Transcriptional Regulator Induced Phenotype screen reveals drug potentiators in Mycobacterium tuberculosis

Transposon-based strategies provide a powerful and unbiased way to study bacterial stress response(1–8), but these approaches cannot fully capture the complexities of network-based behavior. Here, we present a network-based genetic screening approach: the Transcriptional Regulator Induced Phenotype (TRIP) screen, which we used to identify previously uncharacterized network adaptations of Mycobacterium tuberculosis (Mtb) to the first-line anti-TB drug isoniazid (INH). We found regulators that alter INH susceptibility when induced, several of which could not be identified by standard gene disruption approaches. We then focused on a specific regulator, mce3R, which potentiated INH activity when induced. We compared mce3R-regulated genes with baseline INH transcriptional responses and implicated the gene ctpD (Rv1469) as a putative INH effector. Evaluating a ctpD disruption mutant demonstrated a previously unknown role for this gene in INH susceptibility. Integrating TRIP screening with network information can uncover sophisticated molecular response programs.