1887

Abstract

The high phosphate content of cell walls dictates that cell wall metabolism is an important feature of the PhoPR-mediated phosphate limitation response. Here we report the expression profiles of cell-envelope-associated and PhoPR regulon genes, determined by live cell array and transcriptome analysis, in exponentially growing and phosphate-limited cells. Control by the WalRK two-component system confers a unique expression profile and high level of promoter activity on the genes of its regulon with and expression differing both qualitatively and quantitatively from all other autolysin-encoding genes examined. The activity of the PhoPR two-component system is restricted to the phosphate-limited state, being rapidly induced in response to the cognate stimulus, and can be sustained for an extended phosphate limitation period. Constituent promoters of the PhoPR regulon show heterogeneous induction profiles and very high promoter activities. Phosphate-limited cells also show elevated expression of the actin-like protein MreBH and reduced expression of the WapA cell wall protein and WprA cell wall protease indicating that cell wall metabolism in this state is distinct from that of exponentially growing and stationary-phase cells. The PhoPR response is very rapidly deactivated upon removal of the phosphate limitation stimulus with concomitant increased expression of cell wall metabolic genes. Moreover expression of genes encoding enzymes involved in sulphur metabolism is significantly altered in the phosphate-limited state with distinct perturbations being observed in wild-type 168 and AH024 (Δ) cells.

Funding
This study was supported by the:
  • , BaSysBio , (Award LSHG-CT-2006-037469)
  • , Science Foundation Ireland , (Award 08/IN.1/B1859)
  • , Irish Research Council for Science, Engineering and Technology (IRCSET)
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2011-09-01
2020-11-28
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References

  1. Allenby N. E., O’Connor N., Prágai Z., Ward A. C., Wipat A., Harwood C. R. ( 2005). Genome-wide transcriptional analysis of the phosphate starvation stimulon of Bacillus subtilis . J Bacteriol 187:8063–8080 [CrossRef][PubMed]
    [Google Scholar]
  2. Anagnostopoulos C., Spizizen J. ( 1961). Requirements for transformation in Bacillus subtilis . J Bacteriol 81:741–746[PubMed]
    [Google Scholar]
  3. Babé L. M., Schmidt B. ( 1998). Purification and biochemical analysis of WprA, a 52-kDa serine protease secreted by B. subtilis as an active complex with its 23-kDa propeptide. Biochim Biophys Acta 1386:211–219 [CrossRef][PubMed]
    [Google Scholar]
  4. Bhavsar A. P., Brown E. D. ( 2006). Cell wall assembly in Bacillus subtilis: how spirals and spaces challenge paradigms. Mol Microbiol 60:1077–1090 [CrossRef][PubMed]
    [Google Scholar]
  5. Birkey S. M., Liu W., Zhang X., Duggan M. F., Hulett F. M. ( 1998). Pho signal transduction network reveals direct transcriptional regulation of one two-component system by another two-component regulator: Bacillus subtilis PhoP directly regulates production of ResD. Mol Microbiol 30:943–953 [CrossRef][PubMed]
    [Google Scholar]
  6. Bisicchia P., Noone D., Lioliou E., Howell A., Quigley S., Jensen T., Jarmer H., Devine K. M. ( 2007). The essential YycFG two-component system controls cell wall metabolism in Bacillus subtilis . Mol Microbiol 65:180–200 [CrossRef][PubMed]
    [Google Scholar]
  7. Bisicchia P., Lioliou E., Noone D., Salzberg L. I., Botella E., Hübner S., Devine K. M. ( 2010). Peptidoglycan metabolism is controlled by the WalRK (YycFG) and PhoPR two-component systems in phosphate-limited Bacillus subtilis cells. Mol Microbiol 75:972–989 [CrossRef][PubMed]
    [Google Scholar]
  8. Bolstad B. M., Irizarry R. A., Astrand M., Speed T. P. ( 2003). A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19:185–193 [CrossRef][PubMed]
    [Google Scholar]
  9. Botella E., Fogg M., Jules M., Piersma S., Doherty G., Hansen A., Denham E. L., Le Chat L., Veiga P. et al. ( 2010). pBaSysBioII: an integrative plasmid generating gfp transcriptional fusions for high-throughput analysis of gene expression in Bacillus subtilis . Microbiology 156:1600–1608 [CrossRef][PubMed]
    [Google Scholar]
  10. Bouhss A., Trunkfield A. E., Bugg T. D. H., Mengin-Lecreulx D. ( 2008). The biosynthesis of peptidoglycan lipid-linked intermediates. FEMS Microbiol Rev 32:208–233 [CrossRef][PubMed]
    [Google Scholar]
  11. Burguière P., Auger S., Hullo M. F., Danchin A., Martin-Verstraete I. ( 2004). Three different systems participate in l-cystine uptake in Bacillus subtilis . J Bacteriol 186:4875–4884 [CrossRef][PubMed]
    [Google Scholar]
  12. Carballido-López R., Formstone A. ( 2007). Shape determination in Bacillus subtilis . Curr Opin Microbiol 10:611–616 [CrossRef][PubMed]
    [Google Scholar]
  13. Carballido-López R., Formstone A., Li Y., Ehrlich S. D., Noirot P., Errington J. ( 2006). Actin homolog MreBH governs cell morphogenesis by localization of the cell wall hydrolase LytE. Dev Cell 11:399–409 [CrossRef][PubMed]
    [Google Scholar]
  14. Daniel R. A., Errington J. ( 2003). Control of cell morphogenesis in bacteria: two distinct ways to make a rod-shaped cell. Cell 113:767–776 [CrossRef][PubMed]
    [Google Scholar]
  15. D’Elia M. A., Millar K. E., Beveridge T. J., Brown E. D. ( 2006). Wall teichoic acid polymers are dispensable for cell viability in Bacillus subtilis . J Bacteriol 188:8313–8316 [CrossRef][PubMed]
    [Google Scholar]
  16. Divakaruni A. V., Loo R. R., Xie Y., Loo J. A., Gober J. W. ( 2005). The cell-shape protein MreC interacts with extracytoplasmic proteins including cell wall assembly complexes in Caulobacter crescentus . Proc Natl Acad Sci U S A 102:18602–18607 [CrossRef][PubMed]
    [Google Scholar]
  17. Divakaruni A. V., Baida C., White C. L., Gober J. W. ( 2007). The cell shape proteins MreB and MreC control cell morphogenesis by positioning cell wall synthetic complexes. Mol Microbiol 66:174–188 [CrossRef][PubMed]
    [Google Scholar]
  18. Dubrac S., Bisicchia P., Devine K. M., 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 [CrossRef][PubMed]
    [Google Scholar]
  19. Eymann C., Homuth G., Scharf C., Hecker M. ( 2002). Bacillus subtilis functional genomics: global characterization of the stringent response by proteome and transcriptome analysis. J Bacteriol 184:2500–2520 [CrossRef][PubMed]
    [Google Scholar]
  20. Formstone A., Carballido-López R., Noirot P., Errington J., Scheffers D. J. ( 2008). Localization and interactions of teichoic acid synthetic enzymes in Bacillus subtilis . J Bacteriol 190:1812–1821 [CrossRef][PubMed]
    [Google Scholar]
  21. Fukuchi K., Kasahara Y., Asai K., Kobayashi K., Moriya S., Ogasawara N. ( 2000). The essential two-component regulatory system encoded by yycF and yycG modulates expression of the ftsAZ operon in Bacillus subtilis . Microbiology 146:1573–1583[PubMed]
    [Google Scholar]
  22. Fukushima T., Afkham A., Kurosawa S., Tanabe T., Yamamoto H., Sekiguchi J. ( 2006). A new d,l-endopeptidase gene product, YojL (renamed CwlS), plays a role in cell separation with LytE and LytF in Bacillus subtilis . J Bacteriol 188:5541–5550 [CrossRef][PubMed]
    [Google Scholar]
  23. Fukushima T., Szurmant H., Kim E. J., Perego M., Hoch J. A. ( 2008). A sensor histidine kinase co-ordinates cell wall architecture with cell division in Bacillus subtilis . Mol Microbiol 69:621–632 [CrossRef][PubMed]
    [Google Scholar]
  24. Fukushima T., Furihata I., Emmins R., Daniel R. A., Hoch J. A., Szurmant H. ( 2011). A role for the essential YycG sensor histidine kinase in sensing cell division. Mol Microbiol 79:503–522 [CrossRef][PubMed]
    [Google Scholar]
  25. Gentleman R. C., Carey V. J., Bates D. M., Bolstad B., Dettling M., Dudoit S., Ellis B., Gautier L., Ge Y. et al. ( 2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5:R80 [CrossRef][PubMed]
    [Google Scholar]
  26. Hochberg Y., Benjamini Y. ( 1990). More powerful procedures for multiple significance testing. Stat Med 9:811–818 [CrossRef][PubMed]
    [Google Scholar]
  27. Hokamp K., Roche F. M., Acab M., Rousseau M. E., Kuo B., Goode D., Aeschliman D., Bryan J., Babiuk L. A. et al. ( 2004). ArrayPipe: a flexible processing pipeline for microarray data. Nucleic Acids Res 32:Web Server issueW457–W459 [CrossRef][PubMed]
    [Google Scholar]
  28. Howell A., Dubrac S., Andersen K. K., Noone D., Fert J., Msadek T., Devine K. M. ( 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 [CrossRef][PubMed]
    [Google Scholar]
  29. Howell A., Dubrac S., Noone D., Varughese K. I., Devine K. M. ( 2006). Interactions between the YycFG and PhoPR two-component systems in Bacillus subtilis: the PhoR kinase phosphorylates the non-cognate YycF response regulator upon phosphate limitation. Mol Microbiol 59:1199–1215 [CrossRef][PubMed]
    [Google Scholar]
  30. Hulett F. M. ( 2002). The PhoP regulon. Bacillus subtilis and its closest relatives: from genes to cells193–202 Sonenshein A. L., Hoch J. A., Losick R. Washington, DC: American Society for Microbiology; [CrossRef]
    [Google Scholar]
  31. Hullo M. F., Auger S., Soutourina O., Barzu O., Yvon M., Danchin A., Martin-Verstraete I. ( 2007). Conversion of methionine to cysteine in Bacillus subtilis and its regulation. J Bacteriol 189:187–197 [CrossRef][PubMed]
    [Google Scholar]
  32. Jones L. J., Carballido-López R., Errington J. ( 2001). Control of cell shape in bacteria: helical, actin-like filaments in Bacillus subtilis . Cell 104:913–922 [CrossRef][PubMed]
    [Google Scholar]
  33. Jules M., Le Chat L., Aymerich S., Le Coq D. ( 2009). The Bacillus subtilis ywjI (glpX) gene encodes a class II fructose-1,6-bisphosphatase,functionally equivalent to the class III Fbp enzyme. J Bacteriol 191:3168–3171 [CrossRef][PubMed]
    [Google Scholar]
  34. Kawai Y., Asai K., Errington J. ( 2009a). Partial functional redundancy of MreB isoforms, MreB, Mbl and MreBH, in cell morphogenesis of Bacillus subtilis . Mol Microbiol 73:719–731 [CrossRef][PubMed]
    [Google Scholar]
  35. Kawai Y., Daniel R. A., Errington J. ( 2009b). Regulation of cell wall morphogenesis in Bacillus subtilis by recruitment of PBP1 to the MreB helix. Mol Microbiol 71:1131–1144 [CrossRef][PubMed]
    [Google Scholar]
  36. Kent W. J. ( 2002). blat – the blast-like alignment tool. Genome Res 12:656–664[PubMed] [CrossRef]
    [Google Scholar]
  37. Kock H., Gerth U., Hecker M. ( 2004). MurAA, catalysing the first committed step in peptidoglycan biosynthesis, is a target of Clp-dependent proteolysis in Bacillus subtilis . Mol Microbiol 51:1087–1102 [CrossRef][PubMed]
    [Google Scholar]
  38. Lahooti M., Harwood C. R. ( 1999). Transcriptional analysis of the Bacillus subtilis teichuronic acid operon. Microbiology 145:3409–3417[PubMed]
    [Google Scholar]
  39. Leaver M., Errington J. ( 2005). Roles for MreC and MreD proteins in helical growth of the cylindrical cell wall in Bacillus subtilis . Mol Microbiol 57:1196–1209 [CrossRef][PubMed]
    [Google Scholar]
  40. Liu W., Eder S., Hulett F. M. ( 1998). Analysis of Bacillus subtilis tagAB and tagDEF expression during phosphate starvation identifies a repressor role for PhoP-P. J Bacteriol 180:753–758[PubMed]
    [Google Scholar]
  41. Mansilla M. C., de Mendoza D. ( 2000). The Bacillus subtilis cysP gene encodes a novel sulphate permease related to the inorganic phosphate transporter (Pit) family. Microbiology 146:815–821[PubMed]
    [Google Scholar]
  42. Mansilla M. C., Albanesi D., de Mendoza D. ( 2000). Transcriptional control of the sulfur-regulated cysH operon, containing genes involved in l-cysteine biosynthesis in Bacillus subtilis . J Bacteriol 182:5885–5892 [CrossRef][PubMed]
    [Google Scholar]
  43. Müller J. P., An Z., Merad T., Hancock I. C., Harwood C. R. ( 1997). Influence of Bacillus subtilis phoR on cell wall anionic polymers. Microbiology 143:947–956 [CrossRef][PubMed]
    [Google Scholar]
  44. Prágai Z., Harwood C. R. ( 2002). Regulatory interactions between the Pho and σB-dependent general stress regulons of Bacillus subtilis . Microbiology 148:1593–1602[PubMed]
    [Google Scholar]
  45. Rasmussen S., Nielsen H. B., Jarmer H. ( 2009). The transcriptionally active regions in the genome of Bacillus subtilis . Mol Microbiol 73:1043–1057 [CrossRef][PubMed]
    [Google Scholar]
  46. Sambrook J., Fritsch E. F., Maniatis T. ( 1989). Molecular cloning: a laboratory manual Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  47. Serizawa M., Kodama K., Yamamoto H., Kobayashi K., Ogasawara N., Sekiguchi J. ( 2005). Functional analysis of the YvrGHb two-component system of Bacillus subtilis: identification of the regulated genes by DNA microarray and Northern blot analyses. Biosci Biotechnol Biochem 69:2155–2169 [CrossRef][PubMed]
    [Google Scholar]
  48. Shi L., Hulett F. M. ( 1999). The cytoplasmic kinase domain of PhoR is sufficient for the low phosphate-inducible expression of Pho regulon genes in Bacillus subtilis . Mol Microbiol 31:211–222 [CrossRef][PubMed]
    [Google Scholar]
  49. Smyth G. K. ( 2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3:e3[PubMed]
    [Google Scholar]
  50. Soufo H. J., Graumann P. L. ( 2010). Bacillus subtilis MreB paralogues have different filament architectures and lead to shape remodelling of a heterologous cell system. Mol Microbiol 78:1145–1158 [CrossRef][PubMed]
    [Google Scholar]
  51. Sun G., Birkey S. M., Hulett F. M. ( 1996). Three two-component signal-transduction systems interact for Pho regulation in Bacillus subtilis . Mol Microbiol 19:941–948 [CrossRef][PubMed]
    [Google Scholar]
  52. Swoboda J. G., Campbell J., Meredith T. C., Walker S. ( 2010). Wall teichoic acid function, biosynthesis, and inhibition. ChemBioChem 11:35–45 [CrossRef][PubMed]
    [Google Scholar]
  53. Vollmer W., Blanot D., de Pedro M. A. ( 2008). Peptidoglycan structure and architecture. FEMS Microbiol Rev 32:149–167 [CrossRef][PubMed]
    [Google Scholar]
  54. Weidenmaier C., Peschel A. ( 2008). Teichoic acids and related cell-wall glycopolymers in Gram-positive physiology and host interactions. Nat Rev Microbiol 6:276–287 [CrossRef][PubMed]
    [Google Scholar]
  55. Yamamoto H., Miyake Y., Hisaoka M., Kurosawa S., Sekiguchi J. ( 2008). The major and minor wall teichoic acids prevent the sidewall localization of vegetative dl-endopeptidase LytF in Bacillus subtilis . Mol Microbiol 70:297–310 [CrossRef][PubMed]
    [Google Scholar]
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