Intricate genetic programs controlling dormancy inMycobacterium tuberculosis

Abstract

Mycobacterium tuberculosis (MTB), responsible for the deadliest infectious disease worldwide, displays the remarkable ability to transition in and out of dormancy, a hallmark of the pathogen's capacity to evade the immune system and opportunistically exploit immunocompromised individuals. Uncovering the gene regulatory programs that underlie the dramatic phenotypic shifts in MTB during disease latency and reactivation has posed an extraordinary challenge. We developed a novel experimental system to precisely control dissolved oxygen levels in MTB cultures in order to capture the chain of transcriptional events that unfold as MTB transitions into and out of hypoxia-induced dormancy. Using a comprehensive genomewide transcription factor binding location map and insights from network topology analysis, we identified regulatory circuits that deterministically drive sequential transitions across six transcriptionally and functionally distinct states encompassing more than three-fifths of the MTB genome. The architecture of the genetic programs explains the transcriptional dynamics underlying synchronous entry of cells into a dormant state that is primed to infect the host upon encountering favorable conditions. One Sentence Summary: High-resolution transcriptional time-course reveals six-state genetic program that enables MTB to enter and exit hypoxia-induced dormancy.Main Text: Mycobacterium tuberculosis (MTB) kills more people than any other infectious agent, causing ~10 million new cases of active tuberculosis (TB) disease and 1.7 million deaths each year (Murray et al., 2014). TB remains a major human public health burden, in large part due to the sizeable reservoir of latently infected individuals, who may relapse into active disease decades after acquiring the infection. MTB can persist in a stable, non-replicative (often termed dormant) state within the host for months or years without symptoms, and then revive to initiate the production of lesions and active TB disease. Moreover, dormant cells may be responsible for the slow treatment response of patients with active TB. Elucidation of the factors that affect treatment outcome, latency and activation requires a better characterization of functional states adopted by the pathogen during progression of the disease, as well as a mechanistic understanding of the genetic programs that orchestrate transitions between these states.Hypoxia, an environmental stress encountered by MTB within granulomas (Tsai et al., 2006), is sufficient to shift the pathogen into a defined non-growing survival form, which can be reversed upon aeration of the culture (Chao and Rubin, 2010). Therefore, hypoxia has been leveraged as an in vitro approximation to study MTB dormancy and the underlying genetic programs. However, previous transcriptional analyses under in vitro hypoxic conditions (via the Wayne model in which MTB cultures are sealed and gradually depleted of oxygen (Wayne and Hayes, 1996;Wayne and Sohaskey, 2001) or the defined hypoxia model in which nitrogen gas is flowed into...