Comparative genomics of elastin: Sequence analysis of a highly repetitive protein.
Identifieur interne : 001050 ( PubMed/Corpus ); précédent : 001049; suivant : 001051Comparative genomics of elastin: Sequence analysis of a highly repetitive protein.
Auteurs : David He ; Martin Chung ; Esther Chan ; Trevis Alleyne ; Kevin C H. Ha ; Ming Miao ; Richard J. Stahl ; Fred W. Keeley ; John ParkinsonSource :
- Matrix biology : journal of the International Society for Matrix Biology [ 0945-053X ] ; 2007.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Elastin.
- chemical , genetics : Elastin, Xenopus Proteins, Zebrafish Proteins.
- Amino Acid Sequence, Animals, Chickens, Evolution, Molecular, Humans, Molecular Sequence Data, Phylogeny, Ranidae, Xenopus, Zebrafish.
Abstract
Due to the low complexity associated with their sequences, uncovering the evolutionary and functional relationships in highly repetitive proteins such as elastin, spider silks, resilin and abductin represents a significant challenge. Using the polymeric extracellular protein elastin as a model system, we present a novel computational approach to the study of sequence, function and evolutionary relationships in repetitive proteins. To address the absence of accurate sequence annotation for repetitive proteins such as elastin, we have constructed a new database repository, ElastoDB (http://theileria.ccb.sickkids.ca/elastin), dedicated to the storage and retrieval of elastin sequence- and meta-data. To analyse their sequence relationships we have devised an innovative new method, based on the identification of overrepresented 'fuzzy' motifs. Applying this method to elastin sequences derived from mammals, chicken, Xenopus and zebrafish resulted in the identification of both highly conserved, and taxon and species specific motifs that likely represent important functional and/or structural elements. The relative spacing and organization of these elements suggest that exon duplication events have played an important role in the evolution of elastin. Clustering of similarity profiles generated for sets of exons and introns, revealed a pattern of putative duplication events involving exons 15-30 in mammalian and chicken elastins, exons 20-31 in both zebrafish elastins, exons 15-20 in fugu elastin and exons 35-50 in Xenopus elastin 1. The success of this approach for elastin offers a promising route to the elucidation of sequence, structure, function and evolutionary relationships for many other proteins with sequences of low complexity.
DOI: 10.1016/j.matbio.2007.05.005
PubMed: 17628459
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pubmed:17628459Le document en format XML
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Ha</name></author><author><name sortKey="Miao, Ming" sort="Miao, Ming" uniqKey="Miao M" first="Ming" last="Miao">Ming Miao</name></author><author><name sortKey="Stahl, Richard J" sort="Stahl, Richard J" uniqKey="Stahl R" first="Richard J" last="Stahl">Richard J. Stahl</name></author><author><name sortKey="Keeley, Fred W" sort="Keeley, Fred W" uniqKey="Keeley F" first="Fred W" last="Keeley">Fred W. Keeley</name></author><author><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2007">2007</date><idno type="RBID">pubmed:17628459</idno><idno type="pmid">17628459</idno><idno type="doi">10.1016/j.matbio.2007.05.005</idno><idno type="wicri:Area/PubMed/Corpus">001050</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001050</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Comparative genomics of elastin: Sequence analysis of a highly repetitive protein.</title><author><name sortKey="He, David" sort="He, David" uniqKey="He D" first="David" last="He">David He</name><affiliation><nlm:affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, University of Toronto, 555 University Avenue, Toronto, Ontario Canada M5G 1X8.</nlm:affiliation></affiliation></author><author><name sortKey="Chung, Martin" sort="Chung, Martin" uniqKey="Chung M" first="Martin" last="Chung">Martin Chung</name></author><author><name sortKey="Chan, Esther" sort="Chan, Esther" uniqKey="Chan E" first="Esther" last="Chan">Esther Chan</name></author><author><name sortKey="Alleyne, Trevis" sort="Alleyne, Trevis" uniqKey="Alleyne T" first="Trevis" last="Alleyne">Trevis Alleyne</name></author><author><name sortKey="Ha, Kevin C H" sort="Ha, Kevin C H" uniqKey="Ha K" first="Kevin C H" last="Ha">Kevin C H. Ha</name></author><author><name sortKey="Miao, Ming" sort="Miao, Ming" uniqKey="Miao M" first="Ming" last="Miao">Ming Miao</name></author><author><name sortKey="Stahl, Richard J" sort="Stahl, Richard J" uniqKey="Stahl R" first="Richard J" last="Stahl">Richard J. Stahl</name></author><author><name sortKey="Keeley, Fred W" sort="Keeley, Fred W" uniqKey="Keeley F" first="Fred W" last="Keeley">Fred W. Keeley</name></author><author><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name></author></analytic><series><title level="j">Matrix biology : journal of the International Society for Matrix Biology</title><idno type="ISSN">0945-053X</idno><imprint><date when="2007" type="published">2007</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence</term><term>Animals</term><term>Chickens</term><term>Elastin (chemistry)</term><term>Elastin (genetics)</term><term>Evolution, Molecular</term><term>Humans</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Ranidae</term><term>Xenopus</term><term>Xenopus Proteins (genetics)</term><term>Zebrafish</term><term>Zebrafish Proteins (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Elastin</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Elastin</term><term>Xenopus Proteins</term><term>Zebrafish Proteins</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Animals</term><term>Chickens</term><term>Evolution, Molecular</term><term>Humans</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Ranidae</term><term>Xenopus</term><term>Zebrafish</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Due to the low complexity associated with their sequences, uncovering the evolutionary and functional relationships in highly repetitive proteins such as elastin, spider silks, resilin and abductin represents a significant challenge. Using the polymeric extracellular protein elastin as a model system, we present a novel computational approach to the study of sequence, function and evolutionary relationships in repetitive proteins. To address the absence of accurate sequence annotation for repetitive proteins such as elastin, we have constructed a new database repository, ElastoDB (http://theileria.ccb.sickkids.ca/elastin), dedicated to the storage and retrieval of elastin sequence- and meta-data. To analyse their sequence relationships we have devised an innovative new method, based on the identification of overrepresented 'fuzzy' motifs. Applying this method to elastin sequences derived from mammals, chicken, Xenopus and zebrafish resulted in the identification of both highly conserved, and taxon and species specific motifs that likely represent important functional and/or structural elements. The relative spacing and organization of these elements suggest that exon duplication events have played an important role in the evolution of elastin. Clustering of similarity profiles generated for sets of exons and introns, revealed a pattern of putative duplication events involving exons 15-30 in mammalian and chicken elastins, exons 20-31 in both zebrafish elastins, exons 15-20 in fugu elastin and exons 35-50 in Xenopus elastin 1. The success of this approach for elastin offers a promising route to the elucidation of sequence, structure, function and evolutionary relationships for many other proteins with sequences of low complexity.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">17628459</PMID><DateCreated><Year>2007</Year><Month>10</Month><Day>22</Day></DateCreated><DateCompleted><Year>2008</Year><Month>01</Month><Day>31</Day></DateCompleted><DateRevised><Year>2007</Year><Month>10</Month><Day>22</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0945-053X</ISSN><JournalIssue CitedMedium="Print"><Volume>26</Volume><Issue>7</Issue><PubDate><Year>2007</Year><Month>Sep</Month></PubDate></JournalIssue><Title>Matrix biology : journal of the International Society for Matrix Biology</Title><ISOAbbreviation>Matrix Biol.</ISOAbbreviation></Journal><ArticleTitle>Comparative genomics of elastin: Sequence analysis of a highly repetitive protein.</ArticleTitle><Pagination><MedlinePgn>524-40</MedlinePgn></Pagination><Abstract><AbstractText>Due to the low complexity associated with their sequences, uncovering the evolutionary and functional relationships in highly repetitive proteins such as elastin, spider silks, resilin and abductin represents a significant challenge. Using the polymeric extracellular protein elastin as a model system, we present a novel computational approach to the study of sequence, function and evolutionary relationships in repetitive proteins. To address the absence of accurate sequence annotation for repetitive proteins such as elastin, we have constructed a new database repository, ElastoDB (http://theileria.ccb.sickkids.ca/elastin), dedicated to the storage and retrieval of elastin sequence- and meta-data. To analyse their sequence relationships we have devised an innovative new method, based on the identification of overrepresented 'fuzzy' motifs. Applying this method to elastin sequences derived from mammals, chicken, Xenopus and zebrafish resulted in the identification of both highly conserved, and taxon and species specific motifs that likely represent important functional and/or structural elements. The relative spacing and organization of these elements suggest that exon duplication events have played an important role in the evolution of elastin. Clustering of similarity profiles generated for sets of exons and introns, revealed a pattern of putative duplication events involving exons 15-30 in mammalian and chicken elastins, exons 20-31 in both zebrafish elastins, exons 15-20 in fugu elastin and exons 35-50 in Xenopus elastin 1. The success of this approach for elastin offers a promising route to the elucidation of sequence, structure, function and evolutionary relationships for many other proteins with sequences of low complexity.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>He</LastName><ForeName>David</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, University of Toronto, 555 University Avenue, Toronto, Ontario Canada M5G 1X8.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chung</LastName><ForeName>Martin</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Chan</LastName><ForeName>Esther</ForeName><Initials>E</Initials></Author><Author ValidYN="Y"><LastName>Alleyne</LastName><ForeName>Trevis</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Ha</LastName><ForeName>Kevin C H</ForeName><Initials>KC</Initials></Author><Author ValidYN="Y"><LastName>Miao</LastName><ForeName>Ming</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Stahl</LastName><ForeName>Richard J</ForeName><Initials>RJ</Initials></Author><Author ValidYN="Y"><LastName>Keeley</LastName><ForeName>Fred W</ForeName><Initials>FW</Initials></Author><Author ValidYN="Y"><LastName>Parkinson</LastName><ForeName>John</ForeName><Initials>J</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2007</Year><Month>05</Month><Day>25</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Matrix Biol</MedlineTA><NlmUniqueID>9432592</NlmUniqueID><ISSNLinking>0945-053X</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D029867">Xenopus Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D029961">Zebrafish Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-58-3</RegistryNumber><NameOfSubstance UI="D004549">Elastin</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002645" MajorTopicYN="N">Chickens</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004549" MajorTopicYN="N">Elastin</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011898" MajorTopicYN="N">Ranidae</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014981" MajorTopicYN="N">Xenopus</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D029867" MajorTopicYN="N">Xenopus Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015027" MajorTopicYN="N">Zebrafish</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D029961" MajorTopicYN="N">Zebrafish Proteins</DescriptorName><QualifierName UI="Q000235" 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