Title

Computational identification of composite regulatory sites in 16s-rRNA gene promoters of Mycobacterium species

Authors

Neeraja Dwivedi¹, Surya Prakash Dwivedi¹, Ajay kumar¹, Vishwa Mohan Katoch² and Sanjay Mishra^{1, *}

Affiliation

¹Department of Biotechnology, College of Engineering and Technology, IFTM Campus, Lodhipur-Rajput, Delhi Road, Moradabad 244 001, U.P., India; ²National Institute for Leprosy (ICMR) and Other Mycobacterial Diseases, Tajganj, Agra, UP, India

Email

sanjaymishra66@gmail.com

Phone

91 591 6453829; * Corresponding author

Article Type

Hypothesis

Date

received March 25, 2008; revised May 13, 2008; accepted May 15, 2008; published June 16, 2008

Abstract

The availability of completely sequenced genomes allow the use of computational techniques to investigate cis-acting sequences controlling transcription regulation associated with groups of functionally related genes. Theoretical analysis was performed to assign functions to regulatory systems. The identification of such sites is relevant for locating a promoter at the 5' boundary of a gene. They also allow the prediction of specific gene-expression pattern and response to disturbances in a known signaling pathway. Here, we describe the identification of composite transcription factor (TF) binding sites over promoter regions in16s-rRNA gene for mycobacterium species strains ICC47, ICC67, ICC43 and CMVL700.  It is established that the ribosomal gene comprises of sequences that are conserved during evolution and interspersed with divergent regions. Computational identification of known TF-binding sites was performed using TFSITESCAN tool and ooTFD database. The ICC67, ICC47, ICC43 and CMYL700 strains showed 12, 13, 9 and 15 known TF binding sites, respectively. Comparison between strains suggests 9 known TF predicted binding sites to be conserved among them. These data provide basis for the understanding of promoter regulation in 16s-rRNA.

Keywords

Composite TF binding sites; promoter regions; 16s-rRNA gene;  Mycobacteria; Computational DNA; regulatory sites identification

Citation

Dwivedi et al., Bioinformation 2(8): 363-368 (2008)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.