Volume 26, Issue 3 (5-2022)                   IBJ 2022, 26(3): 240-251 | Back to browse issues page

PMID: 35216515
PMCID: PMC9440689

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Background: Tuberculosis infection still represents a global health issue affecting patients worldwide. Strategies for its control may be not as effective as it should be, specifically in case of resistant strains of Mycobacterium tuberculosis (M.tb.) In this regard, the role of mycobacterial methyltransferases (MTases) in TB infection can be fundamental, though it has not been broadly deciphered.
Methods: Five resistant isolates of M.tb were obtained. M.tb H37Rv (ATCC 27249) was used as a reference strain. Seven putative mycobacterial MTase genes (Rv0645c, Rv2966c, Rv1988, Rv1694, Rv3919c, Rv2756c, and Rv3263) and Rv1392 as SAM synthase were selected for analysis. PCR-sequencing and qRT-PCR were performed to compare mutations and expression levels of MTases in different strains. The
2-ΔΔCt method was employed to calculate the relative expression levels of these genes.
Results: Only two mutations were found in isoniazid resistance (INHR) strain for Rv3919c (T to G in codon 341) and Rv1392 (G to A in codon 97) genes. Overexpression of Rv0645c, Rv2756c, Rv3263, and Rv2966c was detected in all sensitive and resistant isolates. However, Rv1988 and Rv3919c decreased and Rv1694 increased in the sensitive strains. The Rv1392 expression level also decreased in INHR isolate.
Conclusion: We found a correlation between mycobacterial MTases expression and resistance to antibiotics in M.tb strains. Some MTases undeniably are virulence factors that specifically hijack the host defense mechanism. Further evaluations are needed to explore the complete impact of mycobacterial MTases within specific strains of M.tb to introduce novel diagnosis and treatment strategies.
Type of Study: Full Length | Subject: Molecular Microbiology

1. Chakaya J, Khan M, Ntoumi F, Aklillu E, Fatima R, Mwaba P, Kapata N, Mfinanga S, Hasnain E, Katoto PDMC, Bulabula ANH, Sam-Agudu N A, Nachega JB, Tiberi S, McHugh TD, Abubakar I, Zumla A. Global Tuberculosis report 2020-reflections on the global TB burden, treatment and prevention efforts. International journal of infectious diseases 2021; 113(Suppl1): S7-S12. [DOI:10.1016/j.ijid.2021.02.107]
2. Tacconelli E, Carrara E, Savoldi A, Harbarth S, Mendelson M, Monnet DL, Pulcini C, Kahlmeter G, Kluytmans J, Carmeli Y, Ouellette M, Outterson K, Patel J, Cavaleri M, Cox EM, Houchens CR, Grayson ML, Hansen P, Singh N, Theuretzbacher U, Magrini N, WHO Pathogens Priority List Working Group. Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. The lancet. infectious diseases 2018; 18(3): 318-327. [DOI:10.1016/S1473-3099(17)30753-3]
3. Tarashi S, Ahmadi Badi S, Moshiri A, Nasehi M, Fateh A, Vaziri F, Siadat SD. The human microbiota in pulmonary tuberculosis: Not so innocent bystanders. Tuberculosis 2018; 113: 215-221. [DOI:10.1016/j.tube.2018.10.010]
4. Vesga JF, Hallett TB, JA Reid M, Singh Sachdeva K, Rao R, Khaparde S, Dave P, Rade k, Kamene M, Omesa E, Masini E, Omale N, Onyango E, Owiti P, Karanja M, Kiplimo R, Alexandru S, Vilc V, Crudu V, Bivol S, Celan C, ArinaminpathyN. Assessing tuberculosis control priorities in high-burden settings: a modelling approach. The lancet. Global health 2019; 7(5): e585-e595. [DOI:10.1016/S2214-109X(19)30037-3]
5. Grover S, Gangwar R, Jamal S, Ali S, Nisaa K, Ehtesham NZ, Hasnain SE. Mycobacterial methyltransferases: significance in pathogenesis and virulence. Mycobacterium tuberculosis: molecular infection biology, pathogenesis, diagnostics and new interventions 2019; 103-122. [DOI:10.1007/978-981-32-9413-4_7]
6. Ding W, Smulan LJ, Hou NS, Taubert S, Watts JL, Walker AK. s-Adenosylmethionine levels govern innate immunity through distinct methylation-dependent pathways. Cell metabolism 2015; 22(4): 633-645. [DOI:10.1016/j.cmet.2015.07.013]
7. Tarashi S, Ahmadi Badi S, Moshiri A, Ebrahimzadeh N, Fateh A, Vaziri F, Aazami H, Siadat SD, Fuso A. The inter-talk between Mycobacterium tuberculosis and the epigenetic mechanisms. Epigenomics 2020; 12(5): 455-469. [DOI:10.2217/epi-2019-0187]
8. Gong Z, Wang G, Zeng J, Stojkoska A, Huang H, Xie J. Differential DNA methylomes of clinical MDR, XDR and XXDR Mycobacterium tuberculosis isolates revealed by using single-molecule real-time sequencing. Journal of drug targeting 2021; 29(1): 69-77. [DOI:10.1080/1061186X.2020.1797049]
9. Edwards J.R., Yarychkivska O, Boulard M, Bestor TH. DNA methylation and DNA methyltransferases. Epigenetics and chromatin 2017; 10(1): 1-10. [DOI:10.1186/s13072-017-0130-8]
10. Grover S, Gupta P, Kahlon PS, Goyal S, Grover A, Dalal K, Sabeeha, Ehtesham NZ, Hasnain SE. Analyses of methyltransferases across the pathogenicity spectrum of different mycobacterial species point to an extremophile connection. Molecular biosystems 2016; 12(5): 1615-1625. [DOI:10.1039/C5MB00810G]
11. Miro-Blanch J, Yanes O. Epigenetic regulation at the interplay between gut microbiota and host metabolism. Frontiers in genetics 2019; 10: 638. [DOI:10.3389/fgene.2019.00638]
12. Kathirvel M, Mahadevan S. The role of epigenetics in tuberculosis infection. Epigenomics 2016; 8(4): 537-549. [DOI:10.2217/epi.16.1]
13. Caceres N, Vilaplana C, Prats C, Marzo E, Llopis I, Valls J, Lopez D, Cardona P-J. Evolution and role of corded cell aggregation in Mycobacterium tuberculosis cultures. Tuberculosis 2013; 93(6): 690-698. [DOI:10.1016/j.tube.2013.08.003]
14. van Klingeren B, Dessens-Kroon M, van der Laan T, Kremer K, Soolingen DV. Drug susceptibility testing of Mycobacterium tuberculosis complex by use of a high-throughput, reproducible, absolute concentration method. Journal of clinical microbiology 2007; 45(8): 2662-2668. [DOI:10.1128/JCM.00244-07]
15. Richter E, Rüsch-Gerdes S, Hillemann D. Drug-susceptibility testing in TB: current status and future prospects. Expert review of respiratory medicine 2009. 3(5): 497-510. [DOI:10.1586/ers.09.45]
16. American Thoracic Society. Diagnostic standards and classification of tuberculosis. The American review of respiratory disease 1990; 142(3); 725-735. [DOI:10.1164/ajrccm/142.3.725]
17. Kozbia PZ, Mushegian AR. Natural history of S-adenosylmethionine-binding proteins. BMC structural biology 2005. 5(1): 1-26. [DOI:10.1186/1472-6807-5-19]
18. Rustad TR, Roberts DM, Liao RP, Sherman DR. Isolation of mycobacterial RNA, in Mycobacteria protocols. Methods in molecular biology 2009; 465: 13-22. [DOI:10.1007/978-1-59745-207-6_2]
19. Yaseen I, Kaur P, Nandicoori VK, Khosla S. Mycobacteria modulate host epigenetic machinery by Rv1988 methylation of a non-tail arginine of histone H3. Nature communications 2015; 6(1): 1-13. [DOI:10.1038/ncomms9922]
20. Shell S.S, Prestwich EG, Baek S-H, Shah RR, Sassetti CM, Dedon PC, Fortune SM. DNA methylation impacts gene expression and ensures hypoxic survival of Mycobacterium tuberculosis. Plos pathogens 2013; 9(7): e1003419. [DOI:10.1371/journal.ppat.1003419]
21. Srivastava R, Gopinathan K, Ramakrishnan T. Deoxyribonucleic acid methylation in mycobacteria. Journal of bacteriology 1981; 148(2): 716-719. [DOI:10.1128/jb.148.2.716-719.1981]
22. Sharma G, Upadhyay S, Srilalitha M, Nandicoori VK, Khosla S. The interaction of mycobacterial protein Rv2966c with host chromatin is mediated through non-CpG methylation and histone H3/H4 binding. Nucleic acids research 2015; 43(8): 3922-3937. [DOI:10.1093/nar/gkv261]
23. Velayati A.A, Farnia P, Ibrahim TA, Haroun RZ, Kuan HO, Ghanavi J, Farnia P, Naghee Kabarei A, Tabarsi P, Omar AR, Varahram M, Masjedi MR. Differences in cell wall thickness between resistant and nonresistant strains of Mycobacterium tuberculosis: using transmission electron microscopy. Chemotherapy 2009; 55(5): 303-307. [DOI:10.1159/000226425]
24. Barkan D, Liu Z, Sacchettini JC, Glickman MS. Mycolic acid cyclopropanation is essential for viability, drug resistance, and cell wall integrity of Mycobacterium tuberculosis. Chemistry and biology 2009; 16(5): 499-509. [DOI:10.1016/j.chembiol.2009.04.001]
25. Barry CE, Crick DC, McNeil MR. Targeting the formation of the cell wall core of M. tuberculosis. Infectious disorders drug targets 2007; 7(2): 182-202. [DOI:10.2174/187152607781001808]
26. Cappelli G, Volpe E, Grassi M, Liseo B, Colizzi V, Mariani F. Profiling of Mycobacterium tuberculosis gene expression during human macrophage infection: upregulation of the alternative sigma factor G, a group of transcriptional regulators, and proteins with unknown function. Research in microbiology 2006; 157(5): 445-455. [DOI:10.1016/j.resmic.2005.10.007]
27. Barkan D, Hedhli D, Yan HG, Huygen K, Glickman MS. Mycobacterium tuberculosis lacking all mycolic acid cyclopropanation is viable but highly attenuated and hyperinflammatory in mice. Infection and immunity 2012. 80(6): 1958-1968. [DOI:10.1128/IAI.00021-12]
28. DiNardo A.R, Rajapakshe K, Nishiguchi T, Grimm SL, Mtetwa G, Dlamini Q, Kahari J, Mahapatra S, Kay A, Maphalala G, Mace EM, Makedonas G, Cirillo JD, Netea MG, R Crevel RV, Coarfa C, Mandalakas AM. DNA hypermethylation during tuberculosis dampens host immune responsiveness. The Journal of clinical investigation 2020; 130(6): 3113-3123. [DOI:10.1172/JCI134622]
29. Ndhlovu V, Kiran A, Sloan D, Mandala W, Nliwasa M, Everett DB, Mwapasa M, Kontogianni K, Kamdolozi M, Corbett EL, Caws M, Davies G. Understanding the diversity of DNA methylation in Mycobacterium tuberculosis. The preprent server for biology 2020. [DOI:10.1101/2020.05.29.117077]
30. Sharma G, Sowpati DT, Singh P, Zahoor Khan M, Ganji R, Upadhyay S, Banerjee Sh, Kumar Nandicoori V, Khosla S. Genome-wide non-CpG methylation of the host genome during M. tuberculosis infection. Scientific reports 2016; 6(1): 1-15. [DOI:10.1038/srep25006]
31. Khan S.H, Bijpuria S, Maurya A, Taneja B. Structural and thermodynamic characterization of a highly
32. stable conformation of Rv2966c, a 16S rRNA methyltransferase, at low pH. International journal of biological macromolecules 2020; 164: 3909-3921. [DOI:10.1016/j.ijbiomac.2020.08.236]
33. Osterman I, Dontsova O, Sergiev PV. rRNA methylation and antibiotic resistance. Biochemistry. Biokhimii︠a︡ 2020; 85(11): 1335-1349. [DOI:10.1134/S000629792011005X]
34. Poehlsgaard J, Douthwaite S. The bacterial ribosome as a target for antibiotics. Nature reviews. Microbiology 2005; 3(11): 870-881. [DOI:10.1038/nrmicro1265]
35. Wong S.Y, JavidB, Addepalli B, Piszczek G, Strader MB, Limbach PA, Barry CA. Functional role of methylation of G518 of the 16S rRNA 530 loop by GidB in Mycobacterium tuberculosis. Antimicrobial agents and chemotherapy 2013; 57(12): 6311-6318. [DOI:10.1128/AAC.00905-13]
36. Witek M.A, Kuiper EG, Minten E, Crispell EK, Conn GA. A novel motif for S-adenosyl-L-methionine binding by the ribosomal RNA methyltransferase TlyA from Mycobacterium tuberculosis. The Journal of biological chemistry 2017; 292(5): 1977-1987. [DOI:10.1074/jbc.M116.752659]
37. Buriánková K, Doucet-Populaire F, Dorson O, Gondran A, Ghnassia JC, Weiser J, Pernodet JL. Molecular basis of intrinsic macrolide resistance in the Mycobacterium tuberculosis complex. Antimicrobial agents and chemotherapy 2004; 48(1): 143-150. [DOI:10.1128/AAC.48.1.143-150.2004]
38. Khosla S, Sharma G, Yaseen I. Learning epigenetic regulation from mycobacteria. Microbial cell 2016; 3(2): 92. [DOI:10.15698/mic2016.02.480]
39. Zhan L, Wang J, Wang L, Qin C. The correlation of drug resistance and virulence in Mycobacterium tuberculosis. Biosafety and health 2020; 2(01): 18-24. [DOI:10.1016/j.bsheal.2020.02.004]
40. Mehta M, Rajmani R.S, Singh A. Mycobacterium tuberculosis WhiB3 responds to vacuolar pH-induced changes in mycothiol redox potential to modulate phagosomal maturation and virulence. The Journal of biological chemistry 2016; 291(6): 2888-2903. [DOI:10.1074/jbc.M115.684597]
41. Nixon M.R, Saionz KW, Koo MS, Szymonifka MJ, Jung H, Roberts JP, Nandakumar M, Kumar A, Liao R, Rustad T, Sacchettini JC, Rhee KY, Freundlich JS, Sherman DR. Folate pathway disruption leads to critical disruption of methionine derivatives in Mycobacterium tuberculosis. Chemistry and biology 2014; 21(7): 819-830. [DOI:10.1016/j.chembiol.2014.04.009]

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