Genome-wide analysis of eukaryote thaumatin-like proteins (TLPs) with an emphasis on poplar.
Identifieur interne : 000068 ( Main/Exploration ); précédent : 000067; suivant : 000069Genome-wide analysis of eukaryote thaumatin-like proteins (TLPs) with an emphasis on poplar.
Auteurs : Benjamin Petre [France] ; Ian Major ; Nicolas Rouhier ; Sébastien DuplessisSource :
- BMC plant biology [ 1471-2229 ] ; 2011.
Descripteurs français
- KwdFr :
- Alignement de séquences (MeSH), Animaux (MeSH), Annotation de séquence moléculaire (MeSH), Champignons (génétique), Données de séquences moléculaires (MeSH), Eucaryotes (génétique), Famille multigénique (MeSH), Génome végétal (MeSH), Modèles moléculaires (MeSH), Phylogenèse (MeSH), Plantes (génétique), Populus (génétique), Protéines végétales (génétique), Structure tertiaire des protéines (MeSH), Séquence d'acides aminés (MeSH).
- MESH :
- génétique : Champignons, Eucaryotes, Plantes, Populus, Protéines végétales.
- Alignement de séquences, Animaux, Annotation de séquence moléculaire, Données de séquences moléculaires, Famille multigénique, Génome végétal, Modèles moléculaires, Phylogenèse, Structure tertiaire des protéines, Séquence d'acides aminés.
English descriptors
- KwdEn :
- Amino Acid Sequence (MeSH), Animals (MeSH), Eukaryota (genetics), Fungi (genetics), Genome, Plant (MeSH), Models, Molecular (MeSH), Molecular Sequence Annotation (MeSH), Molecular Sequence Data (MeSH), Multigene Family (MeSH), Phylogeny (MeSH), Plant Proteins (genetics), Plants (genetics), Populus (genetics), Protein Structure, Tertiary (MeSH), Sequence Alignment (MeSH).
- MESH :
- chemical , genetics : Plant Proteins.
- genetics : Eukaryota, Fungi, Plants, Populus.
- Amino Acid Sequence, Animals, Genome, Plant, Models, Molecular, Molecular Sequence Annotation, Molecular Sequence Data, Multigene Family, Phylogeny, Protein Structure, Tertiary, Sequence Alignment.
Abstract
BACKGROUND
Plant inducible immunity includes the accumulation of a set of defense proteins during infection called pathogenesis-related (PR) proteins, which are grouped into families termed PR-1 to PR-17. The PR-5 family is composed of thaumatin-like proteins (TLPs), which are responsive to biotic and abiotic stress and are widely studied in plants. TLPs were also recently discovered in fungi and animals. In the poplar genome, TLPs are over-represented compared with annual species and their transcripts strongly accumulate during stress conditions.
RESULTS
Our analysis of the poplar TLP family suggests that the expansion of this gene family was followed by diversification, as differences in expression patterns and predicted properties correlate with phylogeny. In particular, we identified a clade of poplar TLPs that cluster to a single 350 kb locus of chromosome I and that are up-regulated by poplar leaf rust infection. A wider phylogenetic analysis of eukaryote TLPs - including plant, animal and fungi sequences - shows that TLP gene content and diversity increased markedly during land plant evolution. Mapping the reported functions of characterized TLPs to the eukaryote phylogenetic tree showed that antifungal or glycan-lytic properties are widespread across eukaryote phylogeny, suggesting that these properties are shared by most TLPs and are likely associated with the presence of a conserved acidic cleft in their 3D structure. Also, we established an exhaustive catalog of TLPs with atypical architectures such as small-TLPs, TLP-kinases and small-TLP-kinases, which have potentially developed alternative functions (such as putative receptor kinases for pathogen sensing and signaling).
CONCLUSION
Our study, based on the most recent plant genome sequences, provides evidence for TLP gene family diversification during land plant evolution. We have shown that the diverse functions described for TLPs are not restricted to specific clades but seem to be universal among eukaryotes, with some exceptions likely attributable to atypical protein structures. In the perennial plant model Populus, we unravelled the TLPs likely involved in leaf rust resistance, which will provide the foundation for further functional investigations.
DOI: 10.1186/1471-2229-11-33
PubMed: 21324123
PubMed Central: PMC3048497
Affiliations:
Links toward previous steps (curation, corpus...)
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last="Major">Ian Major</name></author><author><name sortKey="Rouhier, Nicolas" sort="Rouhier, Nicolas" uniqKey="Rouhier N" first="Nicolas" last="Rouhier">Nicolas Rouhier</name></author><author><name sortKey="Duplessis, Sebastien" sort="Duplessis, Sebastien" uniqKey="Duplessis S" first="Sébastien" last="Duplessis">Sébastien Duplessis</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2011">2011</date><idno type="RBID">pubmed:21324123</idno><idno type="pmid">21324123</idno><idno type="doi">10.1186/1471-2229-11-33</idno><idno type="pmc">PMC3048497</idno><idno type="wicri:Area/Main/Corpus">000068</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000068</idno><idno type="wicri:Area/Main/Curation">000068</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000068</idno><idno 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Ian" sort="Major, Ian" uniqKey="Major I" first="Ian" last="Major">Ian Major</name></author><author><name sortKey="Rouhier, Nicolas" sort="Rouhier, Nicolas" uniqKey="Rouhier N" first="Nicolas" last="Rouhier">Nicolas Rouhier</name></author><author><name sortKey="Duplessis, Sebastien" sort="Duplessis, Sebastien" uniqKey="Duplessis S" first="Sébastien" last="Duplessis">Sébastien Duplessis</name></author></analytic><series><title level="j">BMC plant biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence (MeSH)</term><term>Animals (MeSH)</term><term>Eukaryota (genetics)</term><term>Fungi (genetics)</term><term>Genome, Plant (MeSH)</term><term>Models, Molecular (MeSH)</term><term>Molecular Sequence Annotation (MeSH)</term><term>Molecular Sequence Data (MeSH)</term><term>Multigene Family (MeSH)</term><term>Phylogeny (MeSH)</term><term>Plant Proteins (genetics)</term><term>Plants (genetics)</term><term>Populus (genetics)</term><term>Protein Structure, Tertiary (MeSH)</term><term>Sequence Alignment (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Alignement de séquences (MeSH)</term><term>Animaux (MeSH)</term><term>Annotation de séquence moléculaire (MeSH)</term><term>Champignons (génétique)</term><term>Données de séquences moléculaires (MeSH)</term><term>Eucaryotes (génétique)</term><term>Famille multigénique (MeSH)</term><term>Génome végétal (MeSH)</term><term>Modèles moléculaires (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Plantes (génétique)</term><term>Populus (génétique)</term><term>Protéines végétales (génétique)</term><term>Structure tertiaire des protéines (MeSH)</term><term>Séquence d'acides aminés (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Eukaryota</term><term>Fungi</term><term>Plants</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Champignons</term><term>Eucaryotes</term><term>Plantes</term><term>Populus</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Animals</term><term>Genome, Plant</term><term>Models, Molecular</term><term>Molecular Sequence Annotation</term><term>Molecular Sequence Data</term><term>Multigene Family</term><term>Phylogeny</term><term>Protein Structure, Tertiary</term><term>Sequence Alignment</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term><term>Animaux</term><term>Annotation de séquence moléculaire</term><term>Données de séquences moléculaires</term><term>Famille multigénique</term><term>Génome végétal</term><term>Modèles moléculaires</term><term>Phylogenèse</term><term>Structure tertiaire des protéines</term><term>Séquence d'acides aminés</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Plant inducible immunity includes the accumulation of a set of defense proteins during infection called pathogenesis-related (PR) proteins, which are grouped into families termed PR-1 to PR-17. The PR-5 family is composed of thaumatin-like proteins (TLPs), which are responsive to biotic and abiotic stress and are widely studied in plants. TLPs were also recently discovered in fungi and animals. In the poplar genome, TLPs are over-represented compared with annual species and their transcripts strongly accumulate during stress conditions.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>Our analysis of the poplar TLP family suggests that the expansion of this gene family was followed by diversification, as differences in expression patterns and predicted properties correlate with phylogeny. In particular, we identified a clade of poplar TLPs that cluster to a single 350 kb locus of chromosome I and that are up-regulated by poplar leaf rust infection. A wider phylogenetic analysis of eukaryote TLPs - including plant, animal and fungi sequences - shows that TLP gene content and diversity increased markedly during land plant evolution. Mapping the reported functions of characterized TLPs to the eukaryote phylogenetic tree showed that antifungal or glycan-lytic properties are widespread across eukaryote phylogeny, suggesting that these properties are shared by most TLPs and are likely associated with the presence of a conserved acidic cleft in their 3D structure. Also, we established an exhaustive catalog of TLPs with atypical architectures such as small-TLPs, TLP-kinases and small-TLP-kinases, which have potentially developed alternative functions (such as putative receptor kinases for pathogen sensing and signaling).</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>Our study, based on the most recent plant genome sequences, provides evidence for TLP gene family diversification during land plant evolution. We have shown that the diverse functions described for TLPs are not restricted to specific clades but seem to be universal among eukaryotes, with some exceptions likely attributable to atypical protein structures. In the perennial plant model Populus, we unravelled the TLPs likely involved in leaf rust resistance, which will provide the foundation for further functional investigations.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21324123</PMID><DateCompleted><Year>2011</Year><Month>06</Month><Day>20</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2229</ISSN><JournalIssue CitedMedium="Internet"><Volume>11</Volume><PubDate><Year>2011</Year><Month>Feb</Month><Day>15</Day></PubDate></JournalIssue><Title>BMC plant biology</Title><ISOAbbreviation>BMC Plant Biol</ISOAbbreviation></Journal><ArticleTitle>Genome-wide analysis of eukaryote thaumatin-like proteins (TLPs) with an emphasis on poplar.</ArticleTitle><Pagination><MedlinePgn>33</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2229-11-33</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Plant inducible immunity includes the accumulation of a set of defense proteins during infection called pathogenesis-related (PR) proteins, which are grouped into families termed PR-1 to PR-17. The PR-5 family is composed of thaumatin-like proteins (TLPs), which are responsive to biotic and abiotic stress and are widely studied in plants. TLPs were also recently discovered in fungi and animals. In the poplar genome, TLPs are over-represented compared with annual species and their transcripts strongly accumulate during stress conditions.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Our analysis of the poplar TLP family suggests that the expansion of this gene family was followed by diversification, as differences in expression patterns and predicted properties correlate with phylogeny. In particular, we identified a clade of poplar TLPs that cluster to a single 350 kb locus of chromosome I and that are up-regulated by poplar leaf rust infection. A wider phylogenetic analysis of eukaryote TLPs - including plant, animal and fungi sequences - shows that TLP gene content and diversity increased markedly during land plant evolution. Mapping the reported functions of characterized TLPs to the eukaryote phylogenetic tree showed that antifungal or glycan-lytic properties are widespread across eukaryote phylogeny, suggesting that these properties are shared by most TLPs and are likely associated with the presence of a conserved acidic cleft in their 3D structure. Also, we established an exhaustive catalog of TLPs with atypical architectures such as small-TLPs, TLP-kinases and small-TLP-kinases, which have potentially developed alternative functions (such as putative receptor kinases for pathogen sensing and signaling).</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">Our study, based on the most recent plant genome sequences, provides evidence for TLP gene family diversification during land plant evolution. We have shown that the diverse functions described for TLPs are not restricted to specific clades but seem to be universal among eukaryotes, with some exceptions likely attributable to atypical protein structures. In the perennial plant model Populus, we unravelled the TLPs likely involved in leaf rust resistance, which will provide the foundation for further functional investigations.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Petre</LastName><ForeName>Benjamin</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>INRA†/Nancy Université, Unité Mixte de Recherche 1136 Interactions Arbres/Micro-organismes, Centre INRA de Nancy, F-54280 Champenoux, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Major</LastName><ForeName>Ian</ForeName><Initials>I</Initials></Author><Author ValidYN="Y"><LastName>Rouhier</LastName><ForeName>Nicolas</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Duplessis</LastName><ForeName>Sébastien</ForeName><Initials>S</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType 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name="France"><region name="Grand Est"><name sortKey="Petre, Benjamin" sort="Petre, Benjamin" uniqKey="Petre B" first="Benjamin" last="Petre">Benjamin Petre</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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