PrrA modulates Mycobacterium tuberculosis response to acidic pH and high chloride levels

The purpose of this study was to identify genes that are differentially expressed upon prrA overexpression, to reveal the impact of PrrA on global transcription in acidic pH and/or high chloride conditions. Mtb strain CDC1551 harboring a tetracycline inducible prrA-FLAG construct was grown to an OD600 of ~0.6 in standing, filter-capped T-75 flasks and treated with either ethanol (EtOH) as a carrier control or 200 ng/ml anhydrotetracycline (ATC) for 2 hours. Bacteria were then subcultured to an OD600 = 0.3 in standing, filter-capped T-25 flasks in 7H9, pH 7 media ± 250 mM NaCl, or 7H9, pH 5.7 media ± 250 mM NaCl, with continued presence of EtOH or ATC as appropriate. Exposure to the different media conditions was for 4 hours in a humidified, 37°C, 5% CO2 incubator before RNA was extracted. RNA was prepared by removing the rRNA and library prepping with a TruSeq Stranded kit (Illumina) before high-throughput sequencing with an Illumina HiSeq 2500 (High Output v4) (100 bp single end reads, one lane). Two biological samples per condition were sequenced.