Abstract
Advancement in bioinformatics with the development of computational tools has enabled the in-silico prediction and identification of transcription regulatory factors and other genetic elements with great ease. In this study, computational analysis of sequence homology of 546 bp 5' region of 16SrRNA gene of Bacillus sp. strain SJ-101 resulted in identification of promoter-like sequences within the rrn gene. Using BPROM tool, the regulatory motifs like -35 and -10 boxes were mapped at 392 and 411 positions, respectively. Furthermore, the cis-acting elements as the binding sites for transcription factors (TF) cpxR and argR were identified at positions 413 and 416 at the upstream of an open reading frame (ORF). The probable functions of the putative TFs were predicted through the Uni-Prot/Swiss-Prot protein database. Search for the Shine-Dalgarno sequence (SD) found the presence of highly conserved SD sequence (AATACC), and a short 42 bp coding sequence/ORF bounded with characteristic transcription start site (AAC) and a stop codon (TGA) at positions 426 and 465 downstream to the promoter elements. A 13 amino acid long translation product of a short ORF has exhibited 100% homology with protein sequences of Bacillus spp., while showing some degree of polymorphism with other reference strains. The comparative homology of the small protein exhibited maximum similarity with Prolyl-4 hydroxylase of Chlamydomonas reinhardtii with 4.11 ZSCORE. The highly conserved regulatory elements and the putative ORF predicted within the 16SrRNA gene may help understand the role of relatively unexplored short ORFs within rrn operon, and their functional products in genetic regulatory mechanisms in eubacteria.
Highlights
Bacillus sp. strain SJ-101 isolated from soil, is a nickel (Ni)-tolerant strain with intrinsic potential of plant growth promotion, Ni biosorption and bioaccumulation [1,2]
Computational analysis of 16SrRNA gene fragment for prediction of TF and other vital regulatory motifs suggested the presence of cis-acting sites of promoter sequence, and transcription factors binding sites within 5’ region of the gene
The results corroborate with the observations of Berg et al [11], who have reported the in vivo translation of a segment of E. coli rrnB 16SrRNA gene
Summary
Bacillus sp. strain SJ-101 isolated from soil, is a nickel (Ni)-tolerant strain with intrinsic potential of plant growth promotion, Ni biosorption and bioaccumulation [1,2]. Strain SJ-101 isolated from soil, is a nickel (Ni)-tolerant strain with intrinsic potential of plant growth promotion, Ni biosorption and bioaccumulation [1,2]. This non-pathogenic and culturable microorganism is amenable to reverse genetics for functional analysis and regarded as a model system for numerous industrial, medical, and ecological applications. Overall 88% of Bacillus genome has been predicted to be either translated into protein or transcribed into stable structural RNA [3]. The involvement of rRNA in the transcription regulation and translation process apart from its major role in the organization of ribosome structure is quite intriguing [4,5,6]. In addition to the well known infrastructural RNA types, such as tRNA, rRNA, and snRNA, the RNA molecule performs multifarious biologic functions as micro-(miRNA), small interfering-(siRNA), Piwi interacting-(piRNA) and small modulatory-(sm RNA) [8]
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