Analysis of the laccase gene family and miR397-/miR408-mediated posttranscriptional regulation in Salvia miltiorrhiza.
Identifieur interne : 000B30 ( Main/Exploration ); précédent : 000B29; suivant : 000B31Analysis of the laccase gene family and miR397-/miR408-mediated posttranscriptional regulation in Salvia miltiorrhiza.
Auteurs : Caili Li [République populaire de Chine] ; Dongqiao Li [République populaire de Chine] ; Hong Zhou [République populaire de Chine] ; Jiang Li [République populaire de Chine] ; Shanfa Lu [République populaire de Chine]Source :
- PeerJ [ 2167-8359 ] ; 2019.
Abstract
Salvia miltiorrhiza is one of the most commonly used traditional Chinese medicine materials. It contains important bioactive phenolic compounds, such as salvianolic acids, flavonoids and anthocyanins. Elucidation of phenolic compound biosynthesis and its regulatory mechanism is of great significance for S. miltiorrhiza quality improvement. Laccases (LACs) are multicopper-containing enzymes potentially involved in the polymerization of phenolic compounds. So far, little has been known about LAC genes in S. miltiorrhiza. Through systematic investigation of the whole genome sequence and transcriptomes of S. miltiorrhiza, we identified 65 full-length SmLAC genes (SmLAC1-SmLAC65). Phylogenetic analysis showed that 62 of the identified SmLACs clustered with LACs from Arabidopsis and Populus trichocarpa in seven clades (C1-C7), whereas the other three fell into one S. miltiorrhiza-specific clade (C8). All of the deduced SmLAC proteins contain four conserved signature sequences and three typical Cu-oxidase domains, and gene structures of most LACs from S. miltiorrhiza, Arabidopsis and P. trichocarpa were highly conserved, however SmLACs encoding C8 proteins showed distinct intron-exon structures. It suggests the conservation and diversity of plant LACs in gene structures. The majority of SmLACs exhibited tissue-specific expression patterns, indicates manifold functions of SmLACs played in S. miltiorrhiza. Analysis of high-throughput small RNA sequences and degradome data and experimental validation using the 5' RACE method showed that 23 SmLACs were targets of Smi-miR397. Among them, three were also targeted by Smi-miR408. It suggests the significance of miR397 and miR408 in posttranscriptional regulation of SmLAC genes. Our results provide a foundation for further demonstrating the functions of SmLACs in the production of bioactive phenolic compounds in S. miltiorrhiza.
DOI: 10.7717/peerj.7605
PubMed: 31528508
PubMed Central: PMC6717658
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posttranscriptional regulation in <i>Salvia miltiorrhiza</i>.</title><author><name sortKey="Li, Caili" sort="Li, Caili" uniqKey="Li C" first="Caili" last="Li">Caili Li</name><affiliation wicri:level="3"><nlm:affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Li, Dongqiao" sort="Li, Dongqiao" uniqKey="Li D" first="Dongqiao" last="Li">Dongqiao Li</name><affiliation wicri:level="3"><nlm:affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Zhou, Hong" sort="Zhou, Hong" uniqKey="Zhou H" first="Hong" last="Zhou">Hong Zhou</name><affiliation wicri:level="3"><nlm:affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Li, Jiang" sort="Li, Jiang" uniqKey="Li J" first="Jiang" last="Li">Jiang Li</name><affiliation wicri:level="3"><nlm:affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Lu, Shanfa" sort="Lu, Shanfa" uniqKey="Lu S" first="Shanfa" last="Lu">Shanfa Lu</name><affiliation wicri:level="3"><nlm:affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author></analytic><series><title level="j">PeerJ</title><idno type="ISSN">2167-8359</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><i>Salvia miltiorrhiza</i> is one of the most commonly used traditional Chinese medicine materials. It contains important bioactive phenolic compounds, such as salvianolic acids, flavonoids and anthocyanins. Elucidation of phenolic compound biosynthesis and its regulatory mechanism is of great significance for <i>S. miltiorrhiza</i> quality improvement. Laccases (LACs) are multicopper-containing enzymes potentially involved in the polymerization of phenolic compounds. So far, little has been known about <i>LAC</i> genes in <i>S. miltiorrhiza</i>. Through systematic investigation of the whole genome sequence and transcriptomes of <i>S. miltiorrhiza</i>, we identified 65 full-length <i>SmLAC</i> genes (<i>SmLAC1</i>-<i>SmLAC65</i>). Phylogenetic analysis showed that 62 of the identified SmLACs clustered with LACs from <i>Arabidopsis</i> and <i>Populus trichocarpa</i> in seven clades (C1-C7), whereas the other three fell into one <i>S. miltiorrhiza</i>-specific clade (C8). All of the deduced SmLAC proteins contain four conserved signature sequences and three typical Cu-oxidase domains, and gene structures of most <i>LACs</i> from <i>S. miltiorrhiza</i>, <i>Arabidopsis</i> and <i>P. trichocarpa</i> were highly conserved, however <i>SmLACs</i> encoding C8 proteins showed distinct intron-exon structures. It suggests the conservation and diversity of plant <i>LACs</i> in gene structures. The majority of <i>SmLACs</i> exhibited tissue-specific expression patterns, indicates manifold functions of <i>SmLACs</i> played in <i>S. miltiorrhiza</i>. Analysis of high-throughput small RNA sequences and degradome data and experimental validation using the 5' RACE method showed that 23 <i>SmLACs</i> were targets of Smi-miR397. Among them, three were also targeted by Smi-miR408. It suggests the significance of miR397 and miR408 in posttranscriptional regulation of <i>SmLAC</i> genes. Our results provide a foundation for further demonstrating the functions of <i>SmLACs</i> in the production of bioactive phenolic compounds in <i>S. miltiorrhiza</i>.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">31528508</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>7</Volume><PubDate><Year>2019</Year></PubDate></JournalIssue><Title>PeerJ</Title><ISOAbbreviation>PeerJ</ISOAbbreviation></Journal><ArticleTitle>Analysis of the laccase gene family and miR397-/miR408-mediated posttranscriptional regulation in <i>Salvia miltiorrhiza</i>.</ArticleTitle><Pagination><MedlinePgn>e7605</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.7717/peerj.7605</ELocationID><Abstract><AbstractText><i>Salvia miltiorrhiza</i> is one of the most commonly used traditional Chinese medicine materials. It contains important bioactive phenolic compounds, such as salvianolic acids, flavonoids and anthocyanins. Elucidation of phenolic compound biosynthesis and its regulatory mechanism is of great significance for <i>S. miltiorrhiza</i> quality improvement. Laccases (LACs) are multicopper-containing enzymes potentially involved in the polymerization of phenolic compounds. So far, little has been known about <i>LAC</i> genes in <i>S. miltiorrhiza</i>. Through systematic investigation of the whole genome sequence and transcriptomes of <i>S. miltiorrhiza</i>, we identified 65 full-length <i>SmLAC</i> genes (<i>SmLAC1</i>-<i>SmLAC65</i>). Phylogenetic analysis showed that 62 of the identified SmLACs clustered with LACs from <i>Arabidopsis</i> and <i>Populus trichocarpa</i> in seven clades (C1-C7), whereas the other three fell into one <i>S. miltiorrhiza</i>-specific clade (C8). All of the deduced SmLAC proteins contain four conserved signature sequences and three typical Cu-oxidase domains, and gene structures of most <i>LACs</i> from <i>S. miltiorrhiza</i>, <i>Arabidopsis</i> and <i>P. trichocarpa</i> were highly conserved, however <i>SmLACs</i> encoding C8 proteins showed distinct intron-exon structures. It suggests the conservation and diversity of plant <i>LACs</i> in gene structures. The majority of <i>SmLACs</i> exhibited tissue-specific expression patterns, indicates manifold functions of <i>SmLACs</i> played in <i>S. miltiorrhiza</i>. Analysis of high-throughput small RNA sequences and degradome data and experimental validation using the 5' RACE method showed that 23 <i>SmLACs</i> were targets of Smi-miR397. Among them, three were also targeted by Smi-miR408. It suggests the significance of miR397 and miR408 in posttranscriptional regulation of <i>SmLAC</i> genes. Our results provide a foundation for further demonstrating the functions of <i>SmLACs</i> in the production of bioactive phenolic compounds in <i>S. miltiorrhiza</i>.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y" EqualContrib="Y"><LastName>Li</LastName><ForeName>Caili</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y" EqualContrib="Y"><LastName>Li</LastName><ForeName>Dongqiao</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhou</LastName><ForeName>Hong</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Jiang</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lu</LastName><ForeName>Shanfa</ForeName><Initials>S</Initials><Identifier Source="ORCID">0000-0001-6284-4389</Identifier><AffiliationInfo><Affiliation>Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>08</Month><Day>29</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">Gene expression</Keyword><Keyword MajorTopicYN="N">Laccase</Keyword><Keyword MajorTopicYN="N">Laccase gene family</Keyword><Keyword MajorTopicYN="N">Phenolic compound</Keyword><Keyword MajorTopicYN="N">Phenolic compounds</Keyword><Keyword MajorTopicYN="N">Salvia miltiorrhiza</Keyword><Keyword MajorTopicYN="N">miR397</Keyword><Keyword MajorTopicYN="N">miR408</Keyword></KeywordList><CoiStatement>The authors declare that they have no competing interests.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>02</Month><Day>19</Day></PubMedPubDate><PubMedPubDate 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last="Li">Caili Li</name></noRegion><name sortKey="Li, Dongqiao" sort="Li, Dongqiao" uniqKey="Li D" first="Dongqiao" last="Li">Dongqiao Li</name><name sortKey="Li, Jiang" sort="Li, Jiang" uniqKey="Li J" first="Jiang" last="Li">Jiang Li</name><name sortKey="Lu, Shanfa" sort="Lu, Shanfa" uniqKey="Lu S" first="Shanfa" last="Lu">Shanfa Lu</name><name sortKey="Zhou, Hong" sort="Zhou, Hong" uniqKey="Zhou H" first="Hong" last="Zhou">Hong Zhou</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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