title: In-silico prediction of dual function of DksA like hypothetical protein in V. cholerae O395 genome.
abstract: Cholera, an acute infection of the small intestine, is caused by Vibrio cholerae. The present study identified a hypothetical protein in V. cholerae O395, which was predicted to be acquired through horizontal gene transfer the origin of which was found to be from a phage. Its expression was further confirmed by RT-PCR. Homology based 3D model of the hypothetical protein indicated DksA like homologue. Protein binding site of 3D-model revealed a deep cleft which may influence the dimer formation and interaction with ds-DNA molecule. Also, canonical function of direct interaction with RNA polymerase (RNAP) holoenzyme in complex with ppGpp suggests its dual role in the pathogenesis of cholera.
authors.affiliation: Molecular Genetics Division, CSIR - Indian Institute of Chemical Biology, Kolkata, 700032, West Bengal, India.
authors.forename: Avirup
authors.initials: A
authors.lastname: Dutta
authors.affiliation: Molecular Genetics Division, CSIR - Indian Institute of Chemical Biology, Kolkata, 700032, West Bengal, India.
authors.forename: Atul
authors.initials: A
authors.lastname: Katarkar
authors.affiliation: Molecular Genetics Division, CSIR - Indian Institute of Chemical Biology, Kolkata, 700032, West Bengal, India. Electronic address: keya.chaudhuri@gmail.com.
authors.forename: Keya
authors.initials: K
authors.lastname: Chaudhuri
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism*; D001665:Binding Sites; D003198:Computer Simulation; D004269:DNA, Bacterial / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D060888:Real-Time Polymerase Chain Reaction; D014734:Vibrio cholerae / Q000235:genetics* / Q000502:physiology*
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D012321:DNA-Directed RNA Polymerases
keywords: (p)ppGpp; DksA like protein; Homology modeling; Stringent response; V. cholerae O395