Evolutionary variation of papillomavirus E2 protein and E2 binding sites
Identifieur interne : 000104 ( Pmc/Checkpoint ); précédent : 000103; suivant : 000105Evolutionary variation of papillomavirus E2 protein and E2 binding sites
Auteurs : Adam Rogers [États-Unis] ; Mackenzie Waltke [États-Unis] ; Peter C. Angeletti [États-Unis]Source :
- Virology Journal [ 1743-422X ] ; 2011.
Abstract
In an effort to identify the evolutionary changes relevant to E2 function, within and between papillomavirus genera, we evaluated the E2 binding sites (E2BS)s inside the long-control-region (LCR), and throughout the genomes. We identified E2BSs in the six largest genera of papillomaviruses: Alpha, Beta, Gamma, Delta, Lambda, and Xi-papillomaviruses (128 genomes), by comparing the sequences with a model consensus we created from known functional E2BSs (HPV16, HPV18, BPV1). We analyzed the sequence conservation and nucleotide content of the 4-nucleotide spacer within E2BSs. We determined that there is a statistically significant difference in GC content of the four-nucleotide E2BS spacer, between Alpha and Delta-papillomaviruses, as compared to each of the other groups. Additionally, we performed multiple alignments of E2 protein sequences using members of each genus in order to identify evolutionary changes within the E2 protein.
When a phylogenetic tree was generated from E2 amino acid sequences, it was discovered that the alpha-papillomavirus genera segregates into two distinct subgroups (α1 and α2). When these subgroups were individually analyzed, it was determined that the subgroup α1 consensus E2BS favored a spacer of AAAA, whereas subgroup α2 favored the opposite orientation of the same spacer; TTTT. This observation suggests that these conserved inverted linkers could have functional importance.
Url:
DOI: 10.1186/1743-422X-8-379
PubMed: 21806797
PubMed Central: 3161962
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Evolutionary variation of papillomavirus E2 protein and E2 binding sites</title><author><name sortKey="Rogers, Adam" sort="Rogers, Adam" uniqKey="Rogers A" first="Adam" last="Rogers">Adam Rogers</name><affiliation wicri:level="1"><nlm:aff id="I1">Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900</wicri:regionArea><wicri:noRegion>68583-0900</wicri:noRegion></affiliation></author><author><name sortKey="Waltke, Mackenzie" sort="Waltke, Mackenzie" uniqKey="Waltke M" first="Mackenzie" last="Waltke">Mackenzie Waltke</name><affiliation wicri:level="1"><nlm:aff id="I1">Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900</wicri:regionArea><wicri:noRegion>68583-0900</wicri:noRegion></affiliation></author><author><name sortKey="Angeletti, Peter C" sort="Angeletti, Peter C" uniqKey="Angeletti P" first="Peter C" last="Angeletti">Peter C. Angeletti</name><affiliation wicri:level="1"><nlm:aff id="I1">Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900</wicri:regionArea><wicri:noRegion>68583-0900</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21806797</idno><idno type="pmc">3161962</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3161962</idno><idno type="RBID">PMC:3161962</idno><idno type="doi">10.1186/1743-422X-8-379</idno><date when="2011">2011</date><idno type="wicri:Area/Pmc/Corpus">000138</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000138</idno><idno type="wicri:Area/Pmc/Curation">000138</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000138</idno><idno type="wicri:Area/Pmc/Checkpoint">000104</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000104</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Evolutionary variation of papillomavirus E2 protein and E2 binding sites</title><author><name sortKey="Rogers, Adam" sort="Rogers, Adam" uniqKey="Rogers A" first="Adam" last="Rogers">Adam Rogers</name><affiliation wicri:level="1"><nlm:aff id="I1">Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900</wicri:regionArea><wicri:noRegion>68583-0900</wicri:noRegion></affiliation></author><author><name sortKey="Waltke, Mackenzie" sort="Waltke, Mackenzie" uniqKey="Waltke M" first="Mackenzie" last="Waltke">Mackenzie Waltke</name><affiliation wicri:level="1"><nlm:aff id="I1">Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900</wicri:regionArea><wicri:noRegion>68583-0900</wicri:noRegion></affiliation></author><author><name sortKey="Angeletti, Peter C" sort="Angeletti, Peter C" uniqKey="Angeletti P" first="Peter C" last="Angeletti">Peter C. Angeletti</name><affiliation wicri:level="1"><nlm:aff id="I1">Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900</wicri:regionArea><wicri:noRegion>68583-0900</wicri:noRegion></affiliation></author></analytic><series><title level="j">Virology Journal</title><idno type="eISSN">1743-422X</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>In an effort to identify the evolutionary changes relevant to E2 function, within and between papillomavirus genera, we evaluated the E2 binding sites (E2BS)s inside the long-control-region (LCR), and throughout the genomes. We identified E2BSs in the six largest genera of papillomaviruses: Alpha, Beta, Gamma, Delta, Lambda, and Xi-papillomaviruses (128 genomes), by comparing the sequences with a model consensus we created from known functional E2BSs (HPV16, HPV18, BPV1). We analyzed the sequence conservation and nucleotide content of the 4-nucleotide spacer within E2BSs. We determined that there is a statistically significant difference in GC content of the four-nucleotide E2BS spacer, between Alpha and Delta-papillomaviruses, as compared to each of the other groups. Additionally, we performed multiple alignments of E2 protein sequences using members of each genus in order to identify evolutionary changes within the E2 protein.</p></sec><sec><title>Results</title><p>When a phylogenetic tree was generated from E2 amino acid sequences, it was discovered that the alpha-papillomavirus genera segregates into two distinct subgroups (α1 and α2). When these subgroups were individually analyzed, it was determined that the subgroup α1 consensus E2BS favored a spacer of AAAA, whereas subgroup α2 favored the opposite orientation of the same spacer; TTTT. This observation suggests that these conserved inverted linkers could have functional importance.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Zheng, Zm" uniqKey="Zheng Z">ZM Zheng</name></author><author><name sortKey="Baker, Cc" uniqKey="Baker C">CC Baker</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Day, Pm" uniqKey="Day P">PM Day</name></author><author><name sortKey="Lowy, Dr" uniqKey="Lowy D">DR Lowy</name></author><author><name sortKey="Schiller, Jt" uniqKey="Schiller J">JT Schiller</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bosch, Fx" uniqKey="Bosch F">FX Bosch</name></author><author><name sortKey="Sanjose, S" uniqKey="Sanjose S">S Sanjose</name></author><author><name sortKey="Castellsague, X" uniqKey="Castellsague X">X Castellsague</name></author><author><name sortKey="Moreno, V" uniqKey="Moreno V">V Moreno</name></author><author><name 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Virol J</journal-id><journal-title-group><journal-title>Virology Journal</journal-title></journal-title-group><issn pub-type="epub">1743-422X</issn><publisher><publisher-name>BioMed Central</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">21806797</article-id><article-id pub-id-type="pmc">3161962</article-id><article-id pub-id-type="publisher-id">1743-422X-8-379</article-id><article-id pub-id-type="doi">10.1186/1743-422X-8-379</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research</subject></subj-group></article-categories><title-group><article-title>Evolutionary variation of papillomavirus E2 protein and E2 binding sites</article-title></title-group><contrib-group><contrib contrib-type="author" id="A1"><name><surname>Rogers</surname><given-names>Adam</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>adamrogers2@gmail.com</email></contrib><contrib contrib-type="author" id="A2"><name><surname>Waltke</surname><given-names>Mackenzie</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>mwaltke@bigred.unl.edu</email></contrib><contrib contrib-type="author" corresp="yes" id="A3"><name><surname>Angeletti</surname><given-names>Peter C</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>Pangeletti2@unl.edu</email></contrib></contrib-group><aff id="I1"><label>1</label>Nebraska Center for Virology, School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68583-0900, USA</aff><pub-date pub-type="collection"><year>2011</year></pub-date><pub-date pub-type="epub"><day>1</day><month>8</month><year>2011</year></pub-date><volume>8</volume><fpage>379</fpage><lpage>379</lpage><history><date date-type="received"><day>26</day><month>4</month><year>2011</year></date><date date-type="accepted"><day>1</day><month>8</month><year>2011</year></date></history><permissions><copyright-statement>Copyright ©2011 Rogers et al; licensee BioMed Central Ltd.</copyright-statement><copyright-year>2011</copyright-year><copyright-holder>Rogers et al; licensee BioMed Central Ltd.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><self-uri xlink:href="http://www.virologyj.com/content/8/1/379"></self-uri><abstract><sec><title>Background</title><p>In an effort to identify the evolutionary changes relevant to E2 function, within and between papillomavirus genera, we evaluated the E2 binding sites (E2BS)s inside the long-control-region (LCR), and throughout the genomes. We identified E2BSs in the six largest genera of papillomaviruses: Alpha, Beta, Gamma, Delta, Lambda, and Xi-papillomaviruses (128 genomes), by comparing the sequences with a model consensus we created from known functional E2BSs (HPV16, HPV18, BPV1). We analyzed the sequence conservation and nucleotide content of the 4-nucleotide spacer within E2BSs. We determined that there is a statistically significant difference in GC content of the four-nucleotide E2BS spacer, between Alpha and Delta-papillomaviruses, as compared to each of the other groups. Additionally, we performed multiple alignments of E2 protein sequences using members of each genus in order to identify evolutionary changes within the E2 protein.</p></sec><sec><title>Results</title><p>When a phylogenetic tree was generated from E2 amino acid sequences, it was discovered that the alpha-papillomavirus genera segregates into two distinct subgroups (α1 and α2). When these subgroups were individually analyzed, it was determined that the subgroup α1 consensus E2BS favored a spacer of AAAA, whereas subgroup α2 favored the opposite orientation of the same spacer; TTTT. This observation suggests that these conserved inverted linkers could have functional importance.</p></sec></abstract><kwd-group><kwd>extrachromosomal DNA</kwd><kwd>persistent infection</kwd><kwd>Human papillomavirus</kwd><kwd>E2 Protein</kwd><kwd>DNA binding Domain</kwd></kwd-group></article-meta></front></pmc><affiliations><list><country><li>États-Unis</li></country></list><tree><country name="États-Unis"><noRegion><name sortKey="Rogers, Adam" sort="Rogers, Adam" uniqKey="Rogers A" first="Adam" last="Rogers">Adam Rogers</name></noRegion><name sortKey="Angeletti, Peter C" sort="Angeletti, Peter C" uniqKey="Angeletti P" first="Peter C" last="Angeletti">Peter C. Angeletti</name><name sortKey="Waltke, Mackenzie" sort="Waltke, Mackenzie" uniqKey="Waltke M" first="Mackenzie" last="Waltke">Mackenzie Waltke</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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