Decrypting tubby-like protein gene family of multiple functions in starch root crop cassava.
Identifieur interne : 000A41 ( Main/Exploration ); précédent : 000A40; suivant : 000A42Decrypting tubby-like protein gene family of multiple functions in starch root crop cassava.
Auteurs : Ming-You Dong [République populaire de Chine] ; Xian-Wei Fan [République populaire de Chine] ; Xiang-Yu Pang [République populaire de Chine] ; You-Zhi Li [République populaire de Chine]Source :
- AoB PLANTS [ 2041-2851 ] ; 2019.
Abstract
Tubby-like proteins (TLPs) are ubiquitous in eukaryotes and function in abiotic stress tolerance of some plants. Cassava (Manihot esculenta Crantz) is a high-yield starch root crop and has a high tolerance to poor soil conditions and abiotic stress. However, little is known about TLP gene characteristics and their expression in cassava. We identified cassava TLP genes, MeTLPs, and further analysed structure, duplication, chromosome localization and collinearity, cis-acting elements in the promoter regions and expression patterns of MeTLPs, and three-dimensional structure of the encoded proteins MeTLPs. In conclusion, there is a MeTLP family containing 13 members, which are grouped into A and C subfamilies. There are 11 pairs of MeTLPs that show the duplication which took place between 10.11 and 126.69 million years ago. Two MeTLPs 6 and 9 likely originate from one gene in an ancestral species, may be common ancestors for other MeTLPs and would most likely not be eligible for ubiquitin-related protein degradation because their corresponding proteins (MeTLPs 6 and 9) have no the F-box domain in the N-terminus. MeTLPs feature differences in the number from TLPs in wheat, apple, Arabidopsis, poplar and maize, and are highlighted by segmental duplication but more importantly by the chromosomal collinearity with potato StTLPs. MeTLPs are at least related to abiotic stress tolerance in cassava. However, the subtle differences in function among MeTLPs are predictable partly because of their differential expression profiles, which are coupled with various cis‑acting elements existing in the promoter regions depending on genes.
DOI: 10.1093/aobpla/plz075
PubMed: 31871614
PubMed Central: PMC6920310
Affiliations:
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University, Nanning, Guangxi, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi</wicri:regionArea><wicri:noRegion>Guangxi</wicri:noRegion></affiliation></author><author><name sortKey="Fan, Xian Wei" sort="Fan, Xian Wei" uniqKey="Fan X" first="Xian-Wei" last="Fan">Xian-Wei Fan</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi</wicri:regionArea><wicri:noRegion>Guangxi</wicri:noRegion></affiliation></author><author><name sortKey="Pang, Xiang Yu" sort="Pang, Xiang Yu" uniqKey="Pang X" first="Xiang-Yu" last="Pang">Xiang-Yu Pang</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi</wicri:regionArea><wicri:noRegion>Guangxi</wicri:noRegion></affiliation></author><author><name sortKey="Li, You Zhi" sort="Li, You Zhi" uniqKey="Li Y" first="You-Zhi" last="Li">You-Zhi Li</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi</wicri:regionArea><wicri:noRegion>Guangxi</wicri:noRegion></affiliation></author></analytic><series><title level="j">AoB PLANTS</title><idno type="ISSN">2041-2851</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">Tubby-like proteins (TLPs) are ubiquitous in eukaryotes and function in abiotic stress tolerance of some plants. Cassava (<i>Manihot esculenta</i> Crantz) is a high-yield starch root crop and has a high tolerance to poor soil conditions and abiotic stress. However, little is known about TLP gene characteristics and their expression in cassava. We identified cassava TLP genes, <i>MeTLP</i>s, and further analysed structure, duplication, chromosome localization and collinearity, <i>cis</i>-acting elements in the promoter regions and expression patterns of <i>MeTLP</i>s, and three-dimensional structure of the encoded proteins MeTLPs. In conclusion, there is a <i>MeTLP</i> family containing 13 members, which are grouped into A and C subfamilies. There are 11 pairs of <i>MeTLP</i>s that show the duplication which took place between 10.11 and 126.69 million years ago. Two <i>MeTLP</i>s <i>6</i> and <i>9</i> likely originate from one gene in an ancestral species, may be common ancestors for other <i>MeTLP</i>s and would most likely not be eligible for ubiquitin-related protein degradation because their corresponding proteins (MeTLPs 6 and 9) have no the F-box domain in the N-terminus. <i>MeTLP</i>s feature differences in the number from <i>TLP</i>s in wheat, apple, <i>Arabidopsis</i>, poplar and maize, and are highlighted by segmental duplication but more importantly by the chromosomal collinearity with potato <i>StTLP</i>s. <i>MeTLP</i>s are at least related to abiotic stress tolerance in cassava. However, the subtle differences in function among <i>MeTLP</i>s are predictable partly because of their differential expression profiles, which are coupled with various <i>cis</i>‑acting elements existing in the promoter regions depending on genes.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">31871614</PMID><DateRevised><Year>2020</Year><Month>10</Month><Day>01</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2041-2851</ISSN><JournalIssue CitedMedium="Print"><Volume>11</Volume><Issue>6</Issue><PubDate><Year>2019</Year><Month>Dec</Month></PubDate></JournalIssue><Title>AoB PLANTS</Title><ISOAbbreviation>AoB Plants</ISOAbbreviation></Journal><ArticleTitle>Decrypting tubby-like protein gene family of multiple functions in starch root crop cassava.</ArticleTitle><Pagination><MedlinePgn>plz075</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/aobpla/plz075</ELocationID><Abstract><AbstractText>Tubby-like proteins (TLPs) are ubiquitous in eukaryotes and function in abiotic stress tolerance of some plants. Cassava (<i>Manihot esculenta</i> Crantz) is a high-yield starch root crop and has a high tolerance to poor soil conditions and abiotic stress. However, little is known about TLP gene characteristics and their expression in cassava. We identified cassava TLP genes, <i>MeTLP</i>s, and further analysed structure, duplication, chromosome localization and collinearity, <i>cis</i>-acting elements in the promoter regions and expression patterns of <i>MeTLP</i>s, and three-dimensional structure of the encoded proteins MeTLPs. In conclusion, there is a <i>MeTLP</i> family containing 13 members, which are grouped into A and C subfamilies. There are 11 pairs of <i>MeTLP</i>s that show the duplication which took place between 10.11 and 126.69 million years ago. Two <i>MeTLP</i>s <i>6</i> and <i>9</i> likely originate from one gene in an ancestral species, may be common ancestors for other <i>MeTLP</i>s and would most likely not be eligible for ubiquitin-related protein degradation because their corresponding proteins (MeTLPs 6 and 9) have no the F-box domain in the N-terminus. <i>MeTLP</i>s feature differences in the number from <i>TLP</i>s in wheat, apple, <i>Arabidopsis</i>, poplar and maize, and are highlighted by segmental duplication but more importantly by the chromosomal collinearity with potato <i>StTLP</i>s. <i>MeTLP</i>s are at least related to abiotic stress tolerance in cassava. However, the subtle differences in function among <i>MeTLP</i>s are predictable partly because of their differential expression profiles, which are coupled with various <i>cis</i>‑acting elements existing in the promoter regions depending on genes.</AbstractText><CopyrightInformation>© The Author(s) 2019. Published by Oxford University Press on behalf of the Annals of Botany Company.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Dong</LastName><ForeName>Ming-You</ForeName><Initials>MY</Initials><AffiliationInfo><Affiliation>State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fan</LastName><ForeName>Xian-Wei</ForeName><Initials>XW</Initials><AffiliationInfo><Affiliation>State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pang</LastName><ForeName>Xiang-Yu</ForeName><Initials>XY</Initials><AffiliationInfo><Affiliation>State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>You-Zhi</ForeName><Initials>YZ</Initials><AffiliationInfo><Affiliation>State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>11</Month><Day>25</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>AoB Plants</MedlineTA><NlmUniqueID>101539425</NlmUniqueID></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Cassava</Keyword><Keyword MajorTopicYN="N">evolution</Keyword><Keyword MajorTopicYN="N">gene expression</Keyword><Keyword MajorTopicYN="N">growth and development</Keyword><Keyword MajorTopicYN="N">proteins</Keyword><Keyword MajorTopicYN="N">stress tolerance</Keyword><Keyword MajorTopicYN="N">tubby-like protein gene family</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>06</Month><Day>06</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>11</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>12</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>12</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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