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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


Khan F,1, Agrawal S2 Mishra BN3


1,3Department of Biotechnology, Institute of Engineering & Technology, Lucknow, 2Jawahar Lal Nehru Center of Advanced Research, Bangalore, India.



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.