Computational identification of composite regulatory sites in 16s-rRNA gene promoters of Mycobacterium species

Abstract

The availability of completely sequenced genomes allow the use of computational techniques to investigate cis-acting sequences controlling transcription regulation associated with groups of functionally related genes. Theoretical analysis was performed to assign functions to regulatory systems. The identification of such sites is relevant for locating a promoter at the 5′ boundary of a gene. They also allow the prediction of specific gene-expression pattern and response to disturbances in a known signaling pathway. Here, we describe the identification of composite transcription factor (TF) binding sites over promoter regions in16s-rRNA gene for mycobacterium species strains ICC47, ICC67, ICC43 and CMVL700. It is established that the ribosomal gene comprises of sequences that are conserved during evolution and interspersed with divergent regions. Computational identification of known TF-binding sites was performed using TFSITESCAN tool and ooTFD database. The ICC67, ICC47, ICC43 and CMYL700 strains showed 12, 13, 9 and 15 known TF binding sites, respectively. Comparison between strains suggests 9 known TF predicted binding sites to be conserved among them. These data provide basis for the understanding of promoter regulation in 16s-rRNA.

Comparison of Conventional and Modern Biomedical Tools Used for Diagnosis of Genital Tract Tuberculosis: An Overview

“…Biopsies should be obtained by either laparoscopy or laparotomy if examination of the ascetic fluid could not confirm the diagnosis [6][7][8][9][10]. Although tuberculosis after the Second World War has been almost eradicated in the well developed countries due to vaccination, early diagnosis, proper antibiotics and increase in the life standards [11,12], it still seems one of the major problems in the underdeveloped countries and also in the developing countries such as that of Turkey. Because immigration both from one country to another and also to cities, it seems that genital tuberculosis will reborn in many countries and areas where it is thought to be eradicated.…”

“…Tuberculosis (TB) is still rampant in India [11,12]; and TB of the genital tract is the commonest cause of tubal infertility. TB causes infertility only when it infects the genital tract (Genital TB).…”

“…They have severe Asherman's syndrome (intrauterine adhesions); and this can be diagnosed by doing a hysteroscopy. Unfortunately, there is no effective treatment for this, as endometrial tissue after TB can become very avascular, and the only option for these unfortunate women is either surrogacy or adoption [11,12]. In summary, the diagnosis of TB of the genital tract remains notoriously difficult to make.…”

“…This infection can often be silent, and may not cause any symptoms or signs at all! [11][12][13][14].…”

Regulatory elements in the 5’region of 16SrRNA gene of Bacillus sp. strain SJ-101

“…Lately, the development in computational techniques and availability of whole genome sequences have promoted the in­ silico prediction and identification of the putative cis and/or trans acting elements involved in transcriptional regulation of functional genes. Recently, several regulatory elements within 16S and 23S spacer region have been identified in eubacteria using in-silico tools [9–10]. Also, the in vitro translation studies in E. coli have demonstrated the region within 16SRNA gene encoding for small proteins, and sequence elements characteristics of prokaryotic promoters have been reported [11].…”