The Construction of a Database on the Intracellular Vesicular Transport

One of the most conspicuous morphological differences of eucaryotic cells from procaryotic cells is the presence of several membrane compartments within the cell. In order to maintain these organelles, eucaryotic cells transfer membrane structural elements, such as proteins and lipids, between the organelles. In this transfer system, small-size membrane vesicles containing structural elements bud from the ‘donor’ membrane of the donor organelle, move to the vicinity of the target organelle, and fuse to the ‘target’ membrane to transfer the structural elements. This three-stage system consisting of budding, moving, and fusion is named ‘vesicular transport’ a.k.a. ‘membrane traffic.’ In order for the transport vesicle to fuse only to the precise target membrane, unique mutual recognitions are required between the membranes. Following the ‘SNARE hypothesis’ [1], this mechanism can be described as follows. When a proper vesicle SNARE (v-SNARE) protein and a target SNARE (t-SNARE) protein exist on the transport vesicle and the target membrane, respectively, at an appropriate region in the cell, their unique binding interactions make it possible to recognize mutually and to trigger the membrane fusion. SNARE (Soluble N-ethylmaleimide-sensitive factor Attachment protein REceptor) is the general term for a protein whose function is unique recognition and membrane fusion, so a single cell contains multiple SNARE pairs representing the variety of paths between organelles. In order to understand genomic contents and evolutionary origins of intracellular traffic systems, we have constructed a SNARE database which contains a basic data set of t-SNAREs and v-SNAREs. We have then collected other candidates of SNARE proteins from the protein sequence databases and performed the cluster analysis.