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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,
Onl J Bioinform., 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.