A network perspective on nitrogen metabolism from model to crop plants using integrated 'omics' approaches.
Identifieur interne : 002394 ( Main/Exploration ); précédent : 002393; suivant : 002395A network perspective on nitrogen metabolism from model to crop plants using integrated 'omics' approaches.
Auteurs : Atsushi Fukushima [Japon] ; Miyako Kusano [Japon]Source :
- Journal of experimental botany [ 1460-2431 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
- métabolisme : Acides aminés, Azote, Carbone, Plantes, Produits agricoles.
- Analyse de profil d'expression de gènes, Métabolomique.
English descriptors
- KwdEn :
- MESH :
- chemical , metabolism : Amino Acids, Carbon, Nitrogen.
- metabolism : Crops, Agricultural, Plants.
- Gene Expression Profiling, Metabolomics.
Abstract
Nitrogen (N), as an essential element in amino acids, nucleotides, and proteins, is a key factor in plant growth and development. Omics approaches such as metabolomics and transcriptomics have become a promising way to inspect complex network interactions in N metabolism and can be used for monitoring the uptake and regulation, translocation, and remobilization of N. In this review, the authors highlight recent progress in omics approaches, including transcript profiling using microarrays and deep sequencing, and show recent technical developments in metabolite profiling for N studies. Further, network analysis studies including network inference methods with correlations, information-theoretic measures, and a network concept to examine gene expression clusters in relation to N regulatory systems in plants are introduced, and integrating network inference methods and integrated networks using multiple omics data are discussed. Finally, this review summarizes recent omics application examples using metabolite and/or transcript profiling analysis to elucidate the regulation of N metabolism and signalling and the coordination of N and carbon metabolism in model plants (Arabidopsis and rice), crops (tomato, maize, and legumes), and trees (Populus).
DOI: 10.1093/jxb/eru322
PubMed: 25129130
Affiliations:
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Kantō</region></placeName></affiliation></author><author><name sortKey="Kusano, Miyako" sort="Kusano, Miyako" uniqKey="Kusano M" first="Miyako" last="Kusano">Miyako Kusano</name><affiliation wicri:level="1"><nlm:affiliation>RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehirocho, Tsurumi, Yokohama 230-0045, Japan Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan miyako.kusano@riken.jp.</nlm:affiliation><country wicri:rule="url">Japon</country><wicri:regionArea>RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehirocho, Tsurumi, Yokohama 230-0045, Japan Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan Japan Science and Technology Agency (JST), Precursory 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uniqKey="Fukushima A" first="Atsushi" last="Fukushima">Atsushi Fukushima</name><affiliation wicri:level="1"><nlm:affiliation>RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehirocho, Tsurumi, Yokohama 230-0045, Japan JST, National Bioscience Database Center (NBDC), 5-3, Yonbancho, Chiyoda, Tokyo 102-0081, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehirocho, Tsurumi, Yokohama 230-0045, Japan JST, National Bioscience Database Center (NBDC), 5-3, Yonbancho, Chiyoda, Tokyo 102-0081</wicri:regionArea><placeName><settlement type="city">Tokyo</settlement><region type="région">Région de Kantō</region></placeName></affiliation></author><author><name sortKey="Kusano, Miyako" sort="Kusano, Miyako" uniqKey="Kusano M" first="Miyako" last="Kusano">Miyako Kusano</name><affiliation wicri:level="1"><nlm:affiliation>RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehirocho, Tsurumi, Yokohama 230-0045, Japan Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan miyako.kusano@riken.jp.</nlm:affiliation><country wicri:rule="url">Japon</country><wicri:regionArea>RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehirocho, Tsurumi, Yokohama 230-0045, Japan Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012</wicri:regionArea><wicri:noRegion>Saitama 332-0012</wicri:noRegion></affiliation></author></analytic><series><title level="j">Journal of experimental botany</title><idno type="eISSN">1460-2431</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acids (metabolism)</term><term>Carbon (metabolism)</term><term>Crops, Agricultural (metabolism)</term><term>Gene Expression Profiling (MeSH)</term><term>Metabolomics (MeSH)</term><term>Nitrogen (metabolism)</term><term>Plants (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Acides aminés (métabolisme)</term><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Azote (métabolisme)</term><term>Carbone (métabolisme)</term><term>Métabolomique (MeSH)</term><term>Plantes (métabolisme)</term><term>Produits agricoles (métabolisme)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Amino Acids</term><term>Carbon</term><term>Nitrogen</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Crops, Agricultural</term><term>Plants</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Acides aminés</term><term>Azote</term><term>Carbone</term><term>Plantes</term><term>Produits agricoles</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Profiling</term><term>Metabolomics</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Métabolomique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Nitrogen (N), as an essential element in amino acids, nucleotides, and proteins, is a key factor in plant growth and development. Omics approaches such as metabolomics and transcriptomics have become a promising way to inspect complex network interactions in N metabolism and can be used for monitoring the uptake and regulation, translocation, and remobilization of N. In this review, the authors highlight recent progress in omics approaches, including transcript profiling using microarrays and deep sequencing, and show recent technical developments in metabolite profiling for N studies. Further, network analysis studies including network inference methods with correlations, information-theoretic measures, and a network concept to examine gene expression clusters in relation to N regulatory systems in plants are introduced, and integrating network inference methods and integrated networks using multiple omics data are discussed. Finally, this review summarizes recent omics application examples using metabolite and/or transcript profiling analysis to elucidate the regulation of N metabolism and signalling and the coordination of N and carbon metabolism in model plants (Arabidopsis and rice), crops (tomato, maize, and legumes), and trees (Populus). </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25129130</PMID><DateCompleted><Year>2015</Year><Month>06</Month><Day>08</Day></DateCompleted><DateRevised><Year>2014</Year><Month>09</Month><Day>29</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1460-2431</ISSN><JournalIssue CitedMedium="Internet"><Volume>65</Volume><Issue>19</Issue><PubDate><Year>2014</Year><Month>Oct</Month></PubDate></JournalIssue><Title>Journal of experimental botany</Title><ISOAbbreviation>J Exp Bot</ISOAbbreviation></Journal><ArticleTitle>A network perspective on nitrogen metabolism from model to crop plants using integrated 'omics' approaches.</ArticleTitle><Pagination><MedlinePgn>5619-30</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/jxb/eru322</ELocationID><Abstract><AbstractText>Nitrogen (N), as an essential element in amino acids, nucleotides, and proteins, is a key factor in plant growth and development. Omics approaches such as metabolomics and transcriptomics have become a promising way to inspect complex network interactions in N metabolism and can be used for monitoring the uptake and regulation, translocation, and remobilization of N. In this review, the authors highlight recent progress in omics approaches, including transcript profiling using microarrays and deep sequencing, and show recent technical developments in metabolite profiling for N studies. Further, network analysis studies including network inference methods with correlations, information-theoretic measures, and a network concept to examine gene expression clusters in relation to N regulatory systems in plants are introduced, and integrating network inference methods and integrated networks using multiple omics data are discussed. Finally, this review summarizes recent omics application examples using metabolite and/or transcript profiling analysis to elucidate the regulation of N metabolism and signalling and the coordination of N and carbon metabolism in model plants (Arabidopsis and rice), crops (tomato, maize, and legumes), and trees (Populus). </AbstractText><CopyrightInformation>© The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Fukushima</LastName><ForeName>Atsushi</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehirocho, Tsurumi, Yokohama 230-0045, Japan JST, National Bioscience Database Center (NBDC), 5-3, Yonbancho, Chiyoda, Tokyo 102-0081, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kusano</LastName><ForeName>Miyako</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehirocho, Tsurumi, Yokohama 230-0045, Japan Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan miyako.kusano@riken.jp.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D016454">Review</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>08</Month><Day>16</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>J Exp Bot</MedlineTA><NlmUniqueID>9882906</NlmUniqueID><ISSNLinking>0022-0957</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D000596">Amino Acids</NameOfSubstance></Chemical><Chemical><RegistryNumber>7440-44-0</RegistryNumber><NameOfSubstance UI="D002244">Carbon</NameOfSubstance></Chemical><Chemical><RegistryNumber>N762921K75</RegistryNumber><NameOfSubstance UI="D009584">Nitrogen</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000596" MajorTopicYN="N">Amino Acids</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002244" MajorTopicYN="N">Carbon</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018556" MajorTopicYN="N">Crops, Agricultural</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="Y">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055432" MajorTopicYN="Y">Metabolomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009584" MajorTopicYN="N">Nitrogen</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010944" MajorTopicYN="N">Plants</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Central metabolism</Keyword><Keyword MajorTopicYN="N">RNA-seq</Keyword><Keyword MajorTopicYN="N">deep sequencing</Keyword><Keyword MajorTopicYN="N">metabolite profiling</Keyword><Keyword MajorTopicYN="N">nitrogen metabolism</Keyword><Keyword MajorTopicYN="N">transcript profiling.</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>8</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>8</Month><Day>19</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>6</Month><Day>9</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">25129130</ArticleId><ArticleId IdType="pii">eru322</ArticleId><ArticleId IdType="doi">10.1093/jxb/eru322</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Japon</li></country><region><li>Région de Kantō</li></region><settlement><li>Tokyo</li></settlement></list><tree><country name="Japon"><region name="Région de Kantō"><name sortKey="Fukushima, Atsushi" sort="Fukushima, Atsushi" uniqKey="Fukushima A" first="Atsushi" last="Fukushima">Atsushi Fukushima</name></region><name sortKey="Kusano, Miyako" sort="Kusano, Miyako" uniqKey="Kusano M" first="Miyako" last="Kusano">Miyako Kusano</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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