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. Epub 2021 Jul 22.


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.

Keywords: Bayes Theorem; CRISPR-Cas Systems; Drug Development; Essential genes; Mass Spectrometry; Mycobacterium smegmatis; Mycobacterium tuberculosis; Vulnerability.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acyl-tRNA Synthetases / metabolism
  • Antitubercular Agents / pharmacology
  • Bayes Theorem
  • Biological Evolution
  • Clustered Regularly Interspaced Short Palindromic Repeats / genetics
  • Gene Expression Regulation, Bacterial* / drug effects
  • Gene Silencing / drug effects
  • Genome, Bacterial*
  • Microbial Sensitivity Tests
  • Mycobacterium tuberculosis / drug effects
  • Mycobacterium tuberculosis / genetics*
  • RNA, Guide, CRISPR-Cas Systems / genetics


  • Antitubercular Agents
  • RNA, Guide, CRISPR-Cas Systems
  • Amino Acyl-tRNA Synthetases