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,
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.