MicroRNA Superfamilies Descended from miR390 and Their Roles in Secondary Small Interfering RNA Biogenesis in Eudicots[W]
Identifieur interne : 000A31 ( Pmc/Checkpoint ); précédent : 000A30; suivant : 000A32MicroRNA Superfamilies Descended from miR390 and Their Roles in Secondary Small Interfering RNA Biogenesis in Eudicots[W]
Auteurs : Rui Xia [États-Unis] ; Blake C. Meyers [États-Unis] ; Zhongchi Liu [États-Unis] ; Eric P. Beers [États-Unis] ; Songqing Ye [États-Unis] ; Zongrang Liu [États-Unis]Source :
- The Plant Cell [ 1040-4651 ] ; 2013.
Abstract
This work shows the conservation in eudicots of a miRNA-TAS-PPR-siRNA pathway characterized by a set of 22-nucleotide miRNAs that trigger secondary siRNAs using distinct mechanistic strategies. This super-miR7122 family of miRNAs includes miR173 and originates from miR390, emerging via gene duplication and neofunctionalization, which involved yet another miRNA superfamily (super-miR4376).
Url:
DOI: 10.1105/tpc.113.110957
PubMed: 23695981
PubMed Central: 3694692
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">MicroRNA Superfamilies Descended from miR390 and Their Roles in Secondary Small Interfering RNA Biogenesis in Eudicots<xref ref-type="author-notes" rid="fn1"><sup>[W]</sup></xref></title><author><name sortKey="Xia, Rui" sort="Xia, Rui" uniqKey="Xia R" first="Rui" last="Xia">Rui Xia</name><affiliation wicri:level="2"><nlm:aff id="aff1">Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Virginie</region></placeName><wicri:cityArea>Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="aff2">Appalachian Fruit Research Station, Agricultural Research Service, U.S. Department of Agriculture, Kearneysville, West Virginia 25430</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Virginie-Occidentale</region></placeName><wicri:cityArea>Appalachian Fruit Research Station, Agricultural Research Service, U.S. Department of Agriculture, Kearneysville</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="aff3">Alson H. Smith Agricultural Research and Extension Center, Department of Horticulture, Virginia Polytechnic Institute and State University, Winchester, Virginia 22602</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Virginie</region></placeName><wicri:cityArea>Alson H. Smith Agricultural Research and Extension Center, Department of Horticulture, Virginia Polytechnic Institute and State University, Winchester</wicri:cityArea></affiliation></author><author><name sortKey="Meyers, Blake C" sort="Meyers, Blake C" uniqKey="Meyers B" first="Blake C." last="Meyers">Blake C. Meyers</name><affiliation wicri:level="2"><nlm:aff id="aff4">Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19717</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Delaware</region></placeName><wicri:cityArea>Department of Plant and Soil Sciences, University of Delaware, Newark</wicri:cityArea></affiliation></author><author><name sortKey="Liu, Zhongchi" sort="Liu, Zhongchi" uniqKey="Liu Z" first="Zhongchi" last="Liu">Zhongchi Liu</name><affiliation wicri:level="2"><nlm:aff id="aff5">Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>Department of Cell Biology and Molecular Genetics, University of Maryland, College Park</wicri:cityArea></affiliation></author><author><name sortKey="Beers, Eric P" sort="Beers, Eric P" uniqKey="Beers E" first="Eric P." last="Beers">Eric P. Beers</name><affiliation wicri:level="2"><nlm:aff id="aff1">Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Virginie</region></placeName><wicri:cityArea>Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg</wicri:cityArea></affiliation></author><author><name sortKey="Ye, Songqing" sort="Ye, Songqing" uniqKey="Ye S" first="Songqing" last="Ye">Songqing Ye</name><affiliation wicri:level="2"><nlm:aff id="aff5">Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>Department of Cell Biology and Molecular Genetics, University of Maryland, College Park</wicri:cityArea></affiliation></author><author><name sortKey="Liu, Zongrang" sort="Liu, Zongrang" uniqKey="Liu Z" first="Zongrang" last="Liu">Zongrang Liu</name><affiliation wicri:level="2"><nlm:aff id="aff1">Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Virginie</region></placeName><wicri:cityArea>Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="aff2">Appalachian Fruit Research Station, Agricultural Research Service, U.S. Department of Agriculture, Kearneysville, West Virginia 25430</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Virginie-Occidentale</region></placeName><wicri:cityArea>Appalachian Fruit Research Station, Agricultural Research Service, U.S. Department of Agriculture, Kearneysville</wicri:cityArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23695981</idno><idno type="pmc">3694692</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694692</idno><idno type="RBID">PMC:3694692</idno><idno type="doi">10.1105/tpc.113.110957</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000C86</idno><idno type="wicri:Area/Pmc/Curation">000C85</idno><idno type="wicri:Area/Pmc/Checkpoint">000A31</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">MicroRNA Superfamilies Descended from miR390 and Their Roles in Secondary Small Interfering RNA Biogenesis in Eudicots<xref ref-type="author-notes" rid="fn1"><sup>[W]</sup></xref></title><author><name sortKey="Xia, Rui" sort="Xia, Rui" uniqKey="Xia R" first="Rui" last="Xia">Rui Xia</name><affiliation wicri:level="2"><nlm:aff id="aff1">Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Virginie</region></placeName><wicri:cityArea>Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="aff2">Appalachian Fruit Research Station, Agricultural Research Service, U.S. Department of Agriculture, Kearneysville, West Virginia 25430</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Virginie-Occidentale</region></placeName><wicri:cityArea>Appalachian Fruit Research Station, Agricultural Research Service, U.S. Department of Agriculture, Kearneysville</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="aff3">Alson H. Smith Agricultural Research and Extension Center, Department of Horticulture, Virginia Polytechnic Institute and State University, Winchester, Virginia 22602</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Virginie</region></placeName><wicri:cityArea>Alson H. Smith Agricultural Research and Extension Center, Department of Horticulture, Virginia Polytechnic Institute and State University, Winchester</wicri:cityArea></affiliation></author><author><name sortKey="Meyers, Blake C" sort="Meyers, Blake C" uniqKey="Meyers B" first="Blake C." last="Meyers">Blake C. Meyers</name><affiliation wicri:level="2"><nlm:aff id="aff4">Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19717</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Delaware</region></placeName><wicri:cityArea>Department of Plant and Soil Sciences, University of Delaware, Newark</wicri:cityArea></affiliation></author><author><name sortKey="Liu, Zhongchi" sort="Liu, Zhongchi" uniqKey="Liu Z" first="Zhongchi" last="Liu">Zhongchi Liu</name><affiliation wicri:level="2"><nlm:aff id="aff5">Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>Department of Cell Biology and Molecular Genetics, University of Maryland, College Park</wicri:cityArea></affiliation></author><author><name sortKey="Beers, Eric P" sort="Beers, Eric P" uniqKey="Beers E" first="Eric P." last="Beers">Eric P. Beers</name><affiliation wicri:level="2"><nlm:aff id="aff1">Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Virginie</region></placeName><wicri:cityArea>Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg</wicri:cityArea></affiliation></author><author><name sortKey="Ye, Songqing" sort="Ye, Songqing" uniqKey="Ye S" first="Songqing" last="Ye">Songqing Ye</name><affiliation wicri:level="2"><nlm:aff id="aff5">Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Maryland</region></placeName><wicri:cityArea>Department of Cell Biology and Molecular Genetics, University of Maryland, College Park</wicri:cityArea></affiliation></author><author><name sortKey="Liu, Zongrang" sort="Liu, Zongrang" uniqKey="Liu Z" first="Zongrang" last="Liu">Zongrang Liu</name><affiliation wicri:level="2"><nlm:aff id="aff1">Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Virginie</region></placeName><wicri:cityArea>Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="aff2">Appalachian Fruit Research Station, Agricultural Research Service, U.S. Department of Agriculture, Kearneysville, West Virginia 25430</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Virginie-Occidentale</region></placeName><wicri:cityArea>Appalachian Fruit Research Station, Agricultural Research Service, U.S. Department of Agriculture, Kearneysville</wicri:cityArea></affiliation></author></analytic><series><title level="j">The Plant Cell</title><idno type="ISSN">1040-4651</idno><idno type="eISSN">1532-298X</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>This work shows the conservation in eudicots of a miRNA-TAS-PPR-siRNA pathway characterized by a set of 22-nucleotide miRNAs that trigger secondary siRNAs using distinct mechanistic strategies. This super-miR7122 family of miRNAs includes miR173 and originates from miR390, emerging via gene duplication and neofunctionalization, which involved yet another miRNA superfamily (super-miR4376).</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Plant Cell</journal-id><journal-id journal-id-type="iso-abbrev">Plant Cell</journal-id><journal-id journal-id-type="hwp">plantcell</journal-id><journal-id journal-id-type="publisher-id">aspb</journal-id><journal-title-group><journal-title>The Plant Cell</journal-title></journal-title-group><issn pub-type="ppub">1040-4651</issn><issn pub-type="epub">1532-298X</issn><publisher><publisher-name>American Society of Plant Biologists</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">23695981</article-id><article-id pub-id-type="pmc">3694692</article-id><article-id pub-id-type="publisher-id">110957</article-id><article-id pub-id-type="doi">10.1105/tpc.113.110957</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Articles</subject></subj-group></article-categories><title-group><article-title>MicroRNA Superfamilies Descended from miR390 and Their Roles in Secondary Small Interfering RNA Biogenesis in Eudicots<xref ref-type="author-notes" rid="fn1"><sup>[W]</sup></xref></article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Xia</surname><given-names>Rui</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref><xref ref-type="aff" rid="aff2"><sup>b</sup></xref><xref ref-type="aff" rid="aff3"><sup>c</sup></xref></contrib><contrib contrib-type="author"><name><surname>Meyers</surname><given-names>Blake C.</given-names></name><xref ref-type="aff" rid="aff4"><sup>d</sup></xref></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Zhongchi</given-names></name><xref ref-type="aff" rid="aff5"><sup>e</sup></xref></contrib><contrib contrib-type="author"><name><surname>Beers</surname><given-names>Eric P.</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ye</surname><given-names>Songqing</given-names></name><xref ref-type="aff" rid="aff5"><sup>e</sup></xref><xref ref-type="author-notes" rid="afn2"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Liu</surname><given-names>Zongrang</given-names></name><xref ref-type="aff" rid="aff1"><sup>a</sup></xref><xref ref-type="aff" rid="aff2"><sup>b</sup></xref><xref ref-type="corresp" rid="cor1"><sup>2</sup></xref></contrib><aff id="aff1"><label>a</label>Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061</aff><aff id="aff2"><label>b</label>Appalachian Fruit Research Station, Agricultural Research Service, U.S. Department of Agriculture, Kearneysville, West Virginia 25430</aff><aff id="aff3"><label>c</label>Alson H. Smith Agricultural Research and Extension Center, Department of Horticulture, Virginia Polytechnic Institute and State University, Winchester, Virginia 22602</aff><aff id="aff4"><label>d</label>Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19717</aff><aff id="aff5"><label>e</label>Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742</aff></contrib-group><author-notes><corresp id="cor1"><label>2</label>Address correspondence to <email>zongrang.liu@ars.usda.gov</email>.</corresp><fn id="afn2" fn-type="present-address"><label>1</label><p>Current address: Division of Plant Sciences, University of Missouri, Columbia, MO 65211.</p></fn><fn id="afn1"><p>The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (<ext-link ext-link-type="uri" xlink:href="http://www.plantcell.org">www.plantcell.org</ext-link>) is: Zongrang Liu (<email>zongrang.liu@ars.usda.gov</email>).</p></fn><fn id="fn1"><label>[W]</label><p>Online version contains Web-only data.</p></fn><fn><p><ext-link ext-link-type="uri" xlink:href="http://www.plantcell.org/cgi/doi/10.1105/tpc.113.110957">www.plantcell.org/cgi/doi/10.1105/tpc.113.110957</ext-link></p></fn></author-notes><pmc-comment>Fake ppub date generated by PMC from publisher
pub-date/@pub-type='epub-ppub' </pmc-comment>
<pub-date pub-type="ppub"><month>5</month><year>2013</year></pub-date><pub-date pub-type="epub"><day>21</day><month>5</month><year>2013</year></pub-date><volume>25</volume><issue>5</issue><fpage>1555</fpage><lpage>1572</lpage><history><date date-type="received"><day>25</day><month>2</month><year>2013</year></date><date date-type="rev-recd"><day>23</day><month>4</month><year>2013</year></date><date date-type="accepted"><day>02</day><month>5</month><year>2013</year></date></history><permissions><copyright-statement>© 2013 American Society of Plant Biologists. All rights reserved.</copyright-statement><copyright-year>2013</copyright-year></permissions><self-uri xlink:role="icon" xlink:type="simple" xlink:href="PC_110957_ic1.gif"></self-uri><abstract abstract-type="precis"><p>This work shows the conservation in eudicots of a miRNA-TAS-PPR-siRNA pathway characterized by a set of 22-nucleotide miRNAs that trigger secondary siRNAs using distinct mechanistic strategies. This super-miR7122 family of miRNAs includes miR173 and originates from miR390, emerging via gene duplication and neofunctionalization, which involved yet another miRNA superfamily (super-miR4376).</p></abstract><abstract><p><italic>Trans</italic>-acting small interfering RNAs (<xref ref-type="def" rid="def4">tasiRNAs</xref>) are a major class of small RNAs performing essential biological functions in plants. The first reported <xref ref-type="def" rid="def4">tasiRNA</xref> pathway, that of miR173-<italic>TAS1/2</italic>, produces <xref ref-type="def" rid="def4">tasiRNAs</xref> regulating a set of pentatricopeptide repeat (<italic>PPR</italic>) genes and has been characterized only in <italic>Arabidopsis thaliana</italic> to date. Here, we demonstrate that the microRNA (<xref ref-type="def" rid="def2">miRNA</xref>)-<italic>trans</italic>-acting small interfering RNA gene (<italic>TAS</italic>)-pentatricopeptide repeat-containing gene (<italic>PPR</italic>)-small interfering RNA pathway is a highly dynamic and widespread feature of eudicots. Nine eudicot plants, representing six different plant families, have evolved similar <xref ref-type="def" rid="def4">tasiRNA</xref> pathways to initiate phased small interfering RNA (<xref ref-type="def" rid="def5">phasiRNA</xref>) production from <italic>PPR</italic> genes. The <italic>PPR</italic><xref ref-type="def" rid="def5">phasiRNA</xref> production is triggered by different 22-nucleotide <xref ref-type="def" rid="def2">miRNAs</xref>, including miR7122, miR1509, and fve-PPRtri1/2, and through distinct mechanistic strategies exploiting <xref ref-type="def" rid="def2">miRNA</xref> direct targeting or indirect targeting through <italic>TAS</italic>-like genes (<italic>TASL</italic>), one-hit or two-hit, or even two layers of <xref ref-type="def" rid="def4">tasiRNA</xref>–<italic>TASL</italic> interactions. Intriguingly, although those <xref ref-type="def" rid="def2">miRNA</xref> triggers display high sequence divergence caused by the occurrence of frequent point mutations and splicing shifts, their corresponding <italic>MIRNA</italic> genes show pronounced identity to the <italic>Arabidopsis MIR173</italic>, implying a common origin of this group of <xref ref-type="def" rid="def2">miRNAs</xref> (super-miR7122). Further analyses reveal that super-miR7122 may have evolved from a newly defined miR4376 superfamily, which probably originated from the widely conserved miR390. The elucidation of this evolutionary path expands our understanding of the course of <xref ref-type="def" rid="def2">miRNA</xref> evolution, especially for relatively conserved <xref ref-type="def" rid="def2">miRNA</xref> families.</p></abstract><counts><page-count count="18"></page-count></counts></article-meta><notes><glossary><title>Glossary</title><def-list><def-item><term id="term1">sRNA</term><def id="def1"><p>small RNA</p></def></def-item><def-item><term id="term2">miRNA</term><def id="def2"><p>microRNA</p></def></def-item><def-item><term id="term3">siRNA</term><def id="def3"><p>small interfering RNA</p></def></def-item><def-item><term id="term4">tasiRNA</term><def id="def4"><p><italic>trans</italic>-acting siRNA</p></def></def-item><def-item><term id="term5">phasiRNA</term><def id="def5"><p>phased siRNA</p></def></def-item><def-item><term id="term6">AS</term><def id="def6"><p>alignment score</p></def></def-item><def-item><term id="term7">5′-RLM-RACE</term><def id="def7"><p>RNA ligation mediated rapid amplification of cDNA ends</p></def></def-item><def-item><term id="term8">PARE</term><def id="def8"><p>parallel analysis of RNA ends</p></def></def-item><def-item><term id="term9">Mya</term><def id="def9"><p>million years ago</p></def></def-item><def-item><term id="term10">CMS</term><def id="def10"><p>cytoplasmic male sterility</p></def></def-item><def-item><term id="term11">IGV</term><def id="def11"><p>Integrative Genomics Viewer</p></def></def-item></def-list></glossary></notes></front></pmc><affiliations><list><country><li>États-Unis</li></country><region><li>Delaware</li><li>Maryland</li><li>Virginie</li><li>Virginie-Occidentale</li></region></list><tree><country name="États-Unis"><region name="Virginie"><name sortKey="Xia, Rui" sort="Xia, Rui" uniqKey="Xia R" first="Rui" last="Xia">Rui Xia</name></region><name sortKey="Beers, Eric P" sort="Beers, Eric P" uniqKey="Beers E" first="Eric P." last="Beers">Eric P. Beers</name><name sortKey="Liu, Zhongchi" sort="Liu, Zhongchi" uniqKey="Liu Z" first="Zhongchi" last="Liu">Zhongchi Liu</name><name sortKey="Liu, Zongrang" sort="Liu, Zongrang" uniqKey="Liu Z" first="Zongrang" last="Liu">Zongrang Liu</name><name sortKey="Liu, Zongrang" sort="Liu, Zongrang" uniqKey="Liu Z" first="Zongrang" last="Liu">Zongrang Liu</name><name sortKey="Meyers, Blake C" sort="Meyers, Blake C" uniqKey="Meyers B" first="Blake C." last="Meyers">Blake C. Meyers</name><name sortKey="Xia, Rui" sort="Xia, Rui" uniqKey="Xia R" first="Rui" last="Xia">Rui Xia</name><name sortKey="Xia, Rui" sort="Xia, Rui" uniqKey="Xia R" first="Rui" last="Xia">Rui Xia</name><name sortKey="Ye, Songqing" sort="Ye, Songqing" uniqKey="Ye S" first="Songqing" last="Ye">Songqing Ye</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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