Importance of understanding the main metabolic regulation in response to the specific pathway mutation for metabolic engineering of Escherichia coli

Computational and Structural Biotechnology Journal

Volumn 3, Issue 4, 2012, Pages e201210018-

  Matsuoka, Yu ^a   Shimizu, Kazuyuki ^a,b  

^a KYUSHU INSTITUTE OF TECHNOLOGY   (Japan)

^b KEIO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84893243410     PISSN: None     EISSN: 20010370     Source Type: Journal    
DOI: 10.5936/csbj.201210018     Document Type: Short Survey

References (85)

1. Alper H and Stephanopoulos G (2007) Global transcription machinery engineering: a new approach for improving cellular phenotype. Metab Eng 9: 258-267. (Pubitemid 46809525)
2. Alper H, Moxley J, Nevoigt E, Fink GR, Stephanopoulos G (2006) Engineering yeast transcription machinery for improved ethanol tolerance and production. Science 314: 1565-1568. (Pubitemid 44907143)
3. Alper H, Miyaoka K, Stephanopoulos G (2005a) Construction of lycopene-over producing E. coli strains by combining systematic and combinatorial gene knockout targets. Nat Biotechnol 23: 612-616. (Pubitemid 41724901)
4. Alper H, Fischer C, Nevoigt E, Stephanopoulos G (2005b) Tuning genetic control through promoter engineering. Proc Natl Acad Sci USA 102: 12678-12683. (Pubitemid 41279425)
5. Atsumi S, Wu TY, Machado IM, Huang WC, Chen PY, Pellegrini M, Liao JC (2010) Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli, Mol Syst Biol 6:449.
6. Atsumi S, Hanai T, Liao JC (2008a) Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451: 86-90.
7. Atsumi S, Cann AF, Connor MR, Shen CR, Smith KM, Brynildsen MP, Chou KJ, Hanai T, Liao JC (2008b) Metabolic engineering of Escherichia coli for 1-butanol production. Metab Eng 10: 305-311.
8. Bailey JE, Shurlati A, 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. (Pubitemid 26317945)
9. Bailey JE (1991) Toward a science of metabolic engineering. Science 252: 1668-1675. (Pubitemid 21917084)
10. Beller HR Goh EB, Keasling JD (2010) Genes involved in long-chain alkene biosynthesis in Micrococcus luteus. Appl Environ Microbiol 76: 1212-1223.
11. Becker J, Klopproqqe C, Wittmann C (2008) Metabolic responses to pyruvate kinase deletion in lysine producing Corynebacterium glutamicum. Microb Cell Fact 7:8.
12. Bettenbrock K, Fischer S, Klemling A, Sauter FT, Gilles, ED (2006) A quantitative approach to catabolite repression in Escherichia coli. J. Biol. Chem. 281: 2578-2584. (Pubitemid 43845718)
13. Bruggeman FJ and Westerhoff HV (2006) Approaches to biosimulaiton of cellular processes. J Biol Phys 32: 273-288.
14. Burgard AP, Phakya P, Maranas CD (2003) OptKnock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol. Bioeng. 84: 647-657. (Pubitemid 37420336)
15. Chang MC, Eachus RA, Trieu W, Ro DK, Keasling JD (2007) Engineering Escherichia coli for production of functionalized terpenoids using plant P450s. Nat. Chem. Biol. 3: 274-277. (Pubitemid 46625834)
16. Cunningham DS, Liu Z, Domagalski N, Koepsel RR, Ataai MM, Domach MM (2009): Pyruvate kinase-deficient Escherichia coli exhibits increased plasmid copy number and cyclic AMP levels. / Bacteriol, 191:3041-3049.
17. Dunlop MJ, Dossani ZY, Szmidt HL, Chu HC, Lee TS, Keasling JD, Hadi MZ, Mukhopadhyay A (2011) Engineering microbial biofuel tolerance and export using efflux pumps. Mol Syst Biol 7:487.
18. Edwards MC, Henriksen ED, Yomano LP, Gardner BC, Sharma LN, Ingram LO, Doran Peterson J (2011) Addition of genes for cellobiase and pectinolytic activity in Escherichia coli for fuel ethanol production from pectin-rich lignocellulosic biomass. Appl Environ Microbiol 77: 5184-5191.
19. Escalante A, Calderon R, Valdivia A, de Anda R, Hernandez G, Ramirez OT, Gosset G, Bolivar F (2010) Metabolic engineering for the production of shikimic acid in an evolved Escherichia coli strain lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system. Microb Cell Fact 9:21.
20. Feist AM and Palsson BO (2008) The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli, Nat Biotechnol 26: 659-667. (Pubitemid 351824691)
21. Fell DA (1997) Understanding the control of metabolism (1st ed.) Portland Press
22. Flores N, Leal L, Sigala JC, de Anda R, Escalante A, Martinez A, Ramirez OT, Gosset G, Bolivar F (2007) Growth recovery on glucose under aerobic conditions of an Esherichia coli strain carrying a phosphoenolpyruvate: carbohydrate phosphotransferase system deletion by inactivating arcA and overexpressing the genes coding for glucokinase and galactose permease. J Mol Microbiol Biotechnol 13: 105-116. (Pubitemid 351359839)
23. Fuhrer T, Fischer E, Sauer U (2005) Experimental identification and quantification of glucose metabolism in seven bacterial species. J Bacteriol 187: 1581-1590. (Pubitemid 40289358)
24. Gama-Castro S, Salgado H, Peralta-Gil M, Santos-Zavaleta A, Muniz-Rascado L, Solano-Lira H, Jimenez-Jacinto V, Weiss V, Garcia-Sotelo JS, Lopez-Fuentes A, Porron-Sotelo L, Alquicira-Hernandez S, Medina-Rivera A, Martinez-Flores I, Alquicira-Hernandez K, Martinez-Adame R, Bonavides-Martinez C, Miranda-Rios J, Huerta A, Mendoza-Vargas A, Collado-Torres L, Taboada B, Vega-Alvarado L, Olvera M, Olvera L, Grande R, Morett E, Collado-Vides J (2010) RegulonDB (version 7.0).
25. Geddes CC, Nieves IU, Ingram LO (2011) Advances in ethanol production. Curr Opin Biotechnol 22: 312-319.
26. Gosset G (2005) Improvement of Escherichia coli production strains by modification of the phosphoenolpyruvate: sugar phosphotransferase system. Microb Cell Fact 4:14.
27. Hawkins KM and Smolke CD (2008) Production of benzylisoquinoline alkaloids in Saccharomyces cerevisiae, Nat Chem Biol 4: 564-573.
28. Heinrich R and Schuster S (1996) The regulation of Cellular Systems. Chapman and Hall, New York.
29. Herrgard MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Bluthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novere N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spacic I, Weichart D, Brent R, Broomhead DS, Westerhff HV, Kirdar B, Penttila M, Klipp E, Palsson BO, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol 26: 1155-1160.
30. Hua Q, Yang C, Baba T, Mori H, Shimizu K (2003) Responses of the central carbon metabolism in Escherichia coli to phosphoglucose isomerase and glucose-6-phosphate dehydrogenase knockouts. J Bacteriol 185:7053-7067. (Pubitemid 37509820)
31. Inui M, Suda M, Kimura S, Yasuda K, Suzuki H, Toda H, Yamamoto S, Okino S, Suzuki N, Yukawa H (2008) Expression of Clostridium acetobutylicum butanol synthetic genes in Escherichia coli. Appl Microbiol Biotechnol, 77:1305-1316.
32. Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, Kanai A, Hirasawa T, Naba M, Hirai K, Hoque A, Ho PY, Kakazu Y, Sugawara K, Igarashi S, Harada S, Masuda T, Sugiyama N, Togashi T, Hasegawa M, Takai Y, Yugi K, Arakawa K, Iwata N, Toya Y, Nakayama Y, Nishioka T, Shimizu K, Mori H, Tomita M (2007) Multiple high-throughput analyses monitor the response of £ coli to perturbations. Science 316: 593-597. (Pubitemid 46683144)
33. Kabir M, Ho PY, Shimizu K (2005) Effect of idhA gene deletion on the metabolism of E. coli based on gene expression, enzyme activities, intracellular metabolite concentrations, and metabolic flux distribution. BiochemEngJ26: 1-11. (Pubitemid 41219792)
34. Kabir M and Shimizu K (2004) Fermentation characteristics and protein expression patterns for recombinant E. coli mutant lacking pgi for PHB production. Appl Microbiol Biotechnol 62: 244-255. (Pubitemid 36995179)
35. Kabir M and Shimizu K (2003) Gene expression patterns for metabolic pathway in pgi knockout E. coli with and without phb genes based on RT-PCR. J Biotechnol 105: 11-31. (Pubitemid 37159312)
36. Kao KC, Tran LM, Liao JC (2005) A global regulatory role of gluconeogenic genes in Escherichia coli revealed by transcriptome network analysis. J Biol Chem 280: 36079-36087. (Pubitemid 41633879)
37. Keasling JD (2010) Manufacturing molecules through metabolic engineering. Science 330: 1355-1358.
38. Kedar P, Colah R, Shimizu K (2007) Proteomic investigation on the pyk-F gene knockout Escherichia coli for aromatic amino acid production. Enz Microbial Technol 41: 455-465. (Pubitemid 47033941)
39. Kondo, A, Ishii J, Hara KY, Hasunuma T, Matsuda F (2012) Development of microbial cell factories for bio-refinery through synthetic bioengineering, J. Biotechnol.,in print.
40. Kotte O, Zaugg JB, Heinemann M (2010) Bacterial adaptation through distributed sensing of metabolic fluxes. Mol Sys Biol 6:355.
41. Kremling A, Fischer S, Sauter T, Bettenbrock K, Gilles ED (2004) Time hierarchies in the Escherichia coli carbohydrate uptake and metabolism. BioSystems 73:57-71. (Pubitemid 38077255)
42. Kremling A and Gilles ED (2001) The organization of metabolic reaction networks. II. Signal processing in hierarchical structured functional units. Metab Eng 3:138-150. (Pubitemid 32930969)
43. Laporte DC and Koshland DE (1982) A protein with kinase and phosphatase activities involved in regulation of tricarboxylic acid cycle. Nature 300: 458-460.
44. Lee SJ, Lee DY, Kin TY, Kim BH, Lee J, Lee YS (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. (Pubitemid 41805090)
45. Leonard E, Ajikumar PK, Thayer K, Xiao WH, Mo JD, Tidor B, Stephanopoulos G, Prather KLJ (2010) Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control. Proc. Natl. Acad. Sci. U.S.A. 107: 13654-13659.
46. Li M, Yao S, Shimizu K (2006a) Effect of ipdA gene knockout on the metabolism in Escherichia coli based on enzyme activities, intracellular metabolite concentrations and metabolic flux analysis by 13C-labeling experiments. J Biotechnol 122: 254-266.
47. Li M, Ho PY, Yao S, Shimizu K (2006b) Effect of sucA or sucC gene knockout on the metabolism in Escherichia coli based on gene expressions, enzyme activities, intracellular metabolite concentrations and metabolic fluxes by "C-labeling experiments. Biochem Eng J 30: 286-296. (Pubitemid 43929416)
48. Lu J, Tang J, Liu Y, Zhu X, Zhang T, Zhang X (2012) Combinatorial modulation of galP and glk gene expression for improved alternative glucose utilization, Appl. Microbiol. Biotechnol., 93:2455-2462
49. Lutke-Eversloh T and Stephanopoulos G (2008) Combinatorial pathway analysis for improved L-tyrosine production in Escherichia coli: identification of enzymatic bottlenecks by systematic gene overexpression. Metab Eng 10: 69-77.
50. Martin VJJ, Pitera DJ, Withers ST, Newman JD, Keasling JD (2003) Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol. 21: 796-802. (Pubitemid 36791399)
51. Matsuoka Y and Shimizu K (2011) Metabolic regulation in Escherichia coli in response to culture environments via global regulators. Biotechnol J 6:1330-1341.
52. Meza E, Becker J, Bolivar F, Gosset G, Wittmann C (2012) Consequences of phosphoenolpyruvate: sugar phosphotransferase system and pyruvate kinase isozymes inactivation in central carbon metabolism flux distribution in Escherichia coli. Microb Cell Fact 11:127.
53. Munjal N, Mattam AJ, Pramanik D, Srivastava PS, Yazdani SS (2012) Modulation of endogenous pathways enhances bioethanol yield and productivity in Escherichia coli, Micobial Cell Fact., 11:145
54. Nakamura CE and Whited GM (2003) Metabolic engineering for the microbial production of 1,3-propanediol. Curr. Opin. Biotechnol. 14: 454-459. (Pubitemid 37298028)
55. Nielsen J (2011) Editorial: Industrial systems biology. Biotechnol J 6:255.
56. Nielsen J (2003) It is all about metabolic fluxes. J Bacteriol 185: 7031-7035. (Pubitemid 37521234)
57. Nielsen J and Keasling JD (2011) Synergies between synthetic biology and metabolic engineering. Nat Biotechnol 29: 693-695.
58. Palsson B (2009) Metabolic systems biology. FEBS Lett 583: 3900-3904.
59. Papagianni M (2012) Recent advances in engineering the central carbon metabolism of industrially important bacteria. Microb Cell Fact 11:50.
60. Peng L, Arauzo M, Shimizu K (2004) Metabolic flux analysis for a ppc mutant Escherichia coli based on 13C-labelling experiments together with enzyme acyivity assays and intracellular metabolite measurements. FEMS Microbiol Lett 235: 17-23. (Pubitemid 38668632)
61. Pfeifer BA, Admiraal SJ, Gramajo H, Cane DE, Khosla C (2001) Biosynthesis of complex polyketides in a metabolically engineered strain of E. coli. Science 291: 1790-1792. (Pubitemid 32198984)
62. Pharkya P, Burgard AP, Maranas CD (2004) OptStrain: a computational framework for redesign of microbial production systems. Genome Res 14: 2367-2376. (Pubitemid 39517344)
63. Pharkya P and Maranas CD (2006) An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. Metab Eng 8: 1-13. (Pubitemid 43017837)
64. Ro DK, Paradise EM, Ouellet M, Fischer KJ, Newman L, Ndungu JM, Ho KA, Eachus RA, Ham TS, Kirby J, Chang MCY, Withers ST, Shiba Y, Sarpong R, Keasling JD (2006) Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440: 940-943.
65. Rossell S, van der Weijden CC, Lindenbergh A, van Tuijl A, Francke C, Bakker BM, Westerhoff HV (2006) Unraveling the complexity of flux regulation: a new method demonstrated for nutrient starvation in Saccharomyces cerevisiae. Proc Nad Acad Sci USA 103: 2166-2171. (Pubitemid 43271641)
66. Rossell S, van der Weijden CC, Kruckeberg AL, Bakker BM, Westerhoff HV (2005) Hierarchical and metabolic regulation of glucose influx in starved Saccharomyces cerevisiae. FEMS Yeast Res 5: 611-619. (Pubitemid 40380700)
67. Schirmer A, Rude MA, Li X, Popova E, del Cardayre SB (2010) Microbial biosynthesis of alkanes. Science 329: 559-562.
68. Shimizu K (2009) Toward systematic metabolic engineering based on the analysis of metabolic regulation by the integration of different levels of information. Biochem Eng J 46: 235-251.
69. Shimizu K (2004) Metabolic flux analysis based on 13C labeling experiments and integration of the information with gene and protein expression patterns. Adv Biochem Eng Biotechnol 91:1-49.
70. Shimizu K (2012) Bacterial cellular metabolic systems, Woodhead Publ. Ltd., Oxford.
71. Siddiquee KAZ, Arauzo-Bravo M, Shimizu K (2004a) Metabolic flux analysis of pykF gene knockout Escherichia coli based on 13C-labeled experiment together with measurements of enzyme activities and intracellular metabolite concentrations. Appl Microbiol Biotechnol 63: 407-417. (Pubitemid 38134779)
72. Siddiquee KAZ, Arauzo-Bravo M, Shimizu K (2004b) Effect of pyruvate kinase (pykF gene) knockout mutation on the control of gene expression and metabolic fluxes in Escherichia coli. FEMS Microbiol Lett 235: 25-33. (Pubitemid 38668633)
73. Steen EJ, Kang Y, Bokinsky G, Hu Z, Schirmer A, McClure A, Cardayre SB, Keasling JD (2010) Microbial production of fatty-acid-derived fuels and chemicals from plant biomass. Nature 463: 559-563.
74. Steen EJ, Chan R, Prasad N, Myers S, Petzold CJ, Redding A, Ouellet M, Keasling JD (2008) Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol. Microb Cell Fact 7: 36.
75. Toya Y, Ishii N, Nakahigashi K, Hirasawa T, Soga T, Tomita T, Shimizu K (2010) ' 3C-metabolic flux analysis for batch culture of Escherichia coli and its Pyk and Pgi gene knockout mutants based on mass isotopomer distribution of intracellular metabolites. Biotechnol. Prog. 26: 975-992.
76. Trinh CT, Carlson R, Wlaschin A, Srienc F (2006) Design, construction and performance of the most efficient biomass producing E. coli bacterium. Metab Eng 8: 628-638. (Pubitemid 44512166)
77. Usui Y, Hirasawa T, Furusawa C, Shirai T, Yamamoto N, Mori H, Shimizu H (2012) Investigating the effects of perturbations to pgi and eno gene expression on central carbon metabolism in Escherichia coli using 13C metabolic flux analysis. Microb Cell Fact 11:87.
78. Westerhoff HV, Winder C, Messiha H, Simeonidis E, Adamczyk M, Verma M, Bruggeman FJ, Dunn W (2009) Systems biology: the elements and principles of life. FEBS Lett 583: 3882-3890.
79. Yadav VG, Mey MD, Lim CG, Ajikumar PK, Stephanopoulos G (2012) The future of metabolic engineering and synthetic biology: Towards a systematic practice. Metab Eng 14: 233-241.
80. Yang C, Hua Q, Baba T, Mori H, Shimizu K (2003) Analysis of £ coli anaplerotic dilution rates and pck knockout. Biotechnol Bioeng 84: 129-144.
81. Zambonij N, Heinemann M, Sauer U (2007) Getting closer to the whole picture. Science, 316, 550 - 551. (Pubitemid 46683128)
82. Zhao J, Baba T, Mori H, Shimizu K (2004a) Effect of zwf gene knockout on the metabolism of Escherichia coli grown on glucose or acetate. Metab Eng 6: 164-174. (Pubitemid 38601069)
83. Zhao J, Baba T, Mori H, Shimizu K (2004b) Analysis of metabolic and physiological responses to gnd knockout in £. coli by using C-13 tracer experiment and enzyme activity measurement. FEMS Microbiol Lett 220:295-301. (Pubitemid 36378985)
84. Zhu J and Shimizu K (2005) Effect of a single-gene knockout on the metabolic regulation in E. coli for D-lactate production under microaerobic condition. Metab Eng 7: 104-115. (Pubitemid 40387559)
85. Zhu J and Shimizu K (2004) The effect of pfl genes knockout on the metabolism for optically pure D-lactate production by Escherichia coli. Appl Microbiol Biotechnol 64: 367-375. (Pubitemid 38626461)