Regulation of pneumococcal epigenetic and colony phases by multiple two-component regulatory systems


Autoři: Juanjuan Wang aff001;  Jing-Wen Li aff001;  Jing Li aff001;  Yijia Huang aff001;  Shaomeng Wang aff001;  Jing-Ren Zhang aff001
Působiště autorů: Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing, China aff001
Vyšlo v časopise: Regulation of pneumococcal epigenetic and colony phases by multiple two-component regulatory systems. PLoS Pathog 16(3): e1008417. doi:10.1371/journal.ppat.1008417
Kategorie: Research Article
doi: 10.1371/journal.ppat.1008417

Souhrn

Streptococcus pneumoniae is well known for phase variation between opaque (O) and transparent (T) colonies within clonal populations. While the O variant is specialized in invasive infection (with a thicker capsule and higher resistance to host clearance), the T counterpart possesses a relatively thinner capsule and thereby higher airway adherence and colonization. Our previous study found that phase variation is caused by reversible switches of the “opaque ON-or-OFF” methylomes or methylation patterns of pneumococcal genome, which is dominantly driven by the PsrA-catalyzed inversions of the DNA methyltransferase hsdS genes. This study revealed that switch frequency between the O and T variants is regulated by five transcriptional response regulators (rr) of the two-component systems (TCSs). The mutants of rr06, rr08, rr09, rr11 and rr14 produced significantly fewer O and more T colonies. Further mutagenesis revealed that RR06, RR08, RR09 and RR11 enrich the O variant by modulating the directions of the PsrA-catalyzed inversion reactions. In contrast, the impact of RR14 (RitR) on phase variation is independent of PsrA. Consistently, SMRT sequencing uncovered significantly diminished “opaque ON” methylome in the mutants of rr06, rr08, rr09 and rr11 but not that of rr14. Lastly, the phosphorylated form of RR11 was shown to activate the transcription of comW and two sugar utilization systems that are necessary for maintenance of the “opaque ON” genotype and phenotype. This work has thus uncovered multiple novel mechanisms that balance pneumococcal epigenetic status and physiology.

Klíčová slova:

Gene regulation – Genetic loci – Methylation – Opacity – Phenotypes – Phosphorylation – Regulator genes – Sequence motif analysis


Zdroje

1. Bogaert D, de Groot R, Hermans PWM. Streptococcus pneumoniae colonisation: the key to pneumococcal disease. Lancet Infect Dis. 2004;4(3):144–54. doi: 10.1016/S1473-3099(04)00938-7 14998500

2. Weiser JN. Phase variation in colony opacity by Streptococcus pneumoniae. Microb Drug Resist. 1998;4(2):129–35. doi: 10.1089/mdr.1998.4.129 9651000.

3. Weiser JN, Austrian R, Sreenivasan PK, Masure HR. Phase variation in pneumococcal opacity: relationship between colonial morphology and nasopharyngeal colonization. Infect Immun. 1994;62(6):2582–9. 8188381.

4. Kim JO, Weiser JN. Association of intrastrain phase variation in quantity of capsular polysaccharide and teichoic acid with the virulence of Streptococcus pneumoniae. J Infect Dis. 1998;177(2):368–77. doi: 10.1086/514205 9466523

5. Li J, Li JW, Feng Z, Wang J, An H, Liu Y, et al. Epigenetic switch driven by DNA inversions dictates phase variation in Streptococcus pneumoniae. PLoS Pathog. 2016;12(7):e1005762. doi: 10.1371/journal.ppat.1005762 27427949.

6. Li J, Zhang JR. Phase variation of Streptococcus pneumoniae. Microbiol Spectr. 2019;7(1):GPP3-0005-2018. doi: 10.1128/microbiolspec.GPP3-0005-2018 30737916.

7. Manso AS, Chai MH, Atack JM, Furi L, De Ste Croix M, Haigh R, et al. A random six-phase switch regulates pneumococcal virulence via global epigenetic changes. Nat Commun. 2014;5:5055. doi: 10.1038/ncomms6055 25268848.

8. De Ste Croix M, Vacca I, Kwun MJ, Ralph JD, Bentley SD, Haigh R, et al. Phase-variable methylation and epigenetic regulation by type I restriction-modification systems. FEMS Microbiol Rev. 2017;41(Supp_1):S3–S15. doi: 10.1093/femsre/fux025 28830092.

9. Li JW, Li J, Wang J, Li C, Zhang JR. Molecular mechanisms of hsdS inversions in the cod locus of Streptococcus pneumoniae. J Bacteriol. 2019;201(6):e00581–18. doi: 10.1128/JB.00581-18 30617241.

10. De Ste Croix M, Chen KY, Vacca I, Manso AS, Johnston C, Polard P, et al. Recombination of the phase-variable spnIII locus is independent of all known pneumococcal site-specific recombinases. J Bacteriol. 2019;201(15)e00233–19. doi: 10.1128/JB.00233-19 31085693.

11. Loenen WAM, Dryden DTF, Raleigh EA, Wilson GG. Type I restriction enzymes and their relatives. Nucleic Acids Res. 2014;42(1):20–44. doi: 10.1093/nar/gkt847 24068554

12. Stock AM, Robinson VL, Goudreau PN. Two-component signal transduction. Annu Rev Biochem. 2000;69:183–215. doi: 10.1146/annurev.biochem.69.1.183 10966457.

13. Stock J, Park P, Surette M, Levit M. Two-component signal transduction system: structure-function relationship and mechanisms of catalysis. 1995; p. 25–51. In: Hoch J, Silhavy T (ed), Two-Component Signal Transduction. ASM Press, Washington, DC. doi: 10.1128/9781555818319.ch3

14. Lange R, Wagner C, de Saizieu A, Flint N, Molnos J, Stieger M, et al. Domain organization and molecular characterization of 13 two-component systems identified by genome sequencing of Streptococcus pneumoniae. Gene. 1999;237(1):223–34. doi: 10.1016/s0378-1119(99)00266-8 10524254.

15. Throup JP, Koretke KK, Bryant AP, Ingraham KA, Chalker AF, Ge Y, et al. A genomic analysis of two-component signal transduction in Streptococcus pneumoniae. Mol Microbiol. 2000;35(3):566–76. doi: 10.1046/j.1365-2958.2000.01725.x 10672179.

16. Gomez-Mejia A, Gamez G, Hammerschmidt S. Streptococcus pneumoniae two-component regulatory systems: The interplay of the pneumococcus with its environment. Int J Med Microbiol. 2018;308(6):722–37. doi: 10.1016/j.ijmm.2017.11.012 29221986.

17. Trihn M, Ge X, Dobson A, Kitten T, Munro CL, Xu P. Two-component system response regulators involved in virulence of Streptococcus pneumoniae TIGR4 in infective endocarditis. PLoS One. 2013;8(1):e54320. doi: 10.1371/journal.pone.0054320 23342132.

18. Schnorpfeil A, Kranz M, Kovacs M, Kirsch C, Gartmann J, Brunner I, et al. Target evaluation of the non-coding csRNAs reveals a link of the two-component regulatory system CiaRH to competence control in Streptococcus pneumoniae R6. Mol Microbiol. 2013;89(2):334–49. doi: 10.1111/mmi.12277 23710838.

19. Liu Y, Zeng Y, Huang Y, Gu L, Wang S, Li C, et al. HtrA-mediated selective degradation of DNA uptake apparatus accelerates termination of pneumococcal transformation. Mol Microbiol. 2019. doi: 10.1111/mmi.14364 31396996.

20. Guenzi E, Gasc AM, Sicard MA, Hakenbeck R. A two-component signal-transducing system is involved in competence and penicillin susceptibility in laboratory mutants of Streptococcus pneumoniae. Mol Microbiol. 1994;12(3):505–15. doi: 10.1111/j.1365-2958.1994.tb01038.x 8065267.

21. Sebert ME, Patel KP, Plotnick M, Weiser JN. Pneumococcal HtrA protease mediates inhibition of competence by the CiaRH two-component signaling system. J Bacteriol. 2005;187(12):3969–79. doi: 10.1128/JB.187.12.3969-3979.2005 15937159

22. Pinas GE, Cortes PR, Orio AG, Echenique J. Acidic stress induces autolysis by a CSP-independent ComE pathway in Streptococcus pneumoniae. Microbiology. 2008;154(Pt 5):1300–8. doi: 10.1099/mic.0.2007/015925-0 18451038.

23. Mascher T, Heintz M, Zahner D, Merai M, Hakenbeck R. The CiaRH system of Streptococcus pneumoniae prevents lysis during stress induced by treatment with cell wall inhibitors and by mutations in pbp2x involved in beta-lactam resistance. J Bacteriol. 2006;188(5):1959–68. doi: 10.1128/JB.188.5.1959-1968.2006 16484208.

24. Dagkessamanskaia A, Moscoso M, Henard V, Guiral S, Overweg K, Reuter M, et al. Interconnection of competence, stress and CiaR regulons in Streptococcus pneumoniae: competence triggers stationary phase autolysis of ciaR mutant cells. Mol Microbiol. 2004;51(4):1071–86. doi: 10.1111/j.1365-2958.2003.03892.x 14763981

25. Salvadori G, Junges R, Morrison DA, Petersen FC. Competence in Streptococcus pneumoniae and close commensal relatives: mechanisms and implications. Front Cell Infect Microbiol. 2019;9:94. doi: 10.3389/fcimb.2019.00094 31001492.

26. Pestova EV, Havarstein LS, Morrison DA. Regulation of competence for genetic transformation in Streptococcus pneumoniae by an auto-induced peptide pheromone and a two-component regulatory system. Mol Microbiol. 1996;21(4):853–62. doi: 10.1046/j.1365-2958.1996.501417.x 8878046.

27. Havarstein LS, Gaustad P, Nes IF, Morrison DA. Identification of the streptococcal competence-pheromone receptor. Mol Microbiol. 1996;21(4):863–9. doi: 10.1046/j.1365-2958.1996.521416.x 8878047

28. Gutu AD, Wayne KJ, Sham LT, Winkler ME. Kinetic characterization of the WalRKSpn (VicRK) two-component system of Streptococcus pneumoniae: dependence of WalKSpn (VicK) phosphatase activity on its PAS domain. J Bacteriol. 2010;192(9):2346–58. doi: 10.1128/JB.01690-09 20190050.

29. Wayne KJ, Sham LT, Tsui HC, Gutu AD, Barendt SM, Keen SK, et al. Localization and cellular amounts of the WalRKJ (VicRKX) two-component regulatory system proteins in serotype 2 Streptococcus pneumoniae. J Bacteriol. 2010;192(17):4388–94. doi: 10.1128/JB.00578-10 20622066.

30. Eldholm V, Gutt B, Johnsborg O, Bruckner R, Maurer P, Hakenbeck R, et al. The pneumococcal cell envelope stress-sensing system LiaFSR is activated by murein hydrolases and lipid II-interacting antibiotics. J Bacteriol. 2010;192(7):1761–73. doi: 10.1128/JB.01489-09 20118250.

31. Zheng JJ, Sinha D, Wayne KJ, Winkler ME. Physiological roles of the dual phosphate transporter systems in low and high phosphate conditions and in capsule maintenance of Streptococcus pneumoniae D39. Front Cell Infect Microbiol. 2016;6:63. doi: 10.3389/fcimb.2016.00063 27379215.

32. Novak R, Cauwels A, Charpentier E, Tuomanen E. Identification of a Streptococcus pneumoniae gene locus encoding proteins of an ABC phosphate transporter and a two-component regulatory system. J Bacteriol. 1999;181(4):1126–33. 9973337

33. Standish AJ, Stroeher UH, Paton JC. The two-component signal transduction system RR06/HK06 regulates expression of cbpA in Streptococcus pneumoniae. Proc Natl Acad Sci U S A. 2005;102(21):7701–6. doi: 10.1073/pnas.0409377102 15897461.

34. Ma Z, Zhang JR. RR06 activates transcription of spr1996 and cbpA in Streptococcus pneumoniae. J Bacteriol. 2007;189(6):2497–509. doi: 10.1128/JB.01429-06 17220227.

35. McKessar SJ, Hakenbeck R. The two-component regulatory system TCS08 is involved in cellobiose metabolism of Streptococcus pneumoniae R6. J Bacteriol. 2007;189(4):1342–50. doi: 10.1128/JB.01170-06 17028271

36. de Saizieu A, Gardes C, Flint N, Wagner C, Kamber M, Mitchell TJ, et al. Microarray-based identification of a novel Streptococcus pneumoniae regulon controlled by an autoinduced peptide. J Bacteriol. 2000;182(17):4696–703. doi: 10.1128/jb.182.17.4696-4703.2000 10940007.

37. Reichmann P, Hakenbeck R. Allelic variation in a peptide-inducible two-component system of Streptococcus pneumoniae. Fems Microbiol Lett. 2000;190(2):231–6. doi: 10.1111/j.1574-6968.2000.tb09291.x 11034284

38. Kjos M, Miller E, Slager J, Lake FB, Gericke O, Roberts IS, et al. Expression of Streptococcus pneumoniae bacteriocins is induced by antibiotics via regulatory interplay with the competence system. PLoS Pathog. 2016;12(2):e1005422. doi: 10.1371/journal.ppat.1005422 26840404.

39. Ulijasz AT, Andes DR, Glasner JD, Weisblum B. Regulation of iron transport in Streptococcus pneumoniae by RitR, an orphan response regulator. J Bacteriol. 2004;186(23):8123–36. doi: 10.1128/JB.186.23.8123-8136.2004 15547286.

40. Glanville DG, Han L, Maule AF, Woodacre A, Thanki D, Abdullah IT, et al. RitR is an archetype for a novel family of redox sensors in the streptococci that has evolved from two-component response regulators and is required for pneumococcal colonization. PLoS Pathog. 2018;14(5):e1007052. doi: 10.1371/journal.ppat.1007052 29750817.

41. Blue CE, Mitchell TJ. Contribution of a response regulator to the virulence of Streptococcus pneumoniae is strain dependent. Infect Immun. 2003;71(8):4405–13. doi: 10.1128/IAI.71.8.4405-4413.2003 12874319

42. Hendriksen WT, Silva N, Bootsma HJ, Blue CE, Paterson GK, Kerr AR, et al. Regulation of gene expression in Streptococcus pneumoniae by response regulator 09 is strain dependent. J Bacteriol. 2007;189(4):1382–9. doi: 10.1128/JB.01144-06 17085554

43. Park AK, Lee JH, Chi YM, Park H. Structural characterization of the full-length response regulator spr1814 in complex with a phosphate analogue reveals a novel conformational plasticity of the linker region. Biochem Biophys Res Commun. 2016;473(2):625–9. doi: 10.1016/j.bbrc.2016.03.144 27038544.

44. Tsui HC, Zheng JJ, Magallon AN, Ryan JD, Yunck R, Rued BE, et al. Suppression of a deletion mutation in the gene encoding essential PBP2b reveals a new lytic transglycosylase involved in peripheral peptidoglycan synthesis in Streptococcus pneumoniae D39. Mol Microbiol. 2016;100(6):1039–65. doi: 10.1111/mmi.13366 26933838.

45. Lukat GS, McCleary WR, Stock AM, Stock JB. Phosphorylation of bacterial response regulator proteins by low molecular weight phospho-donors. Proc Natl Acad Sci U S A. 1992;89(2):718–22. doi: 10.1073/pnas.89.2.718 1731345.

46. Feng Z, Li J, Zhang JR, Zhang X. qDNAmod: a statistical model-based tool to reveal intercellular heterogeneity of DNA modification from SMRT sequencing data. Nucleic Acids Res. 2014;42(22):13488–99. doi: 10.1093/nar/gku1097 25404133.

47. Kwun MJ, Oggioni MR, De Ste Croix M, Bentley SD, Croucher NJ. Excision-reintegration at a pneumococcal phase-variable restriction-modification locus drives within- and between-strain epigenetic differentiation and inhibits gene acquisition. Nucleic Acids Res. 2018;46(21):11438–53. doi: 10.1093/nar/gky906 30321375

48. Smith JG, Latiolais JA, Guanga GP, Pennington JD, Silversmith RE, Bourret RB. A search for amino acid substitutions that universally activate response regulators. Mol Microbiol. 2004;51(3):887–901. doi: 10.1046/j.1365-2958.2003.03882.x 14731287.

49. Martin B, Soulet AL, Mirouze N, Prudhomme M, Mortier-Barriere I, Granadel C, et al. ComE/ComE~P interplay dictates activation or extinction status of pneumococcal X-state (competence). Mol Microbiol. 2013;87(2):394–411. doi: 10.1111/mmi.12104 23216914.

50. Hentrich K, Lofling J, Pathak A, Nizet V, Varki A, Henriques-Normark B. Streptococcus pneumoniae senses a human-like sialic acid profile via the response regulator CiaR. Cell Host Microbe. 2016;20(3):307–17. doi: 10.1016/j.chom.2016.07.019 27593514.

51. Sung CK, Morrison DA. Two distinct functions of ComW in stabilization and activation of the alternative sigma factor ComX in Streptococcus pneumoniae. J Bacteriol. 2005;187(9):3052–61. doi: 10.1128/JB.187.9.3052-3061.2005 15838032.

52. Luo P, Li H, Morrison DA. Identification of ComW as a new component in the regulation of genetic transformation in Streptococcus pneumoniae. Mol Microbiol. 2004;54(1):172–83. doi: 10.1111/j.1365-2958.2004.04254.x 15458414.

53. Jeong JK, Kwon O, Lee YM, Oh DB, Lee JM, Kim S, et al. Characterization of the Streptococcus pneumoniae BgaC protein as a novel surface beta-galactosidase with specific hydrolysis activity for the Galbeta1-3GlcNAc moiety of oligosaccharides. J Bacteriol. 2009;191(9):3011–23. doi: 10.1128/JB.01601-08 19270088.

54. Afzal M, Shafeeq S, Ahmed H, Kuipers OP. N-acetylgalatosamine-mediated regulation of the aga operon by AgaR in Streptococcus pneumoniae. Front Cell Infect Microbiol. 2016;6:101. doi: 10.3389/fcimb.2016.00101 27672623.

55. Maruyama Y, Nakamichi Y, Itoh T, Mikami B, Hashimoto W, Murata K. Substrate specificity of streptococcal unsaturated glucuronyl hydrolases for sulfated glycosaminoglycan. J Biol Chem. 2009;284(27):18059–69. doi: 10.1074/jbc.M109.005660 19416976.

56. Marion C, Stewart JM, Tazi MF, Burnaugh AM, Linke CM, Woodiga SA, et al. Streptococcus pneumoniae can utilize multiple sources of hyaluronic acid for growth. Infect Immun. 2012;80(4):1390–8. doi: 10.1128/IAI.05756-11 22311922

57. Agrawal R, Sahoo BK, Saini DK. Cross-talk and specificity in two-component signal transduction pathways. Future Microbiol. 2016;11(5):685–97. doi: 10.2217/fmb-2016-0001 27159035

58. Inniss NL, Prehna G, Morrison DA. The pneumococcal sigma(X) activator, ComW, is a DNA-binding protein critical for natural transformation. J Biol Chem. 2019;294(29):11101–18. doi: 10.1074/jbc.RA119.007571 31160340.

59. Johnson RC. Site-specific DNA inversion by serine recombinases. Microbiol Spectr. 2015;3(1):MDNA3-0047-2014. doi: 10.1128/microbiolspec.MDNA3-0047-2014 26104558.

60. Johnson RC, Bruist MF, Simon MI. Host protein requirements for in vitro site-specific DNA inversion. Cell. 1986;46(4):531–9. doi: 10.1016/0092-8674(86)90878-0 3524854.

61. Zieg J, Silverman M, Hilmen M, Simon M. Recombinational switch for gene expression. Science. 1977;196(4286):170–2. doi: 10.1126/science.322276 322276.

62. Hillyard DR, Edlund M, Hughes KT, Marsh M, Higgins NP. Subunit-specific phenotypes of Salmonella typhimurium HU mutants. J Bacteriol. 1990;172(9):5402–7. doi: 10.1128/jb.172.9.5402-5407.1990 2168381.

63. Haykinson MJ, Johnson RC. DNA looping and the helical repeat in vitro and in vivo: effect of HU protein and enhancer location on Hin invertasome assembly. EMBO J. 1993;12(6):2503–12. doi: 10.1002/j.1460-2075.1993.tb05905.x 8508775.

64. McLean MM, Chang Y, Dhar G, Heiss JK, Johnson RC. Multiple interfaces between a serine recombinase and an enhancer control site-specific DNA inversion. Elife. 2013;2:e01211. doi: 10.7554/eLife.01211 24151546

65. Dhar G, Heiss JK, Johnson RC. Mechanical constraints on Hin subunit rotation imposed by the Fis/enhancer system and DNA supercoiling during site-specific recombination. Mol Cell. 2009;34(6):746–59. doi: 10.1016/j.molcel.2009.05.020 19560425.

66. Johnson RC, Bruist MB, Glaccum MB, Simon MI. In vitro analysis of Hin-mediated site-specific recombination. Cold Spring Harb Symp Quant Biol. 1984;49:751–60. doi: 10.1101/sqb.1984.049.01.085 6099257.

67. Pericone CD, Park S, Imlay JA, Weiser JN. Factors contributing to hydrogen peroxide resistance in Streptococcus pneumoniae include pyruvate oxidase (SpxB) and avoidance of the toxic effects of the fenton reaction. J Bacteriol. 2003;185(23):6815–25. doi: 10.1128/JB.185.23.6815-6825.2003 14617646.

68. Lisher JP, Tsui HT, Ramos-Montanez S, Hentchel KL, Martin JE, Trinidad JC, et al. Biological and chemical adaptation to endogenous hydrogen peroxide production in Streptococcus pneumoniae D39. mSphere. 2017;2(1). doi: 10.1128/mSphere.00291-16 28070562.

69. Overweg K, Pericone CD, Verhoef GG, Weiser JN, Meiring HD, De Jong AP, et al. Differential protein expression in phenotypic variants of Streptococcus pneumoniae. Infect Immun. 2000;68(8):4604–10. doi: 10.1128/iai.68.8.4604-4610.2000 10899862.

70. Chen H, Ma Y, Yang J, O’Brien CJ, Lee SL, Mazurkiewicz JE, et al. Genetic requirement for pneumococcal ear infection. Plos One. 2008;3(8):e2950. doi: 10.1371/journal.pone.0002950 18670623

71. Li J, Wang J, Jiao F, Zhang J-R. Observation of pneumococcal phase variation in colony morphology. Bio-protocol. 2017;7(15):e2434. doi: 10.21769/BioProtoc.2434

72. Liu X, Li JW, Feng Z, Luo Y, Veening JW, Zhang JR. Transcriptional repressor PtvR regulates phenotypic tolerance to vancomycin in Streptococcus pneumoniae. J Bacteriol. 2017;199(14). doi: 10.1128/JB.00054-17 28484041.

73. Schmittgen T. D. Livak K. J. Analyzing real-time PCR data by the comparative CT method. Nat Protoc. 2008;3(6):1101–8. doi: 10.1038/nprot.2008.73 18546601

Přihlášení
Zapomenuté heslo

Nemáte účet?  Registrujte se

Zapomenuté heslo

Zadejte e-mailovou adresu se kterou jste vytvářel(a) účet, budou Vám na ni zaslány informace k nastavení nového hesla.

Přihlášení

Nemáte účet?  Registrujte se