title: Identification of a unique IAHP (IcmF associated homologous proteins) cluster in Vibrio cholerae and other proteobacteria through in silico analysis.
abstract: Previously using global transcription profile approach, the icmF gene of V. cholerae was identified as an in vivo induced gene involved in the regulation of motility, adherence to intestinal epithelial cells. The present report shows that icmF has 27 homologues in the finished and unfinished microbial genome sequences available in the database and among them only Legionella pneumophila IcmF has been partially characterized. We first identified a gene cluster containing 15 genes surrounding IcmF and designated as IcmF associated homologous protein (IAHP), present in nine gram-negative proteo-bacteria that need an intimate contact with the eukaryotic host cells. Only in P. aeruginosa the cluster is present in three different regions of the genome. In Y. pestis CO92 the cluster is in the same orientation as that of V. cholerae. But in E. coli O157:H7 VT2 Sakai, E. coli O157:H7 EDL933 and Y. pestis KIM, the cluster is in the opposite orientation to that of V. cholerae though the relative position of respective ORFs are the same. In other proteobacteria like M. loti, A. tumefaciens, P. aeruginosa and S. typhimurum, the genes are reshuffled indicating the frequent rearrangement in microbial genomes. Annotation, motif and domain prediction suggested a role of the proteins of IAHP cluster in cell surface architecture or secretion. Phylogenetic analysis of each protein belonging to the cluster present in all the nine organisms showed that only E. coli O157:H7 VT2 Sakai, E. coli O157:H7 EDL933, Y. pestis KIM and Y. pestis CO92 are closer to the V. cholerae and this pattern was similar for all proteins in the cluster. Presence of low G + C regions before and after the gene cluster in V. cholerae and both of the E. coli O157: H7 strains provide possibility of transfer of the gene cluster from a foreign source. From our finding it can be speculated that both of the E. coli O157:H7 strains and V. cholerae has a common ancestor, but the other organism where the cluster is reshuffled has undergone a long term of evolution.
authors.affiliation: Human Genetics and Genomics Group, Indian Institute of Chemical Biology, Calcutta, India.
authors.forename: Soumita
authors.initials: S
authors.lastname: Das
authors.forename: Keya
authors.initials: K
authors.lastname: Chaudhuri
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics*; D001482:Base Composition; D016680:Genome, Bacterial; D005810:Multigene Family; D016366:Open Reading Frames; D010802:Phylogeny; D020560:Proteobacteria / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D014734:Vibrio cholerae / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; C464652:IcmF protein, Vibrio cholerae