title: Extracting sequence motifs and the phylogenetic features of SNARE-dependent membrane traffic.
abstract: The SNARE proteins are required for membrane fusion during intracellular vesicular transport and for its specificity. Only the unique combination of SNARE proteins (cognates) can be bound and can lead to membrane fusion, although the characteristics of the possible specificity of the binding combinations encoded in the SNARE sequences have not yet been determined. We discovered by whole genome sequence analysis that sequence motifs (conserved sequences) in the SNARE motif domains for each protein group correspond to localization sites or transport pathways. We claim that these motifs reflect the specificity of the binding combinations of SNARE motif domains. Using these motifs, we could classify SNARE proteins from 48 organisms into their localization sites or transport pathways. The classification result shows that more than 10 SNARE subgroups are kingdom specific and that the SNARE paralogs involved in the plasma membrane-related transport pathways have developed greater variations in higher animals and higher plants than those involved in the endoplasmic reticulum-related transport pathways throughout eukaryotic evolution.
authors.affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan. acyshzw@kuicr.kyoto-u.ac.jp
authors.forename: Akiyasu C
authors.initials: AC
authors.lastname: Yoshizawa
authors.forename: Shuichi
authors.initials: S
authors.lastname: Kawashima
authors.forename: Shujiro
authors.initials: S
authors.lastname: Okuda
authors.forename: Masashi
authors.initials: M
authors.lastname: Fujita
authors.forename: Masumi
authors.initials: M
authors.lastname: Itoh
authors.forename: Yuki
authors.initials: Y
authors.lastname: Moriya
authors.forename: Masahiro
authors.initials: M
authors.lastname: Hattori
authors.forename: Minoru
authors.initials: M
authors.lastname: Kanehisa
mesh_terms: D020816:Amino Acid Motifs; D016000:Cluster Analysis; D010802:Phylogeny; D021381:Protein Transport; D050600:SNARE Proteins / Q000737:chemistry / Q000502:physiology*
chemical_list: D050600:SNARE Proteins