1887

Abstract

Transcriptional specificity in low-G+C Gram-positive bacteria is maintained by RpoE, the delta subunit of the RNA polymerase. Here, we studied the effect of RpoE at the proteome level in the human dental pathogen by comparing the Δ mutant with the wild-type under five conditions: (0) exponential growth, (1) early stationary phase, (2) acid stress, (3) oxidative stress, and (4) combined acid and oxidative stress. A total of 280 cellular protein spots were reproducibly detected, of which 97 differentially expressed protein spots were identified by MALDI-TOF MS. Lack of RpoE caused downregulation of proteins for carbohydrate metabolism and energy production, including phosphoglucomutase (PGM), the phosphopentomutase DeoB and the pyruvate formate-lyase Pfl. The Δ mutant had extensive changes in the abundance of proteins involved in acid and oxidative tolerance and protein turnover, and of chaperones, at exponential phase in the absence of stress, suggesting a potential internal stress. In addition, the mutant had reduced amounts of proteins for adaptation responses, e.g. the multiple sugar transport and metabolism enzymes required for entering early stationary phase, and the proteins for stress-defence mechanisms and glycolysis under oxidative stress. Comparison of the proteome data with the corresponding transcriptome data suggested that the effects were the result of altered transcriptional and post-transcriptional regulation. The data are consistent with the reduced transcriptional specificity of the RNA polymerase in the Δ mutant, and suggest a general impact, but not a specific regulatory role, of RpoE in stress adaptation.

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2012-01-01
2019-10-14
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References

  1. Abranches J. , Chen Y. Y. , Burne R. A. . ( 2004; ). Galactose metabolism by Streptococcus mutans . . Appl Environ Microbiol 70:, 6047–6052. [CrossRef] [PubMed]
    [Google Scholar]
  2. Abranches J. , Lemos J. A. , Burne R. A. . ( 2006; ). Osmotic stress responses of Streptococcus mutans UA159. . FEMS Microbiol Lett 255:, 240–246. [CrossRef] [PubMed]
    [Google Scholar]
  3. Achberger E. C. , Whiteley H. R. . ( 1981; ). The role of the delta peptide of the Bacillus subtilis RNA polymerase in promoter selection. . J Biol Chem 256:, 7424–7432.[PubMed]
    [Google Scholar]
  4. Achberger E. C. , Hilton M. D. , Whiteley H. R. . ( 1982; ). The effect of the delta subunit on the interaction of Bacillus subtilis RNA polymerase with bases in a SP82 early gene promoter. . Nucleic Acids Res 10:, 2893–2910. [CrossRef] [PubMed]
    [Google Scholar]
  5. Ajdić D. , Pham V. T. . ( 2007; ). Global transcriptional analysis of Streptococcus mutans sugar transporters using microarrays. . J Bacteriol 189:, 5049–5059. [CrossRef] [PubMed]
    [Google Scholar]
  6. Ajdić D. , McShan W. M. , McLaughlin R. E. , Savić G. , Chang J. , Carson M. B. , Primeaux C. , Tian R. , Kenton S. . & other authors ( 2002; ). Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen. . Proc Natl Acad Sci U S A 99:, 14434–14439. [CrossRef] [PubMed]
    [Google Scholar]
  7. Biswas I. , Drake L. , Erkina D. , Biswas S. . ( 2008; ). Involvement of sensor kinases in the stress tolerance response of Streptococcus mutans . . J Bacteriol 190:, 68–77. [CrossRef] [PubMed]
    [Google Scholar]
  8. Bizzini A. , Majcherczyk P. , Beggah-Möller S. , Soldo B. , Entenza J. M. , Gaillard M. , Moreillon P. , Lazarevic V. . ( 2007; ). Effects of α-phosphoglucomutase deficiency on cell wall properties and fitness in Streptococcus gordonii . . Microbiology 153:, 490–498. [CrossRef] [PubMed]
    [Google Scholar]
  9. Buchanan J. T. , Stannard J. A. , Lauth X. , Ostland V. E. , Powell H. C. , Westerman M. E. , Nizet V. . ( 2005; ). Streptococcus iniae phosphoglucomutase is a virulence factor and a target for vaccine development. . Infect Immun 73:, 6935–6944. [CrossRef] [PubMed]
    [Google Scholar]
  10. Carmel-Harel O. , Storz G. . ( 2000; ). Roles of the glutathione- and thioredoxin-dependent reduction systems in the Escherichia coli and Saccharomyces cerevisiae responses to oxidative stress. . Annu Rev Microbiol 54:, 439–461. [CrossRef] [PubMed]
    [Google Scholar]
  11. Carpentier S. C. , Witters E. , Laukens K. , Deckers P. , Swennen R. , Panis B. . ( 2005; ). Preparation of protein extracts from recalcitrant plant tissues: an evaluation of different methods for two-dimensional gel electrophoresis analysis. . Proteomics 5:, 2497–2507. [CrossRef] [PubMed]
    [Google Scholar]
  12. Chen P. M. , Chen H. C. , Ho C. T. , Jung C. J. , Lien H. T. , Chen J. Y. , Chia J. S. . ( 2008; ). The two-component system ScnRK of Streptococcus mutans affects hydrogen peroxide resistance and murine macrophage killing. . Microbes Infect 10:, 293–301. [CrossRef] [PubMed]
    [Google Scholar]
  13. De Angelis M. , Gobbetti M. . ( 2004; ). Environmental stress responses in Lactobacillus: a review. . Proteomics 4:, 106–122. [CrossRef] [PubMed]
    [Google Scholar]
  14. Deng D. M. , Liu M. J. , ten Cate J. M. , Crielaard W. . ( 2007a; ). The VicRK system of Streptococcus mutans responds to oxidative stress. . J Dent Res 86:, 606–610. [CrossRef] [PubMed]
    [Google Scholar]
  15. Deng D. M. , ten Cate J. M. , Crielaard W. . ( 2007b; ). The adaptive response of Streptococcus mutans towards oral care products: involvement of the ClpP serine protease. . Eur J Oral Sci 115:, 363–370. [CrossRef] [PubMed]
    [Google Scholar]
  16. Evguenieva-Hackenberg E. , Klug G. . ( 2011; ). New aspects of RNA processing in prokaryotes. . Curr Opin Microbiol 14:, 587–592. [CrossRef] [PubMed]
    [Google Scholar]
  17. Gong Y. , Tian X. L. , Sutherland T. , Sisson G. , Mai J. , Ling J. , Li Y. H. . ( 2009; ). Global transcriptional analysis of acid-inducible genes in Streptococcus mutans: multiple two-component systems involved in acid adaptation. . Microbiology 155:, 3322–3332. [CrossRef] [PubMed]
    [Google Scholar]
  18. Griswold A. R. , Jameson-Lee M. , Burne R. A. . ( 2006; ). Regulation and physiologic significance of the agmatine deiminase system of Streptococcus mutans UA159. . J Bacteriol 188:, 834–841. [CrossRef] [PubMed]
    [Google Scholar]
  19. Gruber T. M. , Gross C. A. . ( 2003; ). Multiple sigma subunits and the partitioning of bacterial transcription space. . Annu Rev Microbiol 57:, 441–466. [CrossRef] [PubMed]
    [Google Scholar]
  20. Hardy G. G. , Caimano M. J. , Yother J. . ( 2000; ). Capsule biosynthesis and basic metabolism in Streptococcus pneumoniae are linked through the cellular phosphoglucomutase. . J Bacteriol 182:, 1854–1863. [CrossRef] [PubMed]
    [Google Scholar]
  21. 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. [CrossRef] [PubMed]
    [Google Scholar]
  22. Higuchi M. , Yamamoto Y. , Kamio Y. . ( 2000; ). Molecular biology of oxygen tolerance in lactic acid bacteria: functions of NADH oxidases and Dpr in oxidative stress. . J Biosci Bioeng 90:, 484–493.[PubMed] [CrossRef]
    [Google Scholar]
  23. Hojo K. , Nagaoka S. , Ohshima T. , Maeda N. . ( 2009; ). Bacterial interactions in dental biofilm development. . J Dent Res 88:, 982–990. [CrossRef] [PubMed]
    [Google Scholar]
  24. Jänsch A. , Korakli M. , Vogel R. F. , Gänzle M. G. . ( 2007; ). Glutathione reductase from Lactobacillus sanfranciscensis DSM20451T: contribution to oxygen tolerance and thiol exchange reactions in wheat sourdoughs. . Appl Environ Microbiol 73:, 4469–4476. [CrossRef] [PubMed]
    [Google Scholar]
  25. Jones A. L. , Needham R. H. , Rubens C. E. . ( 2003; ). The delta subunit of RNA polymerase is required for virulence of Streptococcus agalactiae . . Infect Immun 71:, 4011–4017. [CrossRef] [PubMed]
    [Google Scholar]
  26. Juang Y. L. , Helmann J. D. . ( 1994; ). The delta subunit of Bacillus subtilis RNA polymerase. An allosteric effector of the initiation and core-recycling phases of transcription. . J Mol Biol 239:, 1–14. [CrossRef] [PubMed]
    [Google Scholar]
  27. Kim K. , Yang E. , Vu G. P. , Gong H. , Su J. , Liu F. , Lu S. . ( 2010; ). Mass spectrometry-based quantitative proteomic analysis of Salmonella enterica serovar Enteritidis protein expression upon exposure to hydrogen peroxide. . BMC Microbiol 10:, 166. [CrossRef] [PubMed]
    [Google Scholar]
  28. Korithoski B. , Lévesque C. M. , Cvitkovitch D. G. . ( 2008; ). The involvement of the pyruvate dehydrogenase E1α subunit, in Streptococcus mutans acid tolerance. . FEMS Microbiol Lett 289:, 13–19. [CrossRef] [PubMed]
    [Google Scholar]
  29. Kvint K. , Nachin L. , Diez A. , Nyström T. . ( 2003; ). The bacterial universal stress protein: function and regulation. . Curr Opin Microbiol 6:, 140–145. [CrossRef] [PubMed]
    [Google Scholar]
  30. Lemme A. , Sztajer H. , Wagner-Döbler I. . ( 2010; ). Characterization of mleR, a positive regulator of malolactic fermentation and part of the acid tolerance response in Streptococcus mutans . . BMC Microbiol 10:, 58. [CrossRef] [PubMed]
    [Google Scholar]
  31. Lemme A. , Gröbe L. , Reck M. , Tomasch J. , Wagner-Döbler I. . ( 2011; ). Subpopulation-specific transcriptome analysis of competence-stimulating-peptide-induced Streptococcus mutans . . J Bacteriol 193:, 1863–1877. [CrossRef] [PubMed]
    [Google Scholar]
  32. Lemos J. A. , Burne R. A. . ( 2008; ). A model of efficiency: stress tolerance by Streptococcus mutans . . Microbiology 154:, 3247–3255. [CrossRef] [PubMed]
    [Google Scholar]
  33. Lemos J. A. , Abranches J. , Burne R. A. . ( 2005; ). Responses of cariogenic streptococci to environmental stresses. . Curr Issues Mol Biol 7:, 95–107.[PubMed]
    [Google Scholar]
  34. Len A. C. , Cordwell S. J. , Harty D. W. , Jacques N. A. . ( 2003; ). Cellular and extracellular proteome analysis of Streptococcus mutans grown in a chemostat. . Proteomics 3:, 627–646. [CrossRef] [PubMed]
    [Google Scholar]
  35. Len A. C. , Harty D. W. , Jacques N. A. . ( 2004a; ). Proteome analysis of Streptococcus mutans metabolic phenotype during acid tolerance. . Microbiology 150:, 1353–1366. [CrossRef] [PubMed]
    [Google Scholar]
  36. Len A. C. , Harty D. W. , Jacques N. A. . ( 2004b; ). Stress-responsive proteins are upregulated in Streptococcus mutans during acid tolerance. . Microbiology 150:, 1339–1351. [CrossRef] [PubMed]
    [Google Scholar]
  37. Levander F. , Rådström P. . ( 2001; ). Requirement for phosphoglucomutase in exopolysaccharide biosynthesis in glucose- and lactose-utilizing Streptococcus thermophilus . . Appl Environ Microbiol 67:, 2734–2738. [CrossRef] [PubMed]
    [Google Scholar]
  38. López de Saro F. J. , Woody A. Y. , Helmann J. D. . ( 1995; ). Structural analysis of the Bacillus subtilis delta factor: a protein polyanion which displaces RNA from RNA polymerase. . J Mol Biol 252:, 189–202. [CrossRef] [PubMed]
    [Google Scholar]
  39. López de Saro F. J. , Yoshikawa N. , Helmann J. D. . ( 1999; ). Expression, abundance, and RNA polymerase binding properties of the delta factor of Bacillus subtilis . . J Biol Chem 274:, 15953–15958. [CrossRef] [PubMed]
    [Google Scholar]
  40. Luo P. , Morrison D. A. . ( 2003; ). Transient association of an alternative sigma factor, ComX, with RNA polymerase during the period of competence for genetic transformation in Streptococcus pneumoniae . . J Bacteriol 185:, 349–358. [CrossRef] [PubMed]
    [Google Scholar]
  41. Macarthur D. J. , Jacques N. A. . ( 2003; ). Proteome analysis of oral pathogens. . J Dent Res 82:, 870–876. [CrossRef] [PubMed]
    [Google Scholar]
  42. Marquis R. E. . ( 2004; ). Applied and ecological aspects of oxidative-stress damage to bacterial spores and to oral microbes. . Sci Prog 87:, 153–177. [CrossRef] [PubMed]
    [Google Scholar]
  43. Nakayama K. . ( 1992; ). Nucleotide sequence of Streptococcus mutans superoxide dismutase gene and isolation of insertion mutants. . J Bacteriol 174:, 4928–4934.[PubMed]
    [Google Scholar]
  44. Nyström T. , Neidhardt F. C. . ( 1994; ). Expression and role of the universal stress protein, UspA, of Escherichia coli during growth arrest. . Mol Microbiol 11:, 537–544. [CrossRef] [PubMed]
    [Google Scholar]
  45. Opdyke J. A. , Scott J. R. , Moran C. P. Jr . ( 2001; ). A secondary RNA polymerase sigma factor from Streptococcus pyogenes . . Mol Microbiol 42:, 495–502. [CrossRef] [PubMed]
    [Google Scholar]
  46. Perry J. A. , Lévesque C. M. , Suntharaligam P. , Mair R. W. , Bu M. , Cline R. T. , Peterson S. N. , Cvitkovitch D. G. . ( 2008; ). Involvement of Streptococcus mutans regulator RR11 in oxidative stress response during biofilm growth and in the development of genetic competence. . Lett Appl Microbiol 47:, 439–444. [CrossRef] [PubMed]
    [Google Scholar]
  47. Poole L. B. , Higuchi M. , Shimada M. , Calzi M. L. , Kamio Y. . ( 2000; ). Streptococcus mutans H2O2-forming NADH oxidase is an alkyl hydroperoxide reductase protein. . Free Radic Biol Med 28:, 108–120. [CrossRef] [PubMed]
    [Google Scholar]
  48. Poyart C. , Pellegrini E. , Gaillot O. , Boumaila C. , Baptista M. , Trieu-Cuot P. . ( 2001; ). Contribution of Mn-cofactored superoxide dismutase (SodA) to the virulence of Streptococcus agalactiae . . Infect Immun 69:, 5098–5106. [CrossRef] [PubMed]
    [Google Scholar]
  49. Rabilloud T. , Strub J. M. , Luche S. , van Dorsselaer A. , Lunardi J. . ( 2001; ). A comparison between Sypro Ruby and ruthenium II tris (bathophenanthroline disulfonate) as fluorescent stains for protein detection in gels. . Proteomics 1:, 699–704. [CrossRef] [PubMed]
    [Google Scholar]
  50. Rabilloud T. , Heller M. , Gasnier F. , Luche S. , Rey C. , Aebersold R. , Benahmed M. , Louisot P. , Lunardi J. . ( 2002; ). Proteomics analysis of cellular response to oxidative stress. Evidence for in vivo overoxidation of peroxiredoxins at their active site. . J Biol Chem 277:, 19396–19401. [CrossRef] [PubMed]
    [Google Scholar]
  51. Renzone G. , D’Ambrosio C. , Arena S. , Rullo R. , Ledda L. , Ferrara L. , Scaloni A. . ( 2005; ). Differential proteomic analysis in the study of prokaryotes stress resistance. . Ann Ist Super Sanita 41:, 459–468.[PubMed]
    [Google Scholar]
  52. Russell R. R. . ( 2008; ). How has genomics altered our view of caries microbiology?. Caries Res 42:, 319–327. [CrossRef] [PubMed]
    [Google Scholar]
  53. Santillán M. , Mackey M. C. . ( 2008; ). Quantitative approaches to the study of bistability in the lac operon of Escherichia coli . . J R Soc Interface 5: (Suppl. 1), S29–S39. [CrossRef] [PubMed]
    [Google Scholar]
  54. Saravanan R. S. , Rose J. K. . ( 2004; ). A critical evaluation of sample extraction techniques for enhanced proteomic analysis of recalcitrant plant tissues. . Proteomics 4:, 2522–2532. [CrossRef] [PubMed]
    [Google Scholar]
  55. Seepersaud R. , Needham R. H. , Kim C. S. , Jones A. L. . ( 2006; ). Abundance of the delta subunit of RNA polymerase is linked to the virulence of Streptococcus agalactiae . . J Bacteriol 188:, 2096–2105. [CrossRef] [PubMed]
    [Google Scholar]
  56. Sheng J. , Marquis R. E. . ( 2007; ). Malolactic fermentation by Streptococcus mutans . . FEMS Microbiol Lett 272:, 196–201. [CrossRef] [PubMed]
    [Google Scholar]
  57. Svensäter G. , Sjögreen B. , Hamilton I. R. . ( 2000; ). Multiple stress responses in Streptococcus mutans and the induction of general and stress-specific proteins. . Microbiology 146:, 107–117.[PubMed]
    [Google Scholar]
  58. Taniguchi Y. , Choi P. J. , Li G. W. , Chen H. , Babu M. , Hearn J. , Emili A. , Xie X. S. . ( 2010; ). Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. . Science 329:, 533–538. [CrossRef] [PubMed]
    [Google Scholar]
  59. Tao L. , Sutcliffe I. C. , Russell R. R. , Ferretti J. J. . ( 1993; ). Transport of sugars, including sucrose, by the msm transport system of Streptococcus mutans . . J Dent Res 72:, 1386–1390. [CrossRef] [PubMed]
    [Google Scholar]
  60. Tao L. , Wu X. , Sun B. . ( 2010; ). Alternative sigma factor σH modulates prophage integration and excision in Staphylococcus aureus . . PLoS Pathog 6:, e1000888. [CrossRef] [PubMed]
    [Google Scholar]
  61. Thomas E. L. , Pera K. A. . ( 1983; ). Oxygen metabolism of Streptococcus mutans: uptake of oxygen and release of superoxide and hydrogen peroxide. . J Bacteriol 154:, 1236–1244.[PubMed]
    [Google Scholar]
  62. Toyoda T. , Okano S. , Shibata Y. , Abiko Y. . ( 2010; ). Oxidative stress induces phosphorylation of the ABC transporter, ATP-binding protein, in Porphyromonas gingivalis . . J Oral Sci 52:, 561–566. [CrossRef] [PubMed]
    [Google Scholar]
  63. Tozzi M. G. , Camici M. , Mascia L. , Sgarrella F. , Ipata P. L. . ( 2006; ). Pentose phosphates in nucleoside interconversion and catabolism. . FEBS J 273:, 1089–1101. [CrossRef] [PubMed]
    [Google Scholar]
  64. Wang W. , Sun J. , Hartlep M. , Deckwer W. D. , Zeng A. P. . ( 2003; ). Combined use of proteomic analysis and enzyme activity assays for metabolic pathway analysis of glycerol fermentation by Klebsiella pneumoniae . . Biotechnol Bioeng 83:, 525–536. [CrossRef] [PubMed]
    [Google Scholar]
  65. Wang W. , Hollmann R. , Fürch T. , Nimtz M. , Malten M. , Jahn D. , Deckwer W. D. . ( 2005; ). Proteome analysis of a recombinant Bacillus megaterium strain during heterologous production of a glucosyltransferase. . Proteome Sci 3:, 4. [CrossRef] [PubMed]
    [Google Scholar]
  66. Wang W. , Hollmann R. , Deckwer W. D. . ( 2006; ). Comparative proteomic analysis of high cell density cultivations with two recombinant Bacillus megaterium strains for the production of a heterologous dextransucrase. . Proteome Sci 4:, 19. [CrossRef] [PubMed]
    [Google Scholar]
  67. Watson S. P. , Antonio M. , Foster S. J. . ( 1998; ). Isolation and characterization of Staphylococcus aureus starvation-induced, stationary-phase mutants defective in survival or recovery. . Microbiology 144:, 3159–3169. [CrossRef] [PubMed]
    [Google Scholar]
  68. Weber H. , Engelmann S. , Becher D. , Hecker M. . ( 2004; ). Oxidative stress triggers thiol oxidation in the glyceraldehyde-3-phosphate dehydrogenase of Staphylococcus aureus . . Mol Microbiol 52:, 133–140. [CrossRef] [PubMed]
    [Google Scholar]
  69. Wen Z. T. , Suntharaligham P. , Cvitkovitch D. G. , Burne R. A. . ( 2005; ). Trigger factor in Streptococcus mutans is involved in stress tolerance, competence development, and biofilm formation. . Infect Immun 73:, 219–225. [CrossRef] [PubMed]
    [Google Scholar]
  70. Wen Z. T. , Baker H. V. , Burne R. A. . ( 2006; ). Influence of BrpA on critical virulence attributes of Streptococcus mutans . . J Bacteriol 188:, 2983–2992. [CrossRef] [PubMed]
    [Google Scholar]
  71. Wilkins J. C. , Homer K. A. , Beighton D. . ( 2002; ). Analysis of Streptococcus mutans proteins modulated by culture under acidic conditions. . Appl Environ Microbiol 68:, 2382–2390. [CrossRef] [PubMed]
    [Google Scholar]
  72. Wolf C. , Hochgräfe F. , Kusch H. , Albrecht D. , Hecker M. , Engelmann S. . ( 2008; ). Proteomic analysis of antioxidant strategies of Staphylococcus aureus: diverse responses to different oxidants. . Proteomics 8:, 3139–3153. [CrossRef] [PubMed]
    [Google Scholar]
  73. Xue X. , Tomasch J. , Sztajer H. , Wagner-Döbler I. . ( 2010; ). The delta subunit of RNA polymerase, RpoE, is a global modulator of Streptococcus mutans environmental adaptation. . J Bacteriol 192:, 5081–5092. [CrossRef] [PubMed]
    [Google Scholar]
  74. Xue X. , Sztajer H. , Buddruhs N. , Petersen J. , Rohde M. , Talay S. R. , Wagner-Döbler I. . ( 2011; ). Lack of the delta subunit of RNA polymerase increases virulence related traits of Streptococcus mutans . . PLoS ONE 6:, e20075. [CrossRef] [PubMed]
    [Google Scholar]
  75. Yamada T. , Takahashi-Abbe S. , Abbe K. . ( 1985; ). Effects of oxygen on pyruvate formate-lyase in situ and sugar metabolism of Streptococcus mutans and Streptococcus sanguis . . Infect Immun 47:, 129–134.[PubMed]
    [Google Scholar]
  76. Zhang J. , Biswas I. . ( 2009; ). 3′-Phosphoadenosine-5′-phosphate phosphatase activity is required for superoxide stress tolerance in Streptococcus mutans . . J Bacteriol 191:, 4330–4340. [CrossRef] [PubMed]
    [Google Scholar]
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