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Growth of Escherichia coli MG1655 on LB medium: determining metabolic strategy with transcriptional microarrays

  • Genomics and Proteomics
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Abstract

Expression profiles of genes related to stress responses, substrate assimilation, acetate metabolism, and biosynthesis were obtained by monitoring growth of Escherichia coli MG1655 in Luria–Bertani (LB) medium with transcriptional microarrays. Superimposing gene expression profiles on a plot of specific growth rate demonstrates that the cells pass through four distinct physiological states during fermentation before entering stationary phase. Each of these states can be characterized by specific patterns of substrate utilization and cellular biosynthesis corresponding to the nutrient status of the medium. These data allow the growth phases of the classical microbial growth curve to be redefined in terms of the physiological states and environmental changes commonly occurring during bacterial growth in batch culture on LB medium.

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References

  • Alexander DM, Damerau K, St John AC (1993) Carbohydrate uptake genes in Escherichia coli are induced by carbon starvation. Curr Microbiol 27:335–340

    Article  CAS  Google Scholar 

  • Azam TA, Iwata A, Nishimura A, Ueda S, Ishihama A (1999) Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J Bacteriol 181:6361–6370

    Article  CAS  Google Scholar 

  • Baev MV, Baev D, Jancso Radek A, Campbell JW (2006a) Growth of Escherichia coli MG1655 on LB medium: monitoring utilization of sugars, alcohols and organic acids with transcriptional microarrays. Appl Microbiol Biotechnol (in press). DOI 10.1007/s00253-006-0317-6

  • Baev MV, Baev D, Jancso Radek A, Campbell JW (2006b) Growth of Escherichia coli MG1655 on LB medium: monitoring utilization of amino acids, peptides, and nucleotides with transcriptional microarrays. Appl Microbiol Biotechnol (in press). DOI 10.1007/s00253-005-0310-5

  • Brown TDK, Jones-Mortimer MC, Kornberg HL (1977) The enzymic interconversion of acetate and acetyl-coenzyme A in Escherichia coli. J Gen Microbiol 102:327–336

    Article  CAS  Google Scholar 

  • Brown L, Gentry D, Elliott T, Cashel M (2002) DksA affects ppGpp induction of RpoS at a translational level. J Bacteriol 184:4455–4465

    Article  CAS  Google Scholar 

  • Doelle HW, Ewings KN, Hollywood NW (1982) Regulation of glucose metabolism in bacterial systems. Adv Biochem Eng 23:1–35

    CAS  Google Scholar 

  • Egli T (1995) The ecological and physiological significance of the growth of heterotrophic microorganisms with mixtures of substrates. Adv Microb Ecol 14:305–386

    Article  CAS  Google Scholar 

  • Ferenci T (1999) ‘Growth of bacterial cultures’ 50 years on: towards an uncertainty principle instead of constants in bacterial growth kinetics. Res Microbiol 150:431–438

    Article  CAS  Google Scholar 

  • Ferenci T (2001) Hungry bacteria—definition and properties of a nutritional state. Environ Microbiol 3:605–611

    Article  CAS  Google Scholar 

  • Fisher D, Teich A, Neubauer P, Hengge-Aronis R (1998) The general stress sigma factor σs of Escherichia coli is induced during shift from glucose to lactose. J Bacteriol 180:6203–6206

    Google Scholar 

  • Forst S, Delgado J, Rampersaud A, Inouye M (1990) In vivo phosphorylation of OmpR, the transcription activator of the ompF and ompC genes in Escherichia coli. J Bacteriol 172:3473–3477

    Article  CAS  Google Scholar 

  • Harder W, Dijkhuizen L (1982) Strategies of mixed substrate utilization in microorganisms. Philos Trans R Soc Lond B Biol Sci 297:459–480

    CAS  PubMed  Google Scholar 

  • Harder W, Dijkhuizen L (1983) Physiological responses to nutrient limitation. Annu Rev Microbiol 37:1–23

    Article  CAS  Google Scholar 

  • Harder W, Dijkhuizen L, Veldkamp H (1984) Environmental regulation of microbial metabolism. In: Kelly DP, Carr NG (eds) The microbe 1984. Part II. Procaryotes and eukaryotes. Cambridge University Press, Cambridge, UK, pp 51–95

    Google Scholar 

  • Hengge-Aronis R (2002) Signal transduction and regulatory mechanisms involved in control of the σs (RpoS) subunit of RNA polymerase. Microbiol Mol Biol Rev 66:373–395

    Article  CAS  Google Scholar 

  • Huisman GW, Siegle DA, Zambrano MM, Kolter R (1996) Morphological and physiological changes during stationary phase. In: Neidhardt FC, Curtis R III, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaschter M, Umbarger HE (eds) Escherichia coli and Salmonella: cellular and molecular biology, 2nd edn. ASM, Washington, DC, pp 1672–1682

    Google Scholar 

  • Iyer V, Eisen MB, Ross DT, Shuler G, Moore T, Lee JCF, Trent JM, Staudt LM, Hudson J Jr, Boguski MS, Lashkari D, Shalon D, Botstein D, Brown PO (1999) The transcriptional program in the response of human fibroblasts to serum. Science 283:83–87

    Article  CAS  Google Scholar 

  • Kakuda H, Hosono K, Shiroishi K, Ichihara S (1994) Identification and characterization of the ackA (acetate kinase A)-pta (phosphotransacetylase) operon and complementation analysis of acetate utilization by an ackA-pta deletion mutant of Escherichia coli. J Biochem (Tokyo) 116:916–922

    Article  CAS  Google Scholar 

  • Kleman GL, Strohl WR (1994) Acetate metabolism by Escherichia coli in high-cell-density fermentation. Appl Environ Microbiol 60:3952–3958

    Article  CAS  Google Scholar 

  • Kovarova-Kovar K, Egli T (1998) Growth kinetics of suspended microbial cells: from single-substrate-controlled growth to mixed-substrate kinetics. Microbiol Mol Biol Rev 62:646–666

    Article  CAS  Google Scholar 

  • Kumari S, Tishel R, Eisenbach M, Wolfe AJ (1995) Cloning, characterization, and functional expression of acs, the gene which encodes acetyl coenzyme A synthetase in Escherichia coli. J Bacteriol 177:2878–2886

    Article  CAS  Google Scholar 

  • Kumari S, Beatty CM, Browning DF, Busby SJ, Simel EJ, Hovel-Miner G, Wolfe AJ (2000) Regulation of acetyl coenzyme A synthetase in Escherichia coli. J Bacteriol 182:4173–4179

    Article  CAS  Google Scholar 

  • Lendenmann U, Snozzi M, Egli T (1996) Kinetics of the simultaneous utilization of sugar mixtures by Escherichia coli in continuous culture. Appl Environ Microbiol 62:1493–1499

    Article  CAS  Google Scholar 

  • Lendenmann U, Snozzi M, Egli T (2000) Growth kinetics of Escherichia coli with galactose and several other sugars in carbon-limited chemostat culture. Can J Microbiol 46:72–80

    Article  CAS  Google Scholar 

  • Loewen PC, Hu B, Strutinsky J, Sparling R (1998) Regulation in the rpoS regulon of Escherichia coli. Can J Microbiol 44:707–717

    Article  CAS  Google Scholar 

  • Luli GW, Strohl WR (1990) Comparison of growth, acetate production, and acetate inhibition of Escherichia coli strains in batch and fed-batch fermentations. Appl Environ Microbiol 56:1004–1011

    Article  CAS  Google Scholar 

  • Matin A (1996) Role of alternate sigma factors in starvation protein synthesis-novel mechanisms of catabolite repression. Res Microbiol 147:494–505

    Article  CAS  Google Scholar 

  • Ninfa AJ (1996) Regulation of gene transcription by extracellular stimuli. In: Neidhardt FC, Curtis R III, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaschter M, Umbarger HE (eds) Escherichia coli and Salmonella: cellular and molecular biology, 2nd edn. ASM, Washington, DC, pp 1246–1262

    Google Scholar 

  • Nystrom T (1994) The glucose-starvation stimulon of Escherichia coli: induced and repressed synthesis of enzymes of central metabolic pathways and role of acetyl phosphate in gene expression and starvation survival. Mol Microbiol 12:833–843

    Article  CAS  Google Scholar 

  • Poindexter JS (1987) Bacterial responses to nutrient limitation. In: Fletcher M, Gray TRG, Jones JG (eds) Ecology of microbial communities. Cambridge University Press, Cambridge, UK, pp 283–317

    Google Scholar 

  • Prüß BM (1998) Acetyl phosphate and the phosphorylation of OmpR are involved in the regulation of the cell division rate in Escherichia coli. Arch Microbiol 170:141–146

    Article  Google Scholar 

  • Prüß BM, Wolfe AJ (1994) Regulation of acetyl phosphate synthesis and degradation, and the control of flagellar expression in Escherichia coli. Mol Microbiol 12:973–984

    Article  Google Scholar 

  • Prüß BM, Nelms JM, Park C, Wolfe AJ (1994) Mutations in NADH: ubiquinone oxidoreductase of Escherichia coli affect growth on mixed amino acids. J Bacteriol 176:2143–2150

    Article  Google Scholar 

  • Selinger DW, Cheung KJ, Mei R, Johansson EM, Richmond CS, Blattner FR, Lockhart DJ, Church GM (2000) RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat Biotechnol 18:1262–1268

    Article  CAS  Google Scholar 

  • Shin S, Park C (1995) Modulation of flagellar expression in Escherichia coli by acetyl phosphate and the osmoregulator OmpR. J Bacteriol 177:4696–4702

    Article  CAS  Google Scholar 

  • Tempest DW, Neijssel OM (1978). Eco-physiological aspects of microbial growth in aerobic nutrient-limited environments. Adv Microb Ecol 2:105–153

    Article  Google Scholar 

  • Wanner U, Egli T (1990) Dynamics of microbial growth and cell composition in batch culture. FEMS Microbiol Rev 6:19–43

    Article  CAS  Google Scholar 

  • Wanner BL, Wilmes-Riesenberg MR (1992) Involvement of phosphotransacetylase, acetate kinase, and acetyl phosphate synthesis in control of the phosphate regulon in Escherichia coli. J Bacteriol 174:2124–2130

    Article  CAS  Google Scholar 

  • Webb C, Moreno M, Wilmes-Riesenberg M, Curtis R III, Foster JW (1999) Effects of DksA and ClpP protease on sigma S product and virulence in Salmonella typhimurium. Mol Microbiol 34:112–123

    Article  CAS  Google Scholar 

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Author notes

  1. Dmitry Baev

    Present address: IBM Toronto Software Laboratory, 8200 Warden Ave., Markham, ON,, L6G 1C7, Canada

  2. Agnes Jancso Radek

    Present address: Epicentre Technologies, 726 Post Road, Madison, WI, 53713, USA

  3. John W. Campbell

    Present address: Scarab Genomics LLC, 1202 Ann St., Madison, WI, 53713, USA

Authors and Affiliations

  1. Integrated Genomics Incorporated, 2201 W. Campbell Park Drive, Chicago, IL, 60612, USA

    Mark V. Baev, Agnes Jancso Radek & John W. Campbell

  2. Department of Computer Science, University of Toronto, Ontario, Canada

    Dmitry Baev

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  1. Mark V. Baev
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Correspondence to Mark V. Baev.

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Baev, M.V., Baev, D., Radek, A.J. et al. Growth of Escherichia coli MG1655 on LB medium: determining metabolic strategy with transcriptional microarrays. Appl Microbiol Biotechnol 71, 323–328 (2006). https://doi.org/10.1007/s00253-006-0392-8

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  • DOI: https://doi.org/10.1007/s00253-006-0392-8

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