The Evolution History of Fe-S Cluster A-Type Assembly Protein Reveals Multiple Gene Duplication Events and Essential Protein Motifs.
Identifieur interne : 000027 ( Main/Exploration ); précédent : 000026; suivant : 000028The Evolution History of Fe-S Cluster A-Type Assembly Protein Reveals Multiple Gene Duplication Events and Essential Protein Motifs.
Auteurs : Hui-Meng Lu [République populaire de Chine] ; Jing-Di Li [République populaire de Chine] ; Yu-Dan Zhang [République populaire de Chine] ; Xiao-Li Lu [République populaire de Chine] ; Chang Xu [République populaire de Chine] ; Yuan Huang [République populaire de Chine] ; Michael GribskovSource :
- Genome biology and evolution [ 1759-6653 ] ; 2020.
Abstract
Iron-sulfur (Fe-S) clusters play important roles in electron transfer, metabolic and biosynthetic reactions, and the regulation of gene expression. Understanding the biogenesis of Fe-S clusters is therefore relevant to many fields. In the complex process of Fe-S protein formation, the A-type assembly protein (ATAP) family, which consists of several subfamilies, plays an essential role in Fe-S cluster formation and transfer and is highly conserved across the tree of life. However, the taxonomic distribution, motif compositions, and the evolutionary history of the ATAP subfamilies are not well understood. To address these problems, our study investigated the taxonomic distribution of 321 species from a broad cross-section of taxa. Then, we identified common and specific motifs in multiple ATAP subfamilies to explain the functional conservation and nonredundancy of the ATAPs, and a novel, essential motif was found in Eumetazoa IscA1, which has a newly found magnetic function. Finally, we used phylogenetic analytical methods to reconstruct the evolution history of this family. Our results show that two types of ErpA proteins (nonproteobacteria-type ErpA1 and proteobacteria-type ErpA2) exist in bacteria. The ATAP family, consisting of seven subfamilies, can be further classified into two types of ATAPs. Type-I ATAPs include IscA, SufA, HesB, ErpA1, and IscA1, with an ErpA1-like gene as their last common ancestor, whereas type-II ATAPs consist of ErpA2 and IscA2, duplicated from an ErpA2-like gene. During the mitochondrial endosymbiosis, IscA became IscA1 in eukaryotes and ErpA2 became IscA2 in eukaryotes, respectively.
DOI: 10.1093/gbe/evaa038
PubMed: 32108236
PubMed Central: PMC7144353
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Essential Protein Motifs.</title><author><name sortKey="Lu, Hui Meng" sort="Lu, Hui Meng" uniqKey="Lu H" first="Hui-Meng" last="Lu">Hui-Meng Lu</name><affiliation wicri:level="1"><nlm:affiliation>School of Life Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi'an, Shaanxi, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Life Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi'an, Shaanxi</wicri:regionArea><wicri:noRegion>Shaanxi</wicri:noRegion></affiliation></author><author><name sortKey="Li, Jing Di" sort="Li, Jing Di" uniqKey="Li J" first="Jing-Di" last="Li">Jing-Di Li</name><affiliation wicri:level="1"><nlm:affiliation>School of Life Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi'an, Shaanxi, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Life Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi'an, Shaanxi</wicri:regionArea><wicri:noRegion>Shaanxi</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Yu Dan" sort="Zhang, Yu Dan" uniqKey="Zhang Y" first="Yu-Dan" last="Zhang">Yu-Dan Zhang</name><affiliation wicri:level="1"><nlm:affiliation>School of Life Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi'an, Shaanxi, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Life Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi'an, Shaanxi</wicri:regionArea><wicri:noRegion>Shaanxi</wicri:noRegion></affiliation></author><author><name sortKey="Lu, Xiao Li" sort="Lu, Xiao Li" uniqKey="Lu X" first="Xiao-Li" last="Lu">Xiao-Li Lu</name><affiliation wicri:level="1"><nlm:affiliation>School of Life Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi'an, Shaanxi, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Life Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi'an, Shaanxi</wicri:regionArea><wicri:noRegion>Shaanxi</wicri:noRegion></affiliation></author><author><name sortKey="Xu, Chang" sort="Xu, Chang" uniqKey="Xu C" first="Chang" last="Xu">Chang Xu</name><affiliation wicri:level="1"><nlm:affiliation>College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi</wicri:regionArea><wicri:noRegion>Shaanxi</wicri:noRegion></affiliation></author><author><name sortKey="Huang, Yuan" sort="Huang, Yuan" uniqKey="Huang Y" first="Yuan" last="Huang">Yuan Huang</name><affiliation wicri:level="1"><nlm:affiliation>College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, PR China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi</wicri:regionArea><wicri:noRegion>Shaanxi</wicri:noRegion></affiliation></author><author><name sortKey="Gribskov, Michael" sort="Gribskov, Michael" uniqKey="Gribskov M" first="Michael" last="Gribskov">Michael Gribskov</name><affiliation><nlm:affiliation>Department of Biological Sciences, Purdue University.</nlm:affiliation><wicri:noCountry code="subField">Purdue University</wicri:noCountry></affiliation><affiliation><nlm:affiliation>Department of Computer Science, Purdue University.</nlm:affiliation><wicri:noCountry code="subField">Purdue University</wicri:noCountry></affiliation></author></analytic><series><title level="j">Genome biology and evolution</title><idno type="eISSN">1759-6653</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Iron-sulfur (Fe-S) clusters play important roles in electron transfer, metabolic and biosynthetic reactions, and the regulation of gene expression. Understanding the biogenesis of Fe-S clusters is therefore relevant to many fields. In the complex process of Fe-S protein formation, the A-type assembly protein (ATAP) family, which consists of several subfamilies, plays an essential role in Fe-S cluster formation and transfer and is highly conserved across the tree of life. However, the taxonomic distribution, motif compositions, and the evolutionary history of the ATAP subfamilies are not well understood. To address these problems, our study investigated the taxonomic distribution of 321 species from a broad cross-section of taxa. Then, we identified common and specific motifs in multiple ATAP subfamilies to explain the functional conservation and nonredundancy of the ATAPs, and a novel, essential motif was found in Eumetazoa IscA1, which has a newly found magnetic function. Finally, we used phylogenetic analytical methods to reconstruct the evolution history of this family. Our results show that two types of ErpA proteins (nonproteobacteria-type ErpA1 and proteobacteria-type ErpA2) exist in bacteria. The ATAP family, consisting of seven subfamilies, can be further classified into two types of ATAPs. Type-I ATAPs include IscA, SufA, HesB, ErpA1, and IscA1, with an ErpA1-like gene as their last common ancestor, whereas type-II ATAPs consist of ErpA2 and IscA2, duplicated from an ErpA2-like gene. During the mitochondrial endosymbiosis, IscA became IscA1 in eukaryotes and ErpA2 became IscA2 in eukaryotes, respectively.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">32108236</PMID><DateRevised><Year>2020</Year><Month>07</Month><Day>02</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1759-6653</ISSN><JournalIssue CitedMedium="Internet"><Volume>12</Volume><Issue>3</Issue><PubDate><Year>2020</Year><Month>03</Month><Day>01</Day></PubDate></JournalIssue><Title>Genome biology and evolution</Title><ISOAbbreviation>Genome Biol Evol</ISOAbbreviation></Journal><ArticleTitle>The Evolution History of Fe-S Cluster A-Type Assembly Protein Reveals Multiple Gene Duplication Events and Essential Protein Motifs.</ArticleTitle><Pagination><MedlinePgn>160-173</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/gbe/evaa038</ELocationID><Abstract><AbstractText>Iron-sulfur (Fe-S) clusters play important roles in electron transfer, metabolic and biosynthetic reactions, and the regulation of gene expression. Understanding the biogenesis of Fe-S clusters is therefore relevant to many fields. In the complex process of Fe-S protein formation, the A-type assembly protein (ATAP) family, which consists of several subfamilies, plays an essential role in Fe-S cluster formation and transfer and is highly conserved across the tree of life. However, the taxonomic distribution, motif compositions, and the evolutionary history of the ATAP subfamilies are not well understood. To address these problems, our study investigated the taxonomic distribution of 321 species from a broad cross-section of taxa. Then, we identified common and specific motifs in multiple ATAP subfamilies to explain the functional conservation and nonredundancy of the ATAPs, and a novel, essential motif was found in Eumetazoa IscA1, which has a newly found magnetic function. Finally, we used phylogenetic analytical methods to reconstruct the evolution history of this family. Our results show that two types of ErpA proteins (nonproteobacteria-type ErpA1 and proteobacteria-type ErpA2) exist in bacteria. The ATAP family, consisting of seven subfamilies, can be further classified into two types of ATAPs. Type-I ATAPs include IscA, SufA, HesB, ErpA1, and IscA1, with an ErpA1-like gene as their last common ancestor, whereas type-II ATAPs consist of ErpA2 and IscA2, duplicated from an ErpA2-like gene. During the mitochondrial endosymbiosis, IscA became IscA1 in eukaryotes and ErpA2 became IscA2 in eukaryotes, respectively.</AbstractText><CopyrightInformation>© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Lu</LastName><ForeName>Hui-Meng</ForeName><Initials>HM</Initials><AffiliationInfo><Affiliation>School of Life Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi'an, Shaanxi, PR China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Jing-Di</ForeName><Initials>JD</Initials><AffiliationInfo><Affiliation>School of Life Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi'an, Shaanxi, PR China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Yu-Dan</ForeName><Initials>YD</Initials><AffiliationInfo><Affiliation>School of Life Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi'an, Shaanxi, PR China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lu</LastName><ForeName>Xiao-Li</ForeName><Initials>XL</Initials><AffiliationInfo><Affiliation>School of Life Sciences, Key Laboratory for Space Bioscience and Biotechnology, Northwestern Polytechnical University, Xi'an, Shaanxi, PR China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Chang</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, PR China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Huang</LastName><ForeName>Yuan</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi, PR China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gribskov</LastName><ForeName>Michael</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, Purdue University.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Computer Science, Purdue University.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>figshare</DataBankName><AccessionNumberList><AccessionNumber>10.6084/m9.figshare.11847183</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Genome Biol Evol</MedlineTA><NlmUniqueID>101509707</NlmUniqueID><ISSNLinking>1759-6653</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Fe–S cluster A-type assembly protein</Keyword><Keyword MajorTopicYN="Y">gene duplication</Keyword><Keyword MajorTopicYN="Y">protein family evolution</Keyword><Keyword MajorTopicYN="Y">protein motif</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>02</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>2</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>2</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>2</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32108236</ArticleId><ArticleId IdType="pii">5762613</ArticleId><ArticleId 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last="Huang">Yuan Huang</name><name sortKey="Li, Jing Di" sort="Li, Jing Di" uniqKey="Li J" first="Jing-Di" last="Li">Jing-Di Li</name><name sortKey="Lu, Xiao Li" sort="Lu, Xiao Li" uniqKey="Lu X" first="Xiao-Li" last="Lu">Xiao-Li Lu</name><name sortKey="Xu, Chang" sort="Xu, Chang" uniqKey="Xu C" first="Chang" last="Xu">Chang Xu</name><name sortKey="Zhang, Yu Dan" sort="Zhang, Yu Dan" uniqKey="Zhang Y" first="Yu-Dan" last="Zhang">Yu-Dan Zhang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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