Characterizing escherichia coli DH5α growth and metabolism in a complex medium using genome-scale flux analysis

Biotechnology and Bioengineering

Volumn 102, Issue 3, 2009, Pages 923-934

  Selvarasu, Suresh ^a   Ow, Dave Siak Wei ^b,c   Lee, Sang Yup ^d   Lee, May May ^c   Oh, Steve Kah Weng ^c   Karimi, Iftekhar A ^a   Lee, Dong Yup ^a,b,c  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^c AGENCY FOR SCIENCE   (Singapore)

^d Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

Author keywords

Acetate accumulation; Complex medium; Constraints based flux analysis; Escherichia coli; Genome scale in silico model; Systems biotechnology

Indexed keywords

ACETATE ACCUMULATION; COMPLEX MEDIUM; CONSTRAINTS-BASED FLUX ANALYSIS; GENOME-SCALE IN SILICO MODEL; SYSTEMS BIOTECHNOLOGY;

AMINES; AMINO ACIDS; BIOCHEMISTRY; BIOTECHNOLOGY; CARBOHYDRATES; CELL GROWTH; ESCHERICHIA COLI; GLUCOSE; GROWTH (MATERIALS); INDUSTRIAL MANAGEMENT; METABOLITES; NUTRIENTS; ORGANIC ACIDS;

METABOLISM;

ACETIC ACID; ASPARTIC ACID; CARBOHYDRATE; GLUCOSE; GLUTAMIC ACID; GLYCINE; PYRUVIC ACID; SERINE; TREHALOSE;

AMINO ACID ANALYSIS; AMINO ACID SYNTHESIS; ARTICLE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL METABOLISM; BACTERIAL STRAIN; BIOSYNTHESIS; CELL ENERGY; CELL FUNCTION; COMPUTER MODEL; CULTURE MEDIUM; ENERGY CONSERVATION; ESCHERICHIA COLI; GENOME SCALE FLUX ANALYSIS; METABOLITE; NONHUMAN; NUTRIENT UPTAKE; PRECURSOR; PRODUCTIVITY; PROTEIN INTAKE; SIMULATION;

ACETATES; AMINO ACIDS; BIOREACTORS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; CULTURE MEDIA; ESCHERICHIA COLI; GENOME, BACTERIAL; GLUCOSE; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; SERINE;

ESCHERICHIA COLI;

EID: 60349084386     PISSN: 00063592     EISSN: 10970290     Source Type: Journal    
DOI: 10.1002/bit.22119     Document Type: Article

References (54)

1. Baev MV, Baev D, Radek AJ, Campbell JW. 2006a. Growth of Escherichia coli on LB medium: Monitoring utilization of sugars, alcohols and organic
2. acids with transcriptional microarrays. Appl Microbiol Biotechnol 71:310-316.
3. Baev MV, Baev D, Radek AJ, Campbell JW. 2006b. Growth of Escherichia coli on LB medium: Monitoring utilization of amino acids, peptides, and nucleotides with transcriptional microarrays. Appl Microbiol Biotechnol 71:317-322.
4. Baev MV, Baev D, Radek AJ, Campbell JW. 2006c. Growth of Escherichia coli on LB medium: Determining metabolic strategy using transcriptional microarrays. Appl Microbiol Biotechnol 71:323-328.
5. Boos W, Ehmann U, Forkl H, Klein W, Rimmele M, Postma P. 1990. Trehalose transport and metabolism in Escherichia coli. J Bacteriol 172(6):3450-3461.
6. Chang D-C, 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(21):6656-6663.
7. Cohen SA, Michaud DP. 1993. Synthesis of a fluorescent derivatizing reagent, 6-aminoquinolyl-N-hydroxysuccimidyl carbamate and its application for the analysis of hydrolysate amino acids via high performance liquid chromatography. Anal Biochem 211:279-287.
8. Covert MW, Famili I, Palsson BØ. 2003. Identifying constraints that govern cell behavior: A key to converting conceptual to computational models in biology? Biotechnol Bioeng 84(7):763-772.
9. Dahod SK. 1999. Raw material selection and medium development for industrial fermentation processes. In: Demain AL, Davies JE, editors. Manual of industrial microbiology and biotechnology, 2nd edn. Washington, DC: ASM Press. p 213-220.
10. Delgado J, Liao JC. 1997. Inverse flux analysis for reduction of acetate excretion in Escherichia coli. Biotechnol Prog 13:361-367.
11. Dong T, Kirchhof MG, Schellhorn HE. 2008. RpoS regulation of gene expression during exponential growth of Escherichia coli K12. Mol Genet Genomics 279:267-277.
12. Duarte NC, Herrgård MJ, Palsson BO. 2004. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 14:1298-1309.
13. Eastman EM, Durland RH. 1998. Manufacturing and quality control of plasmid-based gene expression systems. Adv Drug Deliv Rev 30(1-3): 33-48.
14. Edwards JS, Covert M, Palsson BO. 2002. Metabolic modeling ofmicrobes: The flux balance approach. Environ Microbiol 4(3):133-140.
15. Egli T. 1995. The ecological and physiological significance of the growth of heterotrophic microorganisms with mixtures of substrates. Adv Microb Ecol 14:305-386.
16. Fu XY, Wei DZ, Tong WY. 2006. Effect of yeast extract on the expression of thioredoxin-human parathyroid hormone from recombinant Escherichia coli. J Chem Technol Biotechnol 81(12):1866-1871.
17. Hahn-Hagerdal B, Karhumaa K, Larsson CU, Gorwa-Grauslund M, Gorgens J, van Zyl WH. 2005. Role of cultivation media in the development of yeast strains for large-scale industrial use. Microb Cell Fact 4:31.
18. Harder W, Dijkhuizen L. 1982. Strategies of mixed substrate utilization in microorganisms. Philos Trans R Soc Lond B Biol Sci 297:459-480.
19. Herber C, Kornberg HL. 1976. Glucose transport as rate limiting step in growth of Escherichia coli. J Biotechnol 156:447.
20. Kim PJ, Lee D-Y, Kim TY, Lee KH, Jeong H, Lee SY, Park S. 2007. Metabolite essentiality elucidates robustness of Escherichia coli metabolism. Proc Natl Acad Sci 104(34):13638-13642.
21. Kleman GL, Strohl WR. 1994. Acetate metabolism by Escherichia coli in high cell density fermentation. Appl Environ Microbiol 60:3952-3958.
22. Kovorova K, Kach A, Zehnder AJ, Egli T. 1997. Cultivation of Escherichia coli with mixtures of 3-phenylpropionic acid and glucose: Steady-state growth kinetics. Appl Environ Microbiol 63(7):2619-2624.
23. Kumari S, Tishel R, Eisenbach M, Wolfe AJ. 1995. Cloning, characterization and functionalization expression of acs the gene which encodes acetyl coenzymeA. J Bacteriol 177:2878-2886.
24. Kumari S, Beatty CM, Browning DF, Busby SJW, Simel EJ, Galadriel H-M, Wolfe AJ. 2000. Regulation of acetyl coenzyme A synthetase in Escherichia coli. J Bacteriol 182(15):4173-4179.
25. Lee SY. 1996. High cell-density culture of Escherichia coli. Trends Biotechnol 14(3):98 -105.
26. Lee DY, Yun H, Park S, Lee SY. 2003. MetaFluxNet: The management of metabolic reaction information and quantitative metabolic flux analysis. Bioinformatics 19:2144-2146.
27. Lee SY, Lee DY, Kim TY. 2005. Systems biotechnology for strain improvement. Trends Biotechnol 23(7):349-358.
28. 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.
29. Leuchtenberger W, Huthmacher K, Drauz K. 2005. Biotechnological production of amino acids and derivatives: Current status and prospects. Appl Microb Biotechnol 69(1):1-8.
30. Majewski RA, Domach MM. 1990. Simple constrained optimization view of acetate overflow in Escherichia coli. Biotechnol Bioeng 35:732-738.
31. McFall E, Newman E. 1996. Amino acids as carbon sources. In: Neidhardt F, et al. editors. Escherichia coli and Salmonella: Cellular and molecular biology, Vol. 1, 2nd edn. ASM Press. Washington, DC: p 358-379.
32. Mey MD, Maeseneire SD, Soetaert W, Vandamme E. 2007. Minimizing acetate formation in Escherichia coli fermentations. J Ind Microbiol Biotechnol 34:689-700.
33. Miller T, Churchill BW. 1986. Substrates for large-scale fermentations. In: Demain AL, Solomon NA, editors. Manual of industrial microbiology and biotechnology. Washington, DC: ASM Press. p 122-136.
34. Netzer R, Wendisch PP, Eggeling L, Sahm H. 2004. Cometabolism of nongrowth substrate: L-serine utilization by Corneybacterium glutamicum. Appl Environ Microbiol 70(12):7148-7155.
35. Novak L, Loubiere P. 2000. The metabolic network of Lactobacillus. lactis: Distribution of 14C-labelled substrates between catabolic and anabolic pathways. J Bacteriol 182:1136-1143.
36. Ow DSW, Lee RMY, Nissom PM, Philip R, Oh SKW, Yap MGS. 2007. Inactivating FruR global regulator in plasmid-bearing Escherichia coli alters metabolic gene expression and improves growth rate. J Biotechnol 131:261-269.
37. Ow DSW, Lee DY, Yap MGS, Oh SKW. in press-a. Identification of cellular objective for elucidating the physiological state of plasmid-bearing Escherichia coli using genome-scale in silico analysis. Biotechnol Prog.
38. Ow DSW, Yap MGS, Oh SKW. in press-b. Enhancement of plasmid DNA yields during fed-batch culture with a fruR knockout Escherichia coli strain. Biotechnol Appl Biochem.
39. Pizer LI. 1965. Glycine synthesis and metabolism in Escherichia coli. J Bacteriol 89(4):1145-1150.
40. Ponce E. 1999. Effect of growth rate reduction and genetic modifications on acetate accumulation and biomass yields in Escherichia coli. J Biosci Bioeng 87(6):775-780.
41. Ponce E, Martinez A, Bolivar F, Valle F. 1998. Stimulation of glucose catabolism through the pentose phosphate pathway by the absence of two pyruvate kinase isozymes in Escherichia coli. Biotechnol Bioeng 58:292-295.
42. Pruss 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(8):2143-2150.
43. Rahman M, Hasan MR, Shimizu K. 2006. Effect of rpoS gene knockout on the metabolism of Escherichia coli during exponential growth phase and early stationary phase based on gene expressions, enzymes activites and intracellular concentrations. Biotechnol Bioeng 94(3):585-595.
44. Reed JL, Vo TD, Schilling CH, Palsson BO. 2003. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 4:R54.
45. Reiling HE, Laurila H, Fiechter A. 1985. Mass culture of Escherichia coli: Medium development for low and high density cultivation of Escherichia coli B/r in minimal and complex media. J Biotechnol 2:191-206.
46. Rimmele M, Boos W. 1994. Trehalose-6-phoshpate hydrolase of Escherichia coli. J Bacteriol 176(18):5656-5664.
47. Robbins JC, Oxender DL. 1973. Transport systems for alanine, serine and glycine in Escherichia coli. J Bacteriol 116(1):12-18.
48. Schuetz R, Kuepfer L, Sauer U. 2007. Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol Syst Biol 3:119.
49. Seputiene V, Daugelavicius A, Suziedelis K, Suziedeliene E. 2006. Acid response of exponentially growing Escherichia coli K-12. Microbiol Res 161:65 -674.
50. Steinbuchel A, Fuchtenbusch B. 1998. Bacterial and other biological system for polyester production. Trends Biotechnol 16(10):419-427.
51. Suárez DC, Liria CW, Kilikian BV. 1998. Effect of yeast extract on Escherichia coli growth and acetic acid production. World J Microbiol Biotechnol 14:331-335.
52. Varma A, Palsson BO. 1994. Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl Envir Microbiol 60:3724-3731.
53. Zhang J, Reddy J, Buckland B, Greasham R. 2003. Toward consistent and productive complex media for industrial fermentations: Studies on yeast extract for a recombinant yeast fermentation process. Biotechnol Bioeng 82(6):640-652.
54. Zinser ER, Kolter R. 2004. Escherichia coli evolution during stationary phase. Res Microbiol 155:328-336.