Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans.
Identifieur interne : 001982 ( Main/Exploration ); précédent : 001981; suivant : 001983Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans.
Auteurs : Sylvain Raffaele [Royaume-Uni] ; Joe Win ; Liliana M. Cano ; Sophien KamounSource :
- BMC genomics [ 1471-2164 ] ; 2010.
Descripteurs français
- KwdFr :
- Annotation de séquence moléculaire (MeSH), Antienzymes (pharmacologie), Carbonic anhydrases (composition chimique), Carbonic anhydrases (génétique), Carbonic anhydrases (métabolisme), Données de séquences moléculaires (MeSH), Facteurs de virulence (composition chimique), Facteurs de virulence (génétique), Facteurs de virulence (métabolisme), Gènes (MeSH), Génome (génétique), Phytophthora (effets des médicaments et des substances chimiques), Phytophthora (génétique), Phytophthora infestans (effets des médicaments et des substances chimiques), Phytophthora infestans (enzymologie), Phytophthora infestans (génétique), Phytophthora infestans (pathogénicité), Protéines (composition chimique), Protéines (génétique), Protéines (métabolisme), Régulation de l'expression des gènes (effets des médicaments et des substances chimiques), Serine endopeptidases (composition chimique), Serine endopeptidases (génétique), Serine endopeptidases (métabolisme), Similitude de séquences d'acides nucléiques (MeSH), Structure tertiaire des protéines (MeSH), Séquence conservée (génétique), Séquence d'acides aminés (MeSH), Séquences répétées d'acides aminés (MeSH), Virulence (effets des médicaments et des substances chimiques), Virulence (génétique).
- MESH :
- composition chimique : Carbonic anhydrases, Facteurs de virulence, Protéines, Serine endopeptidases.
- effets des médicaments et des substances chimiques : Phytophthora, Phytophthora infestans, Régulation de l'expression des gènes, Virulence.
- enzymologie : Phytophthora infestans.
- génétique : Carbonic anhydrases, Facteurs de virulence, Génome, Phytophthora, Phytophthora infestans, Protéines, Serine endopeptidases, Séquence conservée, Virulence.
- métabolisme : Carbonic anhydrases, Facteurs de virulence, Protéines, Serine endopeptidases.
- pathogénicité : Phytophthora infestans.
- pharmacologie : Antienzymes.
- Annotation de séquence moléculaire, Données de séquences moléculaires, Gènes, Similitude de séquences d'acides nucléiques, Structure tertiaire des protéines, Séquence d'acides aminés, Séquences répétées d'acides aminés.
English descriptors
- KwdEn :
- Amino Acid Sequence (MeSH), Carbonic Anhydrases (chemistry), Carbonic Anhydrases (genetics), Carbonic Anhydrases (metabolism), Conserved Sequence (genetics), Enzyme Inhibitors (pharmacology), Gene Expression Regulation (drug effects), Genes (MeSH), Genome (genetics), Molecular Sequence Annotation (MeSH), Molecular Sequence Data (MeSH), Phytophthora (drug effects), Phytophthora (genetics), Phytophthora infestans (drug effects), Phytophthora infestans (enzymology), Phytophthora infestans (genetics), Phytophthora infestans (pathogenicity), Protein Structure, Tertiary (MeSH), Proteins (chemistry), Proteins (genetics), Proteins (metabolism), Repetitive Sequences, Amino Acid (MeSH), Sequence Homology, Nucleic Acid (MeSH), Serine Endopeptidases (chemistry), Serine Endopeptidases (genetics), Serine Endopeptidases (metabolism), Virulence (drug effects), Virulence (genetics), Virulence Factors (chemistry), Virulence Factors (genetics), Virulence Factors (metabolism).
- MESH :
- chemical , chemistry : Carbonic Anhydrases, Proteins, Serine Endopeptidases, Virulence Factors.
- chemical , genetics : Carbonic Anhydrases, Proteins, Serine Endopeptidases, Virulence Factors.
- chemical , metabolism : Carbonic Anhydrases, Proteins, Serine Endopeptidases, Virulence Factors.
- drug effects : Gene Expression Regulation, Phytophthora, Phytophthora infestans, Virulence.
- enzymology : Phytophthora infestans.
- genetics : Conserved Sequence, Genome, Phytophthora, Phytophthora infestans, Virulence.
- pathogenicity : Phytophthora infestans.
- chemical , pharmacology : Enzyme Inhibitors.
- Amino Acid Sequence, Genes, Molecular Sequence Annotation, Molecular Sequence Data, Protein Structure, Tertiary, Repetitive Sequences, Amino Acid, Sequence Homology, Nucleic Acid.
Abstract
BACKGROUND
Phytophthora infestans is the most devastating pathogen of potato and a model organism for the oomycetes. It exhibits high evolutionary potential and rapidly adapts to host plants. The P. infestans genome experienced a repeat-driven expansion relative to the genomes of Phytophthora sojae and Phytophthora ramorum and shows a discontinuous distribution of gene density. Effector genes, such as members of the RXLR and Crinkler (CRN) families, localize to expanded, repeat-rich and gene-sparse regions of the genome. This distinct genomic environment is thought to contribute to genome plasticity and host adaptation.
RESULTS
We used in silico approaches to predict and describe the repertoire of P. infestans secreted proteins (the secretome). We defined the "plastic secretome" as a subset of the genome that (i) encodes predicted secreted proteins, (ii) is excluded from genome segments orthologous to the P. sojae and P. ramorum genomes and (iii) is encoded by genes residing in gene sparse regions of P. infestans genome. Although including only ~3% of P. infestans genes, the plastic secretome contains ~62% of known effector genes and shows >2 fold enrichment in genes induced in planta. We highlight 19 plastic secretome genes induced in planta but distinct from previously described effectors. This list includes a trypsin-like serine protease, secreted oxidoreductases, small cysteine-rich proteins and repeat containing proteins that we propose to be novel candidate virulence factors.
CONCLUSIONS
This work revealed a remarkably diverse plastic secretome. It illustrates the value of combining genome architecture with comparative genomics to identify novel candidate virulence factors from pathogen genomes.
DOI: 10.1186/1471-2164-11-637
PubMed: 21080964
PubMed Central: PMC3091767
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Sequence</term><term>Genome</term><term>Phytophthora</term><term>Phytophthora infestans</term><term>Virulence</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Carbonic anhydrases</term><term>Facteurs de virulence</term><term>Génome</term><term>Phytophthora</term><term>Phytophthora infestans</term><term>Protéines</term><term>Serine endopeptidases</term><term>Séquence conservée</term><term>Virulence</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Carbonic anhydrases</term><term>Facteurs de virulence</term><term>Protéines</term><term>Serine endopeptidases</term></keywords><keywords scheme="MESH" qualifier="pathogenicity" xml:lang="en"><term>Phytophthora infestans</term></keywords><keywords scheme="MESH" qualifier="pathogénicité" xml:lang="fr"><term>Phytophthora infestans</term></keywords><keywords scheme="MESH" qualifier="pharmacologie" xml:lang="fr"><term>Antienzymes</term></keywords><keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Enzyme Inhibitors</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Genes</term><term>Molecular Sequence Annotation</term><term>Molecular Sequence Data</term><term>Protein Structure, Tertiary</term><term>Repetitive Sequences, Amino Acid</term><term>Sequence Homology, Nucleic Acid</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Annotation de séquence moléculaire</term><term>Données de séquences moléculaires</term><term>Gènes</term><term>Similitude de séquences d'acides nucléiques</term><term>Structure tertiaire des protéines</term><term>Séquence d'acides aminés</term><term>Séquences répétées d'acides aminés</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Phytophthora infestans is the most devastating pathogen of potato and a model organism for the oomycetes. It exhibits high evolutionary potential and rapidly adapts to host plants. The P. infestans genome experienced a repeat-driven expansion relative to the genomes of Phytophthora sojae and Phytophthora ramorum and shows a discontinuous distribution of gene density. Effector genes, such as members of the RXLR and Crinkler (CRN) families, localize to expanded, repeat-rich and gene-sparse regions of the genome. This distinct genomic environment is thought to contribute to genome plasticity and host adaptation.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We used in silico approaches to predict and describe the repertoire of P. infestans secreted proteins (the secretome). We defined the "plastic secretome" as a subset of the genome that (i) encodes predicted secreted proteins, (ii) is excluded from genome segments orthologous to the P. sojae and P. ramorum genomes and (iii) is encoded by genes residing in gene sparse regions of P. infestans genome. Although including only ~3% of P. infestans genes, the plastic secretome contains ~62% of known effector genes and shows >2 fold enrichment in genes induced in planta. We highlight 19 plastic secretome genes induced in planta but distinct from previously described effectors. This list includes a trypsin-like serine protease, secreted oxidoreductases, small cysteine-rich proteins and repeat containing proteins that we propose to be novel candidate virulence factors.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>This work revealed a remarkably diverse plastic secretome. It illustrates the value of combining genome architecture with comparative genomics to identify novel candidate virulence factors from pathogen genomes.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21080964</PMID><DateCompleted><Year>2011</Year><Month>03</Month><Day>07</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>01</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>11</Volume><PubDate><Year>2010</Year><Month>Nov</Month><Day>16</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans.</ArticleTitle><Pagination><MedlinePgn>637</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2164-11-637</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Phytophthora infestans is the most devastating pathogen of potato and a model organism for the oomycetes. It exhibits high evolutionary potential and rapidly adapts to host plants. The P. infestans genome experienced a repeat-driven expansion relative to the genomes of Phytophthora sojae and Phytophthora ramorum and shows a discontinuous distribution of gene density. Effector genes, such as members of the RXLR and Crinkler (CRN) families, localize to expanded, repeat-rich and gene-sparse regions of the genome. This distinct genomic environment is thought to contribute to genome plasticity and host adaptation.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We used in silico approaches to predict and describe the repertoire of P. infestans secreted proteins (the secretome). We defined the "plastic secretome" as a subset of the genome that (i) encodes predicted secreted proteins, (ii) is excluded from genome segments orthologous to the P. sojae and P. ramorum genomes and (iii) is encoded by genes residing in gene sparse regions of P. infestans genome. Although including only ~3% of P. infestans genes, the plastic secretome contains ~62% of known effector genes and shows >2 fold enrichment in genes induced in planta. We highlight 19 plastic secretome genes induced in planta but distinct from previously described effectors. This list includes a trypsin-like serine protease, secreted oxidoreductases, small cysteine-rich proteins and repeat containing proteins that we propose to be novel candidate virulence factors.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">This work revealed a remarkably diverse plastic secretome. It illustrates the value of combining genome architecture with comparative genomics to identify novel candidate virulence factors from pathogen genomes.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Raffaele</LastName><ForeName>Sylvain</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>The Sainsbury Laboratory, John Innes Centre, Norwich NR4 7UH, UK.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Win</LastName><ForeName>Joe</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Cano</LastName><ForeName>Liliana M</ForeName><Initials>LM</Initials></Author><Author ValidYN="Y"><LastName>Kamoun</LastName><ForeName>Sophien</ForeName><Initials>S</Initials></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>2010</Year><Month>11</Month><Day>16</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004791">Enzyme Inhibitors</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D011506">Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D037521">Virulence Factors</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C114880">trypsin-like serine protease</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.4.21.-</RegistryNumber><NameOfSubstance UI="D012697">Serine Endopeptidases</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 4.2.1.1</RegistryNumber><NameOfSubstance UI="D002256">Carbonic Anhydrases</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002256" MajorTopicYN="N">Carbonic Anhydrases</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017124" MajorTopicYN="N">Conserved Sequence</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004791" MajorTopicYN="N">Enzyme Inhibitors</DescriptorName><QualifierName UI="Q000494" MajorTopicYN="N">pharmacology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005786" MajorTopicYN="Y">Gene Expression Regulation</DescriptorName><QualifierName UI="Q000187" MajorTopicYN="N">drug effects</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005796" MajorTopicYN="N">Genes</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016678" MajorTopicYN="N">Genome</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D058977" MajorTopicYN="N">Molecular Sequence Annotation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010838" MajorTopicYN="N">Phytophthora</DescriptorName><QualifierName UI="Q000187" MajorTopicYN="N">drug effects</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D055750" MajorTopicYN="N">Phytophthora infestans</DescriptorName><QualifierName UI="Q000187" MajorTopicYN="N">drug effects</QualifierName><QualifierName UI="Q000201" MajorTopicYN="N">enzymology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000472" MajorTopicYN="Y">pathogenicity</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017434" MajorTopicYN="N">Protein Structure, Tertiary</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011506" MajorTopicYN="N">Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020449" MajorTopicYN="N">Repetitive Sequences, Amino Acid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012689" MajorTopicYN="N">Sequence Homology, Nucleic Acid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012697" MajorTopicYN="N">Serine 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