Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays
Identifieur interne : 001C26 ( Ncbi/Merge ); précédent : 001C25; suivant : 001C27Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays
Auteurs : Sarieh Ghorbani [Belgique] ; Yao-Cheng Lin [Belgique] ; Boris Parizot [Belgique] ; Ana Fernandez [Belgique] ; Maria Fransiska Njo [Belgique] ; Yves Van De Peer [Belgique, Afrique du Sud] ; Tom Beeckman [Belgique] ; Pierre Hilson [Belgique, France]Source :
- Journal of Experimental Botany [ 0022-0957 ] ; 2015.
Abstract
Comparative genome analysis combined with transcriptome mining identified secreted peptides possibly involved in root development. When applied on
Url:
DOI: 10.1093/jxb/erv346
PubMed: 26195730
PubMed Central: 4526923
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id="AF0004"><institution>Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Saclay Plant Sciences</institution>,<addr-line>INRA, route de Saint-Cyr, 78026 Versailles</addr-line>,<country>France</country></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26195730</idno><idno type="pmc">4526923</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4526923</idno><idno type="RBID">PMC:4526923</idno><idno type="doi">10.1093/jxb/erv346</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000113</idno><idno type="wicri:Area/Pmc/Curation">000113</idno><idno type="wicri:Area/Pmc/Checkpoint">000512</idno><idno type="wicri:Area/Ncbi/Merge">001C26</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Expanding the repertoire 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first="Yao-Cheng" last="Lin">Yao-Cheng Lin</name><affiliation wicri:level="1"><nlm:aff id="AF0001"><institution>Department of Plant Systems Biology</institution>,<addr-line>VIB, 9052 Ghent</addr-line>,<country>Belgium</country></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="AF0002"><institution>Department of Plant Biotechnology and Bioinformatics, Ghent University</institution>,<addr-line>9052 Ghent</addr-line>,<country>Belgium</country></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Parizot, Boris" sort="Parizot, Boris" uniqKey="Parizot B" first="Boris" last="Parizot">Boris Parizot</name><affiliation wicri:level="1"><nlm:aff id="AF0001"><institution>Department of Plant Systems Biology</institution>,<addr-line>VIB, 9052 Ghent</addr-line>,<country>Belgium</country></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="AF0002"><institution>Department of Plant Biotechnology and Bioinformatics, Ghent University</institution>,<addr-line>9052 Ghent</addr-line>,<country>Belgium</country></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Fernandez, Ana" sort="Fernandez, Ana" uniqKey="Fernandez A" first="Ana" last="Fernandez">Ana Fernandez</name><affiliation wicri:level="1"><nlm:aff id="AF0001"><institution>Department of Plant Systems Biology</institution>,<addr-line>VIB, 9052 Ghent</addr-line>,<country>Belgium</country></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="AF0002"><institution>Department of Plant Biotechnology and Bioinformatics, Ghent University</institution>,<addr-line>9052 Ghent</addr-line>,<country>Belgium</country></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Njo, Maria Fransiska" sort="Njo, Maria Fransiska" uniqKey="Njo M" first="Maria Fransiska" last="Njo">Maria Fransiska Njo</name><affiliation wicri:level="1"><nlm:aff id="AF0001"><institution>Department of Plant Systems Biology</institution>,<addr-line>VIB, 9052 Ghent</addr-line>,<country>Belgium</country></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="AF0002"><institution>Department of Plant Biotechnology and Bioinformatics, Ghent University</institution>,<addr-line>9052 Ghent</addr-line>,<country>Belgium</country></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name><affiliation wicri:level="1"><nlm:aff id="AF0001"><institution>Department of Plant Systems Biology</institution>,<addr-line>VIB, 9052 Ghent</addr-line>,<country>Belgium</country></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="AF0002"><institution>Department of Plant Biotechnology and Bioinformatics, Ghent University</institution>,<addr-line>9052 Ghent</addr-line>,<country>Belgium</country></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="AF0003"><institution>Genomics Research Institute, University of Pretoria, Hatfield Campus</institution>,<addr-line>Pretoria 0028</addr-line>,<country>South Africa</country></nlm:aff><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Beeckman, Tom" sort="Beeckman, Tom" uniqKey="Beeckman T" first="Tom" last="Beeckman">Tom Beeckman</name><affiliation wicri:level="1"><nlm:aff id="AF0001"><institution>Department of Plant Systems Biology</institution>,<addr-line>VIB, 9052 Ghent</addr-line>,<country>Belgium</country></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="AF0002"><institution>Department of Plant Biotechnology and Bioinformatics, Ghent University</institution>,<addr-line>9052 Ghent</addr-line>,<country>Belgium</country></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author><author><name sortKey="Hilson, Pierre" sort="Hilson, Pierre" uniqKey="Hilson P" first="Pierre" last="Hilson">Pierre Hilson</name><affiliation wicri:level="1"><nlm:aff id="AF0001"><institution>Department of Plant Systems Biology</institution>,<addr-line>VIB, 9052 Ghent</addr-line>,<country>Belgium</country></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="AF0002"><institution>Department of Plant Biotechnology and Bioinformatics, Ghent University</institution>,<addr-line>9052 Ghent</addr-line>,<country>Belgium</country></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="AF0004"><institution>Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Saclay Plant Sciences</institution>,<addr-line>INRA, route de Saint-Cyr, 78026 Versailles</addr-line>,<country>France</country></nlm:aff><country xml:lang="fr">France</country><wicri:regionArea># see nlm:aff country strict</wicri:regionArea></affiliation></author></analytic><series><title level="j">Journal of Experimental Botany</title><idno type="ISSN">0022-0957</idno><idno type="eISSN">1460-2431</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Highlight</title><p>Comparative genome analysis combined with transcriptome mining identified secreted peptides possibly involved in root development. When applied on <italic>Arabidopsis</italic> roots, selected candidates affected growth or branching in specific ways.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Amano, Y" uniqKey="Amano Y">Y Amano</name></author><author><name sortKey="Tsubouchi, H" uniqKey="Tsubouchi H">H Tsubouchi</name></author><author><name sortKey="Shinohara, H" uniqKey="Shinohara H">H Shinohara</name></author><author><name sortKey="Ogawa, M" uniqKey="Ogawa M">M Ogawa</name></author><author><name sortKey="Matsubayashi, Y" uniqKey="Matsubayashi Y">Y Matsubayashi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Atkinson, Ja" uniqKey="Atkinson J">JA Atkinson</name></author><author><name sortKey="Rasmussen, A" uniqKey="Rasmussen A">A Rasmussen</name></author><author><name sortKey="Traini, R" uniqKey="Traini R">R Traini</name></author><author><name sortKey="Vo, U" uniqKey="Vo U">U Voß</name></author><author><name 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<front><journal-meta><journal-id journal-id-type="nlm-ta">J Exp Bot</journal-id><journal-id journal-id-type="iso-abbrev">J. Exp. Bot</journal-id><journal-id journal-id-type="hwp">jexbot</journal-id><journal-id journal-id-type="publisher-id">exbotj</journal-id><journal-title-group><journal-title>Journal of Experimental Botany</journal-title></journal-title-group><issn pub-type="ppub">0022-0957</issn><issn pub-type="epub">1460-2431</issn><publisher><publisher-name>Oxford University Press</publisher-name><publisher-loc>UK</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">26195730</article-id><article-id pub-id-type="pmc">4526923</article-id><article-id pub-id-type="doi">10.1093/jxb/erv346</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Paper</subject></subj-group></article-categories><title-group><article-title>Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Ghorbani</surname><given-names>Sarieh</given-names></name><xref ref-type="aff" rid="AF0001"><sup>1</sup></xref><xref ref-type="aff" rid="AF0002"><sup>2</sup></xref><xref ref-type="corresp" rid="c2">*</xref></contrib><contrib contrib-type="author"><name><surname>Lin</surname><given-names>Yao-Cheng</given-names></name><xref ref-type="aff" rid="AF0001"><sup>1</sup></xref><xref ref-type="aff" rid="AF0002"><sup>2</sup></xref><xref ref-type="corresp" rid="c2">*</xref><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0002-9390-795X</contrib-id></contrib><contrib contrib-type="author"><name><surname>Parizot</surname><given-names>Boris</given-names></name><xref ref-type="aff" rid="AF0001"><sup>1</sup></xref><xref ref-type="aff" rid="AF0002"><sup>2</sup></xref><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0003-1445-6925</contrib-id></contrib><contrib contrib-type="author"><name><surname>Fernandez</surname><given-names>Ana</given-names></name><xref ref-type="aff" rid="AF0001"><sup>1</sup></xref><xref ref-type="aff" rid="AF0002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Njo</surname><given-names>Maria Fransiska</given-names></name><xref ref-type="aff" rid="AF0001"><sup>1</sup></xref><xref ref-type="aff" rid="AF0002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Van de Peer</surname><given-names>Yves</given-names></name><xref ref-type="aff" rid="AF0001"><sup>1</sup></xref><xref ref-type="aff" rid="AF0002"><sup>2</sup></xref><xref ref-type="aff" rid="AF0003"><sup>3</sup></xref><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0003-4327-3730</contrib-id></contrib><contrib contrib-type="author"><name><surname>Beeckman</surname><given-names>Tom</given-names></name><xref ref-type="aff" rid="AF0001"><sup>1</sup></xref><xref ref-type="aff" rid="AF0002"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hilson</surname><given-names>Pierre</given-names></name><xref ref-type="aff" rid="AF0001"><sup>1</sup></xref><xref ref-type="aff" rid="AF0002"><sup>2</sup></xref><xref ref-type="aff" rid="AF0004"><sup>4</sup></xref><xref ref-type="corresp" rid="c1"><sup>†</sup></xref></contrib><aff id="AF0001"><sup>1</sup><institution>Department of Plant Systems Biology</institution>,<addr-line>VIB, 9052 Ghent</addr-line>,<country>Belgium</country></aff><aff id="AF0002"><sup>2</sup><institution>Department of Plant Biotechnology and Bioinformatics, Ghent University</institution>,<addr-line>9052 Ghent</addr-line>,<country>Belgium</country></aff><aff id="AF0003"><sup>3</sup><institution>Genomics Research Institute, University of Pretoria, Hatfield Campus</institution>,<addr-line>Pretoria 0028</addr-line>,<country>South Africa</country></aff><aff id="AF0004"><sup>4</sup><institution>Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Saclay Plant Sciences</institution>,<addr-line>INRA, route de Saint-Cyr, 78026 Versailles</addr-line>,<country>France</country></aff></contrib-group><author-notes><corresp id="c2">* These authors contributed equally to this work.</corresp><corresp id="c1"><sup>†</sup> To whom correspondence should be addressed. E-mail: <email>pierre.hilson@versailles.inra.fr</email></corresp><fn id="fn01"><p>Editor: Ruediger Simon</p></fn></author-notes><pub-date pub-type="ppub"><month>8</month><year>2015</year></pub-date><pub-date pub-type="epub"><day>20</day><month>7</month><year>2015</year></pub-date><pub-date pub-type="pmc-release"><day>20</day><month>7</month><year>2015</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>66</volume><issue>17</issue><issue-title>Special Issue: Peptides take centre stage in Plant Signalling</issue-title><fpage>5257</fpage><lpage>5269</lpage><permissions><copyright-statement>© The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.</copyright-statement><copyright-year>2015</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by/3.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/3.0/">http://creativecommons.org/licenses/by/3.0/</ext-link>), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract abstract-type="precis"><title>Highlight</title><p>Comparative genome analysis combined with transcriptome mining identified secreted peptides possibly involved in root development. When applied on <italic>Arabidopsis</italic> roots, selected candidates affected growth or branching in specific ways.</p></abstract><abstract><p>Plant genomes encode numerous small secretory peptides (SSPs) whose functions have yet to be explored. Based on structural features that characterize SSP families known to take part in postembryonic development, this comparative genome analysis resulted in the identification of genes coding for oligopeptides potentially involved in cell-to-cell communication. Because genome annotation based on short sequence homology is difficult, the criteria for the <italic>de novo</italic> identification and aggregation of conserved SSP sequences were first benchmarked across five reference plant species. The resulting gene families were then extended to 32 genome sequences, including major crops. The global phylogenetic pattern common to the functionally characterized SSP families suggests that their apparition and expansion coincide with that of the land plants. The SSP families can be searched online for members, sequences and consensus (<uri xlink:href="http://bioinformatics.psb.ugent.be/webtools/PlantSSP/">http://bioinformatics.psb.ugent.be/webtools/PlantSSP/</uri>). Looking for putative regulators of root development, <italic>Arabidopsis thaliana</italic> SSP genes were further selected through transcriptome meta-analysis based on their expression at specific stages and in specific cell types in the course of the lateral root formation. As an additional indication that formerly uncharacterized SSPs may control development, this study showed that root growth and branching were altered by the application of synthetic peptides matching conserved SSP motifs, sometimes in very specific ways. The strategy used in the study, combining comparative genomics, transcriptome meta-analysis and peptide functional assays <italic>in planta</italic>, pinpoints factors potentially involved in non-cell-autonomous regulatory mechanisms. A similar approach can be implemented in different species for the study of a wide range of developmental programmes.</p></abstract><kwd-group><title>Key words:</title><kwd>Crops</kwd><kwd>genome annotation</kwd><kwd>meta-analysis</kwd><kwd>plant development</kwd><kwd>signalling peptide.</kwd></kwd-group><counts><page-count count="13"></page-count></counts></article-meta></front></pmc><affiliations><list><country><li>Afrique du Sud</li><li>Belgique</li><li>France</li></country></list><tree><country name="Belgique"><noRegion><name sortKey="Ghorbani, Sarieh" sort="Ghorbani, Sarieh" uniqKey="Ghorbani S" first="Sarieh" last="Ghorbani">Sarieh Ghorbani</name></noRegion><name sortKey="Beeckman, Tom" sort="Beeckman, Tom" uniqKey="Beeckman T" first="Tom" last="Beeckman">Tom Beeckman</name><name sortKey="Beeckman, Tom" sort="Beeckman, Tom" uniqKey="Beeckman T" first="Tom" last="Beeckman">Tom Beeckman</name><name sortKey="Fernandez, Ana" sort="Fernandez, Ana" uniqKey="Fernandez A" first="Ana" last="Fernandez">Ana Fernandez</name><name sortKey="Fernandez, Ana" sort="Fernandez, Ana" uniqKey="Fernandez A" first="Ana" last="Fernandez">Ana Fernandez</name><name sortKey="Ghorbani, Sarieh" sort="Ghorbani, Sarieh" uniqKey="Ghorbani S" first="Sarieh" last="Ghorbani">Sarieh Ghorbani</name><name sortKey="Hilson, Pierre" sort="Hilson, Pierre" uniqKey="Hilson P" first="Pierre" last="Hilson">Pierre Hilson</name><name sortKey="Hilson, Pierre" sort="Hilson, Pierre" uniqKey="Hilson P" first="Pierre" last="Hilson">Pierre Hilson</name><name sortKey="Lin, Yao Cheng" sort="Lin, Yao Cheng" uniqKey="Lin Y" first="Yao-Cheng" last="Lin">Yao-Cheng Lin</name><name sortKey="Lin, Yao Cheng" sort="Lin, Yao Cheng" uniqKey="Lin Y" first="Yao-Cheng" last="Lin">Yao-Cheng Lin</name><name sortKey="Njo, Maria Fransiska" sort="Njo, Maria Fransiska" uniqKey="Njo M" first="Maria Fransiska" last="Njo">Maria Fransiska Njo</name><name sortKey="Njo, Maria Fransiska" sort="Njo, Maria Fransiska" uniqKey="Njo M" first="Maria Fransiska" last="Njo">Maria Fransiska Njo</name><name sortKey="Parizot, Boris" sort="Parizot, Boris" uniqKey="Parizot B" first="Boris" last="Parizot">Boris Parizot</name><name sortKey="Parizot, Boris" sort="Parizot, Boris" uniqKey="Parizot B" first="Boris" last="Parizot">Boris Parizot</name><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name></country><country name="Afrique du Sud"><noRegion><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name></noRegion></country><country name="France"><noRegion><name sortKey="Hilson, Pierre" sort="Hilson, Pierre" uniqKey="Hilson P" first="Pierre" last="Hilson">Pierre Hilson</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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