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Pokeweed Antiviral Protein-Mediated Resistance to Citrus Pathogens

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Pokeweed Antiviral Protein-Mediated Resistance to Citrus Pathogens
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PETERSEN, YOLANDA ( Author, Primary )
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2008

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Antivirals ( jstor )
DNA ( jstor )
Genomes ( jstor )
In vitro fertilization ( jstor )
Polymerase chain reaction ( jstor )
Protoplasts ( jstor )
RNA ( jstor )
Transgenes ( jstor )
Transgenic plants ( jstor )
Viroids ( jstor )

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University of Florida
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University of Florida
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Copyright Yolanda Petersen. Permission granted to the University of Florida to digitize, archive and distribute this item for non-profit research and educational purposes. Any reuse of this item in excess of fair use or other copyright exemptions requires permission of the copyright holder.
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8/1/2004
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POKEWEED ANTIVIRAL PROTEIN-MEDIATED RESISTANCE TO CITRUS PATHOGENS By YOLANDA PETERSEN A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLOR IDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2003

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Copyright 2003 by Yolanda Petersen

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To my parents

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ACKNOWLEDGMENTS The completion of this dissertation would not have been possible without the help and support of many people. First, I would like to express my sincere gratitude and appreciation to my advisor Dr. Richard F. Lee for his support and encouragement, and for having me in his lab. I would like to thank Dr. G. Moore, Dr. D. Pring and Dr. G. Wisler for serving on my committee and reviewing this manuscript. I would like to thank Dr. G. Moore and the members of her lab for always answering my questions; and for their help in facilitating my research. Some people who deserve special mention are Dr. K.L. Manjunath, Dr. V.J. Febres, A. Guerra, Dr. K. Biswas. Their help and understanding during two lab relocations is much appreciated. I want to thank Professor W.O. Dawson and the people in his lab for providing me with the CTV infectious clone and for assisting me with my CTV replication experiment, which I conducted in their laboratory. I thank E. Crawford and E. Philmon for taking care of my plants in the greenhouse and growth rooms, in Gainesville. Without them, a lot more plants would have died. I also want to thank Neil for helping me graft and inoculate my transgenic citrus plants as well as for taking care of these plants in Lake Alfred. I would like to thank the ladies in the main office for their patience and taking care of the numerous problems that arose. I want to thank all the wonderful friends I made in Gainesville as well as friends in Germany, Colorado, New Zealand, and South Africa who were always ready to lend an ear and give me their unconditional support. iv

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My most sincere thanks and appreciation go to my parents and family, for their understanding and support, and for always believing in me. v

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TABLE OF CONTENTS Page ACKNOWLEDGMENTS.................................................................................................iv LIST OF TABLES.............................................................................................................ix LIST OF FIGURES.............................................................................................................x ABSTRACT......................................................................................................................xii CHAPTER 1 LITERATURE REVIEW.............................................................................................1 Introduction...................................................................................................................1 Citrus exocortis viroid (CEVd).....................................................................................1 Movement of Viroids............................................................................................2 Replication of Viroids...........................................................................................3 Citrus tristeza virus (CTV)...........................................................................................4 Classification and Genome Organisation of CTV.................................................5 Replication and Expression Strategy of CTV.......................................................7 Control of CTV......................................................................................................8 Genetic Engineering for Virus/Viroid Resistance...............................................10 Ribosome-Inactivating Proteins (RIPs)...............................................................11 Enzymatic Activities of RIPs..............................................................................12 Antiviral Activity of RIPs...................................................................................13 RIPs in Transgenic Plants....................................................................................14 2 In vitro TRANSLATION OF A Citrus tristeza virus REPLICON AND THE EFFECT OF POKEWEED ANTIVIRAL PROTEIN ON ITS TRANSLATION.....16 Introduction.................................................................................................................16 Materials and Methods...............................................................................................19 Source of Viral Nucleic Acid..............................................................................19 In vitro Transcription and Translation of CTV-Cla..........................................19 In vitro Antiviral Assay.......................................................................................20 Results.........................................................................................................................21 In vitro Translation of CTV-Cla.......................................................................21 PAP Inhibits Translation of CTV-Cla Transcripts............................................23 Discussion...................................................................................................................24 vi

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3 TRANSFORMATION OF Citrus paradisi cv Duncan GRAPEFRUIT WITH POKEWEED ANTIVIRAL PROTEIN......................................................................27 Introduction.................................................................................................................27 Materials and Methods...............................................................................................32 PAP Gene Constructs and Plasmid Expression Vectors.....................................32 Citrus Transformation and Regeneration............................................................33 Seed germination..........................................................................................35 Transformation of epicotyl segments...........................................................35 Selection and regeneration of plantlets........................................................35 Analysis of Transgenic Plants.............................................................................37 Fluorescent microscopy................................................................................37 Polymerase chain reaction (PCR) analysis...................................................37 Southern hybridization........................................................................................38 Reverse-transcription (RT) PCR.........................................................................39 Western blot analysis...........................................................................................39 Grafting and Challenge of Transgenic Plants with CTV.....................................40 Challenge of Transgenic Plants with Citrus exocortis viroid (CEVd)................40 Results.........................................................................................................................42 Transformation and Regeneration.......................................................................42 Southern Blot Analysis and RT-PCR of Transgenic Plants................................46 Protein Expression Analysis................................................................................48 Virus Challenge of Transgenic Plants.................................................................49 Viroid Challenge of Transgenic Plants................................................................51 Discussion...................................................................................................................51 4 THE EFFECT OF POKEWEED ANTIVIRAL PROTEIN ON THE REPLICATION OF Citrus tristeza virus IN Nicotiana benthamiana PROTOPLASTS.........................................................................................................57 Introduction.................................................................................................................57 Materials and Methods...............................................................................................59 Constructs............................................................................................................59 Tobacco Transformation.....................................................................................59 Explant preparation......................................................................................59 Transformation and regeneration of tobacco................................................60 Analysis of Transgenic Plants by PCR................................................................60 Southern Hybridization.......................................................................................61 Reverse-Transcription (RT) PCR........................................................................61 Analysis of Protein Expression...........................................................................62 Determination of Antiviral Properties of Transgenic Plants...............................63 Viral Replication in Transgenic Protoplasts........................................................63 Results.........................................................................................................................64 Transformation and Regeneration.......................................................................64 Molecular Analysis of Transgenic Plants............................................................65 CTV Replication in PAPn-Transgenic N. benthamiana Protoplasts...................69 Discussion...................................................................................................................70 vii

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5 SUMMARY AND CONCLUSIONS.........................................................................73 LIST OF REFERENCES...................................................................................................78 BIOGRAPHICAL SKETCH.............................................................................................90 viii

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LIST OF TABLES Table page 3-1. Expected properties of PAP and PAP mutants...........................................................31 3-2. Sequences of oligonucleotide primers used for amplification and mutagenesis of the PAP gene............................................................................................................33 3-3. Summary of results for the transformation of Citrus paradisi cv. Duncan grapefruit with pokeweed protein (PAP) antiviral constructs..................................45 3-4. CTV antigen levels four months post-inoculation.in transgenic Citrus paradisi plants expressing PAPn............................................................................................51 4-1. Summary of N. benthamiana transformation experiments with the PAP constructs..................................................................................................................65 4-2. TMV antigen levels in transgenic N. benthamiana expressing PAPn following infection with the virus.............................................................................................68 ix

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LIST OF FIGURES Figure page 1-1. Symptoms caused by Citrus tristeza virus...................................................................6 2-1. Schematic representation of the Citrus tristeza virus (CTV) genome........................17 2-2. Optimization of CTV-Cla replicon translation in wheat germ extract.....................22 2-3. Optimization of CTV-Cla translation in rabbit reticulocyte lysate..........................23 2-4. Effect of wild type PAP on translation.......................................................................24 3-1. Cloning strategy of the PAP constructs for plant transformation...............................34 3-2. Agrobacterium-mediated transformation of etiolated Citrus paradisi cv. Duncan grapefruit and regeneration of plants.......................................................................36 3-3. Analysis of GFP expression in citrus shoots regenerated from epicotyl segments transformed with pCambia2202-PAPc and -PAPn..................................................43 3-4. PCR analysis of potentially transgenic shoots containing the PAPn transgene......44 3-5. Phenotypes of plants transformed with the PAPc and PAPv constructs....................47 3-6. Southern analysis to determine transgene copy number in transgenic grapefruit plants transformed with PAPn..................................................................................48 3-7. RT-PCR analysis of transgenic citrus transformed with PAPn to determine gene expression at the level of transcription.....................................................................49 3-8. Western blot analysis of total soluble proteins from transgenic citrus to determine the expression the PAPn transgene..........................................................................49 3-9. RT-PCR analysis of representative viroid-infected PAPn-transgenic plants.............52 4-1. PCR analysis of selected potential transgenic N. benthamiana plants using primers CN444 and CN445...................................................................................................65 4-2. Southern analysis of R0 tobacco plants transformed with PAPn...............................66 x

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4-3. RT-PCR analysis of RNA isolated from selected transgenic plants to determine PAPn expression at the transcriptional level............................................................67 4-4. Northern blot analysis of CTV RNAs in N. benthamiana protoplasts derived from PAPn transgenic R1 plants.......................................................................................69 xi

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Abstract of Dissertation Presented to the Graduate School of the University of Florida in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy POKEWEED ANTIVIRAL PROTEIN-MEDIATED RESISTANCE TO CITRUS PATHOGENS By Yolanda Petersen December 2003 Chair: Richard F. Lee Major Department: Plant Pathology Citrus production is adversely affected by a number of diseases caused by viruses and viroids. This project has employed a ribosome-inactivating protein, pokeweed antiviral protein (PAP) isolated from Phytolacca americana in an effort to control Citrus tristeza virus (CTV) and citrus exocortis viroid (CEVd). PAP has antiviral activity and can act directly on RNA. The applicability of PAP to inhibit CTV translation was evaluated in vitro. In vitro transcription and translation assays using the CTV replicon, CTV-Cla, and wild type PAP showed that viral translation decreased in the presence of increasing concentrations of PAP. In vivo experiments required the production of non-toxic N-terminal (Gly75-Ala), active site (Glu176-Ala) and C-terminal deletion mutants (Trp237-Stop), which were then used to transform Citrus paradisi cv. Duncan by Agrobacterium-mediated transformation. The overall transformation efficiency was low, at 8.6% as determined by the percentage of regenerated plantlets that were PCR-positive for the PAP transgene. Six surviving transgenic plants containing the N-terminal mutant xii

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were obtained and evaluated by virus/viroid challenge. Molecular characterization of these plants showed that the plants contain one to four copies of the mutated PAP gene and that the gene was being expressed at the transcriptional and translational levels. The transgenic citrus plants were challenged with CTV and CEVd by graft-challenge inoculation. Four months post-inoculation the transgenic plants had significantly lower levels of CTV, in comparison to the non-transgenic control plants. All plants supported viroid replication at levels equivalent to that of the non-transgenic controls. To obtain a more accurate view of the effect of the N-terminal mutant on CTV replication, Nicotiana benthamiana was transformed with the mutated PAP gene used for citrus transformation. Five lines of transformed N. benthamiana were selected for protoplast experiments in which CTV virions were used as inoculum for transfection. Results showed that the lines TN5, TN11 and TN23a supported lower levels of CTV replication relative to the non-transgenic control. Thus, the PAPn mutant does not inhibit CEVd replication; and this mutant reduces, but does not completely inhibit the replication of CTV in citrus plants and tobacco protoplasts. xiii

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CHAPTER 1 LITERATURE REVIEW Introduction Diseases caused by viruses and viroids have had major impacts on citrus production. Citrus tristeza virus (CTV) alone has caused the loss of millions of trees worldwide. The propagation of viroid-infected trees has caused economic losses in the Florida citrus industry and is a major threat in regions where susceptible rootstocks are used. Once trees are infected, the disease agents cannot be eliminated. This is of particular economic importance, since citrus trees should have a long productive life. Thus the best control measures would be to prevent the introduction of the disease or propagate plants that are disease resistant. Citrus exocortis viroid (CEVd) Viroids are small unencapsidated circular, highly base-paired RNAs which adopt rod-like structures in their native state (reviewed by Hull, 2001). Viroid RNAs do not encode any proteins. Citrus viroids are grouped into six classes: Citrus exocortis viroid (CEVd, 370-375 nucleotides (nt)), Citrus bent leaf viroid (CBLVd, 315-329 nt; formerly called CVd-I), Hop stunt viroid (HSVd, 295-303 nt; formerly called CVd-II), Citrus viroid III (CVd-III, 291-297 nt), Citrus viroid IV (CVd-IV, 284-286 nt) and Citrus viroid OS (CVd-OS, 329-331 nt) (Duran-Vila et al., 2000; Ito et al., 2000, 2002). CEVd is usually found in combination with other viroids; and in the field causes mild to severe stunting and bark scaling on susceptible rootstocks. The disease is exacerbated on citrus trees propagated on rootstock derived from Poncirus trifoliata or hybrids that have P. 1

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2 trifoliata as one of their parents. These rootstocks are used in many citrus-growing regions. The severe stunting results in a reduced canopy with an adverse effect on fruit yield. Less severe symptoms occur on Citrus sinensis X P. trifoliata (citrange) and Citrus limonia (Rangpur lime) and only mild symptoms are usually seen on Swingle citrumelo (Lee et al., 2003). CEVd and viroids in general are spread primarily via infected budwood and through the use of contaminated cutting tools and equipment. Thus these agents are relatively easily controlled through budwood certification programs and good hygienic practices. CEVd can be detected by biological indexing on the indicator host Citrus medica cv. etrog (Etrog citron), a process that takes 3 to 6 months or via more rapid molecular methods such as analysis by sequential polyacrylamide gel electrophoresis and the reverse transcriptase-polymerase chain reaction. Movement of Viroids From experiments involving fractionating components of viroid-infected cells, confocal laser scanning microscopy, transmission electron microscopy, and in situ hybridisation, it became evident that most viroids are located in the cell nucleus; with the exception of Avocado sunblotch viroid (ASBVd), which is found in the chloroplasts (reviewed by Hull, 2001). CEVd accumulates in the nucleoplasm (Bonfiglioli et al. 1996). Systemic movement of viroids that replicate in the nucleus follows four distinct steps: (1) import into the nucleus via the nuclear pores (2) export out of the nucleus (3) cell-to-cell movement and (4) long-distance movement. Experiments with potato spindle tuber viroid (PSTVd) led to the conclusion that viroids move rapidly from cell to cell via the plasmodesmata; and that the movement is mediated by a specific sequence or structural motif (Ding et al., 1997). The spread of PSTVd in tomato and Nicotiana benthamiana followed the pattern of photoassimilate

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3 transport, suggesting that PSTVd moves long distance through the phloem. (Palukaitis et al., 1987; Zhu et al., 2001). Maniataki et al. (2003) and Owens et al. (2001) showed that PSTVd interacts with host cell proteins and suggested that these proteins might facilitate systemic movement of the viroid. Maniataki et al. (2003) also showed that the region interacting with the host cell protein consisted of eight nucleotides in the TR (terminal right) region of the viroid RNA. The TR region has a bulged hairpin secondary structure reminiscent of micro-RNA precursors, and it is thought that the micro-RNA precursors are capable of systemic movement. Replication of Viroids Despite their small size, the elucidation of viroid replication is remarkably complex. Viroid-infected tissue contains a variety of multimeric RNAs, and replication is thought to proceed via a ‘‘rolling circle’’ mechanism. There are two models for rolling circle replication: (1) the symmetric pathway in which both circular forms of the (+) and (-) strands serve as templates for the synthesis of complementary multimers that are cleaved into monomers and ligated to form circular molecules, and (2) the asymmetric pathway in which the circular (+) strand serves as a template for synthesis of multimeric linear (-) strands, which in turn serve as templates for the synthesis of multimeric (+) strands that are cleaved and ligated to produce the final circular forms. CEVd and other viroids in the family Pospiviroidae replicate via the asymmetric pathway (reviewed by Hull, 2001). Replication does not require a helper virus; and the viroid RNA does not encode any proteins necessary for replication. This suggests that the information necessary for replication resides in the unusual secondary structure of the viroid genome. Localization of CEVd in the nucleus suggests that a host nuclear RNA polymerase may be involved

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4 (Bonfiglioli et al., 1996). The fact that viroid RNA synthesis is inhibited by -amanitin indicates that a host-encoded RNA polymerase II may be required for replication (reviewed by Hull, 2001). Warrilow and Symons (1999) obtained direct evidence for the association of CEVd with a host-encoded RNA polymerase II. Citrus tristeza virus (CTV) Citrus tristeza virus is one of the most important pathogens of citrus. CTV is endemic to most citrus-growing regions and in the past has resulted in devastating economic losses due to decline of sweet orange scions on sour orange rootstock (Bar-Joseph et al., 1989). Hence, the name “tristeza” which in Spanish means “sadness”. CTV causes a number of different symptoms depending on the virus strain and the host/rootstock combination. Decline strains result in decline and death of citrus species on sour orange rootstock as a result of phloem necrosis at the graft union which prevents the movement of nutrients from the canopy to the root system (Figure 1-1 A; Garnsey et al., 1987). Other strains express stem pitting symptoms on either sweet orange and/or grapefruit scions irrespective of the rootstock. Stem pitting reduces tree vigor, fruit yield and quality (Figure 1-1 B and C). Vein corking (Figure 1-1 D) is induced by some strains, and a syndrome called seedling yellows, which is expressed as stunting and chlorosis of grapefruit, lemon and other susceptible varieties. The virus is spread by aphid vectors including Toxoptera citricida (brown citrus aphid), T. aurantii, Aphis gossypii, and A. spiraecola, and by propagation of infected tissue (Bar-Joseph et al., 1989; Roistacher and Bar-Joseph, 1987). T. citricida is the most efficient vector of CTV; and its introduction into Brazil and Argentina in the 1930s caused the death of 16 million trees on sour orange rootstock as a result of the efficient

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5 transmission of decline strains of CTV (Carver, 1978). The brown citrus aphid was first reported in Florida in 1995 (Halbert and Evans, 1996). This vector has been shown to transmit CTV strains that cannot be transmitted by other vectors (Roberts et al., 2001). Thus the presence of the brown citrus aphid may cause a shift in the major viral populations in the state and result in the appearance of CTV strains causing more severe symptoms than in the past. Classification and Genome Organisation of CTV Citrus tristeza virus belongs to the family Closteroviridae within the order Nidovirales. The virus structure is a long flexuous rod 2000 x 11 nm in size. The viral genome consists of a single-stranded, positive-sense RNA and at approximately 19 kb, this genome is one of the largest known for plant viruses (Karasev et al., 1995). The RNA is encapsidated by two coat proteins. Ninety-five percent of the genome is encapsidated by the major coat protein (p25); the remaining 5% is protected by the divergent minor coat protein (p27), which gives the virus a characteristic “rattlesnake” appearance (Febres et al., 1996). The CTV genome has 12 open reading frames with the potential to code for 17 proteins (Karasev et al., 1995; Pappu et al., 1994). Some of the genes have been assigned functions based on sequence homology to other viral genomes. The arrangement and expression strategy of the replicase region of CTV (Karasev et al., 1995) resembles that of the animal Coronaviruses (Lai et al., 1990). ORF1a is expressed as a 349 kDa polyprotein and encodes two papain-like proteases, a methyltransferase-like and a helicase-like domain. ORF1b encodes a RNA-dependent RNA polymerase (RdRp). The protein encoded by the p20 gene is involved in the accumulation of amorphous inclusion bodies in the phloem (Gowda et al., 2000).

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6 The p65 and p61 proteins share homology with the cellular heat shock protein HSP70 and the cellular chaperone HSP90, respectively (Pappu et al., 1994). There is evidence that these proteins are required for efficient virus assembly (Satyanarayana et al., 2000). The gene product of p23 was shown to be an RNA-binding protein involved in the asymmetric accumulation of RNA (Lopez et al., 2000; Satyanarayana et al., 2002b). The functions of other genes remain to be elucidated. The ten 3' genes are expressed via 3' co-terminal subgenomic RNAs (Karasev et al., 1997). Figure 1-1. Symptoms caused by Citrus tristeza virus. A) Decline of sweet orange on sour orange rootstock (R. F Lee). B) Stem pitting on Pera sweet orange (R. F. Lee). C) Reduced fruit quality of a Marsh grapefruit tree infected by severe stempitting isolates, grafted onto rough lemon rootstock (R. F. Lee). D) Vein corking on leaves of a Mexican lime seedling inoculated with a severe seedling yellows isolate (C. N. Roistacher). Photographs were downloaded from http://www.ecoport.org. The names of the authors are given in parentheses.

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7 Replication and Expression Strategy of CTV The small genome size of viruses has led to the evolution of a number of different expression strategies that maximize the number of products encoded by the genome. The genome organization of CTV has similarities with both the animal Coronaviruses and the alpha-supergroup of viruses. The amino acid sequence of the replicase-associated domains and the lack of a common 5' leader sequence in the subgenomic RNAs are similar to the alphavirus supergroup (Dolja et al., 1994). Like the Coronaviruses, the replicase-associated proteins of CTV are expressed as a polyprotein, which is then proteolytically processed into equimolar amounts of nonstructural proteins. The proteolytic activity of the two proteases has been demonstrated in vitro (Vazquez-Ortiz, 2001). The RdRp is expressed via a +1 frameshift that occurs at a frequency of 1-5% (Cevik, 2001). The 3' ORFs are expressed via positive and negative sense 3' co-terminal subgenomic RNAs (Karasev et al., 1995), which are temporally and quantitatively regulated (Navas-Castillo et al., 1997). The phloem-limited nature of the virus, low concentrations in trees, and large complex genome has hindered progress towards understanding the replication strategy of CTV. The development of a full-length cDNA clone and a smaller replicon, designated CTV-Cla (Satyanarayana et al., 1999), has clarified the function of some of the replication-associated genes such as p23, which is involved in the asymmetrical accumulation of RNA (Satyanarayana et al., 2002b); and elucidated replication signals present in the 3' UTR (Satyanarayana et al., 2002a). Also, Satyanarayana et al. (1999) showed that p23, ORFs 1a and 1b and the 5' and 3' UTRs are sufficient to support viral replication. Additionally, the infectious cDNA clones have proved useful in determining

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8 the gene products required for virion assembly (Satyanarayana et al., 2000). CTV produces a complex array of RNAs, including a genome-length negative-sense RNA which acts as a template for further transcription; subgenomic RNAs, both single and double-stranded (Hilf et al., 1995; Mawassi et al., 1995a); positive-sense low molecular weight transcripts (LMTs) and large molecular weight transcripts (LaMTs) (Che et al., 2001; Mawassi et al., 1995b). In total, more than 35 RNA species have been shown to be produced during the replication of CTV. Control of CTV CTV has a complex population structure in its perennial hosts. In nature any one tree is infected by a CTV population that is made up of a number of genetic variants, some of which may exhibit great variation in sequence similarity (Aylln et al., 1999; Brlansky et al., 2003; Hilf et al., 1999). One of these variants might predominate, but it is not known whether the symptoms exhibited by the infected host are due to the predominant strain or a result of an interaction among the different strains. The structure of these populations is subject to change with time, since some CTV strains are more efficiently transmitted by certain aphid species. A number of strategies have been developed to control CTV. The strategies include eradication programs to prevent the spread of the virus, quarantine and budwood certification to prevent the introduction of CTV, the use of CTV-tolerant rootstocks, mild strain cross protection, breeding for resistance, and genetic engineering (reviewed by Ferguson and Garnsey, 1993). Mild strain cross protection is the phenomenon in which a plant is deliberately infected with a mild strain of a virus which then serves to prevent or delay subsequent infection or expression of more severe strains of that virus (Fulton, 1986). This strategy has been used in a number of countries including Australia, Brazil,

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9 South Africa and Florida (Barkley et al., 1990; Costa and Muller, 1980; Lee and Rocha-Pea, 1987). However, this type of protection is not the same as resistance and will eventually break down, resulting in the loss of groves due to the expression of severe strains that may or may not have been present in the original isolate used to protect the trees. A few citrus relatives have been found to be immune to CTV; that is, they do not support replication of the virus (Garnsey et al., 1987). However, only one species (Poncirus trifoliata) is sexually compatible with commercial citrus species. Introgression of the resistance found in P. trifoliata into commercial cultivars has not produced viable scion varieties since genetic breeding introduced undesirable fruit characteristics along with CTV-resistance (Ferguson and Garnsey, 1993). Resistance to CTV has been mapped and shown to be controlled by a single dominant gene, Ctv (Gmitter et al., 1996; Yoshida et al., 1996). The mechanism of action of this gene is currently unknown, since protoplasts of resistant plants support viral replication (Albiach-Marti et al., 1999). The progress that has been made toward mapping the location of Ctv (Deng et al., 1996, 2001; Fang et al., 1998) makes cloning of the gene and using it to transform commercially important citrus cultivars a reality. With the development of an efficient Agrobacterium-mediated citrus transformation protocol (Luth and Moore, 1999), it is now possible to use molecular methods to engineer resistance to CTV. Thus far an attempt at engineering pathogen-derived resistance, using the coat protein gene of various CTV isolates as well as other CTV genomic sequences, has been made (Dominguez et al., 2002; Febres et al., 2003; Gutierrez, 1997).

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10 Genetic Engineering for Virus/Viroid Resistance Recent advances in plant transformation, the study of the molecular genetics of both plants and their pathogens, and the elucidation of the interacting components of the plants’ natural defense mechanisms have given rise to a number of different ways in which to create virusor viroid-resistant plants. Pathogen-derived resistance (PDR), a concept pioneered by Sanford and Johnston (1985), makes use of the information derived from viral genomes to generate specific host resistance. Since many virus genes involved in the important functions of replication and encapsidation have been elucidated, PDR can be achieved by interfering with these processes within host plants. One of the first successful instances of PDR was achieved through the transformation of tobacco with the coat protein (CP) gene of Tobacco mosaic virus (TMV) (Powell-Abel et al., 1986). Successful CP-mediated resistance has since been achieved for a number of RNA viruses including Potato virus X (PVX), Alfalfa mosaic virus, Cucumber mosaic virus (CMV), Tobacco rattle virus, with Papaya ringspot virus being one of the most recent commercial successes (Baulcombe 1996; reviewed in Wilson 1993; Ferreira et al., 2002). Next to CP-mediated resistance, replicase-mediated resistance technology is the most widely applied. Different forms (sense/antisense, translatable/nontranslatable) of the replicase genes from diverse viruses have been used to transform plants and have exhibited a wide range of host responses to viral infection. In certain virus-host systems, the full-length sense construct of the replicase gene provides an adequate level of resistance; while in others it is the antisense, mutated or truncated versions of the replicase that provide a higher level of resistance (Brederode et al., 1995; Chen et al., 2001; Huet et al., 1999; Vazquez Rovere et al., 2000; Wintermantel et al., 1997, 2000). The antisense approach has also been tried for CEVd (Atkins et al., 1995). Instead of

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11 complete resistance, the antisense construct, targeting the negative strand of CEVd, resulted in only a moderate decrease in viroid RNA accumulation, while the construct targeting the positive strand RNA had no effect. Ribozymes, which are RNA molecules that have enzymatic activity and can cleave RNA, have also been used to transform plants in an attempt to produce virusor viroidresistant plants. Resistance to CEVd and PSTVd has previously been achieved (Atkins et al., 1995; Yang et al., 1997). Varying degrees of resistance were seen in ribozyme-expressing plants infected with TMV (de Feyter et al., 1996), CMV (Kwon et al., 1997) and Rice dwarf virus (Han et al., 2001). Sano et al. (1997) and Ishida et al. (2002) produced plants resistant to PSTVd and chrysanthemum stunt viroid by expressing a double-stranded RNA-specific ribonuclease (pacI) from Schizosaccharomyces pombe in transformed potato and chrysanthemums. Thus transformation of plants with proteins or enzymes that act directly on RNA would provide protection against virus or viroid infection. Another approach to engineer resistance is to modify the expression or introduce genes that activate, regulate or directly contribute to defense responses in plants. These genes could be resistance (R) genes, general regulators of signal-transduction pathways or genes that are activated further downstream and confer the actual resistance (for example, PR genes) (reviewed by Campbell et al., 2002). Ribosome-inactivating proteins are another group of plant defense-related genes that have been used to transform heterologous species and shown to confer resistance to viruses. Ribosome-Inactivating Proteins (RIPs) Ribosome-inactivating proteins have been reported from over 50 plant species and include both monocotyledonous and dicotyledonous plants (reviewed by Nielsen and

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12 Boston, 2001). The only plant known to definitely not have RIP activity is Arabidopsis thaliana. RIPs are a group of plant proteins that are toxic to ribosomes as a result of their specific N-glycosidase depurination of the conserved -sarcin loop of large rRNAs (Endo et al., 1987). Depurination of the -sarcin loop interferes with both the elongation factor EF-Tu/EF-1-dependent binding of aminoacyl-tRNA and the GTP-dependent binding of EF-G/EF-2 to ribosomes, arresting protein synthesis at the translocation step and ultimately resulting in cell death (Montanaro et al., 1975; Osborne and Hartley, 1990). This translational inhibitory effect was seen as having potential in the medical field, for use as selective cell-killing agents in anti-tumor therapy (Pastan and Fitzgerald, 1991; Spooner and Lord, 1990). RIPs can be divided into three classes based on their physical properties. Type 1 RIPs, such as pokeweed antiviral protein (PAP) from Phytolacca americana and trichosanthin from Trichosanthes kirilowii, consist of a single polypeptide chain. Type 2 RIPs, such as ricin (from Ricinus communis) have a type 1-like catalytic subunit (A chain) linked to a galactose-binding lectin (B chain) that facilitates adhesion to and penetration of cell membranes (Batelli and Stirpe, 1995). As a result, type 2 RIPs are much more toxic to living cells. Type 3 RIPs, found in maize and barley, are synthesized as inactive precursors that require proteolytic cleavage for activation (Chaudhry et al., 1994; Walsh et al., 1991). Enzymatic Activities of RIPs Extensive studies of the enzymatic activities of RIPs revealed that RNA N-glycosidase activity on the -sarcin loop of rRNA is by no means the only property of these proteins. All RIPs have the ability to act as polynucleotide:adenosine glycosidases. That is, they can remove multiple adenine residues from RNA or DNA (Barbieri et al.,

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13 1997). In addition to removing adenine residues from nucleic acids, PAP is capable of deguanylating ribosomal and viral RNA (Rajamohan et al., 1999a, b). The type 1 RIPs gelonin (from Gelonium multiflorum) and PAP, and the type 2 RIP, ricin, possess DNA glycosylase/AP lyase activity. These proteins, however, do not act in the traditional protective manner of DNA glycosylase/AP lyases. Instead of removing potentially cytotoxic or mutagenic bases, these proteins remove undamaged, non-mispaired bases (Nicolas et al., 1998). Two novel properties have been demonstrated for ricin and trichosanthin (from Trichosanthes kirilowii). Ricin has been shown to act as a phosphatase on lipids and nucleotides (Helmy et al., 1999; reviewed in Peumans et al., 2001), and trichosanthin possesses chitinase activity (Shih et al., 1997). Antiviral Activity of RIPs Perhaps as a consequence of some of the known enzymatic activities, a number of RIPs have also been shown to possess antiviral and/or antifungal properties. The ability of RIPs to inhibit viral infection in plants has been known since 1925, when extracts from Phytolacca americana (pokeweed) were found to inhibit transmission of TMV (reviewed by Nielsen and Boston, 2001; Peumans et al., 2001). The purified forms of many RIPs have proven to be effective against both plant and animal viruses (Barbieri et al., 1993). The antiviral property of the RIPs from pokeweed is being exploited in the medical field as anti-human immunodeficiency virus (HIV) agents, especially since it was found that PAP can inhibit viral replication at concentrations which do not inhibit the translation machinery of the host cells (Rajamohan et al., 1999b; Ucken et al., 1998). Several explanations have been put forward to explain the antiviral activities of RIPs. The first is that RIPs act directly on the viral nucleic acid via their polynucleotide:adenosine glycosidase activity. Second, RIPs could gain selective entry

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14 into virus-infected cells when the cell is damaged upon vector feeding and thus inhibit the protein synthesis machinery of only the infected cell. Third, RIPs may act indirectly through the activation of signal-transduction pathways involved in plant defense. Although there is in vitro evidence for the direct action of RIPs on viral nucleic acid (Rajamohan et al., 1999b), it has not been shown in vivo. Many RIPs are sequestered in the cell wall or cellular storage compartments from host ribosomes. It is not known how the RIPs move from these compartments into the cytosol where they can act on either the viral nucleic acid or the host-cell translational machinery. The most probable theory is that RIPs are defense-related proteins regulated by signalling pathways in plants. It has been demonstrated that RIPs from Phytolacca insularis and barley are induced in vivo by jasmonic acid, a key signalling molecule in the expression of a number of plant defense-related proteins (Chaudhry et al., 1994; Song et al., 2000). Two type 1 RIPs present in Beta vulgaris accumulate in response to treatment of plants with salicylic acid and hydrogen peroxide (two mediators of induced acquired resistance) (Girbs et al., 1996). RIPs in Transgenic Plants The role of RIPs in plant defense and promising in vitro results of RIPs as antiviral proteins prompted exploration into their use as a source of microbial resistance in heterologous plant hosts. Transgenic plants expressing different isoforms (different gene products with the same function and similar or identical sequence) of PAP, and other RIPs including trichosanthin, dianthin, IRIP (Iris-RIP), MOD1 (modified b-32 RIP) and SNA-I' (Sambucus nigra agglutinin I') have been produced and tested for resistance to viruses and fungi (Chen et al., 2002; Desmyter et al., 2003; Hong et al., 1996; Kim et al., 2003; Krishnan et al., 2002; Lodge et al., 1993; Wang et al., 1998). Most researchers chose to transform the model plants N. benthamiana or N. tabacum and study the

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15 antiviral properties of the RIPs by inoculating the plants with TMV. PAP, MOD1 and trichosanthin have been expressed in economically important crops (such as potato and rice) to which they conferred resistance to Potato virus Y (PVY) (Lodge et al., 1993), Rhizoctonia solani (Kim et al., 2003), and Pyricularia oryzae (Yuan et al., 2002), respectively. PAP has been shown to confer resistance to a number of plant viruses including TMV, PVY, PVX, and CMV (Lodge et al., 1993); while the expression of trichosanthin resulted in complete resistance to infection by Turnip mosaic virus (Lam et al., 1996). Dianthin has proven very effective against the geminivirus, African cassava mosaic virus (Hong et al., 1996). Transgenic plants expressing PAP-II and MOD1 are resistant to the fungus, R. solani, with PAP-II also conferring resistance to Sclerotinia homoeocarpa in a turfgrass species (Wang et al., 1998; Kim et al., 2003; Dai et al., 2003). The main objective of this research was to determine the efficacy of PAP as an antiviral agent against CTV and CEVd. More specifically, the efficacy would be evaluated using an in vitro system prior to using PAP mutants to transform Citrus paradisi cv. Duncan grapefruit, which would then be challenged with CTV and CEVd by graft inoculation. The same PAP mutants would be used to transform Nicotiana benthamiana for the purpose of studying the effect of PAP in protoplasts on the replication of CTV.

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CHAPTER 2 In vitro TRANSLATION OF A Citrus tristeza virus REPLICON AND THE EFFECT OF POKEWEED ANTIVIRAL PROTEIN ON ITS TRANSLATION Introduction Citrus tristeza virus (CTV), the largest positive stranded RNA virus of plants, has properties that are intermediate between the animal Nidovirales group, which contains the family Coronaviridae and the alphavirus supergroup, which contains the Tobamoviruses. CTV resembles members of the Coronaviridae because of the similarity of the genes, gene arrangement of ORF1a and 1b, the expression strategy of the RNA-dependent RNA polymerase (RdRp), and the accumulation of double-stranded (ds) RNAs corresponding to subgenomic (sg) RNA. The relationship with the alphaviruses is based on amino acid similarity in the replicase-associated domains and on the lack of a common 5' leader on the sgRNAs (Karasev et al., 1997; Snijder and Horzinek, 1993). The CTV genome is organized into 12 open reading frames (Pappu et al., 1994), with ORF1a being expressed as a 349 kDa polyprotein and ORF1b expressed via a +1 frameshift (Cevik, 2001). The ten 3' genes are expressed via 3' co-terminal sgRNAs (Hilf et al., 1995; Karasev et al., 1997). The study of the biological properties and detailed characterization of CTV at the molecular level have been hampered by the limited host range, the lack of local lesion hosts, the fact that CTV is phloem-limited and not easily mechanically transmissible, and by the large, complex genome of this virus. A full-length infectious cDNA clone was constructed and amplified in E. coli (Satyanarayana et al., 1999). However, the large size 16

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17 of the clone impeded the ready manipulation of the construct and the study of mutants for elucidation of gene functions. As a result, a smaller, more manageable replicon designated CTV-Cla, was generated (Satyanarayana et al., 1999). This clone, retaining only the 5' and 3' UTRs, ORFs 1a and 1b, and a gene fusion between ORF11 and part of ORF2 (Figure 2-1), was able to replicate efficiently in Nicotiana benthamiana mesophyll protoplasts. The use of the infectious CTV clones has, thus far, been used to study replication and gene expression at the transcriptional level in a protoplast system. Figure 2-1. Schematic representation of the Citrus tristeza virus (CTV) genome. A) Full length CTV genome. B) CTV-Cla replicon. Shown are the two papain-like proteases (Pro), the methyltransferase (Met), Helicase (Hel), RNA dependent RNA polymerase (RdRp) and ORFs 2-11. Diagrams were adapted from Satyanarayana et al., 1999. Although the cDNA clone has been used to examine the effect of the product of the ORF11 (p23) on viral replication (Satyanarayana et al., 2002), examination of the events occurring at the translational level in protoplasts is more difficult since visualization of the viral proteins requires the use of antibodies to distinguish viral proteins from other plant proteins. Additionally, only one protein can be studied per western blot.

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18 Development of an efficient in vitro model system would allow the examination of the expression levels of viral proteins and also the effect of exogenous agents, such as other proteins, on the level of translation without the use of antibody-detection methods. Studies at the translation level have been conducted in an in vitro transcription and translation system (Cevik, 2001; Vazquez-Ortiz, 2001). However these experiments used CTV sequences (the two papain-like protease domains and the RdRp, respectively) out of the viral context. There is a possibility that additional viral sequences further upstream or downstream of the gene of interest may have an effect on expression. Thus transcription and translation of the CTV-Cla replicon (which allows for the insertion of other genes) in an in vitro translation system would facilitate the analysis of multiple viral proteins. This would circumvent the need to dually transfect protoplasts with both CTV-Cla and another transcript to examine the effect of the product of the latter transcript on replicon replication. When transfecting protoplasts with two different transcripts, it is unlikely that both transcripts will enter all the cells. This might result in the erroneous interpretation of data. The in vitro approach should facilitate the study of the effect of potential resistance/antiviral gene products on viral translation, and give an initial indication of the efficacy of these proteins without the need for plant transformation and screening of the resultant plants for resistance to CTV (a lengthy and time-consuming process for citrus). Pokeweed antiviral protein (PAP) isolated from the leaves of Phytolacca americana (pokeweed) is a 29 kDa ribosome-inactivating protein that has antiviral properties (reviewed in Nielsen et al., 2001; Tumer et al., 1999). This antiviral effect is not limited to a particular virus or virus group, and is effective against both plant and animal viruses (Chen et al., 1991; Irvin and Uckun, 1992). There is evidence that the

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19 antiviral activity is not solely dependent upon the inactivation of ribosomes (Tumer et al., 1997). In vitro experiments showed that PAP can inhibit translation by directly depurinating the RNA (Rajamohan et al., 1999a); and that although PAP preferentially depurinates capped RNA, it is still capable of inhibiting translation of uncapped viral RNAs by an, as yet, unknown mechanism (Vivanco and Tumer, 2003). The objective of this study was to express the CTV replicon, CTV-Cla, in an in vitro translation system and to test the efficacy of PAP as a potential inhibitor of the translation of this replicon. Materials and Methods Source of Viral Nucleic Acid The CTV-Cla replicon (kindly supplied by Dr. W.O. Dawson) was transformed into E. coli JM109 cells. Large-scale DNA isolation was performed using the Qiagen Midiprep kit according to the manufacturer’s instructions. In vitro Transcription and Translation of CTV-Cla The first attempt to translate the CTV replicon was done in a wheat germ extract TNT coupled in vitro transcription and translation system (Promega, Madison, WI). Different concentrations of DNA were tested in order to optimize the system. A 20 l reaction containing 10 l of wheat germ extract, 0.75 l reaction buffer that contained all the amino acids except leucine, 0.75 l SP6 RNA polymerase, 0.75 l RNAsin ribonuclease inhibitor, and 0.5 Ci/ml 3 H-leucine was incubated at 30C for 1 h. The reactions were then subjected to SDS-PAGE in 12% Tris Ready gels (Bio-Rad) at 150 V for 1.5 h. The radio-labeled proteins were detected using the method described by Bonner and Laskey (1974). Briefly, the gels were fixed in dimethyl sulfoxide (DMSO) and DMSO-2, 5-diphenyloxazole (PPO), dried under vacuum at 70C for 40 min, exposed to

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20 X-ray film overnight at -80C, and developed using a Kodak X-Omat Clinic 1 film processor. Alternatively, the transcription and translation reactions were conducted separately. The plasmid DNA was linearized with the restriction enzyme, NotI (New England Biolabs, Beverly, MA) and transcribed using the RibomaxTM large scale in vitro RNA production system (Promega, Madison, WI) according to the manufacturer’s instructions. Briefly, the transcription reaction was done in a final volume of 25 l, containing 5 l SP6 transcription buffer, 5 l of 25 mM rNTPs, 5 g DNA template, 2 l SP6 enzyme mix and nuclease-free water. The reaction was incubated at 37C for 3 h, stopped by the addition of RNAse-free DNAseI and further incubation at 37C for 15 min. Further purification of the RNA transcripts was done according to the manufacturer’s instructions. Different concentrations of the transcripts were then translated in either wheat germ extract (Promega, Madison, WI) at 25C for 2 h or the Flexi Rabbit reticulocyte lysate system (Promega, Madison, WI) at 37C for 1 h. The transcripts were either capped using the m7GpppG cap analogue (Promega, Madison, WI) or uncapped. For the wheat germ system, different concentrations of potassium acetate were tested; while for the rabbit reticulocyte system, potassium chloride and magnesium acetate concentrations were optimized. The final concentrations of potassium and magnesium used in the translation reactions were established based on the guidelines stipulated by the manufacturer. In vitro Antiviral Assay To determine the direct effect of PAP on CTV-Cla RNA, the transcripts were treated with 0 ng, 20 ng, and 100 ng of wild type (wt) PAP (Worthington, Lakewood, NJ)

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21 per 500 ng of RNA in RIP buffer (50 mM Tris, 50 mM KCl, 10 mM MgCl 2 pH 7.5) and incubated at 30C for 30 min. PAP was removed by phenol-chloroform extraction, and the translation reaction performed in the rabbit reticulocyte lysate system. RNA from Brome mosaic virus (BMV) supplied with the translation kits was used as a control. Results In vitro Translation of CTV-Cla The first attempt at translating CTV-Cla using a wheat germ-based TNT coupled transcription and translation system was unsuccessful. This could be due to the absence of specific co-factors or conditions required by the replicon for translation. Factors that might have a positive effect on translation include varying salt and magnesium concentrations as well as the presence of a capped transcript. For this reason, the transcription and translation reactions were performed separately in two different systems (plant and animal) to optimize the translation reaction. The wheat germ system allowed for optimization of the concentration of the salt, potassium acetate. The combination of 2 g of the DNA template and 53 mM potassium acetate yielded translation products (Figure 2-2). The band of approximately 28 kDa in size might be the product of the fusion of ORF11 with part of ORF2, while the faint high molecular weight band might be the polyprotein or part of the polyprotein since the translation system has an upper limit of approximately 200 kDa. The band at 48 kDa does not correspond to any expected size of products translated from ORF 1a and 1b. Due to the unexpected sizes of the protein bands in the wheat germ system, optimization in a rabbit reticulocyte system was undertaken. The rabbit reticulocyte system allowed for optimization of salt and magnesium concentrations in addition to supporting the translation of larger RNA templates. Two different RNA concentrations

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22 were translated in the absence or the presence of either 70 mM potassium chloride (KCl) or 0.25 mM magnesium acetate (Figure 2-3). Figure 2-2. Optimization of CTV-Cla replicon translation in wheat germ extract. Lane: 1, 1 g RNA with 53 mM potassium acetate; 2, 1 g RNA with 133 mM potassium acetate; 3, 2 g RNA with 53 mM with potassium acetate; 4, 2 g RNA with 133 mM potassium acetate; 5, 4 g RNA with 53 mM potassium acetate; 6, 4 g RNA with 133 mM potassium acetate. Although the standard translation reaction (Figure 2-3, lanes 1 and 4) supported translation of the CTV-Cla transcript, with the higher RNA concentration of 2 g producing more protein, the addition of KCl to 1 g RNA increased translation to the same level produced by 2 g of RNA without any additives. A strong band of approximately 56 kDa was observed in all translation reactions. This band fit the expected size of the proteases and the RdRp expressed by ORF 1a and 1b. The high molecular weight bands seen on the gel were most likely artifacts since they were not consistently observed in subsequent experiments. Due to the higher level of translation,

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23 the appearance of bands closer to the sizes of expected proteins and the reproducibility of the results, it was decided to continue using the rabbit reticulocyte system with the addition of KCl to all further translation reactions. Figure 2-3. Optimization of CTV-Cla translation in rabbit reticulocyte lysate. Lane 1, 1 g RNA; 2, 1 g RNA + 70 mM potassium chloride; 3, 1 g RNA + 0.25 mM magnesium acetate; 4, 2 g RNA; 5, 2 g RNA + 70 mM potassium chloride. RNA was transcribed from the NotI-linearized plasmid containing the CTV-Cla replicon. PAP Inhibits Translation of CTV-Cla Transcripts To determine whether PAP would act as an antiviral agent against CTV translation in vitro, capped CTV-Cla transcripts were treated with commercial wtPAP prior to translation. After incubation with CTV-Cla transcripts, PAP was removed by phenol-chloroform extraction to eliminate the possibility that any observed decrease in translation might be due to the ribosome-inactivating properties of wtPAP. BMV RNA was used as a positive control to confirm the inhibitory effect of the wtPAP preparation. SDS-PAGE analysis of the translation products of wtPAP-treated BMV RNA showed

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24 that 20 ng of wtPAP caused a visible decrease in translation (Figure 2-4 A), indicating that wtPAP had enzymatic activity. The CTV-Cla transcripts treated with 20 ng wtPAP exhibited decreased levels of translation as indicated by the decreased intensity of the major product of the approximately 56 kDa expressed from the CTV-Cla transcript (Figure 2-4). The translation of both BMV and CTV-Cla was completely inhibited by 100 ng of wt PAP (data not shown). Figure 2-4. Effect of wild type PAP on translation. A) BMV translation products B) CTV-Cla translation products. Lane 1, untreated RNA; 2, RNA treated with 20 ng PAP/500 ng RNA. All RNA samples were incubated at 30C for 30 min in RIP buffer followed by a phenol-chloroform extraction. Discussion In vitro translation has played an important role in the elucidation of requirements for viral gene expression. For example, in vitro systems have been used to investigate translational enhancement in Hibiscus chlorotic ringspot virus (Koh et al., 2002), translational frameshifting in Barley yellow dwarf virus (Di et al., 1993; Paul et al., 2001) and the mechanism of cap-independent translation in Tomato bushy stunt virus (Wu and

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25 White, 1999). In addition, in vitro systems are useful when the translation products of viral genomic or subgenomic RNAs are not known (Dinesh-Kumar et al., 1992). Schulte and Kearney (2000) used an in vitro translation system to determine the antiviral potential of a variety of antisense oligonucleotides (ASO). They were able to identify the most effective ASOs before doing more time consuming plant transformation experiments. The objective of this study was to use CTV-Cla transcribed RNA as a reliable template for in vitro translation followed by rapidly testing the efficacy of PAP as an inhibitory agent of CTV translation before proceeding with plant transformation experiments. The results showed that CTV-Cla transcripts can be translated in an in vitro rabbit reticulocyte lysate system. However, the inherent limitations of the system may have prevented the expression of the large polyprotein. Alternatively the two proteases located at the N-terminal end of the polyprotein could have processed the 349 kDa polyprotein into functional proteins of a smaller size (Vazquez-Ortiz, 2001). Using an in vitro translation assay, Hudak et al. (2000) showed that one of the mechanisms by which wtPAP was able to inhibit viral translation was by acting directly on the RNA of BMV and Potato virus X (PVX), removing adenine residues at multiple sites. Therefore, to determine whether PAP could inhibit translation of CTV-Cla RNA by acting directly on the RNA, capped CTV-Cla transcripts were treated with commercial wtPAP prior to translation. A reproducible decrease in the translation of PAP-treated RNA was observed at a concentration of 20 ng of the antiviral protein (Figure 2-4 B). At a concentration of 100 ng, wtPAP completely inhibited translation of BMV and the CTV-Cla replicon (data not shown). However, previous research has

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26 shown that wtPAP is able to almost completely inhibit the translation of 250 ng BMV RNA at a concentration of 5 ng (Hudak et al., 2000). The major difference between that result and the one from this experiment might be explained by differences in the enzymatic activity of the PAP preparation used. Based on the results obtained from the translation of BMV RNA and the possibility that the PAP preparation did not have optimal enzymatic activity, one could extrapolate that a lower concentration of PAP might also have an inhibitory effect on translation. Since the viral RNA will be exposed to the intracellular environment in plants, the in vitro translation result demonstrating the direct effect of PAP on the RNA suggests that transgenic citrus correctly processing and expressing PAP may exhibit reduced levels of CTV.

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CHAPTER 3 TRANSFORMATION OF Citrus paradisi cv Duncan GRAPEFRUIT WITH POKEWEED ANTIVIRAL PROTEIN Introduction Diseases caused by viroids and viruses have had a major impact on citrus production world-wide. Viroids are the smallest known plant pathogens. They consist of unencapsidated, circular, single-stranded RNA molecules that exist as highly base paired rod-like structures. Viroids found in citrus plants can be classified into the following classes: Citrus exocortis viroid (CEVd, 370-375 nucleotides (nt)), Citrus bent leaf viroid (CBLVd, 315-329 nt; formerly called CVd-I), Hop stunt viroid (HSVd, 295-303 nt; formerly called CVd-II), Citrus viroid III (CVd-III, 291-297 nt), Citrus viroid IV (CVd-IV, 284-286 nt) and Citrus viroid OS (CVd-OS, 329-/331 nt) (Duran-Vila et al., 2000; Ito et al., 2000, 2002). In the field, CEVd causes severe stunting and bark scaling of citrus trees on Poncirus trifoliata rootstock. Less severe symptoms occur on Citrus sinensis x P. trifoliata (citrange) and Citrus limonia (Rangpur lime) and only mild symptoms are seen on Swingle citrumelo (Lee et al., 2003). The severe stunting on trifoliate rootstock leads to reduced canopy size and ultimately a reduction in yield. CEVd is spread primarily via infected budwood and contaminated cutting tools and equipment. Resistance to CEVd and potato spindle tuber viroid (PSTVd) has previously been achieved by transforming plants with ribozymes, which are RNA molecules that have enzymatic activity (Atkins et al., 1995; Yang et al., 1997). Sano et al. (1997) and Ishida et 27

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28 al. (2002) produced potato and chrysanthemum plants resistant to PSTVd and chrysanthemum stunt viroid, respectively, by expressing a double-stranded RNA–specific ribonuclease, pacI, from Schizosaccharomyces pombe. Thus transformation of plants with proteins or enzymes that act directly on RNA may provide protection against viroid infection. Citrus tristeza virus (CTV), a member of the genus Closterovirus, is one of the most economically important virus diseases of citrus and has resulted in widespread losses in many citrus-growing regions. The virus is transmitted by six aphid vectors, with Toxoptera citricida being the most efficient vector, as well as by propagation of infected buds (Bar-Joseph et al., 1989). CTV isolates differ in the symptoms they cause depending on the scion/rootstock combination. Certain isolates result in decline and death of citrus species on sour orange rootstock; stem pitting of scions which reduces tree vigour, fruit yield and quality; and a syndrome called seedling yellows which is expressed as stunting and chlorosis of susceptible varieties such as lemon and grapefruit. CTV isolates exist as complex populations consisting of a number of different CTV genotypes, with large sequence variation among the genotypes. Thus CTV isolates are populations of CTV genotypes, in which one genotype may predominate (Aylln et al., 1999; Hilf et al., 1999). A number of strategies have been developed to manage the disease. These strategies include eradication programs, quarantine and budwood certification to prevent the introduction of CTV into a country, the use of CTV tolerant rootstocks, and mild strain cross protection (reviewed by Ferguson and Garnsey, 1993). A source of genetic resistance to CTV has been found in Poncirus trifoliata. This resistance is known to be controlled by a single dominant gene, Ctv (Yoshida et al.,

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29 1996). Although the introgression of the Ctv gene into rootstock species is possible via sexual hybridization, commercially acceptable scions have not yet been produced as a result of the concomitant introgression of undesirable fruit characteristics (Ferguson and Garnsey, 1993). Currently the mechanism of action for Ctv is not known, since protoplasts of virus resistant plants are still able to maintain viral replication (Albiach-Marti et al., 1999). However, cloning the Ctv gene and using it to transform commercially important citrus species should be a successful strategy to develop genetic resistance to CTV. Genetic transformation of woody fruit plants is a promising alternative to conventional breeding practices for the introduction of new traits. This technology circumvents the limitations imposed on breeding by the heterozygosity, long juvenile periods and auto-incompatibility of the plants. With the development of an efficient Agrobacterium-mediated citrus transformation protocol (Luth and Moore, 1999), it is now possible to use molecular methods not only to engineer resistance to CTV, but also to introduce other commercially favorable traits. For example, citrus was successfully transformed with the Arabidopsis thaliana genes LEAFY and APETALA1, both of which reduced the juvenile period of the resultant plants (Pea et al., 2001). Thus far attempts to engineer resistance to CTV has centered on the pathogen-derived resistance approach (PDR); transforming plants with the coat protein gene of various CTV isolates as well as other CTV genomic sequences, (Dominguez et al., 2000, 2002; Febres et al., 2003; Ghorbel et al., 2001; Gutierrez, 1997). Given the complexity of CTV populations, it is possible that a PDR approach may not produce the expected “CTV resistance”.

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30 Ribosome-inactivating proteins (RIPs) with additional antiviral or antifungal properties have been isolated from many different plant species and are enzymes that inhibit protein synthesis in many prokaryotic and eukaryotic cells. This inhibition is due to N-glycosidation activity, which causes the removal of a specific adenine residue from the -sarcin loop, a region conserved in the large rRNAs of both prokaryotes and eukaryotes (Endo et al., 1987; Endo and Tsurugi, 1987). Depurination of the -sarcin loop interferes with both the elongation factor EF-Tu/EF-1-dependent binding of aminoacyl-tRNA and the GTP-dependent binding of EF-G/EF-2 to ribosomes, arresting protein synthesis at the translocation step (Montanaro et al., 1975; Osborne and Hartley, 1990). RIPs can be divided into three classes based on their physical properties. Type 1 RIPs, such as pokeweed antiviral protein (PAP; from Phytolacca americana) and trichosanthin (from Trichosanthes kirilowii) consist of a single polypeptide chain. Type 2 RIPs, such as ricin (from Ricinus communis), have a type 1-like catalytic subunit (A chain) linked to a galactose binding lectin (B chain) that facilitates adhesion to and penetration of cell membranes (Batelli and Stirpe, 1995). As a result, type 2 RIPs are much more toxic to living cells. Type 3 RIPs, found in maize and barley, are synthesized as inactive precursors which require proteolytic cleavage for activation (Chaudhry et al., 1994; Walsh et al., 1991). PAP is a 29-kDa protein produced by Phytolacca americana (pokeweed) and has been shown to exhibit strong antiviral activity against a broad spectrum of plant and animal viruses, including Southern bean mosaic virus, Potato virus X, Cucumber mosaic virus, Tobacco mosaic virus, influenza virus (Tomlinson et al., 1974), poliovirus (Ussery and Hardesty, 1977), herpes simplex virus (Aron and Irvin, 1980) and HIV (Zarling et al.,

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31 1990). A number of PAP mutants have been isolated and tested for toxicity to ribosomes and retention of antiviral properties (Table 3-1; Hur et al. 1995). The most effective mutants with respect to reduced toxicity and inhibition of viral infection are a C-terminal deletion mutant, due to a nonsense mutation (Trp237stop), and an N-terminal mutant (Gly75-Asp). The reason for their efficacy is thought to be due to the fact that the C-terminal deletion removes a region responsible for PAP toxicity to ribosomes, while the N-terminal mutation has been shown to adversely affect the binding of PAP to ribosomes (Zoubenko et al. 2000). Other mutants which have been used include a PAP variant (PAPv) in which a two amino acid change, Lys20-Arg and Trp49-His, causes a slight reduction in toxicity to ribosomes while maintaining the wild type ability to inhibit viral infection, and an active site mutant (PAPx) in which the mutation, Gly176-Val abolished enzymatic activity. Table 3-1. Expected properties of PAP and PAP mutants. Information presented in this table was obtained from Lodge et al. (1993), Tumer et al., (1993) and Zoubenko et al., (2000). Construct Toxicity to ribosomes Translation inhibition Pathogen resistance Wild type PAP Yes Yes Yes PAPv Yes Yes Yes PAPn No Yes Yes PAPc No Yes Yes PAPx No No No The broad-spectrum virus resistance displayed by wild type PAP and its mutants makes it an ideal candidate for the development of virus-resistant plants. To date, PAP has been used to transform Nicotiana benthamiana, N. tabacum cv. Samsun, Solanum tuberosum cv. Russet Burbank and Agrostis stolonifera L. (creeping bentgrass), and the plants have been evaluated for resistance to viruses as well as fungi (Dai et al., 2003; Lodge et al., 1993; Tumer et al., 1997; Zoubenko et al., 2000). Although the mechanism

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32 mediating the antiviral activity of PAP is still under investigation, a number of insights have been gained. PAP has been shown to inhibit translation by directly depurinating viral RNA at multiple sites (Rajamohan et al., 1999a), preferentially depurinating capped RNAs (Hudak et al., 2000; Vivanco and Tumer, 2003), and inhibiting +1 frameshifting in the yeast retrotransposon, TY1 (Tumer et al., 1998). Since CTV has an RNA genome that most probably has a 5' guanosine cap and a RdRp that is expressed via a +1 frameshift, it presents an ideal subject for translational inhibition by PAP in a non-strain specific manner. In this study, four PAP mutants (PAPv, PAPc, PAPn and PAPx), the properties of which are summarized in Table 3-1, were used to transform Citrus paradisi cv. Duncan grapefruit by Agrobacterium tumefaciens-mediated transfer. The resultant transgenic plants were characterized by molecular methods and evaluated for resistance to CTV and CEVd by graft challenge inoculation. Materials and Methods PAP Gene Constructs and Plasmid Expression Vectors All PAP constructs were derived from the PAPv sequence which contains two mutations, Lys20-Arg and Trp49-His. These mutations make the protein slightly less toxic to ribosomes than the wild type (wt) PAP (Tumer et al., 1997). Using a series of oligonucleotide primers (Table 3-2), two mutants, PAPn containing a point mutation that changed residue Gly75 to Ala, and PAPx with Glu176 and Arg170 changed to Ala, were constructed by overlap PCR, while the C-terminal deletion mutant was constructed by changing Trp237 to a translation termination codon, thereby truncating the PAP coding region. The PCR products were cloned into pGEM-T (Promega, Madison, WI) and sequenced to verify the presence of the introduced mutations. The PAP insert was

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33 removed from pGEM-T by digestion with restriction enzymes ApaI and NotI, flanking the PAP coding sequence, and subcloned between the Figwort mosaic virus (FMV) promoter and the Cauliflower mosaic virus (CaMV) 35S termination sequence contained in the pUC118 vector provided by Dr V. J. Febres (Figure 3-1). The PAP expression cassettes containing the PAPv, PAPn, PAPx and PAPc genes were released from pUC118 by digestion with PstI and ligated into the PstI-digested binary expression vector, pCambia2202 (provided by Dr V. J. Febres) which has the kanamycin resistance gene, nptII, as the selection marker and the green fluorescent protein (GFP) as the reporter gene (Figure 3-1). The binary vector containing the PAP constructs were introduced into Agrobacterium tumefaciens strain AGL1 by the cold shock transformation method (Birnboim and Doly, 1979). The bacteria were incubated on LB-agar plates supplemented with 50 g/ml carbenicillin and 100 g/ml chloramphenicol, at 28C for two days to screen for transformants. Table 3-2. Sequences of oligonucleotide primers used for amplification and mutagenesis of the PAP gene Primer Sequence Orientation CN442 GGTATCAGcGGCAGC t gcATTCAAGTAC Sense CN443 GTACTTGAATgc a GCTGCCgCTGATACC Antisense CN444 ATTAGGGCCCGGGAAGATGAAGTCAATGCTTGTG Sense CN445 AATTGCGGCCGCTCAGAATCCTTCAAATAGATC Antisense CN446 AATTGCGGCCGCTCACTTGGCACC Antisense CN447 GTATGTGATGGATTATTCTG Sense CN448 CAGAATAATCCATCACATAC Antisense Lower case letters indicate the mutated nucleotides Citrus Transformation and Regeneration An Agrobacterium-mediated transformation protocol previously developed for Carrizo citrange and Swingle citrumelo (Moore et al. 1992) and subsequently modified for Citrus paradisi cv. Duncan (Luth and Moore, 1999) was followed.

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34 Figure 3-1. Cloning strategy of the PAP constructs for plant transformation. The ApaI/NotI-digested gene fragments were ligated into ApaI/NotI-digested pUC118 between the FMV promoter and CaMV 35 terminator. The resulting expression cassettes were cloned into the PstI restriction site of the binary vector pCambia2202. The black lines on the PAP constructs indicate positions of mutations. All constructs had the mutations Lys20-Arg and Trp49-His. Additional mutations were Gly75-Ala for PAPn, Glu176-Ala and Arg170-Ala for PAPx , and Trp237-Stop for PAPc.

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35 Seed germination Seeds were extracted from mature fruit of Citrus paradisi cv. Duncan grapefruit. The seedcoats were removed from seeds, and the seeds were then sterilized first in 70% ethanol for 2 min, then in a 0.525% sodium hypochlorite solution with 0.05% Tween 20, followed by 3 rinses of 2 min each in sterile water. One or two seeds were placed into test tubes containing half strength MS medium (2.15 g/L MS salts, 50 mg/L myo-inositol, FM stock, 15 g/L sucrose) and 7 g/L agar. The seeds were germinated in the dark for approximately six weeks. Transformation of epicotyl segments Agrobacterium tumefaciens strain AGL1 containing pCambia2202 with the PAPv, PAPn, PAPx or PAPc construct was grown overnight at 28C, in YEP medium (10 g/L bactopeptone, 10 g/L yeast extract, 5 g/L sodium chloride) supplemented with the appropriate antibiotics, to an OD 620nm between 0.4 and 1.0. The cultures were centrifuged at 5000 rpm in a Beckman GSA rotor for 5 min and resuspended to a final concentration of 5x10 8 cfu in MS medium supplemented with 100 M acetosyringone. The epicotyl portions of the etiolated seedlings were cut into 1 cm 2 segments and incubated in the Agrobacterium solution for 1-2 min. The segments were then transferred to co-cultivation medium (MS medium, 7 g/L agar and 100 M acetosyringone) and kept in the dark at room temperature for 2-3 days (Figure 3-2 A and B). Selection and regeneration of plantlets Following co-cultivation, the epicotyl segments were placed onto shoot-inducing medium (MS medium, 7 g/L agar and 0.5 mg/L benzylaminopurine) supplemented with 75 mg/L kanamycin to select for transformed shoots and 500 mg/L claforan to prevent further growth of Agrobacterium (Figure 3-2 C and D).

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36 Figure 3-2. Agrobacterium-mediated transformation of etiolated Citrus paradisi cv. Duncan grapefruit and regeneration of plants. A) Inoculation of stem segments with Agrobacterium strain AGL1 containing pCambia2202 with the PAP construct. B) Co-cultivation. C-D) Regeneration of shoots on selective medium. E) Shoots on root-inducing medium. F) Transgenic plant transferred to soil in the greenhouse.

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37 The plates were incubated at 28C with a 16 h photoperiod provided by cool-white fluorescent lights. The segments were transferred to fresh medium every 4 weeks. Shoots were transferred directly to root-inducing medium (MS medium, 8 g/L agar, 100 mg/L myo-inositol, 0.5 mg/L naphthalene acetic acid), where they remained until they had produced roots (Figure 3-2 E). Upon root production, the plantlets were transferred to covered containers with sterile soil and half strength MS medium and kept at 28C with a 16 h photoperiod until they outgrew the containers. The plants were acclimated by placing them in pots covered by clear plastic bags in a humid growth room with a 16 h photoperiod and a temperature of 28C. After 1-2 weeks, the plastic bags were slashed and after another 1-2 weeks, the bags were completely removed, whereupon the surviving plants were transferred to the greenhouse (Figure 3-2 F). Analysis of Transgenic Plants Fluorescent microscopy The regenerated shoots were examined for GFP expression using a dissecting microscope (Zeiss) equipped with a fluorescent light source with a 515 nm long pass emission filter transmitting red and green light and a 450-490 nm excitation filter. The fluorescent images were captured with a 35 mm camera attached to the microscope. Polymerase chain reaction (PCR) analysis All shoots were tested for the presence of the PAP gene by PCR using gene-specific primers. Some of the shoots were also analysed for the presence of the GFP gene using the gene-specific primers CN462 5'-ATGGTGAGCAAGGGCGAGGAG-3' and CN463 5'-CTTGTACAGCTCGTCCATGCC-3'. DNA was extracted from the plants using a modification of the protocol by Oliveira et al. (2000). Briefly, 0.1 g of tissue was ground in liquid nitrogen. The tissue was resuspended in 300 l of extraction buffer

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38 (100 mM Tris-HCl pH 8.0, 50 mM EDTA pH 8.0, 500 mM NaCl, 140 mM mercaptoethanol, 80 l of 10% SDS), incubated at 65C for 10 min, after which, 100 l of potassium acetate was added and the samples further incubated on ice for 20 min. The samples were centrifuged at 12000 x g for 30 min at 4C. The supernatant was then transferred to a new tube and an equal volume of isopropanol added. The DNA was precipitated by centrifugation at 12000 x g for 20 min at 4C. The DNA pellet was washed with 80% ethanol, dried and resuspended in sterile water containing 2 g/l RNAse. PCR was carried out using primers CN444 and CN446 or CN444 and CN445 (Table 3-1) in a Biometra thermocycler using a profile of 94C for 2 min initial denaturation, 30 cycles of denaturation at 94C for 30 sec, primer annealing at 55C for 45 sec, primer extension at 72C for 45 sec and a final primer extension step of 72C for 5 min. The PCR products were analysed by electrophoresis in 1% agarose gels in TAE buffer. Southern hybridization For Southern hybridization 10 g of total genomic DNA was isolated from transgenic plants and non-transformed control plants using a modification of the protocol by Oliveira et al. (2000). The DNA was digested with BglII (New England Biolabs, Beverly, MA). After agarose gel electrophoresis, the DNA was transferred to nylon membrane (Hybond N+, Fisher Scientific) by capillary action overnight (Sambrook et al. 1989). Using the gene specific primers CN444 and CN446, a digoxigenin (DIG) -labeled probe was produced by PCR amplification according to the manufacturer’s instructions (Roche, Indianapolis, IN). The DIG-labelled probe was denatured and used for a 16 hour hybridisation after 2-4 hours of prehybridisation in DIG Easy Hyb Buffer (Roche). Following hybridization, the membrane was washed twice for 5 min in 2x SSC + 0.1%

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39 SDS at room temperature, and twice for 15 min in 0.5x SSC + 0.1% SDS at 65C. The blot was exposed to X-Ray film and developed using a Kodak X-Omat Clinic 1 film processor. Reverse-transcription (RT) PCR PAP gene expression at the transcriptional level was analysed in the transgenic plants by RT-PCR. Total RNA was isolated from the plants with TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. Prior to RT-PCR, the RNA was treated with DNAse I (Promega, Madison, WI) to eliminate any DNA contaminants, and then phenol-chloroform cleaned to remove the DNAse I. cDNA was prepared using 5 g of RNA, the reverse primer CN446, and MMLV reverse transcriptase (Promega). RNA isolated from a non-transgenic plant was used as a negative control in the RT-PCR reaction. The parameters for the RT reaction were: 1 h at 42C and 15 min at 70C. One tenth of the volume of the RT reaction was used for PCR and the products were analysed on a 1% agarose gel in TAE buffer. Western blot analysis To determine the expression levels of PAP in the transgenic plants, 200 mg of tissue was homogenized in an equal volume of phosphate buffered saline (PBS, 137 mM NaCl, 2.7 mM KCl, 10 mM Na 2 HPO 4 , 2 mM KH 2 PO 4 pH 7.4). Total protein concentration was determined by the Bradford Assay (BioRad, Hercules, CA). Aliquots of the soluble plant extracts containing 100 g total protein were mixed with equal volumes of dissociation buffer (140 mM SDS, 160 mM Tris-HCl pH 7.8, 1% v/v glycerol, 142 mM -mercaptoethanol), boiled for 2 min and separated on a precast 12% polyacrylamide Tris-HCl gel (BioRad). Proteins were transferred to nitrocellulose membrane using a BioRad semi-dry horizontal electrotransfer apparatus according to the

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40 manufacturer’s instructions.Colorimetric immunodetection of the protein was carried out using a 1:500 dilution of 0.5 mg/mL anti-PAP-IgG kindly supplied by Dr Maria Kanieskowski (Monsanto) and the chromogenic substrates -nitro blue tetrazolium (NBT) and 5-bromo-4-chloro-3-indolyl phosphate p-toluidine (BCIP). Grafting and Challenge of Transgenic Plants with CTV Individual transgenic lines were grafted onto Swingle citrumelo rootstock. For challenge with CTV, eight to twenty-eight plants from each replicated line were graft inoculated with the severe strain T66 sub-isolate E (Tsai et al., 2000). Two and four months after inoculation, CTV-inoculated plants on which the grafts had survived were analyzed for infection by direct antibody sandwich indirect-ELISA (DASI-ELISA) (Tsai et al., 2000) using the antibodies, CREC1052 and G604 (provided by R. F. Lee). Plates were coated with a 1:5000 dilution of CREC1052, followed by the addition of 10 mg/100 l of virus-infected tissue, and then a 1:20,000 dilution of G604. Each antibody incubation step was carried out overnight at 4C and was separated from the next step by vigorous washing with water and phosphate-buffered saline supplemented with 0.05% Tween 20. The results were analysed using a BioRad Model 680 ELISA plate reader. The mean absorbance values of the different transgenic citrus lines were compared using the 1-way analysis of variance with Fisher’s Protected Least Significant Difference test. Statistical analysis was done using the SPSS version 8.0 software (Chicago, Illinois). Challenge of Transgenic Plants with Citrus exocortis viroid (CEVd) Ten plants from the transgenic lines, N3, N11, N25, N63 and N71, were challenged with CEVd by graft inoculation. N9 was omitted from the experiment due to a shortage of replicated plants. After one month, RNA was extracted from the viroid-inoculated plants. Briefly, 0.2 g of tissue was ground in liquid nitrogen. Four hundred microliters of

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41 STE (0.01 M Tris-HCl pH8.0, 0.1 M NaCl, 0.01 M EDTA) and phenol, chloroform-isoamyl alcohol (24:1), and 91.4 l of 10% SDS was added to each sample which was briefly vortexed, shaken at room temperature for 10 min and centrifuged at maximum speed at 4C. The supernatant was transferred to a new tube to which 0.02 g of CF-11 powder and ethanol (final concentration of 35%) were added. The samples were shaken at 4C for 30 min, centrifuged and the supernatant discarded. The resultant pellet was washed four times with 1x STE + 35% ethanol. The RNA was precipitated at -20C with 0.1 volume of 3 M sodium acetate pH 5.2 and 2.5 volumes of 95% ethanol. The RNA pellets were resuspended in 20 l of RNAse-free water. Five microlitres of RNA was used in RT reactions with primers CEV D-5 5'-ACGAGCTCCTGTTTCTCCGCTG-3' and CEV D-7 5'CCGGGCGAGGGTGAAAGCCC-3' (Sieburth et al. 2002), and MMLV reverse transcriptase (Invitrogen, Carlsbad, CA). The following parameters were used for the RT reaction: 42C for 15 min, 99C for 5 min and 5C for 5 min. One tenth of the volume of the RT reaction was used for PCR with primers CEV D-5 and CEV D-7. The PCR parameters were as follows: 92C for 5 min, and 30 cycles of 92C for 30 sec, 55C for 45 sec and 72C for 45 sec, with a final extension step at 72C for 3 min. The products were analyzed on a 2% agarose gel. To determine whether there was any difference in the level of viroid in the plants, 1 l of a 1:10, 1:100 and 1:1000 dilution of each RNA sample was spotted onto a Hybond+ membrane, and the procedure for Northern blotting as described in the Roche hybridization manual was followed. The DIG-labeled probe used for hybridization was synthesized by PCR according to the manufacturer’s instructions (Roche) using the primers CEV D-5 and CEV D-7.

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42 Results Transformation and Regeneration For the transformation experiment a total of 10,850 epicotyl segments were used, of which only 3% produced shoots (Table 3-3). Once the regenerated shoots had been transferred to root-inducing medium, they were examined for GFP expression. Only 1.44% of the shoots from the PAPc transformation experiment expressed GFP (Figure 3-3), and this expression was not uniform throughout the shoots. The percentage of PAPn and PAPx-transformed shoots expressing GFP was slightly higher, with two PAPn and one PAPx seedling expressing GPF in all tissues (Table 3-3). Since the process for visualization of GFP expression in citrus tissue was not yet optimized, all shoots were also tested for the presence of the PAP and GFP genes by PCR (Figure 3-4). It was found that there was a comparatively good association between GFP expression and the presence of the GFP transgene. PCR analysis for the presence of the PAP gene in PAPc transformants showed that 9.4% of the regenerated shoots carried the transgene as opposed to 1.44%, which had both PAP and GFP genes (Table 3-3). Shoots that produced roots were transferred from the growth chamber to a growth room with a temperature of 28C and light cycle of 16 h light followed by 8 h of darkness. Once the plants had been acclimatized and transferred to the greenhouse, they were periodically screened for the presence of the PAP transgene by PCR. Results showed that all of the PAPc plants that had initially tested positive for the PAP gene were negative. None of the PAPx and PAPv plants survived after being transferred to soil. Phenotypically, the PAPn plants were indistinguishable from the non-transformants. The PAPc-transformed plants did not exhibit any abnormality except that they grew more slowly than the non-transformed plants (Figure 3-5 A). The PAPv

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43 PCR-positive plants that had been transferred to soil exhibited a severely stunted phenotype (Figure 3-5 B) and did not survive. Figure 3-3. Analysis of GFP expression in citrus shoots regenerated from epicotyl segments transformed with pCambia2202-PAPc and -PAPn. A-C) Transgenic shoots expressing GFP. D) Non-transgenic plant exhibiting auto-fluorescence.

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44 Figure 3-4. PCR analysis of potentially transgenic shoots containing the PAPn transgene. The names of the plants are indicated above the lanes. A) PCR amplification of the PAPn gene using the primers CN444 and CN445. B) PCR amplification of the GFP gene using the primers CN462 and CN463. N14, N15, N17, N18, N19, N20 and N21 were negative for GFP. The plasmid used as a positive control was pCambia2202 containing the PAPn gene.

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Table 3-3. Summary of results for the transformation of Citrus paradisi cv. Duncan grapefruit with pokeweed protein (PAP) antiviral constructs. Construct No. Segments used in transformation experiment No. Segments producing shoots Total no. shoots regenerated No. shoots expressing GFP No. PCR Positive shoots PAP GFP % shoots PAP and GFP positive No. Transgenic survivors in soil PAPc 5000 120 (2.40%) 138 2 13 2 1.44 0 PAPn 4400 196 (4.45%) 215 17 17 22 7.90 6 PAPx 850 11 (1.29%) 14 1 2 1 7.14 0 PAP 600 6 (1.00%) 6 0 2 0 0.00 0 Total 10,850 333 373 20 32 25 6 45

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46 Southern Blot Analysis and RT-PCR of Transgenic Plants Initial information on transgene integration was provided by the PCR results (Table 3-3 and Figure 3-4). However, information on the number of copies of the transgene can only be provided by Southern blot analysis. Nine surviving plants that were PCR-positive for the PAPn gene were analyzed for stable integration of the transgene and its copy number by Southern blot analysis. The plant genomic DNA was digested with BglII, which does not have a cleavage site within the transgene sequence. There was no hybridization of the PAP-derived probe to the non-transformed control (Figure 3-6, lane 1). All the plants were found to be stable transformants resulting from independent integration events and having one to four copies of the PAP sequence present, with the totally GFP-expressing plant, N101, having just one copy of the gene. The four plants, N8, N10, N16 and N101 died. The remaining plants were analyzed for transcript production by RT-PCR. Traditionally, transgene transcripts are analyzed by Northern blotting. However, RT-PCR is increasingly being used as an alternative method, especially when only a qualitative result is sought. To eliminate the possibility that PCR positives might be due to the amplification of contaminating genomic DNA, the RNA was DNAse-treated prior to the RT reaction, and this RNA was then also used as a negative control (No-RT reaction) in the PCR amplification of the PAP gene. As seen in Figure 3-7 no amplification was obtained for the non-transformed control and the No-RT controls. This confirmed that the RT-PCR amplified products observed for N3, N9, N11, N63 and N71 were the result of amplification of DNA complementary to PAP mRNA that had been transcribed in these plants. Plant N25, which has the PAP gene integrated into its genome, did not yield an RT-PCR product, suggesting that the gene had been silenced.

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47 A B Figure 3-5. Phenotypes of plants transformed with the PAPc and PAPv constructs. A) PAPc transformants are on the right and non-transformed plants are on the left. B) A non transformed plant is on the left and a plant transformed with PAPv is on the right.

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48 Figure 3-6. Southern analysis to determine transgene copy number in transgenic grapefruit plants transformed with PAPn. A) Lane 1, non-transformed negative control; 2, N3; 3, N63; 4, N101; 5, plasmid positive control; 6, N10; 7, N16; 8, N8; 9, N11; 10, N9. B) Lane 1, N25; 2, N71; 3, plasmid positive control. Protein Expression Analysis The five plants for which PAP expression had been demonstrated at the level of transcription were further analysed by western blotting for expression of the recombinant protein. Faint bands corresponding to the 29 kDa protein obtained for the wild type positive control were detected for the plants N3, N9, N11, N63, and an extremely faint band was observed for N71, indicating that the protein was being expressed in the transgenic plants, albeit at a very low level (Figure 3-8).

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49 Figure 3-7. RT-PCR analysis of transgenic citrus transformed with PAPn to determine gene expression at the level of transcription. Lane 1, lambda-HindIII; 2, plasmid control; 3, no nucleic acid control; 4, non-transgenic-RT; 5, non-transgenic no-RT; 6, N3-RT; 7, N3 no-RT; 8, N9-RT; 9, N9 no-RT; 10, N11-RT; 11, N11 no-RT; 12, N25-RT; 13, N25 no-RT; 14, N63-RT; 15, N63 no-RT; 16, N71-RT; 17, N71 no-RT. Total RNA was isolated from the plants and cDNA was prepared using 5 g of RNA. Figure 3-8. Western blot analysis of total soluble proteins from transgenic citrus to determine the expression the PAPn transgene. Lane 1, molecular weight marker; 2, 250 ng purified commercial PAP; 3, non-transgenic control; 4, N3; 5, N9; 6, N11; 7, N63; 8, N71. Virus Challenge of Transgenic Plants In vivo antiviral activity of the five transgenic lines expressing PAP, as well as line N25 which contained the PAP transgene but did not express it at detectable levels, was

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50 tested by graft inoculating the multiplied lines with the severe CTV strain, T66 sub-isolate E. Plant samples were tested for viral antigen levels by ELISA two and four months after inoculation. Absorbance values twice that of the healthy control were scored as positive reactions for the presence of CTV. ELISA results after two months showed that almost all of the multiplied plants within each of the five PAP-expressing lines as well as line N25 were positive for the virus as determined by comparison of antigen levels in these lines with that of the non-infected control (mean = 0.03125). Absorbance values (A 405 nm) ranged from 0.0335-1.3235 for N3, 0.0445-1.3915 for N9, 0.0165-0.585 for N25, 0-1.541 for N63 and 0.002-2.165 for N71. Despite scoring an overall positive ELISA reaction for the presence of CTV, approximately 50% of the replicates of the lines N11, N25, and N71 and 25% of those in lines N3, N9, and N63 tested negative for CTV. However, statistical analysis of the absorbance data showed that the viral antigen levels of the transgenic plants were not significantly different from that of the non-transgenic control.lines. After four months, CTV antigen levels decreased in comparison to the antigen levels after two months in lines N3 (87.4%), N9 (105.1%), N11 (115.4%) and N63 (22.3%). An increase in antigen levels was observed for lines N71 (2.4%) and N25 (54.8%) in comparison to the level of CTV antigen present in the plants after two months. Despite the increased antigen level, line N25 maintained one of the lowest levels of CTV after four months, when compared to the non-transgenic control. The mean absorbance values for the transgenic plants were lower than that of the non-transgenic control. The line N9 showed the lowest CTV antigen level as compared to the control (344.1%), followed by N11 (270.9%), N25 (251.6%), N63 (142.8%), N3 (90.0%) and N71 (63.0%).

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51 Statistical analysis showed that the mean absorbance values obtained after four months were significantly lower than that of the non-transgenic control (Table 3-4). Table 3-4. CTV antigen levels four months post-inoculation.in transgenic Citrus paradisi plants expressing PAPn Plant Line Mean Absorbance at 405 nm Non-transgenic control 0.675 a N71 0.414 b N3 0.355 b c N63 0.278 b c d N25 0.192 c d N11 0.182 d N9 0.152 d Mean absorbance values of the different transgenic citrus lines were compared using Fisher’s Protected Least Significant Difference test. Means with the same letter are not significantly different at P=0.05. Eight to twenty-eight plants per transgenic citrus line were graft-inoculated with CTV strain T66 sub-isolate E CTV antigen levels were determined by DASI-ELISA four months post-inoculation. Viroid Challenge of Transgenic Plants Plants were assayed for the presence of viroid RNA by RT-PCR one month after inoculation. The plants from transgenic lines N3, N11, N24, N63 and N71 tested positive for the presence of CEVd (Figure 3-9). To determine whether there were differences in the levels of viroid present in the transgenic plants versus the controls, a Northern dot blot was done using three different 10-fold dilutions of each RNA sample. The transgenic and control plants appeared to have similar levels of viroid RNA, indicating that PAPn had no effect on viroid replication (data not shown). Discussion The broad-spectrum virus resistance displayed by wild type PAP and its mutants makes it an ideal candidate for the development of virus-resistant plants. PAP-expressing transgenic plants have been obtained for N. benthamiana, N. tabacum cv. Samsun, Solanum tuberosum cv. Russet Burbank and Agrostis stolonifera L. (creeping bentgrass).

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52 Figure 3-9. RT-PCR analysis of representative viroid-infected PAPn-transgenic plants. A) Lane 1, 100 bp marker; 2, no DNA control; 3, healthy control; 4, positive control; Lanes 6, 9, 11, line N25; 7, 15, line N3; 8, 13, 16, line N71; 10, 14. line N63. B) Lane 1, 100 bp marker; 2, line N63; 3, 4, line N11; 5-11, infected non-transgenic controls. The plants were graft-inoculated with CEVd and assayed for the presence of the viroid RNA one month later. These plants have been evaluated for resistance to RNA viruses such as TMV, CMV, PVX and PVY as well as the fungi Rhizoctonia solani and Sclerotinia homeocarpa (Dai et al., 2003; Lodge et al., 1993; Tumer et al., 1997; Zoubenko et al., 2000). The objective of this research was to transform Duncan grapefruit with PAP mutants and

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53 determine the efficacy of these mutants as antiviral agents against CTV and CEVd. Both pathogens have RNA-based genomes, albeit with different structures. The percentage of shoots produced in the transformation experiment as a whole was very low at 3%. This value is considerably lower than the 23-29% obtained in C. paradisi transformation experiments by Rosales (2001), Cevik (2001), and Luth and Moore (1999) using the same protocol. Lower percentages of regeneration, ranging between 4% and 13%, were obtained by Febres et al. (2003). Collectively very few transformed shoots were obtained. The only surviving transformants contained the PAPn construct. PAP mutants, PAPn and PAPc, reportedly retain their antiviral activity without the toxic rRNA depurination activity, while PAPv retains both properties and PAPx is an inactive form of the protein (Tumer et al., 1997; Zoubenko et al., 2000). Therefore, one would expect that only the PAPv construct would produce a low number of transformants. Tumer et al. (1997) and Zoubenko et al. (2000) were able to obtain transformation frequencies of approximately 13% in N. tabacum transformed with the non-toxic forms of PAP. Very few transformed tobacco plants and only one transformed potato plant containing the PAPv gene were obtained, and only at low expression levels of PAPv did the plants resemble non-transformed plants (Lodge et al., 1993). Transformation of creeping bentgrass with PAPc produced very few transgenic plants, which ultimately did not exhibit the same level of pathogen resistance as their N. tabacum counterparts (Dai et al., 2003). Therefore, it is possible that the nature of the gene, combined with the inherent problems of transforming a heterologous host such as citrus, may have had an impact on the number of transgenic plants produced.

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54 PCR analysis of the transgenic plants revealed that not all plants had both PAP and GFP genes (Table 3-3). Most of the plants contained only the PAP gene. This discrepancy may be due to the partial integration of T-DNA. It is known that transfer proceeds from the right border of the T-DNA to the left border (reviewed by Gelvin, 2003). Thus one would expect a higher proportion of plants to be positive for the reporter gene, which is closest to the right border. However, transfer can occasionally be initiated from the left border, and the efficiency of transfer depends upon the binary vector and Agrobacterium strain used. All of the PAPc shoots that had been PCR positive for the transgene appeared to eventually have lost the gene. This may be due to the fact that these plants had been chimeras, and new tissue growth did not contain the gene of interest. Alternatively, the gene may have been deleterious to the plants, and chromosomal rearrangements may have led to the loss of the PAP gene. Before evaluating transgenic plants for their performance in field trials, it is important to first characterize the plants with respect to transgene integration and transcript production. A number of stably transformed grapefruit containing 1-4 copies of the transgene per genome were obtained (Figure 3-6) and of the six surviving plants, five had detectable levels of PAPn transcript and protein. Except for N9, all these plants as well as the plant, N25, which retained the transgene in its genome but did not express it at a detectable level, were replicated and challenged with both CEVd and CTV strain T66 sub-isolate E by graft inoculation. The replication of CEVd was not inhibited in the transgenic plants. A possible reason for this result is that the site of replication for viroids in the Pospiviroidae group is the cell nucleus. Thus the replicating viroid RNA may have been protected from PAPn. Vivanco (1999) showed that spraying plants with a RIP from

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55 Mirabilis jalapa prior to inoculation with PSTVd, prevented infection of the plants by the viroid. Thus in this case the RIP had access to the viroid RNA and could have inactivated it via its N-glycosidase activity. Using a rule that an A 405 nm two times higher than the non-inoculated control constituted a positive result for the presence of CTV, 25-50% of the transgenic plants tested negative for the presence of the virus after two months. This result was not completely unexpected, since in many cases PAP-expressing transgenic plants have been shown to accumulate lower levels of virus rather than showing total resistance to infection (Lodge et al., 1993; Tumer et al., 1997). In antifungal tests PAP-expressing plants also showed a lower percentage of disease incidence (Dai et al., 2003; Zoubenko et al., 2000) and in virus and fungal-infected plants, the onset of disease was delayed. Statistical analysis of the ELISA data showed that there was no significant difference in CTV antigen levels in comparison to the non-transgenic controls after two months. Surprisingly, line N25, for which no PAPn transcript was detected, had the lowest level of CTV. After four months, viral antigen levels decreased in lines N3, N9, N11 and N63 and overall, the transgenic plants had significantly lower levels of CTV than the non-transgenic control. After four months, line N25 still had one of the lowest levels of CTV, despite a 54.8% increase in antigen levels. Dai et al. (2003) found that two creeping bentgrass transformants expressing PAPII, an isoform of PAP, showed no detectable protein expression and only a very low level of PAPII mRNA, and yet these plants exhibited restance to Sclerotinia homeocarpa. Thus, the levels of PAPn mRNA and protein in line N25 may have been below the limits of detection by the methods used, since a low level of CTV antigen was detected, indicating aresistance phenotype. The

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56 results obtained suggest that the expression of the PAPn gene in Citrus paradisi causes an antiviral response. From these results, it can be concluded that the PAPn construct does not provide complete resistance to CTV. However, the decrease in viral antigen with time would need to be monitored for a longer period to ascertain the full and accurate effect of PAPn on CTV infection.

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CHAPTER 4 THE EFFECT OF POKEWEED ANTIVIRAL PROTEIN ON THE REPLICATION OF Citrus tristeza virus IN Nicotiana benthamiana PROTOPLASTS Introduction Early attempts to produce virus-resistant plants were based on the pathogen-derived resistance (PDR) approach, which utilizes genes and defective interfering RNAs or DNAs of viral origin (reviewed by Baulcombe, 1996). Since then, researchers have tried to exploit plant genes conferring natural resistance to particular pathogens by transforming these genes into heterologous plant hosts, and also altering the expression of genes involved in plant defense-related signal transduction pathways. A group of proteins that have shown promise as naturally occurring antiviral agents are ribosome-inactivating proteins (RIPs). However, as a result of their N-glycosidase activity, which results in the inactivation of ribosomes and ultimately the cessation of translation, many wild type RIPs cause major phenotypic aberrations when expressed in heterologous hosts. Pokeweed antiviral protein (PAP) is a RIP that adversely affects plant development when expressed in tobacco at concentrations higher than 5 ng/mg of total protein (Lodge et al. 1993). PAP was shown to inhibit infection of plants by seven different viruses, each representing a different virus group (Chen et al., 1991); thus PAP might confer a broad-spectrum of resistance to plants. The potential agronomic value of PAP as a broad-spectrum resistance agent prompted the search for non-toxic mutants that retained their antiviral activity. Several such mutants were identified by random mutagenesis and selection in Saccharomyces cerevisiae (Hur et al., 1995). Two of these mutants, viz. 57

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58 PAPc (Trp237-stop) and PAPn (Gly75-Val), have been used successfully to transform tobacco and produce phenotypically normal plants that exhibited resistance to certain viruses (Tumer et al., 1997; Zoubenko et al., 2000). Two other mutants that were produced, viz. PAPv and PAPx showed reduced toxicity and no enzymatic activity, respectively. Citrus tristeza virus (CTV) is one of the more complex plant viruses. For many years the fragile virions, the limited host range, lack of local lesion hosts, phloem-limitation of virions and a single-stranded RNA genome of approximately 20 kb in size hampered the in depth study of its biology and molecular characteristics. To facilitate the study of CTV replication, two protoplast systems, one from a CTV host, Citrus sinensis cv. Hamlin and the other from a non-host, Nicotiana benthamiana, were developed (Price et al., 1996; Navas-Castillo et al., 1997). Although the general pattern of CTV replication, with respect to the time of accumulation of the viral products was the same in both protoplast systems, the final yields of viral RNAs, proteins and virions were approximately 40 times higher in N. benthamiana (Navas-Castillo et al., 1997). Virions were found to be a better source of inoculum than purified genomic RNA. The lower level of replication observed with RNA as the inoculum is most probably due to the reduced efficiency of protoplast inoculation as a result of the large genome size. The development of a full-length infectious cDNA clone of CTV and smaller CTV replicons has further increased the progress towards understanding the gene functions and replication strategy (Satyanarayana et al., 1999). The smaller replicons are much more efficient at transfecting N. benthamiana protoplasts, indicating that the large genome size may have been a limiting factor in previous work.

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59 The study of the effect of different genes and genetic mutations on replication of CTV can be done in either citrus or N. benthamiana protoplasts. However, if the objective is to study the effect of a stably integrated heterologous gene on CTV replication, it would be more efficient to use the N. benthamiana protoplast system. The relatively short generation time and an established transformation protocol make N. benthamiana an ideal model system in which to study the effect of potential resistance agents on viral replication. The objectives of this study were to transform N. benthamiana with PAP mutants, characterize the resultant transgenic plants by molecular methods and to examine the effect of the expressed recombinant proteins on CTV replication in a protoplast system. Materials and Methods Constructs The four constructs used for transformation, viz. PAPn, PAPc, PAPv and PAPx were described in Chapter 3. The plasmids were transformed into Agrobacterium tumefaciens strain AGL1 by the cold-shock transformation method (Birnboim and Doly, 1979). Tobacco Transformation Explant preparation Nicotiana benthamiana seeds were sterilized by shaking them in 70% ethanol for 10 min, 0.042% sodium hypochlorite solution plus Tween 20 for 20 min and 3 x 2 min in sterile deionized water. The seeds were germinated on half strength MS medium (2.15 g/L MS salts, 50 mg/L myo-inositol, 10 g/L sucrose pH 5.8) supplemented with 6 g/L of agar. The plates were kept in a growth chamber that had a constant temperature of 28C and white fluorescent lighting with a 16 h day and 8 h night cycle. Once the

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60 seedlings had a well developed root, they were transferred to sterile soil in jars and magenta boxes, and grown until the upper leaves reached a size of 2-3 cm across. Transformation and regeneration of tobacco The transformed Agrobacterium cultures were grown overnight at 28C in YEP medium (10 g/L yeast extract, 10 g/L Bacto peptone, 5 g/L sodium chloride) supplemented with 50 g/ml carbenicillin and 100 g/ml chloramphenicol. The cultures were centrifuged at 5000 rpm in a Beckman GSA rotor for 5 min and the cell pellet resuspended in MS medium containing 100 M acetosyringone to give a final concentration of 5x10 8 cfu/ml. The leaves from sterile explants were cut into 1 cm 2 , transferred to the Agrobacterium solution for 1 min, and the excess liquid removed prior to being transferred to regeneration medium (4.3 g/L MS salts, 100 mg/L myo-inositol, 4 mg/L thiamine, 30 g/L sucrose, 1 mg/L IAA, 2 mg/L kinetin). The plates were incubated in the growth chamber for 48 h and then transferred to regeneration medium supplemented with 200 mg/L mefoxin and 50 mg/L kanamycin. The leaf pieces were transferred to fresh medium every two weeks. Shoots were transferred to rooting medium (R1/2N) supplemented with 200 mg/L mefoxin and 50 mg/L kanamycin. After the appearance of the first root, shoots were transferred to soil in pots and covered with a plastic bag which was slashed after a few days to allow the plants to become acclimated to the conditions in the growth room (28C, 16 h photoperiod). Analysis of Transgenic Plants by PCR All the regenerated plants were tested for the presence of the transgene by PCR using either of two gene-specific primer pairs, CN444, 5' ATTAGGGCCCGGGAAGATGAAGTCAATGCTTGTG 3' and CN445 5'

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61 AATTGCGGCCGCTCAGAATCCTTCAAATAGATC 3', or CN444 with CN273 5'-TTATCTGGGAACTACTCACAC 3’, which is specific for the CaMV 35S termination sequence. DNA was extracted from the plants using a modification of the protocol by Oliveira et al. (2000), previously described in chapter 2. PCR was carried out in a Biometra thermocycler using a profile of 94C for 2 min initial denaturation, 29 cycles of denaturation at 94C for 30 sec, primer annealing at 55C for 45 sec, primer extension at 72C for 45 sec and a final primer extension step of 72C for 5 min. The PCR products were analysed by electrophoresis in 1% agarose gels in TAE buffer. Southern Hybridization For Southern hybridization 10 g of total genomic DNA from transgenic plants and non-transformed control plants was digested with BglII (Invitrogen, Carlsbad, CA). After agarose gel electrophoresis the DNA was transferred to nylon membrane (Hybond N+, Fisher Scientific) by capillary action overnight (Sambrook et al., 1989). Using the primers CN444 and CN273, a DIG-labeled probe was produced by PCR amplification according to the manufacturer’s instructions (Roche, Indianapolis, IN). The DIG-labeled probe was denatured and used for a 16 h hybridization following 2-4 hours of prehybridization in DIG Easy Hyb Buffer (Roche). The blot was prepared for visualization on X-ray film according to the protocol provided by Roche. Reverse-Transcription (RT) PCR PAP gene expression at the transcriptional level was analysed in the transgenic plants by RT-PCR. Total RNA was isolated from the plants with TRIzol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions. Prior to RT-PCR, the RNA was treated with DNAse (Promega, Madison, WI) to eliminate any DNA contaminants, and then phenol-chloroform cleaned to remove the DNAseI. cDNA was

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62 prepared using 5 g of RNA, the reverse primer CN273 and MMLV reverse transcriptase (Promega). The parameters for the RT reaction were: 1 hour at 42C and 15 min at 70C. One tenth of the volume of the RT reaction was used for PCR with the primers CN273 and CN444 and the products were analysed on a 1% agarose gel run in TAE buffer. Analysis of Protein Expression PAP expression was analyzed by both Western blotting and ELISA. Protein concentration was determined by the Bradford Assay (BioRad, Hercules, CA). For Western blotting, aliquots of the soluble plant proteins in phosphate buffered saline (PBS, 137 mM NaCl, 2.7 mM KCl, 10 mM Na 2 HPO 4 , 2 mM KH 2 PO 4 , pH 7.4), were mixed with equal volumes of dissociation buffer (140 mM SDS, 160 mM Tris-HCl pH 7.8, 1% v/v glycerol, 142 mM -mercaptoethanol), to give a final concentration of 100 g total protein, which was then boiled for 2 min and separated on a precast 12% polyacrylamide Tris-HCl gel (BioRad). Proteins were transferred to nitrocellulose membrane using a BioRad semi-dry horizontal electrotransfer apparatus according to the manufacturer’s instructions. Colorimetric detection of the protein was carried out using a 1:500 dilution of 0.5 mg/ml anti-PAP-IgG (provided by Dr. Maria Kaniewski) and the substrates NBT and BCIP (Sigma). For ELISA analysis the 96 well plates were coated with either a 1:500 or 1:1000 dilution of anti-PAP-IgG. The plant tissue was extracted in an equal volume of PBS-Tween 20 containing polyvinylpyrrolidone (PVP-40). The PAP-alkaline phosphatase conjugate (provided by Dr Maria Kaniewski) was used at a 1:5000 dilution. All incubations were carried out overnight at 4C. The substrate, -nitrophenyl-o-phosphate

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63 was used at a concentration of 1 mg/ml. The plates were analyzed using a BioRad Model 680 plate reader and associated software. Determination of Antiviral Properties of Transgenic Plants To determine whether the transformed plants exhibited antiviral activity, five plants from the R0 and one from the R1 generation along with a non-transgenic control plant were challenged with Tobacco mosaic virus (TMV), a virus known to be inhibited by the antiviral activity of PAP (Lodge et al., 1993). Infected plant material (0.5 g) was ground in liquid nitrogen, resuspended in 5 ml of PBS containing carborundum, and applied to the leaves. Leaf samples were collected and analysed by ELISA at 7 and 14 days post-inoculation. The 96 well plates were coated with the antigen for 2 h at room temperature, followed by incubations with the TMV-U strain antibody (provided by Dr. Ernest Hiebert) and goat-anti-rabbit-alkaline phospatase conjugate (Sigma) used at a 1:5000 and 1:30 000 dilution respectively. Results were analyzed using a Bio-Rad Model 680 microplate reader. The mean absorbance values obtained from the different tobacco lines were compared using the 1-way analysis of variance with Fisher’s Protected Least Significant Difference test. Statistical analysis was done using the SPSS version 8.0 software (Chicago, Illinois). Viral Replication in Transgenic Protoplasts R1 plants from lines TN5, TN11, TN18, TN23a and TN27a were grown for six weeks under controlled environmental conditions. Fully expanded leaves were sterilized in 70% ethanol and 10% sodium hyperchlorite and washed 3 times in sterile water. The lower surface of the leaves were slashed at approximately 1 mm intervals and incubated overnight in the dark at 25C, in an enzyme solution containing 0.5% Onozuka cellulase RS (Yakult Honsha, Japan) and 0.25% macerase pectinase (Calbiochem, USA) dissolved

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64 in 13% MMC buffer (13% D-mannitol, 5 mM MES, 10 mM CaCl2, pH 5.8). The mesophyll protoplasts were isolated and transfected with CTV virions using polyethylene glycol (PEG) mediated transfection as described by Navas-Castillo et al. (1997) and Satyanarayana et al. (1999). The macerated leaves were centrifuged at 100 x g for 3 min and the supernatant was discarded. The pellet was resuspended in 15 ml of 0.6 MM buffer (0.6M D-mannitol, 5 mM MES, pH 5.8) and centrifuged for 3 min at 100 x g. The pellet was resuspended in 0.6 MM buffer, layered over 20.5% sucrose, centrifuged for 7 min at 100 x g. The protoplasts were collected from the top layer and washed twice with 0.6 MM. Ten microliters of purified CTV virions were added to 200 l of protoplasts. Five hundred microliters of PEG 1540 was then added, and the solution was gently mixed for 20 sec, after which 0.6 MM bufferwas added. The protoplasts were allowed to recover for 10 min and centrifuged at 100 x g for 3 min. The pellet was resuspended in 0.6 MM AOKI (0.6 M D-mannitol, 5 mM MES, 100 ml of 10x AOKI salts to make 1 L of solution, pH 5.8) containing a 1:200 dilution of antibiotic/antimycotic solution (Sigma, St. Louis, MO), centrifuged at 100 x g for 3 min and resuspended in a final volume of 3 ml of 0.6 MM AOKI with antibiotic/antimycotic. The protoplasts were incubated under light and harvested three days post-inoculation (dpi). Total RNA was isolated and Northern hybridization was performed as described by Satyanarayana et al. (1999), using positive and negative sense 3' terminal probes. Results Transformation and Regeneration A total of seventy-four shoots were obtained from all the N. benthamiana transformation experiments. The majority of the shoots produced had been transformed with the PAPn construct and no shoots were obtained from leaf disks transformed with

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65 PAPv (Table 4-2). The potentially transgenic plants were screened only by PCR for the presence of the transgene (Figure 4-1). Although 55 plants initially tested positive for the presence of the transgene, subsequent PCR screens as the plants matured revealed that only 27 continued to test positive. The plants that maintained the transgene after three months (as determined by PCR) had all been transformed with the PAPn mutant. No phenotypic abnormalities were observed for the surviving plants. Figure 4-1. PCR analysis of selected potential transgenic N. benthamiana plants using primers CN444 and CN445. Lane 1, 1 kb marker; 2, no DNA control; 3, plasmid control; 4, non-transgenic control; 5, N5; 6, N6; 7, N7; 8, N8; 9, N9; 10, N10; 11, N11; 12, N12; 13, N13. Table 4-1. Summary of N. benthamiana transformation experiments with the PAP constructs. Construct Total number of shoots Initial PCR Positive PCR positive after 3 months PAPv 0 0 0 PAPc 24 12 (50.0%) 0 PAPx 9 4 (44.4%) 0 PAPn 55 39 (70.9%) 27 (49.1%) Molecular Analysis of Transgenic Plants All the transgenic plants that survived and had been transferred to soil were analyzed by Southern blotting to determine the transgene copy number. No hybridization of the PAP-specific probe was detected in the genomic DNA sample from the

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66 non-transformed control (Figure 4-2). The transgene was stably integrated with the copy number of the PAPn transgene varying from 1-4 copies per genome (Figure 4-2). Having established the genomic integration of the transgene, the plants were analyzed for PAPn transcript production by RT-PCR (Figure 4-3). Total RNA isolated from the transgenic plants was first treated with DNAseI to remove any contaminating DNA that might result in a false positive result. The results showed that the transgene was transcribed in 48.1% of the surviving plants. Figure 4-2. Southern analysis of R0 tobacco plants transformed with PAPn. The names of the plants are indicated above the lanes. TUT is a non-transformed control plant. The positive control is a plasmid containing PAPn, digested with PstI. Since the protein product of the PAP gene is required for antiviral activity, the plants were further analysed by western blotting and ELISA in order to determine whether the protein is being expressed. No protein was detected when the plants were analyzed by western blotting (data not shown). Since ELISA is more sensitive than

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67 western blotting, the plants were screened for protein expression using this technique. In comparison to the colorimetric reaction of purified wild type PAP (Worthington) at concentrations as low as 1 ng, the level of PAPn in the plants tested was not visually detectable. Including purified PAP at different concentrations, and using the ELISA analysis software to construct a standard curve, PAPn levels of 0-25 pg/mg were determined (Table 4-2). Figure 4-3. RT-PCR analysis of RNA isolated from selected transgenic plants to determine PAPn expression at the transcriptional level. Lane 1 is the HindIII molecular weight marker. Lanes 2, 4, 6, 8, 10, 12 and 14 are the no-RT controls for each sample during the PCR reaction. Lane 3, non-transformed control; 5, TN5; 7, TN7; 9, TN11; 11, TN18; 13, TN23a; 15, TC27. The low or undetectable levels of PAPn protein in the transgenic plants raised questions as to whether it would be viable to continue with the CTV replication studies in protoplasts derived from the progeny of these plants. Therefore, it was decided to challenge five R0 plants and one R1 plant with TMV, a virus known to be inhibited by PAP (Lodge et al., 1993). The second and fourth systemically infected leaves were evaluated for virus antigen levels by ELISA at 7 dpi and 14 dpi respectively (Table 4-2). The absorbance values obtained showed that there was no detectable level of TMV in all

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68 the test plants after one week, as compared to the non-transgenic control. Statistical analysis of the mean absorbance values obtained for each plant 14 dpi, using Fisher’s Protected Least Significant Difference test showed that all five transgenic plants had significantly lower levels of virus antigen compared to the control and that the level of virus in TN5, TN11 and TN18 was significantly different from TC27, TN7 and TN23a (Table 4-2). Comparison of the ELISA data obtained 7 and 14 dpi using a one tailed t-test assuming equal variance showed that there was no significant difference in virus antigen levels after the two week period for TN5, TN11, TN18 (Table 4-2). Thus these plants containing the PAPn transgene showed resistance towards TMV, although this resistance was not complete since a low level of viral antigen could be detected by ELISA. These results were the basis for proceeding to study the effect of PAPn on CTV replication. Table 4-2. TMV antigen levels in transgenic N. benthamiana expressing PAPn following infection with the virus. Plant Line PAP (pg/ml) Mean Absorbance 7 dpi 14 dpi Infected non-transgenic control 0 0.0705 0.230a TC27* nd 0.008 0.154b TN23a nd 0.005 0.121b TN7 nd 0.0055 0.117b TN11 25.1 0.006f 1.067x10 -2 cf TN18 5.05 0.0055e 9.33x10 -3 ce TN5 nd 0.006d 8.667x10 -3 cd Mean absorbance values of the different plants 14 dpi were compared using the 1-way analysis of variance with Fisher’s Protected Least Significant Difference test. Means with the same letter are not significantly different at P=0.05. dpi: Days post-inoculation. PAPn levels were quantitated by ELISA. The second and fourth systemically infected leaves were assayed for virus antigen levels by ELISA 7 and 14 dpi, respectively. *This plant was from the R1 generation. All other plants were from the R0 generation. nd=not detectable

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69 CTV Replication in PAPn-Transgenic N. benthamiana Protoplasts The replication of CTV in the protoplasts was assessed by Northern blot analysis. Analysis of RNA extracted from the CTV virion-transfected protoplasts, using a 3' minus sense probe showed no difference between the levels of positive sense RNA in the transgenic plants when compared to the control (Figure 4-4 A). This result may have been influenced by the presence of the positivesense input RNA, which masked the true level of replication. Figure 4-4. Northern blot analysis of CTV RNAs in N. benthamiana protoplasts derived from PAPn transgenic R1 plants. A) Positive sense 3' probe. B) Negative sense 3' probe. Lane 1, inoculated non-transgenic control; 2, TN5; 3, TN7; 4, TN11; 5, TN18; 6, TN23a. Protoplasts were transfected with CTV virions and RNA isolated 3 dpi. The numbers to the left of the figures indicate the subgenomic mRNAs corresponding to ORFs 4-10. The arrow indicates the genomic RNA. Thus, to obtain a more accurate view of replication, a 3' positive-sense probe was used to measure the accumulation of minus strand RNA (Figure 4-4 B). The Northern hybridization results showed that the production of negative-sense subgenomic RNAs

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70 and thus replication was considerably reduced in protoplasts derived from TN11 and TN23a, while replication in TN5 was comparable to that of the control and TN7 and TN18 had higher levels of replication. These results indicate that two PAPn transgenic N. benthamiana lines are able to suppress CTV replication. Discussion N. benthamiana was transformed with four mutants of PAP, a ribosome-inactivating protein reported to confer broad-spectrum resistance to viruses (Lodge et al. 1993). In two of the mutants (PAPc and PAPn) the antiviral activity of PAP has been separated from the toxic ribosome-inactivating activity. The greater proportion of transgenic shoots obtained were from transformation experiments with these two constructs. However, repeated PCR analysis showed that the PAPc plants did not retain the transgene as the plants matured. A similar result was obtained when Citrus paradisi cv. Duncan grapefruit was transformed with the same construct (Chapter 3). There are two possible reasons for this result. First, it is possible that this gene construct is deleterious to the plants. The second reason could be that the plants were chimeras that did not express the transgene in every cell. Lodge et al. (1993) showed that PAPc expressed in transgenic N. tabacum did not have a toxic effect on ribosomes nor did it cause phenotypic abnormalities. Therefore, the most likely reason for the loss of the transgene appears to be that the PAPc plants had been chimeras. Not obtaining any transformants for the PAPv construct was not surprising since PAPv, which has antiviral activity, is only slightly less toxic to ribosomes than wild type PAP. Approximately 48% of the plants produced the PAPn transcript. However, PAPn expression at the protein level was almost undetectable for most of the plants. In other studies where PAP or PAP mutants were expressed in N. tabacum, N. benthamiana or

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71 Solanum tuberosum, PAP levels were usually found to be above 0.6 ng/mg (Lodge et al., 1993; Tumer et al., 1997). However, expression of PAP mutants in creeping bentgrass was either non-existent or undetectable, yet field trials with those plants resulted in the observation of different levels of resistance against the test-pathogen (Dai et al. 2003). To determine whether the transgenic N. benthamiana plants might have any antiviral activity, the plants were inoculated with TMV. These plants behaved similarly to the creeping bentgrass, showing very low levels of accumulation of TMV antigen with time despite having undetectable levels of PAPn. Protoplast systems have played a pivotal role in elucidating viral infection events occurring at the single cell level. Using protoplasts, the effects of salicylic acid on different cell types during the infection process of TMV and Cucumber mosaic virus (CMV) were demonstrated (Murphy and Carr, 2002). Events involved in cell-to-cell movement of CMV and the replication of Cowpea mosaic virus (CoMV) have also been studied in protoplast systems (Carette et al., 2002; Mise et al., 2001). An N. benthamiana protoplast system was developed to facilitate the study of CTV replication (Navas-Castillo et al., 1997). The R1 generation of transgenic plants which had shown inhibition of TMV accumulation was used to produce protoplasts for the study of the effect of PAPn on CTV replication. This approach was undertaken to quickly determine whether PAPn affects CTV replication, as well as to decrease the inoculum pressure as compared to graft inoculation of a plant. Northern blot analysis showed that three lines, TN5, TN11 and TN23a, were able to inhibit replication of CTV. This suggests that PAPn could be an effective antiviral agent against CTV and provides further evidence that the PAPn

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72 construct expressed at very low to undetectable levels does not completely inhibit CTV replication. A higher level of PAPn expression might completely inhibit CTV replication.

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CHAPTER 5 SUMMARY AND CONCLUSIONS Genetic engineering for resistance is often specific for a particular pathogen, e.g. pathogen-derived resistance. Natural selection and the fact that the genomes of RNA viruses are subject to changes as a result of errors introduced by the RNA polymerase suggest that PDR may not be effective as a durable form of resistance. Targeting signal transduction pathways that play a role in the plants’ general defense response, expressing more than one gene in transformed plants or expressing proteins that can function as antiviral agents by more than one mechanism, may prove effective in the longterm. The efficacy of a ribosome-inactivating protein (RIP) from Phytolacca americana, as an antiviral/antiviroid agent against two citrus pathogens was investigated. The RIP, pokeweed antiviral protein (PAP), was reported to have broad-spectrum antiviral activity against plant and animal viruses. The protein was reported to inhibit viral accumulation in a number of ways. In vitro it inhibited viral translation by removing adenine and guanine residues directly from the viral RNA; it recognised and preferentially depurinated RNA that had a 5' methyl-guanosine cap structure; and it inhibited +1 frameshifting in the yeast retrotransposon, TY1. All three of these mechanisms would be applicable to Citrus tristeza virus (CTV), while only the first could be predicted to inhibit replication of a viroid, viz. Citrus exocortis viroid (CEVd). CTV alone has caused the loss of millions of trees worldwide and the propagation of viroid-infected trees has caused economic losses in the Florida citrus industry, and is a major threat in regions where susceptible rootstocks are used. 73

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74 To determine whether it would be viable to transform citrus with PAP, a preliminary experiment to observe the effect of PAP on the translation of CTV was conducted in vitro. The translation of a CTV replicon, CTV-Cla, which retains only the 5' and 3' UTRs, ORFs 1a and 1b and a gene fusion between ORF11 and part of ORF2, was first optimized. CTV-Cla RNA was then incubated in the presence of wild type PAP prior to translation in a rabbit reticulocyte lysate translation system. A decrease in translation was observed at 20 ng PAP per 500 ng of RNA. Compared to previous research, the concentration of PAP required to inhibit translation is very high. However, since a similar result was obtained with the Brome mosaic virus RNA (a virus whose translation in known to be inhibited by PAP) used as a control in this experiment, it was concluded that the preparation of wild type PAP that was used may not have had optimal enzymatic activity or that optimal activity may have been affected by some component of the antiviral assay. Since the viral RNA will be exposed to the intracellular environment in plants, the in vitro translation result demonstrating the direct effect of PAP on the RNA, suggested that transgenic citrus correctly processing and expressing PAP might exhibit reduced levels of CTV. Epicotyl segments of etiolated Duncan grapefruit seedlings were transformed with four PAP mutant constructs by Agrobacterium-mediated transfer. Two of the mutants, PAPn and PAPc reportedly retained their antiviral activity without the deleterious ribosome-inactivating property, while PAPx was an inactive form of the protein, and PAPv which had antiviral activity was only slightly less toxic to ribosomes than wild type PAP. Very few transformed plants were obtained, and those that survived to the pathogen-challenge stage contained only the PAPn transgene. It is possible that the nature

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75 of the gene, combined with the inherent problems of transforming a heterologous host such as citrus, may have had an impact on the number of transgenic plants produced. Southern analysis of the transgenic plants showed them to be stably transformed with 1-4 copies of the PAPn gene per genome. Of the six plants that survived, only five (N3, N9, N11, N63 and N71) expressed PAPn at the protein level. However, all six transgenic plants were replicated in preparation for the graft-challenge experiment. Due to a shortage of plants, all lines except N9 were challenge-inoculated with CEVd. Plants assayed for the presence of the viroid by RT-PCR one month post-inoculation were all positive, indicating that PAPn did not inhibit viroid replication. There has been one other published report of a RIP being tested for antiviroid activity (Vivanco, 1999). However, the research did not involve the in vivo expression of the RIP in transgenic plants. Instead, it was shown that an exogenous application of the RIP prevented viroid infection. Therefore, a possible reason for the failure of PAPn to inhibit CEVd replication may be due to the fact that the site of replication for CEVd is the cell nucleus. Thus the viroid RNA may have been inaccessible to PAPn. All six transgenic plant lines were graft challenged with CTV and viral antigen levels were determined by DASI-ELISA two and four months post inoculation. Using a rule that an A 405 two times higher than the non-inoculated control constituted a positive result for the presence of CTV, 25-50% of the transgenic plants tested negative for the presence of the virus after two months. This result was not completely unexpected, since in many cases PAP-expressing transgenic plants have been shown to accumulate lower levels of virus rather than showing total resistance to infection. Statistical analysis of the ELISA data showed that virus antigen levels were significantly lower than the non

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76 transgenic control plants for the lines N9, N11, N25 and N63. Surprisingly, the plants of line N25, in which the PAPn transcript was not detected, accumulated the lowest level of virus. The reason for this may be the result of the location of the transgene in the plant genome or the RNA transcript levels may have been below the level of detection. However, after four months CTV antigen levels increased in all the lines, indicating a delay in virus accumulation in the plants that had tested negative after two months. Although all the transgenic plants tested positive for the presence of CTV after four months, the levels of CTV present in the transgenic lines were significantly lower than that of the control line. In addition, the mean level of CTV antigen present in each transgenic line was lower than level present after two months. Thus these results indicate that the PAPn construct does not provide complete resistance to CTV. However, continued analysis of the transgenic plants for the presence of CTV is required to determine whether the CTV levels in these plants will continue to decrease or whether they will maintain a consistently lower level of CTV in comparison to the non-transgenic control plants. Replication of CTV in PAPn-transgenic Nicotiana benthamiana protoplasts indicated that three lines, TN5, TN11 and TN23a supported a lower level of replication than the non-transgenic control. This was further evidence that the PAPn construct expressed at very low to undetectable levels did not completely inhibit CTV replication. Thus, a larger pool of transgenic grapefruit plants expressing higher levels of PAPn may have produced plants that did not support CTV replication. Alternatively, expression of PAPn from a phloem-specific promoter or the expression of other RIP candidates that

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77 have antiviral activity, in citrus, may provide resistance to CTV and other pathogens of citrus.

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BIOGRAPHICAL SKETCH Yolanda Petersen was born in 1973 in Cape Town, South Africa. She earned a Bachelor of Science degree in Microbiology and Botany at the University of Cape Town, in December 1994. Her Bachelor of Science (Honors) and Master of Science theses were entitled: “The Characterisation of a novel bacteriophage from the the causal agent of chocolate spot disease of cabbage” and “The Characterisation of a novel Xanthomonas bacteriophage”. The degrees were awarded at the University of Cape Town in 1995 and 1999, respectively. In 1999 she was awarded a scholarship by the USDA-ARS International Programs to pursue the Doctor of Philosophy degree in the field of plant pathology at the University of Florida. 90