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OJB©
Online Journal of Bioinformatics©
Onl J Bioinform©
Established 1995
ISSN 1443-2250
Volume 26 (3) : 96-105, 2025
In silico cis-regulatory elements in Mesorhizobium
loti
Khan F, Agrawal S, Mishra BN.
Institute of Engineering & Technology,
Lucknow, Jawahar Lal Nehru Center of Advanced Research, Bangalore, India.
ABSTRACT
Khan F, Agrawal
S, Mishra BN. In silico cis-regulatory
elements in Mesorhizobium loti, Onl
J Bioinform., 26 (3) : 96-105, 2025. The detection of gene regulatory sites on microbes is a challenge due
to the shortness of the upstream sequence 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.
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