Mycobacterium tuberculosis (Mtb) is the world’s most deadly pathogen. Unlike less virulent mycobacteria, Mtb produces 1-tuberculosinyladenosine (1-TbAd), an unusual terpene nucleoside of unknown function. In the present study 1-TbAd has been shown to be a naturally evolved phagolysosome disruptor. 1-TbAd is highly prevalent among patient-derived Mtb strains, where it is among the most abundant lipids produced. Synthesis of TbAd analogs and their testing in cells demonstrate that their biological action is dependent on lipid linkage to the 1-position of adenosine, which creates a strong conjugate base. Furthermore, C20 lipid moieties confer passage through membranes. 1-TbAd selectively accumulates in acidic compartments, where it neutralizes the pH and swells lysosomes, obliterating their multilamellar structure. During macrophage infection, a 1-TbAd biosynthesis gene (Rv3378c) confers marked phagosomal swelling and intraphagosomal inclusions, demonstrating an essential role in regulating the Mtb cellular microenvironment. Although macrophages kill intracellular bacteria through phagosome acidification, Mtb coats itself abundantly with antacid.
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Institutional review boards require confidentiality of patient data and biological material. Distribution of Mtb strains is subject to biosafety approvals. Otherwise, all data and reagents are available.
Global Tuberculosis Report (WHO, 2018).
Armstrong, J. A. & Hart, P. D. Response of cultured macrophages to Mycobacterium tuberculosis, with observations on fusion of lysosomes with phagosomes. J. Exp. Med. 134, 713–740 (1971).
Sturgill-Koszycki, S. et al. Lack of acidification in Mycobacterium phagosomes produced by exclusion of the vesicular proton-ATPase. Science 263, 678–681 (1994).
Vandal, O. H., Nathan, C. F. & Ehrt, S. Acid resistance in Mycobacterium tuberculosis. J. Bacteriol. 191, 4714–4721 (2009).
McKinney, J. D. et al. Persistence of Mycobacterium tuberculosis in macrophages and mice requires the glyoxylate shunt enzyme isocitrate lyase. Nature 406, 735–738 (2000).
Russell, D. G. Phagosomes, fatty acids and tuberculosis. Nat. Cell Biol. 5, 776–778 (2003).
Behr, M. A. et al. Comparative genomics of BCG vaccines by whole-genome DNA microarray. Science 284, 1520–1523 (1999).
Layre, E. et al. A comparative lipidomics platform for chemotaxonomic analysis of Mycobacterium tuberculosis. Chem. Biol. 18, 1537–1549 (2011).
Galagan, J. E. et al. The Mycobacterium tuberculosis regulatory network and hypoxia. Nature 499, 178–183 (2013).
Layre, E. et al. Molecular profiling of Mycobacterium tuberculosis identifies tuberculosinyl nucleoside products of the virulence-associated enzyme Rv3378c. Proc. Natl Acad. Sci. USA 111, 2978–2983 (2014).
Pan, S. J. et al. Biomarkers for tuberculosis based on secreted, species-specific, bacterial small molecules. J. Infect. Dis. 212, 1827–1834 (2015).
Young, D. C. et al. In vivo biosynthesis of terpene nucleosides provides unique chemical markers of Mycobacterium tuberculosis infection. Chem. Biol. 22, 516–526 (2015).
Layre, E., de Jong, A. & Moody, D. B. Human T cells use CD1 and MR1 to recognize lipids and small molecules. Curr. Opin. Chem. Biol. 23c, 31–38 (2014).
Pethe, K. et al. Isolation of Mycobacterium tuberculosis mutants defective in the arrest of phagosome maturation. Proc. Natl Acad. Sci. USA 101, 13642–13647 (2004).
Vandal, O. H., Pierini, L. M., Schnappinger, D., Nathan, C. F. & Ehrt, S. A membrane protein preserves intrabacterial pH in intraphagosomal Mycobacterium tuberculosis. Nat. Med. 14, (849–854 (2008).
Heyl, A., Riefler, M., Romanov, G. A. & Schmulling, T. Properties, functions and evolution of cytokinin receptors. Eur. J. Cell Biol. 91, 246–256 (2012).
Cekic, C. & Linden, J. Purinergic regulation of the immune system. Nat. Rev. 16, 177–192 (2016).
MacMicking, J. D. Cell-autonomous effector mechanisms against Mycobacterium tuberculosis. Cold Spring Harb. Perspect. Med. 4, a018507 (2014).
Rohde, K., Yates, R. M., Purdy, G. E. & Russell, D. G. Mycobacterium tuberculosis and the environment within the phagosome. Immunol. Rev. 219, 37–54 (2007).
Deretic, V. et al. Immunologic manifestations of autophagy. J. Clin. Invest. 125, 75–84 (2015).
Kapinos, L. E., Operschall, B. P., Larsen, E. & Sigel, H. Understanding the acid–base properties of adenosine: the intrinsic basicities of N1, N3 and N7. Chemistry 17, 8156–8164 (2011).
Martin, M. G. & Reese, C. B. Some aspects of the chemistry of N(1)- and N(6)-dimethylallyl derivatives of adenosine and adenine. J. Chem. Soc. Perkin 1, 1731–1738 (1968).
Winterbourn, C. C., Hampton, M. B., Livesey, J. H. & Kettle, A. J. Modeling the reactions of superoxide and myeloperoxidase in the neutrophil phagosome: implications for microbial killing. J. Biol. Chem. 281, 39860–39869 (2006).
Buter, J. et al. Stereoselective synthesis of 1-tuberculosinyl sdenosine: a virulence factor of Mycobacterium tuberculosis. J. Org. Chem. 81, 6686–6696 (2016).
Tan, S., Yates, R. M. & Russell, D. G. Mycobacterium tuberculosis: readouts of bacterial fitness and the environment within the phagosome. Methods Mol. Biol. 1519, 333–347 (2017).
Podinovskaia, M., Lee, W., Caldwell, S. & Russell, D. G. Infection of macrophages with Mycobacterium tuberculosis induces global modifications to phagosomal function. Cell Microbiol. 15, 843–859 (2013).
de Duve, C. et al. Commentary. Lysosomotropic agents. Biochem. Pharmacol. 23, 2495–2531 (1974).
Nadanaciva, S. et al. A high content screening assay for identifying lysosomotropic compounds. Toxicology In Vitro 25, 715–723 (2011).
Plantone, D. & Koudriavtseva, T. Current and future use of chloroquine and hydroxychloroquine in infectious, immune, neoplastic, and neurological diseases: a mini-review. Clin. Drug Invest. 38, 653–671 (2018).
Feng, X. et al. Antiinfectives targeting enzymes and the proton motive force. Proc. Natl Acad. Sci. USA 112, E7073–E7082 (2015).
Mann, F. M. et al. Edaxadiene: a new bioactive diterpene from Mycobacterium tuberculosis. J. Am. Chem.Soc. 131, 17526–17527 (2009).
Sani, M. et al. Direct visualization by cryo-EM of the mycobacterial capsular layer: a labile structure containing ESX-1-secreted proteins. PLoS Pathog. 6, e1000794 (2010).
Samanovic, M. I. et al. Proteasomal control of cytokinin synthesis protects Mycobacterium tuberculosis against nitric oxide. Mol. Cell 57, 984–994 (2015).
Deretic, V. Autophagy in tuberculosis. Cold Spring Harb. Perspect. Med. 4, a018481 (2014).
van der Wel, N. et al. M. tuberculosis and M. leprae translocate from the phagolysosome to the cytosol in myeloid cells. Cell 129, 1287–1298 (2007).
Murphy, K. C., Papavinasasundaram, K. & Sassetti, C. M. Mycobacterial recombineering. Methods Mol. Biol. 1285, 177–199 (2015).
Guinn, K. M. et al. Individual RD1-region genes are required for export of ESAT-6/CFP-10 and for virulence of Mycobacterium tuberculosis. Mol. Microbiol. 51, 359–370 (2004).
The authors thank H. van Veen and W. Tigchelaar for EM, P. Reinink for phylogenetic graphs and S. Suliman for advice. Work was supported by grant nos. AI116604 (to D.B.M. and N.N.v.d.W.), AI111224 (to D.B.M. and M.M.), GM065307 (to E.O.), CA158191 (to E.O.) and AI114952 (to S.T.), the Dutch Science Foundation NWO-VICI 70.57.443 (to A.J.M.) and a Canadian Institute of Health Research Foundation grant 148362 (to M.A.B.).
The authors declare no competing interests.
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Nature Chemical Biology (2019)