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Online Journal of Bioinformatics©
Volume 6 (2):129-141, 2005.
In silico identification of cis-regulatory elements in Mesorhizobium loti
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.