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Bioinformatics Advance Access published online on March 3, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti375
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received November 18, 2004
Revised January 31, 2005
Accepted March 2, 2005

Discovery note

Computational prediction and experimental verification of novel IdeR binding sites in the upstream sequences of Mycobacterium tuberculosis ORFs

Prachee Prakash 1, Sailu Yellaboina 2, Akash Ranjan 2, and Seyed E. Hasnain 3*

1 Laboratory of Molecular and Cellular Biology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500 076, India
2 Laboratory of Computational and Functional Genomics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500 076, India
3 Laboratory of Molecular and Cellular Biology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, 500 076, India; Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, 560064, India

* To whom correspondence should be addressed.
Seyed E. Hasnain, E-mail: hasnain{at}cdfd.org.in


  Abstract

IdeR (Iron dependent regulator) is a key regulator of virulence factors and iron acquisition systems in M. tuberculosis. Despite the wealth of information available on IdeR regulated genes of Mtb, 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 Mtb. We describe an in silico approach employing positional relative entropy method to identify potential IdeR binding sites in the upstream sequences of all the 3919 ORFs of Mtb. 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, few genes for which there has been no evidence for IdeR regulation were additionally identified. Our results have implications on iron dependent regulatory mechanism of Mtb vis-a-vis the activity of urease operon and novel transcription regulators and transporters.


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[Abstract] [Full Text] [PDF]


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