Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies
Identifieur interne : 006A88 ( Main/Exploration ); précédent : 006A87; suivant : 006A89Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies
Auteurs : Christina D. Fetterman [Canada] ; Bruce Rannala [États-Unis] ; Michael A. Walter [Canada]Source :
- BMC Evolutionary Biology [ 1471-2148 ] ; 2008.
Abstract
Members of the forkhead gene family act as transcription regulators in biological processes including development and metabolism. The evolution of forkhead genes has not been widely examined and selection pressures at the molecular level influencing subfamily evolution and differentiation have not been explored. Here,
Application of site models, which estimate overall selection pressures on individual codons throughout the phylogeny, showed that the amino acid changes observed were either neutral or under negative selection. Branch-site models, which allow estimated selection pressures along specified lineages to vary as compared to the remaining phylogeny, identified positive selection along branches leading to the FoxA3 and Protostomia clades in the FoxA cluster and the branch leading to the FoxO3 clade in the FoxO cluster. Residues that may differentiate paralogs were identified in the FoxA and FoxO clusters and residues that differentiate orthologs were identified in the FoxA cluster. Neutral amino acid changes were identified in the forkhead domain of the FoxA, FoxD and FoxP clusters while positive selection was identified in the forkhead domain of the Protostomia lineage of the FoxA cluster. A series of residues under strong negative selection adjacent to the N- and C-termini of the forkhead domain were identified in all clusters analyzed suggesting a new method for refinement of domain boundaries. Extrapolation of domains among cluster members in conjunction with selection pressure information allowed prediction of residue function in the FoxA, FoxO and FoxP clusters and exclusion of known domain function in residues of the FoxA and FoxI clusters.
Consideration of selection pressures observed in conjunction with known functional information allowed prediction of residue function and refinement of domain boundaries. Identification of residues that differentiate orthologs and paralogs provided insight into the development and functional consequences of paralogs and forkhead subfamily composition differences among species. Overall we found that after gene duplication of forkhead family members, rapid differentiation and subsequent fixation of amino acid changes through negative selection has occurred.
Url:
DOI: 10.1186/1471-2148-8-261
PubMed: 18816404
PubMed Central: 2570691
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies</title><author><name sortKey="Fetterman, Christina D" sort="Fetterman, Christina D" uniqKey="Fetterman C" first="Christina D" last="Fetterman">Christina D. Fetterman</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Medical Genetics, University of Alberta, Edmonton, Alberta</wicri:regionArea><wicri:noRegion>Alberta</wicri:noRegion></affiliation></author><author><name sortKey="Rannala, Bruce" sort="Rannala, Bruce" uniqKey="Rannala B" first="Bruce" last="Rannala">Bruce Rannala</name><affiliation wicri:level="2"><nlm:aff id="I2">Genome Center and Section of Evolution and Ecology, University of California, Davis, California, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Genome Center and Section of Evolution and Ecology, University of California, Davis, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Walter, Michael A" sort="Walter, Michael A" uniqKey="Walter M" first="Michael A" last="Walter">Michael A. Walter</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Medical Genetics, University of Alberta, Edmonton, Alberta</wicri:regionArea><wicri:noRegion>Alberta</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">18816404</idno><idno type="pmc">2570691</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2570691</idno><idno type="RBID">PMC:2570691</idno><idno type="doi">10.1186/1471-2148-8-261</idno><date when="2008">2008</date><idno type="wicri:Area/Pmc/Corpus">002A62</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">002A62</idno><idno type="wicri:Area/Pmc/Curation">002A61</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">002A61</idno><idno type="wicri:Area/Pmc/Checkpoint">003961</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">003961</idno><idno type="wicri:Area/Ncbi/Merge">002F58</idno><idno type="wicri:Area/Ncbi/Curation">002F58</idno><idno type="wicri:Area/Ncbi/Checkpoint">002F58</idno><idno type="wicri:Area/Main/Merge">006B92</idno><idno type="wicri:Area/Main/Curation">006A88</idno><idno type="wicri:Area/Main/Exploration">006A88</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies</title><author><name sortKey="Fetterman, Christina D" sort="Fetterman, Christina D" uniqKey="Fetterman C" first="Christina D" last="Fetterman">Christina D. Fetterman</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Medical Genetics, University of Alberta, Edmonton, Alberta</wicri:regionArea><wicri:noRegion>Alberta</wicri:noRegion></affiliation></author><author><name sortKey="Rannala, Bruce" sort="Rannala, Bruce" uniqKey="Rannala B" first="Bruce" last="Rannala">Bruce Rannala</name><affiliation wicri:level="2"><nlm:aff id="I2">Genome Center and Section of Evolution and Ecology, University of California, Davis, California, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Genome Center and Section of Evolution and Ecology, University of California, Davis, California</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Walter, Michael A" sort="Walter, Michael A" uniqKey="Walter M" first="Michael A" last="Walter">Michael A. Walter</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Medical Genetics, University of Alberta, Edmonton, Alberta</wicri:regionArea><wicri:noRegion>Alberta</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Evolutionary Biology</title><idno type="eISSN">1471-2148</idno><imprint><date when="2008">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Members of the forkhead gene family act as transcription regulators in biological processes including development and metabolism. The evolution of forkhead genes has not been widely examined and selection pressures at the molecular level influencing subfamily evolution and differentiation have not been explored. Here, <italic>in silico </italic>methods were used to examine selection pressures acting on the coding sequence of five multi-species FOX protein subfamily clusters; FoxA, FoxD, FoxI, FoxO and FoxP.</p></sec><sec><title>Results</title><p>Application of site models, which estimate overall selection pressures on individual codons throughout the phylogeny, showed that the amino acid changes observed were either neutral or under negative selection. Branch-site models, which allow estimated selection pressures along specified lineages to vary as compared to the remaining phylogeny, identified positive selection along branches leading to the FoxA3 and Protostomia clades in the FoxA cluster and the branch leading to the FoxO3 clade in the FoxO cluster. Residues that may differentiate paralogs were identified in the FoxA and FoxO clusters and residues that differentiate orthologs were identified in the FoxA cluster. Neutral amino acid changes were identified in the forkhead domain of the FoxA, FoxD and FoxP clusters while positive selection was identified in the forkhead domain of the Protostomia lineage of the FoxA cluster. A series of residues under strong negative selection adjacent to the N- and C-termini of the forkhead domain were identified in all clusters analyzed suggesting a new method for refinement of domain boundaries. Extrapolation of domains among cluster members in conjunction with selection pressure information allowed prediction of residue function in the FoxA, FoxO and FoxP clusters and exclusion of known domain function in residues of the FoxA and FoxI clusters.</p></sec><sec><title>Conclusion</title><p>Consideration of selection pressures observed in conjunction with known functional information allowed prediction of residue function and refinement of domain boundaries. Identification of residues that differentiate orthologs and paralogs provided insight into the development and functional consequences of paralogs and forkhead subfamily composition differences among species. Overall we found that after gene duplication of forkhead family members, rapid differentiation and subsequent fixation of amino acid changes through negative selection has occurred.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Lines, Ma" uniqKey="Lines M">MA Lines</name></author><author><name sortKey="Kozlowski, K" uniqKey="Kozlowski K">K Kozlowski</name></author><author><name sortKey="Walter, Ma" uniqKey="Walter M">MA Walter</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Fang, J" uniqKey="Fang J">J Fang</name></author><author><name sortKey="Dagenais, Sl" uniqKey="Dagenais S">SL Dagenais</name></author><author><name sortKey="Erickson, Rp" uniqKey="Erickson R">RP Erickson</name></author><author><name sortKey="Arlt, Mf" uniqKey="Arlt M">MF Arlt</name></author><author><name sortKey="Glynn, Mw" uniqKey="Glynn M">MW Glynn</name></author><author><name sortKey="Gorski, Jl" uniqKey="Gorski 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uniqKey="Fetterman C" first="Christina D" last="Fetterman">Christina D. Fetterman</name></noRegion><name sortKey="Walter, Michael A" sort="Walter, Michael A" uniqKey="Walter M" first="Michael A" last="Walter">Michael A. Walter</name></country><country name="États-Unis"><region name="Californie"><name sortKey="Rannala, Bruce" sort="Rannala, Bruce" uniqKey="Rannala B" first="Bruce" last="Rannala">Bruce Rannala</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Sante/explor/LymphedemaV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 006A88 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 006A88 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Sante
|area= LymphedemaV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= PMC:2570691
|texte= Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:18816404" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a LymphedemaV1
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