eLife (Nov 2020)

Arrayed CRISPRi and quantitative imaging describe the morphotypic landscape of essential mycobacterial genes

  • Timothy J de Wet,
  • Kristy R Winkler,
  • Musa Mhlanga,
  • Valerie Mizrahi,
  • Digby F Warner

DOI
https://doi.org/10.7554/eLife.60083
Journal volume & issue
Vol. 9

Abstract

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Mycobacterium tuberculosis possesses a large number of genes of unknown or predicted function, undermining fundamental understanding of pathogenicity and drug susceptibility. To address this challenge, we developed a high-throughput functional genomics approach combining inducible CRISPR-interference and image-based analyses of morphological features and sub-cellular chromosomal localizations in the related non-pathogen, M. smegmatis. Applying automated imaging and analysis to 263 essential gene knockdown mutants in an arrayed library, we derive robust, quantitative descriptions of bacillary morphologies consequent on gene silencing. Leveraging statistical-learning, we demonstrate that functionally related genes cluster by morphotypic similarity and that this information can be used to inform investigations of gene function. Exploiting this observation, we infer the existence of a mycobacterial restriction-modification system, and identify filamentation as a defining mycobacterial response to histidine starvation. Our results support the application of large-scale image-based analyses for mycobacterial functional genomics, simultaneously establishing the utility of this approach for drug mechanism-of-action studies.

Keywords