Mapping transcription start site The transcription start site was mapped using the strategy described by Lloyd et al. [41]. Primer extension was carried out on DNA free RNA with fluorescence labeled primers HEX-tsp1 and FAM-tsp2 mapping 100 nucleotides downstream of the translation initiation site PS-341 concentration of Rv0166 and Rv0167 respectively [Additional file 4]. The DNA sequence analysis and Genescan analysis was carried out at the commercial facility of The Centre for Genomic Application, Okhla, New Delhi and Labindia, Udyog Vihar, Gurgaon, India respectively. The Genescan analysis was carried out on 3130×l

Genetic Analyzer from Applied Biosystems with GSLIZ 500 as marker set. The data was analyzed Selleckchem Crizotinib using GeneMapper V4.0. Quantitative RT-PCR The transcriptional activity in log and stationary phase, was estimated by quantitative PCR using cDNA samples. 15 ml cultures of M.tuberculosis H37Rv and VPCI591

from log (day10) and stationary phase (day 20) were harvested at 4°C. RNA isolation was performed using RNeasy Mini Kit (Qiagen) and treated with DNaseI (MBI Fermentas). Absence of amplicons in PCR without reverse transcriptase confirmed the absence of DNA contamination. 500 ng of DNase I treated total RNA samples extracted were retrotranscribed using cDNA synthesis kit (MBI Fermentas) with random hexamer primers. Real Time PCR was performed using SYBR Green PCR master mix (Applied Biosystems, USA); sigA or rpoB was used as endogenous control. The relative expression of mce1 operon genes (Rv0167, Adenosine triphosphate Rv0170 and Rv0178) in M.tuberculosis H37Rv and VPCI591 and lacZ expression from the clones pPrRv and pPr591 in M.smegmatis was determined, using similar protocol. The experiments were repeated three times and the data was analyzed using the ΔΔCt method [42]. Acknowledgements The authors thank Indian Council for Medical Research, Govt. India, for financial support through research grants to MB and VB, Anil Tyagi (Delhi University) for pSD5B and other promoter constructs, Dipanker Chatterji (Indian Institute of Science, Bangalore)

for pSdps1 plasmid and Angel Cataldi (Institute of Biotechnology, Castelar, Argentina) for Rv0165c cloned in pET28a vector. MJ, SB and RP thank Council for Scientific and Industrial Research (CSIR), Govt. India for Senior Research Fellowship. Electronic supplementary material Additional file 1: Detection of putative promoter motif. Output consensus sequences of MEME mapped [bold upper case] on validated promoter sequences. The input sequences are from T6 to PA [gyr]. IGPr is the query sequence. Translation start site (ATG/GTG) of the gene driven by each promoter used as the reference for alignment is shown in capital. (DOC 26 KB) Additional file 2: Comparison of expression level of adjacent genes in different operons.