Transcriptomic and proteomic analysis reveals wall-associated and glucan-degrading proteins with potential roles in Phytophthora infestans sexual spore development.
Identifieur interne : 000629 ( Main/Exploration ); précédent : 000628; suivant : 000630Transcriptomic and proteomic analysis reveals wall-associated and glucan-degrading proteins with potential roles in Phytophthora infestans sexual spore development.
Auteurs : Xiaofan Niu [États-Unis] ; Audrey M V. Ah-Fong [États-Unis] ; Lilianna A. Lopez [États-Unis] ; Howard S. Judelson [États-Unis]Source :
- PloS one [ 1932-6203 ] ; 2018.
Descripteurs français
- KwdFr :
- Analyse de profil d'expression de gènes (MeSH), Glucanes (métabolisme), Glycosidases (génétique), Glycosidases (métabolisme), Gènes fongiques du type conjugant (génétique), Métabolisme glucidique (génétique), Paroi cellulaire (génétique), Paroi cellulaire (métabolisme), Phytophthora infestans (physiologie), Protéome (analyse), Protéomique (MeSH), Reproduction (MeSH), Régulation de l'expression des gènes au cours du développement (MeSH), Régulation de l'expression des gènes fongiques (MeSH), Spores (croissance et développement), Spores (génétique), Spores (métabolisme), Transcriptome (MeSH).
- MESH :
- analyse : Protéome.
- croissance et développement : Spores.
- génétique : Glycosidases, Gènes fongiques du type conjugant, Métabolisme glucidique, Paroi cellulaire, Spores.
- métabolisme : Glucanes, Glycosidases, Paroi cellulaire, Spores.
- physiologie : Phytophthora infestans.
- Analyse de profil d'expression de gènes, Protéomique, Reproduction, Régulation de l'expression des gènes au cours du développement, Régulation de l'expression des gènes fongiques, Transcriptome.
English descriptors
- KwdEn :
- Carbohydrate Metabolism (genetics), Cell Wall (genetics), Cell Wall (metabolism), Gene Expression Profiling (MeSH), Gene Expression Regulation, Developmental (MeSH), Gene Expression Regulation, Fungal (MeSH), Genes, Mating Type, Fungal (genetics), Glucans (metabolism), Glycoside Hydrolases (genetics), Glycoside Hydrolases (metabolism), Phytophthora infestans (physiology), Proteome (analysis), Proteomics (MeSH), Reproduction (MeSH), Spores (genetics), Spores (growth & development), Spores (metabolism), Transcriptome (MeSH).
- MESH :
- chemical , analysis : Proteome.
- chemical , genetics : Glycoside Hydrolases.
- chemical , metabolism : Glucans, Glycoside Hydrolases.
- genetics : Carbohydrate Metabolism, Cell Wall, Genes, Mating Type, Fungal, Spores.
- growth & development : Spores.
- metabolism : Cell Wall, Spores.
- physiology : Phytophthora infestans.
- Gene Expression Profiling, Gene Expression Regulation, Developmental, Gene Expression Regulation, Fungal, Proteomics, Reproduction, Transcriptome.
Abstract
Sexual reproduction remains an understudied feature of oomycete biology. To expand our knowledge of this process, we used RNA-seq and quantitative proteomics to examine matings in Phytophthora infestans. Exhibiting significant changes in mRNA abundance in three matings between different A1 and A2 strains compared to nonmating controls were 1170 genes, most being mating-induced. Rising by >10-fold in at least one cross were 455 genes, and 182 in all three crosses. Most genes had elevated expression in a self-fertile strain. Many mating-induced genes were associated with cell wall biosynthesis, which may relate to forming the thick-walled sexual spore (oospore). Several gene families were induced during mating including one encoding histidine, serine, and tyrosine-rich putative wall proteins, and another encoding prolyl hydroxylases which may strengthen the extracellular matrix. The sizes of these families vary >10-fold between Phytophthora species and one exhibits concerted evolution, highlighting two features of genome dynamics within the genus. Proteomic analyses of mature oospores and nonmating hyphae using isobaric tags for quantification identified 835 shared proteins, with 5% showing >2-fold changes in abundance between the tissues. Enriched in oospores were β-glucanases potentially involved in digesting the oospore wall during germination. Despite being dormant, oospores contained a mostly normal complement of proteins required for core cellular functions. The RNA-seq data generated here and in prior studies were used to identify new housekeeping controls for gene expression studies that are more stable than existing normalization standards. We also observed >2-fold variation in the fraction of polyA+ RNA between life stages, which should be considered when quantifying transcripts and may also be relevant to understanding translational control during development.
DOI: 10.1371/journal.pone.0198186
PubMed: 29897992
PubMed Central: PMC5999078
Affiliations:
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To expand our knowledge of this process, we used RNA-seq and quantitative proteomics to examine matings in Phytophthora infestans. Exhibiting significant changes in mRNA abundance in three matings between different A1 and A2 strains compared to nonmating controls were 1170 genes, most being mating-induced. Rising by >10-fold in at least one cross were 455 genes, and 182 in all three crosses. Most genes had elevated expression in a self-fertile strain. Many mating-induced genes were associated with cell wall biosynthesis, which may relate to forming the thick-walled sexual spore (oospore). Several gene families were induced during mating including one encoding histidine, serine, and tyrosine-rich putative wall proteins, and another encoding prolyl hydroxylases which may strengthen the extracellular matrix. The sizes of these families vary >10-fold between Phytophthora species and one exhibits concerted evolution, highlighting two features of genome dynamics within the genus. Proteomic analyses of mature oospores and nonmating hyphae using isobaric tags for quantification identified 835 shared proteins, with 5% showing >2-fold changes in abundance between the tissues. Enriched in oospores were β-glucanases potentially involved in digesting the oospore wall during germination. Despite being dormant, oospores contained a mostly normal complement of proteins required for core cellular functions. The RNA-seq data generated here and in prior studies were used to identify new housekeeping controls for gene expression studies that are more stable than existing normalization standards. We also observed >2-fold variation in the fraction of polyA+ RNA between life stages, which should be considered when quantifying transcripts and may also be relevant to understanding translational control during development.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29897992</PMID><DateCompleted><Year>2019</Year><Month>01</Month><Day>11</Day></DateCompleted><DateRevised><Year>2019</Year><Month>01</Month><Day>11</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>13</Volume><Issue>6</Issue><PubDate><Year>2018</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>Transcriptomic and proteomic analysis reveals wall-associated and glucan-degrading proteins with potential roles in Phytophthora infestans sexual spore development.</ArticleTitle><Pagination><MedlinePgn>e0198186</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0198186</ELocationID><Abstract><AbstractText>Sexual reproduction remains an understudied feature of oomycete biology. To expand our knowledge of this process, we used RNA-seq and quantitative proteomics to examine matings in Phytophthora infestans. Exhibiting significant changes in mRNA abundance in three matings between different A1 and A2 strains compared to nonmating controls were 1170 genes, most being mating-induced. Rising by >10-fold in at least one cross were 455 genes, and 182 in all three crosses. Most genes had elevated expression in a self-fertile strain. Many mating-induced genes were associated with cell wall biosynthesis, which may relate to forming the thick-walled sexual spore (oospore). Several gene families were induced during mating including one encoding histidine, serine, and tyrosine-rich putative wall proteins, and another encoding prolyl hydroxylases which may strengthen the extracellular matrix. The sizes of these families vary >10-fold between Phytophthora species and one exhibits concerted evolution, highlighting two features of genome dynamics within the genus. Proteomic analyses of mature oospores and nonmating hyphae using isobaric tags for quantification identified 835 shared proteins, with 5% showing >2-fold changes in abundance between the tissues. Enriched in oospores were β-glucanases potentially involved in digesting the oospore wall during germination. Despite being dormant, oospores contained a mostly normal complement of proteins required for core cellular functions. The RNA-seq data generated here and in prior studies were used to identify new housekeeping controls for gene expression studies that are more stable than existing normalization standards. We also observed >2-fold variation in the fraction of polyA+ RNA between life stages, which should be considered when quantifying transcripts and may also be relevant to understanding translational control during development.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Niu</LastName><ForeName>Xiaofan</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Department of Microbiology and Plant Pathology, University of California, Riverside, CA, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ah-Fong</LastName><ForeName>Audrey M V</ForeName><Initials>AMV</Initials><AffiliationInfo><Affiliation>Department of Microbiology and Plant Pathology, University of California, Riverside, CA, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lopez</LastName><ForeName>Lilianna A</ForeName><Initials>LA</Initials><AffiliationInfo><Affiliation>Department of Microbiology and Plant Pathology, University of California, Riverside, CA, United States of America.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Judelson</LastName><ForeName>Howard S</ForeName><Initials>HS</Initials><Identifier Source="ORCID">0000-0001-7865-6235</Identifier><AffiliationInfo><Affiliation>Department of Microbiology and Plant Pathology, University of California, Riverside, CA, United States of America.</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><ArticleDate DateType="Electronic"><Year>2018</Year><Month>06</Month><Day>13</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005936">Glucans</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D020543">Proteome</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.2.1.-</RegistryNumber><NameOfSubstance UI="D006026">Glycoside Hydrolases</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D050260" MajorTopicYN="N">Carbohydrate Metabolism</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002473" MajorTopicYN="N">Cell Wall</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018507" MajorTopicYN="N">Gene Expression Regulation, Developmental</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015966" MajorTopicYN="N">Gene Expression Regulation, Fungal</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D049770" MajorTopicYN="N">Genes, Mating Type, Fungal</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005936" MajorTopicYN="N">Glucans</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006026" MajorTopicYN="N">Glycoside Hydrolases</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D055750" MajorTopicYN="N">Phytophthora infestans</DescriptorName><QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020543" MajorTopicYN="N">Proteome</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="N">analysis</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D040901" MajorTopicYN="N">Proteomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012098" MajorTopicYN="N">Reproduction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013170" MajorTopicYN="N">Spores</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="Y">growth & development</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059467" MajorTopicYN="N">Transcriptome</DescriptorName></MeshHeading></MeshHeadingList><CoiStatement>The authors have declared that no competing interests exist.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>12</Month><Day>29</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>05</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2018</Year><Month>6</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2018</Year><Month>6</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>1</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">29897992</ArticleId><ArticleId IdType="doi">10.1371/journal.pone.0198186</ArticleId><ArticleId IdType="pii">PONE-D-17-45268</ArticleId><ArticleId IdType="pmc">PMC5999078</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>RNA 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Ah-Fong</name><name sortKey="Judelson, Howard S" sort="Judelson, Howard S" uniqKey="Judelson H" first="Howard S" last="Judelson">Howard S. Judelson</name><name sortKey="Lopez, Lilianna A" sort="Lopez, Lilianna A" uniqKey="Lopez L" first="Lilianna A" last="Lopez">Lilianna A. Lopez</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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