Identification and phylogenetic analyses of VASt, an uncharacterized protein domain associated with lipid-binding domains in Eukaryotes
| Autor: | Ludovic Cottret, Sylvain Raffaele, Mehdi Khafif, Claudine Balagué |
|---|---|
| Přispěvatelé: | Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), TULIP [ANR-10-LABX-41], Marie Curie CIG grant [334036], European Research Council (ERC) [336808] |
| Rok vydání: | 2014 |
| Předmět: |
Models
Molecular [SDV.SA]Life Sciences [q-bio]/Agricultural sciences Architecture domain Molecular Sequence Data Protein domain Sequence alignment Biology Biochemistry Genome VASt Conserved sequence 03 medical and health sciences 0302 clinical medicine Protein structure Structural Biology Phylogenetics Animals Humans Amino Acid Sequence VAD1 programmed cell death Molecular Biology Peptide sequence Conserved Sequence Phylogeny 030304 developmental biology Genetics 0303 health sciences Applied Mathematics Eukaryota Proteins protein domain Lipid Metabolism Lipids Agricultural sciences Protein Structure Tertiary Computer Science Applications gram domain Structural Homology Protein bet v1-like Sequence Alignment Sciences agricoles 030217 neurology & neurosurgery Research Article |
| Zdroj: | BMC Bioinformatics BMC Bioinformatics, BioMed Central, 2014, 15, 12 p. ⟨10.1186/1471-2105-15-222⟩ BMC Bioinformatics (15), 12 p.. (2014) |
| ISSN: | 1471-2105 |
| Popis: | Background Several regulators of programmed cell death (PCD) in plants encode proteins with putative lipid-binding domains. Among them, VAD1 is a regulator of PCD propagation harboring a GRAM putative lipid-binding domain. However the function of VAD1 at the subcellular level is unknown and the domain architecture of VAD1 has not been analyzed in details. Results We analyzed sequence conservation across the plant kingdom in the VAD1 protein and identified an uncharacterized VASt (VAD1 Analog of StAR-related lipid transfer) domain. Using profile hidden Markov models (profile HMMs) and phylogenetic analysis we found that this domain is conserved among eukaryotes and generally associates with various lipid-binding domains. Proteins containing both a GRAM and a VASt domain include notably the yeast Ysp2 cell death regulator and numerous uncharacterized proteins. Using structure-based phylogeny, we found that the VASt domain is structurally related to Bet v1-like domains. Conclusion We identified a novel protein domain ubiquitous in Eukaryotic genomes and belonging to the Bet v1-like superfamily. Our findings open perspectives for the functional analysis of VASt-containing proteins and the characterization of novel mechanisms regulating PCD. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|
Full text from SpringerLink