9 kDa GlnR protein in the mutant strain compared with the wild type (Supporting information, Fig. S2). A phenotypic GSK126 growth effect was observed by OD and CFU mL−1 for WT M. smegmatis cells grown in nitrogen-limiting media when compared with nitrogen-excess media (Fig. 1a and b). At the time of external nitrogen run-out, as determined by Aquaquant analysis (Fig. 1e), a reduction in growth rate between the two conditions is evident (Fig. 1a and b). Growth rate in the nitrogen-limiting media was restored to

the same rate as the nitrogen-excess media with the addition of an exogenous nitrogen source to the nitrogen-limiting media at this time point (Fig. 1a and b); no effect on growth rate was seen when exogenous nitrogen was added to the nitrogen-excess

media (data not shown). Further confirmation that our media was nitrogen-limiting and inducing a nitrogen-stress response in WT M. smegmatis cells was obtained by analysing the transcriptomic levels of genes known to be up-regulated in conditions of nitrogen limitation: amt1, amtB and glnA1 (Amon et al., 2008). The transcript levels BKM120 of amt1, amtB and glnA1 were all significantly induced in the nitrogen-limiting media, but not induced in the nitrogen-excess conditions at 13 h, 2 h after nitrogen run-out in the limiting media (Fig. 2). We therefore confirmed that our nitrogen-limiting conditions were stimulating a genetic response to nitrogen limitation in M. smegmatis. Growth kinetics of the M. smegmatis mutant strains in nitrogen-limiting RVX-208 and nitrogen-excess medium were performed. Although the M. smegmatis strains grew similarly in nitrogen-excess conditions (data not shown), the GlnR and GlnR_D48A mutants exhibited a reduced growth

rate when compared with the wild type under nitrogen-limiting conditions (Fig. 1c and d). However, no major growth defect was noted for either mutant strain; this is intriguing, suggesting that the M. smegmatis GlnR-mediated transcriptomic response is not essential for growth during nitrogen limitation. Another interesting observation was the reduced uptake of ammonium from the medium by both mutants. Two ammonium transporters (amtB and amt1) have previously been shown to be up-regulated under nitrogen limitation by GlnR (Amon et al., 2008). The inability of the GlnR mutant strains to induce expression of ammonium transporters could explain the observed reduction in growth rate, suggesting ammonium uptake in these mutants is by diffusion alone. The transcriptomic response of the wild type and mutants during nitrogen limitation was therefore investigated further.