Abstract
Escherichia coli remains the best-established production organism in industrial biotechnology. However, when aerobic fermentation runs at high growth rates, considerable amounts of acetate are accumulated as by-product. This by-product has negative effects on growth and protein production. Over the last 20 years, substantial research efforts have been expended on reducing acetate accumulation during aerobic growth of E. coli on glucose. From the onset it was clear that this quest would not be a simple or uncomplicated one. Simple deletion of the acetate pathway reduced the acetate accumulation, but other by-products were formed. This mini review gives a clear outline of these research efforts and their outcome, including bioprocess level approaches and genetic approaches. Recently, the latter seems to have some promising results.
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Akesson M, Karlsson EN, Hagander P, Axelsson JP, Tocaj A (1999) On-line detection of acetate formation in Escherichia coli cultures using dissolved oxygen responses to feed transients. Biotechnol Bioeng 64:590–598
Dittrich CR, Vadali RV, Bennett GN, San K-Y (2005) Redistribution of metabolic fluxes in the central aerobic metabolic pathway of E. coli mutant strains with deletion of the ackA-pta and poxB pathways for the synthesis of isoamyl acetate. Biotechnol Prog 21:627–631
Eiteman MA, Altman E (2006) Overcoming acetate in Escherichia coli recombinant protein fermentations. Trends Biotechnol 24:530–533
Rose IA, Grunberg-Manago M, Korey SR, Ochoa S (1954) Enzymatic phosphorylation of acetate. J Biol Chem 211:737–756
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 mutation of Escherichia coli. J Biochem (Tokyo) 116:916–922
Avison MB, Horton RE, Walsh TR, Bennett PM (2001) Escherichia coli CreBC is a global regulator of gene expression that responds to growth in minimal media. J Biol Chem 276:26955–26961
Chang D-E, Shin S, Rhee J-S, Pan J-G (1999) Acetate metabolism in a pta mutant of Escherichia coli W3110: Importance of maintaining acetyl coenzyme A flux for growth and survival. J Bacteriol 181:6656–6663
Chang Y-Y, Cronan JE Jr (1983) Genetic and biochemical analyses of Escherichia coli strains having a mutation in the structural gene (poxB) for pyruvate oxidase. J Bacteriol 154:756–762
Chang Y-Y, Wang A-Y, Cronan JE Jr (1994) Expression of Escherichia coli pyruvate oxidase (PoxB) depends on the sigma factor encoded by the rpoS (katF) gene. Mol Microbiol 11:1019–1028
Abdel-Hamid A, Attwood M, Guest J (2001) Pyruvate oxidase contributes to the aerobic growth efficiency of Escherichia coli. Microbiology 147:1483–1498
Contiero J, Beatty CM, Kumari S, DeSanti CL, Strohl WR, Wolfe AJ (2000) Effects of mutations in acetate metabolism on high-cell-density growth of Escherichia coli. J Ind Microbiol Biotechnol 24:421–430
Stephanopoulos G (1998) Metabolic engineering. Biotechnol Bioeng 58:199–120
Diaz-Ricci J, Hiltzmann B, Rinas U, Bailey J (1990) Comparative studies of glucose catabolism by Escherichia coli grown in complex medium under aerobic and anaerobic conditions. Biotechnol Prog 6:326–332
Cherrington C, Hinton M, Pearson G, Chopra I (1991) Short-chain organic acids at pH 5.0 kill Escherichia coli and Salmonella spp. without causing membrane perturbation. J Appl Bacteriol 70:161–165
Wolfe AJ (2005) The acetate switch. Microbiol Mol Biol Rev 69:12–50
Akesson M, Hagander P, Axelsson JP (2001) Avoiding acetate accumulation in Escherichia coli cultures using feedback control of glucose feeding. Biotechnol Bioeng 73:223–230
Farmer WR, Liao JC (1997) Reduction of aerobic acetate production by Escherichia coli. Appl Environ Microbiol 63:3205–3210
Lin HY, Mathiszik B, Xu B, Enfors SO, Neubauer P (2001) Determination of the maximum specific uptake capacities for glucose and oxygen in glucose-limited fed-batch cultivations of Escherichia coli. Biotechnol Bioeng 73:347–357
van de Walle M, Shiloach J (1998) Proposed mechanism of acetate accumulation in two recombinant Escherichia coli strains during high density fermentation. Biotechnol Bioeng 57:71–78
Yee L, Blanch HW (1992) Recombinant protein expression in high cell density fed-batch cultures of Escherichia coli. Biotechnology 10:1550–1556
Kleman GL, Chalmers JJ, Luli GW, Strohl WR (1991) Glucose-stat, a glucose-controlled continuous culture. Appl Environ Microbiol 57:918–923
Kleman GL, Chalmers JJ, Luli GW, Strohl WR (1991) A predictive and feedback control algorithm maintains a constant glucose concentration in fed-batch fermentations. Appl Environ Microbiol 57:910–917
Kleman GL, Horken KM, Tabita FR, Strohl WR (1996) Overexpression of ribulose 1,5-biphosphate carboxylase/oxygenase in glucose-controlled high cell density fermentation. Appl Environ Microbiol 62:3502–3507
Kleman GL, Strohl WR (1992) High cell density and high-productivity microbial fermentation. Curr Opin Biotechnol 3:93–98
Kleman GL, Strohl WR (1994) Acetate metabolism by Escherichia coli in high-cell-density fermentation. Appl Environ Microbiol 60:3952–3958
Lee SY (1996) High cell-density culture of Escherichia coli. Trends Biotechnol 14:98–105
Riesenberg D, Guthke R (1996) High-cell-density cultivation of microorganisms. Appl Microbiol Biotechnol 51:422–30
Kim BS, Lee SC, Lee SY, Chang YK, Chang HN (2004) High cell density fed-batch culyivation of Escherichia coli using exponential feeding combined with pH-stat. Bioprocess Biosyst Eng 26:147–150
Konstantinov K, Kishimoto M, Seki T, Yoshida T (1990) A balanced DO-stat and its application to the control of acetic acid excretion by recombinant Escherichia coli. Biotechnol Bioeng 36:750–758
Lee J, Lee SY, Park S, Middelberg APJ (1999) Control of fed-batch fermentations. Biotechnol Adv 17:29–48
Hahm DH, Pan J, Rhee JS (1994) Characterization and evaluation of a pta (phosphotransacetylase) negative mutant of Escherichia coli HB101 as production host of foreign lipase. Appl Microbiol Biotechnol 42:100–107
Andersen KB, von Meyenburg K (1980) Are growth rates of Escherichia coli in batch cultures limited by respiration? J Bacteriol 144:114–123
Aristidou AA, San K-Y, Bennett GN (1999) Improvement of biomass yield and recombinant gene expression in Escherichia coli by using fructose as the primary carbon source. Biotechnol Prog 15:140–145
Han K, Lim HC, Hong J (1992) Acetic acid formation in Escherichia coli fermentation. Biotechnol Bioeng 39:663–671
Zawada J, Swartz J (2005) Maintaining rapid growth in moderate-density Escherichia coli fermentations. Biotechnol Bioeng 89:407–417
Fuchs C, Koster D, Wiebusch S, Mahr K, Eisbrenner G, Markl H (2002) Scale-up of dialysis fermentation for high cell density cultivation of Escherichia coli. J Biotechnol 93:243–251
Nakano K, Rischke M, Sato S, Maerkl H (1997) Influence of acetic acid on the growth of Escherichia coli K12 during high-cell-density cultivation in a dialysis reactor. Appl Microbiol Biotechnol 48:597–601
Chen X, Cen P, Chen J (2005) Enhanced production of human epidermal growth factor by a recombinant Escherichia coli integrated with in situ exchange of acetic acid by macroporous ion-exchange resin. J Biosci Bioeng 100:579–581
Ko Y-F, Bentley WE, Weigand WA (1993) An integrated metabolic modeling approach to describe the energy efficiency of Escherichia coli fermentations under oxygen-limited conditions: Cellular energetics, carbon flux, and acetate production. Biotechnol Bioeng 42:843–853
Chou C-H, Bennett GN, San K-Y (1994) Effect of modified glucose uptake using genetic engineering techniques on high-level recombinant protein production in Escherichia coli dense cultures. Biotechnol Bioeng 44:953–960
Han C, Zhang WC, You S, Huang LY (2004) Knockout of the ptsG gene in Escherichia coli and cultural characterization of the mutants. Sheng Wu Gong Cheng Xue Bao 20:16–20
Sanchez AM, Bennett GN, San KY (2005) Efficient succinic acid production from glucose through overexpression of pyruvate carboxylase in an Escherichia coli alcohol dehydrogenase and lactate dehydrogenase mutant. Biotechnol Prog 21:358–365
Sigüenza R, Flores N, Hernández G, Martínez A, Bolivar F, Valle F (1999) Kinetic characterization in batch and continuous culture of Escherichia coli mutants affected in phosphoenolpyruvate metabolism: differences in acetic acid production. World J Microbiol Biotechnol 15:587–592
Jeong J-Y, Kim Y-J, Cho N, Shin D, Nam T-W, Ryu S, Seok Y-J (2004) Expression of ptsG encoding the major glucose transporter is regulated by arcA in Escherichia coli. J Biol Chem 279:38513–38518
Vemuri GN, Altman E, Sangurdekar DP, Khodursky AB, Eiteman MA (2006) Overflow metabolism in Escherichia coli during steady-state growth: transcriptional regulation and effect of the redox ratio. Appl Environ Microbiol 72:3653–3661
Vemuri GN, Eiteman MA, Altman E (2006) Increased recombinant protein production in Escherichia coli strains with overexpressed water-forming NADH oxidase and a deleted ArcA regulatory protein. Biotechnol Bioeng 94:538–542
Gokarn RR, Evans JD, Walker JR, Martin SA, Eiteman MA, Altman E (2001) The physiological effects and metabolic alterations caused by the expression of Rhizobium etli pyruvate carboxylase in Escherichia coli. Appl Microbiol Biotechnol 56:188–195
Lin HY, Bennett GN, San KY (2005) Metabolic engineering of aerobic succinate production systems in Escherichia coli to improve process productivity and achieve the maximum theoretical succinate yield. Metabolic Eng 7:116–127
Muñoz M, Ponce E (2003) Pyruvate kinase: current status of regulatory and functional properties. Comp Biochem Physiol B 135:197–218
Emmerling M, Dauner M, Ponti A, Fiaux J, Hochuli M, Szyperski T, Wüthrich K, Bailey JE, Sauer U (2002) Metabolic flux responses to pyruvate kinase knockout in Escherichia coli. J Bacteriol 184:152–164
Ponce E (1999) Effect of growth rate reduction and genetic modifications on acetate accumulation and biomass yields in Escherichia coli. J Biosci Bioeng 87:775–780
Sauer U, Lasko DR, Fiaux J, Hochuli M, Glaser R, Szyperski T, Wuthrich K, Bailey JE (1999) Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism. J Bacteriol 181:6679–6688
Siddiquee KA, Arauzo-Bravo MJ, Shimizu K (2004) Effect of a pyruvate kinase (pykF-gene) knockout mutation on the control of gene expression and metabolic fluxes in Escherichia coli. FEMS Microbiol Lett 235:25–33
El-Mansi EMT, Holms WH (1989) Control of carbon flux to acetate excretion during growth of Escherichia coli in batch and continuous cultures. J Gen Microbiol 135:2875–2884
Noronha SB, Yeh HJC, Spande TF, Shiloach J (2000) Investigation of the TCA cycle and the glyoxylate shunt in Escherichia coli BL21 and JM109 using 13C-NMR/MS. Biotechnol Bioeng 68:316–327
Neidhardt FC (ed) (1996) Escherichia coli, Salmonella. Cellular and molecular biology. ASM Press, Washington
Yang C, Hua Q, Baba T, Mori H, Shimizu K (2003) Analysis of Escherichia coli anaplerotic metabolism and its regulation mechanisms from the metabolic responses to altered dilution rates and phosphoenolpyruvate carboxykinase knockout. Biotechnol Bioeng 84:129–144
Chao Y-P, Liao JC (1994) Metabolic responses to substrate futile cycling in Escherichia coli. J Biol Chem 269:5122–5126
Chao Y-P, Liao JC (1993) Alteration of growth yield by overexpression of phosphoenolpyruvate carboxylase and phosphoenolpyruvate carboxykinase in Escherichia coli. Appl Environ Microbiol 59:4261–4265
De Maeseneire SL, De Mey M, Vandedrinck S, Vandamme EJ (2006) Metabolic characterisation of E. coli citrate synthase and phosphoenolpyruvate-carboxylase mutants in aerobic cultures. Biotechnol Lett 28(23):1945–1953
Holms H (1996) Flux analysis and control of the central metabolic pathways in Escherichia coli. FEMS Microbiol Rev 19:85–116
Fong SS, Nanchen A, Palsson BO, Sauer U (2006) Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes. J Biol Chem 281:8024–8033
Peng L, Arauzo-Bravo MJ, Shimizu K (2004) Metabolic flux analysis for a ppc mutant Escherichia coli based on 13C-labelling experiments together with enzyme activity assays and intracellular metabolite measurements. FEMS Microbiol Lett 235:17–23
Suzuki T (1969) Phosphotransacetylase of Escherichia coli B, activation by pyruvate and inhibition by NADH and certain nucleotids. Biochim Biophys Acta 191:559–569
Yang Y-T, Bennett GN, San K-Y (1999) Effect of inactivation of nuo and ackA-pta on redistribution of metabolic fluxes in Escherichia coli. Biotechnol Bioeng 65:291–297
Kumari S, Beatty CM, Browning DF, Busby SJW, Simel EJ, Hovel-Miner G, Wolfe AJ (2000) Regulation of acetyl coenzyme A synthetase in Escherichia coli. J Bacteriol 182:4173–4179
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
Lin H, Castro NM, Bennett GN, San K-Y (2006) Acetyl-CoA synthetase overexpression in Escherichia coli demonstrates more efficient acetate assimilation and lower acetate accumulation: a potential tool in metabolic engineering. Appl Microbiol Biotechnol 71(6):870–874
Bertagnolli B,Hager L (1991) Activation of Escherichia coli pyruvate oxidase enhances the oxidation of hydroxyethylthiamin pyrophosphate. J Biol Chem 266:10168–10173
Vemuri GN, Minning TA, Altman E, Eiteman MA (2005) Physiological response of central metabolism in Escherichia coli to deletion of pyruvate oxidase and introduction of heterologous pyruvate carboxylase. Biotechnol Bioeng 90:64–76
Lara AR, Leal L, Flores N, Gosset G, Bolivar F, Ramirez OT (2006) Transcriptional and metabolic response of recombinant Escherichia coli to spatial dissolved oxygen tension gradients simulated in a scale-down system. Biotechnol Bioeng 92:372–385
Lee J, Goel A, Ataai MM, Domach MM (1994) Flux adaptations of citrate synthase-deficient Escherichia coli. Ann N Y Acad Sci 745:35–50
Aoshima M, Ishii M, Yamagishi A, Oshima T, Igarashi Y (2003) Metabolic characteristics of an isocitrate dehydrogenase defective derivative of Escherichia coli BL21(DE3). Biotechnol Bioeng 84:732–737
El-Mansi EMT, Dawson GC, Bryce CFA (1994) Steady-state modelling of metabolic flux between the tricarboxylic acid cycle and the glyoxylate bypass in Escherichia coli. Comput Appl Biosci 10:295–299
Berrios-Rivera S, Bennett G, San K (2002) Metabolic engineering of Escherichia coli: increase of NADH availability by overexpressing an NAD+-dependent formate dehydrogenase. Metabolic Eng 4:217–229
Berrios-Rivera SJ, Bennett GN, San KY (2002) The effect of increasing NADH availability on the redistribution of metabolic fluxes in Escherichia coli chemostat cultures. Metabolic Eng 4:230–237
Berrios-Rivera SJ, San KY, Bennett GN (2002) The effect of NAPRTase overexpression on the total levels of NAD, the NADH/NAD+ ratio, and the distribution of metabolites in Escherichia coli. Metabolic Eng 4:238–247
San K-Y, Bennett GN, Berríos-Rivera SJ, Vadali RV, Yang Y-T, Horton E, Rudolph FB, Sariyar B, Blackwood K (2002) Metabolic engineering through cofactor manipulation and its effects on metabolic flux redistribution in Escherichia coli. Metabolic Eng 4:182–192
Abiko Y (1975) Metabolism of coenzyme A, In: Greenburg D (ed) Metabolic pathways. Academic, New York
Koebmann BJ, Westerhoff HV, Snoep JL, Nilsson D, Jensen PR (2002) The glycolytic flux in Escherichia coli is controlled by the demand for ATP. J Bacteriol 184:3909–3916
Bailey JE, Sburlati AR, Hatzimanikatis V, Lee K, Renner WA, Tsai PS (1996) Inverse metabolic engineering: a strategy for directed genetic engineering of useful phenotypes. Biotechnol Bioeng 52:109–121
Alper H, Fischer C, Nevoigt E, Stephanopoulos G (2005) Tuning genetic control through promoter engineering. Proc Natl Acad Sci USA 102:12678–12683
Chassagnole C, Noisommit-Rizzi N, Schmid JW, Mauch K, Reuss M (2002) Dynamic modeling of the central carbon metabolism of Escherichia coli. Biotechnol Bioeng 79:53–73
Fischer C, Alper H, Nevoigt E, Jensen K, Stephanopoulos G (2006) Response to Hammer et al.: tuning genetic control—importance of thorough promoter characterization versus generating promoter diversity. Trends Biotechnol 24:55–56
Hammer K, Mijakovic I, Jensen PR (2006) Synthetic promoter libraries—tuning of gene expression. Trends Biotechnol 24:53–55
Jensen PR, Hammer K (1998) Artificial promoters for metabolic optimization. Biotechnol Bioeng 58:191–195
Jensen PR, Hammer K (1998) The sequence of spacers between the consensus sequences modulates the strength of prokaryotic promotors. Appl Environ Microbiol 64:82–87
Mijakovic I, Petranovic D, Jensen PR (2005) Tunable promoters in system biology. Curr Opin Biotechnol 16:329–335
Rud I, Jensen PR, Naterstad K, Axelsson L (2006) A synthetic promoter library for constituitive gene expression in Lactobacillus plantarum. Microbiology 152:1011–1019
Solem C, Jensen PR (2002) Modulation of gene expression made easy. Appl Environ Microbiol 68:2397–2403
Lee SJ, Lee DY, Kim TY, Kim BH, Lee J, Lee SY (2005) Metabolic engineering of Escherichia coli for enhanced production of succinic acid, based on genome comparison and in silico gene knockout simulation. Appl Environ Microbiol 71:7880–7887
Emmerling M, Bailey JE, Sauer U (1999) Glucose catabolism of Escherichia coli strains with increased activity and altered regulation of key glycolytic enzymes. Metabolic Eng 1:117–127
El-Mansi EMT (1998) Control of metabolic interconversion of isocitrate dehydrogenase between the catalytically active and inactive forms in Escherichia coli. FEMS Microbiol Lett 166:333–339
Chang D-E, Jung H-C, Rhee J-S, Pan J-G (1999) Homofermentative production of d- or l-lactate in metabolically engineered Escherichia coli RR1. Appl Environ Microbiol 65:1384–1389
Zhu J, Shimizu K (2004) The effect of pfl gene knockout on the metabolism for optically pure D-lactate production by Escherichia coli. Appl Microbiol Biotechnol 64:367–375
Zhu J, Shimizu K (2005) Effect of a single-gene knockout on the metabolic regulation in Escherichia coli for D-lactate production under microaerobic conditions. Metabolic Eng 7:104–115
Yang Y-T, Aristidou AA, San K-Y, Bennett GN (1999) Metabolic flux analysis of Escherichia coli deficient in the acetate production pathway and expressing the Bacillus subtilis acetolactate synthase. Metabolic Eng 1:26–34
Hong SH, Lee SY (2001) Metabolic flux analysis for succinic acid production by recombinant Escherichia coli with amplified malic enzyme activity. Biotechnol Bioeng 74:89–95
Diaz Ricci JC, Regan L, Bailey JE (1991) Effect of alteration of the acetic acid synthesis pathway on the fermentation pattern of Escherichia coli. Biotechnol Bioeng 38:1318–1324
Causey TB, Shanmugam KT, Yomano LP, Ingram LO (2004) Engineering Escherichia coli for efficient conversion of glucose to pyruvate. Proc Natl Acad Sci USA 101:2235–2240
Acknowledgments
The authors wish to thank the Institute for the Promotion of Innovation through Science and Technology in Flanders (IWT-Vlaanderen) for financial support in the framework of a Ph.D grant (B/04316/01) to M. De Mey.
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De Mey, M., De Maeseneire, S., Soetaert, W. et al. Minimizing acetate formation in E. coli fermentations. J Ind Microbiol Biotechnol 34, 689–700 (2007). https://doi.org/10.1007/s10295-007-0244-2
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DOI: https://doi.org/10.1007/s10295-007-0244-2