New tricks for "old" domains: how novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM.
Identifieur interne : 000662 ( PubMed/Corpus ); précédent : 000661; suivant : 000663New tricks for "old" domains: how novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM.
Auteurs : Graham Cromar ; Ka-Chun Wong ; Noeleen Loughran ; Tuan On ; Hongyan Song ; Xuejian Xiong ; Zhaolei Zhang ; John ParkinsonSource :
- Genome biology and evolution [ 1759-6653 ] ; 2014.
English descriptors
- KwdEn :
- MESH :
- chemical , metabolism : Extracellular Matrix Proteins.
- genetics : Tandem Repeat Sequences.
- metabolism : Extracellular Matrix.
- Animals, Evolution, Molecular, Humans.
Abstract
The extracellular matrix (ECM) is a defining characteristic of metazoans and consists of a meshwork of self-assembling, fibrous proteins, and their functionally related neighbours. Previous studies, focusing on a limited number of gene families, suggest that vertebrate complexity predominantly arose through the duplication and subsequent modification of retained, preexisting ECM genes. These genes provided the structural underpinnings to support a variety of specialized tissues, as well as a platform for the organization of spatio-temporal signaling and cell migration. However, the relative contributions of ancient versus novel domains to ECM evolution have not been quantified across the full range of ECM proteins. Here, utilizing a high quality list comprising 324 ECM genes, we reveal general and clade-specific domain combinations, identifying domains of eukaryotic and metazoan origin recruited into new roles in approximately two-third of the ECM proteins in humans representing novel vertebrate proteins. We show that, rather than acquiring new domains, sampling of new domain combinations has been key to the innovation of paralogous ECM genes during vertebrate evolution. Applying a novel framework for identifying potentially important, noncontiguous, conserved arrangements of domains, we find that the distinct biological characteristics of the ECM have arisen through unique evolutionary processes. These include the preferential recruitment of novel domains to existing architectures and the utilization of high promiscuity domains in organizing the ECM network around a connected array of structural hubs. Our focus on ECM proteins reveals that distinct types of proteins and/or the biological systems in which they operate have influenced the types of evolutionary forces that drive protein innovation. This emphasizes the need for rigorously defined systems to address questions of evolution that focus on specific systems of interacting proteins.
DOI: 10.1093/gbe/evu228
PubMed: 25323955
Links to Exploration step
pubmed:25323955Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">New tricks for "old" domains: how novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM.</title><author><name sortKey="Cromar, Graham" sort="Cromar, Graham" uniqKey="Cromar G" first="Graham" last="Cromar">Graham Cromar</name><affiliation><nlm:affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada Department of Molecular Genetics, University of Toronto, Ontario, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Wong, Ka Chun" sort="Wong, Ka Chun" uniqKey="Wong K" first="Ka-Chun" last="Wong">Ka-Chun Wong</name><affiliation><nlm:affiliation>Department of Computer Science, University of Toronto, Ontario, Canada Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Ontario, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Loughran, Noeleen" sort="Loughran, Noeleen" uniqKey="Loughran N" first="Noeleen" last="Loughran">Noeleen Loughran</name><affiliation><nlm:affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="On, Tuan" sort="On, Tuan" uniqKey="On T" first="Tuan" last="On">Tuan On</name><affiliation><nlm:affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada Department of Molecular Genetics, University of Toronto, Ontario, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Song, Hongyan" sort="Song, Hongyan" uniqKey="Song H" first="Hongyan" last="Song">Hongyan Song</name><affiliation><nlm:affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Xiong, Xuejian" sort="Xiong, Xuejian" uniqKey="Xiong X" first="Xuejian" last="Xiong">Xuejian Xiong</name><affiliation><nlm:affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Zhaolei" sort="Zhang, Zhaolei" uniqKey="Zhang Z" first="Zhaolei" last="Zhang">Zhaolei Zhang</name><affiliation><nlm:affiliation>Department of Molecular Genetics, University of Toronto, Ontario, Canada Department of Computer Science, University of Toronto, Ontario, Canada Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Ontario, Canada Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name><affiliation><nlm:affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada Department of Molecular Genetics, University of Toronto, Ontario, Canada Department of Biochemistry, University of Toronto, Ontario, Canada john.parkinson@utoronto.ca.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:25323955</idno><idno type="pmid">25323955</idno><idno type="doi">10.1093/gbe/evu228</idno><idno type="wicri:Area/PubMed/Corpus">000662</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000662</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">New tricks for "old" domains: how novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM.</title><author><name sortKey="Cromar, Graham" sort="Cromar, Graham" uniqKey="Cromar G" first="Graham" last="Cromar">Graham Cromar</name><affiliation><nlm:affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada Department of Molecular Genetics, University of Toronto, Ontario, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Wong, Ka Chun" sort="Wong, Ka Chun" uniqKey="Wong K" first="Ka-Chun" last="Wong">Ka-Chun Wong</name><affiliation><nlm:affiliation>Department of Computer Science, University of Toronto, Ontario, Canada Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Ontario, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Loughran, Noeleen" sort="Loughran, Noeleen" uniqKey="Loughran N" first="Noeleen" last="Loughran">Noeleen Loughran</name><affiliation><nlm:affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="On, Tuan" sort="On, Tuan" uniqKey="On T" first="Tuan" last="On">Tuan On</name><affiliation><nlm:affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada Department of Molecular Genetics, University of Toronto, Ontario, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Song, Hongyan" sort="Song, Hongyan" uniqKey="Song H" first="Hongyan" last="Song">Hongyan Song</name><affiliation><nlm:affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Xiong, Xuejian" sort="Xiong, Xuejian" uniqKey="Xiong X" first="Xuejian" last="Xiong">Xuejian Xiong</name><affiliation><nlm:affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Zhaolei" sort="Zhang, Zhaolei" uniqKey="Zhang Z" first="Zhaolei" last="Zhang">Zhaolei Zhang</name><affiliation><nlm:affiliation>Department of Molecular Genetics, University of Toronto, Ontario, Canada Department of Computer Science, University of Toronto, Ontario, Canada Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Ontario, Canada Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name><affiliation><nlm:affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada Department of Molecular Genetics, University of Toronto, Ontario, Canada Department of Biochemistry, University of Toronto, Ontario, Canada john.parkinson@utoronto.ca.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Genome biology and evolution</title><idno type="eISSN">1759-6653</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Evolution, Molecular</term><term>Extracellular Matrix (metabolism)</term><term>Extracellular Matrix Proteins (metabolism)</term><term>Humans</term><term>Tandem Repeat Sequences (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Extracellular Matrix Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Tandem Repeat Sequences</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Extracellular Matrix</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Evolution, Molecular</term><term>Humans</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The extracellular matrix (ECM) is a defining characteristic of metazoans and consists of a meshwork of self-assembling, fibrous proteins, and their functionally related neighbours. Previous studies, focusing on a limited number of gene families, suggest that vertebrate complexity predominantly arose through the duplication and subsequent modification of retained, preexisting ECM genes. These genes provided the structural underpinnings to support a variety of specialized tissues, as well as a platform for the organization of spatio-temporal signaling and cell migration. However, the relative contributions of ancient versus novel domains to ECM evolution have not been quantified across the full range of ECM proteins. Here, utilizing a high quality list comprising 324 ECM genes, we reveal general and clade-specific domain combinations, identifying domains of eukaryotic and metazoan origin recruited into new roles in approximately two-third of the ECM proteins in humans representing novel vertebrate proteins. We show that, rather than acquiring new domains, sampling of new domain combinations has been key to the innovation of paralogous ECM genes during vertebrate evolution. Applying a novel framework for identifying potentially important, noncontiguous, conserved arrangements of domains, we find that the distinct biological characteristics of the ECM have arisen through unique evolutionary processes. These include the preferential recruitment of novel domains to existing architectures and the utilization of high promiscuity domains in organizing the ECM network around a connected array of structural hubs. Our focus on ECM proteins reveals that distinct types of proteins and/or the biological systems in which they operate have influenced the types of evolutionary forces that drive protein innovation. This emphasizes the need for rigorously defined systems to address questions of evolution that focus on specific systems of interacting proteins.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25323955</PMID><DateCreated><Year>2014</Year><Month>11</Month><Day>01</Day></DateCreated><DateCompleted><Year>2015</Year><Month>07</Month><Day>06</Day></DateCompleted><DateRevised><Year>2017</Year><Month>02</Month><Day>20</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1759-6653</ISSN><JournalIssue CitedMedium="Internet"><Volume>6</Volume><Issue>10</Issue><PubDate><Year>2014</Year><Month>Oct</Month><Day>15</Day></PubDate></JournalIssue><Title>Genome biology and evolution</Title><ISOAbbreviation>Genome Biol Evol</ISOAbbreviation></Journal><ArticleTitle>New tricks for "old" domains: how novel architectures and promiscuous hubs contributed to the organization and evolution of the ECM.</ArticleTitle><Pagination><MedlinePgn>2897-917</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/gbe/evu228</ELocationID><Abstract><AbstractText>The extracellular matrix (ECM) is a defining characteristic of metazoans and consists of a meshwork of self-assembling, fibrous proteins, and their functionally related neighbours. Previous studies, focusing on a limited number of gene families, suggest that vertebrate complexity predominantly arose through the duplication and subsequent modification of retained, preexisting ECM genes. These genes provided the structural underpinnings to support a variety of specialized tissues, as well as a platform for the organization of spatio-temporal signaling and cell migration. However, the relative contributions of ancient versus novel domains to ECM evolution have not been quantified across the full range of ECM proteins. Here, utilizing a high quality list comprising 324 ECM genes, we reveal general and clade-specific domain combinations, identifying domains of eukaryotic and metazoan origin recruited into new roles in approximately two-third of the ECM proteins in humans representing novel vertebrate proteins. We show that, rather than acquiring new domains, sampling of new domain combinations has been key to the innovation of paralogous ECM genes during vertebrate evolution. Applying a novel framework for identifying potentially important, noncontiguous, conserved arrangements of domains, we find that the distinct biological characteristics of the ECM have arisen through unique evolutionary processes. These include the preferential recruitment of novel domains to existing architectures and the utilization of high promiscuity domains in organizing the ECM network around a connected array of structural hubs. Our focus on ECM proteins reveals that distinct types of proteins and/or the biological systems in which they operate have influenced the types of evolutionary forces that drive protein innovation. This emphasizes the need for rigorously defined systems to address questions of evolution that focus on specific systems of interacting proteins.</AbstractText><CopyrightInformation>© The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Cromar</LastName><ForeName>Graham</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada Department of Molecular Genetics, University of Toronto, Ontario, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wong</LastName><ForeName>Ka-Chun</ForeName><Initials>KC</Initials><AffiliationInfo><Affiliation>Department of Computer Science, University of Toronto, Ontario, Canada Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Ontario, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Loughran</LastName><ForeName>Noeleen</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>On</LastName><ForeName>Tuan</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada Department of Molecular Genetics, University of Toronto, Ontario, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Song</LastName><ForeName>Hongyan</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xiong</LastName><ForeName>Xuejian</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Zhaolei</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Department of Molecular Genetics, University of Toronto, Ontario, Canada Department of Computer Science, University of Toronto, Ontario, Canada Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Ontario, Canada Banting and Best Department of Medical Research, University of Toronto, Ontario, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Parkinson</LastName><ForeName>John</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada Department of Molecular Genetics, University of Toronto, Ontario, Canada Department of Biochemistry, University of Toronto, Ontario, Canada john.parkinson@utoronto.ca.</Affiliation></AffiliationInfo></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>2014</Year><Month>10</Month><Day>15</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Genome Biol Evol</MedlineTA><NlmUniqueID>101509707</NlmUniqueID><ISSNLinking>1759-6653</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D016326">Extracellular Matrix Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>BMC Evol Biol. 2005;5:31</RefSource><PMID Version="1">15892888</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nature. 2008 Feb 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