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Extracting Sequence Motifs and the Phylogenetic Features of SNARE‐Dependent Membrane Traffic
Author(s) -
Yoshizawa Akiyasu C.,
Kawashima Shuichi,
Okuda Shujiro,
Fujita Masashi,
Itoh Masumi,
Moriya Yuki,
Hattori Masahiro,
Kanehisa Minoru
Publication year - 2006
Publication title -
traffic
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.677
H-Index - 130
eISSN - 1600-0854
pISSN - 1398-9219
DOI - 10.1111/j.1600-0854.2006.00451.x
Subject(s) - biology , vesicular transport proteins , endoplasmic reticulum , sequence motif , conserved sequence , snare complex , sequence alignment , lipid bilayer fusion , membrane protein , phylogenetics , transport protein , consensus sequence , microbiology and biotechnology , computational biology , genetics , peptide sequence , gene , membrane , n terminus
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.