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Genome-wide mRNA profiling in glucose starved Bacillus subtilis cells

Abstract

In this study global changes in gene expression were monitored in Bacillus subtilis cells entering stationary growth phase owing to starvation for glucose. Gene expression was analysed in growing and starving cells at different time points by full-genome mRNA profiling using DNA macroarrays. During the transition to stationary phase we observed extensive reprogramming of gene expression, with ~1000 genes being strongly repressed and ~900 strongly up-regulated in a time-dependent manner. The genes involved in the response to glucose starvation can be assigned to two main classes: (i) general stress/starvation genes which respond to various stress or starvation stimuli, and (ii) genes that respond specifically to starvation for glucose. The first class includes members of the σB-dependent general stress regulon, as well as 90 vegetative genes, which are strongly down regulated in the course of the stringent response. Among the genes in the second class, we observed a decrease in the expression of genes encoding proteins required for glucose uptake, glycolysis and the tricarboxylic acid cycle. Conversely, many carbohydrate utilisation systems that depend on phosphotransferase systems (PTS) or ABC transporters were activated. The expression of genes required for utilisation or generation of acetate indicates that acetate constitutes an important energy source for B. subtilis during periods of glucose starvation. Finally, genome wide mRNA profiling data can be used to predict new metabolic pathways in B. subtilis. Thus, our data suggest that glucose-starved cells are able to degrade branched-chain fatty acids to pyruvate and succinate via propionyl-CoA using the methylcitrate pathway. This pathway appears to link lipid degradation to gluconeogenesis in glucose-starved cells.

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References

  1. Ali NO, Bignon J, Rapoport G, Debarbouille M (2001) Regulation of the acetoin catabolic pathway is controlled by sigma L in Bacillus subtilis. J Bacteriol 183:2497–2504

  2. Anagnostopoulos C, Spizizen J (1961) Requirements for transformation in Bacillus subtilis. J Bacteriol 81:7471–7476

  3. Bandow JE, Brötz H, Hecker M (2002) Bacillus subtilis tolerance of moderate concentrations of rifampin involves the sigma(B)-dependent general and multiple stress response. J Bacteriol 184:459–467

  4. Bernhardt J, Weibezahn J, Scharf C, Hecker M (2003) A movie of the life of Bacillus subtilis during feast and famine: visualisation of protein synthesis during glucose starvation by proteome analysis. Genome Res 13:224–237

  5. Blencke HM, Homuth G, Ludwig H, Mäder U, Hecker M, Stülke J (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab Eng 5:133–149

  6. Bryan EM, Beall BW, Moran CP Jr (1996) A sigma E dependent operon subject to catabolite repression during sporulation in Bacillus subtilis. J Bacteriol 178:4778–4786

  7. Cashel M, Gentry DR, Hernandez VJ, Vinella D (1996) The stringent response. In: Neidhardt FC, Curtiss III R, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE (eds) Escherichia coli and Salmonella: cellular and molecular biology, 2nd edn. ASM Press, Washington DC, pp1458–1496

  8. Conway T, Schoolnik GK (2003) Microarray expression profiling: capturing a genome-wide portrait of the transcriptome. Mol Microbiol 47:879–889

  9. Dauner M, Storni T, Sauer U (2001) Bacillus subtilis metabolism and energetics in carbon-limited and excess-carbon chemostat culture. J Bacteriol 183:7308–7317

  10. Deutscher J, Galinier A, Martin-Verstraete I. (2002) Carbohydrate uptake and metabolism. In: Sonenshein AL, Hoch JA, Losick R (eds) Bacillus subtilis and its closest relatives: from genes to cells. ASM Press, Washington DC, pp 129–150

  11. Drzewiecki K, Eymann C, Mittenhuber G, Hecker M (1998) The yvyD gene of Bacillus subtilis is under dual control of sigmaB and sigmaH. J Bacteriol 180:6674–6680

  12. 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

  13. Gerth U, Krüger E, Derre I, Msadek T, Hecker M (1998) Stress induction of the Bacillus subtilis clpP gene encoding a homologue of the proteolytic component of the Clp protease and the involvement of ClpP and ClpX in stress tolerance. Mol Microbiol 28:787–802

  14. Gropp M, Eizenman E, Glaser G, Samarrai W, Rudner R (1994) A relA(S) suppressor mutant allele of Bacillus subtilis which maps to relA and responds only to carbon limitation. Gene 140:91–96

  15. Hecker M, Völker U (2001) General stress response of Bacillus subtilis and other bacteria. Adv Microb Physiol 44:35–91

  16. Homuth G, Masuda S, Mogk A, Kobayashi Y, Schumann W (1997) The dnaK operon of Bacillus subtilis is heptacistronic. J Bacteriol 179:1153–1164

  17. Horswill AR, Escalante-Semerena JC (1997) Propionate catabolism in Salmonella typhimurium LT2: two divergently transcribed units comprise the prp locus at 8.5 centisomes, prpR encodes a member of the sigma-54 family of activators, and the prpBCDE genes constitute an operon. J Bacteriol 179:928–940

  18. Huynen MA, Dandekar T, Bork P (1999) Variation and evolution of the citric-acid cycle: a genomic perspective. Trends Microbiol 7:281–291

  19. Inaoka T, Matsumura Y, Tsuchido T (1998) Molecular cloning and nucleotide sequence of the superoxide dismutase gene and characterization of its product from Bacillus subtilis . J Bacteriol 180:3697–3703

  20. Kaneda T (1977) Fatty acids of the genus Bacillus: an example of branched-chain preference. Bacteriol Rev 41:391–418

  21. Kaneda T (1991) Iso-fatty and anteiso-fatty acids in bacteria: biosynthesis, function, and taxonomic significance. Microbiol Rev 55:288–302

  22. Kanehisa M, Goto S, Kawashima S, Nakaya A (2002) The KEGG databases at GenomeNet. Nucleic Acids Res 30:42–46

  23. Kim KS, Farrand SK (1996) Ti plasmid-encoded genes responsible for catabolism of the crown gall opine mannopine by Agrobacterium tumefaciens are homologs of the T-region genes responsible for synthesis of this opine by the plant tumor. J Bacteriol 178:3275–3284

  24. Kim HJ, Jourlin-Castelli C, Kim SI, Sonenshein AL (2002) Regulation of the Bacillus subtilis ccpC gene by ccpA and ccpC. Mol Microbiol 43:399–410

  25. Kunst F et al (1997) The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390:249–256

  26. Ludwig H, Homuth G, Schmalisch M, Dyka FM, Hecker M, Stülke J (2001) Transcription of glycolytic genes and operons in Bacillus subtilis: evidence for the presence of multiple levels of control of the gapA operon. Mol Microbiol 41:409–422

  27. Matsunaga I, Ueda A, Fujiwara N, Sumimoto T, Ichihara K (1999) Characterization of the ybdT gene product of Bacillus subtilis: novel fatty acid beta-hydroxylating cytochrome P450. Lipids 34:841–846

  28. Mittenhuber G (2001) Comparative genomics and evolution of genes encoding bacterial (p)ppGpp synthetases/hydrolases (the Rel, RelA and SpoT proteins). J Mol Microbiol Biotechnol 3:585–600

  29. Molle V, Nakaura Y, Shivers RP, Yamaguchi H, Losick R, Fujita Y, Sonenshein AL (2003) Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis. J Bacteriol 185:1911–1922

  30. Moszer I, Jones LM, Moreira S, Fabry C, Danchin A (2002) SubtiList: the reference database for the Bacillus subtilis genome. Nucleic Acids Res 30:62–65

  31. Msadek T (1999) When the going gets tough: survival strategies and environmental signaling networks in Bacillus subtilis. Trends Microbiol 7:201–207

  32. Nishino T, Gallant J, Shalit P, Palmer L, Wehr T (1979) Regulatory nucleotides involved in the Rel function of Bacillus subtilis. J Bacteriol 140:671–679

  33. O’Reilly M, Devine KM (1997) Expression of AbrB, a transition state regulator from Bacillus subtilis, is growth phase dependent in a manner resembling that of Fis, the nucleoid binding protein from Escherichia coli. J Bacteriol 179:522–529

  34. Petersohn A (2003) Funktion SigB-abhängiger Stressproteine in Bacillus subtilis. PhD Thesis. Ernst-Moritz-Arndt-Universität, Greifswald

  35. Petersohn A, Engelmann S, Setlow P, Hecker M (1999) The katX gene of Bacillus subtilis is under dual control of sigmaB and sigmaF. Mol Gen Genet 262:173–179

  36. Petersohn A, Brigulla M, Haas S, Hoheisel JD, Völker U, Hecker M (2001) Global analysis of the general stress response of Bacillus subtilis. J Bacteriol 183:5617–5631

  37. Piggot PJ, Losick R (2002) Sporulation genes and intercompartmental regulation. In: Sonenshein AL, Hoch JA, Losick R (eds) Bacillus subtilis and its closest relatives: from genes to cells. ASM Press, Washington DC, pp 483–517

  38. Price CW, Fawcett P, Ceremonie H, Su N, Murphy CK, Youngman P (2001) Genome-wide analysis of the general stress response in Bacillus subtilis. Mol Microbiol 41:757–774

  39. Reizer J, Bachem S, Reizer A, Arnaud M, Saier MH Jr., Stülke J (1999) Novel phosphotransferase system genes revealed by genome analysis—the complete complement of PTS proteins encoded within the genome of Bacillus subtilis. Microbiology 145:3419–3429

  40. Rosenkrantz MS, Dingman DW, Sonenshein AL (1985) Bacillus subtilis citB gene is regulated synergistically by glucose and glutamine. J Bacteriol 164:55–64

  41. Servant P, Le Coq D, Aymerich S (2004) CcpN (YqzB), a novel regulator for CcpA-independent catabolite repression of Bacillus subtilis gluconeogenic genes. Mol Microbiol, in press

  42. Sonenshein AL (2000) Bacterial sporulation: a response to environmental signals. In: Storz G, Hengge-Aronis R (eds) Bacterial stress responses. ASM Press, Washington DC, pp 199–221

  43. Sonenshein AL (2002) The Krebs citric acid cycle. In: Sonenshein AL, Hoch JS, Losick R (eds) Bacillus subtilis and its closest relatives: from genes to cells. ASM Press, Washington DC, pp 151–162

  44. Stragier P, Losick R (1996) Molecular genetics of sporulation in Bacillus subtilis. Annu Rev Genet 30:297–241

  45. Stülke J, Hillen W (2000) Regulation of carbon catabolism in Bacillus species. Annu Rev Microbiol 54:849–880

  46. Stülke J, Hanschke R, Hecker M (1993) Temporal activation of beta-glucanase synthesis in Bacillus subtilis is mediated by the GTP pool. J Gen Microbiol 139:2041–2045

  47. Tobisch S, Glaser P, Kruger S, Hecker M (1997) Identification and characterization of a new beta-glucoside utilization system in Bacillus subtilis. J Bacteriol 179:496–506

  48. Tobisch S, Zühlke D, Bernhardt J, Stülke J, Hecker M (1999) Role of CcpA in regulation of the central pathways of carbon catabolism in Bacillus subtilis. J Bacteriol 181:6996–7004

  49. Wendrich TM, Marahiel MA (1997) Cloning and characterization of a relA/spoT homologue from Bacillus subtilis. Mol Microbiol 26:65–79

  50. Yoshida K, Kobayashi K, Miwa Y, Kang CM, Matsunaga M, Yamaguchi H, Tojo S, Yamamoto M, Nishi R, Ogasawara N, Nakayama T, Fujita Y (2001) Combined transcriptome and proteome analysis as a powerful approach to study genes under glucose repression in Bacillus subtilis. Nucleic Acids Res 29:683–692

  51. Zhang B, Struffi P, Kroos L (1999) Sigma K can negatively regulate sigE expression by two different mechanisms during sporulation of Bacillus subtilis. J Bacteriol 181:4081–4088

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Acknowledgements

J. Weibezahn and T. Koburger contributed equally to this work. This work was supported by grants from the BMBF (No. 031U107A), the DFG (No. HE1887/7-1) and the “Fonds der Chemischen Industrie” to M.H. We thank Colin Harwood and Jörg Stülke for critically reading the manuscript, and Stéphane Aymerich for providing data before publication. The work was carried out in compliance with the laws governing genetic experimentation in Germany

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Correspondence to Torsten Koburger.

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Communicated by A. Kondorosi

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Koburger, T., Weibezahn, J., Bernhardt, J. et al. Genome-wide mRNA profiling in glucose starved Bacillus subtilis cells. Mol Genet Genomics 274, 1–12 (2005). https://doi.org/10.1007/s00438-005-1119-8

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Keywords

  • Bacillus subtilis
  • Transcription
  • Glucose starvation
  • Regulation
  • Metabolism