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Suppression of autophagy and antigen presentation by Mycobacterium tuberculosis PE_PGRS47

Abstract

Suppression of major histocompatibility complex (MHC) class II antigen presentation is believed to be among the major mechanisms used by Mycobacterium tuberculosis to escape protective host immune responses. Through a genome-wide screen for the genetic loci of M. tuberculosis that inhibit MHC class II-restricted antigen presentation by mycobacteria-infected dendritic cells, we identified the PE_PGRS47 protein as one of the responsible factors. Targeted disruption of the PE_PGRS47 (Rv2741) gene led to attenuated growth of M. tuberculosis in vitro and in vivo, and a PE_PGRS47 mutant showed enhanced MHC class II-restricted antigen presentation during in vivo infection of mice. Analysis of the effects of deletion or over-expression of PE_PGRS47 implicated this protein in the inhibition of autophagy in infected host phagocytes. Our findings identify PE_PGRS47 as a functionally relevant, non-redundant bacterial factor in the modulation of innate and adaptive immunity by M. tuberculosis, suggesting strategies for improving antigen presentation and the generation of protective immunity during vaccination or infection.

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Figure 1: Identification of Mtb cosmid clones that inhibit MHC class II antigen presentation.
Figure 2: Inhibition of autophagy by PE_PGRS47.
Figure 3: Increased acidification and lysosomal fusion of phagosomes containing Mtb ΔPE_PGRS47.
Figure 4: PE_PGRS47 is required for full virulence at late stages of Mtb infection.
Figure 5: Autophagy-dependent enhancement of MHC class II antigen presentation during in vitro infection by the Mtb ΔPE_PGRS47 mutant.
Figure 6: Suppression of CD4+ T-cell responses by PE_PGRS47.

References

  1. 1

    Wolf, A. J. et al. Mycobacterium tuberculosis infects dendritic cells with high frequency and impairs their function in vivo. J. Immunol. 179, 2509–2519 (2007).

    Article  Google Scholar 

  2. 2

    Mogues, T., Goodrich, M. E., Ryan, L., LaCourse, R. & North, R. J. The relative importance of T cell subsets in immunity and immunopathology of airborne Mycobacterium tuberculosis infection in mice. J. Exp. Med. 193, 271–280 (2001).

    Article  Google Scholar 

  3. 3

    Repique, C. J. et al. Susceptibility of mice deficient in the MHC class II transactivator to infection with Mycobacterium tuberculosis. Scand. J. Immunol. 58, 15–22 (2003).

    Article  Google Scholar 

  4. 4

    Scanga, C. A. et al. Depletion of CD4+ T cells causes reactivation of murine persistent tuberculosis despite continued expression of interferon gamma and nitric oxide synthase 2. J. Exp. Med. 192, 347–358 (2000).

    Article  Google Scholar 

  5. 5

    Baena, A. & Porcelli, S. A. Evasion and subversion of antigen presentation by Mycobacterium tuberculosis. Tissue Antigens 74, 189–204 (2009).

    Article  Google Scholar 

  6. 6

    Harding, C. V. & Boom, W. H. Regulation of antigen presentation by Mycobacterium tuberculosis: a role for Toll-like receptors. Nature Rev. Microbiol. 8, 296–307 (2010).

    Article  Google Scholar 

  7. 7

    Pai, R. K., Convery, M., Hamilton, T. A., Boom, W. H. & Harding, C. V. Inhibition of IFN-γ-induced class II transactivator expression by a 19-kDa lipoprotein from Mycobacterium tuberculosis: a potential mechanism for immune evasion. J. Immunol. 171, 175–184 (2003).

    Article  Google Scholar 

  8. 8

    Pennini, M. E. et al. CCAAT/enhancer-binding protein β and δ binding to CIITA promoters is associated with the inhibition of CIITA expression in response to Mycobacterium tuberculosis 19-kDa lipoprotein. J. Immunol. 179, 6910–6918 (2007).

    Article  Google Scholar 

  9. 9

    Dengjel, J. et al. Autophagy promotes MHC class II presentation of peptides from intracellular source proteins. Proc. Natl Acad. Sci. USA 102, 7922–7927 (2005).

    Article  Google Scholar 

  10. 10

    Paludan, C. et al. Endogenous MHC class II processing of a viral nuclear antigen after autophagy. Science 307, 593–596 (2005).

    Article  Google Scholar 

  11. 11

    Schmid, D., Pypaert, M. & Munz, C. Antigen-loading compartments for major histocompatibility complex class II molecules continuously receive input from autophagosomes. Immunity 26, 79–92 (2007).

    Article  Google Scholar 

  12. 12

    Zhou, D. et al. Lamp-2a facilitates MHC class II presentation of cytoplasmic antigens. Immunity 22, 571–581 (2005).

    Article  Google Scholar 

  13. 13

    Singh, S. B., Davis, A. S., Taylor, G. A. & Deretic, V. Human IRGM induces autophagy to eliminate intracellular mycobacteria. Science 313, 1438–1441 (2006).

    Article  Google Scholar 

  14. 14

    Gutierrez, M. G. et al. Autophagy is a defense mechanism inhibiting BCG and Mycobacterium tuberculosis survival in infected macrophages. Cell 119, 753–766 (2004).

    Article  Google Scholar 

  15. 15

    Shin, D. M. et al. Mycobacterium tuberculosis Eis regulates autophagy, inflammation, and cell death through redox-dependent signaling. PLoS Pathogens 6, e1001230 (2010).

    Article  Google Scholar 

  16. 16

    Romagnoli, A. et al. ESX-1 dependent impairment of autophagic flux by Mycobacterium tuberculosis in human dendritic cells. Autophagy 8, 1357–1370 (2012).

    Article  Google Scholar 

  17. 17

    Espert, L., Beaumelle, B. & Vergne, I. Autophagy in Mycobacterium tuberculosis and HIV infections. Front. Cell. Infect. Microbiol. 5, 49 (2015).

    Article  Google Scholar 

  18. 18

    Rudensky, A., Preston-Hurlburt, P., Hong, S. C., Barlow, A. & Janeway, C. A. Jr. Sequence analysis of peptides bound to MHC class II molecules. Nature 353, 622–627 (1991).

    Article  Google Scholar 

  19. 19

    Deretic, V., Saitoh, T. & Akira, S. Autophagy in infection, inflammation and immunity. Nature Rev. Immunol. 13, 722–737 (2013).

    Article  Google Scholar 

  20. 20

    Munz, C. Enhancing immunity through autophagy. Annu. Rev. Immunol. 27, 423–449 (2009).

    Article  Google Scholar 

  21. 21

    Mizushima, N., Yoshimori, T. & Levine, B. Methods in mammalian autophagy research. Cell 140, 313–326 (2010).

    Article  Google Scholar 

  22. 22

    Tian, C. & Jian-Ping, X. Roles of PE_PGRS family in Mycobacterium tuberculosis pathogenesis and novel measures against tuberculosis. Microb. Pathog. 49, 311–314 (2010).

    Article  Google Scholar 

  23. 23

    Brennan, M. J. & Delogu, G. The PE multigene family: a ‘molecular mantra’ for mycobacteria. Trends Microbiol. 10, 246–249 (2002).

    Article  Google Scholar 

  24. 24

    Bardarov, S. et al. Specialized transduction: an efficient method for generating marked and unmarked targeted gene disruptions in Mycobacterium tuberculosis, M. bovis BCG and M. smegmatis. Microbiology 148, 3007–3017 (2002).

    Article  Google Scholar 

  25. 25

    Rusten, T. E. & Stenmark, H. p62, an autophagy hero or culprit? Nature Cell Biol. 12, 207–209 (2010).

    Article  Google Scholar 

  26. 26

    Bold, T. D., Banaei, N., Wolf, A. J. & Ernst, J. D. Suboptimal activation of antigen-specific CD4+ effector cells enables persistence of M. tuberculosis in vivo. PLoS Pathogens 7, e1002063 (2011).

    Article  Google Scholar 

  27. 27

    Reiley, W. W. et al. ESAT-6-specific CD4T cell responses to aerosol Mycobacterium tuberculosis infection are initiated in the mediastinal lymph nodes. Proc. Natl Acad. Sci. USA. 105, 10961–10966 (2008).

    Article  Google Scholar 

  28. 28

    Kruh, N. A., Troudt, J., Izzo, A., Prenni, J. & Dobos, K. M. Portrait of a pathogen: the Mycobacterium tuberculosis proteome in vivo. PLoS ONE 5, e13938 (2010).

    Article  Google Scholar 

  29. 29

    Simeone, R., Bottai, D., Frigui, W., Majlessi, L. & Brosch, R. ESX/type VII secretion systems of mycobacteria: insights into evolution, pathogenicity and protection. Tuberculosis (Edinb.) 95(Suppl 1), S150–S154 (2015).

    CAS  Article  Google Scholar 

  30. 30

    Srivastava, V., Jain, A., Srivastava, B. S. & Srivastava, R. Selection of genes of Mycobacterium tuberculosis upregulated during residence in lungs of infected mice. Tuberculosis (Edinb.) 88, 171–177 (2008).

    Article  Google Scholar 

  31. 31

    Copin, R. et al. Sequence diversity in the pe_pgrs genes of Mycobacterium tuberculosis is independent of human T cell recognition. mBio 5, e00960–e00913 (2014).

    Article  Google Scholar 

  32. 32

    Lee, H. K. et al. In vivo requirement for Atg5 in antigen presentation by dendritic cells. Immunity 32, 227–239 (2010).

    Article  Google Scholar 

  33. 33

    Deretic, V. Autophagy, an immunologic magic bullet: Mycobacterium tuberculosis phagosome maturation block and how to bypass it. Future Microbiol. 3, 517–524 (2008).

    Article  Google Scholar 

  34. 34

    Koul, A., Herget, T., Klebl, B. & Ullrich, A. Interplay between mycobacteria and host signalling pathways. Nature Rev. Microbiol. 2, 189–202 (2004).

    Article  Google Scholar 

  35. 35

    Watson, R. O., Manzanillo, P. S. & Cox, J. S. Extracellular M. tuberculosis DNA targets bacteria for autophagy by activating the host DNA-sensing pathway. Cell 150, 803–815 (2012).

    Article  Google Scholar 

  36. 36

    Ouimet, M. et al. Mycobacterium tuberculosis induces the miR-33 locus to reprogram autophagy and host lipid metabolism. Nature Immunol. 17, 677–686 (2016).

    Article  Google Scholar 

  37. 37

    Kimmey, J. M. et al. Unique role for ATG5 in neutrophil-mediated immunopathology during M. tuberculosis infection. Nature 528, 565–569 (2015).

    Article  Google Scholar 

  38. 38

    Cadieux, N. et al. Induction of cell death after localization to the host cell mitochondria by the Mycobacterium tuberculosis PE_PGRS33 protein. Microbiology 157, 793–804 (2011).

    Article  Google Scholar 

  39. 39

    Braunstein, M., Bardarov, S. S. & Jacobs, W. R. Jr. Genetic methods for deciphering virulence determinants of Mycobacterium tuberculosis. Methods Enzymol. 358, 67–99 (2002).

    Article  Google Scholar 

  40. 40

    Stover, C. K. et al. New use of BCG for recombinant vaccines. Nature 351, 456–460 (1991).

    Article  Google Scholar 

  41. 41

    Hinchey, J. et al. Enhanced priming of adaptive immunity by a proapoptotic mutant of Mycobacterium tuberculosis. J. Clin. Invest. 117, 2279–2288 (2007).

    Article  Google Scholar 

  42. 42

    Lutz, M. B. et al. An advanced culture method for generating large quantities of highly pure dendritic cells from mouse bone marrow. J. Immunol. Methods 223, 77–92 (1999).

    Article  Google Scholar 

  43. 43

    Houben, E. N., Nguyen, L. & Pieters, J. Interaction of pathogenic mycobacteria with the host immune system. Curr. Opin. Microbiol. 9, 76–85 (2006).

    Article  Google Scholar 

  44. 44

    Mizushima, N., Yamamoto, A., Matsui, M., Yoshimori, T. & Ohsumi, Y. In vivo analysis of autophagy in response to nutrient starvation using transgenic mice expressing a fluorescent autophagosome marker. Mol. Biol. Cell 15, 1101–1111 (2004).

    Article  Google Scholar 

  45. 45

    Forestier, C. et al. Improved outcomes in NOD mice treated with a novel Th2 cytokine-biasing NKT cell activator. J. Immunol. 178, 1415–1425 (2007).

    Article  Google Scholar 

  46. 46

    Yuk, J. M. et al. Vitamin D3 induces autophagy in human monocytes/macrophages via cathelicidin. Cell Host Microbe 6, 231–243 (2009).

    Article  Google Scholar 

  47. 47

    Averill, L. E. et al. Screening of a cosmid library of Mycobacterium bovis BCG in Mycobacterium smegmatis for novel T-cell stimulatory antigens. Res. Microbiol. 144, 349–362 (1993).

    Article  Google Scholar 

  48. 48

    Barlow, A. K., He, X. & Janeway, C. Jr. Exogenously provided peptides of a self-antigen can be processed into forms that are recognized by self-T cells. J. Exp. Med. 187, 1403–1415 (1998).

    Article  Google Scholar 

  49. 49

    Clarke, L. & Carbon, J. A colony bank containing synthetic Col El hybrid plasmids representative of the entire E. coli genome. Cell 9, 91–99 (1976).

    Article  Google Scholar 

  50. 50

    Pavelka, M. S. Jr & Jacobs, W. R. Jr. Comparison of the construction of unmarked deletion mutations in Mycobacterium smegmatis, Mycobacterium bovis bacillus Calmette-Guerin, and Mycobacterium tuberculosis H37Rv by allelic exchange. J. Bacteriol. 181, 4780–4789 (1999).

    Google Scholar 

  51. 51

    Prados-Rosales, R. et al. Mycobacteria release active membrane vesicles that modulate immune responses in a TLR2-dependent manner in mice. J. Clin. Invest. 121, 1471–1483 (2011).

    Article  Google Scholar 

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Acknowledgements

The authors thank the staff of the Flow Cytometry Core Facility of the Albert Einstein College of Medicine (supported by the Einstein Cancer Center grant NIH/NCI CA13330). The authors acknowledge the NIH Tetramer Core Facility (contract no. HHSN272201300006C) for provision of the I-Ab/TB9.8 tetramers. This work was supported by NIH grants AI093649 to S.A.P. and AI063537 to S.A.P., W.R.J. and J.C. The authors thank N. Mizushima, Tokyo Medical and Dental University, for providing the GFP-LC3 lentivirus construct and A.Y. Rudensky for providing the Y-Ae hybridoma. The authors also thank P. Jain and P. A. Gonzalez for their suggestions on the construction of the ΔPE_PGRS47 mutant strain and R. Sellers for assistance in analysis of histopathology. A.B. acknowledges support from ‘Estrategia de Sostenibilidad Universidad de Antioquia’. The authors thank R. Prados-Rosales for assistance with EM studies and E. Bejarano for advice on autophagy analysis.

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N.K.S., A.B. and T.W.N. designed and carried out experiments. S.A.P. supervised the design and execution of all experiments. M.M.V., S.C.K., S.K.-V., L.J.C. and J.X. assisted in the execution of selected experiments. J.C., M.H.L. and W.R.J. provided input on the design of experiments and data interpretation. All authors contributed to writing and editing the manuscript.

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Correspondence to Steven A. Porcelli.

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The authors declare no competing financial interests.

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Saini, N., Baena, A., Ng, T. et al. Suppression of autophagy and antigen presentation by Mycobacterium tuberculosis PE_PGRS47. Nat Microbiol 1, 16133 (2016). https://doi.org/10.1038/nmicrobiol.2016.133

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