Domain Architecture of Prokaryotic Single-Spanning Transmembrane Proteins

Single-spanning transmembrane (TM) proteins (single-spannings), which account for as much as 25-30% of individual TM proteomes [1], can be regarded as soluble proteins rooted in the membrane lipid bilayer. There are three types of single-spannings depending on their topology: type I, with signal peptide (SP) and Nout; type II, without SP and Nin; type III, without SP and Nout. The two relatively longer tail loops, i.e., Nand C-tail loops, protrude to both the cytoplasmic and non-cytoplasmic sides from the membrane, and could behave freely with their one open end. Naturally, these loops are expected to have domains that are structural, functional and evolutional units of proteins, some of which should be shared with soluble proteins, with some others specific to only TM proteins. In this study, we assigned Pfam domains [3] to single-spannings predicted from 87 sequenced prokaryotic (bacterial and archaean) genomes, and attempted to carry out comprehensive analyses of the domain architecture of the single-spannings. We focused on the single-spannings with one or two domains on Nand/or C-tail loops, and with no assigned domains.