Fig 3. Global expression of acid-inducible mycobacterial genes require the phoR locus.

(A) RNA-sequencing derived heat-map showing ~ 31 low pH-inducible genes that are differentially regulated in ΔphoR-H37Rv (>2.0 fold; p< 0.05) grown under low pH (pH 4.5) conditions compared to normal conditions (pH 7.0) of growth. The data, which represent average of two biological replicates, list significantly activated pH-inducible genes, majority of which are part of the PhoP regulon. (B) PhoR-dependent expression of acidic pH-inducible genes were examined by comparing expression of representative mycobacterial genes in WT-H37Rv, ΔphoR-H37Rv, and complemented strain, grown under normal and acidic pH conditions. The data show plots of average values from biological duplicates, each performed with one technical repeat (*P≤0.05; **P≤0.01; ***P≤0.001). (C) To examine in vivo recruitment of PhoP within its target promoters, ChIP was carried out using anti-PhoP antibody followed by qPCR using IP samples from WT-H37Rv and ΔphoR-H37Rv (see Methods section for further details). To assess fold enrichment, each data point was compared with the corresponding IP sample without adding antibody. The experiments were carried out as biological duplicates, each with at least one technical repeat (*P≤0.05; **P≤0.01). Non-significant differences are not indicated.