RESEARCH ARTICLE


Genomic Identification of SinR Transcription Factor Binding Sites in Nitrogen Fixing Bacterium Bradyrhizobium japonicum



Khan Feroz1, Sharma Richa1, Shukla Rakesh Kumar2, Meena Abha1, Shasany Ajit Kumar2, Sharma Ashok*, 1
1 Bioinformatics & In Silico Biology Division
2 Genetic Resource Biotechnology Division, Central Institute of Medicinal & Aromatic Plants, Council of Scientific & Industrial Research, Lucknow-226015 (UP), India


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Creative Commons License
© 2009 Feroz et al.

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: https://creativecommons.org/licenses/by/4.0/legalcode. This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

* Address correspondence to this author at the Bioinformatics & In Silico Biology Division, Central Institute of Medicinal & Aromatic Plants, Council of Scientific & Industrial Research, P.O. CIMAP, Kukrail Picnic Spot Road, Lucknow-226015 (UP), India; Tel: +91 522 2717626; Fax: +91 522 2342666; E-mail: ashoksharma@cimap.res.in


Abstract

SinR is a transcription factor which controls expression of stress tolerance sin genes related to alternate development processes under stress condition. Identification of genome wide SinR-box motif and their regulated genes has not been worked out yet in Bradyrhizobium japonicum. For this, a weight matrix of 9 bp was developed from the known promoter sequences of Bacillus subtilis, which was then used for genome wide identification of co-regulated genes. The methodology first involves phylogenetic footprinting of SinR regulated genes and then construction of scoring matrix through ‘Consensus’ and confirmation through MEME & D-Matrix tools. Genomic prediction was done through ‘Patser’ program and confirmation through ‘PossumSearch’ program in Linux system. Results showed that all the 371 predicted genes belongs to 9 different functional classes, in which 221 found in operons with more than 80% Sin-box motif similarity. Similar approach can be used in other bacteria to explore hidden genomic regulatory network.

Keywords: SinR, Transcription factor, Sin-box, Bradyrhizobium japonicum, Stress tolerance.