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OJB©
Online
Journal of Bioinformatics©
Volume 6 (2) : 129-141, 2005
In silico
identification of cis-regulatory elements in Mesorhizobium loti
1,3Department
of Biotechnology,
Khan F, Agrawal S, Mishra BN, In silico
identification of cis-regulatory elements in Mesorhizobium loti, Online J Bioinformatics, 6 (2) : 129-141, 2005. Detection of microbial regulatory sites is a challenge
due to the shortness of the
upstream sequence from the gene and
determination of its limit.
Non-coding regions are of interest since they govern the regulation of gene
expression. A computational method was used to detect over-represented hexanucleotides located within -400 bp
upstream sequences of 4 data set of genes similar to cellular functional
categories of viz. Nitrogen
fixation, Symbiosis, Nitrogen metabolism and Glutamate family in Mesorhizobium loti; a symbiont
to model legume plant Lotus japonicus. The upstream sequences of these genes
were analyzed for known transcription factor (TF) binding sites and verified
statistically with experimental data comparisons using over-represented hexanucleotide frequencies. Eight families of known
TF/binding sites were recognized in all sets as high affinity novel motif patterns.
Genome wide occurrence of the detected patterns had several nif, nod, nitrogen metabolism related and amino acid biosynthetic
genes. These findings in genome of M.
loti may lead to more a more
precise analysis of the regulatory
network involved in symbiotic interaction with the host plant L. japonicus.
KEYWORDS: Regulatory binding motifs, TF binding sites in M. loti, Hexanucleotides motifs,
Nitrogen fixing bacteria.