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Rv1255c, a dormancy-related transcriptional regulator of TetR family in Mycobacterium tuberculosis, enhances isoniazid tolerance in Mycobacterium smegmatis

The Journal of Antibiotics volume 76, pages 720–727 (2023)Cite this article

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Abstract

Mycobacterium tuberculosis is exposed to diverse stresses inside the host during dormancy. Meanwhile, many metabolic and transcriptional regulatory changes occur, resulting in physiological modifications that help M. tuberculosis to adapt to these stresses. The same physiological changes also cause antibiotic tolerance in dormant M. tuberculosis. However, the transcriptional regulatory mechanism of antibiotic tolerance during dormancy remains unclear. Here, we showed that the expression of Rv1255c, an uncharacterised member of the tetracycline repressor family of transcriptional regulators, is upregulated during different stresses and hypoxia-induced dormancy. Antibiotic tolerance and efflux activities of Mycobacterium smegmatis constitutively expressing Rv1255c were analysed, and interestingly, it showed increased isoniazid tolerance and efflux activity. The intrabacterial isoniazid concentrations were found to be low in M. smegmatis expressing Rv1255c. Moreover, orthologs of the M. tuberculosis katG, gene of the enzyme which activates the first-line prodrug isoniazid, are overexpressed in this strain. Structural analysis of isoforms of KatG enzymes in M. smegmatis identified major amino acid substitutions associated with isoniazid resistance. Thus, we showed that Rv1255c helps M. smegmatis tolerate isoniazid by orchestrating drug efflux machinery. In addition, we showed that Rv1255c also causes overexpression of katG isoform in M. smegmatis which has amino acid substitutions as found in isoniazid-resistant katG in M. tuberculosis.

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References

  1. Bates JH, Stead WW. The history of tuberculosis as a global epidemic. Med Clin North Am. 1993;77:1205–17.

    Article  CAS  PubMed  Google Scholar 

  2. WHO. Global Tuberculosis Report 2020 – World. ReliefWeb. 2020;1–232.

  3. World Health Organization. Global Tuberculosis Report 2021. Geneva: ©World Health Organization; 2021. p 57.

  4. Gengenbacher M, Kaufmann SHE. Mycobacterium tuberculosis: success through dormancy. FEMS Microbiol Rev. 2012;36:514–32.

    Article  CAS  PubMed  Google Scholar 

  5. Trutneva KA, Shleeva MO, Demina GR, Vostroknutova GN, Kaprelyans AS. One-year old dormant, “non-culturable” Mycobacterium tuberculosis preserves significantly diverse protein profile. Front Cell Infect Microbiol. 2020;10:26.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Wayne LG, Sohaskey CD. Nonreplicating persistence of Mycobacterium tuberculosis. Annu Rev Microbiol. 2001;55:139–63.

    Article  CAS  PubMed  Google Scholar 

  7. Gopinath V, Raghunandanan S, Gomez RL, Jose L, Surendran A, Ramachandran R, et al. Profiling the proteome of Mycobacterium tuberculosis during dormancy and reactivation. Mol Cell Proteom. 2015;14:2160–76.

    Article  CAS  Google Scholar 

  8. Wayne LG, Hayes LG. An in vitro model for sequential study of shiftdown of Mycobacterium tuberculosis through two stages of nonreplicating persistence. Infect Immun. 1996;64:2062–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Ojha AK, Baughn AD, Sambandan D, Hsu T, Trivelli X, Guerardel Y, et al. Growth of Mycobacterium tuberculosis biofilms containing free mycolic acids and harbouring drug-tolerant bacteria. Mol Microbiol. 2008;69:164–74.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Flentie K, Harrison GA, Tükenmez H, Livny J, Good JAD, Sarkar S, et al. Chemical disarming of isoniazid resistance in Mycobacterium tuberculosis. Proc Natl Acad Sci USA. 2019;116:10510–7.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Voskuil MI, Bartek IL, Visconti K, Schoolnik GK. The response of Mycobacterium tuberculosis to reactive oxygen and nitrogen species. Front Microbiol. 2011;2:105.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Deb C, Lee C-M, Dubey VS, Daniel J, Abomoelak B, Sirakova TD, et al. A novel in vitro multiple-stress dormancy model for Mycobacterium tuberculosis generates a lipid-loaded, drug-tolerant, dormant pathogen. PLoS One. 2009;4:e6077.

    Article  PubMed  PubMed Central  Google Scholar 

  13. Shastri MD, Shukla SD, Chong WC, Dua K, Peterson GM, Patel RP, et al. Role of oxidative stress in the pathology and management of human tuberculosis. Oxid Med Cell Longev. 2018;2018:7695364.

  14. Li G, Zhang J, Guo Q, Jiang Y, Wei J, Zhao LL, et al. Efflux pump gene expression in multidrug-resistant Mycobacterium tuberculosis clinical isolates. PLoS One. 2015;10:e0119013.

    Article  PubMed  PubMed Central  Google Scholar 

  15. Bhandol H, Alindogan J, De Guzman A, Lim R. Review: Structure and transcriptional regulation of the Acr efflux pumps and their role in antibiotic resistance in Escherichia coli. Undergrad J Exp Microbiol Immunol. 2020;6:1–16.

    Google Scholar 

  16. Liu J, Shi W, Zhang S, Hao X, Maslov DA, Shur KV, et al. Mutations in efflux pump Rv1258c (Tap) cause resistance to pyrazinamide, isoniazid, and streptomycin in M. tuberculosis. Front Microbiol. 2019;10:216.

    Article  PubMed  PubMed Central  Google Scholar 

  17. Liu H, Yang M, He Z-G. Novel TetR family transcriptional factor regulates expression of multiple transport-related genes and affects rifampicin resistance in Mycobacterium smegmatis. Sci Rep. 2016;6:27489.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Remm S, Earp JC, Dick T, Dartois V, Seeger MA. Critical discussion on drug efflux in Mycobacterium tuberculosis. FEMS Microbiol Rev. 2022;46:fuab050.

  19. Balhana RJC, Singla A, Sikder MH, Withers M, Kendall SL. Global analyses of TetR family transcriptional regulators in mycobacteria indicates conservation across species and diversity in regulated functions. BMC Genomics. 2015;16:1–12.

    Article  CAS  Google Scholar 

  20. Luo L, Zhu L, Yue J, Liu J, Liu G, Zhang X, et al. Antigens Rv0310c and Rv1255c are promising novel biomarkers for the diagnosis of Mycobacterium tuberculosis infection. Emerg Microbes Infect. 2017;6:1–8.

    Article  Google Scholar 

  21. Rustad TR, Harrell MI, Liao R, Sherman DR. The enduring hypoxic response of Mycobacterium tuberculosis. PLoS One. 2008;3:e1502.

    Article  PubMed  PubMed Central  Google Scholar 

  22. Sun X, Zhang L, Jiang J, Ng M, Cui Z, Mai J, et al. Transcription factors Rv0081 and Rv3334 connect the early and the enduring hypoxic response of Mycobacterium tuberculosis. Virulence. 2018;9:1468.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Galagan JE, Minch K, Peterson M, Lyubetskaya A, Azizi E, Sweet L, et al. The Mycobacterium tuberculosis regulatory network and hypoxia. Nature. 2013;499:178–83.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Martin A, Camacho M, Portaels F, Palomino JC. Resazurin microtiter assay plate testing of Mycobacterium tuberculosis susceptibilities to second-line drugs: rapid, simple, and inexpensive method. Antimicrob Agents Chemother. 2003;47:3616.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Pal S, Misra A, Banerjee S, Dam B. Adaptation of ethidium bromide fluorescence assay to monitor activity of efflux pumps in bacterial pure cultures or mixed population from environmental samples. J King Saud Univ Sci. 2020;32:939–45.

    Article  Google Scholar 

  26. Valdivia RH, Hromockyj AE, Monack D, Ramakrishnan L, Falkow S. Applications for green fluorescent protein (GFP) in the study of host-pathogen interactions. Gene. 1996;173:47–52.

  27. Jose L, Ramachandran R, Bhagavat R, Gomez RL, Chandran A, Raghunandanan S, et al. Hypothetical protein Rv3423.1 of Mycobacterium tuberculosis is a histone acetyltransferase. FEBS J. 2016;283:265–81.

    Article  CAS  PubMed  Google Scholar 

  28. Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE. Tools for integrated sequence-structure analysis with UCSF Chimera. BMC Bioinforma. 2006;7:1–10.

    Article  Google Scholar 

  29. Engohang-Ndong J, Baillat D, Aumercier M, Bellefontaine F, Besra GS, Locht C, et al. EthR, a repressor of the TetR/CamR family implicated in ethionamide resistance in mycobacteria, octamerizes cooperatively on its operator. Mol Microbiol. 2004;51:175–88.

    Article  CAS  PubMed  Google Scholar 

  30. Ramos JL, Martínez-Bueno M, Molina-Henares AJ, Terán W, Watanabe K, Zhang X, et al. The TetR family of transcriptional repressors. Microbiol Mol Biol Rev. 2005;69:326–56.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Bollela VR, Namburete EI, Feliciano CS, Macheque D, Harrison LH, Caminero JA. Detection of katG and inhA mutations to guide isoniazid and ethionamide use for drug-resistant tuberculosis. Int J Tuberc Lung Dis. 2016;20:1099.

    Article  CAS  PubMed  Google Scholar 

  32. Ai JW, Ruan QL, Liu QH, Zhang WH. Updates on the risk factors for latent tuberculosis reactivation and their managements. Emerg Microbes Infect. 2016;5:e10.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Gomez RL, Jose L, Ramachandran R, Raghunandanan S, Muralikrishnan B, Johnson JB, et al. The multiple stress responsive transcriptional regulator Rv3334 of Mycobacterium tuberculosis is an autorepressor and a positive regulator of kstR. FEBS J. 2016;283:3056–71.

    Article  CAS  PubMed  Google Scholar 

  34. Ramaswamy S, Musser JM. Molecular genetic basis of antimicrobial agent resistance in Mycobacterium tuberculosis: 1998 update. Tube Lung Dis. 1998;79:3–29.

    Article  CAS  Google Scholar 

  35. Gao CH, Wei WP, Tao HL, Cai LK, Jia WZ, Hu L, et al. Cross-talk between the three furA orthologs in Mycobacterium smegmatis and the contribution to isoniazid resistance. J Biochem. 2019;166:237–43.

    Article  CAS  PubMed  Google Scholar 

  36. Barozi V, Musyoka TM, Sheik Amamuddy O, Tastan Bishop Ö. Deciphering isoniazid drug resistance mechanisms on dimeric Mycobacterium tuberculosis KatG via post-molecular dynamics analyses including combined dynamic residue network metrics. ACS Omega. 2022;7:13313–32.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

JGR thanks the Department of Science and Technology, Government of India, for the INSPIRE fellowship. KK thanks the Department of Biotechnology, Government of India for the Ramalingaswami fellowship. RAK is grateful to the Department of Biotechnology, Government of India for financial support.

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Authors and Affiliations

  1. Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India

    Jijimole Gopi Reji, Lakshmi K. Edison, Sajith Raghunandanan, Akhil Raj Pushparajan, Krishna Kurthkoti & Ramakrsihnan Ajay Kumar

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  1. Jijimole Gopi Reji
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Correspondence to Ramakrsihnan Ajay Kumar.

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Gopi Reji, J., K. Edison, L., Raghunandanan, S. et al. Rv1255c, a dormancy-related transcriptional regulator of TetR family in Mycobacterium tuberculosis, enhances isoniazid tolerance in Mycobacterium smegmatis. J Antibiot 76, 720–727 (2023). https://doi.org/10.1038/s41429-023-00661-8

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