The Eukaryotic-Like Ser/Thr Kinase PrkC Regulates the Essential WalRK Two-Component System in

English version České info

A central question in bacterial physiology is how bacteria sense and respond to their environment. The archetype of bacterial signaling systems is the two-component signaling system composed of a sensor protein histidine kinase that activates a transcription factor response regulator in response to a specific signal. In addition, bacteria also have signaling systems composed of eukaryotic-like Ser/Thr kinases and phosphatases. Even though these systems do not have dedicated transcription factors, they are capable of affecting gene expression. Here we show that a eukaryotic-like Ser/Thr kinase conserved in all sequenced Gram-positive bacteria converges with an essential two-component signaling system to regulate gene expression in the model organism Bacillus subtilis. We show that this eukaryotic-like Ser/Thr kinase phosphorylates the response regulator of a highly conserved and essential two-component signaling system, thereby increasing its activity. This phosphorylation results in the regulation of genes involved in the essential process of cell wall metabolism. Given that bacterial cell wall metabolism is the target of many known antibiotics, and mutations in both of these signaling systems change the antibiotic sensitivity of a number of important Gram-positive pathogens, we expect that our analysis will suggest novel insight into the emergence of antibiotic resistance.

Vyšlo v časopise: The Eukaryotic-Like Ser/Thr Kinase PrkC Regulates the Essential WalRK Two-Component System in. PLoS Genet 11(6): e32767. doi:10.1371/journal.pgen.1005275
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1005275

Souhrn

Zdroje

1. Mijakovic I, Macek B (2012) Impact of phosphoproteomics on studies of bacterial physiology. FEMS Microbiol Rev 36 : 877–892. doi: 10.1111/j.1574-6976.2011.00314.x 22091997

2. Dworkin J (2015) Ser/Thr phosphorylation as a regulatory mechanism in bacteria. Curr Opin Microbiol 24C: 47–52.

3. Pereira SF, Goss L, Dworkin J (2011) Eukaryote-like serine/threonine kinases and phosphatases in bacteria. Microbiology and molecular biology reviews: MMBR 75 : 192–212. doi: 10.1128/MMBR.00042-10 21372323

4. Donat S, Streker K, Schirmeister T, Rakette S, Stehle T, et al. (2009) Transcriptome and functional analysis of the eukaryotic-type ser/thr kinase PknB in Staphylococcus aureus. J Bacteriol 191 : 4056–4069. doi: 10.1128/JB.00117-09 19376851

5. Saskova L, Novakova L, Basler M, Branny P (2007) Eukaryotic-type serine/threonine protein kinase StkP is a global regulator of gene expression in Streptococcus pneumoniae. J Bacteriol 189 : 4168–4179. 17416671

6. Banu LD, Conrads G, Rehrauer H, Hussain H, Allan E, et al. (2010) The Streptococcus mutans serine/threonine kinase, PknB, regulates competence development, bacteriocin production, and cell wall metabolism. Infect Immun 78 : 2209–2220. doi: 10.1128/IAI.01167-09 20231406

7. Burnside K, Rajagopal L (2012) Regulation of prokaryotic gene expression by eukaryotic-like enzymes. Curr Opin Microbiol 15 : 125–131. doi: 10.1016/j.mib.2011.12.006 22221896

8. Wright DP, Ulijasz AT (2014) Regulation of transcription by eukaryotic-like serine-threonine kinases and phosphatases in Gram-positive bacterial pathogens. Virulence 5 : 863–885. doi: 10.4161/21505594.2014.983404 25603430

9. Jones G, Dyson P (2006) Evolution of transmembrane protein kinases implicated in coordinating remodeling of gram-positive peptidoglycan: inside versus outside. J Bacteriol 188 : 7470–7476. 16936012

10. Yeats C, Finn RD, Bateman A (2002) The PASTA domain: a beta-lactam-binding domain. Trends Biochem Sci 27 : 438. 12217513

11. Maestro B, Novakova L, Hesek D, Lee M, Leyva E, et al. (2011) Recognition of peptidoglycan and beta-lactam antibiotics by the extracellular domain of the Ser/Thr protein kinase StkP from Streptococcus pneumoniae. FEBS Lett 585 : 357–363. doi: 10.1016/j.febslet.2010.12.016 21167155

12. Mir M, Asong J, Li X, Cardot J, Boons GJ, et al. (2011) The extracytoplasmic domain of the Mycobacterium tuberculosis Ser/Thr kinase PknB binds specific muropeptides and is required for PknB localization. PLoS pathogens 7: e1002182. doi: 10.1371/journal.ppat.1002182 21829358

13. Squeglia F, Marchetti R, Ruggiero A, Lanzetta R, Marasco D, et al. (2011) Chemical Basis of Peptidoglycan Discrimination by PrkC, a Key Kinase Involved in Bacterial Resuscitation from Dormancy. Journal of the American Chemical Society 133 : 20676–20679. doi: 10.1021/ja208080r 22111897

14. Shah IM, Laaberki MH, Popham DL, Dworkin J (2008) A eukaryotic-like Ser/Thr kinase signals bacteria to exit dormancy in response to peptidoglycan fragments. Cell 135 : 486–496. doi: 10.1016/j.cell.2008.08.039 18984160

15. Shah IM, Dworkin J (2010) Induction and regulation of a secreted peptidoglycan hydrolase by a membrane Ser/Thr kinase that detects muropeptides. Mol Microbiol 75 : 1232–1245. doi: 10.1111/j.1365-2958.2010.07046.x 20070526

16. Nicolas P, Mader U, Dervyn E, Rochat T, Leduc A, et al. (2012) Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science 335 : 1103–1106. doi: 10.1126/science.1206848 22383849

17. Winkler ME, Hoch JA (2008) Essentiality, bypass, and targeting of the YycFG (VicRK) two-component regulatory system in gram-positive bacteria. J Bacteriol 190 : 2645–2648. doi: 10.1128/JB.01682-07 18245295

18. Dubrac S, Bisicchia P, Devine KM, Msadek T (2008) A matter of life and death: cell wall homeostasis and the WalKR (YycGF) essential signal transduction pathway. Mol Microbiol 70 : 1307–1322. doi: 10.1111/j.1365-2958.2008.06483.x 19019149

19. Fabret C, Hoch JA (1998) A two-component signal transduction system essential for growth of Bacillus subtilis: implications for anti-infective therapy. J Bacteriol 180 : 6375–6383. 9829949

20. Dominguez-Cuevas P, Mercier R, Leaver M, Kawai Y, Errington J (2012) The rod to L-form transition of Bacillus subtilis is limited by a requirement for the protoplast to escape from the cell wall sacculus. Molecular microbiology 83 : 52–66. doi: 10.1111/j.1365-2958.2011.07920.x 22122227

21. Ng WL, Robertson GT, Kazmierczak KM, Zhao J, Gilmour R, et al. (2003) Constitutive expression of PcsB suppresses the requirement for the essential VicR (YycF) response regulator in Streptococcus pneumoniae R6. Molecular microbiology 50 : 1647–1663. 14651645

22. Howell A, Dubrac S, Andersen KK, Noone D, Fert J, et al. (2003) Genes controlled by the essential YycG/YycF two-component system of Bacillus subtilis revealed through a novel hybrid regulator approach. Mol Microbiol 49 : 1639–1655. 12950927

23. Bisicchia P, Noone D, Lioliou E, Howell A, Quigley S, et al. (2007) The essential YycFG two-component system controls cell wall metabolism in Bacillus subtilis. Mol Microbiol 65 : 180–200. 17581128

24. Dubrac S, Boneca IG, Poupel O, Msadek T (2007) 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. Journal of bacteriology 189 : 8257–8269. 17827301

25. Salzberg LI, Powell L, Hokamp K, Botella E, Noone D, et al. (2013) The WalRK (YycFG) and sigma(I) RsgI regulators cooperate to control CwlO and LytE expression in exponentially growing and stressed Bacillus subtilis cells. Mol Microbiol 87 : 180–195. doi: 10.1111/mmi.12092 23199363

26. Bugrysheva J, Froehlich BJ, Freiberg JA, Scott JR (2011) Serine/threonine protein kinase Stk is required for virulence, stress response, and penicillin tolerance in Streptococcus pyogenes. Infection and Immunity 79 : 4201–4209. doi: 10.1128/IAI.05360-11 21788381

27. Szurmant H, Nelson K, Kim EJ, Perego M, Hoch JA (2005) YycH regulates the activity of the essential YycFG two-component system in Bacillus subtilis. J Bacteriol 187 : 5419–5426. 16030236

28. Qazi SN, Counil E, Morrissey J, Rees CE, Cockayne A, et al. (2001) agr expression precedes escape of internalized Staphylococcus aureus from the host endosome. Infect Immun 69 : 7074–7082. 11598083

29. Radeck J, Kraft K, Bartels J, Cikovic T, Durr F, et al. (2013) The Bacillus BioBrick Box: generation and evaluation of essential genetic building blocks for standardized work with Bacillus subtilis. J Biol Eng 7 : 29. doi: 10.1186/1754-1611-7-29 24295448

30. Gaidenko TA, Kim TJ, Price CW (2002) The PrpC serine-threonine phosphatase and PrkC kinase have opposing physiological roles in stationary-phase Bacillus subtilis cells. J Bacteriol 184 : 6109–6114. 12399479

31. Botella E, Hubner S, Hokamp K, Hansen A, Bisicchia P, et al. (2011) Cell envelope gene expression in phosphate-limited Bacillus subtilis cells. Microbiology 157 : 2470–2484. doi: 10.1099/mic.0.049205-0 21636651

32. Yamamoto H, Hashimoto M, Higashitsuji Y, Harada H, Hariyama N, et al. (2008) Post-translational control of vegetative cell separation enzymes through a direct interaction with specific inhibitor IseA in Bacillus subtilis. Mol Microbiol 70 : 168–182. doi: 10.1111/j.1365-2958.2008.06398.x 18761694

33. Kobayashi K, Sudiarta IP, Kodama T, Fukushima T, Ara K, et al. (2012) Identification and characterization of a novel polysaccharide deacetylase C (PdaC) from Bacillus subtilis. J Biol Chem 287 : 9765–9776. doi: 10.1074/jbc.M111.329490 22277649

34. Madec E, Stensballe A, Kjellstrom S, Cladiere L, Obuchowski M, et al. (2003) Mass spectrometry and site-directed mutagenesis identify several autophosphorylated residues required for the activity of PrkC, a Ser/Thr kinase from Bacillus subtilis. J Mol Biol 330 : 459–472. 12842463

35. Prisic S, Dankwa S, Schwartz D, Chou MF, Locasale JW, et al. (2010) Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases. Proc Natl Acad Sci U S A 107 : 7521–7526. doi: 10.1073/pnas.0913482107 20368441

36. Fukushima T, Szurmant H, Kim EJ, Perego M, Hoch JA (2008) A sensor histidine kinase co-ordinates cell wall architecture with cell division in Bacillus subtilis. Molecular microbiology 69 : 621–632. doi: 10.1111/j.1365-2958.2008.06308.x 18573169

37. Fukushima T, Furihata I, Emmins R, Daniel RA, Hoch JA, et al. (2011) A role for the essential YycG sensor histidine kinase in sensing cell division. Mol Microbiol 79 : 503–522. doi: 10.1111/j.1365-2958.2010.07464.x 21219466

38. Szurmant H, Mohan MA, Imus PM, Hoch JA (2007) YycH and YycI interact to regulate the essential YycFG two-component system in Bacillus subtilis. J Bacteriol 189 : 3280–3289. 17307850

39. Szurmant H, Bu L, Brooks CL 3rd, Hoch JA (2008) An essential sensor histidine kinase controlled by transmembrane helix interactions with its auxiliary proteins. Proc Natl Acad Sci U S A 105 : 5891–5896. doi: 10.1073/pnas.0800247105 18408157

40. Toro-Roman A, Mack TR, Stock AM (2005) Structural analysis and solution studies of the activated regulatory domain of the response regulator ArcA: a symmetric dimer mediated by the alpha4-beta5-alpha5 face. J Mol Biol 349 : 11–26. 15876365

41. Bourret RB (2010) Receiver domain structure and function in response regulator proteins. Curr Opin Microbiol 13 : 142–149. doi: 10.1016/j.mib.2010.01.015 20211578

42. Kern D, Volkman BF, Luginbuhl P, Nohaile MJ, Kustu S, et al. (1999) Structure of a transiently phosphorylated switch in bacterial signal transduction. Nature 402 : 894–898. 10622255

43. Casino P, Rubio V, Marina A (2009) Structural insight into partner specificity and phosphoryl transfer in two-component signal transduction. Cell 139 : 325–336. doi: 10.1016/j.cell.2009.08.032 19800110

44. Capra EJ, Perchuk BS, Lubin EA, Ashenberg O, Skerker JM, et al. (2010) Systematic dissection and trajectory-scanning mutagenesis of the molecular interface that ensures specificity of two-component signaling pathways. PLoS Genet 6: e1001220. doi: 10.1371/journal.pgen.1001220 21124821

45. Absalon C, Obuchowski M, Madec E, Delattre D, Holland IB, et al. (2009) CpgA, EF-Tu and the stressosome protein YezB are substrates of the Ser/Thr kinase/phosphatase couple, PrkC/PrpC, in Bacillus subtilis. Microbiology 155 : 932–943. doi: 10.1099/mic.0.022475-0 19246764

46. Pompeo F, Freton C, Wicker-Planquart C, Grangeasse C, Jault JM, et al. (2012) Phosphorylation of CpgA protein enhances both its GTPase activity and its affinity for ribosome and is crucial for Bacillus subtilis growth and morphology. J Biol Chem 287 : 20830–20838. doi: 10.1074/jbc.M112.340331 22544754

47. Ravikumar V, Shi L, Krug K, Derouiche A, Jers C, et al. (2014) Quantitative phosphoproteome analysis of bacillus subtilis reveals novel substrates of the kinase PrkC and phosphatase PrpC. Mol Cell Proteomics 13 : 1965–1978. doi: 10.1074/mcp.M113.035949 24390483

48. Foulquier E, Pompeo F, Freton C, Cordier B, Grangeasse C, et al. (2014) PrkC-mediated Phosphorylation of Overexpressed YvcK Protein Regulates PBP1 Protein Localization in Bacillus subtilis mreB Mutant Cells. J Biol Chem 289 : 23662–23669. doi: 10.1074/jbc.M114.562496 25012659

49. Pietack N, Becher D, Schmidl SR, Saier MH, Hecker M, et al. (2010) In vitro Phosphorylation of Key Metabolic Enzymes from Bacillus subtilis: PrkC Phosphorylates Enzymes from Different Branches of Basic Metabolism. J Mol Microbiol Biotechnol 18 : 129–140. doi: 10.1159/000308512 20389117

50. Kobir A, Poncet S, Bidnenko V, Delumeau O, Jers C, et al. (2014) Phosphorylation of Bacillus subtilis gene regulator AbrB modulates its DNA-binding properties. Mol Microbiol 92 : 1129–1141. doi: 10.1111/mmi.12617 24731262

51. Agarwal S, Agarwal S, Pancholi P, Pancholi V (2012) Strain-specific regulatory role of eukaryote-like serine/threonine phosphatase in pneumococcal adherence. Infect Immun 80 : 1361–1372. doi: 10.1128/IAI.06311-11 22311926

52. Horstmann N, Saldana M, Sahasrabhojane P, Yao H, Su X, et al. (2014) Dual-site phosphorylation of the control of virulence regulator impacts group a streptococcal global gene expression and pathogenesis. PLoS Pathog 10: e1004088. doi: 10.1371/journal.ppat.1004088 24788524

53. Fridman M, Williams GD, Muzamal U, Hunter H, Siu KW, et al. (2013) Two unique phosphorylation-driven signaling pathways crosstalk in Staphylococcus aureus to modulate the cell-wall charge: Stk1/Stp1 meets GraSR. Biochemistry 52 : 7975–7986. doi: 10.1021/bi401177n 24102310

54. Canova MJ, Baronian G, Brelle S, Cohen-Gonsaud M, Bischoff M, et al. (2014) A novel mode of regulation of the Staphylococcus aureus Vancomycin-resistance-associated response regulator VraR mediated by Stk1 protein phosphorylation. Biochem Biophys Res Commun 447 : 165–171. doi: 10.1016/j.bbrc.2014.03.128 24704444

55. Chao JD, Papavinasasundaram KG, Zheng X, Chavez-Steenbock A, Wang X, et al. (2010) Convergence of Ser/Thr and two-component signaling to coordinate expression of the dormancy regulon in Mycobacterium tuberculosis. J Biol Chem 285 : 29239–29246. doi: 10.1074/jbc.M110.132894 20630871

56. Canova MJ, Veyron-Churlet R, Zanella-Cleon I, Cohen-Gonsaud M, Cozzone AJ, et al. (2008) The Mycobacterium tuberculosis serine/threonine kinase PknL phosphorylates Rv2175c: mass spectrometric profiling of the activation loop phosphorylation sites and their role in the recruitment of Rv2175c. Proteomics 8 : 521–533. doi: 10.1002/pmic.200700442 18175374

57. Cohen-Gonsaud M, Barthe P, Canova MJ, Stagier-Simon C, Kremer L, et al. (2009) The Mycobacterium tuberculosis Ser/Thr kinase substrate Rv2175c is a DNA-binding protein regulated by phosphorylation. J Biol Chem 284 : 19290–19300. doi: 10.1074/jbc.M109.019653 19457863

58. Ulijasz AT, Falk SP, Weisblum B (2009) Phosphorylation of the RitR DNA-binding domain by a Ser-Thr phosphokinase: implications for global gene regulation in the streptococci. Mol Microbiol 71 : 382–390. doi: 10.1111/j.1365-2958.2008.06532.x 19040630

59. Lin WJ, Walthers D, Connelly JE, Burnside K, Jewell KA, et al. (2009) Threonine phosphorylation prevents promoter DNA binding of the Group B Streptococcus response regulator CovR. Molecular microbiology 71 : 1477–1495. doi: 10.1111/j.1365-2958.2009.06616.x 19170889

60. Delaune A, Dubrac S, Blanchet C, Poupel O, Mader U, et al. (2012) The WalKR system controls major staphylococcal virulence genes and is involved in triggering the host inflammatory response. Infect Immun 80 : 3438–3453. doi: 10.1128/IAI.00195-12 22825451

61. Friedman L, Alder JD, Silverman JA (2006) Genetic changes that correlate with reduced susceptibility to daptomycin in Staphylococcus aureus. Antimicrob Agents Chemother 50 : 2137–2145. 16723576

62. Jansen A, Turck M, Szekat C, Nagel M, Clever I, et al. (2007) Role of insertion elements and yycFG in the development of decreased susceptibility to vancomycin in Staphylococcus aureus. Int J Med Microbiol 297 : 205–215. 17418637

63. Howden BP, McEvoy CR, Allen DL, Chua K, Gao W, et al. (2011) Evolution of multidrug resistance during Staphylococcus aureus infection involves mutation of the essential two component regulator WalKR. PLoS Pathog 7: e1002359. doi: 10.1371/journal.ppat.1002359 22102812

64. Hafer C, Lin Y, Kornblum J, Lowy FD, Uhlemann AC (2012) Contribution of selected gene mutations to resistance in clinical isolates of vancomycin-intermediate Staphylococcus aureus. Antimicrob Agents Chemother 56 : 5845–5851. doi: 10.1128/AAC.01139-12 22948864

65. Harwood CR, Cutting SM, editors (1990) Molecular biological methods for Bacillus New York: Wiley.