genes related to quorum sensing (da Silva et al. 2002). Attachment of the pa thogen to the host is the initial critical step initiating the process of pathogenicity. The pathogen uses specialized surface structures to survive environmental stresses, attach the plant host and invade the plant intercellular space. These cell surface structures are encoded by extracellular polysaccharide (EPS), lipopolysaccharide (LPS), capsular polysaccharide (CPS), type IV pilli, adhesins and flagella genes. EPS is secreted outside the cell and form s a layer on the outer surface. A cluster of 12 gum genes that produce xanthan gum encodes EPS production in Xanthomonas spp. Besides contributing to the bacterial survival against environmental stresses, EPS is a major component of biofilm of Xanthomonas spp. Mutations of gum genes in Xanthomonas spp. caus es loss of EPS production, change in biofilm and impaired epiphytic survival on hosts (Chou et al. 1997; Dunger et al. 2007; Rigano et al. 2007;

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22 Kim et al. 2009b). EPS is also important as virulence factor and has been shown to suppress callose deposition in the plant cel l wall (Yun et al. 2006). CPS on the other hand, also forms a layer on the cell surface but unlike EPS is bound to the surface via a covalent bond. The capsule helps prevent cell desiccation, and aids in adherence to surface or other cells (Roberts 1996). Though the role of CPS in plant pathogen interaction has not been throughly studied in Xanthomonas mutation of genes like opsX and galU lead to the loss of capsule, changes in LPS and the loss of virulence suggesting that CPS is important for infection (Guo et al. 2010). The gene clusters of Xanthomonas spp. involved in LPS biosynthesis vary in number and sequence similarity (Lu et al. 2008). In Xcc, the two regions involved in LPS synthesis are one with genes encoding transferases, epimera ses, and sugar transporters and another with genes encoding sugar biosynthesis (da Silva et al. 2002). LPS is a major outer membrane component of Gram negative bacteria that contributes to the structural integrity of bacteria and protects it against the at tack of toxic chemicals in environments. Mutations in LPS genes of Xcc leads to reduced biofilm formation, increased sensitivity to environmental stresses and reduction of virulence (Li and Wang 2011). Type IV pili act as fimbrial adhesins helping the ba cteria to adhere and colonize the plant host. The pili are filaments on cell surface that are responsible for bacterial twitching motility (Hirano and Upper 2000). V arious genes including fimA fimT and 26 pil genes encode type IV pilus biosynthesis in Xcc A (da Silva et al. 2002). Nonfimbrial adhesins that are type V secretion system substrates such as autotransporters and two partner secretion substrates can also help in bacterial attachment to the host (Gerlach and Hensel 2007). Xcc contains multiple gene s encoding nonfimbrial adhesins such as

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23 xadA xadB and filamentous hemagglutinins. Mutations in fhaB gene in Xcc abolished adhesion and biofilm formation and reduced virulence of Xcc, indicating that hemagglutinin proteins are important for tissue c oloniza tion (Gottig et al. 2009 ). Xcc has a full set of genes for flagellar biosynthesis and chemotaxis pathway (da Silva et al. 2002). Flagella are used not only for motility but also for surface attachment, biofilm formation and entry into the host (Josenhans a nd Suerbaum 2002). Mutations in fliC and flgE in Xcc, which encode flagellin and hook respectively, resulted in decreased motility and biofilm and also reduced virulence in host (Malamud et al. 2011). The above mentioned bacterial surface structures lik e flagellin and LPS are important for virulence of the pathogens but also act as PAMPs, which can be recognized by plant surface arrayed pattern recognition receptor like kinases and induce PAMP triggered immunity (Schneider and Coll mer 2010). Major PAMP triggered b asal defense responses in plant a include oxidative burst, the production of reactive oxy gen species (ROS) the production of antimicrobial compounds (phytoalexins), thickening of the plant cell wall, and expression of pathogenesis related genes (Newman et al. 2007). Therefore, bacteria have to manipulate virulence traits for better growth in host and also suppress flagellar functions for avoidance of host defense response. Also, the bacteria use type three secretion systme to deliver 15 30 effect ors directly into host cells to circumvent the PAMP triggered immunity and cause disease (Jones and Dangl 200 6 ) Plants in turn develop a more specialized mechanism to detect the effectors translocated by microbes, and activate a second layer of defense known as effector triggered immunity (ETI) or also known as gene for gene resistance (Boller and He

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24 2009) ETI involves the direct or indirect recognition of effector proteins by plant resistance (R) proteins. The R proteins are either nucleotide binding l e ucine rich repeat (NB LRR) proteins or extracellular LRR proteins (Chisholm et al. 2006) ETI also induces oxidative burst, hormonal changes, and transcriptional reprogramming as common plant immune responses (Tsuda and Katagiri 2010). ETI is also associa ted with rapid plant cell death or hypersensitive reaction to restrict patho gen growth (Jones and Dangl 2006 ). ETI induces prolonged ROS production which act s as either signaling molecules or result in pathogen death. ETI also induces prolonged hormone sig naling pathways specially one mediated by salicylic acid that is important for immunity of plants against bacteria (Tsuda and Katagiri 2010). Salycilic acid is the master regulator of the plant immune signaling network and thus suppresses microbial growth (Leon Reyes et al. 2009 ). Not surprisingly, pathogens seem to have adapted effectors to over come ETI by evading recognition and not by attacking ETI signaling (Tsuda and Katagiri 2010). Thus both the plant R genes and pathogen effectors are co evolving in nature (Jones and Dangl 2006 ). The secretion systems have been classified into six types in Gram negative bacteria, type 1 to type 6, according to their composition, function and substrates (Tseng et al. 2009). All six secretion systems, are known to exis t in Xcc (da Silva et al. 2002; Shrivastava and Mande 2008). Type I secretion system (T1SS) is a Sec independent system that exports substrates in a one step process across both membranes of bacteria. It consists of an ATP binding cassette (ABC) transporte r in the inner membrane, an outer membrane factor (OMF) serving as a protein channel and a membrane fusion protein (MFP) connecting the two components. T1SS plays an

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25 important role in pathogenic bacteria by secreting toxins (e.g. hemolysins), lipases and p roteases (Gerlach and Hensel 2007). Altough it has been known to be required for transport of an avirulence factor AvrXa21 which results in a host response in X. oryzae pv. oryzae it has not been demonstrated to contribute to virulence in Xcc (da Silva et al. 2004). Type II secretion system (T2SS) is a Sec dependent system via which various potential virulence factors are secreted, including cell wall degrading enzymes (CWDEs), proteases, lipases and phosphatases. T2SS mediated translocation occurs in tw o steps: substrates with signal peptide are translocated across the inner membrane via the Sec pathway; and then they are exported across the outer membrane via the T2SS translocation pore, which is formed by approximately 12 15 components in the outer mem brane (Sandkvist 2001). Xcc has two independent T2SS, which are encoded by xcs and xps gene clusters. Xcc also encodes for a large number of T2SS substrates most importantly the cell wall degrading enzymes like pectinolytic, cellulolitic and hemicellulolyt ic enzymes (da Silva et al. 2002). Type III secretion system (T3SS) is a key pathogenicity factor conserved in plant and animal pathogenic bacteria such as Yersinia spp., Shigella flexneri Salmonella typhimurium E. coli Ervinia amylovora P. syringae Xanthomonas spp. and others. It is a needle like structure that delivers effector proteins directly from the bacterial cytoplasm into the host cells (Hueck 1998; Buttner and Bonas 2002). In plant pathogens, the T3SS genes are called hrp (hypersensitive r esponse and pathogenicity) genes and hrc (hypersensitive response and conserved) genes. Those genes are required for bacterial pathogenicity and also for induction of hypersensitive response on

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26 hosts and non hosts, respectively (Lindgren et al. 1986; Alfan o and Collmer 1997; Roine et al. 1997). T3SS effectors are secreted into host cells by T3SS. Man y effector genes code avirulence factors that are recognized by specific plant resistance proteins, e.g., AvrBs1 in Xcv (Ronald and Staskawicz 1988). Several ca ndidate effectors have also been identified based on homology to known effectors from other pathogens by in silico prediction (Nol et al. 2003). The major function of T3SS effector proteins is to optimize the host cell environment for bacterial growth eit her by interfering with host defense responses or by modifying the normal cellular function of host proteins (Nomura et al. 2005; Grant et al. 2006). This can be achieved by enzymatic activities of some T3SS effectors to modify host proteins and by transcr iption activator activities of effectors in AvrBs3/PthA family to alter host transcriptome. PthA effector identified in Xcc can confer ability to cause canker lik e symptom to strains that do not cause canker symptoms like Xcam (Swarup et al. 1991). The eff ectors in AvrBs3/PthA family are transcription activators which target host transcription. PthA is the first member of AvrBs3/PthA family which was experimentally identified for its virulence activity (Swarup et al. 1991). It has been demonstrated that Avr Bs3 acts as a transcription activator and bind s to the promoter of upa20 which encodes a transcription factor that induces plant cell hypertrophy (Kay et al. 2007). Type IV secretion system (T4SS), is a one step secretion system that can transport macr omolecules from bacterial cytoplasm into eukaryotic cells or other bacterial cells (Christie et al. 2005). The T4SS in Agrobacterium tumefaciens delivers T DNA with protein from its Ti plasmid into the host to cause the formation of crown gall tumors (Chr istie et al. 2005). There are two T4SS clusters found in Xcc, one on the

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27 chromosome and the other on plasmid pXAC64. However, neither cluster are complete as they lack of virB5 and virB7 in both clusters and the lack of virD4 in the plasmid (da Silva et al 2002). The products of those missing genes are important components for successful translocation of T4SS substrates. Hence, their influence on virulence remains unclear in Xcc (Yeo and Waksman 2004). Type V secretion system (T5SS) is classified into thr ee sub groups based on the secretion mechanisms: T5aSS is the autotransporter system; T5bSS is the two partner system and T5cSS is the oligomeric coiled coil adhesin (Yen et al. 2002). T5aSS is an autotransporter containing three domains: a N terminal sign al peptide, a passenger domain and a translocation unit at C terminal end. In contrast to the single polypeptide of T5aSS, T5bSS consists of two separate proteins (one passenger and one transporter) whereas T5cSS contains trimeric proteins for the formatio n of beta barrel secondary structure. A large number of proteins, which are translocated via T5SS, contribute to bacterial virulence, including enzymes (proteases, peptidases, lipase, esterase), toxins, and adhesins (Gerlach and Hensel 2007). Type VI sec retion system (T6SS), was identified and characterized in V. cholera (Pukatzki et al. 2006) and P. aeruginosa (Mougous et al. 2006). Comparative genomic analysis revealed the presence of T6SS in more than 25% of sequenced bacterial genomes including Xcc (S hrivastava and Mande 2008). T6SS has been speculated to evolve from the bacteriophage base plate, due to the homologies shared by several subunits of T6SS and subunits of the bacteriophage T4 tail spike (Cascales 2008). T6SS forms a phage tail spike like c omplex to inject effector proteins directly into host cytoplasm like T3SS. It is required for virulence in animal and plant pathogenic bacteria

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28 such as V. cholera P. aeruginosa A. tumefaciens X. oryza e and others (Shrivastava and Mande 2008; Pukatzki et al. 2009) Bacteria have evolved global regulatory networks to coordinate the expression of the large number of virulence traits discussed above. A few two component signal transduction systems have been discovered to contribute to the global regulatory n etworks in Xanthomonas spp., including RavS/RavR, ColS/ColR, RpfC/RpfG, and response regulator HrpG. Two component systems usually consist of a membrane bond histidine kinase sensor and a cytoplasmic response regulator. On receiving an external signal, the histidine kinase sensor is autophosphorylated and subsequently transfers the phosphoryl group to the receiver domain response regulator. The activated response regulator then induces physiological changes by regulating the expression of target genes. A nu mber of important physiological activities are under control of two component systems in bacteria, including cell motility, biofilm formation, quorum sensing, and virulence. Quorum sensing (QS) is a cell to cell communication method in response to fluctu ation in cell population. For QS bacteria produce and release diffusible chemical signaling molecules into their environment. When the concentration of signaling molecules reaches a threshold, the bacteria detect and respond to this signal and alter their gene expression. In Xanthomonas two known signaling factors are diffusible signaling factor (DSF), which has been characterized as the unsaturated fatty acid cis 11 methyl dodecenoic acid (Wang et al. 2004) and diffusible factor (DF), which is an uncharac terized butyrolactone molecule. DF controls the production of the yellow pigment xanthomonadin and EPS (Poplawsky and Chun 1997), whereas DSF mediated

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29 QS pathway regulates the production of extracellular enzymes (including proteases, pectinases and endoglu canase) and extracellular polysaccharides (EPS) as well as biofilm formation (Tang et al. 1991; Barber et al. 1997; Slater et al. 2000; Torres et al. 2007). The rpf gene cluster is responsible for DSF production and signal transduction, including the core genes rpfF rpfC and rpfG (Chatterjee and Sonti 2002; He et al. 2006; Siciliano et al. 2006). The rpfF gene encodes a putative enoyl CoA hydratase that catalyzes the synthesis of signal molecule DSF. Extracellular DSF is sensed by a two component signal tr ansduction system consisting of the sensor protein RpfC and response regulator RpfG. The downstream signaling pathway of QS in the bacterial cell is not completely understood The demonstration that the HD GYP domain of RpfG is a cyclic di GMP phosphodiest erase indicates cyclic di GMP i s a second messenger in DSF signal transduction (Dow et al. 2006; Ryan et al. 2006) Cyclic di GMP is synthesized by proteins containing GGDEF domain which has diguanylate cyclase acti vity, whereas cyclic di GMP is degraded by proteins containing EAL or HD GYP domains which have phosphodiesterase. The high levels of cyclic di GMP promote biofilm formation, while low levels promote motility and transcription of virulence factors (Simm et al. 2004; Tischler and Camilli 2004; Rmling et al. 2005) One important target of cyclic di GMP is Clp (cAMP receptor protein like protein) which is a transcriptional activator. Microarray analyse s reveal that Clp is involved in the DSF mediated QS system in Xanthomonas spps. (He et al. 2006; He et al. 2007 ; Guo et al. 2012 ) Cyclic di GMP binds to the Clp to prevent it from DNA binding and the induction of the expression of genes encoding extracellular enzymes, and genes involved in T3SS, and EPS biosynthesis (He et al. 2007). It is known that QS is required for full virulence of

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30 Xcc in planta. A recent comprehensive study has shown that QS temporally regulates the expressio n of a large set of genes, including chemotaxis and flagellar biosynthesis, energy metabolism, T2SS substrates, T5SS adhesins, type IV pili, T3SS and T3SS effectors. The temporal regulation of QS regulon suggests that it is required at different stages of canker infection, including attachment, invasion and growth in host apoplast (Guo et al. 2012) O ther important regulator in Xanthomonas spp. consists of HrpG and HrpX that positively regulate the hrp gene cluster and various other cellular funtions (Wenge lnik and Bonas 1996 a ; Wengelnik et al. 1996b ; Guo et al. 2011 ). HrpG is a response regulator of OmpR family and works with an unknown sensor kinase to detect environmental signals. Significant induction of hrpG expression has been observed in minimal media (XVM2) or in plant apoplast, rather than in rich media or on leaf surface (Wengelnik et al.1996b). The activated HrpG positively controls the expression of hrpX whose product is an AraC type transcriptional activator. HrpX subsequently induces the expres sion of hrp gene cluster (Wengelnik and Bonas 1996 a ). HrpX binds to a conserved cis regulatory element named plant inducible promoter, which is present in the promoter regions of hrp operons (Koebnik et al. 2006). A genome wide microarray analysi s in Xcc s howed that HrpG and HrpX are global regulators in Xanthomonas spp. They control multiple cellular activities responding to the host environment, such as amino acid biosynthesis, oxidative phosphorylation, transport of sugar, iron and potassium, and others thus coordinating the infection of the pathogen (Guo et al. 2011). Project Goals a nd Objectives The present study aims t o use comparative genomics and/or tr a n scriptomics to understand the molecular mechanism responsible for difference in host range and

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31 vir ulence in Xacm and Xcaw as compared to XccA. The hypothesis for the research is that difference s in host specificity and symptoms can be due to strain specific genes and also due to difference s in gene expression/regulation. The goal this research wa s to i dentify critical genes involved in virulence and host specificity in X. citri subsp. citri 306 and related strains. The objectives were to (1) o btain complete genome sequence of X. axonopodis pv. citrumelo strain F1 and compare with other xanthomonads to understand and mine its genome for pathogenicity determinants for citr us bacterial spot disease and, (2) o btain complete genome sequence of Xcaw strain and compare its genome and transcriptome to XccA to investigate the mechanisms responsible for variation in host range and virulence. We applied a combination of techniques like 454 FLX sequencing, Illumina/Solexa sequencing and optical mapping to obtain high quality finished genome sequences of Xacm F1 and Xcaw12879. We then used RNA Seq to compare the expr ession profile of XccA and Xcaw. High throughput sequencing by Illumina was used to compare differences in transcriptomes of the two strains in nutrient rich and plant intrercellular space mimicking media XVM2

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32 CHAPTER 2 COMPARATIVE GENOMIC ANALYSIS OF XANTHOMONAS axonopodis pv citrumelo F1 CAUSING CITRUS BA CTERIAL SPOT AND REL ATED STRAINS I ntroduction Xanthomonas is an important genus of plant pathogenic bacteria (Ryan et al. 2011) These Gram negative rod shaped pathogens belong to class gamma proteobacteria and can infect over 350 species of plants (Chan and Goodwin 1999) Among the diseases on citr us, citrus bacterial canker (CBC) and citrus bacterial spot (CBS) are caused by distinct pathovars of Xanthomonas species. Citrus canker is caused by several pathogenic variants of Xanthomonas citri (Xcc) (syn. Xanthomonas campestris pv citri or Xanthomon as axonopodis pv. citri ) (Schaad et al. 2006; Vauterin et al. 1995) whereas CBS is caused by X. citri pv citrumelo Xac strain 306 with a suspected origin in southeastern Asia causes Asiatic type (A) canker and is the most widespread and virulent form of CBC. It produces corky lesions as a results of hyperplasia and hypertrophy, surrounded by oily or water soaked margins and a yellow halo on leaves, stems, and fruits. In 1984, a disease similar to citrus canker wa s discovered in citrus nurseries in central Florida leading to destruction of millions of seedlings (Sun 1984) This new disease was mistakenly described as a form of citrus canker caused by also known as nursery strain canker. Leaf spots of this strain are irregular to round, 3 5 mm in diameter, flat, water soaked, often necrotic in the center, and usually surrounded by a chlorotic halo. Water soaked elongate d lesions with necrotic centers are also obser ved on twigs but not on fruits (Cubero and Graham 2004) Extensive efforts were put forth to eradicate this disease resulting in destruction of 20 million citrus plants at the cost of $94 million (Schubert 1991)

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33 Strains in this group do not cause hyperplasia and the lesions continue to be flat with time unlike CBC, which results in raised callus like lesions. Further research revealed that the CBS pathogen is variable but widely distributed in the state and does not have the same host range as Asiatic strain (Gottwald et al. 1993) CBS bacteria are most aggressive on trifoliate orange hybrids including Swingle c itrumelo (Graham and Gottwald 1990) Populations of CBS bacteria developed to a lower level and varied in leaves of grapefruit (Schubert et al. 2001) The origin of the strain remains unknown as it is not found outside Florida, and is speculated to have moved to citrus from existing populations of Xanthomonas in Florida (Gottwald and Graham 1990) Further research showed that these strains are serologically, genetically and physiologically distinct from the previously k nown citrus canker pathogenic groups (Graham and Gottwald 1991) and are not susceptible to any of the phages commonly used to differentiate these groups (Graham et al. 1990) Because it affects citrus an d causes symptoms that can be easily confused with canker the disease was wrongly termed as E strain citrus canker (Gottwald et al. 1988) The disease is now recognized as dis tinct from citrus canker and was named citrus bacterial spot caused by Xanthomonas axonopodis pv. citrumelo (Gabriel et al. 1989 ) Other names associated with the bacteria included X. campestris pv. citrumelo and X. alfalfae pv. citrumelonis (Gottwald et al. 1991; Schaad et al. 2006) The nomenclature and classification for the strains of Xanthomonas that infect citrus have undergon e extensive taxonomic revision in recent years and are still under debate (Schaad et al. 2006; Vauterin et al. 2000) Hence, in this report we chose to use classical nomenclature and address the CBS pathogen as Xan thomonas axonopodis

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34 pv. citrumelo ( Xacm (Saddler and Bradbury 2005) Compared to XccA Xacm has much reduced pathogenicity with limited host range. The host range of XccA is broad includ ing most commercial citrus varieties while Xacm does not infect any commercial citrus varieties and it is limited primarily to trifoliate orange, its hybrids, and a few other individual species (Graham et al. 1990) Citrus bacterial spot occurs almost exclusively in nurseries, where young, susceptible tissue is abundant and irrigation is freque nt (Timmer et al. 1991) In field, greenhouse, and growth chamber, Xacm generally does not cause disease when applied as a spr ay. Bacterial populations of bacterial spot strains within lesions on most hosts exc ept Swingle citrumelo decline rapidly with time (Egel et al. 1991) In comparison with XccA the Xacm strains isolated from Florida nurseries were found to vary widely in aggressiveness from each other (Graham and Gottwald 1990) Restriction Fragment Length Polymorphism analysis by Hartung and Civerolo (1989) showed that Xacm strains are not very closely related to XccA and they are not a form of canker. This was further corroborated by comparison of Xacm strains with other xanthomonads using DNA DNA hybridization, which showed that Xacm is only about 60% similar to XccA (Egel et al. 1991) Later, Cubero and Graham deduced that Xacm is much closely related to X. campestris pv. vesi catoria rather than XccA based on 16S rDNA analysis (Cubero and Graham 2002) as well as leucine responsive regulatory protein gene analysis (Cubero and Graham 2004) The mechanism of reduced pathogenicity and limited host range of Xacm compared to XccA remains unknown. To address this question, comparative genomic

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35 study was conducted in this present research by completing the genome sequence of Xacm strain F1 (Graham and Gottwald 1990) In comparison with XccA X. axonopodis pv. citrumelo is a genetically, pathogenically, and serologically distinct pathogen (Alvarez et al. 1991; Gent et al. 2005; Graham and Gottwald 1990; Hartung and Civerolo 1989) We decided to sequence Xacm F1, which is a highly aggressive citrus bacterial spot bacterial strain, thus it is more l ikely to infect cit rus nursery plants as a pathogen. To gain better understanding of ecological and evolutionary relationships between strains and species of Xanthomonas we also compared Xacm with closely related strain of X. campestris pv. vesicatoria str. 85 10 (Xcv) (Syn X. euvesicatoria ; X. axonopodis pv. vesicatoria ) causing bacterial spot on tomato and pepper (Lu et al. 2008; Ryan et al. 2011; Vauterin et al. 2000) M aterials a nd Methods Bacterial Strain a nd DNA Sequencing Th e X. axonopodis pv. citrumelo strain F1 sequenced in this study was isolated from Avon Park, Florida in 1984 and stored in a glycerol stock at 80 C Genomic DNA was extracted from bacterial culture grown over night at 28 C in Nutrient broth medium, using a Wizard DNA purification kit (Promega, Madison, WI, USA.) according to the purity of the DNA was measured spectrophotometrically (Nanodrop ND 1000, NanoDrop Tech. Inc., Wilmington, DE). Whole genome sequencing was performed using two high throughput sequencing techniques, 454 pyrosequencing and Illumina Solexa GA sequencing. Single and paired end reads were generated on a 454 GS FLX Titanium sequencer (454 Life sciences, Branford, CT) in accordance with the manufac Interdisciplinary Center for Biotechnology Research (ICBR), University of Florida.

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36 Paired end Illumina sequence reads were obtained using Illumina Genome Analyzer IIx (Illumina, Hayward, CA, USA) at Yale University Center for Genomics a nd Proteomics. Gap Closure a nd Assembly Validation The 1350 contigs obtained from Illumina were used to confirm the assembly of 454 scaffolds. The Illumina contigs were aligned against the 454 scaffolds using BLASTn to confirm the orientations and integrit y of the assembled sequences and to close gaps and link contigs together within the scaffold. A de novo BamHI optical map of the genome of Xacm was generated by OpGen technologies (Madison, Wisconsin, USA). In silico BamHI restriction maps of the 5 scaffol ds were constructed and aligned to the optical map according to their restriction fragment pattern, using MapSolver v.3.1 software (OpGen Technologies, Inc.). PCR primers were designed and Sanger sequences of these PCR products were used to close the gaps between the scaffolds. Final assembly was correlated with the optical map for further validation. Annotation a nd Curation and gene finding programs, based on Markov chain mode l prediction algorithm at ICBR, UF (Tyson et al. 2004) Predicted proteins were annotated by similarity searches against the NCBI Non redundant (nr) protein database (http://ncbi.nlm.nih.gov) and clusters of orthol ogous groups (COG) database. A function was assigned to a predicted gene if it met the criteria of a minimum cutoff of 50% identity and 80% coverage of the gene length. In a few cases, additional putative protein coding genes were annotated by direct homol ogy search at the nr protein database using BLASTp. Each gene was also functionally classified by assigning a cluster of orthologous group (COG) number. The rRNA genes were annotated by the FgenesB tool based on sequence conservation,

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37 while tRNA genes were detected with the tRNAscan SE program (Lowe an d Eddy 1997) Insertion sequences were identified by submitting the whole genome to the IS Finder website (Siguier et al. 2006) The CGView Server was used to generate graphical views of genome (Grant and Stothard 2008) The results of the automated annotation were examined and curated manual ly using the JGI GenePRIMP pipeline (Pati et al. 2010) Phylogenetic Analysis To determine the position of Xacm within the evolutionary tree of Xanthomonas pathovars, we used protein sequences of nine housekeeping genes uvrD, secA, carA, recA, groEL, dnaK, atpD, gyrB and infB from 10 completely sequenced Xanthomonas spps. We also added sequences fr om three Xylella fastidiosa strains and three Pseudomonas spp. as well as from two Stenotrophomonas maltophilia strains. The sequences of Ralstonia solanacearum strains GMI1000 & PSI07 and Burkholderia cenocepacia strain NCTC 10247 were used as out group s pecies. Amino acid sequences of nine proteins from the above genomes were aligned using clustal W (Larkin et al. 2007) and the resulting alignments were concatenated. Phylogenic tree from concatenated genes was constructed using PAUP 4.0 (Swarup et al. 1992) by the maximum likelihood method. The percentage of replicate trees in which the as sociated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches in the tree. Comparative Analysis For comparative analyses, the sequences of X. campestris pv. vesicatoria str. 85 10 (GenBank accession no. NC_007508) and X citri subsp. citri str. 306 (GenBank accession no. NC_003919), which were determined as closest relatives to X.

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38 campestris pv. citrumelo F1 in BLAST analyses as well as phylogenetic searches; were retrieved from GenBank. Complete genome sequences of all the three Xanthomonas spp. and also specific regions were aligned and visualized in progressive mode using MAUVE (Darling et al. 2010) Pan genome analysis that include s the core genome against sequences of the above genomes. The genes aligned based on amino acid sequence were considered orthologo us if reciprocal BLASTp hits were found between two genes with e value less than or equal to 10 20 and alignments exceeding 80% sequence identity and 80% query gene length. A gene was considered singleton to each strain if it had no hits with an e values less than or equal to 10 5 Additional Sequence Analysis Candidate T3SS effectors were identified using both nucleotide and protein blasts by comparison to the Xanthomonas effector database (http://www.xanthomonas.org) Putative perfect and imperfect PIP box sequences TTCGC N 15 TTCGC and TTCGC N 16 TTCG respectively were identified using custom scripts (Fensela u and Bonas 1995) Pathogenicity islands or g enomic regions with atypical G+C content were identified using the web based software GC profile. It uses a suite of segmentation programs to identify regions with differential G+C content in the genome (Gao and Zhang 2006) Pectate Lyase Assay Cultures were grown on rich medium, nutrient agar at 28C, then suspended in steril e deionized water and adjusted A, B and C which has pectate as the sole carbon source were used to test for pectolytic activity (Hildebrand 1971) T he medium contained bromothymol blue dye, calcium

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39 chloride, 2% sodium polypectae and 0.4% agar. The pH was adjusted to 4.5, 7.0 and 8.5 for the mediu incubated at 28C for 6 days before confirming pitting due to pectate lyase production. Database Submission The complete genome of Xanthomonas axonopodis pv. citrumelo strain F1 has been deposited at Genebank under the accession number CP002914. Results Sequencing and General Features of t he Genome Xacm was sequenced using 454 GS FLX pyrosequencing (both unpaired and paired end) (Margulies et al. 2005) and paired end Illumina/Solexa sequencing (Bently et al. 2006) A total of 367,109 high quality sequences with an average read length of 332 bp, representing more than 21 fold genome coverage were obtained by 454 FLX sequencing. These sequences were assem bled into contigs and scaffolds using the 454 de novo assembler Newbler 2.0 ( Table 2 1 ) Although the genome coverage obtained through Illumina was much higher as compared to 454, the longer GS FLX reads resulted in much better assembly of contigs. In tota l, 72 contigs were generated, of which 61 contigs were larger than 500 bp. The average size of the large contigs was 81 kb. These contigs were further grouped into five scaffolds based on paired end reads. The maximum size of the scaffolds was 2,559,303 ba ses with an average of 990,948 bp. Solexa sequencing generated a total of 37,695,118 high quality filtered sequence reads with an average read length of 74 bp. Average coverage was more than 400 fold. All reads were de novo assembled using CLCbio Genomics Workbench version 4.0, length fraction and similarity set at 0.9 and all the other parameters set as default values. This yielded 1,350 contigs (N 50 = 8,322; maximum length = 36,202; minimum

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40 length = 102). The 72 contigs obtained by 454 sequences were alig ned in the right order to obtain 5 scaffolds using the paired end reads. Aligning 1350 Illumina contigs and using the ones overlapping the 454 contigs solved most gaps within scaffolds. Pyrosequencing has a higher error rate around homopolymers (Huse et al. 2007) resulting in insertion deletion errors in assembly and thus in frame stop codons in genes. Illumina data on the other hand has errors mainly due to mismatches ( Dohm et al. 2008) Hence, it was used to correct the errors in the scaffold sequences by mapping the Illumina reads against the 454 consensus sequences using CLCbio Genomics Workbench version 4.0 (Aury et al. 2008) After all the intensive and time consuming efforts the assembly still contained 5 scaffolds with internal gaps, which were difficult to resolve due to repeat regions. Thus optical mapping was used to obtain a de novo BamHI restriction map with no require ment for previous sequence information (Latreille et al. 2007) The in silico restriction maps of scaffolds were aligned to this structural map to rev eal the correct alignment and orientation of all the contigs as shown in Fig 2 1A. The genome was completely closed by primer walking and validated by manually inspecting a ll areas of imperfect match between the optical map and the sequence assembly (Fig 2 1B). The genome sequence was further corroborated by either high coverage with the 454 and Illumina data or by re sequencing the region X. axonopodis pv. citrumelo strain F1 has a single, circular chromosome of 4,967,469 bp (Fig. 2 2) with no plasmids. D e tails of the general features of the genome are shown in Table 2 2. The G+C content of the chromosome averages 64.92%, which is similar to other Xanthomonas genomes. The chromosome displays a clear GC skew

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41 transition typical of prokaryotic genomes, indic ative of bi directional replication mechanism (Ravin et al. 2003) GC skew analysis and blast comparison was used to locate the origin of replication at the point with an excess of G over C corresponding to the beginning of the leading strand and dnaA was first of the coding sequences (CDS) of the genome. The Xacm genome en codes 4,202 putative coding sequences (CDSs), and 60 structural RNAs (Table 2 2). The genome shows a coding density of 86.53% characteristic of most xanthomonads. There is no asymmetry in the distribution of the CDS on the chromosome between the leading st rand 2,131 (50%) and the lagging strand 2,131 (50%). After FgenesB annotation and manual curation, 3,481 CDSs (82.42%) could be assigned to one or more COG functional classes (Table 2 3) whereas there was not enough evidence for 721 CDSs to be assigned to any COG category. Two sets of 5S 16S 23S rRNA, clustered in operons were found located in a region of approximately 500 kb (between 4,379,256 bp and 4,847,563 bp) on the left replichore. A total of 54 tRNA genes with specificities for all 20 amino acids we re also identified. Phylogenetic Relatedness o f Xacm t o Other Xanthomonads To establish the phylogenetic relationship of Xacm strain F1 with respect to other selected members of completely sequenced Xanthomonas we compared a set of nine housekeeping gen es ( uvrD, secA, carA, recA, groEL, dnaK, atpD, gyrB and infB ) These genes are highly conserved that show no evidence of horizontal transfer among the 10 xanthomonads as well as other plant pathogens sequenced. These genes have provided robust analysis an d resolved evolutionary relationships reliably in other studies (Clarke et al. 2010) For this analysis, we focused on bacteria with complete genomes

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42 and excluded draft genomes due to the limitations of draft genomes (Palmer and McCombie 2002) We created an alignment of the nine proteins, concatenated the sequences and reconstructed the phylogenetic tre e using maximum likelihood method (Fig 2 3). The phylogenetic tree indicates that X. axonopodis pv. citrumelo strain F1 groups most closely with X. campestris pv. vesicatoria and Xanthomonas citri subsp. citri forming a distinct clade from other xanthomon ads. The closest relative of Xacm is Xcv 85 10 that causes bacterial spot disease in tomato and pepper (Thieme et al. 2005) This is consistent with the results by comparison of optical maps of the three chromosome s (Fig. 2 1C). Xacm and Xcv appear to be separated from XccA that is included in this cluster, which is supported by a good bootstrap value of 100 at this node. However, the relationship with XccA is sufficiently close that they share nucleotide sequence i dentity over 98% in most conserved regions. Interestingly, Xacm F1 has been shown to be 56% and 58% similar to XccA strain 9771 and Xcv strain 58, respectively by DNA DNA hybridization analysis (Egel et al. 1991) It is noteworthy that other strains of XccA and Xcv were used in that comparison rather than the sequenced Xcc A strain 306 and Xcv strain 85 10. Interestingly, Gent and colleagues had shown that the pathovars of citrumelo are indistinguishable from a few other X. axonopodis pathovars and they do not form a monophyletic cluster by rep PCR (Gent et al. 2005) However, Xacm F1 sequenced here is an aggressive strain which was not included in the previous study. Comparison of Chromosome Organization o f Xacm To Xcc A a nd Xcv The chromosome organization of Xacm was compared with that of two closely related strains XccA and Xcv using MAUVE in progressive mode. Though most of the genome is collinear, Xacm harbors some translocations and inversions around the

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43 replication terminus of the chromosome (Fig. 2 4). The unequal replichores might have been due from this reorganization. The Xacm genome has one major inversion with a translocation and 2 major deletions as compared to XccA whereas there are 3 inversions with translocations and 2 major deletions compared to Xcv. Many of the rearranged and deleted blocks were flanked by transposons and/or integrases, indicating that this rearrangement may be a result of horizontal gene transfer. The genome of Xacm does not harbor any plasmid. In comparison XccA contains two (pXAC33 and pXAC64) and Xcv contains four (pXCV2, pXCV19, pXCV38, pXCV183) plasmids respectively. Plasmids of xantho monads have been reported to play important roles in pathogenicity. Plasmid pXAC64 of XccA encodes for pthA4 gene, a homolog of pthA which is capable of conferring ability to cause canker like symptoms to strains of Xacm (Swofford 2003) On the other hand plasmids pXCV38 and pXCV183 encode for putative Vir/Tra and Icm/Dot like type IV secretion systems respectively (Thieme et al. 2005) The absence of plasm ids from Xacm may have contributed to the reduced virulence of the CBS strain. Horizontal Gene Transfer ( HGT ) a nd Genome Plasticity Horizontal gene transfer is recognized as one of the major mechanisms for genome plasticity leading to diversification and speciation of the bacteria (Ochman et al. 2000) A simple method to identify potential horizontally transferred genes is to look for regions having atypical G+C content in the genome. The G+C content of Xacm genome ranged from 48.90% to 68.41% with an average of 64.92%. The segmentation results predicted e ight regions of low GC content, which are recognized as genomic islands (Table 2 4). The negative cumulative GC profile of these regions is also different in

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44 comparison to the whole genome (Fig. 2 5A). A sharp drop in the G+C content of these regions disti nctly separates them from the rest of the genome (Fig. 2 5B). These regions vary in size from approximately 3 kb to 64 kb. It was noteworthy that one of the genomic island from 2,970,113 bp to 3,004,362 bp encodes for virB4 virB11 virB9 and virD4 protein s that are part of type IV secretion system and components of type IV pilus like fimT pilE and pilus tip associated proteins. Presence of such genes in genomic regions indicative of horizontal gene transfer is in agreement with earlier reports (Thieme et al. 2005) It was also observed that about 50% of ORFs in the two biggest regions from 1,827,507 to 1,891,340 bp and 3,664,590 to 3,686,175 bp were determined to be orphan genes. Orphan genes have a very limited ph ylogenetic distribution and have no recognizable homologs. A recent study in Escherichia coli demonstrated that most orphan genes encode functional proteins (Daubin and Ochman 2004) Thus orphan genes may encode functional proteins in Xacm and migh t be responsible for virulence or differential host range of the strain. In addition these regions have a high number of integrase and transposase genes, which is a conserved feature of genomic islands. The genome of X. axonopodis pv. citrumelo includes 41 insertion sequence (IS) elements. A majority of these transposases belong to IS3 family including Ixac2 and IS1404. We also found 2 IS elements from IS5 and IS1595 families each and 3 elements belonging to the Tn3 family. Comparison o f Proteins E ncoded b y Xacm t o XccA a nd Xcv We compared proteomes of the above three Xanthomonas spp. using reciprocal BLASTp. A Venn diagram representing the pan genome of all three genomes is shown in Fig. 2 6. The comparison of the predicted protein sequences revealed that 3,292

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45 CDS are shared by all three genomes. These genes represent about three quarters of the genome forming the core set that include conserved housekeeping and virulence genes essential for plant infection. Of the remaining 910 predicted genes in Xacm, 1 19 have homologs only in XccA and are absent from Xcv. These genes may include virulence factors necessary for infecting the common citrus host. The number of homologs in Xcv at 385 is much higher than XccA further confirming that the CBS strain is much cl oser to Xcv as compared to XccA A total of 406 protein coding genes are unique to Xacm as compared to XccA and Xcv of which 298 are hypothetical proteins, 26 are mobile genetic elements and 82 are singletons with predicted functions. Moreover 174 genes sh ow homologs in distinctly related Xanthomonas or other highly related bacteria suggesting their acquisition by horizontal gene transfer. The significant features shared between the genomes as well as the differences between the genomes are discussed in det ail as follows. Type Three Secretion Gene ( T3SS ) Clusters Gram negative bacteria use T3SS to translocate virulence factors into the host cell. In X. axonopodis pv. citrumelo the T3SS is encoded by 27 genes, the organization of which is in close synteny wi th hrp cluster of Xcv and XccA (Fig. 2 7). The cluster includes all nine hrc (hypersensitive response conserved) genes that encode T3SS structural components and all 9 hrp genes some of which encode components of the hrp pilus These genes, present only i n phytopathogenic bacteria, are associated with rapid programmed death of plant cells at the site of infection in most non host or resistant host plants and for pathogenesis in susceptible hosts (Buttner and Bonas 2003) The major difference as compared to XccA is that the Xacm cluster lacks the hypothetical protein upstream of hrpF and instead has three additional genes in the

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46 same locus. These 3 genes consist of XACM_0383, which encodes a hypothetical protein with 97% amino acid identity to a hypothetical protein XPE_2921 in X. perfor ans a pathogen of tomato causing bacterial spot (Jones et al. 1998) ; XACM_0384 that is 99% identical to outer membrane protein F1 (XopF1) from Xcv; and XACM_0385 with no obvious homologs. The final gen e in this cluster, XACM_0407, shares 98% similarity to putative transglycosylase gene hpaH from X. perforans As compared to Xcv, T3SS of Xacm lacks 2 hrp associated genes hpaG and hpaE 2 outer protein genes xopD and xopA and 5 hypothetical genes XCV_0410 XCV_0412, XCV_0436, XCV_0438 and XCV_0439 with no known functions. Loss of these genes from Xacm might have contributed to host range and virulence variation. Repertoire o f T3SS Effectors o f Xacm in Comparison t o XccA a nd Xcv T3SS effectors were identifi ed in the Xacm genome and compared with XccA and Xcv. Considerable differences were observed in the effector repertoires present in these three strains (Table 2 5). Twenty two effectors were identified in Xacm, whereas 25 and 30 effectors were identified i n XccA and Xcv respectively. We subdivided them into three groups of core, partially shared and species specific depending on their presence in the three strains. The core effectors shared by all the three strains consist of 17 effector genes. Of this cor e set, 9 effector genes ( avrBs2, xopK, xopL, xopN, xopP, xopQ, xopR, xopX, xopZ ) are present in genomes of all sequenced Xanthomonas with the exception of X. albilineans and X. campestris pv. armoraciae, the later of which has only xopP and xopR These gen es might be essential effector genes required for pathogenicity of xanthomonads in plant host. The effector avrBs2 belongs to a family known for effector triggered immunity in plants (Swords et al. 1996) It elicits HR in plants carrying Bs2 resistance gene (Minsavage et al. 1990) and is needed for full

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47 virulence of the pathogen on susceptible hosts. Effector xopQ, which be longs to the hopQ1 family from Pseudomonas has also been known as an avirulence determinant in Nicotiana benthamiana since Psedomonas syringae pv. tomato DC3000 deletion mutant of hopQ1 1 acquired the ability to grow to high levels and produce bacterial sp eck lesions in non host N. benthamiana (Wei et al. 2007) XopN has been shown to interact with TARK1 and TFT1 proteins from tomato, thus repressing pathogen associated molecular pattern triggered immunity (Kim et al. 2009) The homologs of effectors x opL, xopP and xopQ have been shown to contribute to pathogenicity in X campestris pv. campestris (Jiang et al. 2009) Both xopX and xopZ potentially interfere with host innate immunity, thus making the plant more susceptible. The remaining 8 core effectors ( xopA, xopE1, xopF2, xopI, xopV, xopAD, xopAE, xopAK ) are not present in all xanthomonads and might be responsible for pathogenicity in some plant hosts while inducing resistance in others (White et al. 2009) It is likely that none of the effectors belonging to the core group are responsible for the difference in virulence and host range of Xacm, Xcc A and Xcv. The partially shared effectors are present in only two of the three strains. This group consists of xopC1 xopF1 and xopAJ shared by Xacm and Xcv only as well as xopE2 shared by XccA and Xcv but absent from Xacm xopF1 is found in all Xanthomo nas species except Xac which encodes a truncated version of the same. In Xacm a homolog of xopF1 is present which shares 99% similarity to that gene in Xcv. The xopAJ homolog of Xacm shares 99% similarity with xopAJ / avrRxo1 of Xcv. This gene is truncated i n Xacm due to a deletion mutation at 1056 bp in the gene that resulted in early termination of the protein at 379 amino acids as opposed to its

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48 homolog of 450 amino acids in Xcv The xopC1 effector gene encodes a haloacid dehalogenase like hydrolase with several phosphoribosyl transferase domains This gene is present in Xacm but is fragmented across the genome (XACM_2129, XACM_2132 and XACM_2248) due to genome rearrangement and transposon insertion and thus is likely to be non functional. xopE2 which has been identified in various xanthomonads has recently been shown to be involved in virulence of Xcv group B strains on tomato but not in that of group A strains (Lin et al. 2011) It has also been related to suppression of HR indicating that it plays a dual role in different host plants ( Lin et al. 2011) Two species specific effectors xopC2 and xopW were found in Xacm. Though homologs of xopC2 are found in both XccA and Xcv, they might be non functional. Xacm consists of a xopC2 gene with its closest homolog in X. perforans which causes bacterial spot only on tomato (Potnis et al. 2011) Xacm also h as a truncated gene XACM_0435 which is a homolog of xopW from X. oryzae pv. oryzicola and might be non functional. Xcv has at least 9 unique effectors as listed in Table 2 5. Some effectors like avrBs1 avrBs1.1 xopJ3 are known avirulence factors. These effectors might be important for pathogenicity in tomato and pepper. XccA possesses four unique effectors avrBs3/pthA, XopE3, XopAI and HrpW which are absent in Xacm and Xcv (Table 2 5) The differences in repertoire of T3SS effectors in Xacm and XccA mi ght contribute to their difference in virulence and host range. T3SS effectors have been known to contribute to pathogenicity and multiplication of pathogens in planta (Gurlebeck et al. 2006) T3SS effectors benefit the pathogens by altering the

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49 physiology of the host cell and suppressing plant defenses (Grant et al. 2006) T3SS effectors might contribute to host range by suppressing host defenses as virulence factors or narrowing the host range when certain effectors are specifically recognized by the plant as avirulence factors (Hajri et al. 2009) Importantly, avrBs3/pthA is present in XccA strain 306 while absent in Xacm F1 and Xcv 85 10. Ho wever, it is noteworthy that many other Xcv strains contain avrBs3 and homologs (Szurek et al. 2002) In XccA strain 306, there are 4 copies of pthA : pthA1 pthA2 pthA3 and pthA4 on two plasmids, whi ch are all absent in Xacm and Xcv PthA4 with 17.5 repeats which is same as PthA is known to play an important role in citrus canker as knockout of pthA4 abolished the development of citrus canker symptom development (Al Saadi et al. 2007) PthA is responsible for development of hypertrophic and hyperplasic symptoms and cell death and its mutation leads to reduction in ability of bacteria to disseminate from infected lesions (Yang and White 2004) PthA also contributes to the epidermal rupture and necrosis, which promotes exudation and dissemination of XccA Interestingly, the pthA gene from XccA strain when introduced to Xacm conferred the ability to cause raised pustules (Swarup et al. 1992) PthA and its homologs do not determine host range according to a previous study (Al Saadi 2005) indicating that neither of the complementing homologs nor any of the noncomplementing paralogs of pthA suppresses avirulence of Xcc A* strain on grapefr uit. However, hssB3 .0, a homolog of pthA was shown to be responsible for host specific suppression of virulence of Xcc A strain KC21 on Citrus grandis cultivars but not on other Citrus species such as Citrus sinensis (Shiotani et al. 2007) This suppression le d to reduced aggressiveness rather

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50 than change in host range since Xcc A strain KC21 still causes citrus canker symptoms on Citrus grandis Other Xacm specific effectors might be contribute to the broader host range of XccA compared to Xacm xopE3 ( avrX acA2 ) is a putative transglutaminase enzyme that belongs to the hopX ( avrPphE ) family and is widespread among phytopathogenic bacteria (Nimchuk et al. 2007 ) XopAI is putative effector protein reported only in the three canker causing strains XccA 306, X. aurantifolii strain B and X. aurantifolii str ain C as well as in one X. vesicatoria str. 1111 (Moriera et al. 2010, Potnis et al. 2011) The role of XopAI in virulence of Xanthomonas remains to be characterized. HrpW is not known to be associated with virule nce, although it contains domains resembling harpins and pectate lyases. It may not function as an intracellular effector but is secreted by the T3SS. HrpW in several other phytopathogens is known to elicit an HR in non host plants (Kim and Beer 1998) Alternately, the limited host range of Xacm might result from the presence of the Xacm specific xopC2 and xopW serving as avirulence factors. The presence of all the species specific effectors in XccA and Xacm may be the main factors determining the host range of the pathogens. Further study is needed to understand their contribution to XccA and Xac m for infecting different hosts. The difference in effector repertoires of Xacm and Xcv might contribute to their different host specificity with Xacm infecting citrus seedlings whereas Xcv 85 10 causing bacterial spot disease on both pepper and tomato pla nts (Potnis et al. 2011; Ryan et al. 2011) It has been suggested that the specific effector set of a given bacterial strain is the potential determinant of host range (Thie me et al. 2007) Compared to Xcv, Xacm contains xopC2 and xopW which are absent in Xcv while

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51 Xacm lacks avrBs1, xopB, xopD, xopG, xopH (avrBs1), xopJ1, xopJ3 (avrRxv), xopO, and xopAA (Table 2 5), which are present in Xcv. avrBs1 is known to encode a 50 kDa protein with homology to AvrA of Pseudomonas syringae pv glycinea This protein specifies avirulence on pepper cultivars containing the resistance gene Bs1 (Napoli and Staskawicz 1987) XopD is known to alter host transcription, promote pathogen growth, and delay develo pment of disease symptoms (Kim et al. 2008) XopB attenuated cell proliferation when expressed in yeast and also cause cell death in N benthamiana leaves but not in tomato (Salomon et al. 2011) XopJ homologs a re known to inhibit host protein secretion and interfere with defense responses (Bartetz ko et al. 2009) Other effectors XopG, XopO, and XopAA have not been studied in detail in Xcv How these effectors contribute to the different host ranges and different virulence of Xacm and Xcv needs further characterization. Other Secretion Sy stems Ass ociated w ith Virulence Xanthomonads have at least five more protein secretion systems including type I to type VI other than the T3SS. Genes involved in all the secretion systems were identified in Xacm F1 genome. Secretion systems are of fundamental impor tance for translocation of proteins and other molecules. They play important roles in virulence of different bacterial pathogens. The relevant features of these virulence associated secretion systems of Xacm shared with XccA and Xcv are presented below. Ty pe 1 Secretion S ystem (T1SS) T1SS has not been shown to contribute to virulence in Xanthomonas spp. (Buttner and Bonas 2010) Instead, T1SS is required for Xa21 mediated immunity in rice against X. oryzae pv oryzae PXO99. The Ax21 (activator of Xa21 mediated immunity) is highly conserved in Xanthomonas spp. and secreted by T1SS. In Xacm the

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52 Ax21 protein (XACM_0208) is 100% identical with XccA and Xcv proteins and 93% identical with X. oryzae pv. oryzae PXO99 protein. In addition, RaxST is required for sulfati on and three genes raxA raxB and raxC are required for secretion of Ax21 (Han et al. 2011) The gene raxgA in Xacm (XACM_1188) may be non functional due to a frameshift mutation whereas the proteins encoded by raxB (XACM_1189), raxC (XACM_3355) and raxST (XACM_1187) are 99 100% identical to Xcv proteins. XccA on the other hand encodes fo r only raxC gene. Type 2 S ec r etion S ystem (T2SS) Xacm is also equipped with the xps and xcs T2SS clusters, which secrete toxins and degradative enzymes. The T2SS clusters in Xacm are very conserved compared to those identified in Xcv and XccA with xps bei ng composed of 11 genes and xcs of 12 genes (Fig 2 8). The xps T2SS that is found in all the sequenced xanthomonads is known to affect virulence in Xcv and also enhance translocation by T3SS. The xcs T2SS, on other hand is restricted to only some Xanthomon as spp. and has no obvious virulence function (Szczesny et al. 2010) The T2SS are known to secrete many plant cell wall degrading enzymes like cellulases, xylanases, lipases and proteases amongst others. Each species has its unique set of enz ymes, which helps degrade components of the plant cell wall, thus assisting in pathogenesis. The range of these enzymes in Xacm was compared to the ones found in Xcv and XccA (Table 2 6). Enzymes such as cellulase, protease and pectate lyase have been know n to promote bacterial nutrition and also virulence (Dow et al. 1990; Ray et al. 2000) XynC, an endoxyalanase in Xcv is known to be secreted by the xps T2SS under the control of hrpG and hrpX and contribute to vir ulence (Szczesny et al. 2010) Xacm contains a homolog of this gene, XACM_0913 that may play a similar role. Most of the enzymes show functional

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53 redundancy and hence loss of one gene might not affect virulence. Rajeshwari et al (Rajeshwari et al. 2005) showed that double mutants of both lipase and xylanase show much reduced virulence as compared to the single mutants in X. oryzae pv. oryzae It is interesting to note that Xacm is deficient in pectate lyase function. In comparison of the four genes in Xcv and three in XccA Xacm shows presence of o nly two genes. However, both the genes XACM_2919 and XACM_3456 are pseudogenes that have stop codons resulting in truncated protein s Thus, these proteins may be non Both X ccA and Xcv produced pitting in the agar at pH 8.5 to confirm pectate lyase activity. Xacm did not produce any pitting as seen in Fig. 2 9, supporting the hypothesis that it is pectate lyase deficient. A pectate lyase homolog xagP has been shown to induce an HR in tobacco and pepper in X. axonopodis pv glycines (Kaewnum et a l. 2006) The role of pectate lyase in citrus pathogens remains to be determined. Several T2SS substrates have been shown to not only affect virulence but also induce plant defense responses. T2SS and its substrates are also controlled by T3SS regulators (Guo et al. 2011) Type 4 Secretion S ystem (T4SS) In bacteria, the T4SS is known to contribute to virulence. Two T4SS clusters are present in both XccA and Xcv. Both the clusters are of Vir type in Xac (Fig. 2 10), where one is located on the chromosome and the other on plasmid (Al Saadi et al. 2007) Xcv on the other hand encodes for one Vir and the other Dot/Icm type cluster (Fig. 2 10), both on plasmids and a partial Vir cluster on chr omosome (Thieme et al. 2005) Xacm encodes for only one Vir type T4SS cluster on the chromosome. The cluster in Xacm does not show high similarity to Vir type T4SS of either XccA or Xcv. With the exception

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54 of virD4 that shows homologs in both XccA and Xcv, most of the predicted T4SS genes in Xacm share sequence similarity with genes in strains of Stenotrophomonas maltophilia which is an aerobic gram negative environmental bacterium commonly found in soil, water and animals (Hauben et al. 1999) Xacm also encodes for a virK and two virJ like prote ins, outside the T4SS cluster. The function of virK protein is unknown and it has been linked to T2SS substrates instead of T4SS (Guo et al. 2011) VirJ is a peri plasmic chaperone believed to mediate the association between the T4S pilus and substrate proteins (Christie et al. 2005) Type 5 Secretion S ystem (T5SS) Both Xac and Xcv encode a two partner secretion system, which belongs to T5SS. It translocates large proteins such as adhesins, and has been identified i n many bacterial pathogens. Xacm encodes for a filamentous hemagglutinin like protein fhaB A complete homolog of this gene can be found in XccA but is inactivated in Xcv by an internal stop codon inducing mutation. In Xacm, the gene is interrupted due to genomic rearrangements, which indicates that it might be inactive. The rearrangement has caused the gene to split with an insertion of 2 hypothetical proteins XACM_1838 and XACM_1839 between the two fhaB fragments. Transposon genes in the vicinity may have instigated this change. fhaB is involved in attachment and biofilm formation in XccA and its loss affects virulence of the bacterium (Gottig et al. 2009) The fhaB gene in Xacm is likely to be inactive due to the insertion and lack of the functional gene could contribute to the lower virulence of Xacm as compared to XccA Type 6 Secretion S ystem (T6SS) Recently a new secretion system was identified in Vibrio cholerae and Pseudomonas aeruginosa named T6SS. T6SS is evolutionarily related to

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55 bacteriophage, likely a reminiscent of phage injection machinery. T6SS has diverse roles in virulence, symbiosis, interbacterial interactions and antipathogenesis in different bacteria (Records 2011) Xcv is found to have two clusters of T6SS; cluster type 1 and cluster type 2, of which the later one is split into two locations. XccA has only cl uster type 2 T6SS, which like Xcv is split into two locations (Boyer et al. 2009) The distribution of the T6SS in all three Xanthomonas is compiled in Table 2 7. Xacm encodes for two clusters, cluster type one from XACM_2098 XACM_2121 and cluster type two from X ACM_4015 XACM_3979. Both the clusters are homologues to the ones found in Xcv. XccA on the other hand has only T6SS cluster type two, encoded from XAC4147 to XAC4112. Bacterial Surface Structures Lipopolysaccharides (LPS) LPS is composed of three distinc t components; membrane anchored lipid A, core oligosaccharide and an O antigen polysaccharide chain LPS serves a dual role as a physical barrier by protecting the bacteria from antibacterial substances produced by plants and also as inducer of plant defen se related genes (Newman et al. 2000). Flanked by highly conserved housekeeping genes for cystathionine gamma lyase ( met ) at one end and electron transport flavoprotein ( etf ) at the other end, the genome of Xacm encodes a cluster of 22 genes that encode ge nes involved in LPS biosynthesis. The LPS gene cluster encoded by 24.5 kb region in Xacm is markedly different both in gene number and composition as compared to the 17 gene cluster in XccA and more so from the 16 gene cluster in Xcv (Fig. 2 11). The flank ing genes of etfB etfA and metB/C are conserved in all the three genomes. The LPS locus of Xacm has at least 6 homologs to XccA and only one to Xcv (Fig. 2 11). The LPS cluster is involved in

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56 synthesis of O antigen polysaccharide. It is known to be import ant for biofilm formation on the host and contributes to virulence. Two such loci XAC3586 and rfbC have been experimentally shown to contribute to virulence of XccA on grapefruit ( Citrus paradisi cv. Duncan grapefruit) (Li and Wang 2011) Xacm does not have homologs for either of these genes This may contribute to the poor survival of Xacm in planta and hence lower virulence as compared to XccA Interestingly, the O antigen ABC transporter encoding wzt gene mutant of XccA showed more water soaking on citrus plants as compared to wild type strain (Laia et al. 2009) XACM_3499 in Xacm is the closest homolog to wzt with a low protein identity of 34% and 41% to its orthologs in XccA and Xcv. Also, the Xacm gene encodes for a truncated protein with half of it missing from the C terminus region as compared to its orthologs and thus, it might be non functional. This may have led to variation in symptoms of Xacm and it shows pronounced water soaki ng as compared to XccA It was also suggested that there is no obvious correlation of the content of the LPS gene cluster with host specificity (Lu et al. 2008) Thus, the variation in the LPS gene cluster among Xacm, XccA and Xcv might contribute to their difference in virulence or symptom development in plant hosts rather than serve as a determinant of their differential host range. In either case, the se diffe rences are consistent with the diversifying selection based on the changes in this locus put forward by Patil et al. stating that LPS locus in plant pathogenic bacteria shows intense interstrain variation due to horizontal gene transfer (Patil et al. 2007) Extracellular P olysaccharides Extracellular polysaccharides (EPS, called xanthan gum in Xanthomonas) are an important component of a biofilm and contributes to epiphytic fitness of Xanthomonas spp. (Rigano et al. 2007) It is postulated to promote colonization of plant tissues by

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57 protecting the pathogens from harsh environmental conditions and to contribute to occlusion of vascular tissues in wilts and blights (Kiraly et al. 1997) Xacm encodes for the complete gum gene cluster from gumA to gumP which is syntenic to those found in XccA and Xcv. The ide ntity of gum genes ranges from 88 100% among the three Xanthomonas species. Since EPS encoding genes are so conserved it is unlikely that EPS plays any role in the difference in virulence and host range of Xacm, XccA and Xcv. Flagella Xanthomonas is kno wn to contain all the genes for flag ellum synthesis and motility. Various genes located in 4 clusters, which are characteristically flanked by transposase genes, encode the flagellum Xacm contains complete flagella structure and motility genes in four sim ilar clusters. The flagellar genes in Xacm are mostly organized in similar order to those in Xcv and XccA (Fig. 2 12). Cluster 1 consists of motA (XACM_3590) and motB (XACM_3592) and cluster 2 of motB (XACM_1939) and motC (XACM_1940). These genes encode fl agellar motor proteins required for rotation of flagella. Cluster 3 in Xacm consists of 24 genes from XACM_1954 to XACM_1977, involved in synthesis and regulation of flagella that is syntenic with XccA and Xcv. The gene fliK in this cluster may be a pseudo gene, which is non functional due to frameshift mutations. Mutations in fliK affect flagellar hook length in animal pathogenic bacteria (Williams et al. 1996) However, no det ectable difference was observed between the motility of XccA and Xacm. Xacm has a cluster comprised of 24 genes from XACM_1991 to XACM_2014, which is highly conserved as compared to both XccA and Xcv.

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58 Interestingly the genes that lie between these cluste rs are different in Xacm as compared to XccA A notable difference includes the absence of homolog of XAC1927 from Xacm. This gene encoding an Fe S oxidoreductase and located on a probable pathogenicity island, has been linked to virulence in XccA (Laia et al. 2009 ) The absence of this gene from Xacm coul d possibly contribute to lower virulence of Xacm pathogen as compared to XccA on citrus. Regulation o f Pathogenicity Factors (Rpf) Cluster The rpf genes control the synthesis of DSF that plays a major role in quorum sensing thus controlling various virule nce factors in XccA (Siciliano et al. 2006) Three core genes rpfF rpfC and rpfG control synthesis of DSF molecule and signal transduction. rpfF is responsible for production of DSF, whereas rpfC / rpfG are two component signaling factors. RpfC is a sensor protein and RpfG is a response regulator. RpfG has a HD GYP domain that regulates the amount of cyclic di GMP. Furthermore this is involved in regulation of the DSF regulon, thus affecting vir ulence of the pathogen XccA (Andrade et al. 2006) In addition to all the rpf genes found in XccA the CBS pathogen Xacm encodes for a functional rpfH which lies nestled between rpfC and rpfG This gene encodes a protein, which is structurally similar to the sensory domain of RpfC. rpfH is also present in Xcv and X. campestris pv. campestris but absent in XccA A study by Slater et al (Slater et al. 2000 ) showed that mutation in rpfH gene in XccA did not affect the DSF pathway and thus its role in this operon is unclear. It would be interesting to study whether its presence affects virulence of Xacm on citrus.

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59 Other Strain Specific Genes that Might Contribute to the Distinct Virulence o f Xcc A a nd Xacm o n Citrus Overall 807 XccA specific genes were missing in Xacm and Xcv. Besides the genes discussed a bove, XccA also contains other genes missing from Xacm that may be responsible for its higher virulence. A plant like natriuretic peptide (XacPNP), which is expressed specifically during the infection process in XccA is one such gene. XAC2654 encodes this plant like hormone that induces changes in host photosynthetic efficiency thereby weakening host defense (Garavaglia et al. 2010b) It has been shown that XacPNP mimics host PNP and results in improved host tissue health and consequently better pathogen survival in the lesions (Garavaglia et al. 2010a) Xacm genome was found to have neither a homolog of XAC2654 nor the surrounding region in its genome. In terestingly, XccA also encodes for genes with putative toxin producing function. The genes syrE1 and syrE2 are similar to those found in Pseudomonas syringae encoding the phytotoxin syringomycin (Etchegaray et al. 2004) These non ribosomal peptide synthetases, which might produce toxins, are absent from Xacm genome. XccA also encodes for haemolysin type calcium binding proteins XAC2197 and XAC2198 along with poten tial secretion genes hlyB and hlyD These genes are also found in the citrus pathogen Xylella fastidiosa and belong to the RTX toxin family (Simpson et al. 2000) They are known to be pore forming cytotoxins which act as virulence factors and individual toxins often exhibit host specificity in eukaryotes (Welch 1991) The region containing the toxin genes is absent from Xacm. Another region of 20 kb from approximately 1.72 to 1.74 Mb is specific to XccA and is not found in Xacm. It contains at least two genes XAC1496 and XAC1507 ( mobL ) that are involved in virulence of the canker pathogen (Yan and Wang 2012) This region has a very low

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60 G+C content of 50% and is surrounded by integrase genes sugg esting that XccA might have acquired it through recent HGT events. These might be potential genes contributing to higher aggression shown by XccA on citrus as compared to Xacm. Conclusion Xanthomonas is a large genus of bacteria that collectively cause di sease on more than 300 plant species. The broad host range of the genus contrasts with stringent host and tissue specificity and differences in symptoms for individual species and pathovars. In the present study we conducted a comprehensive comparative gen omic study to provide insights into the reduced pathogenicity and limited host range of an aggressive strain F1 of Xanthomonas axonopodis pv. citrumelo, causal agent of citrus bacteria spot compared to X. citri subsp. citri strain 306, causal agent of citr us canker. To gain a better understanding of the ecological and evolutionary relationships, we also compared Xacm with the closely related X. campestris pv. vesicatoria strain 85 10 which causes bacterial spot on tomato and pepper. 454 GS FLX pyrosequencin g, paired end Illumina/Solexa sequencing and optical mapping was used to obtain high quality finished genome of Xacm which is 4.9 Mb in size. Phylogenetic relatedness based on a set of nine housekeeping genes from completely sequenced Xanthomonas indicated that Xacm is closely related to XccA and Xcv forming a clade distinct from other xanthomonads. Comparison of chromosome organization using MAUVE showed inversion s (with translocation s ) and major deletions in Xacm compared to XccA and Xcv. Both XccA and Xc v harbor plasmids pXAC64 & pXAC34 and pXCV183, pXCV38, pXCV19 and pXCV2 respectively, containing various genes involved in pathogenesis. The lack of plasmids in Xacm may have contributed to the reduced virulence of the CBS strain. A sharp drop in the G+C c ontent of various regions in the genome of Xacm

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61 indicated that these may have acquired due to horizontal gene transfer. One of the genomic island postulated to be acquired by HGT possess genes encoding for parts of Type IV secretion system (T4SS), componen ts of Type IV pilus and pilus tip associated proteins. Fifty percent of open reading frames in the two biggest regions of the chromosome of Xacm identified to be acquired by HGT were determined as orphan genes. These orphan genes having a very limited phyl ogenetic distribution and no recognizable homologs, may encode functional proteins that might contribute to virulence and/or differential host range of the strain. Comparison of the proteomes of three Xanthomonas spp. using bi directional BLASTp revealed that about three quarters (3,292 CDSs) of the genome of Xacm forms the core set of genes that include conserved house keeping and virulence genes essential for plant infection. Homologs present in both XccA and Xacm may include virulence factors necessary for infecting citrus host. Higher number of similar homologs between Xacm and Xcv compared to Xacm and XccA confirmed the genetic closeness of CBS strain to Xcv. Xacm genome contain 406 unique CDSs, many of which are hypothetical genes and may contribute t o the differences in symptoms and host range. The organization of Type III secretion system (T3SS) gene cluster of Xacm showed close synteny with the hrp cluster of XccA and Xcv, however few major differences were also observed. As compared to Xcv, the T3S S of Xacm lacks several hrp associated outer protein and hypothetical genes; the loss of which might contribute to the variations in host range and virulence. Considerable differences were observed in the effector repertoires present in Xacm, XccA or Xcv s trains. Seventeen effector genes shared by all three strains were defined as core effectors and none of them is likely to be responsible for differences in host

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62 range or virulence among strains. Two species specific effectors, xopC2 and xopW are postulated to play key role in differential virulence and host range of Xacm. E ffectors such as pthA xopE3, xopAI and hrpW were absent from Xacm while present in XccA These effectors might be responsible for survival and the low virulence of this pathogen on citr us compared to that of XccA The contribution of various effectors in determing host range and differences in virulence needs further characterization. Xacm also encodes for several genes involved in Type I and Type II secretion systems. Xacm is deficient in pectate lyase function (belongs to T2SS) as was confirmed by the lack of pitting in Hildebrands agar medium. Type IV secretion system of Xacm codes for one Vir type cluster which shows high similarity to Stenotrophomonas maltophila rather than XccA or X cv. Xacm codes for gene fhaB (belongs to Type V secretion system) which is likely to be inactive due to the insertion. The product of fhaB is a filamentous hemagglutinin protein and the lack of this functional gene could contribute to the low virulence of Xacm compared to XccA which encodes for a fully functional fhaB Xacm codes for two Type VI secretion system clusters both of which are homologs of T6SS of Xcv. The production of LPS is controlled by 22 genes in a cluster in Xacm which is markedly differe nt in number and composition from XccA or Xcv. Several genes in the LPS cluster shown to contribute to the virulence of XccA are either absent or truncated in Xacm which might explain the variation in symptoms between two strains. The organization of 4 clu sters of various genes involved in flagella biosynthesis was similar for all the three strains although differences were observed between the genes which lie between these different clusters. Xacm also lacks various genes, such as syrE1 syrE2 and RTX tox in family genes which are present in XccA The absence of these genes

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63 may be associated with distinct virulence of XccA and Xacm. Overall the comparison of the finished genome sequence of Xacm to those of XccA and Xcv provides insights into the emergence o f new virulent strains with different host range and distinct virulences. Such knowledge contributes to our understanding of bacterial evolution and the role of various systems in virulence and host range of pathogens. These strain specific genes need to b e functionally characterized to understand their roles in virulence and host specificity.

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64 Table 2 1 Overview of sequence data for Xanthomonas axonopodis pv. citrumelo str. F1 Sequencing method 454 sequencing Illumina/Solexa Total reads 367,109 37,695,118 Total sequence output 103,810,015 bp 2,789,438,732 bp Average read length 332 bp 74 bp Genome coverage 20 450 No. of contigs a 72 1350 Note: 454 contigs assembled using Newbler 2.0 and Illumina/Solexa contigs assembled us ing CLCbio Genomics Workbench 4.0 Table 2 2 General features of X. axonopodis pv. citrumelo str. F1 genome Chromosome features XACM Genome Size (bp) 4,967,469 GC content (%) 64.92 Plasmids 0 Protein coding region (%) 86.53 Predicted CDS Protein coding genes 4202 with COGs 3087 with Pfam 3293 with TIGRfam 1314 connected to KEGG pathways 1189 Ribosomal RNA 6 rRNA operons 2 Transfer RNA 54

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65 Table 2 3 Functional classifi cation of annotated sequences in genome of Xanthomonas axonopodis pv citrumelo F1 COG Categories Abbreviation Gene Count % of Total (3481) INFORMATION STORAGE AND PROCESSING Transcription K 233 6.69 Translation, ribosomal structure and biogenesis J 172 4.94 Replication, recombination and repair L 154 4.42 CELLULAR PROCESSES Cell cycle control, cell division, chromosome partitioning D 33 0.95 Cell motility N 129 3.71 Cell wall/membrane/envelope biogenesis M 234 6.72 Posttranslational mod ification, protein turnover, chaperones O 148 4.25 Inorganic ion transport and metabolism P 186 5.34 Signal transduction mechanisms T 260 7.47 METABOLISM Amino acid transport and metabolism E 231 6.64 Carbohydrate transport and metabolism G 21 4 6.15 Energy production and conversion C 194 5.57 Lipid transport and metabolism I 136 3.91 Nucleotide transport and metabolism F 66 1.9 Coenzyme transport and metabolism H 143 4.11 Secondary metabolites biosynthesis, transport and catabolism Q 74 2. 13 POORLY CHARACTERISED Function unknown S 314 9.02 General function prediction only R 373 10.72 Chromatin structure and dynamics B 1 0.03 Cytoskeleton Z 1 0.03 Defense mechanisms V 56 1.61 Intracellular trafficking, secretion, and vesi cular transport U 128 3.68 RNA processing and modification A 1 0.03 Not in COG 1196 27.92

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66 Table 2 4 Coordinates, sizes and G+C contents of the segmented domains of X. axonopodis pv. citrumelo str. F1 genome determined by GC Profile. The eight pote ntially horizontally transferred regions are marked with an asterisk The criteria used for analysis were: Halting parameter = 50; Filtered gap size = 0 bp; Minimum length = 100 bp. Start (bp) Stop (bp) Length (bp) GC content (%) 1 1051658 1051658 65 .58 1051659 1253711 202053 64.01 1253712 1265138 11427 57.66 1265139 1827506 562368 65.27 1827507 1891340 63834 55.09 1891341 2417433 526093 64.72 2417434 2438710 21277 68.41 2438711 2443584 4874 52.11 2443585 26456 28 202044 63.80 2645629 2970112 324484 65.38 2970113 3004362 34250 54.41 3004363 3037313 32951 63.34 3037314 3621975 584662 65.62 3621976 3664589 42614 62.31 3664590* 3686175 21586 57.14 3686176 4550479 864304 65.04 4 550480 4559509 9030 57.70 4559510 4634913 75404 67.92 4634914 4967469 332556 65.49

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67 Table 2 5 Effector repertoire of X. axonopodis pv. citrumelo str. F1, X. citri subsp. citri str. 306 and X. campestris pv. vesicatoria str. 85 10 Effecto r class Xacm XccA Xcv Pfam domains References Core effectors present in all three strains AvrBs2 XACM_0049 XAC0076 XCV0052 Glycerophosphoryl diester phosphodiesterase (Kearney and Staskawicz 1990) Xo pA (Hpa1/HpaG) XACM_0406 XAC0416 XCV0440 (Noel et al. 2002) XopE1 (AvrXacE1) XACM_0271 XAC0286 XCV0294 Putative transglutaminase (Th ieme et al. 2007) XopF2 XACM_2726 XCV2942 (Roden et al. 2004) XopI XACM_0750 XAC0754 XCV0806 F box protein (Thieme et al. 2008) XopK XACM_3001 XAC3085 XCV3215 (Furutani et al. 2009) XopL XACM_3007 XAC3090 XCV3220 LRR protein (Jiang 2007) XopN XACM_2728 XAC2786 XCV2944 ARM/HEAT repeat (Kim et al. 2009) XopP XACM_1178 XAC1208 XCV1236 (Roden et al. 2004) XopQ XACM_4215 XAC4333 XCV4438 Inosine uridine nucleoside N ribohydrolase (Roden et al. 2004) XopR XACM_026 3 XAC0277 XCV0285 (Furutani et al. 2009) XopV XACM_0604 XAC0601 XCV0657 (Furutani et al. 2009) XopX XACM_0532 XAC0543 XCV0572 (Metz et al. 20 05) XopZ XACM_2036 XAC2009 XCV2059 (Furutani et al. 2009) XopAD XACM_4086 XAC4213 SKWP repeat protein (Guidot et al. 2007, Petnicki Ocwieja et al. 2002) XopAE (HpaF/HpaG) XACM_0381 XAC0393 LRR protein (White et al. 2009) XopAK XACM_3563 XAC3666 XCV3786 (Petnicki Ocwieja et al. 2002)

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68 Table 2 5. Continued. Effector class Xacm XccA Xcv Pfam domains References Effectors shar ed by Xacm and Xcv but not present in XccA XopC1 XACM_2129 XACM_2132 XACM_2248 XCV2435 Phosphoribosyl transferase domain and haloacid dehalogenase like hydrolase (Roden et al. 2004) XopF1 (Hpa4) XACM_0384 XCV0414 (Roden et al. 2004) XopAJ (AvrRxo1) XACM_4204 XCV4428 Zeta toxin (Zhao et al. 2004) Effectors shared by XccA and Xcv but not present in Xacm XopE2 (AvrXacE3, AvrXccE1) XACb0011 XCV2280 Putative transglutaminase (Thieme et al. 2007) Effectors unique to XccA PthA (AvrBs3, TAL) XACa0022 (PthA1) XACa0039 (PthA2) XACb0015 (PthA4) XACb0065 (PthA4) Transcriptional activator, nucle ar localization (Algeria et al. 2005) XopE3 (AvrXacE2) XAC3224 Putative transglutaminase (Nimchuk et al. 2007) XopAI XAC3230 Putative ADP ribosyltransferase (Thieme et al. 2005) HrpW (PopW) XAC2922 Pectate lyase (Park et al. 2006)

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69 Table 2 5. Continued Effector class Xacm XccA Xcv Pfam domains References Effectors unique to Xcv AvrBs1 XCVd0104 (Thieme et al. 2005) XopB XCV0581 (Noel et al. 2001) XopD XCV0437 C48 family SUMO c ysteine protease (Ulp1 protease family), EAR motif (Roden et al. 2004) XopG XCV1298 M27 family peptidase clostridium toxin (Thieme et al. 2005) AvrBs1.1 (XopH) XCVd0105 Putative tyrosine phosphatase (Thieme et al. 2005) XopJ1 XCV2156 C55 family cysteine protease or Ser/Thr acetyltransferase (Roden et al. 2004) XopJ3 (AvrRxv) XCV0471 C55 family cysteine protease or Ser/Thr acetyltransferase (Thieme et al. 2005) XopO XCV1055 (Thieme et al. 2005 ) XopAA XCV3785 Early chlorosis factor, proteasome/ cyclosome repeat (Thieme et al. 2005) Effectors unique to Xacm XopC2 XACM_1180 Haloacid dehalogenase like hydrolase (White et al. 2009) XopW XACM_0435 (Furutani et al. 2009) Partial Sequences due to interruption by IS elements during HGT

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70 Table 2 6 Putative Type 2 Secretion System Substrates in X. axonopodis pv. citrumelo str. F1, X. citri subsp. citri str. 306 and X. campestris pv. vesicatoria str. 85 10 Enzymes Gene Xacm XccA Xcv Cellulases egl1 XACM_0030 XAC0028 XCV0029 egl2 XACM_0031 XAC0029 XCV0031 egl3 XACM_0032 XAC0030 XCV0033 XACM_0334 XAC0346 XCV0358 engXCA XACM_0615 XAC0612 XCV0670 XACM_1793 XAC3948 XCV1802 egl4 XACM_2502 XAC25 22 XCV2704 celS XACM_3403 XAC3507 XCV3634 bcsZ XACM_3410 XAC3516 XCV3641 Polygalacturases pgl XACM_0665 XAC0661 XCV0722 pglA -XAC2374 XCV2571 Rhamnogalacturonase rhgB XACM_3402 XAC3505 XCV3632 Beta glucosidase bglS XACM_1437 XA C1448 XCV1505 celD XACM_1816 XAC1793 XCV1823 XACM_2997 XAC3076 XCV3211 bglX XACM_3763 XAC3869 XCV3988 XACM_4105 XAC4231 XCV4337 Pectate lyase --XCV2278 pel -XAC2373 XCV2569 pel1 XACM_2919 pseudogene XAC2986 XCV3132 pel2 XACM_ 3456 pseudogene XAC3562 XCV3687 Xylanase xynC XACM_0913 XAC0933/34 partial XCV0965 XACM_1262 XAC1286 XCV1335 XACM_3080 -XCV3292 aguA XACM_4003 XAC4227 XCV4333 xynA XACM_4122 XAC4249 XCV4355 xynB2 XACM_4125 XAC4252 XCV4358 xynB3 XACM_ 4127 XAC4254 XCV4360

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71 Table 2 6. Continued. Enzymes Gene Xacm XccA Xcv Proteases XACM_0907 XAC0928 XCV0959 XACM_0908 XAC0929 XCV0960 clpA XACM_2027 XAC2001 XCV2049 XACM_2704 XAC2763 XCV2918 XACM_2799 XAC2853 XCV3013 XACM_3437 XAC3 545 XCV3669 htrA XACM_3850 XAC3980 XCV4074 XACM_2775 XAC2831 XCV2993 XACM_0541 XAC0552 XCV0583 xcp XACM_0790 XAC0795 XCV0845 Lipase XACM_0494 XAC0501 XCV0536 Table 2 7 Putative Type 6 Secretion System clusters in X. axonopodis pv. ci trumelo str. F1, X. citri subsp. citri str. 306 and X. campestris pv. vesicatoria str. 85 10 COGs Xcv 85 10 Xacm F1 XccA 306 Cluster 1 Cluster 2 Cluster 1 Cluster 2 Cluster 2 3516 XCV2120 XCV4243 XACM_2098 XACM_4015 XAC4147 3517 XCV2121 XCV4242 XACM_2 099 XACM_4014 XAC4146 3157 XCV2122 XCV4241 XACM_2100 XACM_4013 XAC4145 4455 XCV2123 XCV4240 XACM_2101 XACM_4012 XAC4144 3518 XCV2124 XCV4239 XACM_2102 XACM_4011 XAC4143 3519 XCV2125 XCV4238 XACM_2103 XACM_4010 XAC4142 3520 XCV2126 XCV4237 XACM_2104 XA CM_4009 XAC4141 0542 XCV2127 XCV4236 XACM_2105 XACM_4008 XAC4140 3501 XCV2133 XCV4217 XACM_2111 XACM_3993 XAC4124 3456 XCV2135 XCV4214 XACM_2113 XACM_3991 XAC4122 3522 XCV2136 XCV4211 XACM_2114 XACM_3988 XAC4121 3455 XCV2137 XCV4210 XACM_2115 XACM_398 7 XAC4120 3523 XCV2138 XCV4209 XACM_2116 XACM_3986 XAC4119 3913 XCV2139 XCV4208 XACM_2117 XACM_3985 XAC4118 0631 XCV2140 XCV4207 XACM_2118 XACM_3984 XAC4117 0515 XCV2141 XCV4206 XACM_2119 XACM_3983 XAC4116 3515 XCV2143 XCV4202 XACM_2121 XACM_3979 XAC4 112

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72 Figure 2 1. Alignments between the whole genome optical maps and the in silico genome sequence assemblies at various stages of the project. Dark blue represents cut sites, light blue regions indicate alignment, white regions indicate no alignment. A) An early comparison of an optical map derived from BamH1 digestion of the X. axonopodis pv. citrumelo F1 (Xacm) genome to the assembled scaffolds generated by traditional sequencing technologies. The Xacm optical map derived from BamH1 digestion of the chromosome is presented as a single contig in the center. The sequenced genome contains five scaffolds that have a corresponding match to the optical map. Scaffold 1 is too small to be mapped using current optical map technology. However, during gap closur e it was placed between contigs 3 and 4. The finishing strategy including gap closure was simplified using the optical map as an assembly model. Red arrows indicate where PCR gap closure was done. B ) Comparison of the final assembly of the Xacm genome (top ) to the optical map (bottm) for the BamH1 digest. C ) Comparison of the finished sequence of Xacm (center) to the BamH1 optical map of Xanthomonas axonopodis pv. citri str. 306 (top) and Xanthomonas campestris pv. vesicatoria str. 85 10 (bottom). Dark blue represents cut sites, light blue represents aligned regions, red represents regions aligning to both sequences, and white represents unaligned regions. Alignment lines for inversions and translocations highlighted in pink. Inverted and translocated region s highlighted in yellow.

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73 Figure 2 2. Circular representation of Xanthonomas axonopodis pv. citrumelo F1. Circles from outside to inside: first, scale bar in kilobases; second and third, predicted coding sequences of chromosome on leading and lagging strand respectively (colors according to COGs); fourth, G+C content; fifth, G+C skew.

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74 Figure 2 3. Maximum likelihood tree of the genome of Xanthonomas axonopodis pv. citrumelo F1 showing the relationship to other fully sequenced Xathomonads and rel ated species. The tree was constructed using concatenated protein sequenc es of nine housekeeping genes ( uvrD, secA, carA, recA, groEL, dnaK, atpD, gyrB and i nfB ) aligned using Clustal W. Phylogenic tree from concatenated sequences was constructed in PAUP (version 4.0) using the Maximum likelihood method. The sequences of Ralstonia solanacearum strains GMI1000 & PSI07 and Burkholderia cenocepacia strain NCTC 10247 were used as out group species. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. Horizontal scale bar (0.1) at th e bottom represents number of am ino acid substitutions per site.

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75 Figure 2 4. MAUVE alignment of the genome sequences of the g enome of X. citri subsp. citri str. 306, X. axonopodis pv. citrumelo str. F1 and X. campestris pv. vesicatoria str. 85 10. Conserved and highly related regions are colored and low identity unique region are in white (colorless).

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76 A B Figure 2 5. GC pro file and GC content of XACM genome. A) The negative cumulative GC profile for the genome of XACM marke d with the segmentation points The segmentation points are obtained at t0= 50. B) Plot representing the distributions of G+C content along the XACM genom e. It shows at least six regions of low GC content, which are recognized as genomic island.

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77 Figure 2 6. Venn diagram representing the pan genome of X. axonopodis pv. citrumelo F1 (XACM), X. campestris pv. vesicatoria str. 85 10 (XCV) and X. citri su bsp. citri str. 306 (XCCA). Numbers in brackets represent the protein coding genes on chromosome of each species.

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78 Figure 2 7. Comparison of the hrp gene cluster in the genomes of X. citri subsp. citri str. 306, X. axonopodis pv. citrumelo str. F1 and X. campestris pv. vesicatoria str. 85 10. Arrows indicate individual genes. Homologues genes are colored and low identity or unique genes are white. Figure 2 8. Comparison of the xps and xcs gene cluster in the genomes of X. citri subsp. citri str. 306 X. axonopodis pv. citrumelo str. F1 and X. campestris pv. vesicatoria str. 85 10. Arrows indicate individual genes and homologues genes have same color.

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79 Figure 2 9. Comparison of the pecate lyase production by X. citri subsp. citri str. 306, X. axonop odis pv. citrumelo str. F1 and X. campestris pv. vesicatoria str. 85 10. lyase positive strains are inoculated: XAC and XCV. No pitting is seen for XACM. All str ains were incubated days. Figure 2 10. Comparison of the T4SS gene clusters in the genomes of X. citri subsp. citri str. 306, X. axonopodis pv. citrumelo str. F1 and X. campestris pv. vesicatoria str. 85 10. Arrows indicate indiv idual genes and homologues genes have same color.

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80 Figure 2 11. Relative organization of the LPS gene cluster in the genomes of X axonopodis pv. citrumelo str. F1, X. citri subsp. citri str. 306 and X. campestris pv. vesicatoria str. 85 10. Comparison of LPS gene cluster (not to scale). Conserved and highly related genes are colored and low identity or unique genes are white.

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81 Figure 2 12. Comparison of the flagella gene clusters in the genomes of X. citri subsp. citri str. 306, X. axonopodis pv. citrumelo str. F1 and X. campestris pv. vesicatoria str. 85 10. Arrows indicat e individual genes and homologou s genes that have same color.

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82 CHAPTER 3 GENE CONTENT OR GENE EXPRESSION, WHICH DE TERMINES THE DIFFERENCE IN HOST R ANGE AND VIRULENCE O F STRAINS OF X anthomonas citri subsp citri ? I ntroduction The co evolution of plants and microbes is a dynamic process and results from hundreds of millions years of co existence. Luckily, plants are resistant to most microbes. On the other hand, outbreaks of new d iseases have been common and caused disastrous consequences in human history (Plank et al. 1963; McMullen et al. 1997) Those diseases likely result ed from introduc tion of the pathogens to new areas and to new crops or the endemic pathogens overcoming the plant defense systems. Multiple models have been proposed to describe the co evolu tion of plants and microbes (Chisholm et al. 2006; Jones and Dangl 2006; Barrett et al. 2009; Genin 2010 ). Dramatic effort s have been focused on understanding the mechanism s of how pathogens expand their host range by studying the molecular determinants of virulence and host range of different pathogens (Kay and Bonas 2009; Arnold and Jackson 2011; Ryan et al. 2011; Lindeberg 2012 ). Knowledge of such mechanism s is critical to prevent, slow down, or prepare for the outbreaks of new diseases. Xanthomonas is one important model genus for s tudy ing the host microbe interactions and members of this genus are capable of infecting at least 124 monocotyledonous and 268 dicotyledonous p lants (Chan and Goodwin 1999) Among the diseases caused by Xanthomonas citrus canker caused by X. citri s ubsp citri (Xcc) is an important disease that has severe economic impact on citrus industries worldwide. Asiatic (A) type canker is the most widespread and destructive form of citrus canker It produces hyperplasic and hypertrophic (raised) lesions surro unded by oily or water

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83 soaked margins and a yellow halo on leaves, stems, and fruits. Besides Xcc, X fuscans subsp. aurantifolii (Xau) is also known to cause citrus canker with limited geographic distribution and limited host range. XauB is restricted to South America (Argentina, Uruguay and Paraguay) and causes canker B. It mostly affects lemon ( C. limon ) and Mexican lime ( C. aurantifolia ) but is also found on sweet orange ( C. sinensis ) and grapefruit (Civerolo 1984) XauC is restricted to Brazil and causes canker C only on Mexican lime (Stall 1991) Compared to Xau, XccA has a broad host range and affects most commercial citrus varieties within the Rutaceae family including grapefruit ( C. paradisi ) and M exican lime (Verniere 1998 ; Sun 2004) Two variants of XccA have also been identified. The variant designated A* was found in s outheast Asia in the 1990s infecting C. aurantifolia (Vernire et al. 1998) The second variant was described by S c hubert et al. discovered in Florida in late 1990s (Schubert et al. 2001) This variant designated as the characterized by Sun et al. (2004) This strain of X. citri subsp. citri strain A w (Xcaw) was f ound to be pathogenic to Mexican lime and alemow ( C. macrophyla ) plants, but not to grapefruit and orange. DNA reassociation analysis showed that Xcaw is closely related to XccA and XccA strains as compared to XauB and XauC strains (Sun et al. 2004). Both Xcaw and XccA cause similar symptoms on Mexican lime and the populations were similar in th is susceptible host (Rybak et al. 2009) The Xcaw strain also causes a hypersensitive reaction (HR) in grapefruit ( Rybak et al. 2009 ). AvrGf1 has been shown to be involved in affecting the host range of Xcaw AvrGf1, an avirulence factor, interacts with the grapefruit host plant and induces the hypersensitive response ( HR )

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84 reaction ( Rybak et al. 2009 ). Mutation of a vrGf1 expands the host range of Xcaw to include C. paradasi al though the symptoms are much reduced as compared to XccA ( Rybak et al. 2009 ). Thus, it was suggested that Xcaw contains other unidentified factors that are involved in host range limitation. A comprehensive understanding of the molecular mechan ism s responsible for the differences in virulence and host range of Xcaw and XccA is lacking. Comparative genomic analyses of xanthomona d s have greatly facilita ted our understanding of the suite virulence factors and host range determinants of different p athogens (da Silva et al. 2002; Jalan et al. 2011; Moreira et al. 2011) Comparative genomic analysis of X campestris pv. campestris and Xcc A has been conducted previously to provide a framework for understand ing the mechanisms of differing host range an d pathogenic processes of the two Xanthomonas species which have distinct host specialt y (d a Silva et al. 2002). Compared to Xcc which infect s citrus and caus es citrus canker, X. campestris pv campestris affects crucifers such as Brassica and causes bla ck rot. Numerous species specific genes have been suggested to contribute to the difference s in virulence and host range of the two pathogens. Comparative genomic analysis of Xcc A and X axonopodis pv citrumelo also contributed to the understanding of the m echanism s of bacterial virulence and host specificities. X axonopodis pv citrumelo is the nursery infecting strain and shows low virulence on citrus compared to that of Xcc A. D ifferences in gene contents, such as type III effectors (e.g. PthA), the typ e IV secretion system, and lipopolysaccharide synthesis were identified and may contribute to the difference s in bacterial virulence and host range (Jalan et al. 2011 ; Potnis et al. 2011 ). Furthermore, sequencing of XauB and XauC

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85 strains revealed the con tribution of different virulence factors affecting host range of closely related species (Moreira et al. 2011) As mentioned above, the p revious comparative genomic studies have mainly focused on contribution of the differences in gene content to the diffe rences in virulence and host range (da Silva et al. 2002; Jalan et al. 2011; Moreira et al. 2011; Potnis et al. 2011). The contribution of gene expression due to nucleotide differences in promoter regions and the differences in regulators ha s been largely ignored. It is known that bacteria coordinate different virulence factors using complex regulatory system s to infect plants We hypothesized that not only gene content but also gene expression contribute to the difference s in virulence and host range of ba cterial pathogens In this study, we tested our hypothesis by combining comparative genomic and transcriptome analyses to understand the differences in virulence and host range of Xcaw and XccA strains. We completed genome sequencing of X. citri subsp. c itri strain A w 12879 and compared it with the closely related strain XccA (d a Silva et al. 2002). We further examined the transcriptomes of both XccA and Xcaw by Illumina sequencing of cDNAs via RNA Seq in nutrient rich condition Nutrient broth (NB) and in XVM2 which is known to mimic the conditions in the intercellular space of plant cells (Wengelnik et al. 1996a) Combining comparative genomic and transcriptome analyses provides novel insights in to the mechanism s of virulence and host range of pathogens. Our data suggests that both gene content and gene expression contribute to virulence and host range of bacterial pathogens.

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86 M aterials And Methods Bacterial Strain and DNA S equencing Genomic DNA was extracted from bacterial culture grown over night at 28 C in N B using a Wizard DNA purification kit (Promega, USA.) according to the spectrophotometrically (Nanodrop ND 1000, NanoDrop Tech. Inc., Wilmington, DE). Two high throughput seque ncing techniques, 454 P yrosequencing and Illumina Solexa GA sequencing were used for whole genome sequencing. Single and paired end reads were generated on a 454 GS FLX Titanium sequencer (454 Life sciences, Branford, CT) in accordance with the manufacture Biotechnology Research (ICBR), University of Florida. Paired end Illumina sequence reads were obtained using Illumina Genome Analyzer IIx (Illumina, Hayward, CA, USA) at Yale center for genomic analysis. A de no vo Bam HI optical map of the genome of Xcaw was generated by OpGen technologies (Madison, Wisconsin, USA). Plasmids were extracted using the Wizard Plus SV Minipreps DNA purification system (Promega, Madison, Wisconsin, USA) and sequenced using 454 GS FLX t itanium sequencer giving paired end reads. Data A ssembly and A nnotation The total reads obtained by the two sequencing methods (Table 3 1) were trimmed prior to assembly. For de novo assembly, the 454 sequencing reads were assembled into contigs using Newb ler 2.0 and further grouped into scaffolds using paired end reads. Illumina reads were assembled using CLC Genomics Workbench (V5.0, CLC Bio) with length fraction and frequency set at 0.8 and all other parameters set as default values. The Illumina contigs were aligned against the 454 scaffolds using

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87 BLASTn to confirm the orientations and integrity of the assembled sequences and to close gaps and link contigs together within the scaffold. In silico Bam HI restriction maps of the scaffolds were constructed an d aligned to the optical map according to their restriction fragment pattern, using MapSolver v.3.1 software (OpGen Technologies, Inc.). The orientations of scaffolds were corrected as deemed by the alignment and Illumina contigs were used to close the gap s between the scaffolds. Final assembly was correlated with the optical map for further validation. Annotation was done as described by Jalan et al. (2011). In short the predicted proteins were annotat ed by similarity searches against the NCBI Non redundant (nr) protein database (http://ncbi.nlm.nih.gov) and clusters of orthologous groups (COG) database. The results of the automated annotation were examined and curated manually using the JGI GenePRIMP p ipeline (Pati et al. 2010) Phylogenetic and Comparative A nalysis The deduced pr otein sequences of nine housekeeping genes ( uvrD, secA, carA, recA, groEL, dnaK, atpD, gyrB and infB ) from 11 completely sequenced Xanthomonas spp. were used to determine the position of Xcaw within the evolutionary tree. Additional sequences from two draf t X. aurantifolii strains and three Xylella fastidiosa strains were also used along with Burkholderia mallei NCTC 10247 as out group species. As stated in a previous work by Jalan et al. (2011), amino acid sequences were aligned using clustal W (Larkin et al. 2007) A phylogen et ic tree was constructed from the concatenated sequences using PAUP 4.0 (Swafford 2003) by the maximum likelihood method. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) is shown next to the branches in the tree.

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88 For co mparative analyses, the sequences of XccA strain 306 (GenBank accession no. NC_003919, NC_003921.3 and NC_003922.1) were retrieved from GenBank. Complete genome sequences of XccA and Xcaw were aligned and visualized in progressive mode using MAUVE (Darling et al. 2010) A two way BLAST of the protein sequences was done to identify unique genes in each strain. The genes aligned based on amino acid sequence wer e considered orthologous if reciprocal BLASTp hits was found between two genes with e value less than or equal to 10 20 and alignments exceeding 70% sequence identity and 70% query gene length. A gene was considered singleton or unique to each strain if i t had no hits with an e values less than or equal to 10 5 Preparation of RNA Samples for Transcriptome A nalysis RNA sample preparation and cDNA library generation was performed according to procedures outlined by Filiatrault et al. (2010) with some modif ications. RNA samples were extracted from XccA and Xcaw grown to OD560 of 0.4 in XVM2 medium and NB medium at 28C on shaker at 200 rpm. The starting OD560 for each culture was 0.03. Three biological replicates of each strain in each medium were used for R NA extraction. When the OD560 reached 0.4 for each condition, RNA was stabilized immediately by mixing the culture with two volumes of RNAprotect bacterial reagent (Qiagen, Valencia, CA). The cells were centrifuged at 5000g at 4C and cell pellets were tr eated with lysozyme and RNA extractions were performed using RiboPure bacteria kit (Ambion, Austin, TX) as per manufacturers' instructions. Contaminated genomic DNA was removed by treatment with TURBO DNA free kit (Ambion, Austin, TX). Total RNA samples we re quantified using spectrophotometry (Nanodrop ND 1000, NanoDrop

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89 Tech. Inc.). RNA quality was assessed using the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA). mRNA Enrichment and Library C onstruction mRNA was enriched from total RNA by c omplementary oligonucleotide hybridization using MicrobExpress kit (Ambion) with the Pseudomonas module to remove the 23S and 16S ribosomal RNAs (rRNAs). Removal of rRNAs was assessed using an Agilent Bioanalyzer. Double stranded cDNA synthesis was done us ing the Illumina mRNA Sequencing sample preparation guide method (Cat. No. RS 930 1001) in accordance with the manufacturer's standard protocol. Enriched mRNA was fragmented via incubation for 5 min at 94C with the Illumina supplied fragmentation buffer. The first strand of cDNA was synthesized by reverse transcription using random oligo primers. Second strand synthesis was conducted by incubation with RNAse H and DNA polymerase I. The resulting dsDNA fragments were further end repaired, and A nucleotide o verhangs were added. After the ligation of Illumina adaptors, the samples were run on a denaturing gel and the band correlating to 200 (25) base pairs on the denatured DNA ladder was selected. The selected DNA constructs were amplified by PCR using the pr imers provided in the Illumina library kit. The amplified constructs were purified and the library was validated using Agilent 2100 bioanalyzer. Illumina S equencing and Alignment Paired end, 75 cycle sequencing of the libraries was performed using an Illum ina GAIIx at Yale center for genomic analysis by loading each sample onto a single lane of a flow cell. The raw sequencing reads were further analyzed using CLC Genomics Workbench (V5.0, CLC Bio). The reads were trimmed using the quality score limit of 0.0 8 and maximum limit of 2 ambiguous nucleotides. The trimmed reads were mapped

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90 XccA strain 306 (GenBank accession no. NC_003919, NC_003921.3 and NC_003922.1) and Xcaw strain 12879, with the parameters allo wing mapping of reads to the genome with up to 2 mismatches. The reads mapped to rRNA and the reads not uniquely mapped were removed from further analysis. per kilobase of exon model per m Mortazavi et al. (2008). Differential Gene Expression A nalysis The differential gene expression of the pooled samples from each condition was analyzed using CLC Genomics Workbench (V5.0, CLC Bio). RPKM values we re normalized using quantile normalization and further log 2 transformed for statistical analysis. Box plots, hierarchical clustering of samples and principal component analysis were done to examine data quality and comparability. A t test was performed on log 2 transformed data to identify the genes with significant changes in expression between the two growth conditions and between the two strains. The p values were adjusted for the false discovery rate (FDR) using the Benjamini and Hochberg method (1995). Differentially expressed genes were ranked based on FDR, and genes with FDR < 0.05 and log 2 fold change > 1 were considered as overexpressed whereas those with log 2 fold change < 1 were down regulated Quantitative Real Time One Step RT PCR To verify the RNA Seq result, qRT PCR assays were carried out using the same set s of RNA for RNA Seq analysis. Gene specific primers listed in Table 3 2 were designed to generate sequences of 100 250 bp in length from the XccA genome. qRT PCR was performed for all 3 bi ological replicates of XccA and Xcaw grown in NB and

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91 XVM2 on a 7500 fast real time PCR system (Applied Biosystems) using QuantiTect TM SYBR Green RT was used as an endogenous control. The fold change of gene expression was calculated by using the formula 2 T (Livak and Schmittgen 2001) The fold change was further log 2 transformed to compare with the RNA Seq differential gene expression values. Pathogenicity Assay Pathogenicity assays were conducted in a quarantine greenhouse facility at Citrus Research and Educatio n Center, Lake Alfred, FL XccA, Xcaw, and strains were grown with shaking overnight at 28C in NB, centrifuged down and suspended in sterile tap water and the concentrations were adjusted to 10 8 cfu / ml. T he bacterial solutions were infiltrated into fully expanded, immature leaves of Duncan grapefruit Valencia sweet orange and Hamlin, with needleless syringes (Guo et al. 2011 ) The test was repeated three times with similar results. Disease symptoms were photographed 5, 10, and 1 4 days post inoculation (DPI). Generation of the xopAF M utant and xopAF, avrGf1 Double M utant To construc t the xopA F deletion mutant, the 1096 bp fragment containing entire xopA F gene was amplified using genomic DNA of Xcaw 12879 as template and primers xopAFF1 and xopAFR This resulted in F1, containing a Bam HI restriction site within the xopAF gene. A 422bp fragment containing 347bp of xopA F gene and its downstream region was amplified further from F1 using primers xopAFF2 Bam HI and xopAFR (Table 3 2 ), resulting in F2. Both F1 and F2 were digested with Bam HI and fragments F3 (414bp) and F4 (500bp) were gel p urified. The fragments were ligated and cloned into pGEM T easy vector, resulting in the construct na med pGEM F that was

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92 confirmed by PCR and sequencing From pGEM F, an Apa I Pst I fragment containing xopA F gene with internal deletion was transfer red into Apa I Pst I digested suicide vector pNTPS138 resu lting in pNTPS F. The construct pNTPS F was transformed into E. coli The construct was purified from E. coli an d in a previous study (Rybak et al. 2009) by electroporation. T ransformants were selected on NA med ium supplemented with Kanamycin Positive colonies were replicated on both NA plates supp lemented with 5% (w/v) sucrose and Kanamycin and only NA and Kanamyci n The sucrose sensitive colon ies were selected from NA plus Kanamycin plate and grown in NB medium overnight at 28 C The culture was then dilution plated on NA containing 5% sucrose to select for resolution of the construct by a secon d cross over event. The resulting deletion mutant of xopA F and double mutant of xopAF and avrGf1 was confirmed by PCR. Growth Assay in planta F F strains were grown with shaking overnight at 28C in NB, centrifuged down an d suspended in sterile tap water and the concentrations were adjusted to 10 6 cfu / ml. T he bacterial solutions were infiltrated into fully expanded, immature leaves of Duncan grapefruit Mexican Lime and Valencia sweet orange with needleless syringes (Guo et al. 2011 ) To evaluate the growth of various Xcc strains and mutants in these plants 2 inoculated leaves were collected from each plant at 0, 2, 4, 7, 10, 14 and 21 days. 1 cm 2 leaf disks from inoculated leaves we re cut with a cork borer and then ground in 1 ml sterile water. These were serially diluted and plated on NA plates. The bacterial colonies were

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93 counted after 3 day incubation at 28C The test was repeated three times independently Pectate Lyase and Prot einase A ssay Xcc and Xcaw were grown on nutrient agar at 28C, then suspended in sterile used to test for pectolytic activity (Hildebrand 1971) In short the medium contained bromothymol blue dye, calcium chloride, 2% sodium polypectate and 0.4% agar. The pH was adjusted to 4.5, 7.0 and 8.5 for the medium A, B and C. One were inoculated onto the plates and incubated at 28C for 6 days before confirming pitting due to pectate lyase production. 10% skim milk agar was used to test the ba cterial protease activity. The cultures were grown and suspended in sterile water as explained above. One milk plates and cultured at 28C for 6 days to observe protease activity. D ata A ccess The genome seq uences of Xcaw are available at GenBank under the accession numbers CP003778, CP003779 and CP003780. The RNA Seq data from this study are available in the NCBI's Gene Expression Omnibus database under the accession number GSE41519. R esults Genome S equenci ng of Xcaw Xcaw strain 12879 was isolated from Palm Beach county, Florida prior to 2004 (Sun et al. 2004). To generate a high quality finished genome we combined two independent sequencing approaches; 454 and Illumina sequencing. Table 3 1 shows an overvie w of the reads from both the technologies that were assembled into contigs

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94 separately. The 378 contigs generated by 454 Pyrosequencing were grouped into 17 scaffolds based on paired end reads. De novo assembly of solexa reads yielded 1,426 contigs, which w ere used to confirm the 454 Pyrosequencing scaffolds and close the gaps within them. The 17 scaffolds were further aligned to the Bam HI optical map that revealed several misassembles and changed orientation of the scaffolds (Fig. 3 1A ). The changes were ma de as per the optical map and gaps between the scaffolds were closed using the 454/Illumina contigs and by primer walking. The complete genome was further validated by manually checking a ll areas of imperfect match between the optical map and the sequence assembly (Fig. 3 1B ). Table 3 3 shows the genome features of Xcaw12879, which is comprise d of a single circular chromosome of 5.3 Mb and two plasmids pXcaw19 and pXcaw58 of approx. 19 kb and 58 kb respectively (Fig. 3 2 ). The genome consist s of 4 675 ann otated protein coding sequences (CDS) and 54 structural RNAs (Table 3 3 ). After annotation and manual curation 3,423 CDSs could be assigned to one or more COG functional classes whereas 1,252 could not be assigned to any COG category. M ultil ocus sequenci ng test (M LST ) based phylogenetic analysis was performed for Xcaw12879 and other Xanthomonas using 9 housekeeping genes ( uvrD, secA, carA, recA, groEL, dnaK, atpD, gyrB and infB ) that are highly conserved in bacteria. We aligned the nine nucleotide sequen ces, concatenated them and constructed a maximum likelihood phylogenetic t ree (Fig. 3 3 ). We ascertained that Xcaw is closely related to XccA The two Xcc strains, which are the most closely related, fo rm a separate clade from the other two citrus canker c ausing bacteria XauB and XauC.

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95 Chromosome Organization and Genome P lasticity The genome of Xcaw shows the presence of insertion sequence (IS) elements, phage related genes and plasmids, which are all important sources for genome evolution of bacteria (Mira et al. 2002) Whole genome alignment of Xcaw to closely related XccA using MAUVE in progressive mode revealed many inver sions and translocations (Fig. 3 4 ). Most of the separated blocks in the alignment are assoc iated with integrases and/or IS elements on at least one of their borders. The IS elements have been known to aid horizontal gene transfer and other genome rearrangements as seen in the alignment above. The Xcaw genome also shows various insertions and del etions through out the genome as seen in Fig. 3 4 Xcaw12879 genome consists of two plasmids pXcaw19 and pXcaw58 that are significantly different from the plasmids found in XccA. Plasmid pXcaw19 sequence has no homology with the plasmids of XccA 306 wherea s pXcaw58 is only about 35% similar to pXAC64. Plasmid pXcaw58 consists of pthAw2 gene, a homolog of pthA4 which is capable of conferring the ability to cause canker like symptoms (Al Saadi et al. 2007) However, the plasmid pXcaw58 does not contain the Vir like type IV secretion system genes foun d on pXAC64 (Fig. 3 5 ). The type IV secretion system has been shown to contribute to virulence in X. campestris pv. campestris strain 8004 (Qian et al. 2005) and absence of these genes from the plasmid could affect virulence of Xcaw strain. The BLAST p analysis of all the proteins from Xcaw and XccA revealed various gene clusters specific to each strain. Of the 4 ,76 0 proteins from Xc aw and 4 427 proteins from XccA, 4 034 proteins are found to be orthologous using the cut off, e 20 and ali gnments > 70% sequence identity and, > 70% query gene length.

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96 Xcaw has 726 proteins that are either are non orthologous to proteins from X ccA whereas XccA has 393 such proteins. The hrp and hrc gene s encoding t he TTSS in Xcaw are homologous to the hrp and hrc genes found in XccA. All the genes are found in similar order with the exception in gene annotation between hrpF and hpaB The genom e of XccA contains the annotated gene, XAC0395 between the two, which is a hypothetical protein. The annotation in Xcaw in the same region is on the opposite strand and contains hpaI (XCAW_0080 3 ) and pseudogene xopF1 (XCAW_0080 4 /XCAW_0080 5 ). The nucleotid e sequences in both strains are same and the differences in annotation were confirmed by BLAST similarity of the annotated genes in Xcaw to other xanthomonads. Our RNA Seq data supports our annotation of hpaI and xopF1 (data not shown). The TTSS transloca tes effector proteins into the plant cells These proteins further cause disease in plants via different mechanisms (Bttner and Bonas 2010) The effectors can either aid in nutri ent acquisition and virulence or ac t as avirulence factors that trigger host immune response. The type III effector genes in Xcaw were predicted by BLAST analysis against the known TTSS effector database (http://www.xanthomonas.org). The TTSS effectors of Xcaw showed notable differences i n comparison to effectors in the other three citrus canker causing strains XccA, XauB, and XauC as summarized in Table 3 4 Xcaw contains thirty two effector genes of which nineteen are present in all four sequenced citrus canker causing variants (XccA, Xca w, XauB, and XauC) compared and thus represent the core effector set for Xanthomonas that cause citrus canker. The effector genes avrBs2, xopK, xopL, xopQ, xopR, xopX and xopZ are found in all other

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97 sequenced Xanthomonas genomes and hence the 7 genes might be a core set of effectors required for phytopathogenicity as suggested by Moreira et al. (2010) Twelve effector genes ( xopA, xopE1, xopE3, pthA4 or its functional homologs xopI, xopV, xopAD, xopAI, xopAK, xopAP hpaA and hrpW ) are present in all four genomes that were compared (Xcaw, XccA, XauB and XauC). Thus these effectors might be necessary for causing disease on citrus host but not on other hosts. Some of these 1 2 effectors might act as avirulence genes in other hosts and activate the plant immune system. Two effector genes avr G f1 and xopAF were identified in Xcaw, XauB and XauC but were not present in XccA genome ( Table 3 4 ) Multiple genes clustered into 9 groups were identified in Xcaw but not in XccA (T able 3 5 ) Most genes of the clusters except cluster 1 of Xcaw have homologs with other Xanthomonas species. These regions contain transposase, integrase or phage related genes indicating horizontal gene transfer. The most prominent difference noted in th e above mentioned regions is cluster 8, which encodes for lipopolysaccharide (LPS) biosynthetic pathway. Interestingly, the LPS cluster in Xcaw is chimeric which contains regions orthologous to both XccA and X. oryzae pv. oryzicola BLS256 as shown in Fig. 3 9 which indicates that there has been horizontal gene transfer. The Xcaw unique clusters also encode large numbers of phage related genes (Table 3 5 ) Pathogenicity and Growth Assays The three strains of Xanthomonas affecting citrus, Xcaw, XauB and Xau C but not XccA have either complete avrGf1 o r partial sequence and xopAF genes in their genomes. The gene avrGf1 has been earlier studied in Xcaw and is known to be responsible for HR in grapefruit (Rybak et al. 2009). However its eff ect on other vari e ties of citrus such as sweet orange is unknown. Also, since xopAF is the other

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98 putative effector gene its effect on host limitation was further characterized by pathogenicity and growth assays of Xc Xc aw 1 Pathogenicity assays indicated that Xc aw did not elicit a reaction on Valencia or Hamlin while wild type strain XccA caused typical necrotic raised lesions typical of citrus canker on the leaves at a high bacterial inoculation concentration of 10 8 cfu/ml (Fig. 3 7 ). Xc aw showed a hyper sensitive reaction on Grapefruit leaves that was abolished by deleting avrGf1 gene ( Xc aw visibly reduced as compared to XccA strain. Xc aw reaction on e ither Valencia or Hamlin (Fig. 3 7 ) To check whether mutation of xopAF affects Xcaw growth in planta the wild type strain XccA, Xcaw were inoculated into Grapefruit, Mexican Lime and Vale ncia leaves. As shown in Fig. 3 8A the population of X caw is much lower as compared to XccA in grapefruit. This is restore d to some extent in which causes symptoms on grapefruit. However, the populations of order magnitude lower than that of Xcaw and mutation of xopAF gene has slowed the growth of Xcaw in planta Similar trend was observed in Mexican Lime where the growths of xopAF single and xopAF avrGf1 double mutants were lower as compared to Xcaw and Xcaw 8B ). No significant changes were obse rved in Valencia leaves as neither Xcaw nor any of its mutants grew well in the sweet orange variety as compared to XccA (Fig 3 8 C).

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99 Transcriptome A nalysis of Xcaw and XccA U nder N utr ient Rich (NB) and Plant Intercellular S pace M imic ing (XVM2) C onditions To determine the differential gene expression amongst the strains of X. citri subsp citri we grew Xcaw and XccA under nutrient rich condition in Nutrient Broth (NB) and in XVM2 that mimics the plant intercellular growth environment (Wengelnik et al. 1996 a ) Three biological replicates of the strains were used to collect cells at O.D. 0.4 ( Fig. 3 10 ) and extract the total RNA, enrich for mRNA and sequence cDNA for RNA Seq Over 45 million reads were obtained on ave rage for each sample. After trimming and mapping approximately 96% of the reads were mapped to the genomes (data not shown) indicating th at RNA Seq provides high quality reads suitable for Xanthomonas transcriptomics. Of all the reads over 6.5 million coul d be mapped from each sample to mRNA specifically ( Table 3 6 ) giving the enrichment of mRNA up to 28.5% or less. Overall, the three biological replicates gave an average coverage of approximately 98 times for each gen e, thus resulting in deep sequencing of the Xcc transcriptome which c ould cover majority of the genes transcribed. To quantify the expression of each gene, the reads aligned to each gene were pooled and normalized for gene size by calculating the RPKM values (reads per kilobase CDS length per m illion reads). The values for each gene from all the replicates were further quantile normalized to test them statistically. The resulting values were log 2 transformed and t test was performed on these expression values to compare differential gene express ion (DGE) between XccA and Xcaw under the same growth conditions or between the same strains in NB or XVM 2 growth conditions. High correlation was observed between differential expression values of biological replicates ( Table 3 7 ) signifying that the meth od was reproducible.

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10 0 Principal component analysis indicates that the biological replicates of XccA formed a separate cluster from Xcaw in both the growth conditions ( Fig. 3 11 ). One step quantitative RT PCR (qRT PCR) was used to validate the RNA Seq data. Eight genes were chosen (Table 3 2 ) which were differentially expressed in Xcaw as compared to XccA under both NB and XVM2 growth conditions to compare data obtained from the two methods. The resulting transcriptional ratio from qRT PCR analysis was log 2 t ransformed and t test was performed to compared with the DGE val ues obtained by RNA Seq (Fig. 3 12 ). Although the scale of fold changes between the two techniques is different, high correlation coefficient of 0.87 verifies that the general trend of gene ex pression is consistent for both the data sets. We studied the expression profile of Xcc strains in XVM2 as compared to NB. At the cut off of log 2 showed differential expression (173 up regulated and 119 down regulated in XVM2 compared to NB ) in XccA (Table 3 8 ) and 281 genes (129 up regulated and 152 down regulated in XVM2 compared to NB) for Xcaw ( Table 3 9 ). The entire TTSS cluster consisting of 25 genes except one gene (XAC0395) was up regulated in XVM2 for both XccA and Xcaw strains ascertaining that XVM2 is an excellent hrp inducing medium (Tables 3 8 and 3 9 ). Among all the effectors 16 were induced for XccA whereas 19 effectors were overexpressed for Xcaw in XVM2. As identified in this study, the effectors avrBs2, xopA, xopE1, xopE3, xopI, xopX, xopZ1, xopAD, xopAP, xopAQ, hpaA, xopN and xopP were up regulated in both strains while pthA1 pthA2 avrXacE3 and xopK were induced only in XccA and xopL, xopR, xopAI, xopAK, xopAF and xopAG only in Xcaw strain. In addition, one putative effector gene was identified in XccA in this study.

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101 XccA contains one currently unannotated gene encoding XopAQ between XAC3223 and XAC3224. This region was identified as differentially expressed intergenic region in XVM2 medium as compared to NB. An open reading frame was identified at this region which showed log 2 fold change of 1.8 13 ). BLAST analysis revealed that the ORF encodes for putative XopAQ effector protein, 100% identical to XCAW_03514 in Wellington strain and 85% identical to XGA_2091 from X. gardneri (Potnis et al. 2011). Further BLAST anal ysis also revealed presence of this ORF in XauB located between XAUB_14670 and XAUB_14680. The 11 gene xps cluster encodes f or type II secretion system (T2 SS) in Xanthomonas secreting various enzymes including pectate lyase, cellulase, and xylanase. The x ps genes were down regulated in XVM2 as compared to NB for Xcaw with xpsE being the most significantly down regulated with log 2 fold change 1.07 at FDR = 0.03. XpsE is known to be a key component of T2SS, the loss of which leads to lower virulence in X. o ryzae (Sun et al. 2004). For XccA, the xps genes were not down regulated. Besides the TIISS genes, at least 22 genes encoding TIISS substrates in XccA were overexpressed in XVM2 as compared to only 12 in Xcaw. To the contrary 11 genes for Xcaw and 8 for X ccA were down regulated (Tables 3 8; 3 9 ). Our analysis showed that all the flagella biosynthesis genes encoded by flg and fli motility by mot and chemotaxis by mcp che and tsr were repressed in XVM2 for XccA and Xcaw except cheY (XAC3284 in XccA and XCAW_03412 in Xcaw) and tar (XCAW_03417, XCAW_04009 and XCAW_02497). The genes encoding LPS were down regulated in both strains, whereas the xanthan gum (EPS) genes were overexpressed in both except gumP in XccA. This is in concurrence with the infection

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102 cycle where the bacterial motility will be suppressed to help it attach and colonize with the help of extracellular polysaccharides. LPS also acts as a pathogen associated molecular pattern (PAMP), and might be down regulated in planta to avoid bacterial r ecognition. A few genes encoding outer membrane proteins, which help in adhesion, including ompW blc and hms were up regulated in XVM2 as compared to in NB for both strains while xadA and yapH were induced in XccA but down regulated in Xcaw. The Type IV p illi genes encoded by pil and fim genes except pilB and filamentous haemagglutinin related genes ( fhaB XAC1816 ) were down regulated in both the strains (Tables 3 8 and 3 9 ). In order to further understand the molecular mechanisms determining the differen ces in virulence and host range of Xcaw and XccA, we compared the expression profile of common genes of Xcaw and XccA. Among the 4,034 common genes, when expression of orthologous genes in Xcaw were compared to XccA, 603 genes (426 overexpressed and 177 d own regulat ed) in NB (Table 3 10 ) and 450 genes (319 overexpressed and 131 down regulated) genes in XVM2 (Table 3 11 ) conditions were significantly differentially regulated at cut off value of log 2 the conditions, 126 genes were differentially regulated in Xcaw as compared to XccA irrespective of the growt h conditions (Fig. 3 14 ). Of these 87 were overexpressed in Xcaw and 39 genes were repressed as compared to XccA (Table 3 12 ). Of the 87 genes overexpressed in Xcaw, 35 were virulence related genes including hrpX hrpG phoP phoQ regulatory genes, TIISS substrate genes (XAC2537, XAC2763, XAC2999, XAC4004) (Table 3 12). Of the 39 genes overexpressed in XccA, 21 were virulence

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103 related genes including cellulase genes (XAC0028, XAC0029 and engXCA ), reactive oxygen species (ROS) scavenging enzyme genes e. g. superoxide dismutase gene sodC2 gen es encoding heat shock protein GrpE and heat stress protein Muc. Discussion In this study, we have sequenced Xcaw, one of the variants of XccA causing citrus canker. Currently, genome sequences of XccA and Xcaw are in finished status, whereas XauB and XauC are in draft status, and XccA* is yet to be sequenced. Comparative genomic and transcriptome analyses were conducted to understand the mechanisms underlying the differences in virulence and host range of different bacterial strains. All the citrus canke r causing variants (XccA, Xcaw, XccA*, XauB, and XauC) contain PthA or its functional homologs. Thus, PthA or its functional homologs are likely one of the major pathogenicity determinant of citrus canker pa thogen as suggested in a previous study by Al Saa di et al. ( 2007) which linked the strains of Xanthomonas with different host range together. Al Saadi et al. (2007) have shown that all the variants carry one pthA homolog with 17.5 repeats that determines pathog enicity on citrus and triggers immunity in various other plant species (Swarup et al. 1992) The avrBs3 / pthA family of effectors includes various pth genes but only PthA (Sw arup et al. 1992) is known to induce canker. The functional homolog of this gene in XccA strain 306 (da Silva et al. 2002) is pthA4 which also has three other paral ogs on its two plasmids (Table 3 3 ). We found two homologs pthAw1 and pthAw2 in Xcaw genome both located on plasmid pXcaw58. The gene pthAw2 is 99% identical to pthA4 from XccA and also to pthAW sequenced from another W ellingtion strain 0053 which is able to complement a knockout mutant of pthA in XccA strain 3213 (Al Saadi et al. 2007)

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104 indicating that PthAw2 is the functional homolog of pthA in Xcaw. PthAw2 has the same repeat number (17.5) as other functional homologs PthA4, PthB and PthC from the three respective citrus canker causing strains XccA, Xa uB, and XauC (Moreira et al. 2010) The other homolog P thAw1 in Xcaw has 18.5 tandem repeats which is different from PthA homologs found in XccA that have either 15.5 or 16.5 tandem repeats. The A vrBs3/ P thA family effectors are known as transcription activator like (TAL) effectors since they reprogram host cells by specifically binding to the promoters of plant genes recognized by the central domain of tandem repeats ( Boch an d Bonas 2010 ) Comparing the DNA binding TAL effector codes for PthA from XccA as predicted by Boch and Bonas (2009) to PthAw indicate that the codes for PthA4 and PthAw2 are quite divergent ( Fig. 3 6 ). Al Saadi et al. (2007) predicted that the well conse rved sequence of 17 th repeat in functional PthA might be impo r tant for pathogenicity on citrus and this sequence i s preserved in PthAw2 The rest of the sequence however enco des a DNA binding code that is o nly about 67% similar to the one encoded by PthA4 of XccA ( Fig. 3 6 ). This may result in recognition of different target genes in host plant or differences in strength of induction of plant genes and thus affect virulence of Xcaw and XccA The PthAw1 is very different from all the other sequenced PthA hom ologs in XccA. It remains to be investigated whether PthAw1 affects virulence in Xcaw. Comparative analysis of Xcaw and XccA identified multiple strain specific genes that might contribute to the differences in virulence and host range. Among the genes pr esent in Xcaw, but absent in XccA, t wo effector genes avr G f1 and xopAF were identified in Xcaw, XauB and XauC but were not present in XccA genome (Table 3 3 ) The presence of these effectors in limited host range strains causing citrus canker and

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105 not in t he broader host range XccA makes them prime candidates for effectors that could affect host specificity. Importantly, the role of A vrGf1 in limiting the host range of Xcaw has been confirmed previously (Rybak et al. 2009) The avr G f1 gene in Xcaw belongs to the avrGf1 family and has been shown to trigger hypersensitive reaction in grapefruit (Rybak et al. 2009) A vrGf1 shows only about 45% identity to its homolog XAUC_04910 i n XauC whereas the homolog XAUB_03570 in XauB is interrupted by a transposon and might be non functional. When the mutant strain avr G f1 was inoculated in grapefruit it caused typical canker like symptoms instead of HR, but the symptoms were visibly reduced (Rybak et al. 2009). disease on sweet orange (Valencia and Hamlin) as shown in Figure 3 7 indicating that there are other host limiting factors in the Xcaw genome or other virulence factors are required for XccA to overcome the plant defense and to acquire the nutrients to infect different hosts. Another candidate gene which might contribute to host specificity, is xopAF which belongs to avrXv3 family and is located on the plasmid pXcaw58 in Xcaw. Homologs of xopAF XAUB_02310 and XAUC_00300 are found in XauB and XauC but not in XccA (Table 3 3 ) Thus, it may contribute to restricting host ra nge of all the three strains to limited varieties of citrus as compared to XccA A xopAF homolog avrXv3 from X. campestris pv. vesicatoria is known to induce HR in tomato line Hawaii 7981 and pepper plants (Astua Mo nge et al. 2000) They also ascertained that the gene was plant inducible and regulated by the hrp regulatory system. The C terminal region of the protein encodes for a putative transcription activator domain indicating that it might interact with plant h ost genes. In this study we found that xopAF mutant and xopAF avrGF1 double mutant both have lower growth in planta as compared to Xcaw and

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106 avrGF1 si ngle mutant respectively (Fig. 3 8 ). Though the xopAF mutant did not make the wellington strain pathogenic in sweet orange Valencia it slowed the growth of the pathogen in grapefruit and Mexican lime indicating that it is important for growth of the cells. Both the wellington strain and its mutants maintained their numbers in Valencia and d id not die until 21 d ays (Fig. 3 8 ) indicating possibility of non host like reaction of sweet orange to Xcaw. In addition to the effectors documented above, other effectors that differ in their presence are xopAQ xopE2 xopN xopP and xopAE present in Xcaw, XccA and XauB but not in XauC strain. Also xopB xopE4 and xopJ1 are present in both B and C strains of Xau but missing from XccA and Xcaw. How these effectors contribute to virulence and host range of XccA Xcaw XauB, and XauC requires further investigation The LPS gene clusters of Xcaw and XccA differ (Fig. 3 9 ). Compared to XccA, the LPS cluster in Xcaw contains regions orthologous to both XccA and X. oryzae pv. oryzicola The LPS is an important virulence factor that can affect host range in other Xanthomonads by prot ecting the bacterial cells from plant defense compounds as determined in X. campestris (Kingsley et al. 1993) Hence this variable LPS region of Xcaw is a potential candidate for affecting virulence and host range. LPS is also known to be a PAMP that can be recognized by plant hosts and trigger defense responses such as oxidative burst, and cell wall modifications (Dow et al. 2000; Meyer et al. 2001 ) Hence, the variation in LPS region as compared to XccA might have altered the recognition of Xcaw by plants thus altering its host range. The Xcaw unique clusters also encode large numbers of phage related genes. Bacteriophages are known to facilitate horizontal gene transfer of virulence factors and

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107 other new traits thus leading to evolution of new strains (Krylov 2003) Not surprisingly, the phage related genes showed high nucleotide identity to phage genes from X. campestris pv. campestris and X. oryzae pv. oryzae further indicating that horizontal gene transfer has been responsible for the acquisition of these unique gene clusters. The clusters show presence of several unique transcriptional r egulators ( XCAW_01037, XCAW_0 1129, XCAW_0 1131, XCAW_0 1170) and one two component system (TCS) sensor kinase ( XCAW_0 1148) and its response regulator ( XCAW_0 1150) in Xcaw that are absent in XccA. Transcriptional regulators are known to control gene expressio n in bacteria, whereas two component signal transduction systems are used to modify gene expression in response to environmental conditions (Galperin 2004). These distinct regulators could be involved in regulating the gene expression of the two closely related strains differentially, thus resulting in altered virulence in host plants. Overall, 393 genes from XccA were found to be non orthologous to those found in Xcaw which might contribute to its broad host range of XccA One such gene is the plant like natriuretic peptide (PNP) encoding gene XAC2654 in XccA. XAC2654 is expressed during infection and can modify host proteome by mimic ing plant hormones. It weakens host defense by affecting its photosynthetic capabi lities and maintains host cellular health for better pathogen survival Knockout of XAC2654 caused more necro sis than those observed with the wild type, and bacterial cell death occurred earlier in the mutant. E xpress ion of XacPNP in X. axonopodis pv ves icatoria caused less necrotic lesions in the host than the wild type ( Gottig et al. 2008; Garavaglia et al. 2010 b ) Thus, XacPNP might promote the host expansion of XccA by modifying host defense response. In addi tion, f our genes XAC2673, XAC2903, XAC3263 and

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108 XAC3294 that have previously been shown to be involved in virulence of XccA (Laia et al. 2009 ; Yan and Wang 2011 ) were found to be missing fr om Xcaw. Many genes unique to XccA lie on its two plasmids, of which genes on the plasmid pXAC33 is mostly unique to XccA and pXAC64 has only 29 genes orthologous to genes from Xcaw. In addition to pthA and its functional homologs discussed in detail abov e XccA contains pthA1 pthA2 and pthA3 which are absent in Xcaw. Interestingly, pthA1 and pthA2 were induced in XVM2 compared to NB (Table 3 8 ). It has been suggested that those three PthA variants PthA1, PthA2, and PthA3 might interact with distinct hos t targets and contribute to virulence of XccA ( Domingues et al. 2010 ). T he other important set of genes unique to XccA is the Type IV secretion system (TIVSS) XccA contains two TIVSS clusters, the one on chromosome is homologous to the one found in Xcaw, however the one located on plasmid is completely missing from the Xca w genome (Fig. 3 5 ). Different TIVSS have been found in many pathogenic bacteria with different functional characteristics (Backert and Meyer 2006 ) Alegria et al. (2005) identified protein protein interactions of TIVSS proteins in XccA, where plasmid cluster appears to help in plasmid mobility and the function of the TIVSS cluster on the chromosome is unclear. The TIVSS proteins from plasmid have been shown to interact with other proteins on both plasmids as well as chromosome (Alegria et al. 2005). Furthermore, TIVSS has been shown to contribute to virulence in X. campestris pv. campestris strain 8004 (Qian et al. 2005) Thus, absence of TIVSS region might contribute to the differences in virulence and host range of Xcaw as compared to XccA. Besides the differences in gene content, dramatic difference s w ere observed in gene expression between Xcaw and XccA which might also contribute to the differences

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109 in virulence and host range of the two pathogens. We studied the expression profile of Xcc A and Xcaw strains in XVM2 as compared to NB. At the cut off of log 2 fold change = (173 up regulated and 119 down regulated in XVM2 compared to NB ) in XccA (Table 3 8 ). Among them, 59 virulence related genes were induced in XVM2 compared to N B. In addition, 281 genes (129 up regulated and 152 down regulated in XVM2 compared to NB) were observed for Xcaw (Table 3 9 ). Among them, 40 virulence related genes were induced in XVM2 compared to NB. The differences in gene expression between Xcaw and X ccA probably results from the differences in regulators and promoter sequences (data not shown). The induction of the virulence genes in XVM2 condition compared to nutrient rich NB is supported by previous study (Astua Monge et al. 2005). In the previous study, only 279 genes of XccA potentially associated with pathogenicity and virulence were tested and 31 genes were up regulated in XVM2, while only 7 genes were repressed. In our study, we further expanded the previous study by including all genes of Xc cA and provide a comprehensive picture of Xanthomonas gene regulation. The detailed expression profile of virulence genes of Xcaw and XccA under nutrient rich (NB) and plant intercellular space mimic ing (XVM2) conditions is described below. The entire TT SS cluster consisting of 24 genes was up regulated in XVM2 for both XccA and Xcaw strains ascertaining that XVM2 is an excellent hrp inducing medium. This is consistent with previous report that Xanthomonas hrp genes were induced in XVM2 (Schulte and Bonas 1992; Astua Monge et al. 2005). However, only eight hrp genes of XccA were reported to be upregulated by XVM2 in the previous study

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110 (Astua Monge et al. 2005) compared to 24 induced hrp genes identified in this study. Among all the effectors, 16 were indu ced for XccA whereas 19 effectors were overexpressed for Xcaw in XVM2. In the previous study (Astua Monge et al. 2005), only three effector genes avrXacE1 avrXacE2 and Xac0076 were induced in XVM2. Thus, our study further expanded the knowledge of expre ssion of the hrp and effector genes in plant intercellular space mimic ing (XVM2) condition In order to further understand the molecular mechanisms determining the differences in virulence and host range of Xcaw and XccA, we compare the expression profil e of common virulence genes of Xcaw and XccA. Interestingly, both hrpX and hrpG genes were overexpressed in the Xcaw compared to XccA (Table 3 12 ). Both genes have been shown to be critical for virulence in Xanthomonas spp. (Wengelnik and Bonas 1996b) The hrpX gene encodes an AraC type transcriptional activator and hrpG gene e ncodes an OmpR family regulator, both of which are known to regulate many virulence related genes including TTSS, effector, TIISS substrate flagella, and chemotaxis genes (Guo et al. 2011) Overexpression of Xcaw hrpG in X. perforans elicited HR in grapefruit and Mexican lime leaves by inducing xopA and other avirulence genes (Rybak et al. 2009). Th e xopA gene encodes harpin and was suggested to be a host limiting factor by inducing HR. Its homologues hpaG and hrpN are also known to induce HR. The promoter regions of the xopA genes of Xcaw and XccA are different. However, the xopA gene was not ove rexpressed significantly in Xcaw compared to XccA (Table 3 13 ). The fold change of xopA was more than 2, but the FDR did not pass the cut off value. Five other effector genes xopL xopX xopAD hrpW and xopAQ were overexpressed in Xcaw in XVM2, whereas only one effector gene xopAP was

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111 induced in XccA in NB (Table 3 13 ). Overexpression of those effector genes in Xcaw might contribute to the limited host range of Xcaw. In addition, the phoP phoQ two component system genes were overexpressed in Xcaw compa red to XccA (Table 3 12 ). The phoP gene encoding a response regulator is predicted to interact with various signal sensor proteins in addition to PhoQ. It is known to activate the response regulator hrpG in X. oryzae pv. oryzae and thus lead to a chain rea ction involving activation of various virulence and growth factor genes downstream (Lee et al. 2008) The phoQ gene on the other hand is required for the activity of AvrXA21 in X. oryzae pv. oryzae which determine s host variation of the strain against some rice lines (Lee et al. 2008). Thus in Xcaw, overexpression of phoP phoQ could contribute to activation of certain effector genes mentioned above. TIISS is the major protein secretion system, which secretes toxi ns and various degradative enzymes to breakdown the cell wall in plant hosts ( Bttner and Bonas 2010). TIISS and its substrates have been shown to be important for the virulence of XccA (Yan and Wang 2012). The xps genes were down regulated in XVM2 as comp ared to NB for Xcaw with xpsE being the most significantly down regulated with log 2 fold change 1.07 at FDR = 0.03. XpsE is known to be a key component of T2SS, the loss of which leads to lower virulence in X. oryzae (Sun et al. 2004). For XccA, the xps g enes were not down regulated. Down regulation of xps genes in Xcaw but not in XccA might contribute to differences in virulence on different hosts of Xcaw and XccA. In XccA at least 22 genes encoding TIISS substrates were overexpressed as compared to onl y 12 in Xcaw. On the contrary 11 genes for Xcaw and 8 for XccA were down regulated. Similarly, genes encoding TIISS substrates were found either down

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112 regulated or up regulated (Astua Monge et al. 2005). Specifically, four TIISS substrate protease genes (X AC2537, XAC2763, XAC2999, and XAC4004) were upregulated in Xcaw compared to XccA in both conditions (Table 3 12 ). Consequently, Xcaw showed higher prote ase activity than XccA (Fig. 3 15A ). In contrast, multiple cellulase genes (XAC0028, XAC0029, and engXC A ) were down regulated in Xcaw compared to XccA (Table 3 12 ). Pectate lyase gene pel (XAC03562) was also down regulated in Xcaw compared to XccA in NB medium (Table 3 10 ). Consequently, Xcaw show ed lower pectate lyase activity as compared to XccA ( Fig. 3 1 5 B). The differential regulation of genes encoding TIISS substrates in XVM2 probably results from the different involvement of the TIISS substrates in the infection process of Xanthomonas Collectively, the differences in expression of genes encoding TIIS S and its substrates might contribute to the differences in virulence on different hosts of Xcaw and XccA. Compared to Xcaw, multiple virulence genes were overexpressed in XccA which might contribute to its adaption to a broad host range (Table 3 12 ). Thes e include many reactive oxygen species (ROS) scavenging enzyme genes, e. g. superoxide dismutase gene sodC2 genes encoding heat shock protein GrpE and heat stress protein Muc, which indicates that XccA might be more adapted to stressful conditions due to the host defense responses of different hosts. Attachment of Xanthomonas to plant cell surfaces is important for pathogenicity (Rigano et al. 20007; Li and Wang 2011). Multiple genes involved in adherence were overexpresse d in XccA in NB medium (Table 3 10 ) including filamentous haemagglutinin gene fhaB gum genes ( gumB to gumK gumM ), chemotaxis genes (XAC0611, XAC1666, XAC1891, XAC1893, XAC1894, XAC1895, XAC1896, XAC1897, XAC1899, XAC1900, XAC1902), mcp genes (XAC1996,

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113 XAC2448, XAC2866, XAC3132), cheA (XA C2865), cheR (XAC1890), cheR (XAC2869), cheY (XAC1904) and cheD (XAC1889). These genes are involved in adhesion and biofilm formation of Xcaw in glass tubes as compared to XccA (Li and Wang 2011). Multiple transporter genes which are known to play critical roles for bacteria to acquire nutrients from the intercellular environment were overexpressed in XccA in XVM2 as compared to Xcaw, e.g. t he potassium transporter genes kdpB kdpC and kdpD and the iron siderophore transporter gene fhuA (XAC2185) and XAC283 0 (Table 3 11 ). Altogether, they might contribute to the virulence on broad host of XccA as compared to Xcaw. In conclusion, we have successfully sequenced the genome of X citri subsp. citri strain A w 12879. Comparative genomic analysis of Xcaw and XccA i ndicates that Xcaw strain specific effectors XopAG and XopAF might contribute to its limited host range compared to XccA. In addition, the overexpression of avirulence/effector genes in Xcaw might also contribute to its limited host range. The overexpress ion of genes involved in cell wall degradation, attachment, ROS scavenging, nutrient transportation in XccA might contribute to its expansion of host range. T he differential expression of genes encoding TIISS and its substrates might contribute to the diff erences in virulence and host range of Xcaw and XccA. Our data also demonstrate that virulence genes including genes encoding TTSS and its effectors are induced in the condition mimicing the plant intercellular environment. This study lays foundation to further characterize the mechanisms for virulence and host range of strains of X. citri subsp citri and other bacterial pathogens.

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114 Table 3 1. Overview of sequence data for the genome of Xanthomonas citri subsp. citri A w 12879 Sequencing method 454 sequen cing Illumina/Solexa Total reads 620,233 37,467,584 Total sequence output 129,503,865 bp 2,772,601,216 bp Average read length 240 bp 74 bp Genome coverage 24X 410X No. of contigs a 378 1426 Note: 454 contigs assembled using Newbler 2.0 and Illumina/So lexa contigs assembled using CLCbio Genomics Workbench 5.0 Table 3 2. Primers used in this study For Mutant construction xopAFF1 CGAATCCGAAAAGGCCAT xopAFF2 GAggatccATTATTACACAGGCGAA CG xopAFR AAGTAGTCGTCTCTGAAAGA For qRT PCR gnlF TGGATAAATCGCCGGTCAAGGAGT gnlR ATCGGAGTTGGAGACGTACAAGGT hrpGF ATCGTGCTTGGACGTTTCGATTGC hrpGR ATTGAAAGGCAGCGCAAGGACTTC hrpXF AAGCGTTACTGCTCTACAACCGCT hrpXR TGCGCATTGGTGATCATGTAGCTG nuoMF A CAGGACGACATGAAGAAGCTGGT nuoMR ACGAAACCGTGCGAAATCATCTGC phoPF CTTGCGCGATGAAGGCAAGAAGTT phoPR ACGTGGAACGGCTTGACCAGATAA sodC2F AAGGGTAATGACGTCAAAGGCACG sodC2R ATATTGCCGTGATCGGACTGGGA grpEF GCCTGGACATGACCTACAAGCAAT grpER TTCTGGAACACCTGCACCACAT eglF ACT ACGCCAAGTATTACGGCCACA eglR AGGCTCATTCATCAGCCCGAAGAT 16sF AACGCGAAGAACCTTACCTGGTCT 16sR TGCGGGACTTAACCCAACATCTCA

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115 Table 3 3. General features of Xanthomonas citri subsp. citri A w 12879 genome Chromosome Plasmids Features Xcaw pXcaw19 pXcaw58 Size (bp) 5,321,499 18,869 58,317 GC content (%) 64.71 63.07 61.85 Predicted CDS Protein coding genes 4675 17 69 with COGs 3423 9 25 with Pfam 3552 10 32 with TIGRfam 1377 2 4 connected to KEGG pathways 1194 2 1 Ribosomal RNA 6 0 0 rRNA ope rons 2 0 0 Transfer RNA 54 0 0

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116 Table 3 4. Effector repertoire of X. citri subsp. citri A w 12879 (Xcaw), X. citri subsp. citri str. 306 (XccA), X. fuscans subsp. aurantifolii str. ICPB 11122 (XauB) and X. fuscans subsp. aurantifolii str. ICPB 10535 (Xa uC) Effector class Xcaw XccA XauB XauC Pfam domains References AvrBs2 XCAW_00465 XAC0076 XAUB_16770 XAUC_23650 Glycerophosphoryl diester phosphodiesterase (Kearney and Staskawicz 1990) PthA (AvrBs3, T AL) XCAW_b00018 (PthAw1) XCAW_b00026 (pthAw2) XACa0022 (PthA1) XACa0039 (PthA2) XACb0015 (PthA3) XACb0065 (PthA4) XAUB_40130 XAUB_28490 XAUC_22430 XAUC_24060 XAUC_09900 XAUC_43080 Transcriptional activator, nuclear localization (Algeria et al. 2005) XopA (Hpa1/HpaG) XCAW_00826 XAC0416 XAUB_19280 XAUC_43660 (Noel et al. 2002) XopE1 (AvrXacE1) XCAW_00686 XAC0286 XAUB_37010 XAUC_37580 Putative transglutaminase (Thieme et al. 2007) XopE3 (AvrXacE2) XCAW_03515 XAC3224 XAUB_14680 XAUC_00040 Puta tive transglutaminase (Nimchuk et al. 2007) XopF2 (Roden et al. 2004) XopI XCAW_03828 XAC0754 XAUB_39080 XAUC_07100 F box protein (Thieme 2008) XopK XCAW_03372 XAC3085 XAUB_34090 XAUC_12520 (Furutani et al. 2009) XopL XCAW_03376 XAC3090 XAUB_34130 XAUC_02900/ LRR protein (Jiang 2007) XopQ XCAW_04706 XAC4333 XAUB_10220 XAUC_14670 Inosine uridine nucleoside N ribohydrolase (Roden et al. 2004) XopR XCAW_00677 XAC0277 XAUB_36920 XAUC_3749 0 (Furutani et al. 2009) XopV XCAW_03980 XAC0601 XAUB_23140 XAUC_21260 (Furutani et al. 2009)

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117 Table 3 4. Continued. Effector class Xcaw XccA XauB XauC Pfam domains R eferences XopX XCAW_00956 XAC0543 XAUB_14760 XAUC_20690 (Metz et al. 2005) XopZ1 XCAW_01815 XAC2009 XAUB_11532/ XAUC_25915 (Furutani et al. 2009) XopAD XCAW_00082 XAC4213 XAUB_02510 XAUC_34870 SKWP repeat protein (Guidot et al. 2007, Petnicki Ocwieja et al. 2 002) XopAI XCAW_01099 XAC3230 XAUB_26830 XAUC_23780 Putative ADP ribosyltransferase (Thieme et al. 2005) XopAK XCAW_04369 XAC3666 XAUB_02580 XAUC_32490 (Petnicki Ocwieja et al. 2002) XopAP XCAW_03269 XA C2990 XAUB_13980 XAUC_08760 (Mukaihara et al. 2010) HpaA XCAW_00810 XAC0400 XAUB_19430 XAUC_19990 T3S control protein (Lorenz et al. 2008) HrpW (PopW) XCAW_03200 XAC2922 XAUB_19460 XAUC_20020 Pectate Lyase (Park et al. 2006) XopAQ XCAW_03514 No annotation between XAC3223 and XAC3224 No annotation between XAUB_14670 and XAUB_14680 (Mukaihara et al. 2010) XopE2 (AvrXacE3, AvrXccE1) XCAW_03520 XACb0011 XAUB_31660 Pu tative transglutaminase (Thieme et al. 2007) XopN XCAW_01387 XAC2786 XAUB_07520 ARM/HEAT repeat (Kim et al. 2009) XopP XCAW_ 01310 XAC1208 XAUB_06720 (Roden et al. 2004)

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118 Table 3 4. Continued. Effector class Xcaw XccA XauB XauC Pfam domains References XopAE (HpaF/HpaG) XCAW_00801 XAC0393 XAUB_19500 LRR protein (White et al. 2009) XopC2 Haloacid dehalogenase like hydrolase (White et al. 2009) XopAF (AvrXv3) XCAW_b00003 XAUB_02310 XAUC_00300 (Astua Monge et al. 2000) XopAG (AvrGf1/ AvrGf2) XCAW_00608 XAUC_04910 (Rybak et al. 2009) XopF1 (Hpa4) XCAW_00804/ XCAW_00805 (Roden et al. 2004) XopB XAUB_09070/ XAUC_00260 (Noel et al. 2001) XopE4 XAUB_23330 XAUC_31730 Putative transglutaminase (Moreira et al. 2010) XopJ1 XAUB_20830 XAUC_08850 C55 family cysteine protease or Ser/Thr acetyltransferase (Roden et al. 2004)

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119 Table 3 5. Genes unique to Xcaw clustered in groups Cluster number Locus tag Homologs in other genomes Function 1 XCAW_01029 to XCAW_01071 hypothetical proteins, RhsA family protein, transcr iptional regulator, integrase, adenine specific DNA methylase, type III restriction enzyme: res subunit, ATP dependent exoDNAse, thermonulease 2 XCAW_01118 to XCAW_01171 Some present in X campestris pv. campestris ATCC 33913 transcriptional regulator, ph age related tail proteins, TCS response sensor and regulator, chitinase, Zn peptidase, polymerase V, transcriptional repressor, protein glutamate methylesterase 3 XCAW_01571 to XCAW_01582 Some present in X campestris pv. campestris str. 8004 phage relate d proteins, hypothetical protein 4 XCAW_01620 to XCAW_01631 Some present in Acidovorax sp. JS42 transposases, hypothetical protein, type II restriction enzyme: methylase subunit 5 XCAW_01642 to XCAW_01650 Homologous to X campestris pv. campestris str. 8 004 phage related regulatory proteins, chromosome partitioning related protein, hypothetical protein 6 XCAW_01654 to XCAW_01687 Homologous to X campestris pv. campestris str. 8004 hypothetical proteins, soluble lytic murein transglycosylase 7 XCAW_01691 to XCAW_01719 Homologous to X campestris pv. campestris str. 8004 VirB6 protein, transposases, hypothetical proteins 8 XCAW_04295 to XCAW_04303 Homologous to X oryzae pv. oryzicola BLS256 lipopolysaccharide biosynthesis genes 9 XCAW_04518 to XCAW_0454 4 Homologous to X oryzae pv. oryzae PXO99A phage related proteins, transcriptional regulator, transposases, hypothetical proteins

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120 Table 3 6. Summary of cDNA samples sequenced for RNA Seq Sample No. of Reads No. of reads after trim Avg. read length a fter trim, bp No. of uniquely mapped reads No. of uniquely mapped bps x 10 8 Average coverage mRNA reads % of uniquely mapped reads ANB1 61,102,324 59,054,234 63.8 10,900,571 6.96 147X 18.46% ANB2 34,861,658 34,502,250 71.0 8,505,214 6.04 129X 24.65% ANB 3 55,909,444 54,311,690 65.5 12,850,535 8.42 179X 23.66% AXVM1 59,932,224 57,731,460 64.7 7,002,216 4.53 96X 12.13% AXVM2 60,656,960 58,303,398 62.3 8,453,622 5.27 109X 14.50% AXVM3 59,906,612 58,437,562 65.8 8,721,747 5.74 120X 14.93% WNB1 64,399,896 62,871,274 68.3 14,093,510 9.63 202X 22.42% WNB2 23,499,508 23,341,184 71.9 6,671,456 4.80 101X 28.58% WNB3 52,110,418 48,359,192 43.0 8,185,467 3.52 77X 16.93% WXVM1 59,681,564 58,050,261 65.5 7,998,317 5.24 111X 13.78% WXVM2 67,385,040 62,470,162 61. 5 7,068,123 4.35 95X 11.31% WXVM3 60,841,200 51,076,418 52.0 6,561,478 3.41 79X 12.85%

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121 Table 3 7. Degree of agreement between biological replicates for RNA Seq Sample Repeats compared R 2 value correlation coefficient XccA in NB ANB1 and ANB2 0.9 9673907 ANB2 and ANB3 0.996187926 ANB3 and ANB1 0.996890541 XccA inXVM2 AXVM1 and AXVM2 0.999881083 AXVM2 and AXVM3 0.999844115 AXVM3 and AXVM1 0.999722292 Xcaw in NB WNB1 and WNB2 0.999145975 WNB2 and WNB3 0.999762336 WNB3 and WNB1 0.999658312 Xcaw in XVM2 WXVM1 and WXVM2 0.999227967 WXVM2 and WXVM3 0.999358198 WXVM3 and WXVM1 0.999976985

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122 Table 3 8 Genes differentially expressed in X. citri subsp. citri str. 306 (A) in XVM2 medium (hrp inducing) as compared to NB (nu trient rich condition). Cut off 1.585 for underexpressed genes. Log2 fold change 1.585 3) Locus tag Gene Name Product Log2 Fold Change AXVM/ANB Overexpressed Genes X ACa0031 XACa0031 transposase 91.4244951 XAC3181 lysA diaminopimelate decarboxylase 53.73516607 XAC2259 XAC2259 hypothetical protein 48.47324504 XACb0072 XACb0072 resolvase 13.97339668 XAC0402 hrcR type III secretion system protein 11.17800952 XAC1673 XAC1673 hypothetical protein 9.025178375 XAC3177 XAC3177 hypothetical protein 8.963896246 XAC3226 XAC3226 Tn5044 transposase 8.583043094 XAC2249 XAC2249 hypothetical protein 7.104496978 XAC3180 iucA iron transporter 7.064570216 XAC0403 hrcQ HrcQ prote in 6.540008483 XAC3548 xadA hypothetical protein 5.871344066 XAC3690 XAC3690 hypothetical protein 4.974578776 XAC4256 cirA TonB dependent receptor 4.964583959 XACb0026 XACb0026 hypothetical protein 4.96159489 XAC2653 S phage related tail protein 4.803 492842 XAC3489 fyuA TonB dependent receptor 4.734157783 XAC2280 XAC2280 hypothetical protein 4.713497615 XAC0406 hrcU type III secretion system protein HrcU 4.520513651 XAC0416 hpa1 Hpa1 protein 4.035690704 XAC0825 XAC0825 hypothetical protein 4.00938 0091 XAC2172 XAC2172 NADH dehydrogenase 3.634554453 XAC4338 XAC4338 hypothetical protein 3.554860845 XAC4007 XAC4007 hypothetical protein 3.417379518 XAC0753 XAC0753 hypothetical protein 3.364728257 XAC0398 hrpD6 HrpD6 protein 3.352499507 XAC1009 XAC 1009 hypothetical protein 3.215722675 XAC4157 fldW 4 oxalomesaconate hydratase 3.140707774 XAC0823 phuR outer membrane hemin receptor 3.051667562 XAC3680 XAC3680 hypothetical protein 3.041662946 XAC3490 XAC3490 amylosucrase or alpha amylase 3.010433641 XAC0758 kdpC potassium transporting ATPase subunit C 2.933171867 XAC0754 XAC0754 hypothetical protein 2.916595239 XAC0337 kdgT 2 keto 3 deoxygluconate permease 2.849020751 XAC0257 aceA isocitrate lyase 2.84266408 XAC0400 hpaA HpaA protein 2.738106242

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123 Table 3 8 Continued. Locus tag Gene Name Product Log2 Fold Change AXVM/ANB XAC0255 rbcR transcriptional regulator 2.710976372 XAC0338 XAC0338 hypothetical protein 2.703694796 XAC1766 dgoA 2 dehydro 3 deoxy 6 phosphogalactonate aldolase 2.672151326 XAC2219 XAC2219 hypothetical protein 2.639008605 XAC0822 XAC0822 hypothetical protein 2.599756547 XAC2982 qxtB quinol oxidase subunit II 2.495353682 XAC0328 smeB multidrug efflux transporter 2.457299532 XAC1681 XAC1681 hypothetical protein 2.451022814 XAC1576 pstC ABC transporter phosphate permease 2.430225279 XAC3777 XAC3777 hypothetical protein 2.410883587 XAC2983 XAC2983 quinol oxidase subunit I 2.393931836 XAC1792 phoX alkaline phosphatase 2.37667334 XACa0009 XACa0009 ISxac3 transposase 2.3316 92412 XAC3843 XAC3843 hypothetical protein 2.327542167 XAC3757 XAC3757 hypothetical protein 2.319496966 XAC4303 slyA cryptic hemolysin transcriptional regulator 2.312159867 XAC2267 XAC2267 hypothetical protein 2.274095104 XAC4356 XAC4356 hypothetical protein 2.26803207 XAC3453 ilvM acetolactate synthase isozyme II small subunit 2.263948546 XAC2853 XAC2853 cysteine protease 2.263084895 XAC0757 kdpB potassium transporting ATPase subunit B 2.257681733 XAC4194 XAC4194 hypothetical protein 2.226616628 XAC0334 sflA NADH dependent FMN reductase 2.217978209 XAC1682 rpoE RNA polymerase sigma E factor 2.210265862 XAC1575 pstA ABC transporter phosphate permease 2.19717434 XAC4252 xynB xylanase 2.185687507 XAC4225 xylA xylose isomerase 2.177610014 XAC2838 XAC2838 LysR family transcriptional regulator 2.175983417 XAC3204 XAC3204 hypothetical protein 2.170078675 XAC1579 oprO polyphosphate selective porin O 2.164587442 XAC0545 aroG phospho 2 dehydro 3 deoxyheptonate aldolase 2.144680178 XAC0693 fecA TonB dependent receptor 2.136279222 XAC4306 nodT outer membrane efflux protein 2.081398082 XAC0399 hrpD5 HrpD5 protein 2.080275393 XAC0310 vanB vanillate O demethylase 2.067620126 XAC0364 gctA glutaconate CoA transferase subunit A 2.065093914 XAC1873 XAC18 73 hypothetical protein 2.061601373 XAC2844 mexA multidrug resistance protein 2.056792203

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124 Table 3 8 Continued. Locus tag Gene Name Product Log2 Fold Change AXVM/ANB XAC1197 XAC1197 hypothetical protein 2.038960886 XAC3497 XAC3497 hypothetical protei n 2.035065213 XAC0256 mls malate synthase 2.014744175 XAC0756 kdpA potassium transporting ATPase subunit A 2.01029461 XAC2202 hlyB hemolysin secretion protein B 1.996046182 XAC4254 xynB xylanase 1.986792522 XAC3498 fhuE ferric iron uptake outer membra ne protein 1.982667307 XAC2364 eutP ethanolamin permease 1.981577825 XAC0899 XAC0899 hypothetical protein 1.970885848 XAC0335 XAC0335 hypothetical protein 1.969646672 XAC2218 XAC2218 hypothetical protein 1.950096088 XACa0030 XACa0030 transposase 1.942 874024 XAC4064 ftrA transcriptional activator FtrA 1.9425816 XAC2163 XAC2163 hypothetical protein 1.908393867 XAC0162 dctP C4 dicarboxylate transport system 1.907790828 XAC2143 XAC2143 hypothetical protein 1.906583575 XAC1577 pstS phosphate ABC transp orter substrate binding protein 1.896343446 XAC0336 metE 5 methyltetrahydropteroyltriglutamate -homocysteine S methyltransferase 1.894636436 XAC0537 XAC0537 hypothetical protein 1.892799099 XAC2164 XAC2164 hypothetical protein 1.886338219 XAC4155 fldZ hypothetical protein 1.883749096 XAC0737 XAC0737 transcriptional regulator 1.878535144 XAC2515 XAC2515 AsnC family transcriptional regulator 1.878202166 XAC2949 XAC2949 calcium binding protein 1.875482776 XAC1679 ccmC cytochrome C type biogenesis prot ein 1.865566378 XAC2245 XAC2245 hypothetical protein 1.862058453 XAC3338 XAC3338 hypothetical protein 1.857715429 XAC4253 XAC4253 hypothetical protein 1.841445518 XAC3459 XAC3459 LysR family transcriptional regulator 1.841171539 XAC3692 XAC3692 hypoth etical protein 1.836521986 XAC0413 hrpB7 HrpB7 protein 1.827779479 XAC0560 mdcA malonate decarboxylase subunit alpha 1.825851893 XAC4368 fecA TonB dependent receptor 1.824073349 XAC1790 XAC1790 hypothetical protein 1.820176779 XAC2786 XAC2786 hypothet ical protein 1.817216578 XAC1765 dgoA galactonate dehydratase 1.803114779 XAC1433 asnB asparagine synthetase B 1.802702416 XAC0037 XAC0037 penicillin acylase 1.796506774 XAC2399 htpX heat shock protein HtpX 1.787884005

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125 Table 3 8 Continued. Locus ta g Gene Name Product Log2 Fold Change AXVM/ANB XAC1136 prpR propionate catabolism regulatory protein 1.784579084 XAC2774 XAC2774 TonB like protein 1.780544218 XAC0311 vanA vanillate O demethylase oxygenase 1.774853793 XAC3769 nucA endonuclease 1.7746247 59 XAC3222 XAC3222 hypothetical protein 1.761406582 XAC3737 XAC3737 hypothetical protein 1.757594224 XAC2274 XAC2274 hypothetical protein 1.750527464 XAC2113 XAC2113 hypothetical protein 1.747782429 XAC0543 XAC0543 hypothetical protein 1.747726474 XA C0916 XAC0916 hydrolase 1.743077247 XAC1574 pstB phosphate transporter ATP binding protein 1.743016923 XAC1023 fecA TonB dependent receptor 1.742769966 XAC3085 XAC3085 hypothetical protein 1.741946347 XAC2248 XAC2248 hypothetical protein 1.730250938 X AC3552 XAC3552 hypothetical protein 1.728086337 XAC4305 fusE fusaric acid resistance protein 1.721852333 XAC0396 hpaB HpaB protein 1.720831425 XAC4062 fhuA TonB dependent receptor 1.710547693 XAC3488 suc1 sugar transporter 1.70804397 XAC2285 orf84 hyp othetical protein 1.705264507 XAC3053 XAC3053 hypothetical protein 1.700863999 XAC4350 XAC4350 transcriptional regulator 1.699812386 XAC0297 XAC0297 hypothetical protein 1.694139167 XAC3954 XAC3954 hypothetical protein 1.691303605 XAC1927 aslB Fe S ox idoreductase 1.68552461 XAC4192 XAC4192 hypothetical protein 1.684456718 XAC3176 fecA citrate dependent iron transporter 1.682395955 XAC0074 cirA TonB dependent receptor 1.679957329 XAC4227 aguA alpha glucuronidase 1.673235652 XAC0363 vanA vanillate O demethylase oxygenase 1.672624497 XAC1196 lexA LexA repressor 1.672059517 XAC1770 celA cellulase 1.66986911 XAC2763 XAC2763 extracellular protease 1.668484952 XAC1702 XAC1702 Mg protoporphyrin IX monomethyl ester oxidative cyclase 1.66610193 XAC2626 fimT fimbrial biogenesis protein 1.661546548 XAC3984 XAC3984 hypothetical protein 1.658630042 XAC0492 XAC0492 bacterioferritin associated ferredoxin 1.656523625 XAC2243 orf8 plasmid like protein 1.6549515 XAC0202 XAC0202 hypothetical protein 1.65319071 1

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126 Table 3 8 Continued. Locus tag Gene Name Product Log2 Fold Change AXVM/ANB XAC2746 XAC2746 metallopeptidase 1.651225818 XAC0414 hrcT HrcT protein 1.645206342 XAC2212 topB DNA topoisomerase III 1.63848051 XAC1820 thrA bifunctional aspartokinase I/ homoserine dehydrogenase I 1.636258424 XAC1680 XAC1680 serine protease 1.636225787 XAC3747 ybdR Zn dependent alcohol dehydrogenase 1.630208116 XAC0878 pcaH protocatechuate 4,5 dioxygenase subunit beta 1.626181497 XAC1651 XAC1651 TonB like protein 1.625 943134 XAC1181 XAC1181 hypothetical protein 1.614724598 XAC2843 mexB multidrug efflux transporter 1.614288819 XAC3866 XAC3866 hypothetical protein 1.61071669 XAC4138 XAC4138 transposase 1.608738524 XAC1685 XAC1685 cytochrome C 1.608524014 XAC0612 eng XCA cellulase 1.607513009 XAC2561 blc outer membrane lipoprotein Blc 1.605041752 XAC1161 XAC1161 hypothetical protein 1.597790636 XAC0163 dctQ C4 dicarboxylate membrane transport protein 1.596821527 XAC1789 XAC1789 hypothetical protein 1.589554846 XAC 1578 phoX phosphate binding protein 1.589114245 XAC0917 XAC0917 transcriptional regulator 1.588678732 XAC1160 XAC1160 oxidoreductase 1.587648214 Underexpressed Genes XAC3178 XAC3178 hypothetical protein 16.88666299 XAC4255 exuT hexuranate transport er 7.192282312 XAC0116 XAC0116 hypothetical protein 6.973927206 XAC1814 fhaC outer membrane hemolysin activator protein 6.097046532 XAC2548 XAC2548 oxidoreductase 5.982748884 XAC0824 XAC0824 hypothetical protein 5.53161883 XACb0051 ISxac2 ISxac2 transposase 5.419377359 XAC3754 XAC3754 hypothetical protein 5.146227128 XAC2549 XAC2549 D amino acid oxidase 3.599951465 XAC3520 XAC3520 hypothetical protein 2.896127295 XAC2539 XAC2539 hypothetical protein 2.87796941 XAC0516 XAC0516 hypothetica l protein 2.738068666

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127 Table 3 8 Continued. Locus tag Gene Name Product Log2 Fold Change AXVM/ANB XAC2546 XAC2546 ketoglutarate semialdehyde dehydrogenase 2.678728672 XAC2868 vieA response regulator 2.630814242 XAC3179 yceE transporter 2.6192779 98 XAC0350 XAC0350 hypothetical protein 2.570246784 XAC2541 XAC2541 peptidase 2.4839614 XAC2540 XAC2540 hypothetical protein 2.482935843 XAC2550 XAC2550 hypothetical protein 2.47376968 XAC2545 pepQ proline dipeptidase 2.435703559 XAC2531 btuB To nB dependent receptor 2.398041276 XAC3753 XAC3753 hypothetical protein 2.335154867 XAC2547 dapA dihydrodipicolinate synthetase 2.327334203 XAC0614 XAC0614 diguanylate cyclase 2.319954402 XAC1314 paaF enoyl CoA hydratase 2.273135291 XAC2543 XAC254 3 hypothetical protein 2.227249442 XAC1901 XAC1901 hypothetical protein 2.212326226 XAC1695 XAC1695 hypothetical protein 2.203648497 XAC2544 XAC2544 hypothetical protein 2.196500695 XAC0518 XAC0518 hypothetical protein 2.192309509 XAC1803 XAC1803 hypothetical protein 2.179683683 XAC3635 XAC3635 hypothetical protein 2.162789585 XAC1900 tsr chemotaxis protein 2.162665841 XAC3294 XAC3294 hypothetical protein 2.115589002 XAC0749 ribA 3,4 dihydroxy 2 butanone 4 phosphate synthase 2.110168405 XAC0853 XAC0853 hypothetical protein 2.086058433 XAC2535 btuB TonB dependent receptor 2.075039441 XAC1130 trpE hypothetical protein 2.065691257 XAC1899 tsr chemotaxis protein 2.047540487 XAC0520 XAC0520 acyltransferase 2.043733249 XAC2542 yveA am ino acid permease 2.041106275 XAC1897 tsr chemotaxis protein 2.022977015 XAC1313 fadE9 acyl CoA dehydrogenase 2.015280259 XAC4134 XAC4134 hypothetical protein 1.996637065 XAC3330 cysJ NADPH sulfite reductase flavoprotein subunit 1.98662768 XAC194 0 XAC1940 diguanylate cyclase 1.983751862 XAC1935 flhF flagellar biosynthesis regulator FlhF 1.96685314 XAC1936 flhA flagellar biosynthesis protein FlhA 1.928453971 XAC2144 XAC2144 serine protease 1.912143648 XAC0747 XAC0747 hypothetical protein 1 .904861098

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128 Table 3 8 Continued. Locus tag Gene Name Product Log2 Fold Change AXVM/ANB XAC1315 XAC1315 enoyl CoA hydratase 1.903057101 XAC3662 XAC3662 hypothetical protein 1.895677175 XAC1890 cheR chemotaxis protein methyltransferase 1.895667171 XAC0748 ribE riboflavin synthase subunit alpha 1.895299492 XAC2375 XAC2375 hypothetical protein 1.894255325 XAC1937 flhB flagellar biosynthesis protein FlhB 1.890179824 XAC2866 mcp chemotaxis protein 1.888602271 XAC1941 fliR flagellar biosynthetic protein 1.87915101 XAC0471 XAC0471 hypothetical protein 1.871060264 XAC3444 btuB TonB dependent receptor 1.851599574 XAC2156 XAC2156 hypothetical protein 1.850920329 XAC0107 XAC0107 hypothetical protein 1.850894531 XAC1946 fliN flagellar protein 1.838883742 XAC1985 flgC flagellar basal body rod protein FlgC 1.834499798 XAC1003 XAC1003 hypothetical protein 1.833636126 XAC3120 glk glucokinase 1.831271258 XAC1891 tsr chemotaxis protein 1.830609851 XAC1312 mmsA methylmalonate semialdehyde de hydrogenase 1.809288575 XAC4012 XAC4012 hypothetical protein 1.808698614 XAC1948 fliL flagellar protein 1.802809033 XAC1942 fliQ flagellar biosynthesis 1.80252679 XAC1988 flgA flagellar basal body P ring biosynthesis protein FlgA 1.7766389 XAC026 3 accC biotin carboxylase 1.760031408 XAC3317 XAC3317 acetyltransferase 1.757740341 XAC0860 oppD ABC transporter ATP binding protein 1.756373443 XAC4011 XAC4011 hypothetical protein 1.74650994 XAC2447 cheW chemotaxis protein 1.731056692 XAC1979 f lgI flagellar basal body P ring biosynthesis protein FlgA 1.7296501 XAC1896 tsr chemotaxis protein 1.725885815 XAC2619 virB10 VirB10 protein 1.724072505 XAC1993 XAC1993 hypothetical protein 1.72015485 XAC3072 fucA1 alpha L fucosidase 1.718648011 XAC1816 XAC1816 hemagglutinin/hemolysin like protein 1.718581073 XAC4048 iroN TonB dependent receptor 1.698968733 XAC1980 flgH flagellar basal body L ring protein 1.694451501 XAC3121 fepA TonB dependent receptor 1.685657847 XAC4149 XAC4149 hypothet ical protein 1.684285848 XAC2865 cheA chemotaxis histidine protein kinase 1.682014261

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129 Table 3 8 Continued. Locus tag Gene Name Product Log2 Fold Change AXVM/ANB XAC0205 glnB nitrogen regulatory protein P II 1.677954471 XAC0265 acdA acyl CoA dehyd rogenase 1.662755489 XAC2617 virB1 VirB1 protein 1.661587297 XAC1955 fliE flagellar protein 1.658879997 XAC1396 XAC1396 hypothetical protein 1.654943159 XAC2379 XAC2379 hypothetical protein 1.654198927 XAC0611 tsr chemotaxis protein 1.649954054 XAC1930 cheA chemotaxis protein 1.648894486 XAC2065 acrD transporter 1.646265611 XAC1815 fhaB filamentous hemagglutinin 1.646120848 XAC2534 XAC2534 hypothetical protein 1.643799724 XAC1497 XAC1497 hypothetical protein 1.643559245 XAC1987 cheV ch emotaxis protein 1.642179208 XAC1947 fliM flagellar motor switch protein FliM 1.642060203 XAC0952 pth peptidyl tRNA hydrolase 1.637296939 XAC1389 yfiL ABC transporter ATP binding protein 1.634240173 XAC2622 XAC2622 hypothetical protein 1.625290485 XAC2620 virB9 VirB9 protein 1.622636683 XAC3999 XAC3999 hypothetical protein 1.620704973 XAC1865 recJ single stranded DNA specific exonuclease 1.620226243 XAC3133 yggA membrane transport protein 1.618542941 XAC1146 fecA TonB dependent receptor 1 .616210473 XAC2483 XAC2483 hypothetical protein 1.612738679 XAC1906 cheW chemotaxis protein 1.611391377 XAC4164 XAC4164 hypothetical protein 1.606491793 XAC1945 fliO flagellar protein 1.596788766 XAC0829 XAC0829 ABC transporter substrate binding p rotein 1.594381604 XAC1954 fliF flagellar MS ring protein 1.594165125 XAC2618 virB11 VirB11 protein 1.58976968 XAC2482 rrpX transcriptional regulator 1.589195117 XAC1502 XAC1502 hypothetical protein 1.585753337

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130 Table 3 9 Genes differentially e xpressed in X. citri subsp. citri str. A w 12879 (W) in XVM2 medium (hrp inducing) as compared to NB (nutrient rich condition). Cut 1.585 for underexpressed genes. Log2 fold chang Locus tag Gene Name Product Log 2 Fold Change WXVM/WNB Overexpressed Genes XCAW_01553 czcA silver efflux pump 86.00429147 XCAW_00810 hpaA hpaA protein 48.8765859 XCAW_01579 XCAW_01579 phage replication protein RstA 15.15173 601 XCAW_02384 wbbJ Acetyltransferases (the isoleucine patch superfamily) 12.30102632 XCAW_01571 XCAW_01571 Hypothetical protein 9.398602024 XCAW_02450 XCAW_02450 Hypothetical Protein 8.521995782 XCAW_03444 cirA Outer membrane receptor protein, most ly Fe transport 7.304901959 XCAW_00816 hrcU HrcU protein 6.651595141 XCAW_00738 sflA NADH dependent FMN reductase 5.919992563 XCAW_01386 XCAW_01386 Hypothetical Protein 4.752781261 XCAW_00739 XCAW_00739 Hypothetical Protein 4.238760923 XCAW_02503 X CAW_02503 Hypothetical Protein 3.81974007 XCAW_00731 smeB multidrug efflux transporter 3.634581473 XCAW_02971 XCAW_02971 Hypothetical Protein 3.41784518 XCAW_00656 aceA Isocitrate lyase 3.366724684 XCAW_02513 mhpC hydrolase 3.345425704 XCAW_04531 X CAW_04531 Hypothetical Protein 3.321854834 XCAW_00826 hpa1 Hap1 protein 3.284402619 XCAW_00740 metE Methionine synthase II (cobalamin independent) 3.152363076 XCAW_01800 cirA Outer membrane receptor protein, mostly Fe transport 3.071973882 XCAW_0167 9 XCAW_01679 Hypothetical Protein 2.996833119 XCAW_02390 rpoE RNA polymerase sigma E factor 2.985415596

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131 Table 3 9 Continued. Locus tag Gene Name Product Log2 Fold Change WXVM/WNB XCAW_00817 hrpB1 HrpB1 protein 2.957612445 XCAW_04481 XCAW_04481 H ypothetical protein 2.941814698 XCAW_03573 XCAW_03573 Hypothetical Protein 2.862291397 XCAW_00413 XCAW_00413 Hypothetical Protein 2.773789229 XCAW_00809 hrpD5 HrpD5 protein 2.715655807 XCAW_02099 tra5 transposase 2.64786895 XCAW_03134 XCAW_03134 P AP2 (acid phosphatase) superfamily protein 2.598913765 XCAW_03161 XCAW_03161 Hypothetical Protein 2.556477892 XCAW_01947 XCAW_01947 Hypothetical Protein 2.509564442 XCAW_00498 trxA Thioredoxin 2.498029193 XCAW_01534 araC AraC type DNA binding domain containing protein 2.483440772 XCAW_00913 XCAW_00913 Hypothetical Protein 2.47503809 XCAW_01678 XCAW_01678 Hypothetical Protein 2.446636888 XCAW_04186 cirA Outer membrane receptor protein, mostly Fe transport 2.437688807 XCAW_04216 bcsA Glycosyltra nsferase probably involved in cell wall biogenesis 2.36772409 XCAW_04187 amyA Glycosidase 2.345488068 XCAW_03339 mhpC hydrolase 2.339989105 XCAW_00741 kdgT 2 keto 3 deoxygluconate permease 2.308173551 XCAW_02370 XCAW_02370 Fe S oxidoreductases family 2 2.306884208 XCAW_04628 XCAW_04628 Hypothetical Protein 2.302151917 XCAW_02302 Eda 2 keto 3 deoxy 6 phosphogluconate aldolase 2.291114771 XCAW_03307 XCAW_03307 Hypothetical Protein 2.222122648 XCAW_01319 XCAW_01319 Cysteine protease 2.195405549 XCAW_04201 tra5 transposase 2.174463941 XCAW_00655 aceB Malate synthase 2.148518656 XCAW_01723 xerC Integrase 2.126026528 XCAW_01672 XCAW_01672 Hypothetical Protein 2.120245927 XCAW_03324 mET2 Homoserine acetyltransferase 2.119347649

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132 Table 3 9 Continued. Locus tag Gene Name Product Log2 Fold Change WXVM/WNB XCAW_02038 Pel Pectate lyase 2.105781403 XCAW_01690 radC DNA repair protein 2.089990882 XCAW_03862 betT Choline glycine betaine transporter 2.084851267 XCAW_01112 XCAW_01112 Hypothetic al Protein 2.082537527 XCAW_01646 XCAW_01646 Hypothetical Protein 2.069207669 XCAW_04607 XCAW_04607 Hypothetical Protein 2.064680343 XCAW_03975 Nei Formamidopyrimidine DNA glycosylase 2.063945516 XCAW_00654 lysR Transcriptional regulator 2.06075790 9 XCAW_00806 hpaB HpaB protein 2.060550373 XCAW_00433 XCAW_00433 Hypothetical Protein 2.033307194 XCAW_02392 aprE Subtilisin like serine protease 2.029176025 XCAW_00802 hrpF HrpF protein 2.021961685 XCAW_01387 XCAW_01387 Hypothetical Protein 2.0139 29222 XCAW_00686 avrXacE1 avirulence protein 2.010636575 XCAW_00958 aroG 3 Deoxy D arabino heptulosonate 7 phosphate (DAHP) synthase 1.996777108 XCAW_01632 hepA Superfamily II DNA 1.994982692 XCAW_03756 cirA Outer membrane receptor protein, mostly Fe transport 1.988799152 XCAW_03665 mhpC hydrolase 1.985100655 XCAW_03492 XCAW_03492 Hypothetical Protein 1.958283503 XCAW_01665 XCAW_01665 Hypothetical Protein 1.956543531 XCAW_01110 XCAW_01110 Hypothetical Protein 1.936806015 XCAW_04534 XCAW_04534 Hypothetical Protein 1.928305447 XCAW_01615 syrE1 ATP dependent serine activating enzyme 1.926670915 XCAW_01649 XCAW_01649 Hypothetical Protein 1.920245314 XCAW_00685 XCAW_00685 Hypothetical Protein 1.917812498 XCAW_00528 XCAW_00528 Hypothetical Pr otein 1.915049604 XCAW_03135 yjdB membrane associated, metal dependent hydrolase 1.907833408 XCAW_03112 XCAW_03112 Hypothetical Protein 1.887882446

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133 Table 3 9 Continued. Locus tag Gene Name Product Log2 Fold Change WXVM/WNB XCAW_01271 XCAW_01271 H ypothetical Protein 1.872765196 XCAW_00521 XCAW_00521 Hypothetical Protein 1.863676335 XCAW_02910 asnB Asparagine synthase (glutamine hydrolyzing) 1.860877397 XCAW_04388 XCAW_04388 Hypothetical Protein 1.856936469 XCAW_03828 XCAW_03828 Hypothetical Protein 1.845481551 XCAW_01647 XCAW_01647 Hypothetical Protein 1.837950142 XCAW_00141 fldW 4 oxalomesaconate hydratase 1.833762556 XCAW_00238 ftrA Transcriptional regulator 1.830484771 XCAW_03227 XCAW_03227 Hypothetical Protein 1.821126913 XCAW_0 0100 XCAW_00100 Hypothetical Protein 1.806495705 XCAW_01614 syrE2 ATP dependent serine activating enzyme 1.783262132 XCAW_00750 XCAW_00750 Integrase 1.781219675 XCAW_02422 XCAW_02422 Hypothetical Protein 1.777655981 XCAW_00974 mdcA malonate decarbox ylase subunit alpha 1.759295729 XCAW_00497 atsE Protein required for attachment to host cell 1.756206791 XCAW_00041 cirA Outer membrane receptor protein, mostly Fe transport 1.755436711 XCAW_00769 Hmp Flavodoxin reductases (ferredoxin NADPH reductases) family 1 1.749997983 XCAW_01648 XCAW_01648 Hypothetical Protein 1.746495275 XCAW_01683 XCAW_01683 Hypothetical Protein 1.741760322 XCAW_02651 fimT fimbrial biogenesis protein 1.741740548 XCAW_04317 XCAW_04317 Hypothetical Protein 1.735545735 XCAW _00608 avrGf1 avirulence protein 1.732104322 XCAW_02982 araJ Arabinose efflux permease 1.714674032 XCAW_02746 XCAW_02746 Hypothetical Protein 1.711024522 XCAW_04153 lysR Transcriptional regulator 1.706208886 XCAW_04120 cirA Outer membrane receptor p rotein, mostly Fe transport 1.70382146 XCAW_01772 XCAW_01772 Oxidoreductase 1.693736061 XCAW_04055 blaI transcriptional regulator 1.692014478

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134 Table 3 9 Continued. Locus tag Gene Name Product Log2 Fold Change WXVM/WNB XCAW_00956 XCAW_00956 Hypothet ical Protein 1.686005416 XCAW_03514 XCAW_03514 xanthomonas outer protein AQ 1.653748637 XCAW_02711 citB Response regulator 1.652092283 XCAW_02991 dksA DnaK suppressor protein 1.647424892 XCAW_04318 bioD Dethiobiotin synthetase 1.645368497 XCAW_04 426 XCAW_04426 Hypothetical Protein 1.640092478 XCAW_03037 XCAW_03037 transcriptional regulator 1.638786568 XCAW_04184 proP Permeases of the major facilitator superfamily 1.636778001 XCAW_02192 Lrp Transcriptional regulator 1.634101619 XCAW_01236 p spF Transcriptional regulator 1.632378224 XCAW_01107 gp19 DNA maturase 1.623983311 XCAW_01328 acrA Membrane fusion protein 1.610864633 XCAW_01797 XCAW_01797 Hypothetical Protein 1.610738674 XCAW_04428 XCAW_04428 Hypothetical Protein 1.602655579 XC AW_01722 lysR Transcriptional regulator 1.5958619 XCAW_02168 proP Permeases of the major facilitator superfamily 1.595767988 XCAW_02745 cynT Carbonic anhydrase 1.592269693 XCAW_04389 XCAW_04389 Hypothetical Protein 1.590899382 XCAW_00034 XCAW_00034 Hypothetical Protein 1.590614349 XCAW_00807 hrpE HrpE protein 1.590196171 XCAW_01066 XCAW_01066 Hypothetical Protein 1.589789203 XCAW_01390 XCAW_01390 Hypothetical Protein 1.587621746 XCAW_03704 XCAW_03704 Protein involved in meta pathway of phenol degradation 1.585067241

PAGE 135

135 Table 3 9 Continued. Locus tag Gene Name Product Log2 Fold Change WXVM/WNB Underexpressed Genes XCAW_02378 XCAW_02378 Hypothetical Protein 3140.515625 XCAW_00042 proP Permeases of the major facilitator superfamily 83.0267454 XCAW_00624 XCAW_00624 Hypothetical Protein 35.15380886 XCAW_02461 XCAW_02461 Hypothetical Protein 22.23939813 XCAW_00151 araC AraC type DNA binding domain containing protein 19.75201875 XCAW_01627 XCAW_01627 Hypothetical Protein 11. 82025355 XCAW_02589 fhaC Hemolysin activation 9.636922617 XCAW_01336 araJ Arabinose efflux permease 9.528786753 XCAW_02227 hcaD NAD(FAD) dependent dehydrogenase 9.001986184 XCAW_02229 XCAW_02229 D amino acid oxidase 8.796458825 XCAW_00602 glnK N itrogen regulatory protein PII 7.276308634 XCAW_02376 smtA SAM dependent methyltransferase 5.958742576 XCAW_00168 XCAW_00168 Hypothetical Protein 5.278464915 XCAW_01895 flhF Flagellar GTP binding protein 4.31455307 XCAW_02375 XCAW_02375 Hypothe tical Protein 4.094281955 XCAW_01883 fliN Flagellar motor switch 4.066845786 XCAW_02225 putA NAD dependent aldehyde dehydrogenase 4.031671388 XCAW_00496 XCAW_00496 Hypothetical Protein 3.888352375 XCAW_02221 potE Amino acid transporter 3.324988 986 XCAW_02224 pepP Xaa Pro aminopeptidase 2.973159044 XCAW_03034 paaF Enoyl CoA hydratase 2.965802973 XCAW_02220 dAP2 Dipeptidyl aminopeptidase 2.914007554 XCAW_01230 trpE Anthranilate synthase component I 2.851920531 XCAW_02219 lacA Beta galact osidase 2.823701003 XCAW_03079 rsbW Two component system sensor protein 2.708440947 XCAW_03927 acoR Transcriptional activator of acetoin 2.704095317

PAGE 136

136 Table 3 9 Continued. Locus tag Gene Name Product Log2 Fold Change WXVM/WNB XCAW_02226 dapA Dihyd rodipicolinate synthase 2.637251109 XCAW_03833 ribB 3,4 dihydroxy 2 butanone 4 phosphate synthase 2.586237557 XCAW_02223 XCAW_02223 Hypothetical Protein 2.585904159 XCAW_02230 XCAW_02230 Proline racemase 2.572001105 XCAW_01884 fliO Flagellar bio synthesis 2.489272539 XCAW_00928 pgpB Membrane associated phospholipid phosphatase 2.454176248 XCAW_02222 XCAW_02222 Hypothetical Protein 2.452372612 XCAW_00854 aceF Dihydrolipoamide acyltransferase 2.447742182 XCAW_01847 flgH Flagellar basal bo dy L ring protein 2.432807524 XCAW_00603 amtB Ammonium transporter 2.412986746 XCAW_01848 flgI Flagellar basal body P ring protein 2.340453908 XCAW_00734 cmfA conditioned medium factor 2.33344351 XCAW_00110 XCAW_00110 Metal dependent hydrolase 2.327534492 XCAW_01343 fhuA TonB dependent receptor 2.326107186 XCAW_04243 aprE Subtilisin like serine protease 2.325548227 XCAW_02218 XCAW_02218 Hypothetical Protein 2.319421627 XCAW_02213 cirA Outer membrane receptor protein, mostly Fe transport 2.286199995 XCAW_03834 ribC Riboflavin synthase alpha chain 2.268832606 XCAW_00855 XCAW_00855 Hypothetical Protein 2.257625853 XCAW_00111 Tas oxidoreductases (related to aryl alcohol dehydrogenases) 2.247298472 XCAW_03033 XCAW_03033 Enoyl CoA hydratase 2.230314362 XCAW_01893 flhA Flagellar biosynthesis protein FlhA 2.224098334 XCAW_03987 XCAW_03987 archaeal methyltransferase 2.220823106 XCAW_03775 dAP2 Dipeptidyl aminopeptidase 2.176404655 XCAW_00292 speB Arginase 2.148387728 XCAW_00 927 pldB Lysophospholipase 2.130227195 XCAW_02252 fabH 3 oxoacyl [acyl carrier protein] synthase III 2.120390929 XCAW_02508 Tar Methyl accepting chemotaxis protein 2.113973547

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137 Table 3 9 Continued. Locus tag Gene Name Product Log2 Fold Change WX VM/WNB XCAW_01849 flgJ Flagellum specific muramidase 2.096489665 XCAW_03359 fucA1 Alpha L fucosidase 2.096467276 XCAW_03035 fadE9 Acyl CoA dehydrogenase 2.089155085 XCAW_03815 XCAW_03815 Methyltransferase 2.08866952 XCAW_03032 mmsB 3 hydroxyisob utyrate dehydrogenase 2.059001619 XCAW_01882 fliM Flagellar motor switch protein 2.056316691 XCAW_04041 XCAW_04041 Hypothetical Protein 2.037612969 XCAW_03036 putA NAD dependent aldehyde dehydrogenase 2.006100409 XCAW_01226 fabD Malonyl CoA ACP transacylase 2.004394574 XCAW_00766 glpF Glycerol uptake facilitator and related permeases (Major Intrinsic Protein Family) 1.986165469 XCAW_01854 XCAW_01854 Hypothetical Protein 1.983088897 XCAW_02550 leuA Hydroxymethylglutaryl CoA lyase 1.981592 481 XCAW_00150 uspA Universal stress protein and related nucleotide binding protein 1.980338221 XCAW_02209 cirA Outer membrane receptor protein, mostly Fe transport 1.979295018 XCAW_04455 motB Flagellar motor protein 1.976906999 XCAW_04166 gltP C 4 dicarboxylate transport protein 1.974478906 XCAW_00380 anmK anhydro N acetylmuramic acid kinase 1.935674172 XCAW_02611 sglT sodium/glucose cotransport protein 1.925477209 XCAW_01897 fliA DNA directed RNA polymerase specialized sigma subunit 1.920 358389 XCAW_00099 ndvB Cellobiose phosphorylase 1.919682419 XCAW_01786 XCAW_01786 Adenosine deaminase 1.914461422 XCAW_01900 cheA Chemotaxis protein histidine kinase 1.912684979 XCAW_03381 rimL Acetyltransferase, including N acetylases of ribosoma l protein 1.907245017 XCAW_01996 cycH Cytochrome c biogenesis factor 1.898633138 XCAW_00254 cirA Outer membrane receptor protein, mostly Fe transport 1.885017979 XCAW_01757 XCAW_01757 Cation/multidrug efflux pump 1.867038088 XCAW_00858 nucH extra cellular nuclease 1.857602062

PAGE 138

138 Table 3 9 Continued. Locus tag Gene Name Product Log2 Fold Change WXVM/WNB XCAW_01896 fleN flagellar synthesis regulator 1.843600925 XCAW_00856 acoB Thiamine pyrophosphate dependent dehydrogenase, E1 component beta su bunit 1.825311085 XCAW_01846 flgG Flagellar basal body rod protein 1.817249914 XCAW_03383 cheB Chemotaxis response regulator 1.816912793 XCAW_04726 potE Amino acid transporter 1.815688935 XCAW_04311 Gst Glutathione S transferase 1.812598077 X CAW_01881 fliL Flagellar basal body associated protein 1.798105595 XCAW_04371 yaeE Permease component of an uncharacterized ABC transporter 1.791960586 XCAW_03377 cutC Uncharacterized protein involved in copper resistance 1.791837307 XCAW_04325 fa bA 3 hydroxydecanoyl ACP dehydratase 1.790536413 XCAW_01304 oliA oligopeptide transporter 1.780547639 XCAW_03204 proC Pyrroline 5 carboxylate reductase 1.778101035 XCAW_01009 rimL Acetyltransferase, including N acetylases of ribosomal protein 1.777 243904 XCAW_00910 XCAW_00910 Hypothetical Protein 1.763202433 XCAW_01845 flgF Flagellar basal body rod protein 1.762564656 XCAW_01875 fliF Flagellar MS ring protein 1.752591022 XCAW_00289 XCAW_00289 Hypothetical Protein 1.747286414 XCAW_00957 c irA Outer membrane receptor protein, mostly Fe transport 1.743589863 XCAW_03836 ribD Pyrimidine reductase, riboflavin biosynthesis 1.737362909 XCAW_00507 moxR MoxR like ATPase 1.728262727 XCAW_02022 proP Permeases of the major facilitator superfam ily 1.724564363 XCAW_02044 XCAW_02044 Hypothetical Protein 1.720651997 XCAW_01844 flgE Flagellar basal body and hook protein 1.71809943 XCAW_02214 XCAW_02214 Hypothetical Protein 1.716045903 XCAW_01850 flgK Flagellar hook associated protein Flg K 1.711306816 XCAW_02062 XCAW_02062 Flavoprotein 1.706080685 XCAW_01432 Mrp ATPases involved in chromosome partitioning 1.704145303

PAGE 139

139 Table 3 9 Continued. Locus tag Gene Name Product Log2 Fold Change WXVM/WNB XCAW_02292 XCAW_02292 Hypothetical Pro tein 1.700790245 XCAW_00105 fucP Fucose permease 1.700275909 XCAW_02602 XCAW_02602 Hypothetical Protein 1.697828188 XCAW_04559 Sun tRNA and rRNA cytosine C5 methylase 1.694698627 XCAW_04198 XCAW_04198 Hypothetical Protein 1.690773264 XCAW_03 275 XCAW_03275 Hypothetical Protein 1.679903791 XCAW_03360 XCAW_03360 glycosyl hydrolase 1.67691337 XCAW_04090 Rph Ribonuclease PH 1.670466616 XCAW_03010 ubiH 2 polyprenyl 6 methoxyphenol hydroxylase and related FAD dependent oxidoreductase 1.67 000733 XCAW_00121 actP acetate permease 1.668686991 XCAW_04453 XCAW_04453 Hypothetical Protein 1.665486282 XCAW_00403 XCAW_00403 Hypothetical Protein 1.664782279 XCAW_01899 cheZ Chemotaxis protein 1.661124837 XCAW_04099 XCAW_04099 Hypothetical Protein 1.658567365 XCAW_00615 XCAW_00615 Hypothetical Protein 1.655623816 XCAW_02291 xylB Sugar (pentulose and hexulose) kinase 1.654721931 XCAW_00107 XCAW_00107 L alanine DL glutamate epimerase and related enzymes of enolase superfamily 1.65459 7714 XCAW_02507 XCAW_02507 Hypothetical Protein 1.651152371 XCAW_04042 XCAW_04042 membrane protein 1.649529349 XCAW_03406 Glk Glucokinase 1.649521898 XCAW_00865 hmgA Homogentisate 1,2 dioxygenase 1.646718087 XCAW_01421 yxaH Hypothetical Protei n 1.641362704 XCAW_04244 xadA Autotransporter adhesin 1.640441319 XCAW_02061 XCAW_02061 Uncharacterized protein conserved in bacteria 1.636697842 XCAW_01843 flgD Flagellar hook capping protein 1.635728587 XCAW_00147 XCAW_00147 Uncharacterized p rotein conserved in bacteria 1.634511561

PAGE 140

140 Table 3 9 Continued. Locus tag Gene Name Product Log2 Fold Change WXVM/WNB XCAW_01337 Tas oxidoreductases (related to aryl alcohol dehydrogenases) 1.633424558 XCAW_03630 Pth Peptidyl tRNA hydrolase 1.626 87934 XCAW_02547 caiD Enoyl CoA hydratase 1.626642034 XCAW_04074 pilP Fimbrial assembly protein 1.621647139 XCAW_00149 wbbJ Acetyltransferase (the isoleucine patch superfamily) 1.619862241 XCAW_03363 bglX Beta glucosidase related glycosidase 1.6 19597025 XCAW_00133 XCAW_00133 Uncharacterized protein conserved in bacteria 1.618717367 XCAW_02928 cdsA CDP diglyceride synthetase 1.618284133 XCAW_03384 cheA Chemotaxis protein histidine kinase 1.618182349 XCAW_04326 fabB 3 oxoacyl (acyl carri er protein) synthase 1.617250514 XCAW_02157 proP Permeases of the major facilitator superfamily 1.614914571 XCAW_02612 bglX Beta glucosidase related glycosidase 1.614311211 XCAW_00857 acoA Thiamine pyrophosphate dependent dehydrogenase, E1 componen t alpha subunit 1.610824332 XCAW_01549 yapH filamentous hemagglutinin related protein 1.606880959 XCAW_03382 XCAW_03382 Hypothetical Protein 1.598262704 XCAW_00109 fabG Dehydrogenases with different specificities (related to short chain alcohol deh ydrogenases) 1.588692921 XCAW_03407 cirA Outer membrane receptor protein, mostly Fe transport 1.58604605 XCAW_04454 XCAW_04454 Hypothetical Protein 1.585602168

PAGE 141

141 Table 3 10 Genes differentially expressed between strains X. citri subsp. citri str. 306 (A) and X. citri subsp. citri str. A w 12879 (W) in NB (nutrient rich) medium. Cut off value of Log2 1 Locus tag Gene Name Product Log 2 Fold Change WNB/ANB Overexpressed Genes XAC2219 XAC2219 hypothetical protein 25.64823906 XAC4248 gnl gluconolactonase 10.50680576 XAC1780 amiC N acetylmuramoyl L alanine amidase 7.433611332 XAC3260 mobL plasmid mobilization protein 6.249044118 XAC2372 XAC2372 IS1479 transposase 4.188812122 XAC3474 cit1 citrate carrier protein 2.51470588 XAC3445 XAC34 45 transcriptional regulator 2.499307593 XAC3475 XAC3475 hypothetical protein 2.485473632 XAC1165 XAC1165 hypothetical protein 2.383179166 XAC0338 XAC0338 hypothetical protein 2.276943861 XAC0398 hrpD6 HrpD6 protein 2.189413045 XAC1338 XAC1338 oxidore ductase 2.174773081 XAC0295 XAC0295 hypothetical protein 2.152862049 XAC1576 pstC ABC transporter phosphate permease 2.126602949 XAC3489 fyuA TonB dependent receptor 2.11056609 XAC1575 pstA ABC transporter phosphate permease 2.000651353 XAC1579 oprO p olyphosphate selective porin O 1.99014292 XAC3712 XAC3712 metallopeptidase 1.987497004 XAC3757 XAC3757 hypothetical protein 1.938891939 XAC0999 cirA colicin I receptor 1.927565575 XAC0310 vanB vanillate O demethylase 1.924455658 XAC2835 mocA oxidoredu ctase 1.914657242 XAC0509 XAC0509 MFS transporter 1.911547087 XAC1792 phoX alkaline phosphatase 1.834962219 XAC2520 XAC2520 TonB dependent receptor 1.803981048 XAC0822 XAC0822 hypothetical protein 1.798432741 XAC1577 pstS phosphate ABC transporter sub strate binding protein 1.774309607 XAC2538 XAC2538 hypothetical protein 1.753277012 XAC2113 XAC2113 hypothetical protein 1.749331387 XAC2860 XAC2860 hypothetical protein 1.739794559 XAC3444 btuB TonB dependent receptor 1.737743201 XAC2142 lytS two com ponent system sensor protein 1.703861969 XAC1574 pstB phosphate transporter ATP binding protein 1.693102281 XAC0654 acoR transcriptional regulator AcoR 1.615372055 XAC2763 XAC2763 extracellular protease 1.572651346 XAC3770 XAC3770 hypothetical protein 1.569563197

PAGE 142

142 Table 3 10 Continued. Locus tag Gene Name Product Log2 Fold Change WNB/ANB XAC1266 hrpXct HrpX protein 1.568267693 XAC3501 XAC3501 hypothetical protein 1.566239878 XAC0162 dctP C4 dicarboxylate transport system 1.544128974 XAC1164 XAC11 64 hypothetical protein 1.515862882 XAC4355 XAC4355 hypothetical protein 1.510814239 XAC0298 XAC0298 hypothetical protein 1.500278696 XAC2604 XAC2604 ISxac4 transposase 1.496170371 XAC3028 XAC3028 histidine kinase response regulator hybrid protein 1.49 5944706 XAC3612 XAC3612 peptidase 1.491243942 XAC2141 lytT two component system regulatory protein 1.487417813 XAC1104 mobL plasmid mobilization protein 1.483732088 XAC3490 XAC3490 amylosucrase or alpha amylase 1.474480131 XAC3384 pilN fimbrial assemb ly membrane protein 1.456476503 XAC1137 prpB 2 methylisocitrate lyase 1.455283697 XAC3000 soxR SoxR family transcriptional regulator 1.436934908 XAC0300 XAC0300 serine pyruvate aminotransferase 1.42513523 XAC3382 pilP fimbrial assembly protein 1.422386 632 XAC3754 XAC3754 hypothetical protein 1.419796784 XAC3610 rhlE ATP dependent RNA helicase 1.410457152 XAC3383 pilO fimbrial assembly membrane protein 1.396824265 XAC2423 XAC2423 IS1478 transposase 1.389696936 XAC4009 argI arginase 1.381846267 XAC0 208 ntrC two component system regulatory protein 1.377969174 XAC3312 XAC3312 glycosyl hydrolase 1.367144662 XAC3473 XAC3473 sensor histidine kinase 1.366914397 XAC4127 pknB serine/threonine kinase 1.358906214 XAC3704 XAC3704 DNA polymerase like protein 1.353354957 XAC3647 pheA chorismate mutase 1.348736132 XAC2313 XAC2313 LacI family transcriptional regulator 1.34456622 XAC1196 lexA LexA repressor 1.336678942 XAC3772 XAC3772 LysR family transcriptional regulator 1.333027805 XAC1042 phoB two compone nt system regulatory protein 1.328422784 XAC4257 xylP transporter 1.325096356 XAC4369 phoC phosphatase 1.321836272 XAC3035 XAC3035 hypothetical protein 1.320327487 XAC1910 cirA TonB dependent receptor 1.313206942 XAC3381 pilQ fimbrial assembly protein 1.308210585 XAC2537 XAC2537 peptidase 1.306338218 XAC1130 trpE hypothetical protein 1.299799316 XAC3958 XAC3958 hypothetical protein 1.29895361

PAGE 143

143 Table 3 10 Continued. Locus tag Gene Name Product Log2 Fold Change WNB/ANB XAC3640 ybjZ ABC transporter ATP binding protein 1.298024445 XAC1068 stf phage related tail protein 1.292866904 XAC3240 fimA fimbrillin 1.28994735 XAC4150 nodL nodulation protein 1.289643923 XAC0446 pdhA pyruvate dehydrogenase E1 alpha subunit 1.288140846 XAC3428 XAC3428 hydrola se 1.28366189 XAC0508 XAC0508 LysR family transcriptional regulator 1.279977726 XAC0299 XAC0299 hypothetical protein 1.279487405 XAC3819 gst glutathione S transferase 1.261668538 XAC2500 XAC2500 LacI family transcriptional regulator 1.256706948 XAC044 5 pdhB pyruvate dehydrogenase E1 beta subunit 1.250592984 XAC3064 XAC3064 hypothetical protein 1.247208635 XAC1250 obgE GTPase ObgE 1.244070086 XAC0970 tuf elongation factor Tu 1.241899788 XAC2302 XAC2302 hypothetical protein 1.236512043 XAC0274 XAC02 74 nuclease 1.235937581 XAC2773 oar Oar protein 1.232672974 XAC2324 cycW ABC transporter heme permease 1.228831091 XAC0168 kduI 5 keto 4 deoxyuronate isomerase 1.228597531 XAC1635 hutU urocanate hydratase 1.227454133 XAC3686 XAC3686 hypothetical prote in 1.226668753 XAC1199 dnaE2 DNA polymerase III subunit alpha 1.220359381 XAC3404 XAC3404 hypothetical protein 1.220003008 XAC3339 cysB transcriptional regulator CysB like protein 1.218857138 XAC3791 yncA phosphinothricin acetyltransferase 1.218502295 XAC1637 hutH histidine ammonia lyase 1.218396454 XAC4229 rspA starvation sensing protein 1.214754425 XAC2490 XAC2490 hypothetical protein 1.212956573 XAC3563 rimI ribosomal protein alanine acetyltransferase 1.211869181 XAC4354 yhdG amino acid transpor ter 1.208223002 XAC1774 XAC1774 hypothetical protein 1.206641764 XAC2536 XAC2536 hypothetical protein 1.206097283 XAC1776 xylA xylose isomerase 1.204464335 XAC4272 XAC4272 LacI family transcriptional regulator 1.204316412 XAC2411 acvB virulence protei n 1.20359303 XAC2974 ptsN nitrogen regulatory IIA protein 1.199204521 XAC4190 fucP fucose permease 1.198482604 XAC1265 hrpG HrpG protein 1.194586105 XAC0870 XAC0870 hypothetical protein 1.193665805 XAC2914 XAC2914 hypothetical protein 1.193244983 XAC 2949 XAC2949 calcium binding protein 1.192126089

PAGE 144

144 Table 3 10 Continued. Locus tag Gene Name Product Log2 Fold Change WNB/ANB XAC3331 cysI sulfite reductase subunit beta 1.191296014 XAC3860 XAC3860 N acetylmuramoyl L alanine amidase 1.188397814 XAC231 2 XAC2312 hypothetical protein 1.185492429 XAC2848 XAC2848 hypothetical protein 1.185372734 XAC3166 bfeA ferric enterobactin receptor 1.184298653 XAC1286 XAC1286 alpha L arabinofuranosidase 1.18405598 XAC3928 XAC3928 hypothetical protein 1.182582034 X AC0169 kduD short chain dehydrogenase 1.17965288 XAC1240 XAC1240 hypothetical protein 1.177239607 XAC3433 XAC3433 hypothetical protein 1.177010501 XAC4168 hetI HetI protein 1.176989353 XAC3316 XAC3316 tRNA/rRNA methyltransferase 1.175175543 XAC1232 XA C1232 DNA 3 methyladenine glycosylase 1.174198144 XAC3995 acrE acriflavin resistance protein 1.174020371 XAC1512 XAC1512 serine peptidase 1.173302695 XAC2826 XAC2826 alcohol dehydrogenase 1.171771584 XAC2589 pheT phenylalanyl tRNA synthetase subunit be ta 1.1717389 XAC2341 gaa glutaryl 7 ACA acylase 1.17093649 XAC3733 XAC3733 NtrC family transcriptional regulator 1.167496149 XAC3863 XAC3863 hypothetical protein 1.166631626 XAC1616 XAC1616 hypothetical protein 1.165436305 XAC1449 XAC1449 hypothetical protein 1.165224046 XAC0871 XAC0871 hypothetical protein 1.165180569 XAC1636 hutG formylglutamate amidohydrolase 1.164738375 XAC1793 celD glucan 1,4 beta glucosidase 1.164303373 XAC1329 rumA 23S rRNA 5 methyluridine methyltransferase 1.163782594 XAC3 721 XAC3721 D amino acid oxidase 1.163509009 XAC3391 recG ATP dependent DNA helicase RecG 1.161813634 XAC3072 fucA1 alpha L fucosidase 1.159787168 XAC1794 sglT sodium/glucose cotransport protein 1.157757657 XAC1129 fabF 3 oxoacyl ACP synthase 1.1575648 42 XAC1851 mvaB hydroxymethylglutaryl CoA lyase 1.157385744 XAC3909 dpm1 dolichol phosphate mannosyltransferase 1.155608746 XAC1640 hutC histidine utilization repressor 1.155113338 XAC0025 XAC0025 hypothetical protein 1.151633231 XAC3505 rhgB rhamnoga lacturonase B 1.151359093 XAC3385 pilM fimbrial assembly membrane protein 1.150285388 XAC1638 hutI imidazolonepropionase 1.149561775 XAC0723 dsbA disulfide oxidoreductase 1.149165434 XAC3923 speA arginine decarboxylase 1.149105259 XAC0554 XAC0554 hypo thetical protein 1.14870911

PAGE 145

145 Table 3 10 Continued. Locus tag Gene Name Product Log2 Fold Change WNB/ANB XAC3673 XAC3673 histidine kinase 1.148084876 XAC1835 hisI bifunctional phosphoribosyl AMP cyclohydrolase/phosphoribosyl ATP pyrophosphatase 1.14712 2502 XAC3476 ybhD transcriptional regulator 1.145371713 XAC1471 XAC1471 hypothetical protein 1.143158199 XAC0202 XAC0202 hypothetical protein 1.142130292 XAC4276 pyrF orotidine 5' phosphate decarboxylase 1.141059115 XAC4199 XAC4199 polyvinylalcohol de hydrogenase 1.141037777 XAC0017 XAC0017 hypothetical protein 1.14056938 XAC3313 susB alpha glucosidase 1.140338807 XAC1777 xylE MFS transporter 1.139337986 XAC2752 yxaH transporter 1.138867614 XAC3125 XAC3125 hypothetical protein 1.138848561 XAC2531 btuB TonB dependent receptor 1.138552214 XAC1362 nerA GTN reductase 1.138250538 XAC3862 tcbD chloromuconate cycloisomerase 1.136972174 XAC2707 tpiA triosephosphate isomerase 1.135555794 XAC2830 fhuA TonB dependent receptor 1.135551606 XAC3341 cysK cys teine synthase 1.135197438 XAC4300 XAC4300 hypothetical protein 1.135139198 XAC3578 ipsI IpsJ protein 1.134798188 XAC0070 XAC0070 ankyrin like protein 1.134434828 XAC3241 fimA fimbrillin 1.133014942 XAC2303 XAC2303 beta alanine synthetase 1.132882701 XAC1798 regS two component system sensor protein 1.132438074 XAC0251 XAC0251 TetR family transcriptional regulator 1.132354602 XAC0022 serA D 3 phosphoglycerate dehydrogenase 1.131665742 XAC0600 cycA D alanine/D serine/glycine permease 1.131332249 XAC 2824 XAC2824 phosphodiesterase nucleotide pyrophosphatase 1.131121447 XAC4302 folE GTP cyclohydrolase I 1.131109687 XAC2803 baeR two component system regulatory protein 1.130857165 XAC1113 slp outer membrane protein Slp 1.130749707 XAC3851 XAC3851 hypo thetical protein 1.130178883 XAC2194 XAC2194 hypothetical protein 1.130073359 XAC3376 XAC3376 hypothetical protein 1.130040329 XAC1838 XAC1838 enolase 1.129924845 XAC3379 moxR methanol dehydrogenase regulatory protein 1.128594684 XAC2530 XAC2530 hypot hetical protein 1.12768757

PAGE 146

146 Table 3 10 Continued. Locus tag Gene Name Product Log2 Fold Change WNB/ANB XAC4187 XAC4187 2 hydroxyhepta 2,4 diene 1, 7 dioate isomerase 1.127324344 XAC2522 egl2 cellulase 1.12713615 XAC0952 pth peptidyl tRNA hydrolase 1 .127058666 XAC2877 XAC2877 pirin 1.126419463 XAC3625 fabB beta ketoacyl [ACP] synthase I 1.126179244 XAC3083 XAC3083 hypothetical protein 1.125500518 XAC0254 yjl094C Na+/H+ exchanging protein 1.125157903 XAC1752 XAC1752 hypothetical protein 1.12507902 8 XAC3429 argD acetylornithine transaminase 1.125035412 XAC2019 XAC2019 hypothetical protein 1.12440991 XAC2783 trx thioredoxin 1.123710113 XAC0869 XAC0869 acetoin utilization family protein 1.12367105 XAC3007 XAC3007 hypothetical protein 1.123561922 XAC1582 nth endonuclease III 1.123312544 XAC3850 acrA acriflavin resistance protein 1.121889686 XAC2744 XAC2744 phytoene dehydrogenase 1.121436285 XAC2018 XAC2018 hypothetical protein 1.121230828 XAC3577 ipsJ IpsJ protein 1.121047213 XAC3194 btuB vit amin B transport outer membrane protein 1.1208382 XAC3481 afuA periplasmic iron binding protein 1.120663184 XAC2391 apt adenine phosphoribosyltransferase 1.119220893 XAC0544 XAC0544 hypothetical protein 1.119092736 XAC2329 dsbE C type cytochrome biogen esis protein/thioredoxin 1.118456085 XAC2720 truA tRNA pseudouridine synthase A 1.118171756 XAC3421 acoK transcriptional regulator 1.117750374 XAC1022 tdh L threonine 3 dehydrogenase 1.117170335 XAC3465 htrB lipid A biosynthesis lauroyl acyltransferase 1.116705322 XAC3151 XAC3151 hypothetical protein 1.11644408 XAC1204 XAC1204 alanyl dipeptidyl peptidase 1.11623036 XAC2455 petC ubiquinol cytochrome C oxidoreductase cytochrome C1 subunit 1.115582552 XAC2676 XAC2676 hypothetical protein 1.115566883 X AC2809 XAC2809 hypothetical protein 1.115184493 XAC3327 XAC3327 RND efflux membrane fusion protein 1.114652792 XAC0348 XAC0348 transferase 1.114438071 XAC1619 XAC1619 hypothetical protein 1.113421941 XAC1315 XAC1315 enoyl CoA hydratase 1.112931913 XAC 3705 XAC3705 hypothetical protein 1.112584024

PAGE 147

147 Table 3 10 Continued. Locus tag Gene Name Product Log2 Fold Change WNB/ANB XAC2456 petB ubiquinol cytochrome C oxidoreductase cytochrome B subunit 1.112583372 XAC1843 XAC1843 hypothetical protein 1.11209 6495 XAC0450 XAC0450 hypothetical protein 1.111816831 XAC2973 XAC2973 sigma 54 modulation protein 1.11146047 XAC1252 mviN virulence factor 1.111353917 XAC0174 phhA phenylalanine 4 monooxygenase 1.111002556 XAC4230 xylB arabinosidase 1.110191 XAC2976 XAC2976 hypothetical protein 1.109765725 XAC3913 dut deoxyuridine 5' triphosphate nucleotidohydrolase 1.109605606 XAC0969 fusA elongation factor G 1.109284519 XAC0615 XAC0615 aminopeptidase 1.109124905 XAC0454 hmgA homogentisate 1,2 dioxygenase 1.10906 224 XAC0452 XAC0452 4 hydroxyphenylpyruvate dioxygenase 1.108994714 XAC3644 glmU UDP N acetylglucosamine pyrophosphorylase 1.108805102 XAC3709 wrbA tryptophan repressor binding protein 1.107551541 XAC3987 XAC3987 leucine aminopeptidase 1.10686642 XAC4 373 rnpA ribonuclease P 1.106071395 XAC3463 tolC TolC protein 1.105906894 XAC1239 ate1 arginyl tRNA protein transferase 1.105584562 XAC2305 traB pheromone shutdown protein 1.104288688 XAC3510 def peptide deformylase 1.103200718 XAC2717 trpB tryptophan synthase subunit beta 1.102727484 XAC3887 ctaD cytochrome C oxidase subunit I 1.102617787 XAC2532 XAC2532 peptidase 1.102241954 XAC2681 nadC nicotinate nucleotide pyrophosphorylase 1.101622788 XAC0813 metK S adenosylmethionine synthetase 1.101588425 XAC1797 regR two component system regulatory protein 1.101549049 XAC3869 bglX beta glucosidase 1.101506779 XAC2016 XAC2016 hypothetical protein 1.101444505 XAC2727 XAC2727 hypothetical protein 1.101254486 XAC2545 pepQ proline dipeptidase 1.100225884 X AC3335 XAC3335 sensor histidine kinase 1.100053613 XAC2590 pheS phenylalanyl tRNA synthetase subunit alpha 1.099938956 XAC0731 XAC0731 hypothetical protein 1.099891801 XAC3347 pgk phosphoglycerate kinase 1.099637504 XAC0247 XAC0247 acyltransferase 1.09 896329 XAC2496 XAC2496 hypothetical protein 1.097121352 XAC3813 sppA endopeptidase IV 1.096928553

PAGE 148

148 Table 3 10 Continued. Locus tag Gene Name Product Log2 Fold Change WNB/ANB XAC2398 XAC2398 hypothetical protein 1.095908599 XAC1314 paaF enoyl CoA hyd ratase 1.095898799 XAC2015 ndk nucleoside diphosphate kinase 1.095855212 XAC3189 cobC threonine phosphate decarboxylase 1.095574873 XAC1713 XAC1713 carboxypeptidase like protein 1.095421852 XAC3455 leuA 2 isopropylmalate synthase 1.094712104 XAC3487 c ebR transcriptional regulator 1.093784343 XAC2908 murD UDP N acetylmuramoyl L alanyl D glutamate synthetase 1.092905914 XAC0129 aldA chloroacetaldehyde dehydrogenase 1.092346947 XAC2999 XAC2999 peptidase 1.092100333 XAC3069 XAC3069 16S ribosomal RNA me thyltransferase RsmE 1.092020946 XAC3073 XAC3073 hypothetical protein 1.091729241 XAC0479 XAC0479 hypothetical protein 1.091305768 XAC1032 purF amidophosphoribosyltransferase 1.091145302 XAC2806 XAC2806 beta lactamase 1.090264921 XAC2965 murA UDP N ac etylglucosamine 1 carboxyvinyltransferase 1.090095408 XAC3836 XAC3836 hypothetical protein 1.090065475 XAC1716 pyrG CTP synthetase 1.089830993 XAC2735 rimO ribosomal protein S12 methylthiotransferase 1.089493733 XAC2020 XAC2020 hypothetical protein 1.0 89033283 XAC2345 argH argininosuccinate lyase 1.089027511 XAC0233 fabH 3 oxoacyl ACP synthase 1.08888636 XAC1556 fucP glucose galactose transporter 1.088570635 XAC0591 XAC0591 dipeptidyl peptidase IV 1.088545568 XAC2540 XAC2540 hypothetical protein 1. 087660409 XAC2931 XAC2931 hypothetical protein 1.087452638 XAC3438 pfkA 6 phosphofructokinase 1.087005223 XAC3239 pilB pilus biogenesis protein 1.086446644 XAC3326 acrF acriflavin resistance protein 1.086060973 XAC2959 purM phosphoribosylaminoimidazol e synthetase 1.085947286 XAC4299 XAC4299 hypothetical protein 1.085694007 XAC1090 dnaQ DNA polymerase III subunit epsilon 1.085589405 XAC1139 acnA aconitate hydratase 1.085443877 XAC0751 nusB transcription antitermination protein NusB 1.085066611 XAC3 302 thiG thiazole synthase 1.084474739 XAC0005 XAC0005 hypothetical protein 1.084119954 XAC3848 mtrC membrane fusion protein 1.083463936 XAC0024 XAC0024 hypothetical protein 1.083100501

PAGE 149

149 Table 3 10 Continued. Locus tag Gene Name Product Log2 Fold Cha nge WNB/ANB XAC2745 XAC2745 metallopeptidase 1.082914289 XAC3375 XAC3375 hypothetical protein 1.082173323 XAC2730 XAC2730 hypothetical protein 1.081848637 XAC0635 XAC0635 hypothetical protein 1.081745394 XAC2678 purK phosphoribosylaminoimidazole carbo xylase ATPase subunit 1.08168274 XAC1043 XAC1043 hypothetical protein 1.081681589 XAC4022 phoQ two component system sensor protein 1.081456768 XAC3849 acrD acriflavin resistance protein 1.081189028 XAC4370 trmE tRNA modification GTPase TrmE 1.080532425 XAC3352 gapA glyceraldehyde 3 phosphate dehydrogenase 1.080132309 XAC3871 gcp DNA binding/iron metalloprotein/AP endonuclease 1.079686537 XAC2691 nuoN NADH dehydrogenase subunit N 1.078286647 XAC2713 XAC2713 oxidoreductase 1.077798924 XAC1262 XAC1262 hypothetical protein 1.077651629 XAC2881 cstA carbon starvation protein A 1.077483608 XAC0179 ylmA ABC transporter ATP binding protein 1.077426751 XAC1201 XAC1201 hypothetical protein 1.077311182 XAC3075 XAC3075 beta mannosidase 1.077302533 XAC1282 X AC1282 two component system sensor protein 1.076618737 XAC2022 moeA molybdopterin biosynthesis 1.075617702 XAC2461 XAC2461 (dimethylallyl)adenosine tRNA methylthiotransferase 1.075603939 XAC1214 gcvP glycine dehydrogenase 1.074795455 XAC0943 XAC0943 hy pothetical protein 1.074478864 XAC2542 yveA amino acid permease 1.074168054 XAC2905 ssb single stranded DNA binding protein 1.073988941 XAC2703 nuoB NADH dehydrogenase subunit B 1.073581745 XAC1004 typA GTP binding elongation factor protein 1.072728238 XAC2846 XAC2846 FUR family transcriptional regulator 1.072522739 XAC0944 prfA peptide chain release factor 1 1.072466415 XAC2594 thrS threonyl tRNA synthetase 1.072117274 XAC3560 btuB TonB dependent receptor 1.07058876 XAC2980 mgtE Mg++ transporter 1 .070304477 XAC3047 mtgA monofunctional biosynthetic peptidoglycan transglycosylase 1.069932542 XAC2106 XAC2106 hypothetical protein 1.069628899 XAC0668 lipA lipoyl synthase 1.069207751 XAC4004 XAC4004 peptidase 1.069193407

PAGE 150

150 Table 3 10 Continued. Lo cus tag Gene Name Product Log2 Fold Change WNB/ANB XAC3637 glmS glucosamine -fructose 6 phosphate aminotransferase 1.068626998 XAC1409 lpxA UDP N acetylglucosamine acyltransferase 1.068600973 XAC2008 lolA outer membrane lipoprotein carrier protein 1.068 320953 XAC2543 XAC2543 hypothetical protein 1.067962745 XAC2909 XAC2909 hypothetical protein 1.067469176 XAC0743 glyA serine hydroxymethyltransferase 1.067307853 XAC3442 ppa inorganic pyrophosphatase 1.067266351 XAC0628 XAC0628 prolyl oligopeptidase 1 .066947622 XAC0863 ksgA dimethyladenosine transferase 1.066817843 XAC4023 phoP two component system regulatory protein 1.066440427 XAC1109 dnaX DNA polymerase III subunits gamma and tau 1.06612866 XAC3671 XAC3671 nucleotide binding protein 1.065581085 XAC2878 XAC2878 hypothetical protein 1.065339592 XAC3145 tolQ TolQ protein 1.065185305 XAC3118 XAC3118 hypothetical protein 1.064501937 XAC2847 gltX glutamyl tRNA synthetase 1.064433445 XAC3607 uptC type II secretion system protein like protein 1.0643 25332 XAC3526 gtrB glycosyl transferase 1.064008591 XAC0788 secA preprotein translocase subunit SecA 1.063402126 XAC2053 tex transcription like protein 1.063354974 XAC1826 hisS histidyl tRNA synthetase 1.063333921 XAC2544 XAC2544 hypothetical protein 1.063098061 XAC3071 iroN TonB dependent receptor 1.063003868 XAC0685 XAC0685 histidine kinase response regulator hybrid protein 1.062866613 XAC1017 sbp sulfate ABC transporter substrate binding protein 1.061872022 XAC3357 XAC3357 beta lactamase 1.06176 2926 XAC1428 map methionine aminopeptidase 1.061644888 XAC4217 tatB sec independent translocase 1.061559573 XAC3835 icd isocitrate dehydrogenase 1.06143259 XAC1430 dapD 2,3,4,5 tetrahydropyridine 2,6 carboxylate N succinyltransferase 1.060649377 XAC20 01 clpA ATP dependent Clp protease subunit 1.060164854 XAC1992 XAC1992 c di GMP phosphodiesterase A 1.05948882 XAC3992 XAC3992 hypothetical protein 1.05937852 XAC3602 metB cystathionine gamma synthase 1.059208377 XAC3603 cysB cystathionine beta synthas e 1.0583837 XAC1000 dhs1 family II 2 keto 3 deoxy D arabino heptulosonate 7 phosphate synthase 1.058345599

PAGE 151

151 Table 3 10 Continued. Locus tag Gene Name Product Log2 Fold Change WNB/ANB XAC1539 purB adenylosuccinate lyase 1.055413001 XAC1238 XAC1238 hyp othetical protein 1.055020012 XAC3110 XAC3110 glycosyltransferase 1.053902078 XAC0382 aspH aspartyl asparaginyl beta hydroxylase 1.053845461 XAC3494 aspC aminotransferase 1.05375416 XAC3141 ompP6 outer membrane protein P6 1.053574987 XAC2692 nuoM NADH dehydrogenase subunit M 1.053403547 XAC2683 pnp polynucleotide phosphorylase 1.053215605 XAC1732 hflB cell division protein 1.0531697 XAC2687 infB translation initiation factor IF 2 1.052806459 XAC1804 murB UDP N acetylenolpyruvoylglucosamine reductas e 1.052697606 XAC0221 secB preprotein translocase subunit SecB 1.052151509 XAC0645 pepN aminopeptidase 1.051919733 XAC2698 nuoG NADH dehydrogenase subunit G 1.05135027 XAC1880 rpfB long chain fatty acid CoA ligase 1.050951518 XAC2360 pyrC dihydroorota se 1.050475376 XAC2758 gltT glutamate symporter 1.050231252 XAC1627 ligA NAD dependent DNA ligase LigA 1.04985178 XAC1155 hflK integral membrane protease subunit 1.04957679 XAC3801 def peptide deformylase 1.049531524 XAC2701 nuoD NADH dehydrogenase su bunit D 1.049092169 XAC1040 ppk polyphosphate kinase 1.048546324 XAC2700 nuoE NADH dehydrogenase subunit E 1.047166009 XAC1590 XAC1590 hypothetical protein 1.046648045 XAC4006 trpS tryptophanyl tRNA synthetase 1.046271613 XAC2924 pilT twitching motili ty protein 1.04616725 XAC3493 XAC3493 ribosome associated GTPase 1.045114872 XAC4367 glpQ glycerophosphoryl diester phosphodiesterase 1.041950638 XAC1740 recA recombinase A 1.041511744 XAC2805 yjl094C cation:proton antiporter 1.041157483 XAC3393 spoT pentaphosphate guanosine 3' pyrophosphohydrolase 1.040972721 XAC3912 algC phosphomannomutase 1.03961513 XAC0950 prsA ribose phosphate pyrophosphokinase 1.039604702 XAC2971 yhbG ABC transporter ATP binding protein 1.039398199 XAC3897 tyrS tyrosyl tRNA s ynthetase 1.039046534 XAC2743 oar Oar protein 1.036089137 XAC3650 atpG ATP synthase F0F1 subunit gamma 1.035872908 XAC0120 tldD TldD protein 1.033932809

PAGE 152

152 Table 3 10 Continued. Locus tag Gene Name Product Log2 Fold Change WNB/ANB XAC0989 rpsE 30S rib osomal protein S5 1.033905073 XAC0893 glnS glutaminyl tRNA synthetase 1.02946677 XAC4284 mdoD glucan biosynthesis protein D 1.027224464 XAC0966 rpoC DNA directed RNA polymerase subunit beta' 1.024602274 XAC1551 ugd UDP glucose dehydrogenase 1.023935428 XAC0965 rpoB DNA directed RNA polymerase subunit beta 1.019572533 XAC1623 smc chromosome segregation protein 1.019266918 XAC2298 rpsA 30S ribosomal protein S1 1.014668444 Underexpressed Genes XAC1492 XAC1492 hypothetical protein 10.21684841 XAC3594 XAC3594 hypothetical protein 7.376270824 XAC3593 XAC3593 NAD dependent epimerase/dehydratase/dehydrogenase 6.332084605 XAC1507 mobL plasmid mobilization protein 3.281412651 XAC2868 vieA response regulator 3.275599917 XAC0209 yojM superoxide dismut ase like protein 3.275599917 XAC0048 XAC0048 hypothetical protein 3.031674789 XAC2866 mcp chemotaxis protein 3.016953925 XAC0334 sflA NADH dependent FMN reductase 2.746943112 XAC3273 XAC3273 histidine kinase response regulator hybrid protein 2.657 889437 XAC2865 cheA chemotaxis histidine protein kinase 2.655987946 XAC1891 tsr chemotaxis protein 2.260813095 XAC3323 XAC3323 hypothetical protein 2.235229866 XAC2657 XAC2657 hypothetical protein 2.158660687 XAC0335 XAC0335 hypothetical protein 2.151642626 XAC0029 egl cellulase 2.139857262 XAC0028 egl cellulase 2.12773726 XAC1900 tsr chemotaxis protein 2.07995337 XAC3784 XAC3784 hypothetical protein 1.97520681 XAC1899 tsr chemotaxis protein 1.964518333 XAC1896 tsr chemotaxis protein 1 .959713612 XAC0210 sodC2 superoxide dismutase 1.915635997 XAC1508 XAC1508 hypothetical protein 1.913913416 XAC0691 XAC0691 hypothetical protein 1.904667668 XAC0092 XAC0092 hypothetical protein 1.883234536 XAC2599 aglA alpha glucosidase 1.86774364 2 XAC0098 XAC0098 hypothetical protein 1.843399276 XAC0756 kdpA potassium transporting ATPase subunit A 1.835669295 XAC1890 cheR chemotaxis protein methyltransferase 1.831555873 XAC0050 XAC0050 hypothetical protein 1.781027304

PAGE 153

153 Table 3 10 Contin ued. Locus tag Gene Name Product Log2 Fold Change WNB/ANB XAC3693 motA flagellar motor protein MotA 1.778136017 XAC1146 fecA TonB dependent receptor 1.741489966 XAC1795 XAC1795 hypothetical protein 1.719416095 XAC0336 metE 5 methyltetrahydropteroylt riglutamate -homocysteine S methyltransferase 1.709709626 XAC2448 mcp chemotaxis protein 1.709265955 XAC3741 XAC3741 hypothetical protein 1.703514133 XAC0350 XAC0350 hypothetical protein 1.700503313 XAC2600 btuB TonB dependent receptor 1.69715821 5 XAC1815 fhaB filamentous hemagglutinin 1.679244522 XAC1887 pdeA c di GMP phosphodiesterase A 1.672056227 XAC3365 XAC3365 hypothetical protein 1.671525209 XAC1895 tsr chemotaxis protein 1.653756018 XAC3635 XAC3635 hypothetical protein 1.65125564 4 XAC2869 cheR response regulator for chemotaxis 1.642201143 XAC0611 tsr chemotaxis protein 1.627313159 XAC2597 suc1 transporter 1.613187569 XAC2482 rrpX transcriptional regulator 1.605625375 XAC1902 tsr chemotaxis protein 1.592615948 XAC3725 XA C3725 hypothetical protein 1.584295514 XAC1894 tsr chemotaxis protein 1.570873059 XAC0051 asnB asparagine synthase 1.569680723 XAC0047 XAC0047 galactosyltransferase 1.559099776 XAC0424 XAC0424 hypothetical protein 1.552388457 XAC3726 XAC3726 hypo thetical protein 1.519064447 XAC1993 XAC1993 hypothetical protein 1.514798533 XAC1889 cheD chemoreceptor glutamine deamidase CheD 1.503470372 XAC3922 entF ATP dependent serine activating enzyme 1.496272831 XAC0606 XAC0606 endonuclease 1.493931709 XAC0496 XAC0496 hypothetical protein 1.487092175 XAC0235 dhaA haloalkane dehalogenase 1.483694734 XAC3132 mcp chemotaxis protein 1.474166582 XAC3364 XAC3364 hypothetical protein 1.470066015 XAC3927 XAC3927 hypothetical protein 1.469846529 XAC259 8 XAC2598 hypothetical protein 1.468776033 XAC2027 XAC2027 hypothetical protein 1.468136632 XAC1509 XAC1509 hypothetical protein 1.454251212 XAC1971 XAC1971 hypothetical protein 1.453872449 XAC4283 XAC4283 sensor histidine kinase 1.453084866 XAC2 602 aglA alpha glucosidase 1.433527863 XAC1903 cheA chemotaxis protein 1.389816094

PAGE 154

154 Table 3 10 Continued. Locus tag Gene Name Product Log2 Fold Change WNB/ANB XAC0940 XAC0940 hypothetical protein 1.389037155 XAC0108 atsE AtsE protein 1.382241601 XAC0957 tuf elongation factor Tu 1.376878728 XAC0540 XAC0540 ribonuclease 1.372944605 XAC1193 XAC1193 hypothetical protein 1.364648087 XAC0107 XAC0107 hypothetical protein 1.360547243 XAC3562 pel pectate lyase 1.353706678 XAC3300 estA esterase 1.351414413 XAC2596 cgt cyclomaltodextrin glucanotransferase 1.344697177 XAC1034 XAC1034 peptidyl Asp metalloendopeptidase 1.33483264 XAC1893 tsr chemotaxis protein 1.329618489 XAC1178 XAC1178 oxidoreductase 1.324489879 XAC3763 XAC3763 hypothetica l protein 1.317078785 XAC0690 fecA TonB dependent receptor 1.316467244 XAC3272 XAC3272 hypothetical protein 1.311918746 XAC2026 XAC2026 hypothetical protein 1.311415153 XAC0285 XAC0285 hypothetical protein 1.306554629 XAC2580 gumG GumG protein 1 .30328786 XAC1996 mcp chemotaxis protein 1.300988651 XAC3050 btuB TonB dependent receptor 1.298541812 XAC1905 XAC1905 hypothetical protein 1.295249076 XAC1363 araJ MFS transporter 1.294341225 XAC2577 gumJ GumJ protein 1.287085498 XAC1904 cheY ch emotaxis response regulator 1.28458781 XAC1973 fliS flagellar protein 1.281739723 XAC2582 gumE GumE protein 1.278122361 XAC0394 hrpF HrpF protein 1.27398998 XAC0584 XAC0584 hypothetical protein 1.264705549 XAC1972 XAC1972 hypothetical protein 1. 263599233 XAC3739 XAC3739 hypothetical protein 1.263549906 XAC0798 amy alpha amylase 1.260223514 XAC3324 XAC3324 hypothetical protein 1.255678443 XAC1364 XAC1364 hypothetical protein 1.252810141 XAC1868 XAC1868 hypothetical protein 1.251258578 X AC2494 yieO drug resistance translocase 1.25064029 XAC2585 gumB GumB protein 1.250118598 XAC0747 XAC0747 hypothetical protein 1.246902249 XAC2584 gumC GumC protein 1.24510651 XAC0682 XAC0682 hypothetical protein 1.243210188 XAC1177 XAC1177 hypoth etical protein 1.242395313 XAC2608 XAC2608 VirB6 protein 1.233797995

PAGE 155

155 Table 3 10 Continued. Locus tag Gene Name Product Log2 Fold Change WNB/ANB XAC1666 tsr chemotaxis protein 1.23355901 XAC3615 XAC3615 hypothetical protein 1.232611071 XAC3839 X AC3839 hypothetical protein 1.227809416 XAC3446 XAC3446 hypothetical protein 1.227739588 XAC1810 XAC1810 hypothetical protein 1.226825166 XAC2261 yme plasmid like protein 1.223865173 XAC2812 XAC2812 hypothetical protein 1.222394917 XAC3966 XAC396 6 hypothetical protein 1.22211826 XAC2579 gumH GumH protein 1.219095235 XAC0096 XAC0096 hypothetical protein 1.217779136 XAC3866 XAC3866 hypothetical protein 1.214029647 XAC2359 XAC2359 hypothetical protein 1.2101597 XAC0428 malQ 4 alpha glucanot ransferase 1.206994407 XAC3254 glgX glycogen debranching protein 1.204536333 XAC1319 algU RNA polymerase sigma factor RpoE 1.198589677 XAC0612 engXCA cellulase 1.19584223 XAC1632 XAC1632 hypothetical protein 1.193661007 XAC2581 gumF GumF protein 1.191547922 XAC2583 gumD GumD protein 1.18885598 XAC0610 XAC0610 histidine kinase response regulator hybrid protein 1.187522049 XAC2414 lig3 ATP dependent DNA ligase 1.18464461 XAC2103 XAC2103 DNA recombinase 1.170631164 XAC1321 mucD periplasmic protease 1.165075851 XAC2574 gumM GumM protein 1.163844975 XAC4294 XAC4294 hypothetical protein 1.162498052 XAC1521 grpE heat shock protein GrpE 1.161281031 XAC1654 acpD ACP phosphodieterase 1.160481153 XAC0465 XAC0465 metalloproteinase 1.159209 175 XAC2576 gumK GumK protein 1.156219719 XAC2578 gumI GumI protein 1.156150737 XAC3121 fepA TonB dependent receptor 1.156043879 XAC2122 XAC2122 dehydrogenase 1.143167003 XAC0035 XAC0035 hypothetical protein 1.142783524 XAC0189 iorA indolepyruva te ferredoxin oxidoreductase 1.139472125 XAC0224 poxB pyruvate dehydrogenase 1.135612256 XAC1187 XAC1187 hydroxylase large subunit 1.131635635 XAC0431 glgX glycogen debranching protein 1.129093782 XAC1211 katE catalase 1.128509742 XAC0155 XAC0155 trehalose synthase 1.12365149 XAC3458 leuC isopropylmalate isomerase large subunit 1.122307106

PAGE 156

156 Table 3 10 Continued. Locus tag Gene Name Product Log2 Fold Change WNB/ANB XAC2893 yagR oxidoreductase 1.119474038 XAC0495 XAC0495 two component syste m regulatory protein 1.118411592 XAC2151 yapH YapH protein 1.113301035 XAC1188 XAC1188 hydroxylase molybdopterin containing subunit 1.11308543 XAC3524 XAC3524 hypothetical protein 1.112176282 XAC1495 xrvA virulence regulator 1.102865964 XAC2992 X AC2992 endoproteinase ArgC 1.102233164 XAC1959 XAC1959 hypothetical protein 1.102019808 XAC0122 tldD TldD protein 1.101179671 XAC0154 XAC0154 alpha amylase 1.098686034 XAC2895 yagT xanthine dehydrogenase iron sulfur binding subunit 1.088586864 XA C4204 XAC4204 hypothetical protein 1.083279682 XAC0223 XAC0223 hypothetical protein 1.080628281 XAC1400 XAC1400 PHB depolymerase 1.080212735 XAC0585 XAC0585 hypothetical protein 1.078528777 XAC3243 pilD type IV pre pilin leader peptidase 1.0770507 41 XAC0741 yjjK ABC transporter ATP binding protein 1.072529493 XAC2990 XAC2990 hypothetical protein 1.070915021 XAC1149 XAC1149 bacterioferritin 1.06926196 XAC0264 accD acyl CoA carboxyltransferase subunit beta 1.061441881 XAC2040 yggB small cond uctance mechanosensitive ion channel 1.061111518 XAC2951 comEA DNA transport competence protein 1.059680762 XAC4274 XAC4274 OmpA like protein 1.058356391 XAC1325 rnc ribonuclease III 1.042004593 XAC0711 XAC0711 GntR family transcriptional regulator 1.034955794 XAC1012 mopB hypothetical protein 1.005153155

PAGE 157

157 Table 3 11 Genes differentially expressed between strains X. citri subsp. citri str. 306 (A) and X. citri subsp. citri str. A w 12879 (W) in XVM2 (hrp inducing) medium. Cut off value of Log2 f Locus tag Gene Name Product Log 2 Fold Change WXVM/AXVM Overexpressed Genes XAC4248 gnl gluconolactonase 3.877771021 XAC1689 XAC1689 hypothetical protein 3.775079328 XAC3616 bioD dithiobiotin synthetase 2.768199661 XAC3444 btuB TonB dependent receptor 2.626959105 XAC1696 XAC1696 methyltransferase 2.196872429 XAC2538 XAC2538 hypothetical protein 2.093287334 XAC2860 XAC2860 hypothet ical protein 2.038647836 XAC2603 XAC2603 ISxac4 transposase 1.969683352 XAC2787 XAC2787 hypothetical protein 1.956849632 XAC2604 XAC2604 ISxac4 transposase 1.955367064 XAC1688 XAC1688 hypothetical protein 1.880628405 XAC3475 XAC3475 hypothetical prote in 1.828477254 XAC3712 XAC3712 metallopeptidase 1.815121614 XAC2520 XAC2520 TonB dependent receptor 1.798880957 XAC3445 XAC3445 transcriptional regulator 1.79169953 XAC2891 XAC2891 hypothetical protein 1.790255834 XAC0999 cirA colicin I receptor 1.766 5622 XAC3518 bcsA celullose synthase 1.757482347 XAC3474 cit1 citrate carrier protein 1.73848736 XAC3028 XAC3028 histidine kinase response regulator hybrid protein 1.594045007 XAC3090 XAC3090 leucin rich protein 1.588501578 XAC2423 XAC2423 IS1478 tran sposase 1.569132553 XAC3473 XAC3473 sensor histidine kinase 1.563105005 XAC1068 stf phage related tail protein 1.547879615 XAC2531 btuB TonB dependent receptor 1.52989273 XAC1338 XAC1338 oxidoreductase 1.526369207 XAC2966 XAC2966 hypothetical protein 1.486803374 XAC3133 yggA membrane transport protein 1.479670175 XAC2141 lytT two component system regulatory protein 1.44212119 XAC3162 bla beta lactamase 1.426624097 XAC2024 cirA TonB dependent receptor 1.415070068 XAC4218 tatA twin arginine transloc ation protein TatA 1.414369968 XAC0629 XAC0629 hypothetical protein 1.386558798 XAC3271 tcp chemotaxis transducer 1.380089251 XAC1164 XAC1164 hypothetical protein 1.374341843 XAC1265 hrpG HrpG protein 1.371008805

PAGE 158

158 Table 3 11 Continued. Locus tag Gen e Name Product Log2 Fold Change WXVM/AXVM XAC0503 nudC NADH pyrophosphatase 1.369464533 XAC2098 syrE2 ATP dependent serine activating enzyme 1.361026084 XAC3731 exsF regulatory protein 1.35746756 XAC3166 bfeA ferric enterobactin receptor 1.339825933 X AC2014 XAC2014 TetR family transcriptional regulator 1.339547272 XAC1702 XAC1702 Mg protoporphyrin IX monomethyl ester oxidative cyclase 1.339041029 XAC1680 XAC1680 serine protease 1.333363935 XAC1304 XAC1304 hypothetical protein 1.321989215 XAC3663 XA C3663 hypothetical protein 1.321799017 XAC3129 XAC3129 pseudouridylate synthase 1.32069952 XAC1137 prpB 2 methylisocitrate lyase 1.31928743 XAC2518 XAC2518 hypothetical protein 1.319238004 XAC3993 XAC3993 two component system regulatory protein 1.31453 0614 XAC0151 XAC0151 hypothetical protein 1.302502741 XAC2589 pheT phenylalanyl tRNA synthetase subunit beta 1.300967384 XAC3505 rhgB rhamnogalacturonase B 1.300716685 XAC3704 XAC3704 DNA polymerase like protein 1.300562302 XAC1145 XAC1145 hypothetica l protein 1.29968517 XAC2051 XAC2051 oxidoreductase 1.298496702 XAC3989 prtI ECF sigma factor 1.298447877 XAC2537 XAC2537 peptidase 1.296382 XAC1172 XAC1172 hypothetical protein 1.295504189 XAC3814 norM multidrug efflux protein 1.295412546 XAC3332 cy sH phosphoadenosine phosphosulfate reductase 1.294074263 XAC3255 XAC3255 hypothetical protein 1.290003478 XAC2430 XAC2430 Tn5044 transposase 1.286123031 XAC1388 XAC1388 hypothetical protein 1.28374325 XAC1266 hrpXct HrpX protein 1.282732205 XAC2922 hr pW HrpW protein 1.276470264 XAC2341 gaa glutaryl 7 ACA acylase 1.274288431 XAC1713 XAC1713 carboxypeptidase like protein 1.274030764 XAC3878 XAC3878 disulfide isomerase 1.269624837 XAC3685 XAC3685 hypothetical protein 1.269583318 XAC2761 xseB exodeoxy ribonuclease VII small subunit 1.267073417 XAC4222 XAC4222 hypothetical protein 1.265839654 XAC3448 btuB TonB dependent receptor 1.263428471 XAC0501 XAC0501 hypothetical protein 1.261721563 XAC0435 virK VirK protein 1.259483019 XAC2682 XAC2682 hypothe tical protein 1.254711314

PAGE 159

159 Table 3 11 Continued. Locus tag Gene Name Product Log2 Fold Change WXVM/AXVM XAC2089 kdsB 3 deoxy manno octulosonate cytidylyltransferase 1.25383624 XAC0559 XAC0559 hypothetical protein 1.250733676 XAC0970 tuf elongation fa ctor Tu 1.249217448 XAC1284 XAC1284 two component system regulatory protein 1.244543384 XAC0659 mrdA penicillin binding protein 2 1.242992158 XAC3909 dpm1 dolichol phosphate mannosyltransferase 1.236551411 XAC3433 XAC3433 hypothetical protein 1.2361573 82 XAC1708 exoD ExoD protein 1.233664964 XAC2529 rhsD RhsD protein 1.232430714 XAC4314 Y4JJ plasmid stability protein 1.231372873 XAC2863 XAC2863 hypothetical protein 1.230020862 XAC3923 speA arginine decarboxylase 1.228248127 XAC0150 XAC0150 hypothe tical protein 1.22725162 XAC1054 XAC1054 integrase 1.226369657 XAC0278 XAC0278 hypothetical protein 1.226297939 XAC1275 xylB arabinosidase 1.22533929 XAC3432 XAC3432 serine/threonine protein kinase 1.224225852 XAC2123 XAC2123 hypothetical protein 1.22 3006639 XAC2960 XAC2960 hypothetical protein 1.221089262 XAC0382 aspH aspartyl asparaginyl beta hydroxylase 1.220483682 XAC0186 XAC0186 hypothetical protein 1.22038462 XAC1479 XAC1479 OmpA family protein 1.218418475 XAC1356 XAC1356 hypothetical protei n 1.218271514 XAC2955 XAC2955 nucleotidyl transferase 1.21712065 XAC2345 argH argininosuccinate lyase 1.216795741 XAC1282 XAC1282 two component system sensor protein 1.211033788 XAC4167 XAC4167 hypothetical protein 1.209260576 XAC3136 exsG two compone nt system sensor protein 1.206808147 XAC3972 XAC3972 hypothetical protein 1.205604869 XAC1667 XAC1667 oxidoreductase 1.204126399 XAC2791 XAC2791 transcriptional regulator 1.204061868 XAC0543 XAC0543 hypothetical protein 1.203456667 XAC3465 htrB lipid A biosynthesis lauroyl acyltransferase 1.202356052 XAC0003 recF recombination protein F 1.201714859 XAC2824 XAC2824 phosphodiesterase nucleotide pyrophosphatase 1.201122353 XAC0642 rmrB MFS transporter 1.200503371 XAC3139 XAC3139 radical activating enz yme 1.197609691 XAC3850 acrA acriflavin resistance protein 1.195210554 XAC2321 XAC2321 hydrolase 1.191152444

PAGE 160

160 Table 3 11 Continued. Locus tag Gene Name Product Log2 Fold Change WXVM/AXVM XAC3525 XAC3525 hypothetical protein 1.190776226 XAC2387 XAC23 87 ribonuclease 1.189951672 XAC3430 kch ion transporter 1.189829076 XAC3209 ostB trehalose 6 phosphate phosphatase 1.189748354 XAC3590 XAC3590 oxidoreductase 1.189597864 XAC4073 XAC4073 flavodoxin 1.188859552 XAC2696 nuoI NADH dehydrogenase subunit I 1.187130017 XAC1646 XAC1646 sulfite oxidase subunit YedZ 1.186877136 XAC2066 acrD transporter 1.186361494 XAC4299 XAC4299 hypothetical protein 1.186326261 XAC2494 yieO drug resistance translocase 1.186241703 XAC4371 XAC4371 polysaccharide deacetylase 1.185356334 XAC2087 msbA ABC transporter ATP binding protein 1.18438764 XAC2694 nuoK NADH dehydrogenase subunit K 1.183675966 XAC2949 XAC2949 calcium binding protein 1.182983913 XAC1473 XAC1473 hypothetical protein 1.181749396 XAC3044 XAC3044 hypothet ical protein 1.18077869 XAC3067 nudE ADP ribose diphosphatase NudE 1.179854491 XAC4213 XAC4213 hypothetical protein 1.178728009 XAC3210 XAC3210 hypothetical protein 1.17756792 XAC3368 XAC3368 hypothetical protein 1.176869275 XAC3381 pilQ fimbrial asse mbly protein 1.174243016 XAC3065 mazG nucleoside triphosphate pyrophosphohydrolase 1.174000731 XAC3117 pqqE pyrroloquinoline quinone biosynthesis protein PqqE 1.173512573 XAC3524 XAC3524 hypothetical protein 1.173210162 XAC0482 XAC0482 hypothetical pro tein 1.172459788 XAC3910 XAC3910 hypothetical protein 1.172342832 XAC0262 XAC0262 dipeptidyl anminopeptidase 1.172333892 XAC2692 nuoM NADH dehydrogenase subunit M 1.171712976 XAC3684 XAC3684 hypothetical protein 1.170620368 XAC4151 uvrD DNA dependent helicase II 1.169730092 XAC1242 pthX pathogenicity like protein 1.169659036 XAC1281 cheR chemotaxis protein 1.169622699 XAC1574 pstB phosphate transporter ATP binding protein 1.168429524 XAC3249 colS two component system sensor protein 1.167333473 XAC 1764 XAC1764 regucalcin 1.167191817 XAC2086 exbD biopolymer transport protein 1.167166771 XAC2129 fabG 3 ketoacyl ACP reductase 1.16707058 XAC2312 XAC2312 hypothetical protein 1.166553432

PAGE 161

161 Table 3 11 Continued. Locus tag Gene Name Product Log2 Fold C hange WXVM/AXVM XAC2693 nuoL NADH dehydrogenase subunit L 1.166429198 XAC4204 XAC4204 hypothetical protein 1.166264863 XAC3476 ybhD transcriptional regulator 1.166138952 XAC4080 kefC glutathione regulated potassium efflux system protein 1.16570747 XAC 2370 XAC2370 hypothetical protein 1.164762043 XAC1759 gcvR glycine cleavage system transcriptional repressor 1.163986547 XAC2691 nuoN NADH dehydrogenase subunit N 1.163834219 XAC2216 XAC2216 hypothetical protein 1.163338285 XAC0783 ftsA cell division p rotein 1.163095132 XAC2908 murD UDP N acetylmuramoyl L alanyl D glutamate synthetase 1.162467494 XAC0969 fusA elongation factor G 1.16212181 XAC1283 XAC1283 two component system sensor protein 1.160862998 XAC3490 XAC3490 amylosucrase or alpha amylase 1 .159992676 XAC0025 XAC0025 hypothetical protein 1.15894674 XAC3521 pncB nicotinate phosphoribosyltransferase 1.15811423 XAC3869 bglX beta glucosidase 1.157080382 XAC1516 smpA hypothetical protein 1.157066171 XAC4031 dinG ATP dependent DNA helicase Din G 1.155715443 XAC0338 XAC0338 hypothetical protein 1.154658149 XAC2683 pnp polynucleotide phosphorylase 1.15413532 XAC3796 XAC3796 lipopolysaccharide core biosynthesis glycosyl transferase 1.15356716 XAC3831 rho transcription termination factor Rho 1.1 53021853 XAC1709 tlyC hemolysin 1.151724215 XAC1598 XAC1598 hypothetical protein 1.150619899 XAC1317 czcD cobalt zinc cadmium resistance protein 1.150495839 XAC3027 emrA MFS transporter 1.149954036 XAC2591 rplT 50S ribosomal protein L20 1.149628506 X AC3157 ycaD transmembrane transport protein 1.149427325 XAC0866 ostA organic solvent tolerance protein 1.148219572 XAC3833 ampR B lactamase regulatory protein 1.147739985 XAC2745 XAC2745 metallopeptidase 1.147535942 XAC2019 XAC2019 hypothetical protein 1.147242156 XAC1303 mutS DNA mismatch repair protein MutS 1.147138182 XAC2713 XAC2713 oxidoreductase 1.146816656 XAC3326 acrF acriflavin resistance protein 1.14569161 XAC3110 XAC3110 glycosyltransferase 1.144788182 XAC0234 XAC0234 hypothetical protei n 1.144776321

PAGE 162

162 Table 3 11 Continued. Locus tag Gene Name Product Log2 Fold Change WXVM/AXVM XAC2909 XAC2909 hypothetical protein 1.144705443 XAC4022 phoQ two component system sensor protein 1.142982308 XAC2695 nuoJ NADH dehydrogenase subunit J 1.1422 36467 XAC3487 cebR transcriptional regulator 1.139698561 XAC0944 prfA peptide chain release factor 1 1.139120231 XAC2136 XAC2136 oxidoreductase 1.138862248 XAC3256 xrvA virulence regulator 1.1380708 XAC2939 XAC2939 acetyltransferase 1.137692915 XAC04 76 trpE anthranilate synthase component I 1.137278346 XAC1840 XAC1840 methylthioribulose 1 phosphate dehydratase 1.136880376 XAC2593 infC translation initiation factor IF 3 1.13648463 XAC0997 rplQ 50S ribosomal protein L17 1.134702641 XAC1262 XAC1262 h ypothetical protein 1.132558868 XAC0993 rpsM 30S ribosomal protein S13 1.131512264 XAC1420 XAC1420 hypothetical protein 1.131435935 XAC2054 XAC2054 two component system sensor protein 1.13113872 XAC1629 XAC1629 hypothetical protein 1.130969214 XAC3671 XAC3671 nucleotide binding protein 1.129892218 XAC2419 traY hypothetical protein 1.129882215 XAC2388 XAC2388 hypothetical protein 1.129166509 XAC2728 psd phosphatidylserine decarboxylase 1.128263004 XAC2697 nuoH NADH dehydrogenase subunit H 1.12790819 4 XAC2825 yadQ chloride channel 1.127738383 XAC2020 XAC2020 hypothetical protein 1.127625306 XAC2969 XAC2969 hypothetical protein 1.127114885 XAC0772 mraW S adenosyl methyltransferase MraW 1.126654813 XAC3788 rpoD RNA polymerase sigma factor RpoD 1.12 527377 XAC2700 nuoE NADH dehydrogenase subunit E 1.125103265 XAC2999 XAC2999 peptidase 1.124990925 XAC3343 XAC3343 hypothetical protein 1.124350982 XAC2768 XAC2768 hypothetical protein 1.123518953 XAC3142 tolB translocation protein TolB 1.123326621 X AC4074 nrdF ribonucleotide diphosphate reductase subunit beta 1.12192923 XAC3846 queF 7 cyano 7 deazaguanine reductase 1.121473748 XAC0431 glgX glycogen debranching protein 1.119466319 XAC3971 XAC3971 hypothetical protein 1.118465117 XAC3462 pcm L isoa spartate protein carboxylmethyltransferase 1.116530484 XAC4069 XAC4069 hypothetical protein 1.116032713 XAC0683 XAC0683 two component system sensor protein 1.115904391

PAGE 163

163 Table 3 11 Continued. Locus tag Gene Name Product Log2 Fold Change WXVM/AXVM XAC3 589 XAC3589 hypothetical protein 1.115465221 XAC4004 XAC4004 peptidase 1.115410915 XAC0937 rbn ribonuclease BN/unknown domain fusion protein 1.114810365 XAC3386 mrcA penicillin binding protein 1A 1.114091738 XAC0771 XAC0771 cell division protein MraZ 1 .113965299 XAC3037 XAC3037 hydrolase 1.113581621 XAC2010 XAC2010 recombination factor protein RarA 1.113459243 XAC0630 aspC hypothetical protein 1.112720509 XAC4336 recB exodeoxyribonuclease V subunit beta 1.112518148 XAC0547 XAC0547 hypothetical prot ein 1.111918403 XAC0144 iroN TonB dependent receptor 1.11172718 XAC3464 kdtA 3 deoxy D manno octulosonic acid transferase 1.11084302 XAC0779 murG undecaprenyldiphospho muramoylpentapeptide beta N acetylglucosaminyltransferase 1.110547021 XAC2320 XAC23 20 glutamine cyclotransferase 1.109835366 XAC0731 XAC0731 hypothetical protein 1.109562937 XAC1098 moaC molybdenum cofactor biosynthesis protein MoaC 1.109033631 XAC3986 XAC3986 hydrolase 1.108097884 XAC2420 XAC2420 hypothetical protein 1.104359751 XA C3877 XAC3877 hypothetical protein 1.102492558 XAC4081 zwf glucose 6 phosphate 1 dehydrogenase 1.102461044 XAC0280 XAC0280 ATPase 1.102358355 XAC0678 XAC0678 hypothetical protein 1.102022482 XAC1428 map methionine aminopeptidase 1.101376515 XAC2625 uv rB excinuclease ABC subunit B 1.100974109 XAC3561 slt soluble lytic murein transglycosylase 1.100402961 XAC1783 pcnB polynucleotide adenylyltransferase 1.100281171 XAC0785 lpxC UDP 3 O [3 hydroxymyristoyl] N acetylglucosamine deacetylase 1.098602988 XA C0774 ftsI penicillin binding protein 3 1.098434576 XAC0992 secY preprotein translocase subunit SecY 1.098276194 XAC2614 virB4 VirB4 protein 1.098231486 XAC2980 mgtE Mg++ transporter 1.098077476 XAC2763 XAC2763 extracellular protease 1.097871294 XAC17 16 pyrG CTP synthetase 1.097814907 XAC2701 nuoD NADH dehydrogenase subunit D 1.096469297 XAC2389 uup ABC transporter ATP binding protein 1.096419143

PAGE 164

164 Table 3 11 Continued. Locus tag Gene Name Product Log2 Fold Change WXVM/AXVM XAC4286 mutM formamidop yrimidine DNA glycosylase 1.09597188 XAC2332 metX homoserine O acetyltransferase 1.094871985 XAC2857 XAC2857 hypothetical protein 1.09458925 XAC1224 minE cell division topological specificity factor MinE 1.094411718 XAC2698 nuoG NADH dehydrogenase subu nit G 1.093780318 XAC3393 spoT pentaphosphate guanosine 3' pyrophosphohydrolase 1.093113891 XAC1408 lpxB lipid A disaccharide synthase 1.092309972 XAC2377 ubiG 3 demethylubiquinone 9 3 methyltransferase 1.092111048 XAC3463 tolC TolC protein 1.092037251 XAC0842 thyA thymidylate synthase 1.091613283 XAC0626 XAC0626 outer membrane lipoprotein 1.09029366 XAC3408 XAC3408 cell division protein ZapA 1.089478643 XAC0631 ptrB oligopeptidase B 1.088612894 XAC0865 surA peptidyl prolyl cis trans isomerase 1.08 8038778 XAC1089 rnhA ribonuclease H 1.087115047 XAC0728 gsh1 glutamate cysteine ligase 1.086568153 XAC1459 msbA ABC transporter ATP binding protein 1.083506505 XAC1911 XAC1911 hypothetical protein 1.080916219 XAC2911 lysA bifunctional aspartate kinase /diaminopimelate decarboxylase 1.08036793 XAC2428 XAC2428 hypothetical protein 1.078949686 XAC4075 nrdA ribonucleotide diphosphate reductase subunit alpha 1.078866378 XAC0667 lipB lipoate protein ligase B 1.078675178 XAC2551 XAC2551 transcriptional reg ulator 1.0778973 XAC0307 XAC0307 nucleoside hydrolase 1.077279637 XAC4308 kgtP dicarboxylate transport protein 1.077142988 XAC3140 XAC3140 hypothetical protein 1.075377886 XAC3141 ompP6 outer membrane protein P6 1.074840946 XAC3145 tolQ TolQ protein 1 .073781118 XAC2699 nuoF NADH ubiquinone oxidoreductase NQO1 subunit 1.073471956 XAC2717 trpB tryptophan synthase subunit beta 1.072698883 XAC0466 XAC0466 lytic enzyme 1.072323551 XAC0987 rplF 50S ribosomal protein L6 1.06960567 XAC0499 XAC0499 iron su lfur cluster insertion protein ErpA 1.068741717 XAC2092 uvrC excinuclease ABC subunit C 1.068561306 XAC0926 XAC0926 hypothetical protein 1.068110137

PAGE 165

165 Table 3 11 Continued. Locus tag Gene Name Product Log2 Fold Change WXVM/AXVM XAC0664 dacC penicillin binding protein 6 1.066853695 XAC2053 tex transcription like protein 1.063685457 XAC1863 greA transcription elongation factor GreA 1.063135125 XAC4045 XAC4045 hypothetical protein 1.062585408 XAC3851 XAC3851 hypothetical protein 1.061810454 XAC0979 r plP 50S ribosomal protein L16 1.061276053 XAC2530 XAC2530 hypothetical protein 1.059660422 XAC1739 lexA LexA repressor 1.057997036 XAC0978 rpsC 30S ribosomal protein S3 1.055386761 XAC1876 lysS lysyl tRNA synthetase 1.055250006 XAC2386 sodM superoxida se dismutase 1.054560193 XAC3352 gapA glyceraldehyde 3 phosphate dehydrogenase 1.053735208 XAC3575 etf QO flavoprotein ubiquinone oxidoreductase 1.052411511 XAC2293 XAC2293 dehydratase 1.049383309 XAC1653 serS seryl tRNA synthetase 1.048983343 XAC4023 phoP two component system regulatory protein 1.04705924 XAC2077 sdhA succinate dehydrogenase flavoprotein subunit 1.037306851 XAC1348 atoB acetoacetyl CoA thiolase 1.036315471 XAC2767 tldD TldD protein 1.031928917 XAC3804 smg hypothetical protein 1.03 1496226 Underexpressed Genes XAC3260 mobL plasmid mobilization protein 15.87890005 XAC3594 XAC3594 hypothetical protein 3.566676924 XAC3298 XAC3298 integrase 3.49094522 XAC4225 xylA xylose isomerase 3.361963503 XAC3593 XAC3593 NAD dependent epime rase/dehydratase/dehydrogenase 3.088200659 XAC1492 XAC1492 hypothetical protein 2.634526927 XAC1507 mobL plasmid mobilization protein 2.109894919 XAC0210 sodC2 superoxide dismutase 2.035026214 XAC0029 egl cellulase 1.932933038 XAC0753 XAC0753 hyp othetical protein 1.92587448 XAC0540 XAC0540 ribonuclease 1.911336018 XAC0757 kdpB potassium transporting ATPase subunit B 1.838565045 XAC2151 yapH YapH protein 1.800840033 XAC3323 XAC3323 hypothetical protein 1.774277616 XAC0758 kdpC potassium t ransporting ATPase subunit C 1.718279526 XAC3273 XAC3273 histidine kinase response regulator hybrid protein 1.699159905

PAGE 166

166 Table 3 11 Continued. Locus tag Gene Name Product Log2 Fold Change WXVM/AXVM XAC0048 XAC0048 hypothetical protein 1.562063358 XAC2598 XAC2598 hypothetical protein 1.540700322 XAC3364 XAC3364 hypothetical protein 1.51892591 XAC0028 egl cellulase 1.490864678 XAC0759 kdpD two component system sensor protein 1.48694649 XAC1034 XAC1034 peptidyl Asp metalloendopeptidase 1.4648 26868 XAC2364 eutP ethanolamin permease 1.438426647 XAC1927 aslB Fe S oxidoreductase 1.418653513 XAC4176 actP acetate permease 1.415778246 XAC0957 tuf elongation factor Tu 1.415709759 XAC0051 asnB asparagine synthase 1.39410184 XAC0465 XAC0465 m etalloproteinase 1.382134115 XAC0612 engXCA cellulase 1.377531737 XAC0346 XAC0346 degenerated cellulase 1.364460865 XAC2596 cgt cyclomaltodextrin glucanotransferase 1.356697125 XAC3300 estA esterase 1.354623982 XAC2600 btuB TonB dependent recepto r 1.341832005 XAC0928 XAC0928 extracellular protease 1.337385083 XAC0235 dhaA haloalkane dehalogenase 1.334338186 XAC1821 thrB homoserine kinase 1.325952422 XAC2992 XAC2992 endoproteinase ArgC 1.32122178 XAC2185 fhuA ferrichrome iron receptor 1. 316586488 XAC0122 tldD TldD protein 1.306361106 XAC2830 fhuA TonB dependent receptor 1.303722242 XAC4052 XAC4052 TonB like protein 1.298382438 XAC0190 XAC0190 hypothetical protein 1.297342465 XAC0202 XAC0202 hypothetical protein 1.296144882 XAC3 460 XAC3460 hypothetical protein 1.284270434 XAC1321 mucD periplasmic protease 1.274712139 XAC1011 XAC1011 oxidoreductase 1.274101511 XAC3868 yliI dehydrogenase 1.269934908 XAC0067 mdpB microcystin dependent protein 1.265598564 XAC4177 XAC4177 hy pothetical protein 1.265503813 XAC2597 suc1 transporter 1.263762776 XAC0082 XAC0082 short chain oxidoreductase 1.259455421 XAC3768 XAC3768 chemotaxis protein 1.251708156 XAC3471 dctA C4 dicarboxylate transporter DctA 1.247329501 XAC0445 pdhB pyru vate dehydrogenase E1 beta subunit 1.237752177 XAC4172 XAC4172 transcriptional regulator 1.236557695 XAC3457 leuD isopropylmalate isomerase small subunit 1.236156678 XAC2152 XAC2152 hypothetical protein 1.230846451

PAGE 167

167 Table 3 11 Continued. Locus ta g Gene Name Product Log2 Fold Change WXVM/AXVM XAC1978 flgJ flagellar rod assembly protein/muramidase 1.229827393 XAC1021 XAC1021 hypothetical protein 1.222576427 XAC3458 leuC isopropylmalate isomerase large subunit 1.221916323 XAC4271 XAC4271 hypo thetical protein 1.221079227 XAC1951 fliI flagellar protein 1.219981228 XAC1655 XAC1655 transcriptional regulator 1.217452535 XAC1287 galM aldose 1 epimerase 1.216073189 XAC1107 XAC1107 integrase 1.207377939 XAC3715 XAC3715 hypothetical protein 1.204304527 XAC0495 XAC0495 two component system regulatory protein 1.201603841 XAC2489 XAC2489 beta alanine -pyruvate transaminase 1.199071845 XAC2984 XAC2984 peptidase 1.196915053 XAC0129 aldA chloroacetaldehyde dehydrogenase 1.193030153 XAC1344 XAC1344 hypothetical protein 1.186168829 XAC3887 ctaD cytochrome C oxidase subunit I 1.185672826 XAC1983 flgE flagellar hook protein FlgE 1.183647066 XAC2878 XAC2878 hypothetical protein 1.180721753 XAC0229 XAC0229 MFS transporter 1.18039229 XAC 0112 XAC0112 hypothetical protein 1.178652766 XAC0360 glpD glycerol 3 phosphate dehydrogenase 1.175973943 XAC0498 XAC0498 hypothetical protein 1.174623036 XAC3449 tar chemotaxis protein 1.171887227 XAC3454 tdcB threonine dehydratase 1.171761775 X AC0609 XAC0609 zinc protease 1.16848306 XAC1910 cirA TonB dependent receptor 1.168184575 XAC3514 XAC3514 serine protease 1.165623897 XAC0189 iorA indolepyruvate ferredoxin oxidoreductase 1.164978089 XAC3459 XAC3459 LysR family transcriptional regul ator 1.160188916 XAC1427 pru protein U 1.156274735 XAC3888 ctaC cytochrome C oxidase subunit II 1.151497442 XAC2192 XAC2192 two component system sensor protein 1.150089667 XAC0226 ntrC two component system regulatory protein 1.145996196 XAC1462 c ynT carbonic anhydrase 1.142486217 XAC0287 XAC0287 quinone oxidoreductase 1.141434126 XAC2764 XAC2764 hypothetical protein 1.141007932 XAC3609 uptA fumarylacetoacetate hydrolase 1.140044507 XAC0312 XAC0312 LysR family transcriptional regulator 1.1 33991752 XAC1519 recN recombination protein N 1.128044065 XAC3450 ggt gamma glutamyltranspeptidase 1.125846979 XAC1245 XAC1245 hypothetical protein 1.125528858 XAC0254 yjl094C Na+/H+ exchanging protein 1.120567337

PAGE 168

168 Table 3 11 Continued. Locus ta g Gene Name Product Log2 Fold Change WXVM/AXVM XAC2103 XAC2103 DNA recombinase 1.119674933 XAC3998 XAC3998 hypothetical protein 1.118410688 XAC0224 poxB pyruvate dehydrogenase 1.118133461 XAC2503 fruA PTS system fructose specific transporter subunit IIBC 1.118046447 XAC1981 flgG flagellar basal body rod protein FlgG 1.118019747 XAC1537 XAC1537 hypothetical protein 1.114259852 XAC0032 gltD glutamate synthase subunit beta 1.111298379 XAC0033 gltB glutamate synthase subunit alpha 1.10933767 XA C3313 susB alpha glucosidase 1.108486383 XAC3309 XAC3309 aminopeptidase 1.103704073 XAC0868 XAC0868 hypothetical protein 1.103538809 XAC3268 XAC3268 hypothetical protein 1.103342387 XAC4305 fusE fusaric acid resistance protein 1.102472813 XAC4179 acs acetyl CoA synthetase 1.102184211 XAC1521 grpE heat shock protein GrpE 1.101307396 XAC3239 pilB pilus biogenesis protein 1.100613941 XAC3739 XAC3739 hypothetical protein 1.09922564 XAC2881 cstA carbon starvation protein A 1.094372426 XAC0555 XAC0555 hypothetical protein 1.093597616 XAC3959 XAC3959 hypothetical protein 1.092511912 XAC3652 atpH ATP synthase F0F1 subunit delta 1.091840333 XAC4342 yrbC toluene tolerance protein 1.09134779 XAC3889 XAC3889 hypothetical protein 1.089138387 XAC2758 gltT glutamate symporter 1.082657383 XAC1254 ileS isoleucyl tRNA synthetase 1.072014975 XAC0887 XAC0887 gluconolactonase 1.071876929 XAC2068 edd phosphogluconate dehydratase 1.069481164 XAC1123 fabH 3 oxoacyl ACP synthase 1.067882822 XAC 3626 XAC3626 hypothetical protein 1.066740144 XAC2723 asd aspartate semialdehyde dehydrogenase 1.060890441 XAC1047 XAC1047 hypothetical protein 1.044681666 XAC2872 XAC2872 metallopeptidase 1.041077088 XAC3236 sucC succinyl CoA synthetase subunit be ta 1.02693388

PAGE 169

169 Table 3 12 Differentially expressed genes shared between strains X. citri subsp. citri str. 306 (A) and X. citri subsp. citri str. A w 12879 (W) in both NB (nutrient rich) medium and XVM2 (hrp inducing) medium. Cut off value of Log2 fold 1 for underexpressed genes. Log2 2). Locus tag of only strain A is used for ease of comparison. Locus tag Gene Name Product Log 2 Fold Change WNB/ANB Log 2 Fold Change WXVM/ AXVM Overe xpressed Genes XAC4248 gnl gluconolactonase 10.5068058 3.87777102 XAC3474 cit1 citrate carrier protein 2.51470588 1.73848736 XAC3445 XAC3445 transcriptional regulator 2.49930759 1.79169953 XAC3475 XAC3475 hypothetical protein 2.48547363 1.82847725 XAC 0338 XAC0338 hypothetical protein 2.27694386 1.15465815 XAC1338 XAC1338 oxidoreductase 2.17477308 1.52636921 XAC3712 XAC3712 metallopeptidase 1.987497 1.81512161 XAC0999 cirA colicin I receptor 1.92756557 1.7665622 XAC3229 orfT cointegrate resolution p rotein T 1.92060358 1.53265533 XAC2520 XAC2520 TonB dependent receptor 1.80398105 1.79888096 XAC2538 XAC2538 hypothetical protein 1.75327701 2.09328733 XAC2860 XAC2860 hypothetical protein 1.73979456 2.03864784 XAC3444 btuB TonB dependent receptor 1.73 77432 2.6269591 XAC1574 pstB phosphate transporter ATP binding protein 1.69310228 1.16842952 XAC2763 XAC2763 extracellular protease 1.57265135 1.09787129 XAC1266 hrpXct HrpX protein 1.56826769 1.2827322 XAC1164 XAC1164 hypothetical protein 1.51586288 1 .37434184 XAC2604 XAC2604 ISxac4 transposase 1.49617037 1.95536706 XAC3028 XAC3028 histidine kinase response regulator hybrid protein 1.49594471 1.59404501 XAC2141 lytT two component system regulatory protein 1.48741781 1.44212119 XAC3490 XAC3490 amylo sucrase or alpha amylase 1.47448013 1.15999268 XAC1137 prpB 2 methylisocitrate lyase 1.4552837 1.31928743 XAC2423 XAC2423 IS1478 transposase 1.38969694 1.56913255 XAC3473 XAC3473 sensor histidine kinase 1.3669144 1.56310501

PAGE 170

170 Table 3 12 Continued. L ocus tag Gene Name Product Log2 Fold Change WNB/ANB Log2 Fold Change WXVM/ AXVM XAC3704 XAC3704 DNA polymerase like protein 1.35335496 1.3005623 XAC3381 pilQ fimbrial assembly protein 1.30821059 1.17424302 XAC2537 XAC2537 peptidase 1.30633822 1.296382 XAC1068 stf phage related tail protein 1.2928669 1.54787962 XAC0970 tuf elongation factor Tu 1.24189979 1.24921745 XAC1265 hrpG HrpG protein 1.19458611 1.3710088 XAC2949 XAC2949 calcium binding protein 1.19212609 1.18298391 XAC2312 XAC2312 hypothetical protein 1.18549243 1.16655343 XAC3166 bfeA ferric enterobactin receptor 1.18429865 1.33982593 XAC3433 XAC3433 hypothetical protein 1.1770105 1.23615738 XAC2589 pheT phenylalanyl tRNA synthetase subunit beta 1.1717389 1.30096738 XAC2341 gaa glutaryl 7 ACA acylase 1.17093649 1.27428843 XAC3909 dpm1 dolichol phosphate mannosyltransferase 1.15560875 1.23655141 XAC0025 XAC0025 hypothetical protein 1.15163323 1.15894674 XAC3505 rhgB rhamnogalacturonase B 1.15135909 1.30071669 XAC3923 speA arginine decarb oxylase 1.14910526 1.22824813 XAC3476 ybhD transcriptional regulator 1.14537171 1.16613895 XAC2531 btuB TonB dependent receptor 1.13855221 1.52989273 XAC2824 XAC2824 phosphodiesterase nucleotide pyrophosphatase 1.13112145 1.20112235 XAC3851 XAC3851 hyp othetical protein 1.13017888 1.06181045 XAC2530 XAC2530 hypothetical protein 1.12768757 1.05966042 XAC2019 XAC2019 hypothetical protein 1.12440991 1.14724216 XAC3850 acrA acriflavin resistance protein 1.12188969 1.19521055 XAC3465 htrB lipid A biosynth esis lauroyl acyltransferase 1.11670532 1.20235605 XAC0969 fusA elongation factor G 1.10928452 1.16212181 XAC3463 tolC TolC protein 1.10590689 1.09203725 XAC2717 trpB tryptophan synthase subunit beta 1.10272748 1.07269888 XAC3869 bglX beta glucosidase 1.10150678 1.15708038

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171 Table 3 12 Continued. Locus tag Gene Name Product Log2 Fold Change WNB/ANB Log2 Fold Change WXVM/ AXVM XAC0731 XAC0731 hypothetical protein 1.0998918 1.10956294 XAC1713 XAC1713 carboxypeptidase like protein 1.09542185 1.274030 76 XAC3487 cebR transcriptional regulator 1.09378434 1.13969856 XAC2908 murD UDP N acetylmuramoyl L alanyl D glutamate synthetase 1.09290591 1.16246749 XAC2999 XAC2999 peptidase 1.09210033 1.12499093 XAC1716 pyrG CTP synthetase 1.08983099 1.09781491 X AC2020 XAC2020 hypothetical protein 1.08903328 1.12762531 XAC2345 argH argininosuccinate lyase 1.08902751 1.21679574 XAC3326 acrF acriflavin resistance protein 1.08606097 1.14569161 XAC4299 XAC4299 hypothetical protein 1.08569401 1.18632626 XAC2745 XAC 2745 metallopeptidase 1.08291429 1.14753594 XAC4022 phoQ two component system sensor protein 1.08145677 1.14298231 XAC3352 gapA glyceraldehyde 3 phosphate dehydrogenase 1.08013231 1.05373521 XAC2691 nuoN NADH dehydrogenase subunit N 1.07828665 1.1638342 2 XAC2713 XAC2713 oxidoreductase 1.07779892 1.14681666 XAC1262 XAC1262 hypothetical protein 1.07765163 1.13255887 XAC1282 XAC1282 two component system sensor protein 1.07661874 1.21103379 XAC0944 prfA peptide chain release factor 1 1.07246641 1.1391202 3 XAC2980 mgtE Mg++ transporter 1.07030448 1.09807748 XAC4004 XAC4004 peptidase 1.06919341 1.11541091 XAC2909 XAC2909 hypothetical protein 1.06746918 1.14470544 XAC4023 phoP two component system regulatory protein 1.06644043 1.04705924 XAC3671 XAC3671 nucleotide binding protein 1.06558108 1.12989222 XAC3145 tolQ TolQ protein 1.06518531 1.07378112 XAC2053 tex transcription like protein 1.06335497 1.06368546 XAC1428 map methionine aminopeptidase 1.06164489 1.10137652 XAC3110 XAC3110 glycosyltransfera se 1.05390208 1.14478818

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172 Table 3 12 Continued. Locus tag Gene Name Product Log2 Fold Change WNB/ANB Log2 Fold Change WXVM/ AXVM XAC0382 aspH aspartyl asparaginyl beta hydroxylase 1.05384546 1.22048368 XAC3141 ompP6 outer membrane protein P6 1.05357 499 1.07484095 XAC2692 nuoM NADH dehydrogenase subunit M 1.05340355 1.17171298 XAC2683 pnp polynucleotide phosphorylase 1.0532156 1.15413532 XAC2698 nuoG NADH dehydrogenase subunit G 1.05135027 1.09378032 XAC2701 nuoD NADH dehydrogenase subunit D 1.049 09217 1.0964693 XAC2700 nuoE NADH dehydrogenase subunit E 1.04716601 1.12510326 XAC3393 spoT pentaphosphate guanosine 3' pyrophosphohydrolase 1.04097272 1.09311389 Underexpressed Genes XAC1492 XAC1492 hypothetical protein 10.21684841 2.634526927 XA C3594 XAC3594 hypothetical protein 7.376270824 3.566676924 XAC3593 XAC3593 NAD dependent epimerase/dehydratase/dehydrogenase 6.332084605 3.088200659 XAC3291 XAC3291 hypothetical protein 3.922051423 2.181287589 XAC1507 mobL plasmid mobilization pro tein 3.281412651 2.109894919 XAC0048 XAC0048 hypothetical protein 3.031674789 1.562063358 XAC3273 XAC3273 histidine kinase response regulator hybrid protein 2.657889437 1.699159905 XAC2636 XAC2636 hypothetical protein 2.452389885 2.843259344 XA C3323 XAC3323 hypothetical protein 2.235229866 1.774277616 XAC0029 egl cellulase 2.139857262 1.932933038 XAC0028 egl cellulase 2.12773726 1.490864678 XAC0094 XAC0094 hypothetical protein 1.966999614 1.591122466 XAC0210 sodC2 superoxide dismutas e 1.915635997 2.035026214 XAC0201 adh alcohol dehydrogenase 1.802254241 2.387744174 XAC2597 suc1 transporter 1.613187569 1.263762776 XAC0051 asnB asparagine synthase 1.569680723 1.39410184 XAC2600 btuB TonB dependent receptor 1.522112982 1.34 1832005 XAC0235 dhaA haloalkane dehalogenase 1.483694734 1.334338186

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173 Table 3 12 Continued. Locus tag Gene Name Product Log2 Fold Change WNB/ANB Log2 Fold Change WXVM/ AXVM XAC3364 XAC3364 hypothetical protein 1.470066015 1.51892591 XAC2598 XAC 2598 hypothetical protein 1.468776033 1.540700322 XAC0957 tuf elongation factor Tu 1.376878728 1.415709759 XAC0540 XAC0540 ribonuclease 1.372944605 1.911336018 XAC3300 estA esterase 1.351414413 1.354623982 XAC2596 cgt cyclomaltodextrin glucanot ransferase 1.344697177 1.356697125 XAC1034 XAC1034 peptidyl Asp metalloendopeptidase 1.33483264 1.464826868 XAC0422 XAC0422 ABC transporter substrate binding protein 1.276605046 1.199270308 XAC3739 XAC3739 hypothetical protein 1.263549906 1.0992 2564 XAC0612 engXCA cellulase 1.19584223 1.377531737 XAC2103 XAC2103 DNA recombinase 1.170631164 1.119674933 XAC1321 mucD periplasmic protease 1.165075851 1.274712139 XAC1521 grpE heat shock protein GrpE 1.161281031 1.101307396 XAC0465 XAC0465 metalloproteinase 1.159209175 1.382134115 XAC0189 iorA indolepyruvate ferredoxin oxidoreductase 1.139472125 1.164978089 XAC0224 poxB pyruvate dehydrogenase 1.135612256 1.118133461 XAC3458 leuC isopropylmalate isomerase large subunit 1.122307106 1.221916323 XAC0495 XAC0495 two component system regulatory protein 1.118411592 1.201603841 XAC2151 yapH YapH protein 1.113301035 1.800840033 XAC2992 XAC2992 endoproteinase ArgC 1.102233164 1.32122178 XAC0122 tldD TldD protein 1.101179671 1.30 6361106

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174 Table 3 13 Differential expression of effctor genes shared between strains X. citri subsp. citri str. 306 (A) and X. citri subsp. citri str. A w 12879 (W) in both NB (nutrient rich) medium and XVM2 (hrp inducing) medium. FDR values are in paren thesis. The ones that pass cut off value of 0.05 are marked in green Effector class Xcaw XccA Log 2 fold change(FDR) WNB/ANB Log 2 fold change (FDR) WXVM/AXVM Promoter region AvrBs2 XCAW_00465 XAC0076 1.04 (0.72) 1.2 (0.08) Different 10 XopA (Hpa1/HpaG) X CAW_00826 XAC0416 1.48 (0.53) 1.14 (0.16) Different 35 XopE1 (AvrXacE1) XCAW_00686 XAC0286 1.03 (0.77) 1.19 (0.06) Same XopE3 (AvrXacE2) XCAW_03515 XAC3224 1.01 (1.0) 1.04 (0.38) Same XopF2 1.21 (0.21) 2.39 (0.19) Same XopI XCAW_03828 XAC0754 1.74 (0.06) 1.15 (0.46) Same XopK XCAW_03372 XAC3085 1.23 (0.48) 1.04 (0.83) Same XopL XCAW_03376 XAC3090 1.04 (0.82) 1.59 (0.03) Same XopQ XCAW_04706 XAC4333 1.05 (0.72) 1.0 7 (0.19) Same XopR XCAW_00677 XAC0277 1.01 (1.0) 1.23 (0.14) Same XopV XCAW_03980 XAC0601 1.17 (0.21) 1.43 (0.08) Same XopX XCAW_00956 XAC0543 1.20 (0.20) 1.20 (0.05) Same XopZ1 XCAW_01815 XAC2009 1.03 (0.85) 1.16 (0.09) Same XopAD XCAW_00082 XAC421 3 1.03 (0.87) 1.18 (0.02) Same XopAI XCAW_01099 XAC3230 1.02 (0.85) 1.09 (0.10) Same XopAK XCAW_04369 XAC3666 1.01 (0.96) 1.13 (0.12) Same XopAP XCAW_03269 XAC2990 1.07 (0.04) 1.01 (1.0) Same HpaA XCAW_00810 XAC0400 7.31 (0.26) 1.07 (0.81) Same HrpW(PopW) XCAW_03200 XAC2922 1.03 (0.60) 1.28 (0.02) Same XopAQ XCAW_03514 No annotation between XAC3223 and XAC3224 1.02 (0.81) 1.41 (0.04) Same XopE2 (AvrXacE3, AvrXccE1) XCAW_03520 XACb0011 1.00 (1.0) 1.02 (0.56) Different 35 XopN XCAW_01387 X AC2786 1.23 (0.16) 1.40 (0.06) Same XopP XCAW_01310 XAC1208 1.06 (0.36) 1.16 (0.10) Same XopAE (HpaF/HpaG) XCAW_00801 XAC0393 1.10 (0.69) 1.04 (0.56) Same XopC2 -1.02 (0.99) -1.04 (0.64) Same

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175 Figure 3 1. Alignments between the whole genome optical maps and the in silico genome sequence assemblies at various stages of the project. Dark blue represents cut sites, light blue regions indicate alignment, white regions indicate no alignment. Alignment lines for inversions and translocations are highlighted in pink. Panel A: An early comparison of the optical map derived from Bam H1 digestion of the X. citri subsp. citri A w 12879 ( Xcaw) genome to the assembled scaffolds generated by traditional sequencing technologies. The Xcaw optical map derived from BamH1 digestion of the chromosome is presented as a single contig in the center. The sequenced genome contains 17 scaffolds of which 10 have a corresponding match to the optical map. Other scaffolds are too small in size to be mapped using current optical map technology. However, during gap closure they were placed between contigs to fill gaps or hit to plasmids. The finishing strategy including gap closure was simplified using the optical map as an assembly model. The contigs were broken and inverted as indicated by the mapping and the gaps filled by PCR sequencing. Panel B: Comparison of the final assembly of the Xcaw genome (bottom) to the optical map (top) for the BamH1 digest.

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176 Figure 3 2. Circular representation of X. citri subsp. citri str. A w 12879 genome and plasmids pXcaw19 & pXcaw58. Circles from outside to inside: first and second, predicted coding sequences of chr omosome and plasmids on leading and lagging strands respectively (colors according to COGs); third, G+C content; forth, G+C skew; fifth, scale bar in kilobases.

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177 Figure 3 3. Maximum likelihood tree of the genome of Xanthonomas citri subsp. citri A w 12879 showing the relationship to other fully sequenced Xathomonads (except XauB and XauC) and related species. The tree was constructed using concatenated protein sequenc es of nine housekeeping genes ( uvrD, secA, carA, recA, groEL, dnaK, atpD, g yrB and i nfB ) aligned using Clustal W. Phylogenic tree from concatenated sequences was constructed in PAUP (version 4.0) using the Maximum likelihood method. The sequence of Burkholderia mallei NCTC 10247 was used as out group species. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. Horizontal scale bar (0.1) at the bottom represents number of amino acid substitutions per site.

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178 Figure 3 4. MAUVE alignment o f the genome sequences of X. citri subsp. citri str. 306 and X. citri subsp. citri A w 12879. Conserved and highly related regions are colored and low identity unique region are in white (colorless). The colored lines indicate translocations of the genome s ections. Same colored blocks on opposite sides of the line indicate inversion. Figure 3 5. Comparison of the T4SS gene clusters of X. citri subsp. citri str. 306 (A), and X. citri subsp. citri str. A w Arrows indicate individual genes and homologues genes have same color. Aw does not contain the T4SS genes encoded by the plasmid Xac64 of XccA.

PAGE 179

179 Figure 3 6. Prediction and comparison of the TAL effector codes encoded by pthA genes of X. citri subsp. citri str. 306, and X. citri subsp. citri str. A w Panel A: Prediction of TAL effector codes of PthAw1 and PthAw2. Panel B: The known TAL effector codes of PthA genes from XccA. Panel C: Comparison of the TAL effector codes of PthAw2 and PthA4, homologs in Xcaw and XccA respectively (Red residues show hom ology)

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180 Figure 3 7. Inoculation by pressure infiltration of X. citri subsp. citri str. 306, X. citri subsp. citri str. A w and X. citri subsp. citri str. A w avrGf1 deletion mutant on young Grapefruit, Valencia and Hamlin leaves. The culture concentration of 108 was used for inoculation in plants were incubalted for 2 weeks. XccA infects all three citrus varities, Xcaw shows hypersencitive reaction only on Grapefruit. Xcaw avrGf1 deletion mutant shows reduced symptoms as co mpared to XccA on Grapefruit and no symptoms on Valencia and Hamlin. Grapefruit Valencia H amlin XccA Xcaw X caw

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181 Figure 3 8 Neighbor joining tree of XopAF protein sequences. The tree was constructed using clustal aligned protein sequences of XopAF and its homologs. Bootstrap values are d isplayed at nodes. Xcaw, X. citri subsp. citri strain A w 12879; XauB, XauC, X. fuscans subsp. aurantifolii strains B and C; XooBLS, X. oryzae pv. oryzicola BLS256; Xcv, X. campestris pv. vesicatoria ; Xcm, X. campestris pv. musacearum NCPPB 4381; Xcv, X. ca mpestris pv. vasculorum NCPPB 702; Xe, X. euvesicatoria ; Xp91, X. perforans strain 91 118; Ac, Acidovorax citrulli AAC00 1; PstDC, P. syringae pv. tomato DC3000; PssB728, P. syringae pv. syringae B728. Horizontal scale bar (0.5) at the bottom represents nu mber of amino acid substitutions per site.

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182 Figure 3 9. Comparison of the LPS gene clusters of X. citri subsp. citri str. 306, X. citri subsp. citri A w 12879 and X. oryzae pv. oryzicola str. BLS256. Conserved and highly related genes (over 70% identity) are colored

PAGE 183

183 Figure 3 10 Growth of X. citri subsp. citri str. 306 (blue), and X. citri subsp. citri str. A w 12879 (red) under NB and XVM2 conditions. Arrows indicate where the cells were harvested for RNA purification (O.D. 0.4 at 560 nm in each con dition). Figure 3 11 Principal component analysis of DEG of X. citri subsp. citri str. 306 (A), and X. citri subsp. citri str. A w 12879 (Aw) under NB and XVM2 conditions. The genes expressed by Aw cluster separately from A in both the NB and XVM2 con ditions indicating that orthologous genes are differentially expressed.

PAGE 184

184 Figure 3 12 RNA seq validation by qRT PCR. Comparison of gene expression by quantitative reverse transcription polymerase chain reaction (qRT PCR) and RNA seq. The log2 fold chang e of each gene was derived from comparison of either WNB vs ANB or WXVM2 vs AXVM2. The 16S rRNA gene was used as an endogenous control in qRT PCR. Values of log2 fold change are means of three biological replicates. Error bars indicate standard deviation. Blue bars represent values from RNA seq and yellow bars are values from qRT PCR.

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185 Figure 3 13 Identification of new genes by RNA seq. Comparison of gene expression by aligning reads for XccA in NB and XVM2 medium to the genome. Differential expression was seen in intergenic region between ISxac3 transposase and avrXacE2 genes under different conditions (gray coverage scales below the read alignment). Blast analysis revealed presence of a putative effector protein encoding xopAQ gene. The log2 fold chang e of xopAQ

PAGE 186

186 Figure 3 14 Number of differentially expressed genes when comparing expression of common genes in X. citri subsp. citri str. A w 12879 against X. citri subsp. citri str. 306 in NB and XVM2 growth conditions. Gene expression of orthologous genes between Xcc Aw (W) and XccA (A) was compared when grown in Nutrient broth (NB, nutrient rich medium) and XVM2 (XVM, plant mimic medium).

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187 Figure 3 15 Protease and Pectate lyase activity of X. cit ri subsp. citri str. 306, and X. citri subsp. citri str. A w 12879. A) Protease activity was tested by inoculating 1 l culture on 10% milk agar plates at 28C for 6 days. Zone of clearance was used as the measure of protease activity. B) Pectate lyase acti vity was tested More pitting can be seen on medium at pH 8.5 for XccA strain as compared to Xcaw.

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188 CHAPTER 4 SUMMARY AND CONCLUSI ON Citrus canker caused by Xcc is one of the most s erious diseases of citrus. XccA is distinguished into different variants primarily by host range. XccA has a wide host range and is most virulent, whereas Xcaw strain has host range restricted to Mexican lime and alemow. Xacm is another citrus pathogen cau sing citrus bacterial spot disease with limited host range and virulence. Both Xacm amd Xcaw are geographically restricted within the state of Florida. The goals of this study are to use comparative genomics and transcriptomics to understand the molecular mechanisms responsible for the difference in host range and virulence of these closely related Xanthomonas strains. It has been previously known that avirulence genes can affect host range of Xanthomonas and other plant pathogenic bacteria. Also various ge nes involved in virulence such as T1SS T6SS, T3SS effectors, EPS, LPS, adhesins, flagellum and other have been previously identified by molecular as well as in silico studies. None of the studies however focused on the effect of gene expression on host r ange and virulence of the phytopathogen. We hypothesized that gene expression along with gene content can contribute to virulence and host range of closely related strains. In order to identify potential host range and virulence affecting factors we condu cted a comprehensive comparative genomic study of an aggressive bacterial spot strain Xacm F1 to XccA. Illumina, 454 sequencing and optical mapping were used to obtain complete genome of Xacm strain F1 which is 4.9Mb chromosome with no plasmid. Phylogeneti c studies indicated that Xacm is closely related to Xcv strain 85 10, which causes bacterial spot on tomato and pepper. Comparison of chromosome organization using MAUVE showed inversion (with translocation) and major deletions in

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189 Xacm compared to XccA and Xcv. Comparison of the proteins of three Xanthomonas spp. showed differences in T3SS effectors, T4SS, LPS and others. In addition to pthA effectors such as xopE3 xopAI and hrpW were absent in Xacm, which might be responsible for reduced virulence of thi s pathogen compared to XccA. We also identified unique effectors like xopC2 and xopW in Xacm that may be restricted its host range. Xacm also lacks various toxin related genes, such as syrE1 syrE2 and RTX toxin family genes which are present in XccA. The absence of these genes may be associated with distinct virulence of XccA and Xacm. We also sequenced the genome of Xcaw (5.3 Mb chromosome and two plasmids pXcaw19 and pXcaw58). Whole genome comparison of A w to A strain, disclosed numerous genome rearran gements and insertion/deletion regions indicating genome plasticity. Comparative genomic analysis of Xcaw and XccA indicate that Xcaw strain specific effectors XopAG and XopAF might contribute to its limited host range compared to XccA. Also various change s in genes encoding LPS and T4SS for Xcaw were observed. RNA seq was used to compare expression profile of Xcaw and XccA strains in nutrient rich (NB) and plant intercellular space mimicking (XVM2) conditions using Il lumina sequencing. We found 5 avirulenc e/effector genes overexpressed in Xcaw compared to XccA. This might also contribute to its limited host range. The overexpression of genes involved in cell wall degradation, attachment, ROS scavenging, nutrient transportation in XccA might contribute to it s expanding of host range. Our data also demonstrate that virulence genes including genes encoding TIIISS and its effectors are induced in the condition mimicking the plant intercellular environment.

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190 Overall the comparison of the finished genomes of Xacm and Xcaw to XccA provides valuable insights into the emergence of new virulent strains with different host range and distinct virulences. It was observed that both the strong and weak citrus pathogens were capable of infecting Mexican lime effectively. Th is indicates that either Mexican lime is not equipped with various immunity realted genes or the pat hogen can easily circumvent this immunity. Thus comparison of Mexican lime with other comparatively resistant varities of citrus should help uncover the pla nt genes important in fighting the citrus canker infection. Our transcriptome data also suggests that both gene content and gene expression contribute to difference in virulence and host range of different bacterial strains and this might be further true f or plant genes especially those related to immunity. This study also l ays foundation to further characterize the specific genes and the mechanism of difference in virulence and host range of stains of X. citri subsp citri and other bacterial pathogens.

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191 APPENDIX MEDIA COMPOSITION NUTRIENT AGAR (NA) Beef Extract 3.0 g Peptone 5.0 g Agar 15.0 g DDW 1000 ml NUTRIENT BROTH (NB) Beef Extract 3.0 g Peptone 5.0 g DDW 1000 ml XVM2 Sodium chloride 1.16 g Ammonium sulphate 1.32 g Magnesium sulp hate 0.6 g Calcium c hloride 0.147 g Potassium dihydrogen phosphate 160 l of 1 M stock DiPotassium hydrogen phosphate 320 l of 1 M stock Ferrous sulphate 40 l of 250 mM stock DDW 980 ml Adjust pH to 6.7, autoclave and cool Fructose 10 ml of 1 M stock Sucrose 10 ml of 1 M stock Casaminoacid 1 ml of 30% stock HILDEBRAND'S MEDIUM (3 different pH media) DDW 1000 ml Heat to near boiling Bromothymol blue 1.5% alcoholic solution Calcium c hloride 6 ml of 10% stock Sodium polypectate 22 g Agar 100 ml of 4% solution Adjust pH for two to 4.5 4.7 and 6.9 7.1 with 1N HCl solution and autoclave Autoclave the third and adjust pH 8.3 8.5 with 1N NaOH SKIM MILK AGAR PLATE Nutrient Agar 500 ml. Autoclave Pour basa l plate (thin layer) and cool. 2X Nutrient Agar 250 ml Skim milk Dissolve 50 gm skim milk powder completely in 250 ml warm DDW Autoclave and m ix st. skim milk with 2X NA to get 10% Skim milk agar and pour top layer on basal plates.

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192 LIST OF REFERENCES A chor DS, Browning HW, and Albrigo L G. 1996. Anatomical and histological modification in citrus leaves caused by larval feeding of citrus leaf miner ( Phyllocnistis citrella Staint ). Page 69 in: Proc Int Conf Citrus Leafminer Orlando, Florida, April 23 25 Al Saadi A. 2005. Phenotypic characterization and sequence analysis of pthA homologs from five pathogenic variant groups of Xanthomonas citri University of Florida, Gainesville, Florida Al Saadi A, Reddy JD, Duan YP, Brunings AM, Yuan Q, and Gabriel DW. 2007. All five host range variants of Xanthomonas citri carry one pthA homolog with 17.5 repeats that determines pathogenicity on citrus, but none determine host range variation. Mol Plant Microbe Interact 20: 934 943. Alegria M Souza D Andrade M Docena C Khater L Ramos C da Silva A Farah C 2005. Identification of new protein protein interactions involving the products of the chromosome and plasmid encoded type IV secretion loci of the phytopathogen Xanthomonas axonopodis pv. citri J Bacteriol 187: 2 315 2325. Alfano JR, Collmer A. 1997. The type III (Hrp) secretion pathway of plant pathogenic bacteria: trafficking harpins, Avr proteins, and death. J. Bacteriol 179 :5655 5662. Alvarez AM Benedict AA Mizumoto CY, Pollard LW Civerolo EL 1991. Analysi s of Xanthomonas campestris pv. citri and X. c. citrumelo with monoclonal antibodies. Phytopathology 81: 9. Andrade M Alegria M Guzzo C Docena C Rosa M Ramos C, Farah C 2006. The HD GYP domain of RpfG mediates a direct linkage between the Rpf quorum s ensing pathway and a subset of diguanylate cyclase proteins in the phytopathogen Xanthomonas axonopodis pv citri Mol Microbiol 62: 537 551. Arnold DL, Jackson RW. 2011. Bacterial genomes: evolution of pathogenicity. Current opinion in Plant Biology 14 : 385 391. Astua Monge G, Minsavage GV, Stall RE, Davis MJ, Bonas U, Jones JB. 2000. Resistance of tomato and pepper to T3 strains of Xanthomonas campestris pv. vesicatoria is specified by a plant inducible avirulence gene. Mol Plant Microbe Interact 13 :911 621. Astua Monge G, Feritas Astua J, Bacocina G, Roncoletta J, Carvalho SA, Machado MA. 2005. Expression profiling of virulence and pathogenecity related genes of Xanthomonas axonopodis pv. citri J Bacteriol 187 :1201 1205. Aury JM Cruaud C Barbe V Rogier O Mangenot S Samson G, Poulain J Anthouard, Scarpelli VC Artiguenave F Wincker P 2008. High quality draft sequences for

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211 BIOGRAPHICAL SKETCH Neha Jalan was born in Mumbai, Maharashtra, India in 1983. She obtained her bachelor's degree in micr obiology in 2003 from Mithibai C ollege, Univ ersity of Mumbai, India. She continued to pursue her master's degree at University of Mumbai. During this time she worked on treatment of starchy wastewater by amylase producing soil isolates. She completed her master's de gree in 2005 and joined Sophia C ol lege, University of Mumbai as a lecturer in industrial microbiology. During this time she co wrote a grant and was awarded to do research on microbial degradation of methyl parathion: characterization of its metabolites and their effects on biological sys tem. In November 2006 she started working as Junior resea rch fellow jointly at Bhavan's C ollege, University of Mumbai and ISOMED, Bhabha Atomic Research Center. The research focused on production of fructooligosaccharide by gamma radiation processing of mi crobial levan and radiation effect studies on its use as prebiotic. In August 2008, she joined the Ph.D. program in the Department of Microbiology and Cell Science at the University of Florida. She worked under the guidance of Dr. Nian Wang focusing her re search on comparative genomics and transcriptomics of host specific xanthomonads causing citrus canker and citrus bacterial spot. As a graduate student she presented her work at departmental symposiums and 2010 2012 American Phytopathological Society annua l meetings. She was awarded the 2nd best oral and poster presentation award at the department of MCS graduate student symposium in 2010 and 2012, respectively. Neha is a member of American Phytopathological Society (APS) and American Society of Microbiolog y (ASM).