Survey for G-Proteins in the Prokaryotic Genomes: Prediction of Functional Roles Based on Classification

ABSTRACT The members of the family of G-proteins are characterized by their ability to bind and hydrolyze guanosine triphosphate (GTP) to guanosine diphosphate (GDP). Despite a common biochemical function of GTP hydrolysis shared among themembers of the family of G-proteins, they are associated with diverse biological roles. The current work describes the identification and de-tailed analysis of the putative G-proteins encoded in the completely sequenced prokaryotic genomes. In-ferences on the biological roles of these G-proteins have been obtained by their classification into known functional subfamilies. We have identified 497 G-proteins in 42 genomes. Seven small GTP-binding protein homologues have been identified in prokaryotes with at least two of the diagnostic sequence motifs of G-proteins conserved. The trans-lation factors have the largest representation (234 sequences) and are found to be ubiquitous, which is consistent with their critical role in protein synthe-sis. The GTP_OBG subfamily comprises of 79 se-quences in our dataset. A total of 177 sequences belong to the subfamily of GTPase of unknown function and 154 of these could be associated with domains of known functions such as cell cycle regu-lation and t-RNA modification. The large GTP-binding proteins and the -subunit of heterotri-meric G-proteins are not detected in the genomes of the prokaryotes surveyed. Proteins 2003;52:585–597. © 2003Wiley-Liss, Inc. Key words: proteins; genomeanalysis; GTPases; pro-karyotes; protein Families; protein structure