Retroviral oligonucleotide distributions correlate with biased nucleotide compositions of retrovirus sequences, suggesting a duplicative stepwise molecular evolution.
Identifieur interne : 000295 ( France/Analysis ); précédent : 000294; suivant : 000296Retroviral oligonucleotide distributions correlate with biased nucleotide compositions of retrovirus sequences, suggesting a duplicative stepwise molecular evolution.
Auteurs : I. Laprevotte [France] ; S. Brouillet ; C. Terzian ; A. HénautSource :
- Journal of molecular evolution [ 0022-2844 ] ; 1997.
Descripteurs français
- KwdFr :
- ADN viral (), ADN viral (génétique), Animaux, Composition en bases nucléiques, Données de séquences moléculaires, Oligodésoxyribonucléotides (génétique), Phylogénie, Retroviridae (génétique), Séquence consensus (génétique), Séquences répétées d'acides nucléiques (génétique), Vertébrés, Évolution moléculaire.
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA, Viral.
- genetics : Consensus Sequence, DNA, Viral, Oligodeoxyribonucleotides, Repetitive Sequences, Nucleic Acid, Retroviridae.
- Animals, Base Composition, Evolution, Molecular, Molecular Sequence Data, Phylogeny, Vertebrates.
Abstract
A computer-assisted analysis was made of 24 complete nucleotide sequences selected from the vertebrate retroviruses to represent the ten viral groups. The conclusions of this analysis extend and strengthen the previously made hypothesis on the Moloney murine leukemia virus: The evolution of the nucleotide sequence appears to have occurred mainly through at least three overlapping levels of duplication: (1) The distributions of overrepresented (3-6)-mers are consistent with the universal rule of a trend toward TG/CT excess and with the persistence of a certain degree of symmetry between the two strands of DNA. This suggests one or several original tandemly repeated sequences and some inverted duplications. (2) The existence of two general core consensuses at the level of these (3-6)-mers supports the hypothesis of a common evolutionary origin of vertebrate retroviruses. Consensuses more specific to certain sequences are compatible with phylogenetic trees established independently. The consensuses could correspond to intermediary evolutionary stages. (3) Most of the (3-6)-mers with a significantly higher than average frequency appear to be internally repeated (with monomeric or oligomeric internal iterations) and seem to be at least partly the cause of the bias observed by other researchers at the level of retroviral nucleotide composition. They suggest a third evolutionary stage by slippage-like stepwise local duplications.
DOI: 10.1007/pl00006138
PubMed: 9069182
Affiliations:
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pubmed:9069182Le document en format XML
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Brouillet</name></author><author><name sortKey="Terzian, C" sort="Terzian, C" uniqKey="Terzian C" first="C" last="Terzian">C. Terzian</name></author><author><name sortKey="Henaut, A" sort="Henaut, A" uniqKey="Henaut A" first="A" last="Hénaut">A. 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Laprevotte</name><affiliation wicri:level="1"><nlm:affiliation>Laboratoire Rétrovirus et Rétrotransposons des Vertébrés, UPR 43 CNRS, Université Paris 7, Hôpital Saint Louis, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Laboratoire Rétrovirus et Rétrotransposons des Vertébrés, UPR 43 CNRS, Université Paris 7, Hôpital Saint Louis</wicri:regionArea><wicri:noRegion>Hôpital Saint Louis</wicri:noRegion><wicri:noRegion>Hôpital Saint Louis</wicri:noRegion></affiliation></author><author><name sortKey="Brouillet, S" sort="Brouillet, S" uniqKey="Brouillet S" first="S" last="Brouillet">S. Brouillet</name></author><author><name sortKey="Terzian, C" sort="Terzian, C" uniqKey="Terzian C" first="C" last="Terzian">C. Terzian</name></author><author><name sortKey="Henaut, A" sort="Henaut, A" uniqKey="Henaut A" first="A" last="Hénaut">A. Hénaut</name></author></analytic><series><title level="j">Journal of molecular evolution</title><idno type="ISSN">0022-2844</idno><imprint><date when="1997" type="published">1997</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Base Composition</term><term>Consensus Sequence (genetics)</term><term>DNA, Viral (chemistry)</term><term>DNA, Viral (genetics)</term><term>Evolution, Molecular</term><term>Molecular Sequence Data</term><term>Oligodeoxyribonucleotides (genetics)</term><term>Phylogeny</term><term>Repetitive Sequences, Nucleic Acid (genetics)</term><term>Retroviridae (genetics)</term><term>Vertebrates</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN viral ()</term><term>ADN viral (génétique)</term><term>Animaux</term><term>Composition en bases nucléiques</term><term>Données de séquences moléculaires</term><term>Oligodésoxyribonucléotides (génétique)</term><term>Phylogénie</term><term>Retroviridae (génétique)</term><term>Séquence consensus (génétique)</term><term>Séquences répétées d'acides nucléiques (génétique)</term><term>Vertébrés</term><term>Évolution moléculaire</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA, Viral</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Consensus Sequence</term><term>DNA, Viral</term><term>Oligodeoxyribonucleotides</term><term>Repetitive Sequences, Nucleic Acid</term><term>Retroviridae</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN viral</term><term>Oligodésoxyribonucléotides</term><term>Retroviridae</term><term>Séquence consensus</term><term>Séquences répétées d'acides nucléiques</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Base Composition</term><term>Evolution, Molecular</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Vertebrates</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN viral</term><term>Animaux</term><term>Composition en bases nucléiques</term><term>Données de séquences moléculaires</term><term>Phylogénie</term><term>Vertébrés</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">A computer-assisted analysis was made of 24 complete nucleotide sequences selected from the vertebrate retroviruses to represent the ten viral groups. The conclusions of this analysis extend and strengthen the previously made hypothesis on the Moloney murine leukemia virus: The evolution of the nucleotide sequence appears to have occurred mainly through at least three overlapping levels of duplication: (1) The distributions of overrepresented (3-6)-mers are consistent with the universal rule of a trend toward TG/CT excess and with the persistence of a certain degree of symmetry between the two strands of DNA. This suggests one or several original tandemly repeated sequences and some inverted duplications. (2) The existence of two general core consensuses at the level of these (3-6)-mers supports the hypothesis of a common evolutionary origin of vertebrate retroviruses. Consensuses more specific to certain sequences are compatible with phylogenetic trees established independently. The consensuses could correspond to intermediary evolutionary stages. (3) Most of the (3-6)-mers with a significantly higher than average frequency appear to be internally repeated (with monomeric or oligomeric internal iterations) and seem to be at least partly the cause of the bias observed by other researchers at the level of retroviral nucleotide composition. They suggest a third evolutionary stage by slippage-like stepwise local duplications.</div></front></TEI><affiliations><list><country><li>France</li></country></list><tree><noCountry><name sortKey="Brouillet, S" sort="Brouillet, S" uniqKey="Brouillet S" first="S" last="Brouillet">S. Brouillet</name><name sortKey="Henaut, A" sort="Henaut, A" uniqKey="Henaut A" first="A" last="Hénaut">A. Hénaut</name><name sortKey="Terzian, C" sort="Terzian, C" uniqKey="Terzian C" first="C" last="Terzian">C. Terzian</name></noCountry><country name="France"><noRegion><name sortKey="Laprevotte, I" sort="Laprevotte, I" uniqKey="Laprevotte I" first="I" last="Laprevotte">I. 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