1887

Abstract

We report on the use of the chemostat as an optimal device to create time-invariant conditions that allow accurate sampling for various omics assays in , in combination with recording of the dynamics of the physiological transition in the organism under study that accompany the initiation of glucose repression. cells respond to the addition of glucose not only with the well-known transcriptional response, as was revealed through quantitative PCR analysis of the transcript levels of key genes from the CRP (cAMP receptor protein) regulon, but also with an increased growth rate and a transient decrease in the efficiency of its aerobic catabolism. Less than half of a doubling time is required for the organism to recover to maximal values of growth rate and efficiency. Furthermore, calculations based on our results show that the specific glucose uptake rate () and the H/e ratio increase proportionally, up to a growth rate of 0.4 h, whilst biomass yield on glucose ( ) drops during the first 15 min, followed by a gradual recovery. Surprisingly, the growth yields after the recovery phase show values even higher than the maximum theoretical yield. Possible explanations for these high yields are discussed.

Funding
This study was supported by the:
  • Higher Education Commission of Thailand
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2014-06-01
2024-05-03
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References

  1. Abdel-Hamid A. M., Attwood M. M., Guest J. R. ( 2001). Pyruvate oxidase contributes to the aerobic growth efficiency of Escherichia coli. Microbiology 147:1483–1498[PubMed]
    [Google Scholar]
  2. Alexeeva S., Hellingwerf K. J., Teixeira de Mattos M. J. ( 2003). Requirement of ArcA for redox regulation in Escherichia coli under microaerobic but not anaerobic or aerobic conditions. J Bacteriol 185:204–209 [View Article][PubMed]
    [Google Scholar]
  3. Balázsi G., Barabási A. L., Oltvai Z. N. ( 2005). Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. Proc Natl Acad Sci U S A 102:7841–7846 [View Article][PubMed]
    [Google Scholar]
  4. Bekker M., Kramer G., Hartog A. F., Wagner M. J., de Koster C. G., Hellingwerf K. J., Teixeira de Mattos M. J. ( 2007). Changes in the redox state and composition of the quinone pool of Escherichia coli during aerobic batch-culture growth. Microbiology 153:1974–1980 [View Article][PubMed]
    [Google Scholar]
  5. Boer V. M., de Winde J. H., Pronk J. T., Piper M. D. ( 2003). The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur. J Biol Chem 278:3265–3274 [View Article][PubMed]
    [Google Scholar]
  6. Buchholz A., Hurlebaus J., Wandrey C., Takors R. ( 2002). Metabolomics: quantification of intracellular metabolite dynamics. Biomol Eng 19:5–15 [View Article][PubMed]
    [Google Scholar]
  7. Castrillo J. I., Zeef L. A., Hoyle D. C., Zhang N., Hayes A., Gardner D. C., Cornell M. J., Petty J., Hakes L. & other authors ( 2007). Growth control of the eukaryote cell: a systems biology study in yeast. J Biol 6:4 [View Article][PubMed]
    [Google Scholar]
  8. Chassagnole C., Noisommit-Rizzi N., Schmid J. W., Mauch K., Reuss M. ( 2002). Dynamic modeling of the central carbon metabolism of Escherichia coli. Biotechnol Bioeng 79:53–73 [View Article][PubMed]
    [Google Scholar]
  9. Chirgwin J. M., Przybyla A. E., MacDonald R. J., Rutter W. J. ( 1979). Isolation of biologically active ribonucleic acid from sources enriched in ribonuclease. Biochemistry 18:5294–5299 [View Article][PubMed]
    [Google Scholar]
  10. Delgado J., Liao J. C. ( 1997). Inverse flux analysis for reduction of acetate excretion in Escherichia coli. Biotechnol Prog 13:361–367 [View Article][PubMed]
    [Google Scholar]
  11. Deutscher J., Francke C., Postma P. W. ( 2006). How phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria. Microbiol Mol Biol Rev 70:939–1031 [View Article][PubMed]
    [Google Scholar]
  12. Evans C. G. T., Herbert D., Tempest D. W. ( 1970). The continuous cultivation of micro-organisms: 2. Construction of a chemostat. Methods Microbiol 2:277–327 [View Article]
    [Google Scholar]
  13. Flamholz A., Noor E., Bar-Even A., Liebermeister W., Milo R. ( 2013). Glycolytic strategy as a tradeoff between energy yield and protein cost. Proc Natl Acad Sci U S A 110:10039–10044 [View Article][PubMed]
    [Google Scholar]
  14. Görke B., Stülke J. ( 2008). Carbon catabolite repression in bacteria: many ways to make the most out of nutrients. Nat Rev Microbiol 6:613–624 [View Article][PubMed]
    [Google Scholar]
  15. Gosset G., Zhang Z., Nayyar S., Cuevas W. A., Saier M. H. Jr ( 2004). Transcriptome analysis of Crp-dependent catabolite control of gene expression in Escherichia coli. J Bacteriol 186:3516–3524 [View Article][PubMed]
    [Google Scholar]
  16. Gottesman S. ( 1984). Bacterial regulation: global regulatory networks. Annu Rev Genet 18:415–441 [View Article][PubMed]
    [Google Scholar]
  17. Hayes A., Zhang N., Wu J., Butler P. R., Hauser N. C., Hoheisel J. D., Lim F. L., Sharrocks A. D., Oliver S. G. ( 2002). Hybridization array technology coupled with chemostat culture: tools to interrogate gene expression in Saccharomyces cerevisiae. Methods 26:281–290 [View Article][PubMed]
    [Google Scholar]
  18. Herbert D., Phipps P. J., Strange R. E. ( 1971). Chemical analysis of microbial cells. Methods Microbiol 26:209–344 [View Article]
    [Google Scholar]
  19. Hoskisson P. A., Hobbs G. ( 2005). Continuous culture – making a comeback?. Microbiology 151:3153–3159 [View Article][PubMed]
    [Google Scholar]
  20. Kayser A., Weber J., Hecht V., Rinas U. ( 2005). Metabolic flux analysis of Escherichia coli in glucose-limited continuous culture. I. Growth-rate-dependent metabolic efficiency at steady state. Microbiology 151:693–706 [View Article][PubMed]
    [Google Scholar]
  21. Khankal R., Chin J. W., Ghosh D., Cirino P. C. ( 2009). Transcriptional effects of CRP* expression in Escherichia coli. J Biol Eng 3:13 [View Article][PubMed]
    [Google Scholar]
  22. Kolkman A., Olsthoorn M. M., Heeremans C. E., Heck A. J., Slijper M. ( 2005). Comparative proteome analysis of Saccharomyces cerevisiae grown in chemostat cultures limited for glucose or ethanol. Mol Cell Proteomics 4:1–11 [View Article][PubMed]
    [Google Scholar]
  23. Lange H. C., Eman M., van Zuijlen G., Visser D., van Dam J. C., Frank J., de Mattos M. J., Heijnen J. J. ( 2001). Improved rapid sampling for in vivo kinetics of intracellular metabolites in Saccharomyces cerevisiae. Biotechnol Bioeng 75:406–415 [View Article][PubMed]
    [Google Scholar]
  24. Lendenmann U., Egli T. ( 1995). Is Escherichia coli growing in glucose-limited chemostat culture able to utilize other sugars without lag?. Microbiology 141:71–78 [View Article][PubMed]
    [Google Scholar]
  25. Liu M., Durfee T., Cabrera J. E., Zhao K., Jin D. J., Blattner F. R. ( 2005). Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli. J Biol Chem 280:15921–15927 [View Article][PubMed]
    [Google Scholar]
  26. Livak K. J., Schmittgen T. D. ( 2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25:402–408 [View Article][PubMed]
    [Google Scholar]
  27. Monod J. ( 1949). The growth of bacterial cultures. Annu Rev Microbiol 3:371–394 [View Article]
    [Google Scholar]
  28. Niklas J., Schräder E., Sandig V., Noll T., Heinzle E. ( 2011). Quantitative characterization of metabolism and metabolic shifts during growth of the new human cell line AGE1.HN using time resolved metabolic flux analysis. Bioprocess Biosyst Eng 34:533–545 [View Article][PubMed]
    [Google Scholar]
  29. Novick A., Szilard L. ( 1950). Experiments with the Chemostat on spontaneous mutations of bacteria. Proc Natl Acad Sci U S A 36:708–719 [View Article][PubMed]
    [Google Scholar]
  30. Oh M. K., Rohlin L., Kao K. C., Liao J. C. ( 2002). Global expression profiling of acetate-grown Escherichia coli. J Biol Chem 277:13175–13183 [View Article][PubMed]
    [Google Scholar]
  31. Piper M. D., Daran-Lapujade P., Bro C., Regenberg B., Knudsen S., Nielsen J., Pronk J. T. ( 2002). Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of Saccharomyces cerevisiae. J Biol Chem 277:37001–37008 [View Article][PubMed]
    [Google Scholar]
  32. Postma E., Scheffers W. A., van Dijken J. P. ( 1989). Kinetics of growth and glucose transport in glucose-limited chemostat cultures of Saccharomyces cerevisiae CBS 8066. Yeast 5:159–165 [View Article][PubMed]
    [Google Scholar]
  33. Postma P. W., Lengeler J. W., Jacobson G. R. ( 1993). Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria. Microbiol Rev 57:543–594[PubMed]
    [Google Scholar]
  34. Puustinen A., Finel M., Virkki M., Wikström M. ( 1989). Cytochrome o (bo) is a proton pump in Paracoccus denitrificans and Escherichia coli. FEBS Lett 249:163–167 [View Article][PubMed]
    [Google Scholar]
  35. Richards G. R., Patel M. V., Lloyd C. R., Vanderpool C. K. ( 2013). Depletion of glycolytic intermediates plays a key role in glucose-phosphate stress in Escherichia coli. J Bacteriol 195:4816–4825 [View Article][PubMed]
    [Google Scholar]
  36. Sauer U., Lasko D. R., Fiaux J., Hochuli M., Glaser R., Szyperski T., Wüthrich K., Bailey J. E. ( 1999). Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism. J Bacteriol 181:6679–6688[PubMed]
    [Google Scholar]
  37. Schaefer U., Boos W., Takors R., Weuster-Botz D. ( 1999). Automated sampling device for monitoring intracellular metabolite dynamics. Anal Biochem 270:88–96 [View Article][PubMed]
    [Google Scholar]
  38. Schaub J., Reuss M. ( 2008). In vivo dynamics of glycolysis in Escherichia coli shows need for growth-rate dependent metabolome analysis. Biotechnol Prog 24:1402–1407 [View Article][PubMed]
    [Google Scholar]
  39. Schlegel H. G. ( 1993). General Microbiology, 7th edn. Cambridge: Cambridge University Press.
    [Google Scholar]
  40. Schulze K. L., Lipe R. S. ( 1964). Relationship between substrate concentration, growth rate, and respiration rate of Escherichia coli in continuous culture. Arch Mikrobiol 48:1–20 [View Article][PubMed]
    [Google Scholar]
  41. Sharma P., Hellingwerf K. J., Teixeira de Mattos M. J., Bekker M. ( 2012). Uncoupling of substrate-level phosphorylation in Escherichia coli during glucose-limited growth. Appl Environ Microbiol 78:6908–6913 [View Article][PubMed]
    [Google Scholar]
  42. Silva J. C., Denny R., Dorschel C., Gorenstein M. V., Li G. Z., Richardson K., Wall D., Geromanos S. J. ( 2006). Simultaneous qualitative and quantitative analysis of the Escherichia coli proteome: a sweet tale. Mol Cell Proteomics 5:589–607 [View Article][PubMed]
    [Google Scholar]
  43. Sunya S., Delvigne F., Uribelarrea J. L., Molina-Jouve C., Gorret N. ( 2012). Comparison of the transient responses of Escherichia coli to a glucose pulse of various intensities. Appl Microbiol Biotechnol 95:1021–1034 [View Article][PubMed]
    [Google Scholar]
  44. Vanderpool C. K. ( 2007). Physiological consequences of small RNA-mediated regulation of glucose-phosphate stress. Curr Opin Microbiol 10:146–151 [View Article][PubMed]
    [Google Scholar]
  45. Vollmer M., Nägele E., Hörth P. ( 2003). Differential proteome analysis: two-dimensional nano-LC/MS of E. coli proteome grown on different carbon sources. J Biomol Tech 14:128–135[PubMed]
    [Google Scholar]
  46. Wick L. M., Quadroni M., Egli T. ( 2001). Short- and long-term changes in proteome composition and kinetic properties in a culture of Escherichia coli during transition from glucose-excess to glucose-limited growth conditions in continuous culture and vice versa. Environ Microbiol 3:588–599 [View Article][PubMed]
    [Google Scholar]
  47. Wikström M. ( 1984). Two protons are pumped from the mitochondrial matrix per electron transferred between NADH and ubiquinone. FEBS Lett 169:300–304 [View Article][PubMed]
    [Google Scholar]
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