MtrA regulation of essential peptidoglycan cleavage in Mycobacterium tuberculosis during infection [pH]

The success of Mycobacterium tuberculosis (Mtb) is largely due to its ability to withstand numerous stresses imposed by host immunity. Here, we present a data-driven model that captures these adaptive mechanisms and reveals the dynamic interplay of host-derived stresses and genome-encoded regulatory programs in Mtb. The model captures the genome-wide distribution of cis-acting gene regulatory elements and the conditional influences of transcription factors at those elements to elicit environment-specific responses. Analysis of transcriptional responses that may be essential for Mtb's survival in acidic conditions identified regulatory control by the MtrAB two-component signal system. This data is a comparison of transcriptional differences (RNA-seq) between low pH (pH 5.6) and neutral pH (pH7) of Mtb Overall design: To investigate gene expression changes of M. tuberculosis at acidic pH, cultures of M. tuberculosis were cultured in standard 7H9-rich media to mid-log phase, washed three times in 1x PBS and diluted back to OD600 = 0.1 into either neutral or acidic pH media. Samples, in biological triplicate, were collected right after transfer and after 24 hours in neutral or acidic pH media. Samples were centrifuged at high speed for 5 min, supernatant was discarded and the cell pellet was immediately flash frozen in liquid nitrogen. Cell pellets were stored at -80° C until RNA extraction was performed. The sequence reads that passed quality filters were aligned with Bowtie2 and processed using the R package DuffyNGS.