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INGEST IEID EHFX8XRWX_LTX7PS INGEST_TIME 2014-10-09T23:59:12Z PACKAGE AA00025790_00001
AGREEMENT_INFO ACCOUNT UF PROJECT UFDC
ADENOVIRUS INDUCED ADENO-ASSOCIATED VIRUS GENE EXPRESSION IS
NOT DEPENDENT ON AAV NON-STRUCTURAL REP PROTEIN
DANIEL FRANCIS LACKNER
A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL
OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT
OF THE REQUIREMENTS FOR THE DEGREE OF
DOCTOR OF PHILOSOPHY
UNIVERSITY OF FLORIDA
Daniel Francis Lackner
This work is dedicated to both of my parents, John and Sally Lackner.
In my lab, I would like to thank a great number of people. First, I would like to
thank Bill McDonald. He was the unfortunate postdoc that had to sit next to me as a first
year graduate student. He answered every stupid question I ever asked and taught me to
form the really important ones. Two other important postdocs were Christian and
Corrina. Dr. Teshendorf introduced me to the wonders and peculiarity of the European
lifestyle from the German perspective. He will be the measure to which I compare all
future medical doctors. Corrina has exposed me to the Spanish version of the European
lifestyle and created my entire knowledge of the neuroscience field.
I have enjoyed the large number of Chinese postdocs in the lab, which introduced
me to the Chinese culture. Wei-jin, Pei, Wu, Yan, and Long-Gon have taught me the
limited amount of Mandarin that I can speak in everyday conversation. More
importantly, they showed me the similarities of China and American society but also the
differences between the two cultures. This exposure to a different culture has been one of
the most rewarding experiences in the Muzyczka lab.
Rodney and Opie have always been my lab mates and have made the experience
one to long remember. They have been a great deal of entertainment and have made the
process of getting a Ph.D. a great deal of fun. I would choose no one else to spend these
years with at UF and they will always make me laugh.
Ken and Kevin have been great mentors even through we are the same age. I
respect their opinions and have had no better time than discussing any aspect of AAV
biology with these two great postdocs. They have taught me more than they know and I
know they will do great in their future careers.
Without question, the enduring support of my parents, John and Sally, has
enabled me to complete this Ph.D. dissertation. During many phone calls, their own
interest in my work has inspired me to explain many different aspects of basic AAV and
Adenovirus biology. I cannot thank them enough for everything they have done for me.
I would like to give a very important acknowledgement and thanks to my wife,
Dr. Cari Aspacher Lackner. From the beginning of my graduate career, she has been a
great source of happiness and a great companion in scientific research. I have always had
her as a research consultant and aspired to be her equal as a bench scientist.
TABLE OF CONTENTS
Eukaryotic Gene Expression 1
The Chromatin Template 1
Activation and Repression 5
Chromatin Modification 9
Basal Transcription Factors 11
RNA Polymerase II Holoenzyme 14
Adeno-Associated Virus 15
Adenovirus Helper Functions 18
AAV Rep Proteins 19
AAV Transcription without Adenovirus 20
AAV Transcription with Adenovirus 20
Model for Activation of an AAV Productive Infection from Latency 28
MATERIALS AND METHODS 35
Cell Lines and Virus 35
CAT Reporter Assays 40
Analysis of Adeno-Associated Virus Transcription 41
Define Rep Binding Element as Enhancer or Proximal Promoter Element 41
The p5 RBE is not an upstream activation signal 50
Activation of pl9 is not due to read through from p5 54
Transactivation of pi 9 can be modeled in the absence of Rep 60
Which p5 element is primarily responsible for Rep mediated induction of pi 9? .... 64
Transcriptional Analysis of Mutant Rep Proteins 67
Generation of Rep Mutant Plasmids 68
Transcriptional Activation of the pi 9 Promoter by Rep Mutants 71
Repression of the p5 promoter.
The RBE is not a typical upstream activation signal 79
The p5 RBE is probably an architectural element designed to bring the p5 and the pi9
promoters together 81
Rep Protein Domains in AAV Transcriptional Regulation 87
Future Directions 96
TABLE OF ABBREVIATIONS 104
LIST OF REFERENCES 105
BIOGRAPHICAL SKETCH 125
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
ADENOVIRUS INDUCED ADENO-ASSOCIATED VIRUS GENE EXPRESSION IS
NOT DEPENDENT ON AAV NON-STRUCTURAL REP PROTEIN
Daniel Francis Lackner
Chairman: Nicholas Muzyczka, Ph.D.
Major Department: Molecular Genetics and Microbiology
The normal lifecycle of Adeno-Associated Virus (AAV) alternates between a
latent, repressed provirus and an actively transcribing viral genome. This switch in gene
expression is the combination of cellular and viral factors to promote AAV replication.
Previous studies of AAV have indicated regulatory pathways, which maintain the correct
AAV transcription levels for productive infection. Autoregulation of the AAV genome is
controlled by Rep protein interactions with cellular proteins. The addition of Adenovirus
helper activities induce changes in both cellular and AAV transcriptional regulation.
This combination of regulatory factors allows the dissection of a complex transcriptional
regulation mechanism in a relatively simple genetic system. The dissection of the AAV
transcriptional regulation was performed by a series of promoter constructs that would
access the factors required for transcriptional activation of the AAV pi 9 promoter.
Initially, the first promoter constructs containing a single AAV Rep protein binding site
were used to determine if the nonstructural Rep protein would function as a
transcriptional activator of AAV gene expression. The Rep protein was determined not
to be a transcriptional activator but instead to function as a position-dependent inhibitor
of pl9 promoter activity. This position-dependent inhibition of the AAV pl9 promoter
activity suggested that the previously characterized Rep and Spl interaction might not be
the direct cause of Rep-mediated transactivation. In order to prove that the previous
characterized Rep and Spl interaction was not responsible for induction of the pi 9
promoter, a novel system of hybrid transcription factors was used to replace the Rep and
Spl proteins. The novel hybrid transcription factors modified from the yeast two-hybrid
system, consisted of two different proteins containing a GAL4-DNA binding domain
fused to either an interaction domain from p53 or T-antigen. The replacement of the Rep
and Spl binding sites with GAL4 binding sequences in the pi9 promoter showed that
Rep and Spl were not required for transactivation. We conclude that the Rep and Spl
transcription factors function as architectural proteins facilitating a DNA loop to form
between the Rep binding site in the p5 promoter and the Spl site within the pi9
Eukaryotic Gene Expression
The regulation of eukaryotic gene expression has been shown to be far more
complex than the original protein fractionations for RNA polymerase activities
suggested. Initial fractionation protocols discovered three distinct RNA polymerases and
their respective General or Basal Transcription Factors (GTFs). However, purification of
these factors did not restore the complex regulation of transcription in vitro indicating
that more factors were required for proper transcriptional regulation. More recent studies
have observed that the RNA polymerase II holoenzyme (RNAP II) is about the same size
as the ribosome and many other factors are critical for correct gene expression. DNA
condensation into chromatin has been shown to regulate gene expression and the
exposure of DNA sequences allows the assembly of transcriptional regulators to recruit
the complete RNA polymerase II holoenzyme.
The Chromatin Template
The DNA template of most promoters for protein-encoding genes contains three
important features. The first component is the transcription initiation site that directs the
initiation of polymerization of mRNA, which is catalyzed by the RNA polymerase II
holoenzyme. The second component is the TATA box which regulates the binding of the
TATA binding protein (TBP). The last component is the regulatory sequences
surrounding the transcription initiation site and the TATA box of the expressed gene
The transcription initiation site and the TATA box are defined as the core
promoter elements. This core element averages about 100 base pairs (bp) in length for
most protein encoding genes. The AT-rich sequence named the TATA box is usually
found about 25 to 30 bp upstream of the transcription initiation site in higher eukaryotic
organisms (179). The TATA box was initially characterized for its ability to bind the
TATA binding protein (TBP), a component of the TFIID complex that is important for
initiating the formation of the RNA polymerase II holoenzyme. The binding activity of
this AT-rich region was named for its apparently canonical sequence of TATA but it has
been recently observed that TBP can bind to a range of sequences no longer defined by a
simple sequence match to the TATA box region (58, 170, 208). In addition to the more
common TATA box, many promoters can have an initiator element (Inr) that covers the
transcriptional start site and recruits regulatory factors and the RNA polymerase II (171,
172). The core promoter can therefore comprise a TATA and Inr elements (composite),
either element alone (TATA- or Inr-directed), or neither element (null) (135). Most viral-
encoded proteins have composite promoters, most cellular RNAP II genes are TATA-
directed promoters, and many null promoters have many different transcriptional initiator
sites reflecting variable TBP binding positions (51, 79, 111).
The majority of gene regulation on protein-encoding genes functions at the level
of upstream activating sequences, upstream repressing sequences, silencers, or locus
control regions. Upstream activating sequences (UAS) are defined as sequences of DNA
that bind specific transcription factors that promote the recruitment of the RNAP II at the
core promoter element and activate the initiation of gene expression. These activating
sequences can be relatively close to the initiation site which allows activators to bind near
the core promoter, thus defining this subgroup of UASs as proximal promoter elements
(129, 179). Another subgroup of UASs, defined as enhancers, consist of binding sites for
one or more transcriptional activators that function independent of their orientation and
can be separated by DNA sequences of 85 kilobasepairs (kb) (15). Upstream repressing
sequences (URSs) are DNA sequence elements that function negatively toward the
recruitment and assembly of the RNA polymerase II holoenzyme at the nearby proximal
core promoter element. In contrast to active recruitment by activators, the repressive
elements that bind to URSs function in preventing gene expression by different
mechanisms. The first mechanism is the passive exclusion of activator binding, thereby
preventing the activator from RNA pol II recruitment. Most commonly, the repressor
will have a binding site sequence that is nearby or overlaps the activator, thereby
excluding its binding by steric interference of their binding sites. Another active
repressor mechanism is the modification of chromatin structure by histone deacetylation,
which prevents transcriptional activators from binding their respective DNA sequences.
Silencers are defined as DNA sequence elements that repress promoter activity in
an orientation- and position-independent manner (136). The silencer elements contain
binding sites that recognize specific protein factors. These protein factors bind the
silencer element and interact with chromatin histones H3 and H4. The result of this
interaction is a deacetylation of the H3 and H4 histones inducing a condensation of the
chromatin structure, thus preventing access and binding of any transcriptional activators.
Locus control regions (LCRs) are positive activators of expression for proximal
genes but differ from upstream activating sequences in several aspects. After these LCR
elements are integrated into cellular chromatin, the enhancer sequences function in an
orientation and distance independent manner but the level of gene expression is
influenced by the actual site of integration This effect of integration is defined as
position effect variegation because the structure of chromatin can overwhelm the
enhancerâ€™s effect and the accessibility of transcriptional activators to the enhancer
sequence. In contrast to enhancer elements, the locus control regions can always activate
transcription when integrated into cellular chromatin because the LCR elements directly
interact with the formation of the chromatin structure (44, 49, 55).
The last major chromatin element is the Insulator element which can limit the
effects of the other regulator elements. The Insulator elements allow the chromatin
template to be subdivided into different functional domains. Each chromatin domain is
regulated by various enhancers, UASs, URSs, or LCRs and those respective elements are
separated not by distance but by the function of the Insulator elements (10, 11, 182).
Chromatin structure is comprised of a series of nucleoprotein complexes called
nucleosomes. A nucleosome contains 146 bp of genomic DNA wrapped around an
octomer of histone proteins (92, 226). The octomer is arranged in a cylinder shape
composed of two heterodimers of histones H3 and H4 and another two heterodimers of
histones H2A and H2B. The nucleosome crystal structure shows DNA wrapped around
the cylinder and the contact is maintained by interactions with the histone proteins and
the phosphate backbone of the DNA (116). The DNA is bound so that the N-terminus of
the histones can interact with other neighboring nucleosomes to form higher order
structures. In addition, the DNA and histone interactions are not fixed allowing some
promoter sequences to be exposed for gene expression. The degree of chromatin
structure and condensation within a promoter region is usually related to the level of
transcriptional activation (Fig. 1, A) (56, 142, 152, 212). Many in vitro experiments have
observed that transcriptional templates preincubated with chromatin fractions inhibit the
initiation of RNA polymerases. In complementing experiments, in vivo yeast
experiments which depleted histone proteins increase the transcriptional activity of many
different genes (60, 61, 214). These experiments demonstrate how tight histone-DNA
contacts and the organization of nucleosomes into higher order structures can limit and
sterically inhibit binding of transcription factors to the promoter region.
Activation and Repression
An activator is composed of two different functional protein domains (187). The
first domain binds the specific DNA sequence within the upstream activating sequence
and the second domain functions to recruit or stimulate the activity of the RNA
polymerase II holoenzyme. A single activator can be used in order to activate multiple
genes throughout the genome allowing synchronization of many different gene products.
On the other hand, a single gene in the genome can be regulated by many separate
transcriptional activators providing the genome a mechanism for variable control.
The main function of transcriptional activators is the binding and recruitment of
the transcription initiation apparatus (Fig. 1, B) (151). This function has been
demonstrated by direct binding between the activation domains of transcription factors
and components of the transcription machinery (3, 59). Further evidence for the role of
activation domains in binding and recruiting the transcription apparatus is provided by
replacing the activation domains with an artificial activator such as a fusion protein
Fig. 1. A model for the role of activators in transcriptional initiation. A, Genomic
DNA is packaged into nucleosomes an higher ordered chromatin structures. B,
Transcriptional activators bind to promoter sequences and can have a positive influence
on promoter activity. C, Activators bind and recruit chromatin remodeling and
modifying complexes that influence local chromatin structure. D, Activators bind and
recruit the transcriptional initiation apparatus to promoters through the interactions of a
few large complexes. E, Activators can affect the promoter clearance and RNA
Polymerase II holoenzyme processivity.
High-Order Chromatin Structures
chromatin Activator Binding
between a DNA binding domain and corresponding domains from the transcriptional
machinery. This artificial activator can substitute for the actual activator in vivo by
exhibiting the same functional role in transcriptional activation (5, 26, 215).
Repressors of transcriptional activity usually function in either a general activity
or in a very gene-specific manner (105). The general repressors of transcription interact
with the TBP. In yeast, Motl represses transcription of some genes by directly binding
the TBP-DNA complex and inducing dissociation of TBP from the TATA-box sequence
(2, 131, 194). In large eukaryotic organisms, the Drl protein is another general negative
regulator of RNA polymerase II transcription. The Drl protein binds the basic repeat
domain of TBP bound to promoter DNA and prevents the assembly of the RNA
polymerase II holoenzyme (53, 80, 85).
Gene-specific repressors can function by direct physical interaction with
transcriptional activators or by competition for activator binding sites. One classic model
of gene-specific repression is the GAL4 and GAL80 interaction in yeast. The GAL4
transactivator stimulates the expression of yeast genes with a GAL4 binding site.
However, the activity of GAL4 can be inhibited by its direct physical interaction with
GAL80 (117). The GAL80 protein represses the GAL4 activator by binding and masking
a portion of its activation domain (169). Another repressor, chaperone Hsp90, functions
by a different mechanism to inhibit the activity of the transcriptional activator Hsfl.
Instead of an interaction which masks the activation domain, the Hsp90 protein prevents
the formation of Hsfl trimers required for the binding of the Hsfl activators to its
respective DNA element (227). These are two examples of how direct interaction or
inhibition of an activator can lower transcriptional activity in a gene-specific manner.
Another method of gene-specific repression is steric interference at the level of
DNA binding activity. In this mechanism, no direct interaction between an activation
and a repressor is necessary. Two transcription factor groups representing activator and
repressor activities compete for neighboring DNA promoter sequence. An example of
this type of regulation is found between the Acrl repressor and the ATF/CREB activator
(193). Promoters that use steric interference for transcriptional regulation have
overlapping Acrl and ATF/CREB sites within their promoter regions.
The interaction between activation and repression is also strongly dependent on
the expression and concentration levels of the positive and negative transcription factors.
A strong experimental example of this interplay between activation and repression can be
found in yeast mutational screens that create loss-of-function alleles in negative
transcription factors and are complemented by mutations in positive transcriptional
activators (104, 149, 150).
The compression of genomic DNA into nucleosomes and higher order chromatin
organization provides yet another level of transcriptional regulation. The interactions
between the N-terminus of histone proteins allows many different chromatin complexes
to form based on the ability of the histones to contact one another. The majority of this
variable chromatin structure is regulated by the aceytlation of the N-terminal domains of
histones (130, 188, 225). The acetylation of histones induces the disruption of tight,
high-order chromatin structures and increases transcription activity. On the other hand,
various factors causing histone deacetylation allows the formation of higher-order
chromatin structure and results in the repression of transcription.
Histone proteins are modified by acetylation, phosphorylation, methylation, and
ubiquitination. The acetylation modification is the best understood with several lysines
on the N-terminus of each histone protein reversibly acetylated (176). After acetylation,
the nucleosomes are less likely to undergo physical interactions and condensation so the
exposed DNA sequences may allow increased recruitment of the transcriptional
machinery (Fig. 1, C) (63, 224). Additionally, acetylation of histones neutralizes the
positively charged lysine groups thereby decreasing the histones affinity for DNA (56,
116). Acetylated histones may also directly interact with transcriptional activators
increasing their binding affinities and inducing more RNA polymerase II holoenzyme
Histone acetyltransferases (HATs) were first identified with transcriptional
activation by the structure and function studies of the Tetrahymena protein, p55. The p55
protein was known to function as a histone acetyltransferase but later studies showed it
was related in sequence to the yeast transcriptional cofactor Gcn5 (16). The relationship
between these two proteins correlated the activities of histone acetylation and increased
transcriptional activation. For experimental evidence, the Gcn5-dependent promoters
were shown to have increased acetylation of histones. Additionally, mutations in the
HAT domain inhibited the ability of Gcn5 to activate transcription and acetylate promoter
histones (96, 200). Several transcriptional coactivators that bind to activators, such as
p300 and CBP, have HAT activity. The HAT activity enables them to alter the chromatin
structure of proximal promoters after activators bind to DNA (43, 52, Ogryzko, 1996
#3438). Histone Deacetylases (HDACs) were first correlated to transcriptional
repression by the identification of purified HDACs that have similarity to transcriptional
cofactors (156). As more cellular histone deacetylases were isolated, many were found to
be components of corepressors recruited by transcription factors.
Basal Transcription Factors
In order for any promoter sequence to function, a number of general transcription
factors are required to direct RNA polymerase II to the specific site of transcriptional
initiation. The general transcription factors, comprised of TFIIA, TFIIB, TFIID, TFIIE,
TFIIF, and TFIIH, are necessary for assembly of RNA polymerase at the core promoter
and for transcription initiation (Fig 1, D) (34). The combination of the RNA polymerase
II and the basal transcription factors melts the core promoter sequence to create a open
complex in which 12 to 15 basepairs (bp) of DNA unwind to form a single-stranded
bubble (33, 54, 189). This open complex allows initiation to occur by catalyzing a
number of phosphodiester bonds in messenger RNA (mRNA). In most cases of
transcription initiation, RNA polymerase II and associated factors initiate transcription
and release small mRNA fragments from the open promoter complex (118). Finally, the
RNA polymerase II overcomes these abortive initiations to synthesize longer mRNA
which extends past the open promoter complex. After 25 to 30 bp, the elongating
complex pauses and usually requires stimulation from transcription factors in the
promoter complex and modification of the RNAPII to undergo promoter escape and
create the entire mRNA transcript (189).
One of the most critical factors for initiating transcriptional activity is the TATA-
Binding Protein. The TBP is similar to a symmetrical molecular saddle on the core
promoter DNA (25, 134). When the TBP is bound to a TATA box, the molecular saddle
binds the promoter and causes a sharp bend in the DNA strands which induces a partial
unwinding of base pairing at the initiation site (84). Along with TBP, the TFIID complex
contains the TBP-associated factors or TAFs (18, 192). The TAFs regulate the ability of
the TBP to select the specific site of transcriptional initiation. The requirement for the
TAFs is most clearly seen in the difference between the TATA-directed core promoters
and the Inr-directed or null core promoter elements. The TBP protein is able to initiate
transcription on TATA box elements, independent on any TAF proteins in the TFIID
fraction. However, for Inr-dependent promoters or null core promoter sequences, the
TAF proteins are required for transcriptional activation and interaction with the
transcription factors in the URSs (119).
The TFIIA fraction acts directly with TBP and stabilizes the TBP-DNA
interaction (120). The protein subunits within TFIIA have direct contacts with
transcriptional activators (140, 220). TFIIA may inhibit general transcriptional repressors
by displacing or blocking those proteins from their respective effects on TFIID activity
(139). The TFIIB fraction has been shown to directly influence the selection and site of
trancriptional activation (12, 146). The TFIIB subunit structure seems to set the distance
between the core promoter element and the transcriptional start site. This observation is
proven by TFIIB mutants which shift the site of initiation because they no longer allow
interactions between RNA Polymerase II and the TFIIB fraction (4, 17, 19). Recent
crystal structure experiments have shown that the actual distance between TFIIB and the
RNA polymerase II catalytic site is about 32 bp which is the average distance between
most core promoter TATA box elements and the transcriptional start site (107). TFIIB is
able to interact with a large number of transcriptional activators and the resulting
interaction is a measure of the effectiveness for that activator in the upstream activating
sequence (110, 213).
The TFIIF fraction functions to stabilize the preinitiation complex on the core
promoter element. This stabilization may be the result of altering the DNA topology.
Experiments that crosslink the preinitiation complex to the DNA show that the DNA is
wrapped in one complete turn around the preinitiation complex (153). TFIIF is required
for this tight wrapping that causes stress in the DNA resulting in promoter melting and
open complex formation. The TFIIF factors also function as a transcription elongation
factor. This elongation activity may be regulated by its DNA wrapping ability or an
intrinsic kinase activity (154).
The TFIIE function may be related to a zinc ribbon motif within its protein
sequence (95). TFIIE can bind single-stranded regions of DNA and enable melting of the
core promoter sequence. From experimental data, the requirement of TFIIE in
maintaining an open promoter complex can be overcome by a synthetic, premelted
promoter sequence (72, 141). The induction and stability of an open promoter complex is
related to the actual promoter sequence and the TFIIE requirement has been shown to
vary between specific promoter sequences (158, 185). Other functions of the TFIIE
fraction may be linked to the TFIIH fraction. TFIIE assembles into the RNA Polymerase
II preinitiation complex before TFIIH and may stimulate TFIIH recruitment or the CTD
kinase and ATPase activities of TFIIH.
The TFIIH fraction has been characterized into two separate functional
complexes. The first complex encompasses the core TFIIH functions and the second
complex acts in a kinase/cyclin function. The core TFIIH contains a DNA-dependent
ATPase, an ATP-dependent helicase, and a CTD kinase activity (32). The proteins
responsible for these activities, XPB/ERCC3 and XPB/ERCC2, are found within the
nucleotide excision repair complex. The XPB helicase is required for promoter opening
in vitro and is critical for the conversion from abortive transcription initiation to
transcriptional elongation (42, 57, Bradsher, 2000 #3377, 71, 73). The TFIIH
kinase/cyclin activities are found within the Cdk7/cyclin H proteins (155, 162, 167). The
role of these proteins is to phosphorylate the RNA polymerase carboxy-terminal domain
(CTD) (32). The degree of RNA polymerase II CTD phosphorylation is related to the
ability to switch from transcription initiation to elongation.
RNA Polymerase II Holoenzyme
The purified eukaryotic core RNA polymerase II contains between 10 and 12
different subunits that catalyze DNA-dependent RNA synthesis in vitro. However, the
lack of general transcription factors prevents any specific core promoter recognition. The
largest subunit of the RNA polymerase II has a carboxy-terminal domain (CTD) that
contains tandem repeats of a consensus peptide sequence (Tyr-Ser-Pro-Thr-Ser-Pro-Ser)
(35, 221). The CTD domain is essential for cell growth and there are 52 repeats of the
consensus peptide sequence in the human RNA Polymerase II (1, 6, 223). CTD
regulation is controlled by the amount of phosphorylation on the repeat sequences (37).
Within transcription initiation complexes, the RNA polymerase II CTD domains are not
phosphorylated and appear to recruit the Srb/Mediator complexes to the RNA polymerase
(86, 127). The Srb/Mediator complex functions to transmit the signals from the upstream
transcriptional activators to the components of the RNA polymerase II and its basal
After the recruitment and assembly of the RNA polymerase II preinitiation
complex, the holoenzyme switches from a transcription initiation complex to an
elongation complex through the modification of the CTD phosphorylation state. The two
kinases responsible for the CTD phosphorylation are Cdk7 and the Cdk8 proteins (46).
The Cdk7 kinase is located within the general transcription factor, TFIIH (115). The
TFIIH activity is required for the switch into a stable elongation complex and the Cdk7
kinase phosphorates the CTD subunit allowing release from the initiation complex (42).
The Cdk8 protein is a subunit within the Srb/Mediator complex and may regulate
transcription elongation through upstream activation factors (Fig. 1, E) (78, 115, 183).
After these two kinases have phosphorylated the RNA polymerase II CTD, the
hyperphosphorylated CTD domain promotes the formation of DNA-dependent RNA
synthesis along the protein coding sequence. The phosphorylated RNAPII recruits the
mRNA capping enzyme to the newly formed transcript and allows mRNA capping to
take place soon after promoter clearance (30, 126). In addition to mRNA capping events,
the CTD phosphorylation alters the factors and subunits associated with the RNA
polymerase II enzyme (137, 208). The Srb/Mediator complex only interacts with the
hypophosphorylated CTD and is released with phosphorylation of the CTD. Elongation
complexes containing TFIIS are associated with hyperphorylated CTD regions.
Adeno-associated virus (AAV) is a human, single-stranded DNA virus. It has a
genome size of 4.7kb that encodes only two open reading frames (ORF), rep and cap
(133). These two ORFs are flanked by two inverted terminal repeats that are required for
genome replication, integration, and viral packaging (Fig. 2) (219). An AAV productive
infection requires the activities of another virus to alter the cellular replication and
transcriptional mechanisms. The most widely characterized helper virus for AAV is
Fig. 2. Structure of the Adeno-Associated Virus Genome. In the upper section of the
diagram, the two different open reading frames within AAV are shown by rectangles
named Rep and Cap. The locations of the p5, pi9, and p40 promoters are demonstrated
by bent arrows. The terminal repeats (TR) sequences are diagrammed as darkened boxes
at both ends of the AAV genome. The lower portion of the diagram shows the AAV
transcripts initiated at their relative promoter location. The left side indicates the
transcript size and the molecular weight of the protein is on the right.
p5 p19 p40
Adenovirus. Clinically, AAV is only isolated from patients with adenovirus (Ad)
infections (13, 14, 148). However, AAV infection alone has never been associated with
any disease. If adenovirus is not present during primary AAV infection, an abortive
infection results in an integrated proviral structure (28, 125, 128). Most AAV provirus
genomes exhibit site-specific integration events in the human genome (93, 160, 165,
204). These genomes can be rescued by superinfection with adenovirus, which induces
both proviral rescue and replication (28, 101, 128).
Adenovirus Helper Functions
Several adenovirus genes have been identified that possess specific helper
functions during AAV coinfection (48, 132, 133). The adenovirus El A gene product
functions as a trans-activator for both Ad and AAV promoters. The El A 289 amino-acid
protein expressed during an adenovirus infection binds to transcription factors on the
AAV p5 promoter and induces AAV gene expression. The E1B 55-kd protein regulates
the post-transcriptional export of viral mRNAs into the cytoplasm. The E2 region
encodes the Ad DNA binding protein (Ad DBP). The Ad DP promotes transcriptional
activation from the AAV promoters and may enhance AAV DNA replication. The E4
region influences many cellular activities to support both Ad and AAV productive
infections. The E4 ORF6 gene product increases the degradation of cyclin A and inhibits
the kinase activity of Cdc2 that promotes the cell to remain in late S phase of the cell
cycle. The induction into S phase will result in the expression of more DNA replication
proteins that will convert the single-stranded viral genomes into double-stranded DNA
templates Finally, the VA RNAs of Adenovirus enable the initiation of AAV protein
synthesis by overcoming Ad interferon-induced host cell shutdown of translation.
AAV Rep Proteins
The AAV genome has three different promoters identified by their map positions
of p5, pl9, and p40. The p5 and pl9 promoters transcribe the rep open reading frame.
Rep 78 and its alternatively spliced transcript Rep68 are produced from the p5 promoter.
The Rep52 and its spliced transcript Rep40 are transcribed from the internal pl9
promoter. The larger Rep78/68 proteins have many different activities during AAV
infection (9, 64, 67, 70, 97, 98, 100, 123). Rep78 and Rep68 have specific DNA binding
activity, site- and strand-specific endonuclease activity, DNA and RNA helicase activity,
and an ATPase activity (76, 89, 157, 175, 209). In the absence of adenovirus coinfection,
the large Rep proteins repress the AAV promoters (74, 98, 143, 205). However, during
Ad infection, Rep78/68 exhibit the dual abilities of transcriptional repression on the p5
promoter and transactivation for the p5, pi9, and p40 promoters. Additionally, a model
of AAV replication has been proposed in which the Rep78/68 proteins are responsible for
nicking the terminal repeats. The site-specific endonuclease activity of the larger Rep
proteins nick the terminal repeats thus creating a free 3'OH for AAV genome replication.
In contrast, the smaller Rep52 and Rep40 proteins have fewer characterized
activities during AAV replication. In the absence of adenovirus infection, these proteins
have the ability to repress AAV promoters while not exhibiting any site specific DNA
binding activity (74, 77, 97, 98, 138). Recently, Rep52 has been shown to exhibit
ATPase and helicase activity. Additionally, the Rep52/40 proteins have been shown to
increase the levels of single-stranded monomer during AAV infection. Since single-
stranded genome formation correlates with the packaging of AAV particles, Rep52/40
may function in packaging viral particles (27, 74, 98). Recently, King et al. have
demonstrated that the Rep52 helicase activity is probably directly involved in AAV
AAV Transcription without Adenovirus
The p5 promoter is the most widely studied promoter in the AAV genome
because of its direct role in the switch between latent and productive infection in the viral
lifecycle. Many previous studies demonstrated that no transcripts are detected during the
latent state of AAV (31, 100, 123). The initial studies of the p5 promoter determined that
the promoter contained a Major Late Transcription Factor (MLTF) binding site and a
previously unknown element which was responsive to the El A trans-activator of
adenovirus. The subsequent cloning of this transcription factor resulted in the
identification of the YY1 protein (Ying-Yang protein) named for its dual activities of
repression and activation on a downstream promoter (168).
Previous studies in our lab resulted in the identification of another protein binding
site in the p5 promoter, the Rep binding element (p5RBE). DNasel protection and gel
shift assays determined that the binding site consisted of a 22 bp sequence (125). Initially,
the determination of the p5RBE was performed using purified Rep68 from baculovirus
expression vectors. Sequence analysis of the entire AAV genome showed that similar
binding sites were located in the A-stem of the terminal repeat as well as the three AAV
promoters. The A-stem RBE affinity was shown to be 20 fold higher than the p5RBE
while the pl9 and p40 binding affinities were 160- and 80- fold less than the A-stem
RBE, respectively (125).
AAV Transcription with Adenovirus
Initial analysis of the pi 9 and p40 promoters was performed in our lab by a novel
complementation system (123). Mutational analysis of the two promoters caused direct
alterations of the Rep protein sequence in the AAV genome. In order to prevent this
problem, the Rep protein was supplied in trans by another plasmid pl9/40S which
contained silent mutations in the Rep protein downstream of the pl9 and p40 start sites.
To analyze the effects of the deletions within the pi 9 and p40 promoters, primers were
selected that would distinguish between the pi9 and p40 mutant promoter transcripts and
the transcripts from the Rep complementing plasmid, pl9/40S. This allowed the
measurement of transcripts by primer extension that were synthesized only from the pi 9
and p40 promoter deletions.
The deletion analysis of both the pi 9 and p40 promoters was performed in a
series of 5 contiguous 30 bp intervals proximal to each start site. For the pi9 promoter,
two separated 60 bp regions were necessary for the Rep-mediated activity. One region
was identified between positions -153 to -94 and the other was the region from -63 to -4,
both upstream of the pi 9 start site (Fig. 3 A). For the p40 promoter, two regions of Rep-
mediated induction were identified through deletion analysis. One region was the
immediately upstream -60 bp region of p40 while the other region required the -153 to -
94 region upstream of the pi 9 promoter.
Another deletion analysis for both pi9 and p40 promoters were performed by
progressively larger proximal 5' deletions. The initial deletion named pIM29 dll-320
eliminated the p5 promoter and resulted in pi9 and p40 transcript levels that were 5% of
wild type levels. This data revealed a vital element for transactivation of the pi 9 and p40
promoters that was within the p5 promoter region. Subsequent serial deletions resulted in
no greater Rep-mediated induction of pl9 or p40 eliminating the possibility of a
transcription factor binding site that represses the pi9 and p40 promoters (Fig. 3B). In
Fig. 3. AAV Promoters and Promoter Deletion. A, A portion of the plasmid pIM29,
containing wild type AAV nucleotides 191 to 4484, is shown with an expanded view of
the pi9 and p40 promoters. The relative positions of the pl9 and p40 promoters are
shown by arrows. The locations of the 30bp deletions are diagrammed by lines denoting
the nucleotide position relative to the promoter initiation site which precedes each
deletion. Below each 30bp deletion, the relative strength of that specific promoter mutant
is shown as a precentage of wild type pi9 or p40 promoter activity. B, The plasmid
pIM29 is shown with the Rep coding region shaded. The relative positions of the p5,
pi9, and p40 promoters are marked by arrows, and the intron is represented by a bent
arrow. Below pIM29, the 5â€™deletions used in that study and the AAV restriction sites
used in their construction are shown in the diagram. They are designated by 29dl
followed by the numbers of AAV nucleotides deleted. The relative transcriptional
activity of each promoter mutant plasmid was shown as a percentage of the wild type
pIM29 plasmid strength.
-154 -124 -94 -64 -34
\ \ \ \ \
-154 -124 -94 -64 -34
p19 10 10 100 10 <2
p40 10 30 150 100 100
100 100 100 100 100
92 65 25 10 <2
P19 p40 4484
29dl 1-687 f
â– //â– 1
contrast, the last two deletion constructs named pIM29 dll-1044 and pIM29 dl3-23 differ
only by the presence of a terminal repeat. The presence of the terminal repeat caused the
Rep-mediated induction of the p40 promoter at wild type levels.
The exact determination of the transcription factors proximal of the pi 9 promoter
was performed by DNase I protection. This biochemical analysis identified the
transcription elements SP1-50, GGT-110, SP1-130, and CArG-140 sites relative to the
pi 9 start site (145). Direct determination for some of these protected regions as true SP1
binding sites was performed by competitive gel shifts using SP1 oligos and labeled wt
AAV fragments. As a result, the -50, -110, and -130 sites were positively identified as
SP1 binding sites upstream of the pi 9 promoter. The CArG-140 site remained bound
during competitive gel shift assays containing a serum response element (SRE) that
normally contains authentic CArG-like elements. The next step in the CArG-140
identification procedure was an UV cross-linking experiment, which identified a protein
larger than 34kDa. The combination of a CArG-like binding site and a protein mass of
34 kDa indicated a previously uncharacterized protein. After the identification of each
binding site, the actual in vivo function for each site on pi9 activity was tested using
mutants in each transcription factor site. In order to do this in vivo, the pl9/40S
complementation assay was used to compare the effect of Rep-mediated induction on
each pi9 promoter mutant. The average pi9 transcript level using the wt AAV genome
without terminal repeats (pIM45) complemented with pl9/40S was normalized to one.
The ratio of pi 9 transcripts in each of the pi 9 promoter mutants with or without Rep+
pl9/40S was calculated to determine which elements were responsible for Rep-mediated
induction. If the ratio was relatively unaffected, the pl9 element would be vital for Rep-
mediated induction of pi 9. From this data, only two sites were greatly affected by the
Rep+ pl9/40S induction of the pi 9 promoter. These two sites were the SP1-50 and
CArG-140. Each resulted in the reduction of pl9 transcripts to 20% of wt pi9 promoter
Analysis of the p40 promoter by Dnase I protection assay determined a number of
protected elements. These elements were identified as API-40, SP1-50, GGT-70, and
MLTF-100 binding sites. Two additional biochemical assays, competitive gel shift
analysis and UV cross-linking, were performed to confirm the identity of the sites.. The
combination of these two procedures determined that the SP1-50, GGT-70, and MLTF-
100 sites did have transcription factor binding activities. To test the Rep-mediated
response of the p40 promoter in vivo, transcription factor binding mutants were produced
for each site. Using the pl9/40S complementation assay, Rep induction depended only
on the SP -50 and TATA -30 binding sites. Additionally, the p40 activity was dependent
on the CArG-140 element of pl9 correlating directly with the previous -153 to -94 bp
p40 promoter deletion mutant (144).
This extensive deletion analysis determined that the Rep-mediated induction of
both the p 19 and p40 promoters required three separate elements. One required region is
the proximal SP1-50 element at or in front of each promoter. Another element is a
common -153 to -94 p 19 region defined as the CArG-140 site. The third and final
element appears to be a RBE that can be located in either the left terminal repeat's A-stem
RBE or the p5RBE.
To distinguish between the effects of either the p5RBE or the A-stem RBE on the
AAV promoters, a series of RBE mutants were created to define Rep-mediated elements
responsible for trans-activation of the p5, pi 9 and p40 promoters. The AAV genomic
subclone lacking terminal repeats (pIM45) was normalized to one for transcript levels
from each promoter. The first mutant targeted the p5RBE. As result, the p5 promoter
transcription increased by 3.2-fold while the pi9 and p40 promoters decreased by 5-fold.
This result indicated the p5RBE had a repressive effect on the p5 promoter while
simultaneously transactivating the pl9 and p40 promoters. The next RBE construct had
an intact, wild type p5RBE and a wild type A-stem RBE resembling the fully functional
AAV terminal repeat. This construct restored the pi9 and p40 transcripts to pIM45
levels while raising the p5 promoter to 3-fold. The final construct had a wild type A-
stem RBE and a mutated p5RBE. As a result, this construct exhibited a 8-fold increase in
the level of p5 transcripts relative to the pIM45 subclone. Additionally, the pi9 and p40
promoters had a 2-fold increase in transcription compared to pIM45 levels. This last
construct showed the p5RBE had a direct repressive effect on p5 transcription while the
more distal A-stem RBE transactivated the p5 promoter. However, the p5RBE and the
A-stem RBE appear to be equivalent and redundant transcriptional elements in Rep-
mediated transactivation of the pl9 and p40 promoters. During adenovirus infection, Rep
78 or Rep 68 appeared to behave as a transcription factor that can be both a repressor (of
p5) and a transactivator (of pl9 and p40).
Analysis of the Rep binding abilities on both the terminal repeat RBE and the
p5RBE show that either the Rep78 or Rep68 proteins were required for trans-activation
of the three AAV promoters. The Rep78 and Rep68 proteins were known to interact but
no analysis had been performed on the ability of the larger Reps to bind either Rep52/40
or any cellular proteins. The initial analysis for large and small Rep interaction was
performed using immunoprecipitation against the larger Rep protein domains and by
detecting any Rep proteins with an antibody against the common Rep protein carboxy-
terminal end. From this immunoprecipitation, the larger Rep proteins were only able to
precipitate the Rep52 protein. The in vivo interaction between the large Rep78 and 68
proteins and Rep52 indicated a method of interaction between the Rep78/68 binding
element within the TR and the p5RBE, the large Rep proteins, and the smaller Rep52
protein. To detect Rep78/68 effects on the p5RBE, a p5 promoter CAT construct was coÂ¬
transfected with a constant amount of Rep78/68-expressing plasmid and increasing
amounts of a Rep52 plasmid. The result of this titration was the derepression of the p5
promoter through an increasing gradient of Rep52 concentration.
Another suspected Rep78/68 interaction was the common SP1-50 binding site that
is conserved within the parvovirus family. The initial analysis of a Rep78/68 and SP1
interaction was performed using a gel supershift assay with an Spl-50 binding site. The
positive supershifting gel fragment indicated a direct role for the Rep78/68 interaction
with Spl. Trans-activation of the p 19 and p40 promoters could result from the Rep78/68
bound to the upstream RBEs and each of the SP1-50 binding sites proximal to each
promoter. In order to test a model for DNA looping, an AAV genome fragment
containing the p5RBE and the SP1-50 pi9 was incubated with purified Rep68 and SP1
proteins. The mixture was examined by electron microscopy and analyzed by digitized
measurements. These measurements showed a conserved DNA looping structure
correlating to the direct interaction between the large Rep proteins bound at the p5RBE
and the Spl protein at the pi9 -50 binding site.
Model for Activation of an AAV Productive Infection from Latency
For this model, the proviral structure of AAV is limited to one proximal terminal
repeat containing a single A-stem RBE site. The cellular YY1 and MLTF transcription
factors are bound to their sites within the p5 promoter. In the absence of adenovirus
infection, YY1 bound at the -60 position of the p5 promoter acts as strong repressor of
Rep78/68 transcription (Fig. 4, A) (168). The specific activity of the YY1 -60 binding
prevents any trans-activation of the p5, pi 9, or p40 promoters through either the terminal
repeat or the p5RBE.
During adenovirus infection, the Ad early proteins are responsible for the switch
between AAV latency and productive infection. The El A trans-activating protein
provides the first helper function for AAV transcription. The El A protein has three
conserved domains for interaction with cellular cell cycle control proteins. The El A CR1
and CR2 regions bind the pRB and pi 07 proteins. Expression of the adenovirus El A
protein prevents E2F:pRB complex formation. E2F displacement allows the protein to
act as a transcription factor for many cellular replication proteins. However, the CR3
region of El A interacts with the p300 protein in infected cells. This physical interaction
between El A and p300 is important because the YY1 repressor protein has been shown
previously to bind p300. The last 17 amino acids of YY1 are responsible for this
interaction and YY1 binding mutants are unable to show an ElA-mediated response. As
a result, the El A protein binds specifically with a p300:YYl complex on the p5 promoter
(24, 103, 108, 168). This binding activity induces a conformational change upon the
YY1 protein in a repressive state to expose its activation domain. This change induces p5
promoter trans-activation (Fig. 4, B). After the exposure of the -60 YY1 activation
domain, p5 transcription occurs through a mechanism involving the YY1 initiator
Fig. 4. Loss of AAV Promoter Repression through Adenovirus Infection. A, In the
absence of Adenovirus infection, YY1 and Rep proteins bound at the p5 promoter act as
strong repressors of AAV gene expression. B, during Adenovirus infection, the Ad El A
protein binds to the YY 1 proteins and converts their function as repressors to activators
of AAV gene expression.
element. The YY1 initiator element binds to DNA and interacts with the TFIIB complex.
The YY1 protein is stabilized by its TFIIB interaction facilitating pre-initiation complex
formation at the p5 promoter (191).
Induction of the p5 promoter results in the increased cellular concentration of
Rep78/68. These two proteins bind the RBEs within the AAV genome as a direct
function of their increased concentrations. The first RBE bound is the terminal repeat A-
stem. The binding of Rep 78 and/or Rep 68 trans-activates the p5, pi 9, and p40
promoters. As a direct result, the levels of larger Reps are increased through
transcriptional activation (Fig. 5, A). In addition, the Rep 52/40 and capsid proteins are
increased by the A-stem RBE trans-activation upon the p 19 and p40 promoters. Rep68 is
shown to specifically bind the p5RBE and trans-activate the pi9 and p40 promoters.
After p5RBE binding, the p5 transcription levels decrease while pi9 and p40
transcription levels increase (Fig. 5, B).
As the relative levels of p 19 and p40 promoter directed transcription increase, the
Rep 52 and Rep 40 proteins alleviate the repression on the p5 promoter. Previous studies
in our lab demonstrated complex formation between the Rep78/68 proteins and Rep52.
In addition, the Rep78/68 proteins repress the p5 promoter. However, titration of
increasing levels of Rep52 causes derepression of the p5 promoter. The present model
supports a feedback mechanism in which the rising amounts of Rep52/40 act on the
Rep78/68 proteins bound at the p5RBE. The Rep52 protein would cause an alteration of
the large Reps on the p5RBE to eliminate repression of the p5 promoter (Fig. 5, C).
This feedback loop model between the products of the p5 and p 19 promoters
creates a steady-state level of transcripts. The molar transcript ratios of 1:10:100 for the
Fig. 5. Model of Rep Feedback Regulation between the p5 and pl9 Promoters. A,
Rep 78/68 bound to TR A-stem sequence transactivates the p5, pi9, and p40 promoters.
B, Increase of Rep protein concentration allows Rep 78/68 binding to p5 promoter
repressing the p5 promoter. Rep bound at p5 promoter transactivates the pi9 and p40
promoters. C, Higher pi9 transcription creates more Rep52 protein which derepresses
the p5 promoter.
p5, pi9, and p40 promoters maintain four relationships. First, the lower level of p5
transcription creates enough Rep78/68 to resolve the terminal repeats while preventing
excess endonuclease and helicase activity from eliminating any transcriptionally
competent AAV genomes. Second, the increasing Rep78/68 levels are autoregulated by
their repression of the p5 promoter. Third, the synthesis of higher levels of Rep52/40
transcripts resulting from p5RBE trans-activation causes the derepression of the p5
promoter thereby increasing the Rep78/68 levels. Fourth, the p40 promoter is relatively
unaffected by this feedback inhibition allowing constant transactivation of p40 and
synthesis of the capsid transcripts.
MATERIALS AND METHODS
Cell Lines and Virus.
Human A549 cells (ATCC #CCL 185) were maintained in Dulbecoâ€™s modified
essential media (DMEM, Gibco BRL) containing 10% bovine calf serum (BCS, HyClone
Laboratories Inc.) at 37Â°C in 100mm culture dishes. Adenovirus 5 was grown and titered
on 293 cells.
The p5CAT plasmid is the same as the p5CAT190 plasmid described by Chang et
al. (24) and was kindly provided by Tom Shenk. It contains AAV2 nucleotides 190-310
followed by the CAT expression cassette.
The pIM45 plasmid contains the AAV-2 nucleotides 145-4373 in a pBS M13+
vector (Stratagene Corporation). It essentially contains all of the AAV genome except
for the terminal repeats.
pAXX is a modified pIM45 plasmid in which stop codons have been inserted by
site specific mutagenesis at Rep78 amino acid 71 and at Rep52 amino acid 14. Thus,
pAXX is incapable of producing either p5 or pi 9 Rep proteins, and it was used for the
construction of all of the CAT containing plasmids below. pAXX, pIM45 and all other
plasmids used in this study were sequenced to insure that the AAV sequences were
correct and to confirm the positions of the mutations.
The pl9CAT3 plasmid was created by inserting synthetic oligonucleotides within
the pCAT3BASIC plasmid (Promega Corporation) that together reconstructed the
essential elements of the p 19 promoter. The pi 9 synthetic sequence was created with
three pairs of oligonucleotides that were annealed and then ligated together. The first
oligonucleotide pair (cAAP-140) had the sequence 5'-
CGTCACAAAGACCAGAAATGGCGCCGTCTCGAGTGACAATT-3' that contains
AAV nucleotides 722-756 with a mutation that destroys the SP1-130 binding site and
converts it into an Xhol restriction site. The second pair of oligonucleotides
(pl9XbaSac) had the sequence 5'-
GAGCT-3' that contains AAV nucleotides 757-814 with the GGT-110 binding site
converted into an Xbal restriction site. The third pair of oligonucleotides (SP1-50CAT),
had the sequence 5'-
CCAGTGGGCGTGGACCCGCGGGGAACAGTATTTAAGCGCCTA-3' that contained
AAV nucleotides 815-869 with the TATA-35 site mutated into a SacII restriction site.
The Spl-130, GGT-110 and TATA-35 sites had been shown previously to have little
effect on pl9 transcription. All three oligonucleotide pairs were heated to 90Â°C and
annealed together by slowly cooling to room temperature. They were then ligated using
T4 DNA ligase (Life Technologies). After ligation, a small amount of the DNA product
was used as template in a PCR reaction performed with two primers, pl9XmaI 5'-
ATACCCGGGCACAAAGACCAGAAATGGCG-3' and pl9BglII 5'-
ATAAGATCTCGTGAGATTCAAACAGGCGCTT-3'. The PCR reaction amplified the
synthetic pi9 promoter, which was digested with Xmal and Bglll and cloned into
pCAT3BASIC (Promega Corp.) vector that had been digested with the same restriction
The pl9CAT3-700 plasmid was created by subcloning an oligonucleotide
containing the wild type p5 promoter Rep binding element (p5RBE) sequence, 5â€™-
AAGCCCGAGTGAGCACGCAGGGTCTAGTACT-3 â€™, into the BsaAI restriction site of
the pl9CAT3 plasmid 700 nucleotides upstream of the start of transcription of pi 9. The
pl9CAT3-145 plasmid was created by subcloning the wild type p5RBE sequence into the
Mlul site at the -145 site of pl9CAT3. The pl9CAT3-100 plasmid was created by
subcloning the wild type p5RBE sequence into the Xhol site at the -100 site of
pl9CAT3. The pl9CAT3+25 plasmid was created by subcloning the p5RBE sequence
into the Bglll site at the +25 nucleotide site of pl9CAT3. The pl9CAT3+1225 plasmid
was created by subcloning the p5RBE sequence into the +1225 site of pl9CAT3.
The pIM45CAT3 plasmid was constructed by first digesting pAXX with Bell,
which cleaves at AAV nucleotide 965. The linear pAXX DNA was ligated to the BamHI
and Bell fragment of pcDNA3.1(+)CAT (Invitrogen Corporation) which contains the
CAT gene. pIM45 contains AAV nucleotides 145-965 (including all of the p5 and pl9
promoters) followed by the CAT gene. The psub262CAT3 plasmid was created in the
same way by ligation of the BamHI and Bell fragment from pcDNA3.1(+)CAT into the
psub262 plasmid, which contains a mutant p5 RBE.
The pIM45CAT3poly A plasmid was created in two steps. The Smal to Nrul
fragment from pAXX containing the AAV p5 promoter as well as a portion of the Rep
gene (AAV bp 145- 658) was inserted into the BsaAI site of pl9CAT3; this plasmid was
called p5_pl9CAT3. Then, the Smal and Sfil fragment from the p5_pl9CAT3 plasmid
(containing AAV bp 145-544 and the late polyadenylation signal of SV40) was
substituted for the Nrul to Sfil fragment (containing AAV nucleotides 544-658) in the
pIM45CAT vector. The resulting pIM45CAT3poly A contained AAV nucleotides 145-
544, followed by the SV40 late poly A site (563 bp), followed by AAV nucleotides 722-
869 from pl9CAT3 containing substitutions at Spl-120, GGT-110 and TATA-20,
followed by the CAT gene.
The 2xGAL4 plasmid was created by site-directed mutagenesis of the p5RBE and
the pi9 SP1-50 sites of pIM45CAT3 to GAL4 DNA binding sites. The p5RBE within
pIM45CAT3 was mutated to a GAL4 DNA binding element using the oligonucleotide
CTCC-3â€™. The pl9 promoter SP1-50 site within pIM45CAT3 was mutated to a GAL4
DNA binding site using the oligonucleotide sequence 5â€™-
The pM-53 plasmid expressed a fusion protein of the GAL4 DNA binding domain
and the mouse p53 protein containing p53 amino acids 72 to 390. It was supplied in the
Mammalian MATCHMAKER Two-Hybrid Assay Kit (Clontech Laboratories). The pM-
Tg plasmid contains the GAL4 DNA binding domain fused to SV40 T antigen amino
acids 87-708. The SV40 T-antigen DNA fragment containing amino acids 87 to 708 was
removed from the pVP16-T plasmid (Clontech Laboratories) by EcoRI and Sail digestion
and inserted by directional cloning into EcoRI and Sail digested pM plasmid (Clontech
The 2xGAL4 subMLTF plasmid was created by site-directed mutagenesis of
pIM45CAT3 2xGAL4 using the oligonucleotide 5â€™-
GGT CT AG AGGT CCT GT ATT AG AT AC AC GCGT GTCGTTTT GCG AC ATTTTGCG A
CACC-3â€™ that resulted in the replacement of the p5RBE site with the Mlul restriction
site. The 2xGAL4 subYYl-60 plasmid was mutated at the YY1-60 binding site within
the p5 promoter to EcoRI and BamHI sites using the oligonucleotide 5â€™-
CCTGTATT AG AT AC ACGCGT GTCGTT GAATTCT GGGATCCGAC ACC AT GT GGT
CACGC-3â€™. The 2xGAL4 subMLTF, YY1-60 plasmid was created by the site-directed
mutagenesis of the 2xGAL4 subMLTF plasmid using the subYYl-60 oligonucleotide
CACGC-3â€™. The 2xGAL4 subMLTF, YY1-60, YY1+1 plasmid was created by site-
directed mutagenesis of the 2xGAL4 subMLTF, YY1 -60 plasmid using the
oligonucleotide sequence of 5â€™-
CGGCGG AAGACTCTCCTCCGAGGGTCT AAATTTTGAAG-3 â€™.
Plasmid transfections were performed using cationic liposomes (LipofectAMINE
Plus, Life Technologies). Twenty-four hours before transfection, A549 cells were plated
in 60mm dishes so the cells were 75% to 90% confluent on the day of transfection. The
A549 cell media was removed and 2 ml of serum-free DMEM was added for the
transfection procedure. Plasmid DNA was mixed with 250 pi of serum free DMEM
containing 8 pi Plus Reagent (Life Technologies) and incubated at room temperature for
15 minutes. The plasmid DNA and Plus Reagent mixture was mixed with 250 pi of
serum-free DMEM containing 12 pi of LipofectAMINE and incubated for another 15
min. The entire 500 pi of plasmid DNA/Lipo feet AMINE mixture then was incubated
with the A549 cells without serum for three hours. At three hours post-transfection, 2.5
ml of DMEM with 20% bovine serum with or without Adenovirus 5 at a multiplicity of
infection (MOI) of 5 pfu/cell was added to the A549 cells. To control for transfection
efficiency, each transfection contained 1 pg ofpcDNA 3.1(+)gfp and 1.5 pg of
pcDNA3.1(+)P gal. Extracts were then assayed for (3 gal activity using ONPG (Promega)
to normalize for the transfection efficiency. In those cases where a linear CAT reporter
plasmid was used, a linear p gal plasmid was also used.
CAT Reporter Assays
Forty-eight hours post-transfection, the A549 cells were washed with 2 mL PBS
and lysed in 400 pi of lysis buffer (CAT Reporter Lysis Buffer, Promega Corporation).
The whole cell extracts were vortexed for twenty seconds and heated at 65Â°C for 10
minutes to inactivate endogenous deacetylases. After heat inactivation, the extracts were
centrifuged for 2 minutes and the clarified supernatant was transferred to a new tube.
CAT activity was measured by a standard chloramphenicol acetylation reaction, which
contained in 125 pi: lx lysis buffer (Promega Corp.), 0.2 mM n-Butyryl Coenzyme A
(Promega), 10 pM l4C-chloramphenicol (Amersham Pharmacia Biotech, 58 mCi/mmol)
and either 4 pg of protein from an adenovirus-infected extract or 20 pg of protein from an
uninfected extract. The reaction was incubated for 24 hr at 37Â°C and then extracted with
300 pi of mixed xylenes (Fisher Scientific). The entire upper organic phase containing
the acetylated chloramphenicol was back extracted two times with 100 pi of 0.25M Tris-
HC1 pH 8. The amount of acetylated chloramphenicol in 200 pi of the mixed xylenes
phase was determined by liquid scintillation counting. Each construct was tested by
transfection and CAT assay a minimum of three times. The average CAT activity (as
cpm of acetylated product) was calculated after correction for the amount of extract used,
and is reported +/- one standard deviation.
Analysis of Adeno-Associated Virus Transcription
The overall goal of my research was to understand the regulation of the Adeno-
Associated Virus promoters. In order to perform this analysis, the different AAV
promoter elements were to placed upstream of reporter gene constructs which gauged the
relative influence of the DNA sequence upon gene expression. In the previous studies of
AAV transcriptional regulation, the analysis was performed by isolating a single AAV
promoter region and mutating a series of single transcription factor binding sites (123).
Another study focused on the effects of a single transcription factor upon all three AAV
promoters was performed in the global genomic context of the AAV genome (143). In
the context of the AAV genome, redundant transcription factor effects would not be
detected through the loss of the single transcription factor. To address the combinatorial
effects of multiple regulating factors on the AAV genome, my research goals focused on
the determination of the non-structural AAV protein Rep as a transcriptional activator,
defining the activity of Rep in AAV gene expression, and the role of a Rep-Spl
interaction in the direct mechanism of AAV transcriptional regulation.
Define Rep Binding Element as Enhancer or Proximal Promoter Element
AAV must convert quickly from a latent virus, presumably integrated in
chromosome 19 (93, 160), to a productive, replicating genome following Ad infection
(133). To accomplish this, the virus appears to use two factors as a switch. The first is
Rep protein, which in addition to YY1 and MLTF, binds upstream of the p5 promoter
(Fig. 6) to shut off p5 transcription during latency (23, 97, 168). Thus, in the absence of
Ad, Rep78 and 68 cooperate with cellular proteins to completely inhibit p5 transcription
(143, 203). The second is adenovirus infection. Ad infection leads to Ela and Ad DBP
mediated activation of p5 (23, 24, 102), which accomplishes two things. It increases
transcription from the p5 and pi 9 promoters to produce increased levels of the four Rep
proteins (9, 23, 102). Rep78 and 68, in turn, increase transcription from the pi9 and p40
promoters to an even higher level (100, 123, 143, 203), while reducing transcription from
the p5 promoter (143, 203). Ad infection also independently activates pi9 transcription
(9). Thus the p5 and pl9 promoters are repressed by Rep in the absence of Ad and
differentially regulated in the presence of helper virus. During the proviral stage, Rep
autorepresses its synthesis to prevent excision of the provirus and expression of its gene
products. In the presence of the helper virus, Rep induces the synthesis of the pl9
proteins that required are for encapsidation and maintains the p5 Rep proteins at a lower
level to optimize the level of replicating intermediates.
The p5 promoter (Fig. 6) has been shown previously to contain three elements
involved in p5 regulation, an MLTF site at -80, a YY1 site at -60, and an RBE at -20
(23, 97, 125, 143, 168). In the absence of Ad infection, specifically Ela gene expression,
all three factors (YY1, MLTF and Rep) repress p5 transcription (24, 74, 97, 98, 143). In
the presence of an adenovirus coinfection, YY1 and MLTF both activate p5 transcription
(24). In the case of YY1, this apparently occurs via an interaction of YY1 and Ela with
the cellular p300 protein (103). Rep, however, continues to repress p5 when bound to the
p5 RBE, but is now capable of activating the two downstream promoters, pl9 and
Fig. 6. Sequences of the p5 and pi9 promoters. The known transcription elements in
the p5 and pl9 promoters are diagrammed along with their approximate positions
upstream of the mRNA start sites. p5CAT plasmid contains only the p5 promoter
elements driving CAT expression, while pIM45CAT3 contains both the p5 and pl9
promoter elements with the pi9 promoter driving CAT expression. Dotted lines indicate
intervening sequences that are not shown. Shown in italics are substitutions within the
pl9CAT3 promoter at -120, -110, and -20 that were previously demonstrated to have
little effect on pi9 transcription and the sub262 substitution within the p5 RBE that no
longer binds Rep protein. Shown in bold italics are the GAL4 substitutions in 2xGAL4
that replace the p5 RBE and the pi9 SP1-50 sites. A CREB/ATF site, which has been
mapped upstream of the MLTF site in p5, is not shown.
onR MLTF-80 YY1-60
TATA-20 RBE YY1+1
GAATTCTGGATCCACT AA 294
730 cAAP-140 SP1-130 GGT-110
SP1-50 TATA-35 TATA-20
730 cAAP-140 subSP1-130 subGGT-110
SP1-50 TATA-35 subTATA-20
... CC ApT G G G CGTG G^CfTA ATATp G AAC AG fcCGCGQ/GC
p40 (98, 143, 203). In addition to the YY1, RBE and MLTF sites, p5 contains a
conventional TATA site (-30) and a YY1 responsive initiator site (+1) (164, 178). In the
presence of Rep and Ad gene expression, only mutations in the TATA, YY1-60 and
MLTF sites significantly affect p5 transcription (143).
The pi9 promoter (Fig. 6) contains two TATA sites (-30 and -35), which are
redundant, two Spl sites (-50 and -130) and a site at -140 that binds an unidentified
cellular AAV activating protein (cAAP) (27, 145, 178). Transactivation of the pi 9
promoter by Rep appears to require both the -50 Spl site and the -140 cAAP site (145).
It also requires the p5 RBE (143). In the absence of the p5 RBE, the TR, presumably via
its RBE, can transactivate all three promoters (9, 123, 143, 145, 203). Evidence that the
RBE within the TR is probably responsible for transactivation comes from deletion
analyses of the TR (9, 203). The two RBE elements appear to be redundant with respect
to pl9 transactivation at low Adenovirus MOIs but the TR predominates at high Ad MOI
(>10) (9, 143, 203). Furthermore, at high multiplicities of infection of Adenovirus (>25),
the effect of Rep78 or 68 expression on pl9 activity is no longer seen; that is, expression
of Ad factors can substitute for Rep78 or 68 (203). Finally, it has been shown that Rep
and Spl can directly interact (68, 145), and that Rep bound to the p5 RBE can form a
DNA loop with Spl at pi9 (144).
Repression by Rep proteins is more complex. In contrast to transactivation,
which appears to require either Rep78 or 68 plus Ad infection, repression of the p5 and
pi 9 promoters occurs in the absence of Ad regardless of which Rep protein is expressed
(74, 97). Repression of the p5 promoter depends in part on Rep binding to the p5 RBE
but also requires a functional Rep ATPase (97, 98). However, repression of p5 can be
seen in the absence of a functional p5 RBE. Furthermore, the pi 9 promoter, which does
not have an efficient RBE binding site, can be repressed by all four Rep proteins,
including Rep52 and 40, which lack an RBE binding domain and contain only the Rep
helicase and ATPase domains (74, 77, 97, 174).
Our initial hypothesis was that the upstream p5 RBE-Rep complex might behave
like an enhancer sequence that activates transcription from downstream promoters. To
determine if this were true we made a series of pi 9 CAT constructs (Figs. 7 and 8) in
which CAT gene expression was driven by the pi 9 promoter. The first set of constructs
(Fig. 7) was made to be certain that the CAT constructs would accurately reflect the
control of p5 and pi9 transcription that is seen with the parental TR minus pIM45
plasmid or with wild type AAV. In this set of constructs (Fig. 7), all of the sequences
upstream of the pl9 mRNA start site were identical to those of wild type AAV
(pIM45CAT3) or contained a mutation in the p5 RBE (psub262CAT3) that eliminated
Rep binding (125, 143). To prevent expression of aberrant Rep proteins from
pIM45CAT3 and psub262CAT3, both plasmids contained an amber mutation at amino
acid 71 of Rep78. This mutation terminated the synthesis of Rep78 while the CAT
insertion prevented synthesis of Rep52, so that no Rep proteins could be detected in the
absence of a Rep expressing plasmid. With the exception of the terminal repeat, these
constructs contain all the sequences necessary for pi9 regulation and pl9 transactivation
by Rep (123, 143, 145). The p5CAT plasmid described by Chang et al. (24) was used to
monitor expression from the p5 promoter (Fig. 7). It contained all of the sequences
upstream of the p5 promoter that have been shown to be necessary for p5 regulation with
the exception of the TRs. All of the plasmids used in this study were missing the AAV
Fig. 7. Activity of the wild type p5 and pl9 promoters. A, Diagram of the p5 and pi 9
promoter elements in the CAT reporter constructs p5CAT, pIM45CAT3 and
psub262CAT3. The asterisk indicates a stop codon in the Rep78 open reading frame at
amino acid position 71. B-D, Graphic representation of CAT activity from the p5CAT,
pIM45CAT3, and psub262CAT3 reporter constructs after transfection in A549 cells in
the presence of plasmid alone (Mock), or with the addition of 1 mg of pfM45 (Rep),
Adenovirus at an MOI=5 (Ad), or 1 mg of pIM45 and Adenovirus at an MOI=5 (Ad &
CAT Activity (cpm)
p5CAT plM45CAT3 psub262CAT3
TRs because we and others have shown that the TRs are redundant activation elements
that promote excision and replication, thereby changing the template copy number
available for transcription (9, 123, 143, 159, 203).
The three plasmids (p5CAT, pIM45CAT3 and psub262CAT3) were transfected
into A549 cells in the presence or absence of a coinfection with Adenovirus (MOI=5) or
in the presence or absence of a cotransfection with the wild type Rep expressing plasmid
pIM45 (Fig. 7). pIM45 was chosen because we and others have shown that the four Rep
proteins Rep78, 68, 52, and 40 are expressed at different levels and have differential
effects on repression and transactivation of pl9 during productive infection (74, 97, 143),
and because pIM45 expresses the Rep proteins at approximately the same relative levels
that are seen during wild type viral infection (123, 203). Cells were harvested
approximately 40 hours after plasmid transfection and Ad infection and cell free extracts
were assayed for CAT activity as described in Methods.
As expected, coinfection with Ad alone significantly induced p5 transcription,
approximately 4 fold (Fig. 7 B). This presumably occurs through the interaction of the
El a proteins of Ad with the p300-YYl complex bound to the p5 promoter (24, 103, 168).
Cotransfection with a Rep expressing plasmid repressed p5 transcription both in the
absence (20 fold) and in the presence (12 fold) of Ad coinfection. This has also been
observed previously (9, 74, 98, 143) and is due in part to binding of Rep to the p5 RBE.
In contrast, pi9 transcription was significantly induced by Rep expression both in the
presence and the absence of Ad coinfection, about 5-6 fold (Fig. 7 C). This induction did
not occur if the p5 RBE was mutated so that it could no longer bind the Rep protein (Fig.
7 D). Ad coinfection alone also significantly induced pi9 transcription, approximately
80 fold, and this occurred to approximately the same level regardless of whether the p5
RBE element was intact (Fig. 7, C and D). The induction by Ad and Rep appeared to be
multiplicative and together they induced transcription from the pi 9 promoter by almost
450 fold (Fig. 7 C). p 19 CAT activity in the presence of Rep and Ad was approximately
20 fold higher than p5 CAT activity. This 20 fold difference was approximately the same
as that seen late after infection during normal wild type AAV infections when transcripts
are compared by other methods such as Northerns (9, 100). Thus, the CAT constructs
used in this study seemed to accurately reflect mRNA steady state levels seen during wild
type AAV infections or those seen with TR minus plasmid transfections.
Finally, we noted that when basal expression from the psub262CAT3 plasmid was
compared with that seen in the presence of the Rep expressing plasmid, there was
approximately a 2 fold inhibition of p 19 transcription (Fig. 7 D). Similarly, when the
level of expression in the presence of Ad was compared with expression in the presence
of Ad plus Rep, there was approximately a 2 fold inhibition of p 19 transcription by Rep
protein. Thus, expression of the Rep protein caused inhibition of the pi 9 promoter in the
absence of the p5 RBE. This has also been reported previously (9, 97).
The p5 RBE is not an upstream activation signal.
Having confirmed that the p5 RBE was essential for Rep mediated induction of
p5 transcription, we then asked whether the p5 RBE behaved like a position independent
enhancer or like an upstream activation signal. If the p5 RBE behaved like a
conventional enhancer or upstream activation sequence, we expected that an artificial
construct containing all of the essential pi 9 proximal promoter elements would continue
to respond to an upstream RBE in the presence of Ad and Rep gene expression. For this
purpose we designed a series of CAT constructs in which the pl9 proximal promoter
elements were left intact but the upstream AAV sequences, including the p5 promoter
were substituted with bacterial DNA. In these constructs the pi9 sequences up to -150 bp
of the mRNA start site were essentially the same as the wild type sequence (present in
pIM45CAT3) except that the TATA site at -35, the GGT site at -110 and the Spl site at -
130 were mutated (Fig. 6). These sites had been shown previously to be non-essential for
Rep induction or basal pl9 activity (145). The CAT coding sequence was inserted at +92
of the pi 9 message and a poly A signal was inserted upstream of the p 19 promoter to
prevent read through from fortuitous upstream polymerase II promoters in the bacterial
sequences. The p5 RBE signal was then inserted at various positions upstream or
downstream of the pl9 promoter. In the control plasmid, pl9CAT3, the p5 RBE was
The level of pi 9 activation seen with the pl9CAT3 plasmid in the presence of
either Rep or Ad alone was similar to that seen with the parental pIM45CAT3 plasmid
that contained all of the upstream AAV sequences including the p5 promoter elements.
As expected, Rep did not significantly induce p 19 when Rep and Ad were present
together if there was no upstream RBE (Fig. 8 B). Surprisingly, Rep also did not induce
pi 9 transcription in the presence of both Rep and Ad when an RBE was inserted at -700
upstream of the p 19 promoter. This is approximately the same position that the p5 RBE
occupies in the parental plasmid pIM45CAT3. Furthermore, Rep did not activate pl9
transcription (compare Ad only with Ad plus Rep lanes) regardless of where the RBE
was inserted upstream or downstream of the pi 9 mRNA start site. Instead, the RBE
acted like a repressor element at most of the positions tested in the presence of both Rep
and Ad, and the level of repression increased dramatically as the RBE was inserted closer
Fig. 8. Effect of RBE position on pl9 activity. A, Diagram of transcription elements
within the wild type p5 and pl9 promoters. B-G, Diagrams of the parental plasmid
pl9CAT3 (B) and derivatives of pl9CAT3 C-G, in which an RBE was inserted at various
positions with respect to the start of p 19 transcription (-700 to +1225). The pl9CAT3
plasmid has the minimum pl9 promoter elements as shown in Fig. 6 and no p5 promoter
elements. The CAT activity of each construct was determined after transfection into
A549 cells in the presence of plasmid alone (Mock), pIM45 (Rep), Adenovirus (Ad) or
pIM45 and Ad (Ad & Rep).
â– 600 p5 p19 CAT Activity (cpm)
A I W
qS> qC? -fP qC?
-O ** CAT -1 P19CAT3
^ nâ€”cat I P5RBE *
p, ^ cat | p5RBE
n n catt^p5RBE
to the pi9 promoter. The most dramatic repression was seen when the RBE was placed
at -100 upstream of the pl9 start site (compare Fig. 8 B, Ad + Rep with 8 E, Ad + Rep).
When the RBE was placed downstream of the pi 9 start site (Fig. 8 F and G), some of the
pi9 activity was recovered but the RBE continued to generally repress p 19 transcription
even when it was placed far downstream at +1225. Curiously, in the presence of only
Rep gene expression, pi9 activity was significantly induced over basal levels by Rep
when the RBE was placed at -700 or -145.
We concluded from these experiments that the RBE was not a conventional
upstream activation signal or an enhancer. It did appear, however, to have the ability to
act as a general repression signal in the presence of adenovirus infection under almost all
conditions tested when it was closer than 700 bp upstream or 1200 bp downstream of the
pl9 promoter. Our data also suggested that Rep itself was probably not an activator and
left open the question of how the p5 RBE could transactivate pi 9 in the context of the
normal AAV sequence.
Activation of pl9 is not due to read through from p5.
We considered two other possible mechanisms of pi 9 activation by the p5 RBE.
One was that transcription from the p5 promoter activated pi9 by a read through
mechanism. Although poorly understood, this has been shown to occur in the case of the
adenovirus Elb gene. In this case, active transcription of the El a promoter causes read
through activation of the Elb promoter in a cis-dependent manner (45, 121). Ela
transcription appears to alter the adenovirus genome into a transcriptionally competent
template before Ad DNA replication and late transcription have begun. This possibility
was not likely in the case of the p5/p 19 promoters because the p5 RBE inhibited CAT
expression (Fig. 7) from the p5 promoter at the same time that it induced CAT expression
from the pl9 promoter. However, it remained possible that CAT expression in this study
(as well as other steady state mRNA measurements done previously) did not reflect the
true firing rate of the p5 promoter. In order to address the possibility that p5 transcription
may be transactivating pi 9, two kinds of experiments were done. In the first experiment,
we compared pi 9 CAT activity from the pIM45CAT3 plasmid in the presence of Ad or
Ad plus Rep when the physical connection between the p5 and pl9 promoters was
removed by a restriction digest (Fig. 9). The pIM45CAT3 plasmid was transfected either
uncut, cut with Sphl, which cuts outside both the p5 and pi9 promoters, or cut with
Nrul, which cuts between the p5 and pl9 promoters. As before, the supercoiled uncut
plasmid showed strong activation of the pl9 promoter by Rep in the presence of Ad.
This was not seen when the plasmid was linearized by restriction digestion at either
restriction site even after the input DNA levels were normalized (see Methods). Thus,
Rep induction appeared to require a superhelical template. The difference in CAT
expression between the Sphl and Nrul cut plasmids in the presence of adenovirus alone
or Ad plus Rep was 2-3 fold. Thus, read through activation was not likely to contribute
more than 2-3 fold to pi9 activity.
In the second experiment, we inserted a poly A site between the p5 and p 19
promoters of pIM45CAT3 and psub262CAT3. Insertion of a poly A site between p5 and
pl9 in the psub262CAT3 plasmid had a minimal (2-3 fold) effect on p 19 activity (Fig. 10
D and E). This suggested again that relatively little if any pi 9 transcription relied on read
through from the upstream p5 promoter. In contrast, when the p5 RBE was present (Fig.
10 B and C), insertion of the poly A site decreased pi 9 activity by 10-20 fold under all
conditions tested. Regardless of whether a poly A site was inserted, the plasmids that
Fig. 9. Linearization of pIM45CAT3 plasmid to inhibit read through
transactivation, pi9 CAT activity from A549 cells transfected with supercoiled
pIM45CAT3 plasmid. A, or plasmid that had been linearized by digestion with Nrul (B)
or SphI (C). For each case the activity in the presence of Adenovirus infection, MOI=5
(Ad) is compared with the activity in the presence Ad infection and transfection with 1
mg of pIM45 (Ad & Rep). The values in (A) are the same as those in Fig. 7C and are
presented for comparison.
PIM45CAT3 plM45CAT3-Sphl plM45
CAT Activity (cpm)
Fig. 10. Effect of poly A insertion to inhibit read though activation. A, Poly A
sequence was inserted into pIM45CAT3 and psub262CAT3 between the p5 and pi9
promoters to determine the effect of a poly A signal on pi9 activity when the plasmid
was transfected by itself (Mock), in the presence of the Rep expressing plasmid pIM45
(Rep), in the presence of Ad at an MOI of 5 (Ad), or in the presence of both pIM45 and
Ad (Rep & Ad). The asterisks indicate that the Rep coding sequence has a stop codon at
Rep78 amino acid position 71 to prevent Rep expression from the CAT reporter
plasmids. The values in (B) and (Q are the same as those in Fig. 7 C and D and are
presented here for comparison.
B OWT1 Rep'â€”*-0 rr^Â°
C Q-ewX iâ€”
D (KHT 1 Rep'â€”Lonoa
E OQf1 P,,n, 'jn rAT 1
CAT Activity (cpm)
1C? 102 103 104 105 106
1â€”> * tmtl 1 t t mui i i i mill 1 i i mui i l muJ
contained a p5 RBE both showed a Rep mediated induction of pi 9 in the presence of Ad.
Taken together, our results suggested that modification of the pi 9 plasmid template by a
method that could change the secondary structure of the plasmid (restriction digestion) or
potentially create new protein complexes in the region between p5 and pi 9 (insertion of a
poly A site) reduced pl9 activity. However, they did not suggest read through activation
as a likely mechanism for pl9 induction.
Transactivation of pl9 can be modeled in the absence of Rep.
Thus far, our data were not consistent with the p5 RBE being a conventional
upstream activation signal or with the possibility that it stimulated pl9 transcription by
read through from the p5 promoter. If Rep bound to the p5 RBE was not itself a
transactivator, we then considered the possibility that it had an architectural role. We had
shown previously that Rep bound to the p5 RBE could form a DNA loop via protein
interaction with Spl bound to the pi9 promoter (144). It was possible that the interaction
between Rep and Spl served primarily to bring the other p5 transcriptional elements
(namely the MLTF and YY1 complexes) to the pi 9 promoter, and that one of these
elements was primarily responsible for pi 9 activation. If this were true, then it should be
possible to substitute the Rep and Spl sites with alternative elements that bound proteins
that were capable of interacting.
To test this possibility we substituted both the p5 RBE and the p 19 -50 Spl site
within the parental plasmid pIM45CAT3 with Gal4 binding elements to make the
plasmid called 2xGAL (Fig. 11). Substitution of the RBE and Spl sites was done so that
the spacing in the p5 and pi9 promoters remained the same (Fig. 6). We then tested for
p 19 activation in the presence of two Gal4 fusion proteins that contained the well
characterized interaction domains of SV40 T antigen and p53 (47, 109) but did not
Fig. 11. Replacement of Rep & Spl with Hybrid GAL4 Factors. A, The diagram
illustrates that the RBE in the p5 promoter and the Spl-50 site in the pl9 promoter of
pIM45CAT were both replaced with GAL4 binding sites. See Fig. 6 for specific
sequence modifications. In the presence of hybrid GAL4-p53 and GAL4-Tag fusion
proteins, the remaining p5 promoter elements and their associated protein complexes
would be brought into close proximity with the pi9 promoter resulting in a DNA loop
structure. B, Transactivation of the pIM45CAT3 reporter plasmid when transfected alone
(Mock), with lmg of pIM45 plasmid (Rep), with an adenovirus infection, MOI=5 (Ad),
or an Adenovirus infection at MOI=5 + pIM45 transfection (Ad & Rep). (This data is
identical to that in Fig. 7 B and is presented here for comparison.) C, Transactivation of
the 2xGAL plasmid when transfected alone (Mock), with 1 mg of pM-53 plasmid (p53),
with 1 mg of pM-Tg plasmid (T-Ag), with 1 mg of both pM-53 and pM-Tg plasmid (p53
& T-Ag), with Ad infection at MOI=5 (Ad), with Ad infection at MOI=5 and the two
hybrid plasmids (Ad, p53, T-Ag) or with Ad at MOI=5 and either 1 mg pM-53 (Ad &
p53) or 1 mg pM-Tg (Ad & T-Ag).
YY1+1 YY1-60 MLTF
n n n
â€”â€¢ l I |VlV0)t_
jAd'Ã¡ \ S
H cat i
15333 p53 & T-Ag
Ad & p53
Ad & T-Ag
themselves contain transcriptional activation domains. Substitution of GAL4 binding
sites for the p5RBE and pi9 Spl -50bp binding sites within the pIM45CAT3 reporter
plasmid was expected to allow the GAL4 DNA binding domains to bind DNA and create
a DNA loop between the two promoters through the p53 and SV40 T-Antigen interaction
domains (Fig. 11A).
As expected, basal pi9 CAT activity from the 2xGAL plasmid was low and
comparable to that seen with the parental pIM45CAT3 plasmid (Fig. 11, B and C,
compare Mock lanes). Expression of the Gal4 DNA binding proteins alone induced pi 9
activity by approximately 20 fold while infection with Ad alone induced pl9 activity by
approximately 30 fold. However, when both the Gal4 fusion proteins and Ad were
present, pi9 activity was induced by 350 fold over the basal level. Transfection with
only one of the GAL4 fusion plasmids (p53 or T-ag) and infection with Ad did not induce
pi9 activation. These results demonstrated that an interaction between an activated p5
promoter, which occurs in the presence of Ad infection, and the pi 9 promoter was
essential for pi 9 activation, and that this could be engineered in the absence of Rep and
Spl elements. It also suggested that Rep and Spl probably function primarily as
architectural proteins and activate p 19 by bringing other p5 elements into close proximity
with the pi9 promoter.
The level of pi 9 activity seen in the presence of the two Gal4 fusion proteins and
Ad was approximately half of that seen in the parental pIM45CAT3 plasmid in the
presence of Rep and Ad (compare Fig. 1 IB, Rep with 11C, Ad, p53, T-ag). This was
consistent with the fact that unlike the pIM45CAT3 plasmid, which binds Rep and Spl at
distinct sites, the 2xGAL plasmid could bind the same fusion protein (either T antigen or
p53) at each GAL4 binding site (p5 and pi9). When this happened it would lead to little
or no interaction between p5 and pi9, and presumably no activation. This would
theoretically occur 50% of the time; thus, the 2xGAL plasmid was expected to be
activated about half as well as the parental pIM45CAT3 plasmid. Indeed, transfection
with only one of the GAL4 fusion proteins in the presence of Ad inhibited the activation
normally seen with Ad (Fig. 11C, Ad & p53 or Ad & T-ag lanes). Alternatively, the Spl-
50 site may contribute to the basal level of the pi 9 promoter or to its ability to be induced
by the Ad El a gene product independently of an interaction with the p5 promoter
Which p5 element is primarily responsible for Rep mediated induction of pi9?
If the role of the p5 RBE is to bring some other element to the pi 9 promoter,
which of the known p5 promoter elements (MLTF, TATA or YY1) is primarily
responsible for Rep induced activation in the presence of adenovirus? To determine this
we constructed a series of 2xGAL plasmids in which one or more of the other p5
transcription elements were mutated to eliminate binding of its cognate transcription
factor (Fig. 6). Mutation of the p5 MLTF site had little effect (about 2 fold) on the final
level of pi 9 activity (Fig. 12A and B). Furthermore, pl9 activity was induced in the
presence of Ad and both of the hybrid GAL4 fusion proteins, suggesting that MLTF was
not critical for pi9 induction (Fig. 12B). In contrast, any mutant that included a defective
YY1-60 site was defective for induction in the presence of both Ad and the GAL4 factors
(Fig. 12C, D, E). This suggested that at least one of the critical elements within the p5
promoter for pl9 activation by a putative Rep-Spl interaction was the YY1-60 site.
Two other points became clear from an examination of the mutants. First,
mutation of the YY1-60 site had a major effect on the basal activity of the pl9 promoter.
Fig 12. Transactivation of the 2xGAL pl9 promoter by mutant p5 promoters. The
2xGAL plasmid containing a wild type or mutant p5 promoter was transfected alone
(Mock), with 1 mg each of the hybrid GAL4-p53 and GAL4-Tag expressing plasmids,
pM-53 and pM-Tg (Hybrid), with an Adenovirus infection at MOI=5 (Ad), or with an
Adenovirus infection at MOI=5 and the hybrid GAL4 expressing plasmids (Ad &
Hybrid). See Fig. 6 for specific sequence modifications. A, Transactivation of the
2xGAL4 plasmid containing a wild type p5 promoter. (These values are extracted from
Fig. 6B and presented here for comparison.) B, Transactivation of the 2xGAL reporter
construct lacking the p5 promoter MLTF binding site. C, Transactivation of the 2xGAL
reporter construct lacking the p5 promoter YY1 -60 binding site. D, Transactivation of
the 2xGAL reporter construct lacking the p5 promoter MLTF and YY1 -60 binding sites.
E, Transactivation of the 2xGAL reporter construct lacking the p5 promoter MLTF, YY1
-60, and YY1+1 binding sites.
CAT Activity (cpm)
I I Mock
I I Hybrid
I 1 Ad
Mutation of this site in the p5 promoter increased basal transcription from the pl9
promoter by 100 fold (compare Fig. 12A mock with 12C mock), and in the presence of
Ad, pl9 transcription was increased 10 fold (Fig. 12A, Ad and 12C, Ad). The YY1-60
element has been shown previously (24, 168) to repress the p5 promoter in the absence of
Ad or Rep. Our data (Figs. 12A, C) indicates that the YY1-60 site also has a negative
effect on pi 9 transcription both in the presence and the absence of Ad. In these two
cases, no GAL4 fusion proteins were present; thus, interaction between the p5 and pl9
elements through the Gal4 sites was not possible. This means that other kinds of
interactions between p5 and pl9 must be occurring in addition to those that occur
between the Gal4 sites (ie., the p5 RBE and the pi 9 Spl sites). Second, mutation of the
MLTF site also produced an increase (15 fold) in the basal level of pi 9 expression (Fig.
12A and B, mock lanes). Like the YY1 site, the MLTF site had been shown previously
to repress p5 in the absence of Ad (24). Our results indicate that it also represses the pi 9
promoter in the absence of Ad, possibly by a set of p5/pl9 interactions that are distinct
from those mediated by the YY1 site and the Gal4 (Rep/Spl) sites.
Transcriptional Analysis of Mutant Rep Proteins
Multiple studies of the AAV Rep proteins have demonstrated that the enzymatic
activites of Rep could be localized into functional subunits within the protein. However,
the complete elimination of one biological activity usually results in the loss of several
others. The best example of this interactive effect is the nucleotide binding domain
mutations. The loss of this ATPase domain removes Rep trs endonuclease activity and
DNA replication but also creates a defect in transcriptional transactivation for both the
pi 9 and p40 promoters (124). As result, a more detailed mutagenesis of the AAV Rep
protein was required to identify discrete protein domains for each individual enzymatic
A previous study used the common method of charge-to-alanine mutagenesis for
the production of temperature sensitive mutations. After an initial screening of 10
different Rep mutants, they isolated 2 mutants with separate conditional lethal
phenotypes. The first mutant had an initial protein instability defect that was
characterized as a Mg2+ binding mutation (50). This Mg dependent mutant was not
required for Rep DNA binding or helicase but was critical for terminal repeat
endonuclease activity. The second mutant was identified as a temperature sensitive
mutation that was defective for intracellular replication of AAV. This temperature
sensitivity created a 3-log titer difference between the permissive 32C temperature and
nonpermissive 39C temperature.
Generation of Rep Mutant Plasmids.
In order to produce a large number of possible AAV Rep ts mutants, a charge-to-
alanine amino acid mutagenesis approach was performed on the Rep open reading frame.
This process is believed to disrupt functional domains on the protein surface and result in
conditional lethal mutants. Within the plasmid backbone of pIM45, a noninfectious
genomic subclone of the AAV-2 genome, 20 different clusters of charged amino acids
were substituted with alanine amino acids (Table 1). The pIM45 plasmid allowed the
resulting protein sequence changes to be expressed in all four Rep proteins. Mutagenesis
in every Rep protein would allow possible conditional lethals to be assayed for in vivo
biological effects. The expression of both Rep78/68 and Rep52/40 mutant proteins could
be used to detect conditional lethals within assays for terminal repeat endonuclease
activity, DNA replication, and viral transcription. Previous research and site-directed
Table 1. Biochemical Activities of Rep Alanine Scanning Mutagenesis Panel. In this
Table, each Rep mutant was assayed for its ability to function as a possible mutant in
Adeno-Associated Virusâ€™s known biochemical activities. Within the plasmid backbone
of pIM45, a noninfectious genomic subclone of the AAV-2 genome, 21 different clusters
of charged amino acids were substituted with alanine amino acids.
Amino Acid Change(s)
in vivo Replication
mutagenesis of the AAV Rep protein has resulted in the preliminary identification of a
temperature sensitive mutant (50). This mutant D40A, D42A, D44A had a delayed
replication phenotype that resulted in a 3 log difference in viral titer between 32C and
39C. We have determined the enzymatic activity affected by this protein sequence
change as well as screened a panel of 20 new Rep charge-to-alanine mutants. We have
assayed their ability to exhibit a temperature sensitive phenotype and localized the
specific enzymatic activities affected within these replication defective mutants.
Transcriptional Activation of the pi9 Promoter by Rep Mutants.
In order to directly examine the transcriptional activation of each charge-to-
alanine mutant on the pi9 promoter, pIM45CAT3 was used to assay each Rep mutant for
its ability to specifically transactivate the p 19 promoter during Adenovirus infection. The
pIM45CAT3 construct had a strong level of Rep mediated transactivation that is
comparable to previously published results ( Fig. 13 Lanes 1 and 2) (Lackner and
Muzyczka in press). However, the cotransfection of several replication defective mutants
during an Adenovirus infection resulted in even higher levels of pi 9 transcriptional
activation (Fig. 13 lanes 3,4,5,6, and 11). One of these mutants, K340H, is the well
characterized nucleotide binding mutant (27, 38, 41, 74, 83, 90, 190, 195, 196, 203, 204).
Previous studies have shown that this mutant is defective for both ATPase and M13
helicase activity but retains DNA binding activity. Weger et al. (203) have assayed its
ability to transactivate the pi9 and p40 promoters which resulted in much higher levels of
AAV gene expression. Although this same K340H mutant was unable to stimulate gene
expression in an AAV construct containing the terminal repeats, the loss of
transcriptional activation was believed to be the result of the loss of DNA replication on
the transcriptional template and not its inability to transactivate the pl9 promoter.
Fig. 13. Transcriptional Activation of the pi9 Promoter by Rep Mutant Panel.
pIM45CAT3 reporter plasmid was used to assay each Rep mutant protein for its ability to
transactivate the pi9 promoter. A Rep protein expression plasmid, pIM45, containing the
various alanine scanning mutants was co-transfected with Adenovirus to transactivate the
pi 9 promoter.
Another mutant construct, Y156F, was used as an experimental control in the
pIM45CAT3 transcriptional assay. This mutant has specifically targeted the tyrosine
residue at amino acid position 156, which has direct role in the endonuclease cleavage
reaction during AAV DNA replication. The AAV terminal repeat is cleaved by the
tyrosine residue and substitution of a phenylalanine at this position created a replication
defective mutant (39, 173, 195). The Y156F mutant had no significant difference in its
ability to transactivate the p 19 promoter in the pIM45CAT3 plasmid background (Fig. 13
lane 7). This mutant has a functional ATPase and helicase activity (39, 173, 195.)
The three other mutants retain their ATPase and helicase activity but also express
much higher levels of pi 9 gene expression (Fig. 13 lanes 3, 4, and 5). All three of these
mutants are able to bind the terminal repeat but are unable to nick at the trs site. One
reason for this higher expression could be an alteration in Rep-DNA binding on the p5
promoter. The formation of stable Rep protein complexes on the p5 RBE may allow the
DNA loop between the p5 and pi9 promoters to occur more often and transactivate the
pl9 promoter through Spl at a much higher rate. Another reason for a higher level of
pi9 transactivation may be a difference in binding affinity between the mutated Rep
proteins and the Spl protein bound at the pi9 promoter.
The most interesting result was the dramatic decrease in pl9 promoter
transactivation for the E345A, H349A and D371 A, K372A mutants. These mutants have
maintained their DNA binding, ATPase, and helicase activities although they are
defective in pi9 promoter transactivation. The pi9 promoter assay using the
pIM45CAT3 reporter gene plasmid was defective for both of these mutants as compared
to the wt Rep protein. Although they were above the level of pi 9 transactivation with
Adenovirus alone, the mutants did not completely complement the ability of Rep to
mediate pi 9 transactivation (Fig. 13 lanes 8 and 9). The disruption of Rep mediated
transactivation in both of these mutants may be in different protein domain but may affect
a similar overall function. The E345A, H349A mutant has an interesting characteristic in
that it mutates a potential HMG box that may contribute to a possible mechanism of
transactivation. The potential HMG box domain may be responsible for separation of
DNA strands and the initiation of gene expression for this mutant Rep protein. The
alteration of this protein domain may prevent the correct level of p 19 transactivation
through the action of Rep invading the DNA strands at the p5 or terminal repeat. The
HMG box may permit the correct Rep protein complex to form on the p5 promoter and
correctly contact the Spl bound at the pi 9 promoter. This requirement of strand invasion
may be dependent on helicase activity as well as a functional HMG protein domain.
The D371A, K372A does not appear to directly affect any identifiable protein
domains but its location is close to both a strong Rep-Rep interaction domain and a
previously identified topoisomerase protein sequence. This protein domain could be
responsible for the assembly of large Rep protein complexes that form on the various
RBEs within the AAV genome. This mutant does not initially appear to target a critical
domain required for Rep-Rep interactions but it appears to have multiple problems
regulating the transcriptional activation of the pi 9 promoter as well as the ability of Rep
to repress the p5 promoter.
Repression of the p5 promoter.
One of the most important characteristics of the AAV lifecycle is to repress the
expression of the Rep gene in the absence of an Adenovirus infection (98, 143). In order
to localize the Rep protein domain responsible for this biological activity, the entire Rep
mutant panel was assayed for its ability to repress p5 transcription in the absence of an
Adenovirus coinfection. In this assay of the p5 promoter, the p5CAT3 promoter was
transfected into A549 cells and assayed for its ability to be repressed in the presence of a
mutant Rep protein. As a negative control, the nonsense mutant Rep, dAXX, was
transfected to determine the basal strength of the p5-190CAT promoter (Fig 14 lane 1).
When the wt Rep protein was transfected into A549 cells, the transcriptional activity of
the p5 promoter is 6% of its basal activity demonstrating a strong level of repression by
the Rep protein (Fig. 14 lane 2). It was interesting to note that all of the Rep replication
mutants that were defective in transactivation of pl9 were also greatly reduced in their
ability to repress the p5 promoter. Strikingly, the two mutants E345A, H349A and
D371A,K372A exhibited much lower Rep mediated transactivation of the pl9 promoter
and were unable to repress the p5 promoter through Rep-DNA binding activity. Each of
these two mutants had 7-fold higher levels of p5 promoter expression resulting from the
inability of these Rep proteins to correctly bind the p5 RBE and repressing the promoter
(Fig 14 E345A, H349A and D371A,K372A ). The modification of the HMG box may
result in Rep protein which is unable to correctly assemble large Rep complexes and
repress the p5 promoter. The highest degree of lower repression of the p5 promoter is
directly related to its distance to the HMG box domain.
Fig. 14. Transcriptional Repression of the p5 Promoter by Rep Mutant Panel.
p5CAT reporter plasmid was co-transfected with various Rep alanine scanning
mutations. The basal level of p5 promoter activity was graphically shown as 1.0-fold of
activity. The ability of each Rep mutant to repress the p5 promoter was shown as a
percentage of p5 basal activity.
Percent of Basal p5 Promoter Activity
O O O O O -I
b K> ^ b) bo o
i l i i i i i l i l
To learn more about how the Rep protein controls AAV transcription, we tested
several mechanisms of transcriptional control. Using the CAT gene as a reporter, we first
confirmed that activation of the pi 9 promoter by Rep was dependent on a functional RBE
within the p5 promoter (Fig. 7). As expected pi9 activity was significantly reduced in
the absence of Rep or in the absence of the p5 RBE, provided that the cells had been
infected with adenovirus. This confirmed the results of several previous studies
including our own (100, 123, 143, 203). In addition, we measured accurately the
induction of the pi 9 promoter by Ad infection and Rep expression, and the range from
basal to fully induced was almost 3 logs.
The RBE is not a typical upstream activation signal.
We initially expected that Rep would activate the pi9 promoter in the same way
that its homologue in the autonomous parvovirus family transactivates the p38 capsid
promoter. The MVM Rep analog, NS1, has been shown to induce transcription from the
p38 capsid promoter by binding to a nearby NS1 binding site and interacting with an Spl
-50 site upstream of p38 (94, 113, 114). In the case of NS1, it is clear that a C terminal
activation domain is essential for induction (106) and that NS1 binding sites behave like
upstream activation signals.
To test this possibility for Rep, the RBE was placed at several positions upstream
or downstream of an artificial p 19 promoter that contained the key pi 9 promoter
elements required for Rep activation (Fig. 8). However, surprisingly, the RBE resulted
primarily in repression of the p 19 promoter, and in general, repression was most severe
when the RBE was closest to the p 19 start site. Several points are worth noting about this
experiment. First, in the presence of adenovirus infection. Rep was not capable of
transactivating the p 19 promoter when only the RBE was inserted into the construct.
This clearly showed that the RBE-Rep complex alone was not sufficient for
transactivation. It is also consistent with the fact that, to date an activation domain has
not been found in Rep. Only the C terminal end of Rep has been found to activate
transcription in two hybrid experiments and this region, which is absent in Rep68, is not
essential for p 19 or p40 activation (29, 202, 203).
The second point worth noting is that the level of repression depended on the
conditions of measurement and the distance of the RBE from the start of the pi 9 mRNA.
When Ad infected cells were compared with cells infected with Ad and expressing Rep,
the repression was modest, at most 4 fold (in the case of the -145 position). When Rep
was expressed by itself (in the absence of Ad) there was a 3-7 fold induction of p 19
activity (except in the case of the -100 construct). However, it was clear that placement
of the RBE close to the p 19 promoter had a severe effect on pl9 activity. This was true
even in the absence of Rep expression when Ad was present (Fig. 8, Ad only lanes),
suggesting that a cellular factor as well as Rep were able to interact with the RBE to
cause repression. When the RBE was inserted at the -100 position within the p 19
promoter, a region previously shown to have no effect on transcription (144), p 19 activity
was lower than the basal level under all conditions tested.
Repression by Rep protein has been demonstrated for a variety of heterologous
promoters as well as the endogenous AAV promoters. These include the SV40, c-ras, c-
myc, c-fos, HPV, HIV and Ad early promoters (7, 8, 66, 74, 82, 91, 97, 143). The
mechanism of repression is not clear. Rep has been shown to interact with TBP (69), and
one report suggests that Rep may prevent assembly of TFIID complexes on DNA (181).
Rep also has been shown to bind to the transcriptional activators PC4 (202), Spl (68,
145) and Topors (201), and to the protein kinases PKA and PrKX (29, 40). Recently,
Cathomen et al. (21, 22) identified a cellular transcription factor ZF5 that binds to the
RBE and may contribute to the cellular repression of pi 9 seen here in the absence of Rep.
Rep has also been shown to stimulate some promoters, for example c-sis and CMV (210,
211). At least two mechanisms appear to be involved in Rep mediated repression as first
suggested by Kyostio et al. (98). The first mechanism involves binding of Rep to an RBE
as in the case of the p5 promoter. The second does not require an RBE but does require a
functional ATP binding site in Rep. Presumably, the ATP binding site is needed either to
modify the structure of Rep protein-DNA complexes or to modify the transcriptional
template via the Rep associated DNA and RNA helicase activities (75, 209). Consistent
with the helicase idea, mutations in the Rep proteinâ€™s helicase motifs have been shown to
be negative for transactivation and repression (98, 124).
The p5 RBE is probably an architectural element designed to bring the p5 and the
pi9 promoters together.
Our failure to induce pi9 activation in artificial constructs that contained only an
upstream RBE suggested two other alternatives, read through activation from the p5
promoter and activation by other elements present in the p5 promoter via a looping
mechanism. We found no compelling evidence of read through activation from the p5
promoter (Figs. 9 and 10). However, several experiments suggested that the p5 RBE
served as a scaffold to bring the p5 promoter elements to the pi9 promoter.
Previous work had shown that if purified Rep and Spl are incubated with DNA
containing the p5 and pi9 promoters, a DNA loop can form between the two promoters
via Rep-Spl interaction (144). In this report, we showed that both the p5 RBE and the
pl9 Spl-50 site can be substituted with GAL4 sites. When this was done, activation of
the pi 9 promoter no longer required Rep but depended instead on the presence of hybrid
GAL4 fusion proteins containing p53 and T antigen interaction domains. Neither fusion
protein contained an activation domain of its own, and neither protein could activate pi 9
on its own. However, together the two fusion proteins activated pi9 transcription nearly
as well as Rep and Spl (Fig. 11). This demonstrated that the role of the Rep-Spl
interaction was probably to bring transcription complexes assembled on the p5 promoter
to the pi9 promoter.
Mutagenesis of the p5 promoter identified at least one element essential for pi 9
activation, the YY1 -60 site. Mutation of this element eliminated activation by the GAL4
hybrid proteins (Fig. 12). In contrast mutation of the p5 MLTF site did not eliminate
activation by the hybrid proteins although it did reduce the level of activation. Our
experiments did not exclude the possibility that the YY1+1 site or the TATA site was
also involved in activation. However, the combination of mutants in YY1-60 and MLTF
or YY1-60, MLTF, and YY1 + 1 were not substantially different the YY1-60 mutant by
In addition to eliminating pi9 activation by Ad and the hybrid proteins, mutation
of the YY1-60 site also produced a substantial increase in basal pl9 expression and Ad
induced p 19 expression (Fig. 12). The implication of this is that there are alternative Rep
independent interactions between the p5 and pi 9 promoters and one of these is mediated
by the YY1-60 site in the p5 promoter. The net effect of this interaction is to repress pl9
promoter basal and Ad induced activity. Thus, the p5 YY1 -60 site represses both the
proximal p5 promoter and the downstream pi9 promoter.
Comparison of the YY1-60 mutant with the parental 2xGAL4 plasmid illustrates
one reason for the complexity of AAV transcriptional regulation (Fig. 12). Elimination
of this site by mutation increases pi 9 activity in the presence of Ad to the level seen in
the parental plasmid in the presence of Ad and the hybrid factors. Thus, pi 9 could be
induced to the level needed during AAV replication without the need for further
activation mechanisms (such as Rep) if the YY1-60 site were not present. Flowever, as
mentioned above, elimination of the YY1-60 also increases the basal level of p5
transcription and reduces the Ad induced level of p5 (168). Increasing the basal level of
p5 transcription would lead to a virus that is less likely to maintain the latent state
because of inappropriate p5 Rep expression. Decreasing the Ad induced level of p5
transcription would reduce the level of AAV DNA replication during productive
To illustrate how p5/p 19 interactions might promote activation or repression of
pl9 under different conditions, we have drawn the model in Fig. 15. The model
compares the interaction in pIM45CAT3, which contains wild type p5 and pi9
sequences, with that in psub262CAT3, which has a mutant p5 RBE. In the wild type p5
promoter (pIM45CAT), Rep binds to the p5 RBE and forms a complex with Spl bound
to the Spl-50 site in the pi9 promoter. This places several potential activation regions
Fig 15. Model of pl9 promoter transactivation by interaction with transcription
factor complexes bound to p5. See text for details.
YY1 REP TATA YY1 MLTF
including those of YY1, MLTF, and El a near the pi 9 TATA box to activate pi 9
transcription. Meanwhile, within the p5 promoter, Rep binding inhibits p5 transcription
either by steric hindrance of basal transcription factors (98), by an enzymatic mechanism
involving the Rep ATPase activity (98) or by inhibitory contacts with YY1 or El a.
When the RBE is absent (psub262C AT) or in the absence of Rep gene expression, the
interaction between p5 and pi9 is either absent or occurs between different proteins, for
example, YY1 and Spl (163). The YYl-Spl interaction places activating p5 complexes
in a different position with respect to the pi9 basal transcription machinery, which may
inhibit pi9 rather than activating it. Meanwhile, within the p5 promoter, the absence of
Rep binding leads to derepression of the p5 promoter (98, 143). The model does not
include the contribution of p300 (103) as well as several other cellular and Ad proteins
that are likely to be involved, for example, PC4 (202) and DBP (23). In addition, it is
likely that other as yet unidentified cellular factors are involved in the complexes that
form on the p5 and pl9 promoters. However, the model does illustrate how alternative
interactions can be established between the two promoters that lead to repression or
activation and emphasizes the role of Rep and YY1. The next logical step will be to
determine precisely what is present in the p5/pl9 complexes in uninfected and Ad
Finally, our data also explains a puzzling observation made by Beaton et al (9).
This group replaced the p5 promoter sequences upstream of the RBE (including the
TATA, YY1-60, and MLTF sites), with the SV40 ori region containing the promoter
elements for early SV40 transcription. Surprisingly, this construct was indistinguishable
from wild type AAV, but only if it contained an intact terminal repeat. Deletions of the
terminal repeat that removed the TR Rep binding elements were completely defective for
AAV transcription. On the other hand, constructs that contained a wild type p5 promoter
showed no effect on transcription when the same TR deletions were analyzed. The
results obtained with the SV40-AAV hybrids are entirely consistent with our finding that
the p5 YY1 site plays a key role in activation of pi 9. Because the TRs are redundant
activation elements that contain an RBE, they substituted for the YY1 complex that was
missing in the SV40-AAV hybrid constructs. However, deletions in the TR that removed
the RBE presumably prevented their interaction with the AAV promoters, and thus
eliminated AAV transcription. This begs the question as to what transcription elements
are present in the TR that can substitute for the p5 elements.
Rep Protein Domains in AAV Transcriptional Regulation
A previous study established that two different Rep mutants were created in this
manner and resulted in different phenotypes. One mutant contained a magnesium
binding mutation that affected the Rep protein in its trs endonuclease activity (50). The
mutation did not affect the ability of the Rep protein to bind the terminal repeat or its
helicase activity. However, it was demonstrated that the D412A mutant had a diminished
ability to interact with Mg2+ ions and an interaction between the Rep D412A mutant and
Mg2+ was essential for efficient trs endonuclease cleavage. This data was the first
suggestion that a portion of the active DNA cleavage site required a Mg2+ ion and the
D412A amino acid.
The second phenotype identified was the first identified conditional lethal
mutation within the AAV-2 Rep protein. The D40A,D42A,D44A mutant was found to
demonstrate a 3-log difference in rAAV titer between 32C and 39C. Examination of this
mutant in a replication assay showed a fairly strong delay in DNA replication at the
permissive temperature of 32C (50) (Lackner in prep). However, the ts Rep mutant
showed a complete lack of activity at 39C. In order to better understand the exact
alterations in the D40A,D42A, D44A mutant, we analyzed each of the biochemical
activities within this protein. We discovered that the temperature sensitivity was mainly
dependent on a defect in DNA binding (Lackner in prep). Alteration of the protein
sequence inhibited DNA binding of Rep to a synthetic terminal repeat in the AAV
genome. The reduced level of DNA binding resulted in a complete loss of Rep
endonuclease activity of the AAV terminal repeat.
An important aspect of this D40A, D42A, D44A mutation could be inferred from
its sequence homology with other unrelated proteins such as E. coli DNA J and SV40 T-
Antigen (Fig. 16). The AAV-2 Rep sequences from amino acids 38 to 42 have a high
degree of homology to the chaperone protein domain of DNA J in E. coli and a similar
domain of SV40 T-Antigen (20, 166, 177). Based on this protein sequence alignment,
the temperature sensitivity of the mutant Rep protein was a result of the disruption of this
potential J domain. Similar to its role in SV40 T-Antigen, the potential J-domain within
Rep78 may have a direct and stable interaction with the cellular chaperone protein,
Hsp70 (62). The J-domain within most polyoma viruses makes direct contacts with the
ATPase domain of Hsp70 (20, 88, 122, 161, 166, 197). It has been established through
previous studies that the J-domain within SV40 T-Antigen is critical to SV40 DNA
replication (20). T-Antigen mutations that affect the J-domain prevent the T-Antigen
transactivation of E2F responsive promoters and their subsequent induction in the
progression of the cell cycle (177, 180, 222). These same J-domain mutations were
Fig. 16. Sequence Diagram of Rep Mutagenesis Results. See text for descriptions.
Rep 78/52 Functional Map
j-domain I helix 2
1 |mpgfyeivik vpsdldehlp gisdsfvnwv aekewe 1|PP&) sfflnQlnlieg
Â¡ijiij jijij ;t: molil 2
51 dpltvaeklq rdfltewrrv1 skap'Ã©Ã¡lffv gfekgesyfb mhvllvettqv
101 ksmvlgrfls qirei< liqri yrgieptlpn wfavtktrng a
j=-i -â– Â»- Rep/PC4
Â¡ ^ ! helix 3
no AAV5 homology
nmeqylsacl nlterkrlva qhlthvsqtq^
REPJ* :'t J <â€”
201 legnkenqnpn sdppvirstct sarwnÃ©Xvgw lvdkgitsek qWiqedqasy
:x; Rep/cap Â¿
. â€¢ _ _ j i _ _ j
251 isfnaasnsr sqikaaldna gkimsltkta pdylvgqqpv edissnriyk
^ ' â€¢ p-ioop ] i
301 ilelngydpq yaasvflgwa 'tkkfgkrnti wlfg^attgfe tfria.aeai.aht Q,
D| I topo domain 1 GG box
351 ^vpfygcvnwt nenfpfndcv dkmviwwg0g (jkfrntakv|vesa -kail ggjskvr
C I ; >Jr ; Mg+2 TPGR box C DEAD box I I
401 vdqÂ®ckssaq idp|tpvivt|s ntnmca|vi dg] n sttfehqqp 1 m fÂ®fel
ii â€¢ j, l_
451 trrl@h@fgk vt0q0v00ff rwa0^i vv Â©v 0#Tyvkkgg akkrpapsda
Nu Lo -Mâ€”
501 disepkrvre svaqpstsdal easinyadry qnkcsrhvgm nlmlfpcrqc
551 ermnqnsnic fthgqkdcle cfpvsesqpv svvkkayqkl cyihhimgkv
601 pdactacdlv nvdlddcife q (larghsl)
Cjlep/ Reg) Interaction
HSV6rep / Hox Homologies
Â¡ Transactivation j â€¢
deficient in their capability to bind to Hsp70. The J-domain on SV40 T-Antigen has been
identified as a necessary requirement for nuclear localization (216). Direct interaction of
the T-Antigen J-domain with Hsp70, results in complementation of a SV40 T-Antigen
mutant containing a nuclear translocation and cellular transformation mutation (81).
Although the nuclear localization domain of Rep has been localized to amino acids 483 to
519, this J-domain may explain many of the roles for Rep in DNA replication and
modification of the cell cycle (99, 186, 198, 199, 206, 207). In SV40, this region has
been shown to function as a molecular chaperone mediating phosphorylation of the T-
Antigen associated proteins pi07 and pi30 (180). This same protein domain in Rep may
explain its role in interference with viral replication and oncogenicity in SV40,
papilloma, and herpesviruses (65, 90, 100, 217, 218). The most likely explanation of the
ability of Rep to inhibit cellular transformation after SV40 coinfection could be through a
domain negative phenotype. The ability of T-Antigen to promote oncogenesis depends
on two factors, the J-domain and the pRB-binding motif (147). The presence of another
J-domain containing protein, Rep78, would act as a domain negative protein during an
AAV and SV40 coinfection. The Rep78 protein could possibly interact with pi07 and
pi 30 but would be unable to fully overcome the G1 arrest or E2F-repression of the cell
cycle promoters as a result of its inability to bind pRB. However, in regards to the
D40A,D42A,D44A replication mutant, this targeted mutation may disrupt both DNA
binding and direct assembly of replication complexes on the AAV terminal repeats. We
have demonstrated that the mutation directly inhibits DNA binding and as a result
prevents trs endonuclease activity. In addition to its defect in DNA binding, this Rep ts
mutant may be defective in its ability to recruit active replication complexes due to this J-
domain mutation. It has suggested that T-Antigen uses its J-domain to support SV40
DNA replication in a manner that is strikingly similar to the use of Escherichia coli DnaJ
by bacteriophage lambda in DNA replication (20). In addition to the polyoma virus
family, the HPV replication initiator, El helicase, has enhanced binding to the origin of
replication by the direct interactions of hsp70 proteins (112). This data suggests a strong
role for chaperones in viral DNA replication through contacts in a functional J-domain.
As result, the inability of this mutant Rep78 to bind the synthetic AAV terminal repeats
may be a function of their reduced affinity for the chaperone proteins, Hsp70. Without a
possible Hsp70 interaction through the J-domain, the Rep protein complexes may not be
correctly assembled for DNA binding and trs endonuclease activity.
The second mutant E345A, E349A affects a possible HMG box in the Rep protein
sequence. Between amino acids 340 to 350 of Rep78, protein sequence alignment has
identified a possible HMG box that may have multiple roles in the enzymatic activities
and biological roles of Rep throughout the AAV lifecycle. Previous research
demonstrated that most of the activities associated with the Rep protein are enhanced
with the presence and co-expression of the HMG-1 protein (36). This study discovered
that the presence of HMG-1 stimulated Rep-mediated trs endonuclease cleavage, ATPase
activity, DNA binding, and p5 transcriptional repression. Since the activities of Rep were
assayed both in vivo and in vitro, the HMG-1 and Rep protein HMG box may have very
similar functional roles in which they recognize the cruciform structures of AAV terminal
repeat and form stable nucleoprotein structures. HMG-1 has a general DNA binding
activity but an extremely high affinity for cruciform structures and bends in DNA. The
sole function of HMG-1 enhancement may be to recognize these odd DNA fragments
within the cell and recruit Rep proteins to form multimeric protein complexes on Rep
binding elements. This Rep recruitment would affect every type of RBE within the AAV
genome and influence both the latent and lytic lifecycle. The transient transfection of
HMG-1 in the presence of a p5 promoter assay was shown to have a stronger level of p5
repression but only in the presence of the Rep protein (36). This data indicates that the
assembly of the Rep protein complexes may be more stable in the presence of HMG-1 or
may be recruited by HMG-1 bound to the AAV genome.
It was suggested that HMG-1 and HMG-2 interact with transcription factors that
contain HMG boxes to stimulate DNA binding and form a DNA bend (184).
Transcriptional regulators that contain HMG boxes such as the AAV Rep protein may
recruit the HMG-1 protein through protein-protein interactions thereby increasing the
affinity of transcription factors to their DNA binding sequence. This increase in
transcription factor binding affinity would be dependent on the induction of DNA
bending by HMG-1. After the stabilization of transcription factor binding, the DNA bend
could recruit a second unrelated transcription factor to another site within the DNA
sequence (184). In the case of the E345A,E349A Rep mutant, modification of the HMG
box may prevent any possible Rep and HMG-1 protein interaction either in the AAV
terminal repeat or the p5RBE. Without the HMG-1 protein to alter the structure of DNA
and allow Rep to correctly bind the RBE, a number of biological activities would fail to
occur. First, the mutant would have a much lower level of p5 promoter repression as we
have shown by transient transfection (Fig. 14, E345A,E349A). The lower level of Rep
protein binding would affect both replication and transcription. The defect in pi9
transactivation could be the result of failure to produce the proper DNA loop between the
p5 and pl9 promoters. If HMG-1 stimulates the Rep protein to tightly bind its RBE,
mutation of the HMG box in the Rep protein sequence may prevent a possible p 19
transactivation complex. We believe previous studies demonstrating the stable
interaction between Spl and Rep on AAV support this model (145). However, in vivo
conditions may require that the DNA loop created between the p5 and pi9 promoter for
pi 9 transactivation be stabilized through the activities of the HMG-1 proteins. This
E345A,E349A Rep mutant would support this model because it maintains helicase
activities but it is unable to repress or transactivate the AAV promoters (Fig. 13 and 14).
Remarkably, the in vitro binding assays between Rep and HMG-1 have indicated that a
possible interaction domain between these two protein lies around the proposed Rep
HMG box sequence (36).
The next mutant in our charge-to-alanine scanning mutagenesis was the E371 A,
E372A Rep protein. Although this region of the Rep protein does not contain any known
protein motifs, it is in a close proximity to a Rep-Rep interaction domain and the
previously discussed HMG box. This mutation caused a replication negative phenotype
but did not result in a conditional lethal virus. The E371 A, E372A mutant was capable of
both DNA binding and helicase activities. However, two very important biological
activities were found to be greatly reduced. First, the protein was extremely deficient in
its ability to express the Rep 52 and 40 proteins. As further proof for this disruption of
the pi9 promoter, the pIM45CAT3 reporter construct was unable to transactivate this
promoter at a level significantly higher than with Adenovirus alone (Fig. 13). The most
interesting effect was the complete lack of transcriptional repression on the p5 promoter.
The E371 A,E372A mutant was 7-fold higher in its level of p5 promoter expression
compared to the wt level of p5 activity. Interestingly, all of the replication defective
mutants had p5 promoter expression that was 3-fold higher than wild type. Although the
highest levels of defective p5 promoter repression were focused around the
E371 A,E372A mutant and the potential HMG box at E345A, E349A (Fig. 13,
E345A,E349A and E371A,E372A), other important areas in the Rep protein sequence
that targeted specific p5 repression activity colocalized with motifs based on AAV Rep
and Rolling Circle Replication (RCR) proteins (Fig. 16). Motif 1 from Rep amino acids
10 to 14 corresponds to the K10A,D14A mutant and motif 2 corresponds with amino
acids 90 to 94 similar to the H90A,H92A mutant. Both of these mutations are unable to
replicate viral DNA, transactivate the pi9 promoter, or repress p5. This combination of
mutants would indicate a defect in the assembly of Rep protein complexes similar to the
other RCR proteins. The assembly mutants could be unable to tightly bind DNA, have a
reduced interaction with possible chaperone activities of HMG-1, or lose the ability to
recruit replication machinery to the AAV terminal repeat.
Due to the difficulty in producing large amounts of pure Rep78 for protein
crystalization, we are limited in our dissection of the enzymatic activities to protein
sequence alignment with other unrelated viral proteins. Based on limited homology with
SV40 T-Antigen, previous mutagenesis studies have created ATPase mutants in the Rep
protein. However, the elimination of the ATPase function of Rep created a wide variety
of lost biochemical activities within the Rep78 protein. The ATPase mutants in those
studies also lost DNA helicase activity, the trs endonuclease cleavage at the terminal
repeat, and all transactivation from the p 19 and p40 promoters (124). Based on
homology to those SV40 T-Antigen ATPase mutations, all of the enzymatic activities of
Rep appeared to be dependent on a functional ATPase activity. A new strategy called
charge-to-alanine mutagenesis was indiscriminant to helicase homology and targeted
only charged amino acid clusters within Rep78 in the hope of creating conditional lethal
mutations. Previous work was able to identify an unknown Mg2+ binding site whose
mutation resulted in a lack of endonuclease cleavage at the terminal repeat but was
completely wild type in other aspects for Rep78 activity. This work has continued to
characterize several potential new protein domains within the Rep78 protein. A single
HMG box was localized to a specific domain without the loss of any helicase activity and
it may have a direct effect in stablizing the DNA loop between the p5 and pl9 promoters.
Another Rep mutant suggested the role of a J-domain in a temperature sensitive mutant
that could influence the ability of the Rep protein in binding to the terminal repeat, trs
endonuclease activity, and the recruitment of DNA replication factors at the terminal
repeat. However, until the crystalization of Rep78 is performed further localization and
biochemical characterization of Rep protein domains will be dependent on continued
mutagenesis of the entire protein sequence.
During various cellular conditions, there are a large number of different protein
complexes bound to the p5 promoter. One of most important and least examined
questions in AAV biology is the actual organization of proteins within the p5
transcriptional complex. One experimental protocol to define the factors bound to this
sequence of DNA would be to isolate and purify the p5 promoter. After purification, the
p5 promoter element could be incubated in a cellular extract for one of four cellular
conditions. The first condition would be a mock extract containing neither an
Adenovirus or Adeno-Associated Virus infection. The second and third conditions would
be an single viral infection extract of Ad or AAV, respectively. The last cellular extract
would be a combined infection of both Adenovirus and AAV.
With these four types of cellular extract, the p5 DNA sequence could be incubated
with them to allow DNA-protein complexes to form on the p5 promoter. After a
sufficient time for incubation, the protein complexes formed on the DNA would be fixed
by the addition of a reversible cross-linking agent. The DNA sequence could be
precipitated after the cross-linking event to isolate the protein complexes. By reversing
the mechanism of cross-linking, the DNA-protein complexes could be disassembled and
the proteins within this protein complex could be analyzed by various methods. One
method of analysis could be a simple Western blot for antibodies of suspected proteins in
these complexes. Other methods of analysis could be a 2-D gel electrophoresis or Mass
Spectroscopy to gain possible protein sequence information on the proteins precipitated
with the p5 promoter DNA.
Another process of p5 promoter transcription complex isolation could be the use
of DNA labeled with biomagnetic beads. The purification of the p5 promoter could
occur through restriction enzyme digestion. The ends of the restriction enzyme site could
be filled by Klenow to incorporate biotinylated labeled dNTPs into the p5 promoter
sequence. The biotinylated p5 promoter could be incubated with streptavidin-conjugated
Dynabeads. Through the use of a magnet, the labeled p5 promoter could be precipitated,
washed, and released from bound DNA-protein complexes after incubation with Ad or
AAV infected cells. This biotinylated DNA approach would allow great variety in
protein purification by the use of many salt wash conditions. The washed protein
complexes could be purified and analyzed for protein sequence information without
reversible cross-linking procedures.
Another protocol for isolating the protein complexes formed on the p5 promoter is
the use of DNA affinity column chromatography. The cross-linking of a large number of
p5 promoter oligonucleotides to column matrix would enable the formation and
purification of proteins bound to the DNA sequence. The four different cellular extracts
would be poured over the p5 promoter column and washed with various buffer solutions.
The isolation of protein complexes could proceed a number of different ways. One, a
reversible cross-linking agent could fix the complexes and later release them after many
successive column washings. Second, the washed protein complexes could be
fractionated by step or gradient elutions with various salt solutions. Either of these
purification protocols would isolate proteins to be sequenced or identified by Western
These three protocols of p5 promoter protein complexes could be analyzed in a
number of different ways. First, the structure and composition of these protein
complexes could be compared in the four cellular conditions. The composition of these
complexes could differ greatly during an Adenovirus infection, Rep protein expression or
the combination of both situations. The El A, E4orf6/7, or any other Adenovirus gene
product could influence the structure of these complexes. The stringency of the salt
elution or the concentration of cross-linking reagent could determine the overall order of
protein binding on the p5 promoter. Second, another interesting assay would be the
comparison between the psub262 and p5 promoter. This differential of the two
promoters could define the role of Rep in forming various protein complexes as well as
the role of steric interference in p5 transcription factor binding. In combination with the
four different cellular extracts, the p5 and psub262 promoters could exhibit and
characterize a large number of protein complexes. The analysis of the differential
between the mutant sub262 promoter and the wild type p5 promoter in every cellular
condition should demonstrate the order of addition in the assembly of transcriptional
complexes on the active p5 promoter.
The regulation of gene expression for the Adeno-Associated Virus is one of the
most complex and compact transcriptional mechanisms in molecular biology. The entire
AAV genome is only 4.5kb in size and contains only three promoter elements. In
addition to this relatively minor genome, the lifecycle of AAV can alternate between a
latent, repressed proviral state and an actively lytic infection. The regulation for this
wide range of transcriptional state is controlled by only one single open reading frame in
the AAV genome. The nonstructural proteins of AAV manage every aspect of its
lifecycle as well as influence the infected cell environment. These proteins process the
cellular stasis of the infected host and decide a wide range of viral responses. If the host
cell is healthy, the AAV genome will be directed to site-specifically integrate and repress
all viral transcription. If the host cell is coinfected or superinfected with Adenovirus, the
AAV genome will respond to the Ad proteins, rapidly replicate its viral DNA, and escape
the host cell when the Adenovirus lyzes the host cell. All of these aspects of the AAV
lifecycle are processed and directly controlled by the one nonstructural protein, Rep.
The major rate controlled step in the AAV lifecycle is the transcriptional
regulation of the p5 promoter. This promoter expresses the largest Rep protein and
determines the rate of Rep and Capsid protein expression. Without Adenovirus, the p5
promoter produces a very minute amount of Rep, which represses the expression of the
p5 promoter. However, an Adenovirus infection will induce a large number of changes
in p5 transcription. The Early Ad protein, El A, directly binds to the YY1 repressors on
the p5 promoter converting them into activators of Rep expression. The combination of
large Rep expression and p5 promoter activation induces the other two promoters of
AAV to express their gene products.
The most fascinating AAV promoter is the pl9 promoter. The pi9 promoter
expresses the Rep52 and Rep40 proteins that regulate the expression of the p5 promoter.
During Ad infection, the large Rep proteins are expressed from the p5 promoter and
inhibit their own expression. In addition to feedback inhibition of the p5 promoter, the
large Rep proteins bind the same inhibitory location on the p5 inducing expression from
the pi9 promoter. The pl9 promoter will produce the Rep52 protein which depresses the
p5 promoter by directly interacting with the large Rep proteins on the p5 promoter. This
regulation and interplay with the p5 and pi9 gene products allows the constant
expression of large and small Rep proteins. These Rep protein concentrations permit a
number of conditions in the lytic phase of AAV. First, the large Rep protein is expressed
enough to nick and initiate the replicating pool of AAV genomes. Second, the Rep52
protein concentration is high enough to depress the p5 promoter but low enough to
prevent packaging of the entire AAV genome replication pool. Third, the p40 promoter
producing Capsid protein is always expressed at excess. The maintenance of this
complex transcriptional regulation is controlled by the p5 and pi9 promoters.
In previous work, it was shown that Adenovirus always induced high levels of p5
expression. In contrast, the large Rep proteins seemed to exclusively repress the p5
promoter. This data appears opposite to the requirement of Rep for AAV gene
expression. This question was addressed in a series of assays to determine if Rep
functioned as an enhancer or proximal promoter element.
The Rep binding element was moved to various locations next to the pi9
promoter. In the correct genomic location, the p5RBE did not transactivate the pl9
promoter. The series of pl9CAT3 constructs indicated that as the p5RBE was placed
closer to the transcriptional start site, it caused a much higher level of transcriptional
repression. These constructs would support the conclusion that the Rep protein does not
have any transcriptional activation domain but instead functions exclusively as a
The lack of any transcriptional activation supported the hypothesis that the Rep
protein does not exclusively or directly activate transcription. It may function to connect
or join two proteins which directly recruit the RNA polymerase II holoenzyme at the p 19
promoter. Since the Rep is bound to the p5RBE site in the latent proviral state, the other
p5 transcription factors may induce the p 19 promoter during an Adenovirus infection.
This hypothesis was tested by the subcloning of the p5 promoter elements into the correct
spacing in the synthetic pl9CAT3 plasmid. With Ad and Rep gene expression, these
constructs fail to induce the correct transcriptional regulation. At this point of pi 9
promoter analysis, it was believed the synthetic nature of the pl9CAT3 promoter may
lack the correct transcription factor for gene expression. As a result, the CAT reporter
gene was subcloned into the AAV genomic subclone plasmid, pIM45.
This pIM45CAT3 plasmid expressed the correct transcriptional regulation with
Ad and Rep gene expression. This result implies the sequence of the synthetic pl9
promoters cannot exhibit correct pl9 gene expression or their Rep-Spl interaction is
incorrect. The Rep and Spl proteins were replaced in the pIM45CAT3 plasmid and
replaced with GAL4 hybrid transcription factors. Without any Rep or Spl protein
sequences, it was shown these two proteins have no direct influence on transcriptional
activation of the pi 9 promoter. The genomic organization of the p5 and pl9 promoters
form a stable DNA loop through the protein interaction of Rep-SPl or GAL4 Hybrid
transcription factors. This stable DNA loop allows the protein complexes on the Ad-
induced p5 promoter to contact and stimulate the formation of a RNA polymerase II
holoenzyme at the pi9 promoter.
This observation of the p5 promoter transcription factors stimulating the pi 9 and
p40 promoters supports the strong role of p5 induction by the Adenovirus El A proteins.
The mutagenesis of the p5 transcription factors in the GAL4 hybrid reporter plasmid
showed several unique facts. First, the mutation of the MLTF site did not affect the Ad
and Rep induced transactivation of the p 19 promoter. Second, the mutagenesis of both
YY1 -60bp and YY1+1 caused the loss of this Ad and Rep induced transactivation.
Third, the mutation of the YY1 -60bp induced an extremely high basal transcriptional
activity for the p5 promoter. All of these results support the hypothesis that the El A
proteins bound to the two YY1 proteins at the p5 promoter perform the direct
transactivation of the pi 9 promoter.
This series of conclusions has a very profound effect on understanding the basic
biology of the Adeno-Associated Virus. First, the nonstructural protein, Rep, exhibits no
transcriptional transactivation activity or domains for the AAV promoters. With or
without Ad infection, the large Rep proteins inhibit the transcriptional activity of the p5
promoter. In the context of the pi 9 promoter, the Rep protein does not transactivate the
promoter and will inhibit transcriptional activity when its binding site moved closer to the
transcriptional start site. Second, separation of the p5 and pi 9 promoters by a PolyA
Signal influences both a synthetic pi9 promoter and the genomic pIM45 backbone. For
the genomic plasmids, it strongly decreases the degree of all transcriptional activation.
This observation would support the idea that the presence of a terminating RNA
polymerase II holoenzyme would inhibit the stable DNA loop formed between Rep and
Spl. The synthetic pi 9 promoters had a very different result because the lack of a Rep
binding element induced the strongest level of Ad and Rep induced transactivation. This
effect could be the result of different DNA sequences or the disruption of proper wild
type protein-protein interactions. Third, the Rep and Spl proteins exhibit no requirement
on Ad and Rep induced p 19 transactivation. The sole function of these two proteins is to
bind DNA sequences at the p5 and pi9 promoters and form a stable DNA loop structure.
Any other protein complex which performs this same function can replace the role of Rep
and Spl in AAV transcription. The substitution of GAL4 hybrid transcription factors for
Rep and Spl proteins supports the hypothesis that the Rep and Spl proteins act as
architectural proteins in the regulation of AAV gene expression.
TABLE OF ABBREVIATIONS
chloramphenicol acetyl transferase
Heat Shock Protein 90
Locus Control Region
Minute Virus of Mice
Rep binding element
TATA binding protein
Ying Yang Protein 1
Upstream Activating Sequence
Upstream Repressing Sequence
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Daniel Francis Lackner was bom on September 28, 1971 in Midland, Michigan.
He spent the first four years of his life in Michigan until his parents moved to Madison,
Indiana. He attended Pope John XXII Elementary School and Madison Junior High
School in Indiana. While he was fourteen years old, his parents moved back to Midland,
Michigan where he finished school at Northeast Junior High School and Midland Public
High School. During the fall of 1990, Dan enrolled in college undergraduate studies at
Delta College in University Center, Michigan. After the first two years of Delta College,
he transferred to Michigan State University in East Lansing, Michigan. He received a
Bachelor of Science degree with High Honors in Biochemistry in the spring of 1994.
After earning a Biochemistry degree, he obtained a job as a Laboratory Technician at the
University of Rochester Biology Department in Rochester, New York. He spent one year
in the laboratory of Susan Zusman studying the functions of Integin proteins within the
model organism, Drosophilia melanogaster. He began his graduate career by joining the
Center of Mammalian Genetics at the University of Florida in the fall of 1995. He joined
the laboratory of Nicholas Muzyczka in the summer of 1996. In October of 1999, he
married Cari Lynn Aspacher, a fellow graduate student in the Department of Molecular
Genetics. In August of 2002, he received a Ph.D in biomedical science.
I certify that I have read this study and that in my opinion it conforms to
acceptable standards of scholarly presentation and is fully adequate, in scope and quality,
as a dissertation for the degree of Doctor of Philosophy.
C ^ '
Nicholas Muzyczka, Chair
Eminent Scholar and Professor of
Molecular Genetics and Microbiology
I certify that I have read this study and that in my opinion it conforms to
acceptable standards of scholarly presentation and is fully adequate, in scope and quality,
as a dissertation for the degree of Doctor of Philosophy.
Professor of Pathology, Immunology, and
I certify that I have read this study and that in my opinion it conforms to
acceptable standards of scholarly presentation and is fully adequate/m scope and quality,
as a dissertation for the degree of Doctor of Philosophy. y
Eminent Scholar and Professor of
Molecular Genetics and Microbiology
I certify that I have read this study and that in my opinion it conforms to
acceptable standards of scholarly presentation and is fully adequate,in^scppe and quality,
as a dissertation for the degree of Doctor of Philosophy.
Professor of Molecular Genetics and
This dissertation was submitted to the Graduate Faculty of the College of
Agricultural and Life Sciences and to the Graduate School and was accepted as partial
fulfillment of the requirements for the degree of Doctor of Philosophy.
August 2002 'yifnMr^jSViA C
Dean, CÃ³llege of Medicine
Dean, Graduate School
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