Genome-wide gene expression tuning reveals diverse vulnerabilities of M. tuberculosis

Cell. 2021 Aug 19;184(17):4579-4592.e24. doi: 10.1016/j.cell.2021.06.033. | PubMed

Barbara Bosch¹, Michael A DeJesus¹, Nicholas C Poulton¹, Wenzhu Zhang², Curtis A Engelhart³, Anisha Zaveri³, Sophie Lavalette³, Nadine Ruecker³, Carolina Trujillo³, Joshua B Wallach³, Shuqi Li¹, Sabine Ehrt³, Brian T Chait², Dirk Schnappinger⁴, Jeremy M Rock⁵

1. Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA.
2. Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA.
3. Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA.
4. Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA. Electronic address: dis2003@med.cornell.edu.
5. Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA. Electronic address: rock@rockefeller.edu.

Abstract

Antibacterial agents target the products of essential genes but rarely achieve complete target inhibition. Thus, the all-or-none definition of essentiality afforded by traditional genetic approaches fails to discern the most attractive bacterial targets: those whose incomplete inhibition results in major fitness costs. In contrast, gene "vulnerability" is a continuous, quantifiable trait that relates the magnitude of gene inhibition to the effect on bacterial fitness. We developed a CRISPR interference-based functional genomics method to systematically titrate gene expression in Mycobacterium tuberculosis (Mtb) and monitor fitness outcomes. We identified highly vulnerable genes in various processes, including novel targets unexplored for drug discovery. Equally important, we identified invulnerable essential genes, potentially explaining failed drug discovery efforts. Comparison of vulnerability between the reference and a hypervirulent Mtb isolate revealed incomplete conservation of vulnerability and that differential vulnerability can predict differential antibacterial susceptibility. Our results quantitatively redefine essential bacterial processes and identify high-value targets for drug development.

Presented By Barbara Bosch and Michael A. DeJesus | ORCID iD