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OJB©
Online Journal of Bioinformatics©
Onl J Bioinform©
Established 1995
ISSN 1443-2250
Volume 25 (1) : 1-18, 2024.
Non-coding
in silico cis-regulatory elements in Mesorhizobium
loti
1,3Department of
Biotechnology,
Khan F, Agrawal S, Mishra BN, Non-coding in silico cis-regulatory
elements in Mesorhizobium loti, Onl J Bioinform, 25 (1) : 1-18, 2024. Detection of
microbial regulatory sites is a challenge due
to short upstream gene sequences and determination of its limit.
Non-coding regions can control regulation of gene expression. We constructed a
model to detect over-represented hexanucleotides
located -400 bp upstream sequences of 4 data sets of
genes similar to cellular functional nitrogen fixation, symbiosis, nitrogen
metabolism and glutamate in Mesorhizobium
loti; a symbiont model legume of Lotus
japonicus. The upstream sequences of these genes
were analyzed for known transcription factor (TF) binding sites 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 a more precise
analysis of regulatory network involved in symbiotic interaction with host L.
japonicus.
KEYWORDS: Regulatory binding motifs, TF
binding sites in M. loti, Hexanucleotides motifs, Nitrogen fixing bacteria.