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Current Genetics

, Volume 65, Issue 4, pp 871–876 | Cite as

Spx, a versatile regulator of the Bacillus subtilis stress response

  • Heinrich Schäfer
  • Kürşad TurgayEmail author
Mini-Review

Abstract

Spx is a central regulator of the Bacillus subtilis stress response. By binding to the alpha subunits of RNA polymerase, it regulates the expression of many stress response genes, while concurrently interfering with various developmental processes. The recent observation that Spx also represses transcription of ribosomal RNA adds a direct link between stress response and the control of translation in B. subtilis. Here, we discuss the significance of the regulation of translation and the transcription of translation-related genes during the bacterial stress response and the role of Spx in this process. Furthermore, we compare Spx with the role of DksA during stress response in proteobacteria.

Keywords

Heat shock response Bacillus subtilis Spx Transcriptional regulation DksA Stringent response 

Notes

References

  1. Akanuma G, Kazo Y, Tagami K et al (2016) Ribosome dimerization is essential for the efficient regrowth of Bacillus subtilis. Microbiol Read Engl 162:448–458.  https://doi.org/10.1099/mic.0.000234 CrossRefGoogle Scholar
  2. Amato SM, Orman MA, Brynildsen MP (2013) Metabolic control of persister formation in Escherichia coli. Mol Cell 50:475–487.  https://doi.org/10.1016/j.molcel.2013.04.002 CrossRefPubMedGoogle Scholar
  3. Balaban NQ, Merrin J, Chait R et al (2004) Bacterial persistence as a phenotypic switch. Science 305:1622–1625.  https://doi.org/10.1126/science.1099390 CrossRefGoogle Scholar
  4. Beckert B, Abdelshahid M, Schäfer H et al (2017) Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization. EMBO J 36:2061–2072.  https://doi.org/10.15252/embj.201696189 CrossRefPubMedPubMedCentralGoogle Scholar
  5. Bernhardt J, Volker U, Volker A et al (1997) Specific and general stress proteins in Bacillus subtilis - a two-dimensional protein electrophoresis study. Microbiology 143:999–1017.  https://doi.org/10.1099/00221287-143-3-999 CrossRefPubMedGoogle Scholar
  6. Bourret TJ, Porwollik S, McClelland M et al (2008) Nitric oxide antagonizes the acid tolerance response that protects Salmonella against innate gastric defenses. PloS One 3:e1833.  https://doi.org/10.1371/journal.pone.0001833 CrossRefPubMedPubMedCentralGoogle Scholar
  7. Bremer H, Dennis PP (2008) Modulation of chemical composition and other parameters of the cell at different exponential growth rates. EcoSal Plus.  https://doi.org/10.1128/ecosal.5.2.3 CrossRefPubMedGoogle Scholar
  8. Chi BK, Gronau K, Mäder U et al (2011) S-bacillithiolation protects against hypochlorite stress in Bacillus subtilis as revealed by transcriptomics and redox proteomics. Mol Cell Proteom MCP 10:M111.009506.  https://doi.org/10.1074/mcp.M111.009506 CrossRefGoogle Scholar
  9. Crawford MA, Henard CA, Tapscott T et al (2016a) DksA-dependent transcriptional regulation in salmonella experiencing nitrosative stress. Front Microbiol 7:444.  https://doi.org/10.3389/fmicb.2016.00444 CrossRefPubMedPubMedCentralGoogle Scholar
  10. Crawford MA, Tapscott T, Fitzsimmons LF et al (2016b) Redox-active sensing by bacterial DksA transcription factors is determined by cysteine and zinc content. mBio.  https://doi.org/10.1128/mBio.02161-15 CrossRefPubMedPubMedCentralGoogle Scholar
  11. Elsholz AKW, Michalik S, Zühlke D et al (2010) CtsR, the gram-positive master regulator of protein quality control, feels the heat. EMBO J 29:3621–3629.  https://doi.org/10.1038/emboj.2010.228 CrossRefPubMedPubMedCentralGoogle Scholar
  12. Engman J, von Wachenfeldt C (2015) Regulated protein aggregation: a mechanism to control the activity of the ClpXP adaptor protein YjbH. Mol Microbiol 95:51–63.  https://doi.org/10.1111/mmi.12842 CrossRefPubMedGoogle Scholar
  13. Fitzsimmons LF, Liu L, Kim J-S et al (2018) Salmonella reprograms nucleotide metabolism in its adaptation to nitrosative stress. mBio 9:e00211–e00218.  https://doi.org/10.1128/mBio.00211-18 CrossRefPubMedPubMedCentralGoogle Scholar
  14. Fridman O, Goldberg A, Ronin I et al (2014) Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations. Nature 513:418–421.  https://doi.org/10.1038/nature13469 CrossRefPubMedGoogle Scholar
  15. Furman R, Danhart EM, NandyMazumdar M et al (2015) pH dependence of the stress regulator DksA. PloS One 10:e0120746.  https://doi.org/10.1371/journal.pone.0120746 CrossRefPubMedPubMedCentralGoogle Scholar
  16. Gaballa A, Antelmann H, Hamilton CJ, Helmann JD (2013) Regulation of Bacillus subtilis bacillithiol biosynthesis operons by Spx. Microbiol Read Engl 159:2025–2035.  https://doi.org/10.1099/mic.0.070482-0 CrossRefGoogle Scholar
  17. Gallant J, Palmer L, Pao CC (1977) Anomalous synthesis of ppGpp in growing cells. Cell 11:181–185CrossRefGoogle Scholar
  18. Garg SK, Kommineni S, Henslee L et al (2009) The YjbH protein of Bacillus subtilis enhances ClpXP-catalyzed proteolysis of Spx. J Bacteriol 191:1268–1277.  https://doi.org/10.1128/JB.01289-08 CrossRefPubMedGoogle Scholar
  19. Germain E, Castro-Roa D, Zenkin N, Gerdes K (2013) Molecular mechanism of bacterial persistence by HipA. Mol Cell 52:248–254.  https://doi.org/10.1016/j.molcel.2013.08.045 CrossRefPubMedGoogle Scholar
  20. Gohara DW, Yap M-NF (2018) Survival of the drowsiest: the hibernating 100S ribosome in bacterial stress management. Curr Genet 64:753–760.  https://doi.org/10.1007/s00294-017-0796-2 CrossRefPubMedGoogle Scholar
  21. Gourse RL, Gaal T, Bartlett MS et al (1996) rRNA transcription and growth rate–dependent regulation of ribosome synthesis in Escherichia coli. Annu Rev Microbiol 50:645–677.  https://doi.org/10.1146/annurev.micro.50.1.645 CrossRefPubMedGoogle Scholar
  22. Gourse RL, Chen AY, Gopalkrishnan S et al (2018) Transcriptional responses to ppGpp and DksA. Annu Rev Microbiol 72:163–184.  https://doi.org/10.1146/annurev-micro-090817-062444 CrossRefPubMedPubMedCentralGoogle Scholar
  23. Harms A, Fino C, Sørensen MA et al (2017) Prophages and growth dynamics confound experimental results with antibiotic-tolerant persister cells. mBio.  https://doi.org/10.1128/mBio.01964-17 CrossRefPubMedPubMedCentralGoogle Scholar
  24. Hartl FU, Bracher A, Hayer-Hartl M (2011) Molecular chaperones in protein folding and proteostasis. Nature 475:324–332.  https://doi.org/10.1038/nature10317 CrossRefGoogle Scholar
  25. Hecker M, Schumann W, Völker U (1996) Heat-shock and general stress response in Bacillus subtilis. Mol Microbiol 19:417–428CrossRefPubMedGoogle Scholar
  26. Hecker M, Pané-Farré J, Völker U (2007) SigB-dependent general stress response in Bacillus subtilis and related gram-positive bacteria. Annu Rev Microbiol 61:215–236.  https://doi.org/10.1146/annurev.micro.61.080706.093445 CrossRefPubMedGoogle Scholar
  27. Henard CA, Vázquez-Torres A (2012) DksA-dependent resistance of Salmonella enterica serovar Typhimurium against the antimicrobial activity of inducible nitric oxide synthase. Infect Immun 80:1373–1380.  https://doi.org/10.1128/IAI.06316-11 CrossRefPubMedPubMedCentralGoogle Scholar
  28. Henard CA, Bourret TJ, Song M, Vázquez-Torres A (2010) Control of redox balance by the stringent response regulatory protein promotes antioxidant defenses of Salmonella. J Biol Chem 285:36785–36793.  https://doi.org/10.1074/jbc.M110.160960 CrossRefPubMedPubMedCentralGoogle Scholar
  29. Henard CA, Tapscott T, Crawford MA et al (2014) The 4-cysteine zinc-finger motif of the RNA polymerase regulator DksA serves as a thiol switch for sensing oxidative and nitrosative stress. Mol Microbiol 91:790–804.  https://doi.org/10.1111/mmi.12498 CrossRefPubMedPubMedCentralGoogle Scholar
  30. Höper D, Völker U, Hecker M (2005) Comprehensive characterization of the contribution of individual SigB-dependent general stress genes to stress resistance of Bacillus subtilis. J Bacteriol 187:2810–2826.  https://doi.org/10.1128/JB.187.8.2810-2826.2005 CrossRefPubMedPubMedCentralGoogle Scholar
  31. Kang PJ, Craig EA (1990) Identification and characterization of a new Escherichia coli gene that is a dosage-dependent suppressor of a dnaK deletion mutation. J Bacteriol 172:2055–2064CrossRefPubMedPubMedCentralGoogle Scholar
  32. Kim J-S, Liu L, Fitzsimmons LF et al (2018) DksA-DnaJ redox interactions provide a signal for the activation of bacterial RNA polymerase. Proc Natl Acad Sci USA 115:E11780–E11789.  https://doi.org/10.1073/pnas.1813572115 CrossRefPubMedGoogle Scholar
  33. Kobayashi K (2019) Inactivation of cysL inhibits biofilm formation by activating the disulfide stress regulator Spx in Bacillus subtilis. J Bacteriol.  https://doi.org/10.1128/JB.00712-18 CrossRefPubMedGoogle Scholar
  34. Krásný L, Gourse RL (2004) An alternative strategy for bacterial ribosome synthesis: Bacillus subtilis rRNA transcription regulation. EMBO J 23:4473–4483.  https://doi.org/10.1038/sj.emboj.7600423 CrossRefPubMedPubMedCentralGoogle Scholar
  35. Krüger E, Hecker M (1998) The first gene of the Bacillus subtilis clpC operon, ctsR, encodes a negative regulator of its own operon and other class III heat shock genes. J Bacteriol 180:6681–6688PubMedPubMedCentralGoogle Scholar
  36. Larsson JT, Rogstam A, von Wachenfeldt C (2007) YjbH is a novel negative effector of the disulphide stress regulator, Spx, in Bacillus subtilis. Mol Microbiol 66:669–684.  https://doi.org/10.1111/j.1365-2958.2007.05949.x CrossRefPubMedGoogle Scholar
  37. Leichert LIO, Scharf C, Hecker M (2003) Global characterization of disulfide stress in Bacillus subtilis. J Bacteriol 185:1967–1975CrossRefPubMedPubMedCentralGoogle Scholar
  38. Lemaux PG, Herendeen SL, Bloch PL, Neidhardt FC (1978) Transient rates of synthesis of individual polypeptides in E. coli following temperature shifts. Cell 13:427–434CrossRefPubMedGoogle Scholar
  39. Liu J, Zuber P (2000) The ClpX protein of Bacillus subtilis indirectly influences RNA polymerase holoenzyme composition and directly stimulates sigma-dependent transcription. Mol Microbiol 37:885–897CrossRefPubMedGoogle Scholar
  40. Liu J, Cosby WM, Zuber P (1999) Role of lon and ClpX in the post-translational regulation of a sigma subunit of RNA polymerase required for cellular differentiation in Bacillus subtilis. Mol Microbiol 33:415–428CrossRefPubMedGoogle Scholar
  41. Lopez JM, Dromerick A, Freese E (1981) Response of guanosine 5′-triphosphate concentration to nutritional changes and its significance for Bacillus subtilis sporulation. J Bacteriol 146:605–613PubMedPubMedCentralGoogle Scholar
  42. Maaβ S, Wachlin G, Bernhardt J et al (2014) Highly precise quantification of protein molecules per cell during stress and starvation responses in Bacillus subtilis. Mol Cell Proteom 13:2260–2276.  https://doi.org/10.1074/mcp.M113.035741 CrossRefGoogle Scholar
  43. Mogk A, Homuth G, Scholz C et al (1997) The GroE chaperonin machine is a major modulator of the CIRCE heat shock regulon of Bacillus subtilis. EMBO J 16:4579–4590.  https://doi.org/10.1093/emboj/16.15.4579 CrossRefPubMedPubMedCentralGoogle Scholar
  44. Mogk A, Huber D, Bukau B (2011) Integrating protein homeostasis strategies in prokaryotes. Cold Spring Harb Perspect Biol.  https://doi.org/10.1101/cshperspect.a004366 CrossRefPubMedPubMedCentralGoogle Scholar
  45. Molière N, Hoßmann J, Schäfer H, Turgay K (2016) Role of Hsp100/Clp protease complexes in controlling the regulation of motility in Bacillus subtilis. Front Microbiol.  https://doi.org/10.3389/fmicb.2016.00315 CrossRefPubMedPubMedCentralGoogle Scholar
  46. Mostertz J, Scharf C, Hecker M, Homuth G (2004) Transcriptome and proteome analysis of Bacillus subtilis gene expression in response to superoxide and peroxide stress. Microbiol Read Engl 150:497–512.  https://doi.org/10.1099/mic.0.26665-0 CrossRefGoogle Scholar
  47. Nakano MM, Zhu Y, Liu J et al (2000) Mutations conferring amino acid residue substitutions in the carboxy-terminal domain of RNA polymerase alpha can suppress clpX and clpP with respect to developmentally regulated transcription in Bacillus subtilis. Mol Microbiol 37:869–884CrossRefPubMedGoogle Scholar
  48. Nakano MM, Hajarizadeh F, Zhu Y, Zuber P (2001) Loss-of-function mutations in yjbD result in ClpX- and ClpP-independent competence development of Bacillus subtilis. Mol Microbiol 42:383–394CrossRefPubMedGoogle Scholar
  49. Nakano S, Küster-Schöck E, Grossman AD, Zuber P (2003a) Spx-dependent global transcriptional control is induced by thiol-specific oxidative stress in Bacillus subtilis. Proc Natl Acad Sci USA 100:13603–13608.  https://doi.org/10.1073/pnas.2235180100 CrossRefPubMedGoogle Scholar
  50. Nakano S, Nakano MM, Zhang Y et al (2003b) A regulatory protein that interferes with activator-stimulated transcription in bacteria. Proc Natl Acad Sci USA 100:4233–4238.  https://doi.org/10.1073/pnas.0637648100 CrossRefPubMedGoogle Scholar
  51. Nakano S, Erwin KN, Ralle M, Zuber P (2005) Redox-sensitive transcriptional control by a thiol/disulphide switch in the global regulator. Spx Mol Microbiol 55:498–510.  https://doi.org/10.1111/j.1365-2958.2004.04395.x CrossRefPubMedGoogle Scholar
  52. Pamp SJ, Frees D, Engelmann S et al (2006) Spx is a global effector impacting stress tolerance and biofilm formation in Staphylococcus aureus. J Bacteriol 188:4861–4870.  https://doi.org/10.1128/JB.00194-06 CrossRefPubMedPubMedCentralGoogle Scholar
  53. Paul BJ, Barker MM, Ross W et al (2004) DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell 118:311–322.  https://doi.org/10.1016/j.cell.2004.07.009 CrossRefPubMedGoogle Scholar
  54. Paul BJ, Berkmen MB, Gourse RL (2005) DksA potentiates direct activation of amino acid promoters by ppGpp. Proc Natl Acad Sci USA 102:7823–7828.  https://doi.org/10.1073/pnas.0501170102 CrossRefPubMedGoogle Scholar
  55. Perederina A, Svetlov V, Vassylyeva MN et al (2004) Regulation through the secondary channel–structural framework for ppGpp-DksA synergism during transcription. Cell 118:297–309.  https://doi.org/10.1016/j.cell.2004.06.030 CrossRefPubMedGoogle Scholar
  56. Pöther D-C, Liebeke M, Hochgräfe F et al (2009) Diamide triggers mainly S Thiolations in the cytoplasmic proteomes of Bacillus subtilis and Staphylococcus aureus. J Bacteriol 191:7520–7530.  https://doi.org/10.1128/JB.00937-09 CrossRefPubMedPubMedCentralGoogle Scholar
  57. Potrykus K, Cashel M (2008) (p)ppGpp: still magical? Annu Rev Microbiol 62:35–51.  https://doi.org/10.1146/annurev.micro.62.081307.162903 CrossRefGoogle Scholar
  58. Ratnayake-Lecamwasam M, Serror P, Wong KW, Sonenshein AL (2001) Bacillus subtilis CodY represses early-stationary-phase genes by sensing GTP levels. Genes Dev 15:1093–1103.  https://doi.org/10.1101/gad.874201 CrossRefPubMedPubMedCentralGoogle Scholar
  59. Reyes DY, Zuber P (2008) Activation of transcription initiation by Spx: formation of transcription complex and identification of a cis-acting element required for transcriptional activation. Mol Microbiol 69:765–779.  https://doi.org/10.1111/j.1365-2958.2008.06330.x CrossRefPubMedPubMedCentralGoogle Scholar
  60. Rochat T, Nicolas P, Delumeau O et al (2012) Genome-wide identification of genes directly regulated by the pleiotropic transcription factor Spx in Bacillus subtilis. Nucleic Acids Res 40:9571–9583.  https://doi.org/10.1093/nar/gks755 CrossRefPubMedPubMedCentralGoogle Scholar
  61. Rojas-Tapias DF, Helmann JD (2018a) Induction of the Spx regulon by cell wall stress reveals novel regulatory mechanisms in Bacillus subtilis. Mol Microbiol 107:659–674.  https://doi.org/10.1111/mmi.13906 CrossRefPubMedPubMedCentralGoogle Scholar
  62. Rojas-Tapias DF, Helmann JD (2018b) Stabilization of Bacillus subtilis Spx under cell wall stress requires the anti-adaptor protein YirB. PLoS Genet 14:e1007531.  https://doi.org/10.1371/journal.pgen.1007531 CrossRefPubMedPubMedCentralGoogle Scholar
  63. Runde S, Molière N, Heinz A et al (2014) The role of thiol oxidative stress response in heat-induced protein aggregate formation during thermotolerance in B acillus subtilis: Thiol oxidation in protein aggregate formation. Mol Microbiol 91:1036–1052.  https://doi.org/10.1111/mmi.12521 CrossRefGoogle Scholar
  64. Schäfer H, Heinz A, Sudzinová P et al (2019) Spx, the central regulator of the heat and oxidative stress response in B. subtilis, can repress transcription of translation-related genes. Mol Microbiol 111:514–533.  https://doi.org/10.1111/mmi.14171 CrossRefPubMedGoogle Scholar
  65. Schmid R, Bernhardt J, Antelmann H et al (1997) Identification of vegetative proteins for a two-dimensional protein index of Bacillus subtilis. Microbiol Read Engl 143(Pt 3):991–998.  https://doi.org/10.1099/00221287-143-3-991 CrossRefGoogle Scholar
  66. Shah D, Zhang Z, Khodursky A et al (2006) Persisters: a distinct physiological state of E. coli. BMC Microbiol 6:53.  https://doi.org/10.1186/1471-2180-6-53 CrossRefPubMedPubMedCentralGoogle Scholar
  67. Yang X, Ishiguro EE (2003) Temperature-sensitive growth and decreased thermotolerance associated with relA mutations in Escherichia coli. J Bacteriol 185:5765–5771.  https://doi.org/10.1128/JB.185.19.5765-5771.2003 CrossRefPubMedPubMedCentralGoogle Scholar
  68. Zhang Y, Xiao Z, Zou Q et al (2017) Ribosome profiling reveals genome-wide cellular translational regulation upon heat stress in Escherichia coli. Genom Proteom Bioinform 15:324–330.  https://doi.org/10.1016/j.gpb.2017.04.005 CrossRefGoogle Scholar
  69. Zuber P (2004) Spx-RNA polymerase interaction and global transcriptional control during oxidative stress. J Bacteriol 186:1911–1918CrossRefPubMedPubMedCentralGoogle Scholar
  70. Zuber P, Chauhan S, Pilaka P et al (2011) Phenotype enhancement screen of a regulatory spx mutant unveils a role for the ytpQ gene in the control of iron homeostasis. PloS One 6:e25066.  https://doi.org/10.1371/journal.pone.0025066 CrossRefPubMedPubMedCentralGoogle Scholar

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© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Institute of MicrobiologyLeibniz Universität HannoverHannoverGermany

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