Mo-MuLV nucleotide sequence exhibits three levels of oligomeric repetitions, suggesting a stepwise molecular evolution
Identifieur interne : 000051 ( Istex/Corpus ); précédent : 000050; suivant : 000052Mo-MuLV nucleotide sequence exhibits three levels of oligomeric repetitions, suggesting a stepwise molecular evolution
Auteurs : Ivan LaprevotteSource :
- Journal of Molecular Evolution [ 0022-2844 ] ; 1992-11-01.
English descriptors
- KwdEn :
- Teeft :
- Actual compositions, Chain analysis, Coding, Coding part, Coding sectorsb, Codon, Codon usage, Complementary strands, Consensus ccagacc, Consensus sequence, Construction principle, Core consensus, Doublet frequencies, Eukaryotic viruses, Feline leukemia virus, Further investigation, Gene conversion, Genetic variation, Genome, High number, Hsrv, Human genes, Human spumaretrovirus, Intermediary stage, Intragenic duplications, Laprevotte, Local duplications, Local repetitions, Major source, Markov, Markov chain, Markov chain analysis, Molecular evolution, Noncoding, Noncoding part, Noncoding sectorsb, Nonoverlapping positions, Nucleic acids, Nucleotide, Nucleotide sequence, Ohno, Oligomeric, Oligomeric repetitions, Oligomers, Original tandemly, Overrepeated, Overrepresented, Overrepresented oligomers, Proc natl acad, Purine, Putative tandem repetitions, Pyrimidine, Relative frequencies, Relative frequency, Repetitive, Residual, Residual value, Residual values, Same length, Slippagelike mechanisms, Successive values, Tandem, Tandem repetitions, Threshold value, Total number, Trimeric distribution, Unequal crossover, Universal rule, Whole sequence.
Abstract
Summary: An exhaustive computer-assisted analysis of the Moloney murine leukemia virus nucleotide sequence shows numerous deviations in the oligomeric distribution, suggesting three overlapping levels of a stepwise duplicative evolution. (1) The sequence fits the universal rule of TG/CT excess which has been proposed as the construction principle of all sequences, and maintains some degree of symmetry between the two complementary strands. (2) Oligomeric repeating units share a core consensus regularly scattered throughout the sequence. This consensus is not merely predictable from the doublet frequencies and codon usage, but could correspond to an intermediary stage in a so-called periodic-to-chaotic transition. (3) Probable stepwise local duplications could be accounted for by slippagelike mechanisms. Comparison with the human spumaretrovirus (HSRV) shows similar segments in the overrepresented oligomers of the two sequences. The intermediary stage of transition oligomeric repeating units is not so clearly suggested in HSRV, perhaps because of numerous stepwise local duplications. In any case, a common evolutionary origin for the two viruses is not ruled out.
Url:
DOI: 10.1007/BF00171820
Links to Exploration step
ISTEX:E293A76D253FD6A367EAB60BE64C82FFB0510DE2Le document en format XML
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(1) The sequence fits the universal rule of TG/CT excess which has been proposed as the construction principle of all sequences, and maintains some degree of symmetry between the two complementary strands. (2) Oligomeric repeating units share a core consensus regularly scattered throughout the sequence. This consensus is not merely predictable from the doublet frequencies and codon usage, but could correspond to an intermediary stage in a so-called periodic-to-chaotic transition. (3) Probable stepwise local duplications could be accounted for by slippagelike mechanisms. Comparison with the human spumaretrovirus (HSRV) shows similar segments in the overrepresented oligomers of the two sequences. The intermediary stage of transition oligomeric repeating units is not so clearly suggested in HSRV, perhaps because of numerous stepwise local duplications. 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(1) The sequence fits the universal rule of TG/CT excess which has been proposed as the construction principle of all sequences, and maintains some degree of symmetry between the two complementary strands. (2) Oligomeric repeating units share a core consensus regularly scattered throughout the sequence. This consensus is not merely predictable from the doublet frequencies and codon usage, but could correspond to an intermediary stage in a so-called periodic-to-chaotic transition. (3) Probable stepwise local duplications could be accounted for by slippagelike mechanisms. Comparison with the human spumaretrovirus (HSRV) shows similar segments in the overrepresented oligomers of the two sequences. The intermediary stage of transition oligomeric repeating units is not so clearly suggested in HSRV, perhaps because of numerous stepwise local duplications. 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(1) The sequence fits the universal rule of TG/CT excess which has been proposed as the construction principle of all sequences, and maintains some degree of symmetry between the two complementary strands. (2) Oligomeric repeating units share a core consensus regularly scattered throughout the sequence. This consensus is not merely predictable from the doublet frequencies and codon usage, but could correspond to an intermediary stage in a so-called periodic-to-chaotic transition. (3) Probable stepwise local duplications could be accounted for by slippagelike mechanisms. Comparison with the human spumaretrovirus (HSRV) shows similar segments in the overrepresented oligomers of the two sequences. The intermediary stage of transition oligomeric repeating units is not so clearly suggested in HSRV, perhaps because of numerous stepwise local duplications. In any case, a common evolutionary origin for the two viruses is not ruled out.</p></abstract><textClass xml:lang="en"><keywords scheme="keyword"><list><head>Key words</head><item><term>Mo-MuIV</term></item><item><term>HSRV</term></item><item><term>DNA</term></item><item><term>Computer-assisted analysis</term></item><item><term>Core consensus</term></item><item><term>TG/CT excess</term></item><item><term>Symmetry</term></item><item><term>Markov analysis</term></item></list></keywords></textClass><textClass><keywords scheme="Journal Subject"><list><head>Life Sciences</head><item><term>Cell Biology</term></item><item><term>Microbiology</term></item><item><term>Plant Sciences</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="1992-01-18">Created</change><change when="1992-11-01">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/ark:/67375/1BB-8LB0JKGV-Q/fulltext.txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="corpus springer-journals not found" wicri:toSee="no header"><istex:xmlDeclaration>version="1.0" encoding="UTF-8"</istex:xmlDeclaration><istex:docType PUBLIC="-//Springer-Verlag//DTD A++ V2.4//EN" URI="http://devel.springer.de/A++/V2.4/DTD/A++V2.4.dtd" name="istex:docType"></istex:docType><istex:document><Publisher><PublisherInfo><PublisherName>Springer-Verlag</PublisherName><PublisherLocation>New York</PublisherLocation></PublisherInfo><Journal><JournalInfo JournalProductType="ArchiveJournal" NumberingStyle="Unnumbered"><JournalID>239</JournalID><JournalPrintISSN>0022-2844</JournalPrintISSN><JournalElectronicISSN>1432-1432</JournalElectronicISSN><JournalTitle>Journal of Molecular Evolution</JournalTitle><JournalAbbreviatedTitle>J Mol Evol</JournalAbbreviatedTitle><JournalSubjectGroup><JournalSubject Type="Primary">Life Sciences</JournalSubject><JournalSubject Type="Secondary">Cell Biology</JournalSubject><JournalSubject Type="Secondary">Microbiology</JournalSubject><JournalSubject Type="Secondary">Plant Sciences</JournalSubject></JournalSubjectGroup></JournalInfo><Volume><VolumeInfo VolumeType="Regular" TocLevels="0"><VolumeIDStart>35</VolumeIDStart><VolumeIDEnd>35</VolumeIDEnd><VolumeIssueCount>6</VolumeIssueCount></VolumeInfo><Issue IssueType="Regular"><IssueInfo TocLevels="0"><IssueIDStart>5</IssueIDStart><IssueIDEnd>5</IssueIDEnd><IssueArticleCount>11</IssueArticleCount><IssueHistory><CoverDate><Year>1992</Year><Month>11</Month></CoverDate></IssueHistory><IssueCopyright><CopyrightHolderName>Springer-Verlag</CopyrightHolderName><CopyrightYear>1992</CopyrightYear></IssueCopyright></IssueInfo><Article ID="Art6"><ArticleInfo Language="En" ArticleType="OriginalPaper" NumberingStyle="Unnumbered" TocLevels="0" ContainsESM="No"><ArticleID>BF00171820</ArticleID><ArticleDOI>10.1007/BF00171820</ArticleDOI><ArticleSequenceNumber>6</ArticleSequenceNumber><ArticleTitle Language="En">Mo-MuLV nucleotide sequence exhibits three levels of oligomeric repetitions, suggesting a stepwise molecular evolution</ArticleTitle><ArticleFirstPage>420</ArticleFirstPage><ArticleLastPage>428</ArticleLastPage><ArticleHistory><RegistrationDate><Year>2004</Year><Month>7</Month><Day>2</Day></RegistrationDate><Received><Year>1992</Year><Month>1</Month><Day>18</Day></Received><Revised><Year>1992</Year><Month>5</Month><Day>6</Day></Revised></ArticleHistory><ArticleCopyright><CopyrightHolderName>Springer-Verlag New York Inc</CopyrightHolderName><CopyrightYear>1992</CopyrightYear></ArticleCopyright><ArticleGrants Type="Regular"><MetadataGrant Grant="OpenAccess"></MetadataGrant><AbstractGrant Grant="OpenAccess"></AbstractGrant><BodyPDFGrant Grant="Restricted"></BodyPDFGrant><BodyHTMLGrant Grant="Restricted"></BodyHTMLGrant><BibliographyGrant Grant="Restricted"></BibliographyGrant><ESMGrant Grant="Restricted"></ESMGrant></ArticleGrants><ArticleContext><JournalID>239</JournalID><VolumeIDStart>35</VolumeIDStart><VolumeIDEnd>35</VolumeIDEnd><IssueIDStart>5</IssueIDStart><IssueIDEnd>5</IssueIDEnd></ArticleContext></ArticleInfo><ArticleHeader><AuthorGroup><Author AffiliationIDS="Aff1"><AuthorName DisplayOrder="Western"><GivenName>Ivan</GivenName><FamilyName>Laprevotte</FamilyName></AuthorName></Author><Affiliation ID="Aff1"><OrgDivision>UPR 41 CNRS “Recombinaisons Génétiques,”</OrgDivision><OrgName>Centre Hayem Hôpital Saint-Louis</OrgName><OrgAddress><Postcode>75475</Postcode><City>Paris cedex 10</City><Country>France</Country></OrgAddress></Affiliation></AuthorGroup><Abstract ID="Abs1" Language="En"><Heading>Summary</Heading><Para>An exhaustive computer-assisted analysis of the Moloney murine leukemia virus nucleotide sequence shows numerous deviations in the oligomeric distribution, suggesting three overlapping levels of a stepwise duplicative evolution. (1) The sequence fits the universal rule of TG/CT excess which has been proposed as the construction principle of all sequences, and maintains some degree of symmetry between the two complementary strands. (2) Oligomeric repeating units share a core consensus regularly scattered throughout the sequence. This consensus is not merely predictable from the doublet frequencies and codon usage, but could correspond to an intermediary stage in a so-called periodic-to-chaotic transition. (3) Probable stepwise local duplications could be accounted for by slippagelike mechanisms. Comparison with the <Emphasis Type="Italic">h</Emphasis>uman <Emphasis Type="Italic">s</Emphasis>puma<Emphasis Type="Italic">r</Emphasis>etrovirus (HSRV) shows similar segments in the overrepresented oligomers of the two sequences. The intermediary stage of transition oligomeric repeating units is not so clearly suggested in HSRV, perhaps because of numerous stepwise local duplications. In any case, a common evolutionary origin for the two viruses is not ruled out.</Para></Abstract><KeywordGroup Language="En"><Heading>Key words</Heading><Keyword>Mo-MuIV</Keyword><Keyword>HSRV</Keyword><Keyword>DNA</Keyword><Keyword>Computer-assisted analysis</Keyword><Keyword>Core consensus</Keyword><Keyword>TG/CT excess</Keyword><Keyword>Symmetry</Keyword><Keyword>Markov analysis</Keyword></KeywordGroup></ArticleHeader><NoBody></NoBody></Article></Issue></Volume></Journal></Publisher></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Mo-MuLV nucleotide sequence exhibits three levels of oligomeric repetitions, suggesting a stepwise molecular evolution</title></titleInfo><titleInfo type="alternative" contentType="CDATA"><title>Mo-MuLV nucleotide sequence exhibits three levels of oligomeric repetitions, suggesting a stepwise molecular evolution</title></titleInfo><name type="personal"><namePart type="given">Ivan</namePart><namePart type="family">Laprevotte</namePart><affiliation>UPR 41 CNRS “Recombinaisons Génétiques,”, Centre Hayem Hôpital Saint-Louis, 75475, Paris cedex 10, France</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="research-article" displayLabel="OriginalPaper" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-1JC4F85T-7">research-article</genre><originInfo><publisher>Springer-Verlag</publisher><place><placeTerm type="text">New York</placeTerm></place><dateCreated encoding="w3cdtf">1992-01-18</dateCreated><dateIssued encoding="w3cdtf">1992-11-01</dateIssued><copyrightDate encoding="w3cdtf">1992</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><abstract lang="en">Summary: An exhaustive computer-assisted analysis of the Moloney murine leukemia virus nucleotide sequence shows numerous deviations in the oligomeric distribution, suggesting three overlapping levels of a stepwise duplicative evolution. (1) The sequence fits the universal rule of TG/CT excess which has been proposed as the construction principle of all sequences, and maintains some degree of symmetry between the two complementary strands. (2) Oligomeric repeating units share a core consensus regularly scattered throughout the sequence. This consensus is not merely predictable from the doublet frequencies and codon usage, but could correspond to an intermediary stage in a so-called periodic-to-chaotic transition. (3) Probable stepwise local duplications could be accounted for by slippagelike mechanisms. Comparison with the human spumaretrovirus (HSRV) shows similar segments in the overrepresented oligomers of the two sequences. The intermediary stage of transition oligomeric repeating units is not so clearly suggested in HSRV, perhaps because of numerous stepwise local duplications. In any case, a common evolutionary origin for the two viruses is not ruled out.</abstract><subject lang="en"><genre>Key words</genre><topic>Mo-MuIV</topic><topic>HSRV</topic><topic>DNA</topic><topic>Computer-assisted analysis</topic><topic>Core consensus</topic><topic>TG/CT excess</topic><topic>Symmetry</topic><topic>Markov analysis</topic></subject><relatedItem type="host"><titleInfo><title>Journal of Molecular Evolution</title></titleInfo><titleInfo type="abbreviated"><title>J Mol Evol</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><originInfo><publisher>Springer</publisher><dateIssued encoding="w3cdtf">1992-11-01</dateIssued><copyrightDate encoding="w3cdtf">1992</copyrightDate></originInfo><subject><genre>Life Sciences</genre><topic>Cell Biology</topic><topic>Microbiology</topic><topic>Plant Sciences</topic></subject><identifier type="ISSN">0022-2844</identifier><identifier type="eISSN">1432-1432</identifier><identifier type="JournalID">239</identifier><identifier type="IssueArticleCount">11</identifier><identifier type="VolumeIssueCount">6</identifier><part><date>1992</date><detail type="volume"><number>35</number><caption>vol.</caption></detail><detail type="issue"><number>5</number><caption>no.</caption></detail><extent unit="pages"><start>420</start><end>428</end></extent></part><recordInfo><recordOrigin>Springer-Verlag, 1992</recordOrigin></recordInfo></relatedItem><identifier type="istex">E293A76D253FD6A367EAB60BE64C82FFB0510DE2</identifier><identifier type="ark">ark:/67375/1BB-8LB0JKGV-Q</identifier><identifier type="DOI">10.1007/BF00171820</identifier><identifier type="ArticleID">BF00171820</identifier><identifier type="ArticleID">Art6</identifier><accessCondition type="use and reproduction" contentType="copyright">Springer-Verlag New York Inc, 1992</accessCondition><recordInfo><recordContentSource authority="ISTEX" authorityURI="https://loaded-corpus.data.istex.fr" valueURI="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-3XSW68JL-F">springer</recordContentSource><recordOrigin>Springer-Verlag New York Inc, 1992</recordOrigin></recordInfo></mods><json:item><extension>json</extension><original>false</original><mimetype>application/json</mimetype><uri>https://api.istex.fr/ark:/67375/1BB-8LB0JKGV-Q/record.json</uri></json:item></metadata><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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