Computational investigation of small RNAs in the establishment of root nodules and arbuscular mycorrhiza in leguminous plants.
Identifieur interne : 000A29 ( Main/Corpus ); précédent : 000A28; suivant : 000A30Computational investigation of small RNAs in the establishment of root nodules and arbuscular mycorrhiza in leguminous plants.
Auteurs : Danfeng Jin ; Xianwen Meng ; Yue Wang ; Jingjing Wang ; Yuhua Zhao ; Ming ChenSource :
- Science China. Life sciences [ 1869-1889 ] ; 2018.
English descriptors
- KwdEn :
- Computational Biology (MeSH), Databases, Genetic (MeSH), Fabaceae (microbiology), Gene Expression Regulation, Plant (MeSH), MicroRNAs (genetics), MicroRNAs (metabolism), Mycorrhizae (genetics), Mycorrhizae (physiology), Plant Proteins (genetics), Plant Proteins (metabolism), Root Nodules, Plant (genetics), Root Nodules, Plant (metabolism), Root Nodules, Plant (microbiology), Symbiosis (MeSH).
- MESH :
- chemical , genetics : MicroRNAs, Plant Proteins.
- chemical , metabolism : MicroRNAs, Plant Proteins.
- genetics : Mycorrhizae, Root Nodules, Plant.
- metabolism : Root Nodules, Plant.
- microbiology : Fabaceae, Root Nodules, Plant.
- physiology : Mycorrhizae.
- Computational Biology, Databases, Genetic, Gene Expression Regulation, Plant, Symbiosis.
Abstract
Many small RNAs have been confirmed to play important roles in the development of root nodules and arbuscular mycorrhiza. In this study, we carried out the identification of certain small RNAs in leguminous plants (Medicago truncatula, soybean, peanut and common bean), such as miRNAs, tRFs and srRNAs, as well as the computational investigation of their regulations. Thirty miRNAs were predicted to be involved in establishing root nodules and mycorrhiza, and 12 of them were novel in common bean and peanut. The generation of tRFs in M. truncatula was not associated with tRNA gene frequencies and codon usage. Six tRFs exhibited different expressions in mycorrhiza and root nodules. Moreover, srRNA5.8S in M. truncatula was generated from the regions with relatively low conservation at the rRNA 3' terminal. The protein-protein interactions between the proteins encoded by the target genes of miRNAs, tRFs and srRNAs were computed. The regulation of these three types of sRNAs in the symbiosis between leguminous plants and microorganisms is not a single regulation of certain signaling or metabolic pathways but a global regulation for the plants to own growth or specific events in symbiosis.
DOI: 10.1007/s11427-017-9203-7
PubMed: 29305786
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Life sciences</title><idno type="eISSN">1869-1889</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology (MeSH)</term><term>Databases, Genetic (MeSH)</term><term>Fabaceae (microbiology)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>MicroRNAs (genetics)</term><term>MicroRNAs (metabolism)</term><term>Mycorrhizae (genetics)</term><term>Mycorrhizae (physiology)</term><term>Plant Proteins (genetics)</term><term>Plant Proteins (metabolism)</term><term>Root Nodules, Plant (genetics)</term><term>Root Nodules, Plant (metabolism)</term><term>Root Nodules, Plant (microbiology)</term><term>Symbiosis (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>MicroRNAs</term><term>Plant Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>MicroRNAs</term><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Mycorrhizae</term><term>Root Nodules, Plant</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Root Nodules, Plant</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Fabaceae</term><term>Root Nodules, Plant</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Mycorrhizae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computational Biology</term><term>Databases, Genetic</term><term>Gene Expression Regulation, Plant</term><term>Symbiosis</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Many small RNAs have been confirmed to play important roles in the development of root nodules and arbuscular mycorrhiza. In this study, we carried out the identification of certain small RNAs in leguminous plants (Medicago truncatula, soybean, peanut and common bean), such as miRNAs, tRFs and srRNAs, as well as the computational investigation of their regulations. Thirty miRNAs were predicted to be involved in establishing root nodules and mycorrhiza, and 12 of them were novel in common bean and peanut. The generation of tRFs in M. truncatula was not associated with tRNA gene frequencies and codon usage. Six tRFs exhibited different expressions in mycorrhiza and root nodules. Moreover, srRNA<sup>5.8S</sup> in M. truncatula was generated from the regions with relatively low conservation at the rRNA 3' terminal. The protein-protein interactions between the proteins encoded by the target genes of miRNAs, tRFs and srRNAs were computed. The regulation of these three types of sRNAs in the symbiosis between leguminous plants and microorganisms is not a single regulation of certain signaling or metabolic pathways but a global regulation for the plants to own growth or specific events in symbiosis.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29305786</PMID><DateCompleted><Year>2018</Year><Month>12</Month><Day>13</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1869-1889</ISSN><JournalIssue CitedMedium="Internet"><Volume>61</Volume><Issue>6</Issue><PubDate><Year>2018</Year><Month>06</Month></PubDate></JournalIssue><Title>Science China. Life sciences</Title><ISOAbbreviation>Sci China Life Sci</ISOAbbreviation></Journal><ArticleTitle>Computational investigation of small RNAs in the establishment of root nodules and arbuscular mycorrhiza in leguminous plants.</ArticleTitle><Pagination><MedlinePgn>706-717</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s11427-017-9203-7</ELocationID><Abstract><AbstractText>Many small RNAs have been confirmed to play important roles in the development of root nodules and arbuscular mycorrhiza. In this study, we carried out the identification of certain small RNAs in leguminous plants (Medicago truncatula, soybean, peanut and common bean), such as miRNAs, tRFs and srRNAs, as well as the computational investigation of their regulations. Thirty miRNAs were predicted to be involved in establishing root nodules and mycorrhiza, and 12 of them were novel in common bean and peanut. The generation of tRFs in M. truncatula was not associated with tRNA gene frequencies and codon usage. Six tRFs exhibited different expressions in mycorrhiza and root nodules. Moreover, srRNA<sup>5.8S</sup> in M. truncatula was generated from the regions with relatively low conservation at the rRNA 3' terminal. The protein-protein interactions between the proteins encoded by the target genes of miRNAs, tRFs and srRNAs were computed. The regulation of these three types of sRNAs in the symbiosis between leguminous plants and microorganisms is not a single regulation of certain signaling or metabolic pathways but a global regulation for the plants to own growth or specific events in symbiosis.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Jin</LastName><ForeName>Danfeng</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang, 330096, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Meng</LastName><ForeName>Xianwen</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Yue</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Jingjing</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Yuhua</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Zhejiang University, Hangzhou, 310058, China. yhzhao225@zju.edu.cn.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Ming</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Zhejiang University, Hangzhou, 310058, China. mchen@zju.edu.cn.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>01</Month><Day>03</Day></ArticleDate></Article><MedlineJournalInfo><Country>China</Country><MedlineTA>Sci China Life Sci</MedlineTA><NlmUniqueID>101529880</NlmUniqueID><ISSNLinking>1674-7305</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D035683">MicroRNAs</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D030541" MajorTopicYN="N">Databases, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D007887" MajorTopicYN="N">Fabaceae</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="Y">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D035683" MajorTopicYN="N">MicroRNAs</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D038821" MajorTopicYN="N">Mycorrhizae</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D053204" MajorTopicYN="N">Root Nodules, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013559" MajorTopicYN="N">Symbiosis</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">arbuscular mycorrhiza</Keyword><Keyword MajorTopicYN="Y">leguminous plant</Keyword><Keyword MajorTopicYN="Y">root nodule</Keyword><Keyword MajorTopicYN="Y">small RNA</Keyword><Keyword MajorTopicYN="Y">symbiosis</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>09</Month><Day>07</Day></PubMedPubDate><PubMedPubDate 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