05. Hypoxic cultures (standing) were established by dispensing 200 μL culture aliquots into 96-well black, clear-bottom microtitre plates and incubating the plates at 37 °C. The aerobic promoter activity was measured in cultures that were simultaneously grown in 50-mL tubes (5 mL of culture). Culture aliquots of 200 μL were sampled at 48 h and the GFP fluorescence was measured in a spectrofluorimeter (Molecular Devices, Sunnyvale, CA) with an excitation wavelength of 483 nm and an emission wavelength of 515 nm. The 178-bp narK2 promoter region was amplified LBH589 clinical trial by PCR using NarK2R1 and NarK2F

primers (Fig. 1, Table 2) and genomic DNA of the various standard or clinical strains. The PCR conditions were a 10-min initial denaturation phase at 94 °C, followed by 40 cycles of 30 s at 94 °C, 30 s at 60 °C and 30 s at 72 °C and, finally, 7 min at 72 °C. selleck screening library A 10-μL aliquot of

the PCR product was digested with NheI for 90 min, electrophoresed on a 6% nondenaturing polyacrylamide gel and visualized using ethidium bromide. Mycobacterium bovis AN5 was complemented with the integrating plasmid pNarG-GM1 expressing the M. tb narGHJI operon (Sohaskey & Modesti, 2009) or the pNarK2X plasmid expressing the M. tb narK2X operon, (see Table 1) or both pNarG-GM1 and pNarK2X. To construct pNarK2X, the region encompassing the coding regions of narK2 and narX along with a 280-bp upstream promoter was amplified by PCR using Fusion DNA polymerase (NEB, UK) and M. tb H37Rv DNA and cloned in the EcoR1 and Clomifene HindIII sites of pFPV27 mycobacterial shuttle vector. The resultant plasmid was electroporated into M. bovis or M. bovis-harbouring pNarG-GM1. Nitrate reductase assay was performed with aerobic

shaking and 48-h standing cultures (hypoxic). Briefly, the cultures were grown aerobically as described above in the presence of 5 mM nitrate and standing cultures (starting OD595 nm, 0.05) were maintained for 48 h in 96-well microtitre plates as described previously (Chauhan & Tyagi, 2008b). The nitrite concentration was determined using the Griess reaction as described (Wayne & Doubek, 1965). Briefly, 50 μL of sulfanilamide was added to 50 μL of cultures (both aerobic and standing) and incubated at room temperature for 5–10 min. Next, 50 μL of N-1-napthylethylenediamine dihydrochloride was added and the A595 nm was measured in a plate reader (Biorad). To test the hypothesis that the lack of hypoxic induction of narK2 and narX in M. bovis/BCG is because of a −6T/C SNP in the narK2X promoter region, we mutated the M. tb narK2 promoter by changing thymine at the −6 position to cytosine (−6TC) in the narK2 promoter plasmid, pnarK2, to mimic the observed mutation at this site in M. bovis/BCG. The effect of this mutation on promoter activity was assessed in M. tb H37Rv under hypoxic conditions using the GFP reporter assay. The −6TC mutation completely abolished the hypoxic induction of pnarK2 (Fig.