Tandem clusters of membrane proteins in complete genome sequences

The distribution of genes coding for membrane proteins was investigated in 16 complete genomes: 4 archaea, 11 bacteria, and 1 eukaryote. Membrane prot eins were identified by our new method of predicting transmembrane segments (Kihara et al. 1998) after the removal of amino-terminal signal peptides. Interestingly, about half of the membrane protein genes in each genome were found to be located next to another, Forming tandem clusters. Roughly 10%- 30% of the tandem clusters were conserved among organisms, and most of the conserved tandem clusters belonged to one of the three functional groups, n amely, transporters, the electron transport system, and cell motility. A ta ndem cluster sometimes contained paralogous membrane proteins, in which cas e the cluster size and the number of transmembrane segments could be relate d to a functional category, especially to transporters. In addition to the clustering of membrane proteins, the clustering of membrane proteins and AT P-binding proteins in the complete genomes was also analyzed. Although this clustering was not statistically significant, it was useful to identify ca ndidate membrane protein partners of isolated ATP-binding protein component s in the ABC transporters. Possible implications of tandem cluster organiza tion of membrane protein genes are discussed including the complex formatio n and other functional coupling of protein products and the mechanism of pr otein translocation to the cell membrane.