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Journal of Virology, March 2004, p. 2620-2626, Vol. 78, No. 5
0022-538X/04/$08.00+0 DOI: 10.1128/JVI.78.5.2620-2626.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Roles of the E6 and E7 Proteins in the Life Cycle of Low-Risk Human Papillomavirus Type 11
Stephen T. Oh, Michelle S. Longworth, and Laimonis A. Laimins*
Department of Microbiology-Immunology, The Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
Received 9 September 2003/
Accepted 21 October 2003

ABSTRACT
Many important functions have been attributed to the high-risk
human papillomavirus (HPV) E6 and E7 proteins, including binding
and degradation of p53 as well as interacting with Rb proteins.
In contrast, the physiological roles of the low-risk E6 and
E7 proteins remain unclear. Previous studies demonstrated that
the high-risk E6 and E7 proteins also play roles in the productive
life cycle by facilitating the maintenance of viral episomes
(J. T. Thomas, W. G. Hubert, M. N. Ruesch, and L. A. Laimins,
Proc. Natl. Acad. Sci. USA 96:8449-8454, 1999). In order to
determine whether low-risk E6 or E7 is similarly necessary for
the stable maintenance of episomes, HPV type 11 (HPV-11) genomes
that contained translation termination mutations in E6 or E7
were constructed. Upon transfection into normal human keratinocytes,
genomes in which E6 function was abolished were unable to be
maintained episomally. Transfection of genomes containing substitution
mutations in amino acids conserved in high- and low-risk HPV
types suggested that multiple protein domains are involved in
this process. Examination of cells transfected with HPV-11 genomes
in which E7 function was inhibited were found to exhibit a more
complex phenotype. At the second passage following transfection,
mutant genomes were maintained as episomes but at significantly
reduced levels than in cells transfected with the wild-type
HPV-11 genome. Upon further passage in culture, however, the
episomal forms of these E7 mutant genomes quickly disappeared.
These findings identify important new functions for the low-risk
E6 and E7 proteins in the episomal maintenance of low-risk HPV-11
genomes and suggest that they may act in a manner similar to
that observed for the high-risk proteins.

INTRODUCTION
Human papillomaviruses (HPVs) are small, double-stranded DNA
viruses that induce hyperproliferative lesions in epithelial
tissues (
16,
56). More than 100 types of HPV have been identified,
with each differing by at least 10% in the coding sequence of
the major capsid gene, L1 (
28,
35,
55). High-risk HPV types,
including HPV type 16 (HPV-16), HPV-18, HPV-31, HPV-33, and
HPV-42, induce lesions in the genital tract that can progress
to malignancy. In contrast, low-risk HPV types, such as HPV-6
and HPV-11, which also infect genital epithelia, primarily induce
benign lesions (
16,
28,
55).
In the high-risk HPV types, E6 and E7 have been shown to function as oncoproteins (18, 25). E7 acts by binding to members of the Rb tumor suppressor protein family and inhibiting their ability to modulate the function of E2F transcription factors (7, 34). The low-risk E7 proteins have also been shown to bind to Rb but with a 10-fold-lower affinity (15). One of the primary activities of the high-risk forms of E6 is to target p53 for degradation (32, 43, 53), which is mediated by complex formation with the cellular ubiquitin ligase E6-AP (19, 20, 28, 41, 42). Although degradation of p53 by E6 is specific to high-risk HPV types, some evidence suggests that low-risk forms of E6 may be able to bind to p53 with a low affinity (2, 30, 53). E6 from high-risk types has also been shown to activate telomerase via upregulation of hTERT expression (13, 24, 36, 52). Furthermore, the high-risk E6 proteins have been shown to interact with a number of other cellular proteins, such as the putative calcium-binding protein E6-BP, the focal adhesion protein paxillin, p300/CBP, and PDZ domain proteins such as hDLG, MUPP-1, MAGI-1, and hScrib (1, 11, 12, 14, 23, 29, 39, 40, 48-51, 54). While the majority of these interactions have been shown to be specific for the high-risk forms of E6, several reports have described cellular binding partners for low-risk E6 proteins, such as zyxin, GPS2, Bak, and MCM7 (4, 5, 26, 27, 37, 47). In addition, it has been reported that high-risk and low-risk forms of E6 can bind to p73 (37), although this has not been seen in other studies (33). The physiological relevance of each of these interactions of the low-risk E6 proteins is not yet fully understood.
The HPV life cycle is closely linked to the differentiation status of its target epithelial tissue (28). Infection is thought to occur in cells in the basal layer of stratified epithelia where viral genomes are established as episomes and are replicated synchronously with chromosomal DNA. Following cell division, one of the infected daughter cells migrates away from the basal layer and begins to differentiate, resulting in the activation of late gene expression, amplification of the viral genomes, and virion assembly. In addition to their roles in immortalization, recent work has demonstrated that E6 and E7 play important roles in the HPV life cycle (9, 45). Using a genetic system involving transfection of cloned HPV genomes into keratinocytes, it has been demonstrated that expression of functional high-risk E6 and E7 proteins are required to maintain HPV-31 genomes as stably replicating episomes (45). Although HPV-31 genomes lacking E6 or E7 can be replicated in transient assays, they cannot be maintained in long-term stable replication assays. In addition, spontaneously immortalized keratinocytes transfected with HPV-16 genomes containing mutations in E7 are unable to amplify viral DNA upon differentiation, suggesting that E7 may also be involved in later stages of the viral life cycle (9).
The mechanism by which E6 and E7 contribute to the maintenance of episomes in the viral life cycle is not fully understood. HPV-31 genomes containing a point mutation in E6 that eliminates the ability to target p53 for degradation cannot be maintained episomally, suggesting a role for p53 in this process (45). However, when a second mutation in the E7 open reading frame (ORF) that converted its Rb binding affinity to that of the low-risk E7 was introduced into the genome, the ability to be stably maintained was restored (38). These findings suggest that a complex interplay between viral proteins can contribute to facilitating a cellular environment conducive to episomal maintenance. As with E6, genomes containing point mutations in E7 that abolish binding to Rb are unable to be stably maintained as episomes, suggesting that inactivation of Rb is also important for stable replication (45). Recent work has shown that the low-risk HPV-11 genome can also be stably maintained as an episome following transfection of normal human keratinocytes (46). Since high- and low-risk E6 and E7 proteins probably share some common functions in the productive life cycle, we have investigated the effects of inhibiting translation of these proteins in the context of the complete viral genome (Fig. 1).

Loss of episomal maintenance in cells containing HPV-11 E6 and E7 mutant genomes.
We initially constructed two mutant HPV-11 genomes that inhibited
E6 or E7 function. In HPV11E6-
NheI, the E6 start codon was substituted
with a TAG stop codon that then generates an
NheI site. In HPV-11,
the start codon for E7 is located within the E6 ORF, so in order
to inhibit E7 function, we inserted a translation termination
codon 25 nucleotides downstream of the end of the E6 coding
sequence to generate HPV11E7-
NheI. Wild-type and mutant HPV-11
genomes were cotransfected with pSV
2Neo into normal human foreskin
keratinocytes (HFKs) and selected for neomycin resistance as
previously described (
8,
46). Within each experiment, a single
donor isolate was used. Following selection for 8 days, resistant
colonies were pooled and expanded for analyses. Cells were grown
to confluence and passaged once per week. Each passage of confluent
cells represents approximately 3 or 4 population doublings.
In previous studies, using similar transfection methods, Frattini
et al. demonstrated that all clonal isolates of HPV-31-transfected
cells examined contained HPV DNA at copy numbers similar to
those observed for pooled cultures (
10). Therefore, we believe
it is likely that the majority of cells within our transfected
pools contain HPV-11 DNA. However, we cannot totally exclude
the possibility that some neomycin-resistant cells contain no
HPV-11 DNA.
A representative Southern blot analysis of cells transfected with HPV11, HPV11E6-NheI, or HPV11E7-NheI plasmid is shown in Fig. 2. Cells transfected with the wild-type HPV-11 genome were found to harbor both episomal and integrated forms of the genome at the second passage after transfection (Fig. 2, left). However, no extrachromosomal copies of the genome were detected in cells at the same passage transfected with the HPV11E6-NheI genome, and these cells maintained only small numbers of integrated copies. This suggests that HPV-11 E6 expression is important for episomal maintenance. In cells transfected with the HPV11E7-NheI genome, there was a significant decrease observed in episomal copy number, although low levels of episomes were still detected. Similar results were seen in three separate transfections using different donor keratinocytes. These findings suggest that low-risk E6 and E7 play significant roles in episomal maintenance, as measured at the second passage following transfection.
In order to confirm that these findings were not the result
of
cis effects due to the sequences used to generate the mutations,
we examined the effects of a second set of mutant genomes in
our transfection assays. In HPV11E6-3xTAA, three TAA stop codons
were inserted in place of the E6 start codon, while HPV11E7-3xTAA
contains three TAA stop codons 27 nucleotides downstream of
the E7 initiation codon (Fig.
1). HFKs were transfected with
wild-type HPV-11 genomes or the HPV11E6-
NheI, HPV11E6-3xTAA,
HPV11E7-
NheI, and HPV11E7-3xTAA mutant genomes. As shown in
Fig.
2, cells transfected with wild-type HPV-11 maintained high
levels of episomes along with some integrated forms. In contrast,
at the same passage number, no episomal copies of the genome
were detected in cells transfected with either the HPV11E6-
NheI
or HPV11E6-3xTAA mutant genome, and these cells had only low
levels of integrated DNA. These findings confirm that E6 function
is critical for episomal maintenance of the low-risk HPV-11
genome. In cells transfected with either of the HPV11E7 mutant
genomes, we consistently detected a significantly lower level
of episomal DNA than that seen with cells transfected with wild-type
HPV-11. These findings indicate that in the absence of E7 expression,
cells were impaired in the ability to maintain episomes, although
low levels could still be detected. Similar effects were observed
in three independent experiments at similar passage numbers.
In this study, our use of two types of mutations to eliminate E6 and E7 function ensured that the phenotype we observed was truly due to the lack of E6 or E7 protein and not due to the alteration of a cis element important for other viral functions. Although we have previously shown that disruption of splice donor and acceptor sites within the E6 ORF in the high-risk HPV-31 genome leads to a loss of E1 and/or E2 expression, no such splice sites or splicing patterns in E6 have been found in the low-risk HPV-11 genome (17, 45). Thus, while we cannot completely exclude the possibility that expression of other viral genes may have been affected by these mutations, we believe that the similarity of our findings with two different types of mutations makes this possibility less likely.

HPV11E6 and HPV11E7 mutant genomes cannot be maintained episomally over extended time in culture.
The above experiments demonstrated that HPV11E6 mutant genomes
could no longer be maintained extrachromosomally within two
passages following transfection. Although episomal maintenance
of HPV11E7 mutant genomes was also impaired, low levels of episomal
DNA could still be detected at the same passage. We thus examined
whether the reduced levels of viral episomes seen in cells transfected
with HPV11E7 mutant genomes could be maintained upon further
passage in culture. As shown in Fig.
3, wild-type HPV-11-transfected
cells harbored both episomal and integrated copies of the genome
at two and three passages after transfection. Consistent with
the results seen at earlier passages, no episomal DNA was detected
at either passage for the HPV11E6-
NheI genome. In cells transfected
with the HPV11E7-
NheI genome, a very low level of episomal DNA
could be detected at the second passage, but by the following
passage, there were no longer any episomal copies detected,
suggesting that the lack of E7 function leads to a more severe
defect in episomal maintenance over time. We did not extensively
analyze the state of episomal DNA beyond passage three, but
in all passages where the wild-type HPV-11 genome was compared
with the HVP11E6 or HVP11E7 mutant genome, we detected levels
of episomal DNA that were significantly higher for the wild-type
genome. In the experiment shown in Fig.
3, we were unable to
detect episomal DNA at passage six for the wild-type HPV-11
genome. In a previous study, Thomas et al. detected episomal
forms of HPV-11 at later passages (
46). We believe that the
different results observed in this study are due to the specific
host keratinocytes used for each experiment. Similar findings
were observed with the HPV11E6-3xTAA and HPV11E7-3xTAA mutants
(data not shown), and comparable results were found in six other
independent experiments comparing the wild-type HPV-11 genome
with the HPV11E6-
NheI mutant genome. These findings indicate
that E6 and E7 play an important role in the episomal maintenance
of the HPV-11 genome, such that genomes lacking either E6 or
E7 function cannot be maintained beyond three passages following
transfection.

Stable replication of HPV-11 genomes containing point mutations in E6.
We next sought to investigate the mechanisms by which the HPV-11
E6 protein contributes to episomal maintenance. We focused on
E6, since elimination of its activity led to rapid loss of episomes.
In order to identify domains within the HPV-11 E6 protein that
are important for episomal maintenance, a series of substitution
mutations within the E6 ORF in the context of the HPV-11 genome
was made. We reasoned that since both the high-risk HPV-31 E6
protein and the low-risk HPV-11 E6 protein are important for
stable episomal maintenance, they might bind to a common partner
or act by a shared pathway through conserved amino acids. Comparison
of the amino acid sequences of the high-risk HPV-31, HPV-16,
and HPV-18 E6 types with the low-risk HPV-11 and HPV-6 E6 types
indicated a lack of extensive homology between the two sets
of proteins (Fig.
4). Indeed, the majority of amino acids common
between all five types are scattered within the protein, rather
than clustered into domains. The two major motifs conserved
between all five forms of the protein are the two zinc finger
regions (Cys-X-X-Cys-29 amino acids-Cys-X-X-Cys). However, previous
mutational analysis with the high-risk E6 proteins suggested
that these residues are important for structural integrity rather
than protein-protein interaction domains (
3,
31). We identified
several amino acids that are conserved in the different forms
of E6 (amino acids W133, CC67/137, L111) that have already been
studied in the context of the high-risk E6 proteins. Mutation
of amino acid 133 (W133R) has been shown to inhibit the ability
of HPV-16 E6 to both bind p53 and target it for degradation
(
3), while the CC67/137GG mutation blocks p53- or p73-dependent
transactivation (
37). The L111Q mutation eliminates most E6
activities, including binding and degradation of p53, as well
as binding to E6-AP and E6-BP (
31). In addition, in the context
of the complete HPV-16 genome, the L111Q mutation inhibits episomal
maintenance (
37,
38). Finally, we identified two additional
amino acids (R56 and R78) that are conserved in low-risk and
high-risk forms of E6 but have not been examined previously.
Mutant genomes that incorporated these mutations individually
into the E6 ORF in the context of the complete HPV-11 genome
were constructed. Wild-type and mutant HPV-11 genomes were then
cotransfected with pSV
2Neo into HFKs and selected for neomycin
resistance as in previous experiments. Resistant colonies were
pooled and expanded for Southern blot analyses. As shown in
Fig.
5, cells transfected with the HPV11E6-
NheI mutant genome
contained little to no episomal DNA at the second passage after
transfection. In contrast, cells transfected with the HPV11E6-R56A
mutant genome contained episomal DNA at levels similar to those
of cells transfected with the wild-type HPV-11 genome, suggesting
that this mutation has little effect on episomal maintenance
at this passage number. In contrast, Southern blot analysis
performed at the second passage following transfection of genomes
containing the L111Q, CC66/137GG, W133R, and R78A mutations
revealed impaired episomal maintenance (Fig.
5). Cells transfected
with these mutant genomes contained little to no episomal DNA
compared to cells transfected with the wild-type HPV-11 genome.
These findings suggest that mutation of these residues significantly
impairs, but does not totally inhibit, the ability of E6 to
facilitate HPV-11 stable replication at this passage number.
Similar effects were seen in three independent experiments for
each mutant genome with the exception of the HPV11E6-R56A mutant,
which was examined once. In the rightmost Southern blot shown
in Fig.
5, we detected high levels of open circle and linear
HPV-11 DNA as opposed to supercoiled forms, which we believe
was due to nicking that occurred during the DNA extraction process.
At later passages, cells transfected with the HPV11E6-L111Q,
-CC66/137GG, -W133R, and -R78A mutant genomes lost the ability
to maintain episomes, while cells transfected with wild-type
HPV-11 still retained significant levels of extrachromosomal
viral DNA (data not shown). We have therefore identified four
mutations in E6 that impair its function in episomal maintenance.
In this study, we have identified a function for the low-risk
HPV-11 E6 protein in modulating the stable maintenance of viral
episomes. This is one of the first functions that has been demonstrated
for low-risk E6 in the context of the viral life cycle. As E6
proteins have shown only weak nonspecific DNA binding activity,
we do not believe that E6 acts directly to modulate episome
replication or segregation. Rather, we suspect that E6 acts
to alter the cellular environment to allow for the long-term
maintenance of extrachromosomal elements. The presence of extrachromosomal
DNAs in normal cells is not tolerated and is likely sensed as
a DNA damage stimulus. Papillomaviruses must therefore block
these normal cellular checkpoints to allow for persistence of
viral episomes. Given that high-risk E6 proteins have been shown
to act in a manner similar to low-risk E6 in modulating the
maintenance of viral episomes, they may target similar cellular
pathways. It is likely that these functions are mediated through
the binding of E6 proteins to cellular factors, and the studies
described provide important tools to identify these factors.
Our analysis of the HPV-11 E6 protein identified four amino acid substitution mutations that resulted in significantly impaired episomal maintenance. These mutants will be of particular importance in the future in facilitating the identification of cellular binding partners that mediate these functions of E6. The four substitution mutations induced a significant reduction in episomal copy number, but not a total loss of episomal maintenance at early passage. These individual mutations therefore did not induce as severe a phenotype as did the complete translation stop mutants. This could indicate that multiple activities of E6 are required for its role in episomal maintenance or that some of the mutations we have examined induce structural changes in E6 that indirectly affect its function leading to a loss of episomes. Finally, we cannot exclude the possibility that some of these mutations alter protein stability, but our inability to immunoprecipitate the HPV-11 E6 protein from cells precludes testing this hypothesis. Our observation that some substitution mutations in E6 result in a phenotype similar to that seen with stop codon mutations further suggests that these effects are not due to nonsense-mediated decay. Further work characterizing the ability of these different E6 mutants to bind to cellular proteins is necessary to better elucidate the mechanism by which the low-risk E6 protein facilitates episomal maintenance.
We also observed an effect on episomal maintenance when E7 function was inhibited. The effects we observed with HPV11E7 were, however, less severe than those seen with HPV11E6 mutant genomes, resulting initially in only a partial reduction in the levels of viral episomes. However, within three passages following transfection, episomal DNA was no longer detected. As in the case of E6, the specific manner in which E7 contributes to the HPV-11 viral life cycle is unclear. Previous studies have shown that low-risk forms of E7 bind to Rb, although this occurs with a greatly reduced affinity compared to that of high-risk forms of E7 (15). Therefore, it is possible that binding of Rb family members is responsible for the role of E7 in facilitating episomal maintenance; this is supported by studies in HPV-31 (45). Two early promoters are present in the HPV-11 genome, and one directs transcription of messages that contain E7 as the first ORF (6, 44). In contrast, in the high-risk HPV-31 genome, there is only a single early promoter, and E7 is found on transcripts as the second ORF with E6 or E6* upstream (21, 22). It is therefore possible that due to the configuration of early transcripts in low-risk viruses, the low-risk E7 proteins are synthesized at higher levels than their high-risk counterparts, leading to similar effects on Rb action. The testing of this hypothesis, however, will require the development of efficient antibodies to HPV-11 E7 to accurately determine levels in cells.
The study of episomal maintenance in the low-risk HPV-11 types is complicated by the lack of immortalizing capability of these viral types. This makes it important to compare the effects of various HPV-11 mutants on episomal maintenance as a function of passage number, as we have done in this study. For instance, inhibition of HPV-11 E7 function did not result in an immediate loss of episomal maintenance, but rather this was manifested only over extended passage in culture. However, at all passages examined, wild-type HPV-11 genomes were maintained extrachromosomally at significantly higher copy numbers than episomal forms of E7 mutant genomes. We are confident that the comparisons made in this study represent physiologically important activities of the low-risk E6 and E7 gene products. Upon extended passage of cells in culture, we also observed that the levels of wild-type HPV-11 episomes decreased, although they consistently remained higher than the levels of HPV11E6 or HPV11E7 mutant genomes at the same passage. Thus, we believe the differences we observed reflect true differences in episomal maintenance. We also observed some variation in the levels of wild-type HPV-11 episomal DNA between transfection experiments that we suspect was due to differences in the donor keratinocytes used. However, in experiments using the same donor isolate, we saw consistent differences between wild-type and mutant genomes. Thus, we believe that accurate comparisons can be made between wild-type and mutant genomes within a single experiment. In summary, we have identified novel functions for the low-risk E6 and E7 proteins in the HPV life cycle. These activities are similar to those previously observed for high-risk HPV proteins and may reflect common pathways utilized by both types of viruses during their productive life cycles.

ACKNOWLEDGMENTS
We thank members of the Laimins laboratory for helpful comments
and technical advice.
This study was supported by a grant from the NCI and a grant from the NIAID-supported Sexually Transmitted Disease Cooperative Research Center to L.A.L. (CA74202). S.T.O. was supported by a NIH/NRSA Carcinogenesis Training Grant (5 T32 CA09560-15) to Northwestern University.

FOOTNOTES
* Corresponding author. Mailing address: Department of Microbiology-Immunology, The Feinberg School of Medicine, Northwestern University, Morton 6-681, 303 E. Chicago Ave., Chicago, IL 60611. Phone: (312) 503-0648. Fax: (312) 503-0649. E-mail:
l-laimins{at}northwestern.edu.


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Journal of Virology, March 2004, p. 2620-2626, Vol. 78, No. 5
0022-538X/04/$08.00+0 DOI: 10.1128/JVI.78.5.2620-2626.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
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