High Level of Conservation of Mitochondrial RNA Editing Sites Among Four Populus Species.
Identifieur interne : 000913 ( Main/Exploration ); précédent : 000912; suivant : 000914High Level of Conservation of Mitochondrial RNA Editing Sites Among Four Populus Species.
Auteurs : Wolfram Georg Brenner [Allemagne] ; Malte Mader [Allemagne] ; Niels Andreas Müller [Allemagne] ; Hans Hoenicka [Allemagne] ; Hilke Schroeder [Allemagne] ; Ingo Zorn [Allemagne] ; Matthias Fladung [Allemagne] ; Birgit Kersten [Allemagne]Source :
- G3 (Bethesda, Md.) [ 2160-1836 ] ; 2019.
Descripteurs français
- KwdFr :
- ARN des plantes (métabolisme), ARN mitochondrial (métabolisme), Analyse de profil d'expression de gènes (MeSH), Analyse de séquence d'ARN (MeSH), Mitochondries (génétique), Mitochondries (métabolisme), Phylogenèse (MeSH), Polymorphisme de nucléotide simple (MeSH), Populus (génétique), Populus (métabolisme), Édition des ARN (MeSH).
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , metabolism : RNA, Mitochondrial, RNA, Plant.
- genetics : Mitochondria, Populus.
- metabolism : Mitochondria, Populus.
- Gene Expression Profiling, Phylogeny, Polymorphism, Single Nucleotide, RNA Editing, Sequence Analysis, RNA.
Abstract
RNA editing occurs in the endosymbiont organelles of higher plants as C-to-U conversions of defined nucleotides. The availability of large quantities of RNA sequencing data makes it possible to identify RNA editing sites and to quantify their editing extent. We have investigated RNA editing in 34 protein-coding mitochondrial transcripts of four Populus species, a genus noteworthy for its remarkably small number of RNA editing sites compared to other angiosperms. 27 of these transcripts were subject to RNA editing in at least one species. In total, 355 RNA editing sites were identified with high confidence, their editing extents ranging from 10 to 100%. The most heavily edited transcripts were ccmB with the highest density of RNA editing sites (53.7 sites / kb) and ccmFn with the highest number of sites (39 sites). Most of the editing events are at position 1 or 2 of the codons, usually altering the encoded amino acid, and are highly conserved among the species, also with regard to their editing extent. However, one SNP was found in the newly sequenced and annotated mitochondrial genome of P. alba resulting in the loss of an RNA editing site compared to P. tremula and P. davidiana This SNP causes a C-to-T transition and an amino acid exchange from Ser to Phe, highlighting the widely discussed role of RNA editing in compensating mutations.
DOI: 10.1534/g3.118.200763
PubMed: 30617214
PubMed Central: PMC6404595
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Grosshansdorf</wicri:noRegion></affiliation></author><author><name sortKey="Schroeder, Hilke" sort="Schroeder, Hilke" uniqKey="Schroeder H" first="Hilke" last="Schroeder">Hilke Schroeder</name><affiliation wicri:level="1"><nlm:affiliation>Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Thünen Institute of Forest Genetics, 22927 Grosshansdorf</wicri:regionArea><wicri:noRegion>22927 Grosshansdorf</wicri:noRegion><wicri:noRegion>22927 Grosshansdorf</wicri:noRegion><wicri:noRegion>22927 Grosshansdorf</wicri:noRegion></affiliation></author><author><name sortKey="Zorn, Ingo" sort="Zorn, Ingo" uniqKey="Zorn I" first="Ingo" last="Zorn">Ingo Zorn</name><affiliation wicri:level="1"><nlm:affiliation>Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Thünen Institute of Forest Genetics, 22927 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Forest Genetics, 22927 Grosshansdorf, Germany birgit.kersten@thuenen.de.</nlm:affiliation><country wicri:rule="url">Allemagne</country><wicri:regionArea>Thünen Institute of Forest Genetics, 22927 Grosshansdorf</wicri:regionArea><wicri:noRegion>22927 Grosshansdorf</wicri:noRegion><wicri:noRegion>22927 Grosshansdorf</wicri:noRegion><wicri:noRegion>22927 Grosshansdorf</wicri:noRegion></affiliation></author></analytic><series><title level="j">G3 (Bethesda, Md.)</title><idno type="eISSN">2160-1836</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Gene Expression Profiling (MeSH)</term><term>Mitochondria (genetics)</term><term>Mitochondria (metabolism)</term><term>Phylogeny (MeSH)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Populus (genetics)</term><term>Populus (metabolism)</term><term>RNA Editing (MeSH)</term><term>RNA, Mitochondrial (metabolism)</term><term>RNA, Plant (metabolism)</term><term>Sequence Analysis, RNA (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN des plantes (métabolisme)</term><term>ARN mitochondrial (métabolisme)</term><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Analyse de séquence d'ARN (MeSH)</term><term>Mitochondries (génétique)</term><term>Mitochondries (métabolisme)</term><term>Phylogenèse (MeSH)</term><term>Polymorphisme de nucléotide simple (MeSH)</term><term>Populus (génétique)</term><term>Populus (métabolisme)</term><term>Édition des ARN (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>RNA, Mitochondrial</term><term>RNA, Plant</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Mitochondria</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Mitochondries</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Mitochondria</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ARN des plantes</term><term>ARN mitochondrial</term><term>Mitochondries</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Profiling</term><term>Phylogeny</term><term>Polymorphism, Single Nucleotide</term><term>RNA Editing</term><term>Sequence Analysis, RNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Analyse de séquence d'ARN</term><term>Phylogenèse</term><term>Polymorphisme de nucléotide simple</term><term>Édition des ARN</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">RNA editing occurs in the endosymbiont organelles of higher plants as C-to-U conversions of defined nucleotides. The availability of large quantities of RNA sequencing data makes it possible to identify RNA editing sites and to quantify their editing extent. We have investigated RNA editing in 34 protein-coding mitochondrial transcripts of four <i>Populus</i> species, a genus noteworthy for its remarkably small number of RNA editing sites compared to other angiosperms. 27 of these transcripts were subject to RNA editing in at least one species. In total, 355 RNA editing sites were identified with high confidence, their editing extents ranging from 10 to 100%. The most heavily edited transcripts were <i>ccmB</i> with the highest density of RNA editing sites (53.7 sites / kb) and <i>ccmFn</i> with the highest number of sites (39 sites). Most of the editing events are at position 1 or 2 of the codons, usually altering the encoded amino acid, and are highly conserved among the species, also with regard to their editing extent. However, one SNP was found in the newly sequenced and annotated mitochondrial genome of <i>P. alba</i> resulting in the loss of an RNA editing site compared to <i>P. tremula</i> and <i>P. davidiana</i> This SNP causes a C-to-T transition and an amino acid exchange from Ser to Phe, highlighting the widely discussed role of RNA editing in compensating mutations.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30617214</PMID><DateCompleted><Year>2019</Year><Month>07</Month><Day>08</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>09</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2160-1836</ISSN><JournalIssue CitedMedium="Internet"><Volume>9</Volume><Issue>3</Issue><PubDate><Year>2019</Year><Month>03</Month><Day>07</Day></PubDate></JournalIssue><Title>G3 (Bethesda, Md.)</Title><ISOAbbreviation>G3 (Bethesda)</ISOAbbreviation></Journal><ArticleTitle>High Level of Conservation of Mitochondrial RNA Editing Sites Among Four <i>Populus</i> Species.</ArticleTitle><Pagination><MedlinePgn>709-717</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1534/g3.118.200763</ELocationID><Abstract><AbstractText>RNA editing occurs in the endosymbiont organelles of higher plants as C-to-U conversions of defined nucleotides. The availability of large quantities of RNA sequencing data makes it possible to identify RNA editing sites and to quantify their editing extent. We have investigated RNA editing in 34 protein-coding mitochondrial transcripts of four <i>Populus</i> species, a genus noteworthy for its remarkably small number of RNA editing sites compared to other angiosperms. 27 of these transcripts were subject to RNA editing in at least one species. In total, 355 RNA editing sites were identified with high confidence, their editing extents ranging from 10 to 100%. The most heavily edited transcripts were <i>ccmB</i> with the highest density of RNA editing sites (53.7 sites / kb) and <i>ccmFn</i> with the highest number of sites (39 sites). Most of the editing events are at position 1 or 2 of the codons, usually altering the encoded amino acid, and are highly conserved among the species, also with regard to their editing extent. However, one SNP was found in the newly sequenced and annotated mitochondrial genome of <i>P. alba</i> resulting in the loss of an RNA editing site compared to <i>P. tremula</i> and <i>P. davidiana</i> This SNP causes a C-to-T transition and an amino acid exchange from Ser to Phe, highlighting the widely discussed role of RNA editing in compensating mutations.</AbstractText><CopyrightInformation>Copyright © 2019 Brenner et al.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Brenner</LastName><ForeName>Wolfram Georg</ForeName><Initials>WG</Initials><Identifier Source="ORCID">0000-0001-8934-9417</Identifier><AffiliationInfo><Affiliation>Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mader</LastName><ForeName>Malte</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Müller</LastName><ForeName>Niels Andreas</ForeName><Initials>NA</Initials><AffiliationInfo><Affiliation>Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hoenicka</LastName><ForeName>Hans</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schroeder</LastName><ForeName>Hilke</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zorn</LastName><ForeName>Ingo</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fladung</LastName><ForeName>Matthias</ForeName><Initials>M</Initials><Identifier Source="ORCID">0000-0001-9301-8581</Identifier><AffiliationInfo><Affiliation>Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kersten</LastName><ForeName>Birgit</ForeName><Initials>B</Initials><Identifier Source="ORCID">0000-0001-9900-9133</Identifier><AffiliationInfo><Affiliation>Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany birgit.kersten@thuenen.de.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>figshare</DataBankName><AccessionNumberList><AccessionNumber>10.25387/g3.7166141</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>03</Month><Day>07</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>G3 (Bethesda)</MedlineTA><NlmUniqueID>101566598</NlmUniqueID><ISSNLinking>2160-1836</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D000077278">RNA, Mitochondrial</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018749">RNA, Plant</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008928" MajorTopicYN="N">Mitochondria</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="Y">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017393" MajorTopicYN="Y">RNA Editing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000077278" MajorTopicYN="N">RNA, Mitochondrial</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018749" MajorTopicYN="N">RNA, Plant</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017423" MajorTopicYN="N">Sequence Analysis, 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