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
Article Information
Identifiers and Pagination:
Year: 2009Volume: 3
First Page: 8
Last Page: 17
Publisher ID: TOBIOIJ-3-8
DOI: 10.2174/1875036200903010008
Article History:
Received Date: 27/12/2008Revision Received Date: 14/03/2009
Acceptance Date: 19/03/2009
Electronic publication date: 05/05/2009
Collection year: 2009
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.
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.