A systems biology approach identifies new regulators of poplar root development under low nitrogen.
Identifieur interne : 001F08 ( Main/Exploration ); précédent : 001F07; suivant : 001F09A systems biology approach identifies new regulators of poplar root development under low nitrogen.
Auteurs : Madhumita Dash [États-Unis] ; Yordan S. Yordanov [États-Unis] ; Tatyana Georgieva [États-Unis] ; Sapna Kumari [États-Unis] ; Hairong Wei [États-Unis] ; Victor Busov [États-Unis]Source :
- The Plant journal : for cell and molecular biology [ 1365-313X ] ; 2015.
Descripteurs français
- KwdFr :
- MESH :
- métabolisme : Azote, Populus, Racines de plante.
- méthodes : Biologie des systèmes.
- Régulation de l'expression des gènes végétaux.
English descriptors
- KwdEn :
- MESH :
- chemical , metabolism : Nitrogen.
- metabolism : Plant Roots, Populus.
- methods : Systems Biology.
- Gene Expression Regulation, Plant.
Abstract
In Populus, low nitrogen (LN) elicits rapid and vigorous lateral root (LR) proliferation, which is closely mirrored by corresponding transcriptomic changes. Using transcriptomic data, we built a genetic network encompassing a large proportion of the differentially regulated transcriptome. The network is organized in a hierarchical fashion, centered on 11 genes. Transgenic manipulations of only three of the 11 genes had a strong impact on root development under LN. These three genes encoded an F-box protein similar to Hawaiian Skirt (PtaHWS) and two transcription factors (PtaRAP2.11 and PtaNAC1). Up- and downregulation of the three genes caused increased and decreased root proliferation under LN conditions, respectively. The transgenic manipulations had a strong positive effect on growth under greenhouse conditions including increased shoot and root biomass. The three genes appeared to encompass a putative yet-unknown mechanism that underlies root development under LN. Specifically, the genes are predominantly expressed in roots and have a similar temporal response to LN. More importantly, transgenic manipulation for each of the three genes had a highly significant impact on the expression of the other two. The transgenic manipulations appear to also affect the expression of the regulatory miRNA (PtamiRNA164e) of one of the transcription factors (PtaNAC1), albeit in an opposite fashion. Consistent with a putative function of PtaHWS in proteasome degradation, treatment with proteasome inhibitor reversed the expression changes in the transgenic plants. The insights from this study will allow genetic modifications of root architecture for more efficient and dynamic nitrogen foraging in biofuel crops like poplar.
DOI: 10.1111/tpj.13002
PubMed: 26315649
Affiliations:
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Yordanov</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biological Sciences, Eastern Illinois University, Charleston, IL, 61920, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Eastern Illinois University, Charleston, IL, 61920</wicri:regionArea><wicri:noRegion>61920</wicri:noRegion></affiliation></author><author><name sortKey="Georgieva, Tatyana" sort="Georgieva, Tatyana" uniqKey="Georgieva T" first="Tatyana" last="Georgieva">Tatyana Georgieva</name><affiliation wicri:level="1"><nlm:affiliation>Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931</wicri:regionArea><wicri:noRegion>49931</wicri:noRegion></affiliation></author><author><name sortKey="Kumari, Sapna" sort="Kumari, Sapna" uniqKey="Kumari S" first="Sapna" last="Kumari">Sapna Kumari</name><affiliation wicri:level="1"><nlm:affiliation>Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931</wicri:regionArea><wicri:noRegion>49931</wicri:noRegion></affiliation></author><author><name sortKey="Wei, Hairong" sort="Wei, Hairong" uniqKey="Wei H" first="Hairong" last="Wei">Hairong Wei</name><affiliation wicri:level="1"><nlm:affiliation>Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931</wicri:regionArea><wicri:noRegion>49931</wicri:noRegion></affiliation></author><author><name sortKey="Busov, Victor" sort="Busov, Victor" uniqKey="Busov V" first="Victor" last="Busov">Victor Busov</name><affiliation wicri:level="1"><nlm:affiliation>Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931</wicri:regionArea><wicri:noRegion>49931</wicri:noRegion></affiliation></author></analytic><series><title level="j">The Plant journal : for cell and molecular biology</title><idno type="eISSN">1365-313X</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Gene Expression Regulation, Plant (MeSH)</term><term>Nitrogen (metabolism)</term><term>Plant Roots (metabolism)</term><term>Populus (metabolism)</term><term>Systems Biology (methods)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Azote (métabolisme)</term><term>Biologie des systèmes (méthodes)</term><term>Populus (métabolisme)</term><term>Racines de plante (métabolisme)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Nitrogen</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Plant Roots</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Systems Biology</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Azote</term><term>Populus</term><term>Racines de plante</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Biologie des systèmes</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Regulation, Plant</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Régulation de l'expression des gènes végétaux</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">In Populus, low nitrogen (LN) elicits rapid and vigorous lateral root (LR) proliferation, which is closely mirrored by corresponding transcriptomic changes. Using transcriptomic data, we built a genetic network encompassing a large proportion of the differentially regulated transcriptome. The network is organized in a hierarchical fashion, centered on 11 genes. Transgenic manipulations of only three of the 11 genes had a strong impact on root development under LN. These three genes encoded an F-box protein similar to Hawaiian Skirt (PtaHWS) and two transcription factors (PtaRAP2.11 and PtaNAC1). Up- and downregulation of the three genes caused increased and decreased root proliferation under LN conditions, respectively. The transgenic manipulations had a strong positive effect on growth under greenhouse conditions including increased shoot and root biomass. The three genes appeared to encompass a putative yet-unknown mechanism that underlies root development under LN. Specifically, the genes are predominantly expressed in roots and have a similar temporal response to LN. More importantly, transgenic manipulation for each of the three genes had a highly significant impact on the expression of the other two. The transgenic manipulations appear to also affect the expression of the regulatory miRNA (PtamiRNA164e) of one of the transcription factors (PtaNAC1), albeit in an opposite fashion. Consistent with a putative function of PtaHWS in proteasome degradation, treatment with proteasome inhibitor reversed the expression changes in the transgenic plants. The insights from this study will allow genetic modifications of root architecture for more efficient and dynamic nitrogen foraging in biofuel crops like poplar. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26315649</PMID><DateCompleted><Year>2016</Year><Month>07</Month><Day>26</Day></DateCompleted><DateRevised><Year>2015</Year><Month>10</Month><Day>08</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1365-313X</ISSN><JournalIssue CitedMedium="Internet"><Volume>84</Volume><Issue>2</Issue><PubDate><Year>2015</Year><Month>Oct</Month></PubDate></JournalIssue><Title>The Plant journal : for cell and molecular biology</Title><ISOAbbreviation>Plant J</ISOAbbreviation></Journal><ArticleTitle>A systems biology approach identifies new regulators of poplar root development under low nitrogen.</ArticleTitle><Pagination><MedlinePgn>335-46</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/tpj.13002</ELocationID><Abstract><AbstractText>In Populus, low nitrogen (LN) elicits rapid and vigorous lateral root (LR) proliferation, which is closely mirrored by corresponding transcriptomic changes. Using transcriptomic data, we built a genetic network encompassing a large proportion of the differentially regulated transcriptome. The network is organized in a hierarchical fashion, centered on 11 genes. Transgenic manipulations of only three of the 11 genes had a strong impact on root development under LN. These three genes encoded an F-box protein similar to Hawaiian Skirt (PtaHWS) and two transcription factors (PtaRAP2.11 and PtaNAC1). Up- and downregulation of the three genes caused increased and decreased root proliferation under LN conditions, respectively. The transgenic manipulations had a strong positive effect on growth under greenhouse conditions including increased shoot and root biomass. The three genes appeared to encompass a putative yet-unknown mechanism that underlies root development under LN. Specifically, the genes are predominantly expressed in roots and have a similar temporal response to LN. More importantly, transgenic manipulation for each of the three genes had a highly significant impact on the expression of the other two. The transgenic manipulations appear to also affect the expression of the regulatory miRNA (PtamiRNA164e) of one of the transcription factors (PtaNAC1), albeit in an opposite fashion. Consistent with a putative function of PtaHWS in proteasome degradation, treatment with proteasome inhibitor reversed the expression changes in the transgenic plants. The insights from this study will allow genetic modifications of root architecture for more efficient and dynamic nitrogen foraging in biofuel crops like poplar. </AbstractText><CopyrightInformation>© 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Dash</LastName><ForeName>Madhumita</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yordanov</LastName><ForeName>Yordan S</ForeName><Initials>YS</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, Eastern Illinois University, Charleston, IL, 61920, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Georgieva</LastName><ForeName>Tatyana</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kumari</LastName><ForeName>Sapna</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wei</LastName><ForeName>Hairong</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Busov</LastName><ForeName>Victor</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Plant J</MedlineTA><NlmUniqueID>9207397</NlmUniqueID><ISSNLinking>0960-7412</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>N762921K75</RegistryNumber><NameOfSubstance UI="D009584">Nitrogen</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009584" MajorTopicYN="N">Nitrogen</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018517" MajorTopicYN="N">Plant Roots</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D049490" MajorTopicYN="N">Systems Biology</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Populus tremula × P. alba</Keyword><Keyword MajorTopicYN="N">lateral root growth</Keyword><Keyword MajorTopicYN="N">microRNA</Keyword><Keyword MajorTopicYN="N">nitrogen stress</Keyword><Keyword MajorTopicYN="N">proteasome</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>06</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2015</Year><Month>08</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>08</Month><Day>20</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>8</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>9</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>7</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26315649</ArticleId><ArticleId IdType="doi">10.1111/tpj.13002</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country></list><tree><country name="États-Unis"><noRegion><name sortKey="Dash, Madhumita" sort="Dash, Madhumita" uniqKey="Dash M" first="Madhumita" last="Dash">Madhumita Dash</name></noRegion><name sortKey="Busov, Victor" sort="Busov, Victor" uniqKey="Busov V" first="Victor" last="Busov">Victor Busov</name><name sortKey="Georgieva, Tatyana" sort="Georgieva, Tatyana" uniqKey="Georgieva T" first="Tatyana" last="Georgieva">Tatyana Georgieva</name><name sortKey="Kumari, Sapna" sort="Kumari, Sapna" uniqKey="Kumari S" first="Sapna" last="Kumari">Sapna Kumari</name><name sortKey="Wei, Hairong" sort="Wei, Hairong" uniqKey="Wei H" first="Hairong" last="Wei">Hairong Wei</name><name sortKey="Yordanov, Yordan S" sort="Yordanov, Yordan S" uniqKey="Yordanov Y" first="Yordan S" last="Yordanov">Yordan S. 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