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Inhibition of innate immune cytosolic surveillance by an M. tuberculosis phosphodiesterase

Nature Chemical Biology volume 13, pages 210–217 (2017)Cite this article

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Abstract

Mycobacterium tuberculosis infection leads to cytosolic release of the bacterial cyclic dinucleotide (CDN) c-di-AMP and a host-generated CDN, cGAMP, both of which trigger type I interferon (IFN) expression in a STING-dependent manner. Here we report that M. tuberculosis has developed a mechanism to inhibit STING activation and the type I IFN response via the bacterial phosphodiesterase (PDE) CdnP, which mediates hydrolysis of both bacterial-derived c-di-AMP and host-derived cGAMP. Mutation of cdnP attenuates M. tuberculosis virulence, as does loss of a host CDN PDE known as ENPP1. CdnP is inhibited by both US Food and Drug Administration (FDA)-approved PDE inhibitors and nonhydrolyzable dinucleotide mimetics specifically designed to target the enzyme. These findings reveal a crucial role of CDN homeostasis in governing the outcome of M. tuberculosis infection as well as a unique mechanism of subversion of the host's cytosolic surveillance pathway (CSP) by a bacterial PDE that may serve as an attractive antimicrobial target.

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Figure 1: M. tuberculosis CdnP hydrolyzes both bacterial and host CDNs.
Figure 2: Disruption of CdnP activity leads to virulence attenuation of M. tuberculosis.
Figure 3: CdnP activity regulates host CSP activation and type I IFN responses.
Figure 4: Regulation of intramacrophage CDN homeostasis by bacterial CdnP and host ENPP1.
Figure 5: Inhibition of CdnP by PDE inhibitors and ApA analogs.
Figure 6: A schematic model for regulation of CDN signaling and inhibition of cGAS-mediated innate surveillance by M. tuberculosis CdnP.

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Acknowledgements

We gratefully acknowledge support from NIAID (grants AI037856, AI097138, and AI036973 to W.R.B.), the Howard Hughes Medical Institute (W.R.B.), and the NSF (grants CHE 1307218 and CHE 1636752 to H.O.S.). Funding from the Camille and Dreyfus Foundation (Teacher-Scholar fellowship to H.O.S.) is also acknowledged. Y.Z. is supported by a Mehta Research Award. J.Z. is supported by a University of Maryland Graduate Dean's Dissertation Fellowship. We thank B. Roembke at UMD for help with dinucleotide synthesis. We thank H.W. Virgin IV and D. MacDuff (Washington University School of Medicine, St. Louis, Missouri, USA) for generously providing bone marrow cells from cGAS-deficient mice. We thank A. Sher and K. Mayer-Barber (NIH, Bethesda, Maryland, USA) for generously providing Ifnar1−/− mice. We thank K.-P. Hopfner (Department of Biochemistry and Gene Center, Ludwig-Maximilians-University, Munich, Germany) for providing the plasmid to make DisA. We thank A. Gründling (Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK) for providing the plasmid to make GdpP. We thank Z.-X. Liang (Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore) for providing the plasmid to make YybT. We thank S. Pelly for editing the manuscript.

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Author notes

  1. Bappaditya Dey & Yue Zheng

    Present address: Present addresses: National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA (B.D.); National Institutes of Health, Bethesda, Maryland, USA (Y.Z.).,

  2. Ruchi Jain Dey, Bappaditya Dey and Yue Zheng: These authors contributed equally to this work.

Authors and Affiliations

  1. Center for Tuberculosis Research, Johns Hopkins University, Baltimore, Maryland, USA

    Ruchi Jain Dey, Bappaditya Dey, Laurene S Cheung, Pankaj Kumar, Haidan Guo, Gyanu Lamichhane & William R Bishai

  2. Howard Hughes Medical Institute, Chevy Chase, Maryland, USA

    Ruchi Jain Dey, Bappaditya Dey & William R Bishai

  3. Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland, USA

    Yue Zheng, Jie Zhou, David Sayre & Herman O Sintim

  4. Department of Chemistry and Institute for Drug Discovery, Purdue University, West Lafayette, Indiana, USA

    Yue Zheng, Jie Zhou & Herman O Sintim

  5. Purdue Institute of Inflammation, Immunology and Infectious Disease, West Lafayette, Indiana, USA

    Herman O Sintim

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Contributions

R.J.D., B.D., and Y.Z. designed the experiments in consultation with W.R.B. and H.O.S. Molecular biology, microbiology, cell culture, and animal-based experiments were performed by R.J.D. and B.D. Y.Z. performed biochemical enzymatic assays. J.Z. and D.S. performed chemical synthesis of compounds. L.S.C. contributed to mass spectrometry experiments. P.K. and G.L. contributed to isothermal titration calorimetry experiments. H.G. contributed to mouse experiments. R.J.D. and B.D. wrote the manuscript with input from Y.Z., J.Z., D.S., P.K., L.S.C., H.O.S., and W.R.B. W.R.B. provided overall supervision of the study. All the authors contributed to editing of the manuscript and approved the conclusions.

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Correspondence to Herman O Sintim or William R Bishai.

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Supplementary Results, Supplementary Tables 1–4 and Supplementary Figures 1–19. (PDF 1856 kb)

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Dey, R., Dey, B., Zheng, Y. et al. Inhibition of innate immune cytosolic surveillance by an M. tuberculosis phosphodiesterase. Nat Chem Biol 13, 210–217 (2017). https://doi.org/10.1038/nchembio.2254

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