title: Evolution of the Rab family of small GTP-binding proteins.
abstract: Rab proteins are small GTP-binding proteins that form the largest family within the Ras superfamily. Rab proteins regulate vesicular trafficking pathways, behaving as membrane-associated molecular switches. Here, we have identified the complete Rab families in the Caenorhabditis elegans (29 members), Drosophila melanogaster (29), Homo sapiens (60) and Arabidopsis thaliana (57), and we defined criteria for annotation of this protein family in each organism. We studied sequence conservation patterns and observed that the RabF motifs and the RabSF regions previously described in mammalian Rabs are conserved across species. This is consistent with conserved recognition mechanisms by general regulators and specific effectors. We used phylogenetic analysis and other approaches to reconstruct the multiplication of the Rab family and observed that this family shows a strict phylogeny of function as opposed to a phylogeny of species. Furthermore, we observed that Rabs co-segregating in phylogenetic trees show a pattern of similar cellular localisation and/or function. Therefore, animal and fungi Rab proteins can be grouped in "Rab functional groups" according to their segregating patterns in phylogenetic trees. These functional groups reflect similarity of sequence, localisation and/or function, and may also represent shared ancestry. Rab functional groups can help the understanding of the functional evolution of the Rab family in particular and vesicular transport in general, and may be used to predict general functions for novel Rab sequences.
authors.affiliation: Cell and Molecular Biology Section, Division of Biomedical Sciences, Faculty of Medicine, Imperial College, London, SW7 2AZ, UK.
authors.forename: J B
authors.initials: JB
authors.lastname: Pereira-Leal
authors.forename: M C
authors.initials: MC
authors.lastname: Seabra
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000235:genetics; D029742:Caenorhabditis elegans Proteins / Q000737:chemistry / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D017124:Conserved Sequence; D029721:Drosophila Proteins / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D005091:Exons / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics; D010802:Phylogeny; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics; D029702:Schizosaccharomyces pombe Proteins / Q000737:chemistry / Q000235:genetics; D016415:Sequence Alignment; D020691:rab GTP-Binding Proteins / Q000737:chemistry* / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins; D029742:Caenorhabditis elegans Proteins; D029721:Drosophila Proteins; D029701:Saccharomyces cerevisiae Proteins; D029702:Schizosaccharomyces pombe Proteins; D020691:rab GTP-Binding Proteins