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Online Journal of Bioinformatics

Volume 4: 106-114, 2003

Identification of GltC transcription factor binding DNA motifs and its novel co-regulated genes in nitrogen fixing bacteria.


Khan F,  Agrawal S,  Mishra BN.


Biotechnology Program, Institute of Engineering & Technology,Sitapur road, Lucknow-22, India





Khan F,  Agrawal S,  Mishra BN, Identification of GltC transcription factor binding DNA motifs and its novel co-regulated genes in nitrogen fixing bacteria. Onl J Bioinform., 7: 106-115, 2003. GltC transcription factor regulating expression of glutamate synthase (GS) has been experimentally verified only in Bacillus subtilis, which also represses transcription of its own gene. Glutamate synthase significantly participates in nitrogen metabolism of different microbes specially nitrogen fixing bacteria. Therefore, other bacteria including nitrogen-fixing bacteria are needed to study GltC/GltC like motifs and co-regulated genes.  We report genome wide localization of GltC, its binding sites and related co-regulated genes using computational methods. The upstream genomes of bacteria showed several novel genes containing GltC motifs. It is also assumed that at a lower threshold value, the detection of glutamate synthase as GltC co-regulated genes can be attained in nitrogen fixing bacteria. The bacterial genomes also showed presence of GltC like proteins categorized as transcription regulators of LysR family. These predicted LysR proteins revealed identification of characteristic LysR domains, which were conserved with one another. The difference in binding motif patterns of GltC like motifs can be described to amino acid variation of LysR domain of the GltC like proteins who may cause expression of different set of proteins in different bacteria. There is further scope to perform specific comparative analysis of GltC binding motif elements in these nitrogen-fixing bacteria in order to describe the nature of patterns of expression of related co-regulated genes. Such computational studies are needed to be verified through precise experimentations. 


KEY WORDS: GltC factor, Glutamic acid biosynthesis, computational localization of transcription factor, nitrogen-fixing bacteria.