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Open Access Research article

Identification and phylogenetic analyses of VASt, an uncharacterized protein domain associated with lipid-binding domains in Eukaryotes

Mehdi Khafif12, Ludovic Cottret12, Claudine Balagué12 and Sylvain Raffaele12*

Author Affiliations

1 INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, 24 Chemin de Borde Rouge – Auzeville, CS52627, F31326 Castanet Tolosan Cedex, France

2 CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, 24 Chemin de Borde Rouge – Auzeville, CS52627, F31326 Castanet Tolosan Cedex, France

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BMC Bioinformatics 2014, 15:222  doi:10.1186/1471-2105-15-222

Published: 26 June 2014

Abstract

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.

Keywords:
VASt; VAD1; Protein domain; Programmed cell death; GRAM domain; Bet v1-like