Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms.
We have carried out detailed statistical analyses of integral membrane proteins of the helix-bundle class from eubacterial, archaean, and eukaryotic organisms for which genome-wide sequence data are available. Twenty to 30% of all ORFs are predicted to encode membrane proteins, with the larger genomes containing a higher fraction than the smaller ones. Although there is a general tendency that proteins with a smaller number of transmembrane segments are more prevalent than those with many, uni-cellular organisms appear to prefer proteins with 6 and 12 transmembrane segments, whereas Caenorhabditis elegans and Homo sapiens have a slight preference for proteins with seven transmembrane segments. In all organisms, there is a tendency that membrane proteins either have many transmembrane segments with short connecting loops or few transmembrane segments with large extra-membraneous domains. Membrane proteins from all organisms studied, except possibly the archaeon Methanococcus jannaschii, follow the so-called "positive-inside" rule; i.e., they tend to have a higher frequency of positively charged residues in cytoplasmic than in extra-cytoplasmic segments.
Wallin
E
E
Department of Biochemistry, Stockholm University, Sweden.
von Heijne
G
G
D000818:Animals; D019843:Archaeal Proteins; D001426:Bacterial Proteins; D017173:Caenorhabditis elegans / Q000737:chemistry; D016208:Databases, Factual; D005057:Eukaryotic Cells / Q000737:chemistry; D016678:Genome; D006801:Humans; D008565:Membrane Proteins / Q000737:chemistry*; D016366:Open Reading Frames / Q000235:genetics; D017433:Protein Structure, Secondary
D019843:Archaeal Proteins; D001426:Bacterial Proteins; D008565:Membrane Proteins