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Abstract

Cyclic-di-guanosine monophosphate (c-di-GMP) plays an important role in bacterial signalling networks. C-di-GMP exerts a regulatory function through binding to diverse molecules that include transcription factors, riboswitches and sensor kinases (SKs), thereby regulating diverse processes. Here, we demonstrate the crosstalk between c-di-GMP and the SK MtrB of . MtrB phosphorylates and regulates its cognate response regulator MtrA. C-di-GMP binds directly to the cytosolic domain of MtrB to inhibit its autophosphorylation. C-di-GMP levels in were manipulated by overexpressing a c-di-GMP synthesizing enzyme and a degrading enzyme . We demonstrate that overexpression of lowers growth of the bacterium both and in grown in macrophages. This is in conformity with lowered expression of and selected genes of the regulon involved in cell wall turnover in the -overexpressing strain compared to the parent strain. We also demonstrate that overexpression of in hinders biofilm formation, whereas overexpression of has the opposite effect. Neither of the two genes could rescue the biofilm defective phenotype of the MtrB knock out mutant (), suggesting that c-di-GMP exerts its role on biofilm formation through MtrB. Finally, we show by fluorescence microscopy that the trafficking of overexpressing is significantly higher than that of the parent strain and that this is linked to reduced expression of the MtrB-dependent genes and , which play a role in subversion of lysosomal trafficking of . These results provide important new insight into the crosstalk between c-di-GMP and MtrB in .

Funding
This study was supported by the:
  • Indian Council of Medical Research (Award BMI/11(90)/2022)
    • Principal Award Recipient: MalSoumya
  • Indian Council of Medical Research (Award 45/1/2020-IMM/BMS)
    • Principal Award Recipient: Kumar SharmaArun
  • Indian Council of Medical Research (Award 45/8/2019-PHY/BMS)
    • Principal Award Recipient: BagchiShreya
  • Council for Scientific and Industrial Research, Government of India (Award 21(1088)/19/EMR-II)
    • Principal Award Recipient: KunduManikuntala
  • Department of Biotechnology, Ministry of Science and Technology, India (Award BT/PR20242/MED/29/1062/2016)
    • Principal Award Recipient: KunduManikuntala
  • Science and Engineering Research Board (Award JBR/2021/000020)
    • Principal Award Recipient: BasuJoyoti
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. The Microbiology Society waived the open access fees for this article.
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/content/journal/micro/10.1099/mic.0.001532
2025-02-07
2026-02-19

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References

  1. World Health Organization Global Tuberculosis Report 2022.
  2. Kundu M. The role of two-component systems in the physiology of Mycobacterium tuberculosis. IUBMB Life 2018; 70:710–717 [View Article] [PubMed]
    [Google Scholar]
  3. Stupar M, Furness J, De Voss CJ, Tan L, West NP. Two‐component sensor histidine kinases of Mycobacterium tuberculosis: beacons for niche navigation. Mol Microbiol 2022; 117:973–985
    [Google Scholar]
  4. Dubrac S, Bisicchia P, Devine KM, Msadek T. A matter of life and death: cell wall homeostasis and the WalKR (YycGF) essential signal transduction pathway. Mol Microbiol 2008; 70:1307–1322
    [Google Scholar]
  5. Fukushima T, Furihata I, Emmins R, Daniel RA, Hoch JA et al. A role for the essential yycg sensor histidine kinase in sensing cell division. Mol Microbiol 2011; 79:503–522
    [Google Scholar]
  6. Dubrac S, Boneca IG, Poupel O, Msadek T. New insights into the WalK/WalR (YycG/YycF) essential signal transduction pathway reveal a major role in controlling cell wall metabolism and biofilm formation in Staphylococcus aureus. J Bacteriol 2007; 189:8257–8269 [View Article] [PubMed]
    [Google Scholar]
  7. Möker N, Brocker M, Schaffer S, Krämer R, Morbach S et al. Deletion of the genes encoding the MtrA–MtrB two‐component system of Corynebacterium glutamicum has a strong influence on cell morphology, antibiotics susceptibility and expression of genes involved in osmoprotection. Mol Microbiol 2004; 54:420–438 [View Article]
    [Google Scholar]
  8. Banerjee SK, Lata S, Sharma AK, Bagchi S, Kumar M et al. The sensor kinase MtrB of Mycobacterium tuberculosis regulates hypoxic survival and establishment of infection. J Biol Chem 2019; 294:19862–19876 [View Article] [PubMed]
    [Google Scholar]
  9. Fol M, Chauhan A, Nair NK, Maloney E, Moomey M et al. Modulation of Mycobacterium tuberculosis proliferation by MtrA, an essential two‐component response regulator. Mol Microbiol 2006; 60:643–657 [View Article] [PubMed]
    [Google Scholar]
  10. Rajagopalan M, Dziedzic R, Al Zayer M, Stankowska D, Ouimet M-C et al. Mycobacterium tuberculosis origin of replication and the promoter for immunodominant secreted antigen 85B are the targets of MtrA, the essential response regulator. J Biol Chem 2010; 285:15816–15827 [View Article]
    [Google Scholar]
  11. Plocinska R, Purushotham G, Sarva K, Vadrevu IS, Pandeeti EVP et al. Septal localization of the Mycobacterium tuberculosis MtrB sensor kinase promotes MtrA regulon expression. J Biol Chem 2012; 287:23887–23899 [View Article] [PubMed]
    [Google Scholar]
  12. Chatterjee A, Sharma AK, Mahatha AC, Banerjee SK, Kumar M et al. Global mapping of MtrA-binding sites links MtrA to regulation of its targets in Mycobacterium tuberculosis. Microbiology 2018; 164:99–110 [View Article] [PubMed]
    [Google Scholar]
  13. Sharma AK, Chatterjee A, Gupta S, Banerjee R, Mandal S et al. MtrA, an essential response regulator of the MtrAB two-component system, regulates the transcription of resuscitation-promoting factor B of Mycobacterium tuberculosis. Microbiology 2015; 161:1271–1281 [View Article] [PubMed]
    [Google Scholar]
  14. Plocinska R, Martinez L, Gorla P, Pandeeti E, Sarva K et al. Mycobacterium tuberculosis MtrB sensor kinase interactions with FtsI and Wag31 proteins reveal a role for MtrB distinct from that regulating MtrA activities. J Bacteriol 2014; 196:4120–4129 [View Article] [PubMed]
    [Google Scholar]
  15. Sankhe GD, Raja R, Singh DP, Bheemireddy S, Rana S et al. Sequestration of histidine kinases by non-cognate response regulators establishes a threshold level of stimulation for bacterial two-component signaling. Nat Commun 2023; 14:4483 [View Article]
    [Google Scholar]
  16. Johnson RM, McDonough KA. Cyclic nucleotide signaling in Mycobacterium tuberculosis: an expanding repertoire. Pathog Dis 2018; 76:fty048 [View Article] [PubMed]
    [Google Scholar]
  17. Valentini M, Filloux A. Multiple roles of c-di-GMP signaling in bacterial pathogenesis. Annu Rev Microbiol 2019; 73:387–406 [View Article]
    [Google Scholar]
  18. Römling U, Galperin MY, Gomelsky M. Cyclic di-GMP: the first 25 years of a universal bacterial second messenger. Microbiol Mol Biol Rev 2013; 77:1–52 [View Article]
    [Google Scholar]
  19. Lori C, Ozaki S, Steiner S, Böhm R, Abel S et al. Cyclic di-GMP acts as a cell cycle oscillator to drive chromosome replication. Nature 2015; 523:236–239 [View Article] [PubMed]
    [Google Scholar]
  20. Kaczmarczyk A, Hempel AM, von Arx C, Böhm R, Dubey BN et al. Precise timing of transcription by c-di-GMP coordinates cell cycle and morphogenesis in Caulobacter. Nat Commun 2020; 11:816 [View Article]
    [Google Scholar]
  21. Cheng ST, Wang FF, Qian W. Cyclic-di-GMP binds to histidine kinase RavS to control RavS-RavR phosphotransfer and regulates the bacterial lifestyle transition between virulence and swimming. PLoS Pathog 2019; 15:e1007952 [View Article]
    [Google Scholar]
  22. Lichtenberg M, Kragh KN, Fritz B, Kirkegaard JB, Tolker-Nielsen T et al. Cyclic-di-GMP signaling controls metabolic activity in Pseudomonas aeruginosa. Cell Rep 2022; 41:111515 [View Article] [PubMed]
    [Google Scholar]
  23. Li W, Li M, Hu L, Zhu J, Xie Z et al. HpoR, a novel c-di-GMP effective transcription factor, links the second messenger’s regulatory function to the mycobacterial antioxidant defense. Nucleic Acids Res 2018; 46:3595–3611 [View Article] [PubMed]
    [Google Scholar]
  24. Ling X, Liu X, Wang K, Guo M, Ou Y et al. Lsr2 acts as a cyclic di-GMP receptor that promotes keto-mycolic acid synthesis and biofilm formation in mycobacteria. Nat Commun 2024; 15:695 [View Article]
    [Google Scholar]
  25. Zhang J, Hu L, Zhang H, He Z-G. Cyclic di-GMP triggers the hypoxic adaptation of Mycobacterium bovis through a metabolic switching regulator ArgR. Environ Microbiol 2022; 24:4382–4400 [View Article]
    [Google Scholar]
  26. Flores-Valdez MA, Peterson EJR, Aceves-Sánchez MdeJ, Baliga NS, Morita YS et al. Comparison of the transcriptome, lipidome, and c-di-GMP production between BCGΔBCG1419c and BCG, with mincle- and Myd88-dependent induction of proinflammatory cytokines in murine macrophages. Sci Rep 2024; 14:11898 [View Article] [PubMed]
    [Google Scholar]
  27. Hariharan VN, Yadav R, Thakur C, Singh A, Gopinathan R et al. Cyclic di-GMP sensing histidine kinase PdtaS controls mycobacterial adaptation to carbon sources. FASEB J 2021; 35:e21475 [View Article] [PubMed]
    [Google Scholar]
  28. Sharma AK, Mal S, Sahu SK, Bagchi S, Majumder D et al. Mycobacterial peptidyl prolyl isomerase A activates STING-TBK1-IRF3 signaling to promote IFNβ release in macrophages. FEBS J 2025; 292:94–114 [View Article] [PubMed]
    [Google Scholar]
  29. Manikandan K, Prasad D, Srivastava A, Singh N, Dabeer S et al. The second messenger cyclic di‐AMP negatively regulates the expression of Mycobacterium smegmatis recA and attenuates DNA strand exchange through binding to the C‐terminal motif of mycobacterial RecA proteins. Mol Microbiol 2018; 109:600–614 [View Article]
    [Google Scholar]
  30. Agrawal R, Pandey A, Rajankar MP, Dixit NM, Saini DK. The two-component signalling networks of Mycobacterium tuberculosis display extensive cross-talk in vitro. Biochem J 2015; 469:121–134 [View Article] [PubMed]
    [Google Scholar]
  31. Ning H, Wang L, Zhou J, Lu Y, Kang J et al. Recombinant BCG with bacterial signaling molecule cyclic di-AMP as endogenous adjuvant induces elevated immune responses after Mycobacterium tuberculosis infection. Front Immunol 201910,1519.
    [Google Scholar]
  32. Cholo MC, Rasehlo SSM, Venter E, Venter C, Anderson R. Effects of cigarette smoke condensate on growth and biofilm formation by Mycobacterium tuberculosis. Biomed Res Int 20208237402 [View Article] [PubMed]
    [Google Scholar]
  33. Rohde KH, Abramovitch RB, Russell DG. Mycobacterium tuberculosis invasion of macrophages: linking bacterial gene expression to environmental cues. Cell Host Microbe 2007; 2:352–364
    [Google Scholar]
  34. Burdette DL, Monroe KM, Sotelo-Troha K, Iwig JD, Eckert B et al. STING is a direct innate immune sensor of cyclic di-GMP. Nature 2011; 478:515–518
    [Google Scholar]
  35. Waturuocha UW, Athira PJ, Singh KK, Malhotra V, Krishna MS et al. A high-frequency single nucleotide polymorphism in the MtrB sensor kinase in clinical strains of Mycobacterium tuberculosis alters its biochemical and physiological properties. PLoS One 2021; 16:e0256664
    [Google Scholar]
  36. Römling U. Cyclic di- GMP signaling— where did you come from and where will you go. Mol Microbiol 2023; 120:564–574 [View Article] [PubMed]
    [Google Scholar]
  37. Gupta K, Kumar P, Chatterji D. Identification, activity and disulfide connectivity of C-di-GMP regulating proteins in Mycobacterium tuberculosis. PLoS One 2010; 5:e15072 [View Article] [PubMed]
    [Google Scholar]
  38. Zähringer F, Massa C, Schirmer T. Efficient enzymatic production of the bacterial second messenger c-di-GMP by the diguanylate cyclase YdeH from E. coli. Appl Biochem Biotechnol 2011; 163:71–79 [View Article] [PubMed]
    [Google Scholar]
  39. Gorla P, Plocinska R, Sarva K, Satsangi AT, Pandeeti E et al. MtrA response regulator controls cell division and cell wall metabolism and affects susceptibility of Mycobacteria to the first line antituberculosis drugs. Front Microbiol 2018; 9:2839 [View Article] [PubMed]
    [Google Scholar]
  40. Singh KK, Athira PJ, Bhardwaj N, Singh DP, Watson U et al. Acetylation of response regulator protein MtrA in M. tuberculosis regulates its repressor activity. Front Microbiol 2020; 11:516315 [View Article] [PubMed]
    [Google Scholar]
  41. Zahrt TC, Deretic V. An essential two-component signal transduction system in Mycobacterium tuberculosis. J Bacteriol 2000; 182:3832–3838 [View Article] [PubMed]
    [Google Scholar]
  42. Valentini M, Filloux A. Biofilms and cyclic di-GMP(c-di-GMP) signaling: lessons from Pseudomonas aeruginosa and other bacteria. J Biol Chem 2016; 291:12547–12555 [View Article]
    [Google Scholar]
  43. Flores-Valdez MA, Aceves-Sánchez MdeJ, Pedroza-Roldán C, Vega-Domínguez PJ, Prado-Montes de Oca E et al. The cyclic di-GMP phosphodiesterase gene Rv1357c/BCG1419c affects BCG pellicle production and in vivo maintenance. IUBMB Life 2015; 67:129–138 [View Article] [PubMed]
    [Google Scholar]
  44. Segura-Cerda CA, Aceves-Sánchez MdeJ, Marquina-Castillo B, Mata-Espinoza D, Barrios-Payán J et al. Immune response elicited by two rBCG strains devoid of genes involved in c-di-GMP metabolism affect protection versus challenge with M. tuberculosis strains of different virulence. Vaccine 2018; 36:2069–2078 [View Article] [PubMed]
    [Google Scholar]
  45. Mehra A, Zahra A, Thompson V, Sirisaengtaksin N, Wells A et al. Mycobacterium tuberculosis type VII secreted effector EsxH targets host ESCRT to impair trafficking. PLoS Pathog 2013; 9:e1003734 [View Article] [PubMed]
    [Google Scholar]
  46. Li S, Poulton NC, Chang JS, Azadian ZA, DeJesus MA et al. CRISPRi chemical genetics and comparative genomics identify genes mediating drug potency in Mycobacterium tuberculosis. Nat Microbiol 2022; 7:766–779 [View Article] [PubMed]
    [Google Scholar]
  47. Petchiappan A, Mahapa A, Chatterji D. In Chou SH, Guilani N, Lee VT, Romling U. eds Cyclic Dinucleotide Signaling in Mycobacteria Microbial Cyclic Di-Nucleotide Signaling in Microbial Cyclic Di-Nucleotide Signalling Romling (Springer International Publishing); 2020 pp 3–25
    [Google Scholar]
  48. Hu Q, Zhang J, Chen Y, Hu L, Li W et al. Cyclic di-GMP co-activates the two-component transcriptional regulator DevR in Mycobacterium smegmatis in response to oxidative stress. J Biol Chem 2019; 294:12729–12742 [View Article] [PubMed]
    [Google Scholar]
  49. Dubey BN, Agustoni E, Böhm R, Kaczmarczyk A, Mangia F et al. Hybrid histidine kinase activation by cyclic di-GMP–mediated domain liberation. Proc Natl Acad Sci USA 2020; 117:1000–1008 [View Article]
    [Google Scholar]
  50. Bretl DJ, Demetriadou C, Zahrt TC. Adaptation to environmental stimuli within the host: two-component signal transduction systems of Mycobacterium tuberculosis. Microbiol Mol Biol Rev 2011; 75:566–582 [View Article] [PubMed]
    [Google Scholar]
  51. Sankhe GD, Dixit NM, Saini DK. Activation of bacterial histidine kinases: insights into the kinetics of the cis autophosphorylation mechanism. mSphere 2018; 3:00111–00118 [View Article] [PubMed]
    [Google Scholar]
  52. Yan J, Bassler BL. Surviving as a community: antibiotic tolerance and persistence in bacterial biofilms. Cell Host Microbe 2019; 26:15–21 [View Article] [PubMed]
    [Google Scholar]
  53. Sambandan D, Dao DN, Weinrick BC, Vilchèze C, Gurcha SS et al. Keto-mycolic acid-dependent pellicle formation confers tolerance to drug-sensitive Mycobacterium tuberculosis. mBio 2013; 4:e00222–13 [View Article] [PubMed]
    [Google Scholar]
  54. Chakraborty P, Bajeli S, Kaushal D, Radotra BD, Kumar A. Biofilm formation in the lung contributes to virulence and drug tolerance of Mycobacterium tuberculosis. Nat Commun 2021; 12:1606 [View Article] [PubMed]
    [Google Scholar]
  55. Mishra R, Hannebelle M, Patil VP, Dubois A, Garcia-Mouton C et al. Mechanopathology of biofilm-like Mycobacterium tuberculosis cords. Cell 2023; 186:5135–5150 [View Article] [PubMed]
    [Google Scholar]
  56. Aceves-Sánchez MdeJ, Flores-Valdez MA, Pedroza-Roldán C, Creissen E, Izzo L et al. Vaccination with BCGΔBCG1419c protects against pulmonary and extrapulmonary TB and is safer than BCG. Sci Rep 2021; 11:12417 [View Article]
    [Google Scholar]
  57. Aceves-Sánchez MdeJ, Barrios-Payán JA, Segura-Cerda CA, Flores-Valdez MA, Mata-Espinosa D et al. BCG∆BCG1419c and BCG differ in induction of autophagy, c-di-GMP content, proteome, and progression of lung pathology in Mycobacterium tuberculosis HN878-infected male BALB/c mice. Vaccine 2023; 41:3824–3835 [View Article]
    [Google Scholar]
  58. Zhang H-N, Xu Z-W, Jiang H-W, Wu F-L, He X et al. Cyclic di-GMP regulates Mycobacterium tuberculosis resistance to ethionamide. Sci Rep 2017; 7:5860 [View Article] [PubMed]
    [Google Scholar]
  59. Deng J, Bi L, Zhou L, Guo S, Fleming J et al. Mycobacterium tuberculosis proteome microarray for global studies of protein function and immunogenicity. Cell Rep 2014; 9:2317–2329 [View Article] [PubMed]
    [Google Scholar]
  60. Cassio Barreto de Oliveira M, Balan A. The ATP-binding cassette (ABC) transport systems in Mycobacterium tuberculosis: structure, function, and possible targets for therapeutics. Biology 2020; 9:443 [View Article]
    [Google Scholar]
  61. Böth D, Schneider G, Schnell R. Peptidoglycan remodeling in Mycobacterium tuberculosis: comparison of structures and catalytic activities of RipA and RipB. J Mol Biol 2011; 413:247–260 [View Article] [PubMed]
    [Google Scholar]
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