Transcriptional response of mce3R induction and ctpD disruption in Mycobacterium tuberculosis CDC1551

We identified mce3R and ctpD as genes that could alter M tuberculosis (Mtb) response to isoniazid when perturbed using a regulatory network-based TRIP screen [see associated data at PRJNA483505]. To investigate the mechanisms underlying this response, we performed RNAseq on genetically perturbed mutant strains either in the presence or absence of isoniazid. Overall design: RNAseq analysis was performed on two Mtb mutant strains in the CDC1551 background: 1) CDC1551 transformed with an episomal plasmid that could induce mce3R (Rv1963c) expression upon supplementation with anhydrotetracycline (ATc), and 2) a ctpD (Rv1469) transposon disruption strain in the CDC1551 background (CDC1551::1469tn) transformed with an episomal plasmid that could induce mce3R expression upon ATc supplementation. Bacteria were harvested at 1 day after being exposed to isoniazid (3.6µM) or no drug, as indicated in each sample title. RNA was isolated and gene expression quantified by sequencing.