title: Computational prediction and experimental verification of novel IdeR binding sites in the upstream sequences of Mycobacterium tuberculosis open reading frames.
abstract: IdeR (iron-dependent regulator) is a key regulator of virulence factors and iron acquisition systems in Mycobacterium tuberculosis. Despite the wealth of information available on IdeR-regulated genes of M.tuberculosis, there is still an underlying possibility that there are novel genes/pathways that have gone undetected, the identification of which could give new insights into understanding the pathogenesis of M.tuberculosis. We describe an in silico approach employing the positional relative entropy method to identify potential IdeR binding sites in the upstream sequences of all the 3919 ORFs of M.tuberculosis. While many of the predictions made by this approach overlapped with the ones already identified by microarray experiments and binding assays, pointing to the accuracy of our method, a few genes for which there has been no evidence for IdeR regulation were additionally identified. Our results have implications on the iron-dependent regulatory mechanism of M.tuberculosis vis-a-vis the activity of urease operon and novel transcription regulators and transporters.
authors.affiliation: Laboratory of Molecular and Cellular Biology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500 076, India.
authors.forename: Prachee
authors.initials: P
authors.lastname: Prakash
authors.forename: Sailu
authors.initials: S
authors.lastname: Yellaboina
authors.forename: Akash
authors.initials: A
authors.lastname: Ranjan
authors.forename: Seyed E
authors.initials: SE
authors.lastname: Hasnain
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism*; D001665:Binding Sites; D003198:Computer Simulation; D004269:DNA, Bacterial / Q000235:genetics* / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology; D008954:Models, Biological; D008956:Models, Chemical; D009169:Mycobacterium tuberculosis / Q000235:genetics / Q000378:metabolism; D016366:Open Reading Frames / Q000235:genetics; D011485:Protein Binding; D012097:Repressor Proteins / Q000235:genetics* / Q000378:metabolism*; D017422:Sequence Analysis, DNA / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; C096348:IdeR protein, Mycobacterium tuberculosis; D012097:Repressor Proteins