Genome-wide identification and expression profile analysis of CCH gene family in Populus.
Identifieur interne : 001365 ( Main/Exploration ); précédent : 001364; suivant : 001366Genome-wide identification and expression profile analysis of CCH gene family in Populus.
Auteurs : Zhiru Xu [République populaire de Chine] ; Liying Gao [République populaire de Chine] ; Mengquan Tang [République populaire de Chine] ; Chunpu Qu [République populaire de Chine] ; Jiahuan Huang [République populaire de Chine] ; Qi Wang [République populaire de Chine] ; Chuanping Yang [République populaire de Chine] ; Guanjun Liu [République populaire de Chine] ; Chengjun Yang [République populaire de Chine]Source :
- PeerJ [ 2167-8359 ] ; 2017.
Abstract
Copper plays key roles in plant physiological activities. To maintain copper cellular homeostasis, copper chaperones have important functions in binding and transporting copper to target proteins. Detailed characterization and function analysis of a copper chaperone, CCH, is presently limited to Arabidopsis. This study reports the identification of 21 genes encoding putative CCH proteins in Populus trichocarpa. Besides sharing the conserved metal-binding motif MXCXXC and forming a βαββαβ secondary structure at the N-terminal, all the PtCCHs possessed the plant-exclusive extended C-terminal. Based on their gene structure, conserved motifs, and phylogenetic analysis, the PtCCHs were divided into three subgroups. Our analysis indicated that whole-genome duplication and tandem duplication events likely contributed to expansion of the CCH gene family in Populus. Tissue-specific data from PlantGenIE revealed that PtCCH genes had broad expression patterns in different tissues. Quantitative real-time RT-PCR (qRT-PCR) analysis revealed that PnCCH genes of P. simonii × P. nigra also had different tissue-specific expression traits, as well as different inducible-expression patterns in response to copper stresses (excessive and deficiency). In summary, our study of CCH genes in the Populus genome provides a comprehensive analysis of this gene family, and lays an important foundation for further investigation of their roles in copper homeostasis of poplar.
DOI: 10.7717/peerj.3962
PubMed: 29085758
PubMed Central: PMC5661435
Affiliations:
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xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin</wicri:regionArea><wicri:noRegion>HarBin</wicri:noRegion></affiliation></author><author><name sortKey="Gao, Liying" sort="Gao, Liying" uniqKey="Gao L" first="Liying" last="Gao">Liying Gao</name><affiliation wicri:level="1"><nlm:affiliation>College of Life Science, Northeast Forestry University, HarBin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Science, Northeast Forestry University, HarBin</wicri:regionArea><wicri:noRegion>HarBin</wicri:noRegion></affiliation></author><author><name sortKey="Tang, Mengquan" sort="Tang, Mengquan" uniqKey="Tang M" first="Mengquan" last="Tang">Mengquan Tang</name><affiliation wicri:level="1"><nlm:affiliation>College of Life Science, Northeast Forestry University, HarBin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Science, Northeast Forestry University, HarBin</wicri:regionArea><wicri:noRegion>HarBin</wicri:noRegion></affiliation></author><author><name sortKey="Qu, Chunpu" sort="Qu, Chunpu" uniqKey="Qu C" first="Chunpu" last="Qu">Chunpu Qu</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin</wicri:regionArea><wicri:noRegion>HarBin</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>School of Forestry, Northeast Forestry University, HarBin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Forestry, Northeast Forestry University, HarBin</wicri:regionArea><wicri:noRegion>HarBin</wicri:noRegion></affiliation></author><author><name sortKey="Huang, Jiahuan" sort="Huang, Jiahuan" uniqKey="Huang J" first="Jiahuan" last="Huang">Jiahuan Huang</name><affiliation wicri:level="1"><nlm:affiliation>College of Life Science, Northeast Forestry University, HarBin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Life Science, Northeast Forestry University, HarBin</wicri:regionArea><wicri:noRegion>HarBin</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Qi" sort="Wang, Qi" uniqKey="Wang Q" first="Qi" last="Wang">Qi Wang</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin</wicri:regionArea><wicri:noRegion>HarBin</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>School of Forestry, Northeast Forestry University, HarBin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Forestry, Northeast Forestry University, HarBin</wicri:regionArea><wicri:noRegion>HarBin</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Chuanping" sort="Yang, Chuanping" uniqKey="Yang C" first="Chuanping" last="Yang">Chuanping Yang</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin</wicri:regionArea><wicri:noRegion>HarBin</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>School of Forestry, Northeast Forestry University, HarBin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Forestry, Northeast Forestry University, HarBin</wicri:regionArea><wicri:noRegion>HarBin</wicri:noRegion></affiliation></author><author><name sortKey="Liu, Guanjun" sort="Liu, Guanjun" uniqKey="Liu G" first="Guanjun" last="Liu">Guanjun Liu</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin</wicri:regionArea><wicri:noRegion>HarBin</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>School of Forestry, Northeast Forestry University, HarBin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Forestry, Northeast Forestry University, HarBin</wicri:regionArea><wicri:noRegion>HarBin</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Chengjun" sort="Yang, Chengjun" uniqKey="Yang C" first="Chengjun" last="Yang">Chengjun Yang</name><affiliation wicri:level="1"><nlm:affiliation>School of Forestry, Northeast Forestry University, HarBin, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Forestry, Northeast Forestry University, HarBin</wicri:regionArea><wicri:noRegion>HarBin</wicri:noRegion></affiliation></author></analytic><series><title level="j">PeerJ</title><idno type="ISSN">2167-8359</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Copper plays key roles in plant physiological activities. To maintain copper cellular homeostasis, copper chaperones have important functions in binding and transporting copper to target proteins. Detailed characterization and function analysis of a copper chaperone, CCH, is presently limited to <i>Arabidopsis</i>. This study reports the identification of 21 genes encoding putative CCH proteins in <i>Populus trichocarpa</i>. Besides sharing the conserved metal-binding motif MXCXXC and forming a βαββαβ secondary structure at the N-terminal, all the PtCCHs possessed the plant-exclusive extended C-terminal. Based on their gene structure, conserved motifs, and phylogenetic analysis, the PtCCHs were divided into three subgroups. Our analysis indicated that whole-genome duplication and tandem duplication events likely contributed to expansion of the <i>CCH</i> gene family in <i>Populus</i>. Tissue-specific data from PlantGenIE revealed that <i>PtCCH</i> genes had broad expression patterns in different tissues. Quantitative real-time RT-PCR (qRT-PCR) analysis revealed that <i>PnCCH</i> genes of <i>P. simonii</i> × <i>P. nigra</i> also had different tissue-specific expression traits, as well as different inducible-expression patterns in response to copper stresses (excessive and deficiency). In summary, our study of <i>CCH</i> genes in the <i>Populus</i> genome provides a comprehensive analysis of this gene family, and lays an important foundation for further investigation of their roles in copper homeostasis of poplar.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">29085758</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2167-8359</ISSN><JournalIssue CitedMedium="Print"><Volume>5</Volume><PubDate><Year>2017</Year></PubDate></JournalIssue><Title>PeerJ</Title><ISOAbbreviation>PeerJ</ISOAbbreviation></Journal><ArticleTitle>Genome-wide identification and expression profile analysis of <i>CCH</i> gene family in <i>Populus</i>.</ArticleTitle><Pagination><MedlinePgn>e3962</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.7717/peerj.3962</ELocationID><Abstract><AbstractText>Copper plays key roles in plant physiological activities. To maintain copper cellular homeostasis, copper chaperones have important functions in binding and transporting copper to target proteins. Detailed characterization and function analysis of a copper chaperone, CCH, is presently limited to <i>Arabidopsis</i>. This study reports the identification of 21 genes encoding putative CCH proteins in <i>Populus trichocarpa</i>. Besides sharing the conserved metal-binding motif MXCXXC and forming a βαββαβ secondary structure at the N-terminal, all the PtCCHs possessed the plant-exclusive extended C-terminal. Based on their gene structure, conserved motifs, and phylogenetic analysis, the PtCCHs were divided into three subgroups. Our analysis indicated that whole-genome duplication and tandem duplication events likely contributed to expansion of the <i>CCH</i> gene family in <i>Populus</i>. Tissue-specific data from PlantGenIE revealed that <i>PtCCH</i> genes had broad expression patterns in different tissues. Quantitative real-time RT-PCR (qRT-PCR) analysis revealed that <i>PnCCH</i> genes of <i>P. simonii</i> × <i>P. nigra</i> also had different tissue-specific expression traits, as well as different inducible-expression patterns in response to copper stresses (excessive and deficiency). In summary, our study of <i>CCH</i> genes in the <i>Populus</i> genome provides a comprehensive analysis of this gene family, and lays an important foundation for further investigation of their roles in copper homeostasis of poplar.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Zhiru</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>College of Life Science, Northeast Forestry University, HarBin, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gao</LastName><ForeName>Liying</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>College of Life Science, Northeast Forestry University, HarBin, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tang</LastName><ForeName>Mengquan</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>College of Life Science, Northeast Forestry University, HarBin, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Qu</LastName><ForeName>Chunpu</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>School of Forestry, Northeast Forestry University, HarBin, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Huang</LastName><ForeName>Jiahuan</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>College of Life Science, Northeast Forestry University, HarBin, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Qi</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>School of Forestry, Northeast Forestry University, HarBin, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Chuanping</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>School of Forestry, Northeast Forestry University, HarBin, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Guanjun</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, HarBin, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>School of Forestry, Northeast Forestry University, HarBin, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Chengjun</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>School of Forestry, Northeast Forestry University, HarBin, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>10</Month><Day>27</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PeerJ</MedlineTA><NlmUniqueID>101603425</NlmUniqueID><ISSNLinking>2167-8359</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Copper chaperone</Keyword><Keyword MajorTopicYN="N">Copper homeostasis</Keyword><Keyword MajorTopicYN="N">Copper stress</Keyword><Keyword MajorTopicYN="N">Expression profile</Keyword><Keyword MajorTopicYN="N">Populus</Keyword></KeywordList><CoiStatement>The authors declare there are no completing interests.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>07</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>10</Month><Day>05</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>11</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>11</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>11</Month><Day>1</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">29085758</ArticleId><ArticleId IdType="doi">10.7717/peerj.3962</ArticleId><ArticleId IdType="pii">3962</ArticleId><ArticleId 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uniqKey="Xu Z" first="Zhiru" last="Xu">Zhiru Xu</name><name sortKey="Yang, Chengjun" sort="Yang, Chengjun" uniqKey="Yang C" first="Chengjun" last="Yang">Chengjun Yang</name><name sortKey="Yang, Chuanping" sort="Yang, Chuanping" uniqKey="Yang C" first="Chuanping" last="Yang">Chuanping Yang</name><name sortKey="Yang, Chuanping" sort="Yang, Chuanping" uniqKey="Yang C" first="Chuanping" last="Yang">Chuanping Yang</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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