Phytophthora infestans specific phosphorylation patterns and new putative control targets.
Identifieur interne : 000B55 ( Main/Exploration ); précédent : 000B54; suivant : 000B56Phytophthora infestans specific phosphorylation patterns and new putative control targets.
Auteurs : Itziar Frades [Suède] ; Erik Andreasson [Suède]Source :
- Fungal biology [ 1878-6146 ] ; 2016.
Descripteurs français
- KwdFr :
- MESH :
- analyse : Phosphoprotéines, Protéome.
- composition chimique : Phytophthora infestans.
- Maturation post-traductionnelle des protéines, Phosphorylation, Régulation de l'expression des gènes, Réseaux de régulation génique.
English descriptors
- KwdEn :
- MESH :
- chemical , analysis : Phosphoproteins, Proteome.
- chemistry : Phytophthora infestans.
- Gene Expression Regulation, Gene Regulatory Networks, Phosphorylation, Protein Processing, Post-Translational.
Abstract
In this study we applied biomathematical searches of gene regulatory mechanisms to learn more about oomycete biology and to identify new putative targets for pesticides or biological control against Phytophthora infestans. First, oomycete phylum-specific phosphorylation motifs were found by discriminative n-gram analysis. We found 11.600 P. infestans specific n-grams, mapping 642 phosphoproteins. The most abundant group among these related to phosphatidylinositol metabolism. Due to the large number of possible targets found and our hypothesis that multi-level control is a sign of usefulness as targets for intervention, we identified overlapping targets with a second screen. This was performed to identify proteins dually regulated by small RNA and phosphorylation. We found 164 proteins to be regulated by both sRNA and phosphorylation and the dominating functions where phosphatidylinositol signalling/metabolism, endocytosis, and autophagy. Furthermore we performed a similar regulatory study and discriminative n-gram analysis of proteins with no clear orthologs in other species and proteins that are known to be unique to P. infestans such as the RxLR effectors, Crinkler (CRN) proteins and elicitins. We identified CRN proteins with specific phospho-motifs present in all life stages. PITG_12626, PITG_14042 and PITG_23175 are CRN proteins that have species-specific phosphorylation motifs and are subject to dual regulation.
DOI: 10.1016/j.funbio.2016.01.003
PubMed: 27020162
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Phytophthora infestans specific phosphorylation patterns and new putative control targets.</title><author><name sortKey="Frades, Itziar" sort="Frades, Itziar" uniqKey="Frades I" first="Itziar" last="Frades">Itziar Frades</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, SE-230 53, Sweden. Electronic address: itziar.frades@gmail.com.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, SE-230 53</wicri:regionArea><wicri:noRegion>SE-230 53</wicri:noRegion></affiliation></author><author><name sortKey="Andreasson, Erik" sort="Andreasson, Erik" uniqKey="Andreasson E" first="Erik" last="Andreasson">Erik Andreasson</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, SE-230 53, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, SE-230 53</wicri:regionArea><wicri:noRegion>SE-230 53</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2016">2016</date><idno type="RBID">pubmed:27020162</idno><idno type="pmid">27020162</idno><idno type="doi">10.1016/j.funbio.2016.01.003</idno><idno type="wicri:Area/Main/Corpus">000C36</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000C36</idno><idno type="wicri:Area/Main/Curation">000C36</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000C36</idno><idno type="wicri:Area/Main/Exploration">000C36</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Phytophthora infestans specific phosphorylation patterns and new putative control targets.</title><author><name sortKey="Frades, Itziar" sort="Frades, Itziar" uniqKey="Frades I" first="Itziar" last="Frades">Itziar Frades</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, SE-230 53, Sweden. Electronic address: itziar.frades@gmail.com.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, SE-230 53</wicri:regionArea><wicri:noRegion>SE-230 53</wicri:noRegion></affiliation></author><author><name sortKey="Andreasson, Erik" sort="Andreasson, Erik" uniqKey="Andreasson E" first="Erik" last="Andreasson">Erik Andreasson</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, SE-230 53, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, SE-230 53</wicri:regionArea><wicri:noRegion>SE-230 53</wicri:noRegion></affiliation></author></analytic><series><title level="j">Fungal biology</title><idno type="ISSN">1878-6146</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Gene Expression Regulation (MeSH)</term><term>Gene Regulatory Networks (MeSH)</term><term>Phosphoproteins (analysis)</term><term>Phosphorylation (MeSH)</term><term>Phytophthora infestans (chemistry)</term><term>Protein Processing, Post-Translational (MeSH)</term><term>Proteome (analysis)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Maturation post-traductionnelle des protéines (MeSH)</term><term>Phosphoprotéines (analyse)</term><term>Phosphorylation (MeSH)</term><term>Phytophthora infestans (composition chimique)</term><term>Protéome (analyse)</term><term>Régulation de l'expression des gènes (MeSH)</term><term>Réseaux de régulation génique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>Phosphoproteins</term><term>Proteome</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>Phosphoprotéines</term><term>Protéome</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Phytophthora infestans</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Phytophthora infestans</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Regulation</term><term>Gene Regulatory Networks</term><term>Phosphorylation</term><term>Protein Processing, Post-Translational</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Maturation post-traductionnelle des protéines</term><term>Phosphorylation</term><term>Régulation de l'expression des gènes</term><term>Réseaux de régulation génique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">In this study we applied biomathematical searches of gene regulatory mechanisms to learn more about oomycete biology and to identify new putative targets for pesticides or biological control against Phytophthora infestans. First, oomycete phylum-specific phosphorylation motifs were found by discriminative n-gram analysis. We found 11.600 P. infestans specific n-grams, mapping 642 phosphoproteins. The most abundant group among these related to phosphatidylinositol metabolism. Due to the large number of possible targets found and our hypothesis that multi-level control is a sign of usefulness as targets for intervention, we identified overlapping targets with a second screen. This was performed to identify proteins dually regulated by small RNA and phosphorylation. We found 164 proteins to be regulated by both sRNA and phosphorylation and the dominating functions where phosphatidylinositol signalling/metabolism, endocytosis, and autophagy. Furthermore we performed a similar regulatory study and discriminative n-gram analysis of proteins with no clear orthologs in other species and proteins that are known to be unique to P. infestans such as the RxLR effectors, Crinkler (CRN) proteins and elicitins. We identified CRN proteins with specific phospho-motifs present in all life stages. PITG_12626, PITG_14042 and PITG_23175 are CRN proteins that have species-specific phosphorylation motifs and are subject to dual regulation. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">27020162</PMID><DateCompleted><Year>2016</Year><Month>12</Month><Day>13</Day></DateCompleted><DateRevised><Year>2017</Year><Month>09</Month><Day>01</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">1878-6146</ISSN><JournalIssue CitedMedium="Internet"><Volume>120</Volume><Issue>4</Issue><PubDate><Year>2016</Year><Month>Apr</Month></PubDate></JournalIssue><Title>Fungal biology</Title><ISOAbbreviation>Fungal Biol</ISOAbbreviation></Journal><ArticleTitle>Phytophthora infestans specific phosphorylation patterns and new putative control targets.</ArticleTitle><Pagination><MedlinePgn>631-644</MedlinePgn></Pagination><ELocationID EIdType="pii" ValidYN="Y">S1878-6146(16)00015-5</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.funbio.2016.01.003</ELocationID><Abstract><AbstractText>In this study we applied biomathematical searches of gene regulatory mechanisms to learn more about oomycete biology and to identify new putative targets for pesticides or biological control against Phytophthora infestans. First, oomycete phylum-specific phosphorylation motifs were found by discriminative n-gram analysis. We found 11.600 P. infestans specific n-grams, mapping 642 phosphoproteins. The most abundant group among these related to phosphatidylinositol metabolism. Due to the large number of possible targets found and our hypothesis that multi-level control is a sign of usefulness as targets for intervention, we identified overlapping targets with a second screen. This was performed to identify proteins dually regulated by small RNA and phosphorylation. We found 164 proteins to be regulated by both sRNA and phosphorylation and the dominating functions where phosphatidylinositol signalling/metabolism, endocytosis, and autophagy. Furthermore we performed a similar regulatory study and discriminative n-gram analysis of proteins with no clear orthologs in other species and proteins that are known to be unique to P. infestans such as the RxLR effectors, Crinkler (CRN) proteins and elicitins. We identified CRN proteins with specific phospho-motifs present in all life stages. PITG_12626, PITG_14042 and PITG_23175 are CRN proteins that have species-specific phosphorylation motifs and are subject to dual regulation. </AbstractText><CopyrightInformation>Copyright © 2016 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Frades</LastName><ForeName>Itziar</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, SE-230 53, Sweden. Electronic address: itziar.frades@gmail.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Andreasson</LastName><ForeName>Erik</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, SE-230 53, Sweden.</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>2016</Year><Month>01</Month><Day>18</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Fungal Biol</MedlineTA><NlmUniqueID>101524465</NlmUniqueID></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010750">Phosphoproteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D020543">Proteome</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D005786" MajorTopicYN="N">Gene Expression Regulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D053263" MajorTopicYN="N">Gene Regulatory Networks</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010750" MajorTopicYN="N">Phosphoproteins</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="Y">analysis</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010766" MajorTopicYN="N">Phosphorylation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055750" MajorTopicYN="N">Phytophthora infestans</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011499" MajorTopicYN="Y">Protein Processing, Post-Translational</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020543" MajorTopicYN="N">Proteome</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="Y">analysis</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Crinklers</Keyword><Keyword MajorTopicYN="N">Discriminative n-grams</Keyword><Keyword MajorTopicYN="N">Pesticide targets</Keyword><Keyword MajorTopicYN="N">Phosphoproteomics</Keyword><Keyword MajorTopicYN="N">small RNA</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2015</Year><Month>10</Month><Day>05</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2015</Year><Month>12</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>01</Month><Day>06</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>3</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>3</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>12</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27020162</ArticleId><ArticleId IdType="pii">S1878-6146(16)00015-5</ArticleId><ArticleId IdType="doi">10.1016/j.funbio.2016.01.003</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Suède</li></country></list><tree><country name="Suède"><noRegion><name sortKey="Frades, Itziar" sort="Frades, Itziar" uniqKey="Frades I" first="Itziar" last="Frades">Itziar Frades</name></noRegion><name sortKey="Andreasson, Erik" sort="Andreasson, Erik" uniqKey="Andreasson E" first="Erik" last="Andreasson">Erik Andreasson</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Bois/explor/PhytophthoraV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000B55 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000B55 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Bois
|area= PhytophthoraV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:27020162
|texte= Phytophthora infestans specific phosphorylation patterns and new putative control targets.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:27020162" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a PhytophthoraV1
| This area was generated with Dilib version V0.6.38. |  |