Subcellular Relocalization and Positive Selection Play Key Roles in the Retention of Duplicate Genes of Populus Class III Peroxidase Family.
Identifieur interne : 002036 ( Main/Exploration ); précédent : 002035; suivant : 002037Subcellular Relocalization and Positive Selection Play Key Roles in the Retention of Duplicate Genes of Populus Class III Peroxidase Family.
Auteurs : Lin-Ling Ren [République populaire de Chine] ; Yan-Jing Liu [République populaire de Chine] ; Hai-Jing Liu [République populaire de Chine] ; Ting-Ting Qian [République populaire de Chine] ; Li-Wang Qi [République populaire de Chine] ; Xiao-Ru Wang [Suède] ; Qing-Yin Zeng [République populaire de Chine]Source :
- The Plant cell [ 1532-298X ] ; 2014.
Abstract
Gene duplication is the primary source of new genes and novel functions. Over the course of evolution, many duplicate genes lose their function and are eventually removed by deletion. However, some duplicates have persisted and evolved diverse functions. A particular challenge is to understand how this diversity arises and whether positive selection plays a role. In this study, we reconstructed the evolutionary history of the class III peroxidase (PRX) genes from the Populus trichocarpa genome. PRXs are plant-specific enzymes that play important roles in cell wall metabolism and in response to biotic and abiotic stresses. We found that two large tandem-arrayed clusters of PRXs evolved from an ancestral cell wall type PRX to vacuole type, followed by tandem duplications and subsequent functional specification. Substitution models identified seven positively selected sites in the vacuole PRXs. These positively selected sites showed significant effects on the biochemical functions of the enzymes. We also found that positive selection acts more frequently on residues adjacent to, rather than directly at, a critical active site of the enzyme, and on flexible regions rather than on rigid structural elements of the protein. Our study provides new insights into the adaptive molecular evolution of plant enzyme families.
DOI: 10.1105/tpc.114.124750
PubMed: 24934172
PubMed Central: PMC4114941
Affiliations:
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Chine</country><wicri:regionArea>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Liu, Yan Jing" sort="Liu, Yan Jing" uniqKey="Liu Y" first="Yan-Jing" last="Liu">Yan-Jing Liu</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Liu, Hai Jing" sort="Liu, Hai Jing" uniqKey="Liu H" first="Hai-Jing" last="Liu">Hai-Jing Liu</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Qian, Ting Ting" sort="Qian, Ting Ting" uniqKey="Qian T" first="Ting-Ting" last="Qian">Ting-Ting Qian</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Qi, Li Wang" sort="Qi, Li Wang" uniqKey="Qi L" first="Li-Wang" last="Qi">Li-Wang Qi</name><affiliation wicri:level="1"><nlm:affiliation>Laboratory of Cell Biology, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Laboratory of Cell Biology, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Wang, Xiao Ru" sort="Wang, Xiao Ru" uniqKey="Wang X" first="Xiao-Ru" last="Wang">Xiao-Ru Wang</name><affiliation wicri:level="1"><nlm:affiliation>Department of Ecology and Environmental Science, UPSC, Umeå University, SE-90187 Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Ecology and Environmental Science, UPSC, Umeå University, SE-90187 Umeå</wicri:regionArea><wicri:noRegion>SE-90187 Umeå</wicri:noRegion></affiliation></author><author><name sortKey="Zeng, Qing Yin" sort="Zeng, Qing Yin" uniqKey="Zeng Q" first="Qing-Yin" last="Zeng">Qing-Yin Zeng</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China qingyin.zeng@ibcas.ac.cn.</nlm:affiliation><country wicri:rule="url">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author></analytic><series><title level="j">The Plant cell</title><idno type="eISSN">1532-298X</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Gene duplication is the primary source of new genes and novel functions. Over the course of evolution, many duplicate genes lose their function and are eventually removed by deletion. However, some duplicates have persisted and evolved diverse functions. A particular challenge is to understand how this diversity arises and whether positive selection plays a role. In this study, we reconstructed the evolutionary history of the class III peroxidase (PRX) genes from the Populus trichocarpa genome. PRXs are plant-specific enzymes that play important roles in cell wall metabolism and in response to biotic and abiotic stresses. We found that two large tandem-arrayed clusters of PRXs evolved from an ancestral cell wall type PRX to vacuole type, followed by tandem duplications and subsequent functional specification. Substitution models identified seven positively selected sites in the vacuole PRXs. These positively selected sites showed significant effects on the biochemical functions of the enzymes. We also found that positive selection acts more frequently on residues adjacent to, rather than directly at, a critical active site of the enzyme, and on flexible regions rather than on rigid structural elements of the protein. Our study provides new insights into the adaptive molecular evolution of plant enzyme families.</div></front></TEI><pubmed><MedlineCitation Status="Publisher" Owner="NLM"><PMID Version="1">24934172</PMID><DateRevised><Year>2019</Year><Month>11</Month><Day>20</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1532-298X</ISSN><JournalIssue CitedMedium="Internet"><Volume>26</Volume><Issue>6</Issue><PubDate><Year>2014</Year><Month>Jun</Month></PubDate></JournalIssue><Title>The Plant cell</Title><ISOAbbreviation>Plant Cell</ISOAbbreviation></Journal><ArticleTitle>Subcellular Relocalization and Positive Selection Play Key Roles in the Retention of Duplicate Genes of Populus Class III Peroxidase Family.</ArticleTitle><Pagination><MedlinePgn>2404-2419</MedlinePgn></Pagination><Abstract><AbstractText>Gene duplication is the primary source of new genes and novel functions. Over the course of evolution, many duplicate genes lose their function and are eventually removed by deletion. However, some duplicates have persisted and evolved diverse functions. A particular challenge is to understand how this diversity arises and whether positive selection plays a role. In this study, we reconstructed the evolutionary history of the class III peroxidase (PRX) genes from the Populus trichocarpa genome. PRXs are plant-specific enzymes that play important roles in cell wall metabolism and in response to biotic and abiotic stresses. We found that two large tandem-arrayed clusters of PRXs evolved from an ancestral cell wall type PRX to vacuole type, followed by tandem duplications and subsequent functional specification. Substitution models identified seven positively selected sites in the vacuole PRXs. These positively selected sites showed significant effects on the biochemical functions of the enzymes. We also found that positive selection acts more frequently on residues adjacent to, rather than directly at, a critical active site of the enzyme, and on flexible regions rather than on rigid structural elements of the protein. Our study provides new insights into the adaptive molecular evolution of plant enzyme families.</AbstractText><CopyrightInformation>© 2014 American Society of Plant Biologists. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ren</LastName><ForeName>Lin-Ling</ForeName><Initials>LL</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Yan-Jing</ForeName><Initials>YJ</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Hai-Jing</ForeName><Initials>HJ</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Qian</LastName><ForeName>Ting-Ting</ForeName><Initials>TT</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Qi</LastName><ForeName>Li-Wang</ForeName><Initials>LW</Initials><AffiliationInfo><Affiliation>Laboratory of Cell Biology, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Xiao-Ru</ForeName><Initials>XR</Initials><AffiliationInfo><Affiliation>Department of Ecology and Environmental Science, UPSC, Umeå University, SE-90187 Umeå, Sweden.</Affiliation></AffiliationInfo></Author><Author 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Liu</name><name sortKey="Liu, Yan Jing" sort="Liu, Yan Jing" uniqKey="Liu Y" first="Yan-Jing" last="Liu">Yan-Jing Liu</name><name sortKey="Qi, Li Wang" sort="Qi, Li Wang" uniqKey="Qi L" first="Li-Wang" last="Qi">Li-Wang Qi</name><name sortKey="Qian, Ting Ting" sort="Qian, Ting Ting" uniqKey="Qian T" first="Ting-Ting" last="Qian">Ting-Ting Qian</name><name sortKey="Zeng, Qing Yin" sort="Zeng, Qing Yin" uniqKey="Zeng Q" first="Qing-Yin" last="Zeng">Qing-Yin Zeng</name></country><country name="Suède"><noRegion><name sortKey="Wang, Xiao Ru" sort="Wang, Xiao Ru" uniqKey="Wang X" first="Xiao-Ru" last="Wang">Xiao-Ru Wang</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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