Number Distribution of Transmembrane Helices in Prokaryote Genomes

Number distribution of transmembrane helices represents genetic feature of survival strategy, because the number of transmembrane helices is closely related to the functional group of membrane proteins: for example, most of membrane proteins that have six transmembrane helices belong to transporter functional group. Survival strategies were obtained by evolutionary mechanism that changes the genome sequences. Comparisons of number distributions of transmembrane helices among species that have different survival strategies help us to understand the evolutionary mechanism that has increased the categories of membrane proteins. Some studies about how the categories of protein functions have been increased during evolution were performed using protein database (Chothia et al., 2003; Huynen & van Nimwegen, 1998; Koonin et al., 2002; Qian et al., 2001; Vogel et al., 2005). However, these studies were carried out by the analysis almost for soluble proteins. Classification of protein function groups are often carried out by the empirical methods such as sequence homology that use sequence information of three-dimensional structure resolved proteins as template sequences for each functional group. However three-dimensional structure resolved membrane proteins were much less than that for the soluble proteins because of experimental difficulty of membrane proteins. In the previous study, we developed membrane protein prediction system SOSUI and signal peptide prediction system SOSUIsignal (Gomi et al., 2004; Hirokawa et al., 1998). By combination of those systems, number of transmembrane helices can be predicted based not on empirical but on physicochemical parameters. Therefore, it is possible to investigate the number distribution of transmembrane regions in membrane proteins comprehensively among various genomes by using SOSUI and SOSUIsignal.