Article

Network analysis identifies Rv0324 and Rv0880 as regulators of bedaquiline tolerance in Mycobacterium tuberculosis

  • Nature Microbiology 1, Article number: 16078 (2016)
  • doi:10.1038/nmicrobiol.2016.78
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Abstract

The resilience of Mycobacterium tuberculosis (MTB) emerges from its ability to effectively counteract immunological, environmental and antitubercular challenges. Here, we demonstrate that MTB can tolerate drug treatment by adopting a tolerant state that can be deciphered through systems analysis of its transcriptional responses. Specifically, we demonstrate how treatment with the antitubercular drug bedaquiline activates a regulatory network that coordinates multiple resistance mechanisms to push MTB into a tolerant state. Disruption of this network, by knocking out its predicted transcription factors, Rv0324 and Rv0880, significantly increased bedaquiline killing and enabled the discovery of a second drug, pretomanid, that potentiated killing by bedaquiline. We demonstrate that the synergistic effect of this combination emerges, in part, through disruption of the tolerance network. We discuss how this network strategy also predicts drug combinations with antagonistic interactions, potentially accelerating the discovery of new effective combination drug regimens for tuberculosis.

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Acknowledgements

The authors thank members of the Baliga and Sherman laboratories for discussions, T. Rustad, J. Winkler and S. Hobbs for generating knockout and overexpressing strains, and Z. Simon, M. Sarvothama and R. Liao for technical help. Funding was provided by the National Institute of Allergy and Infectious Diseases of the National Institutes of Health (U19 AI10676, U19 AI111276 and ISBpilot-10135) and the National Institute of General Medical Sciences of the National Institutes of Health (P50GM076547).

Author information

Author notes

    • Eliza J. R. Peterson
    •  & Shuyi Ma

    These authors contributed equally to this work.

Affiliations

  1. Institute for Systems Biology, Seattle, Washington 98109, USA

    • Eliza J. R. Peterson
    •  & Nitin S. Baliga
  2. Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington 98109, USA

    • Shuyi Ma
    •  & David R. Sherman
  3. Interdisciplinary Program of Pathobiology, Department of Global Health, University of Washington, Seattle, Washington 98195, USA

    • David R. Sherman
  4. Molecular and Cellular Biology Program, Departments of Microbiology and Biology, University of Washington, Seattle, Washington 98195, USA

    • Nitin S. Baliga
  5. Lawrence Berkeley National Laboratories, Berkeley, California 94720, USA

    • Nitin S. Baliga

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Contributions

E.J.R.P. led the design and drafted the manuscript. E.J.R.P. and S.M. generated results and analysed data. S.M. helped design the study and helped draft online methods. D.R.S. helped designed the study, discussed results and commented on the manuscript. N.S.B. conceived of the study, discussed the results and drafted the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Nitin S. Baliga.

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