Genome-wide characterization of Phytophthora infestans metabolism: a systems biology approach.
Identifieur interne : 000760 ( Main/Exploration ); précédent : 000759; suivant : 000761Genome-wide characterization of Phytophthora infestans metabolism: a systems biology approach.
Auteurs : Sander Y A. Rodenburg [Pays-Bas] ; Michael F. Seidl [Pays-Bas] ; Dick De Ridder [Pays-Bas] ; Francine Govers [Pays-Bas]Source :
- Molecular plant pathology [ 1364-3703 ] ; 2018.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Phytophthora infestans.
- métabolisme : Phytophthora infestans.
- méthodes : Biologie des systèmes.
- Analyse de profil d'expression de gènes.
English descriptors
- KwdEn :
- MESH :
- genetics : Phytophthora infestans.
- metabolism : Phytophthora infestans.
- methods : Systems Biology.
- Gene Expression Profiling.
Abstract
Genome-scale metabolic models (GEMs) provide a functional view of the complex network of biochemical reactions in the living cell. Initially mainly applied to reconstruct the metabolism of model organisms, the availability of increasingly sophisticated reconstruction methods and more extensive biochemical databases now make it possible to reconstruct GEMs for less well-characterized organisms, and have the potential to unravel the metabolism in pathogen-host systems. Here, we present a GEM for the oomycete plant pathogen Phytophthora infestans as a first step towards an integrative model with its host. We predict the biochemical reactions in different cellular compartments and investigate the gene-protein-reaction associations in this model to obtain an impression of the biochemical capabilities of P. infestans. Furthermore, we generate life stage-specific models to place the transcriptomic changes of the genes encoding metabolic enzymes into a functional context. In sporangia and zoospores, there is an overall down-regulation, most strikingly reflected in the fatty acid biosynthesis pathway. To investigate the robustness of the GEM, we simulate gene deletions to predict which enzymes are essential for in vitro growth. This model is an essential first step towards an understanding of P. infestans and its interactions with plants as a system, which will help to formulate new hypotheses on infection mechanisms and disease prevention.
DOI: 10.1111/mpp.12623
PubMed: 28990716
PubMed Central: PMC6638193
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Initially mainly applied to reconstruct the metabolism of model organisms, the availability of increasingly sophisticated reconstruction methods and more extensive biochemical databases now make it possible to reconstruct GEMs for less well-characterized organisms, and have the potential to unravel the metabolism in pathogen-host systems. Here, we present a GEM for the oomycete plant pathogen Phytophthora infestans as a first step towards an integrative model with its host. We predict the biochemical reactions in different cellular compartments and investigate the gene-protein-reaction associations in this model to obtain an impression of the biochemical capabilities of P. infestans. Furthermore, we generate life stage-specific models to place the transcriptomic changes of the genes encoding metabolic enzymes into a functional context. In sporangia and zoospores, there is an overall down-regulation, most strikingly reflected in the fatty acid biosynthesis pathway. To investigate the robustness of the GEM, we simulate gene deletions to predict which enzymes are essential for in vitro growth. This model is an essential first step towards an understanding of P. infestans and its interactions with plants as a system, which will help to formulate new hypotheses on infection mechanisms and disease prevention.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28990716</PMID><DateCompleted><Year>2019</Year><Month>03</Month><Day>04</Day></DateCompleted><DateRevised><Year>2020</Year><Month>02</Month><Day>25</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1364-3703</ISSN><JournalIssue CitedMedium="Internet"><Volume>19</Volume><Issue>6</Issue><PubDate><Year>2018</Year><Month>06</Month></PubDate></JournalIssue><Title>Molecular plant pathology</Title><ISOAbbreviation>Mol Plant Pathol</ISOAbbreviation></Journal><ArticleTitle>Genome-wide characterization of Phytophthora infestans metabolism: a systems biology approach.</ArticleTitle><Pagination><MedlinePgn>1403-1413</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/mpp.12623</ELocationID><Abstract><AbstractText>Genome-scale metabolic models (GEMs) provide a functional view of the complex network of biochemical reactions in the living cell. Initially mainly applied to reconstruct the metabolism of model organisms, the availability of increasingly sophisticated reconstruction methods and more extensive biochemical databases now make it possible to reconstruct GEMs for less well-characterized organisms, and have the potential to unravel the metabolism in pathogen-host systems. Here, we present a GEM for the oomycete plant pathogen Phytophthora infestans as a first step towards an integrative model with its host. We predict the biochemical reactions in different cellular compartments and investigate the gene-protein-reaction associations in this model to obtain an impression of the biochemical capabilities of P. infestans. Furthermore, we generate life stage-specific models to place the transcriptomic changes of the genes encoding metabolic enzymes into a functional context. In sporangia and zoospores, there is an overall down-regulation, most strikingly reflected in the fatty acid biosynthesis pathway. To investigate the robustness of the GEM, we simulate gene deletions to predict which enzymes are essential for in vitro growth. This model is an essential first step towards an understanding of P. infestans and its interactions with plants as a system, which will help to formulate new hypotheses on infection mechanisms and disease prevention.</AbstractText><CopyrightInformation>© 2017 THE AUTHORS. MOLECULAR PLANT PATHOLOGY PUBLISHED BY BRITISH SOCIETY FOR PLANT PATHOLOGY AND JOHN WILEY & SONS LTD.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Rodenburg</LastName><ForeName>Sander Y A</ForeName><Initials>SYA</Initials><AffiliationInfo><Affiliation>Laboratory of Phytopathology, Wageningen University, Wageningen 6708 PB, the Netherlands.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Bioinformatics Group, Wageningen University, Wageningen 6708 PB, the Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Seidl</LastName><ForeName>Michael F</ForeName><Initials>MF</Initials><AffiliationInfo><Affiliation>Laboratory of Phytopathology, Wageningen University, Wageningen 6708 PB, the Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>de Ridder</LastName><ForeName>Dick</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Bioinformatics Group, Wageningen University, Wageningen 6708 PB, the Netherlands.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Govers</LastName><ForeName>Francine</ForeName><Initials>F</Initials><Identifier Source="ORCID">0000-0001-5311-929X</Identifier><AffiliationInfo><Affiliation>Laboratory of Phytopathology, Wageningen University, Wageningen 6708 PB, the Netherlands.</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></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>01</Month><Day>30</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mol Plant Pathol</MedlineTA><NlmUniqueID>100954969</NlmUniqueID><ISSNLinking>1364-3703</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055750" MajorTopicYN="N">Phytophthora infestans</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><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="Y">Phytophthora infestans</Keyword><Keyword MajorTopicYN="Y">metabolic model</Keyword><Keyword MajorTopicYN="Y">metabolism</Keyword><Keyword MajorTopicYN="Y">oomycete</Keyword><Keyword MajorTopicYN="Y">systems biology</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>07</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2017</Year><Month>09</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>10</Month><Day>04</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>10</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>3</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>10</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">28990716</ArticleId><ArticleId IdType="doi">10.1111/mpp.12623</ArticleId><ArticleId IdType="pmc">PMC6638193</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Annu Rev Genomics Hum Genet. 2001;2:343-72</Citation><ArticleIdList><ArticleId 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IdType="pubmed">9918945</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>Pays-Bas</li></country><region><li>Gueldre (province)</li></region><settlement><li>Wageningue</li></settlement><orgName><li>Université de Wageningue</li></orgName></list><tree><country name="Pays-Bas"><region name="Gueldre (province)"><name sortKey="Rodenburg, Sander Y A" sort="Rodenburg, Sander Y A" uniqKey="Rodenburg S" first="Sander Y A" last="Rodenburg">Sander Y A. Rodenburg</name></region><name sortKey="De Ridder, Dick" sort="De Ridder, Dick" uniqKey="De Ridder D" first="Dick" last="De Ridder">Dick De Ridder</name><name sortKey="Govers, Francine" sort="Govers, Francine" uniqKey="Govers F" first="Francine" last="Govers">Francine Govers</name><name sortKey="Rodenburg, Sander Y A" sort="Rodenburg, Sander Y A" uniqKey="Rodenburg S" first="Sander Y A" last="Rodenburg">Sander Y A. Rodenburg</name><name sortKey="Seidl, Michael F" sort="Seidl, Michael F" uniqKey="Seidl M" first="Michael F" last="Seidl">Michael F. Seidl</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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