Perspectives in metabolic engineering: Understanding cellular regulation towards the control of metabolic routes

Applied Biochemistry and Biotechnology

Volumn 169, Issue 1, 2013, Pages 55-65

  Zadran, Sohila ^a   Levine, Raphael D ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Bioenergetics; Bioengineering; Gene networks; Metabolic flux analysis; Metabolomics

Indexed keywords

BIOCHEMICAL REACTIONS; BIOENERGETICS; CELLULAR REGULATION; CHEMICAL PROCESS; CHEMICAL SYNTHESIS; CURRENT LIMITATION; GENE NETWORKS; GENOME-SCALE MODEL; GREEN CHEMISTRY; HIGH YIELD; KINETIC MODELING; MANUFACTURING PROCESS; METABOLIC FLUX; METABOLIC FLUX ANALYSIS; METABOLIC PATHWAYS; METABOLIC ROUTES; METABOLOMICS; MULTI-DISCIPLINARY APPROACH; SIMPLE SYSTEM; SMALL MOLECULES;

BIOCHEMISTRY; BIODIESEL; CHEMICAL ENGINEERING; METABOLISM; MOLECULAR BIOLOGY; SYSTEMS SCIENCE;

METABOLIC ENGINEERING;

AMPHOTERICIN B; ARTEMISININ; BENZYLISOQUINOLINE DERIVATIVE; DOXORUBICIN; ELEUTHEROBIN; EPIRUBICIN; ERYTHROMYCIN; ISOPRENOID; MITHRAMYCIN; PACLITAXEL; POLYKETIDE; RAPAMYCIN; RIFAMYCIN; TERPENE; TETRACYCLINE; TYLOSIN;

AMINO ACID SYNTHESIS; ANTIBIOTIC BIOSYNTHESIS; ARTICLE; BIOMEDICINE; BREAST CANCER; CARDIOTOXICITY; CELL METABOLISM; CHEMICAL ANALYSIS; CHEMICAL REACTION KINETICS; COST; DRUG MANUFACTURE; DRUG SYNTHESIS; HUMAN; MELANOMA; METABOLIC CONTROL ANALYSIS; METABOLIC ENGINEERING; METABOLIC FLUX ANALYSIS; METABOLIC REGULATION; NONHUMAN; OVARY CANCER; SCALE UP; STOCHASTIC MODEL; THEORETICAL MODEL;

BACTERIA; FUNGI; METABOLIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS;

EID: 84873086193     PISSN: 02732289     EISSN: 15590291     Source Type: Journal    
DOI: 10.1007/s12010-012-9951-x     Document Type: Article

References (76)

1. Bailey, J. E. (1991). Toward a science of metabolic engineering. Science, 252, 1668-1674.
2. Hutchinson, C. R. (1998). Combinatorial biosynthesis for new drug discovery. Current Opinion in Microbiology, 1(3), 319-329.
3. Jacobson, J. R.; Khosla, C. (1998). New directions in metabolic engineering. Current Opinion in Chemical Biology, 2, 133-137.
4. Keasling, J. D. (2010). Manufacturing molecules through metabolic engineering. Science, 330, 1355-1358.
5. Nerem, R. M. (1991). Cellualr engineering. Annals of Biomedical Engineering, 19, 529-545.
6. Koffas, M.; Roberge, C.; Lee, K.; Stephanopoulos, G. (1999). Metabolic engineering. Annual Review of Biomedical Engineering, 01, 535-557.
7. Price, N. D.; et al. (2004). Genome-scale models of microbial cells: evaluating the consequences of constraints. Nature Reviews Microbiology, 2, 886-897.
8. Kosla, C.; Keasling, J. D. (2003). Metabolic engineering for drug discovery and development. Nature Reviews, 2, 1019-1024.
9. Van der Oost, J.; Ciaramella, M.; Moracci, M.; Pisani, F. M.; Rossi, M.; de Vos, W. M. (1998). Molecular biology of hyperthermophillic Archaea. Advances in Biochemical Engineering/Biotechnology, 61, 87-115.
10. Colon, G. E.; Nguyen, T. T.; Jetten, M. S. M.; Sinskey, A. J.; Stephanopoulos, G. (1995). Production of isoleucine by overexpression of ilvA in a Corynebacterium lactofermentum threonine producer. Applied Microbiology and Biotechnology, 43, 482-488.
11. MacQuitty, J. J. (1988). Impact of biotechnology on the chemical industry. ACS Symposium Series, 362, 221-233.
12. Stephanopoulos, G. (1999). Metabolic fluxes and metabolic engineering. Metabolic Engineering, 1, 1-11.
13. Nielson, J. (1994). Physiological engineering-towards a new science, pp. 30-38. Proc. The 1994 IChemE Research Event, London.
14. Cameron, D. C.; Tong, I. T. (1993). Cellular and metabolic engineering. Applied Biochemistry and Biotechnology, 38, 105-140.
15. Hutchinson, C. R. (1994). Drug synthesis by genetically engineered microorganisms. Bio/Technology, 12, 375-380.
16. Craig, G. M.; Newman, D. J.; Snader, K. M. (1997). Natural products in drug discovery and development. Journal of Natural Products, 60, 52-60.
17. McCaskill, D.; Croteau, R. (1997). Prospects for the bioengineering of isoprenoid biosynthesis. Advances in Biochemical Engineering/Biotechnology, 55, 107-146.
18. Yarmush, M. L.; Berthiaume, F. (1997). Metabolic engineering and human disease. Nature Biotechnology, 15, 525-528.
19. Maynard, N. D.; Gutschow, M. V.; Birch, E. W.; Professor, M. W. C. (2010). The virus as metabolic engineering. Biotechnology Journal, 5, 686-694.
20. Lee, S. Y.; Kim, H. U.; Park, J. H.; Park, J. M.; Kim, T. Y. (2009). Metabolic engineering of microorganisms: general strategies and drug production. Drug Discovery Today, 14, 81-89.
21. Zhang, F.; Keasling, J. (2011). Biosensors and their applications in microbial metabolic engineering. Trends in Microbiology, 19, 323-329.
22. Shaw, A. J.; Podkaminer, K. K.; Desai, S. G.; Bardsley, J. S.; Rogers, S. R.; Thorne, P. G.; Hogsetti, D. A.; Lynd, L. R. (2008). Metabolic engineering of a thermophilic bacterium to produce ethanol at high yield. Proceedings of the National Academy of Sciences USA, 105, 13669-13774.
23. Haggart, C. R.; Bartel, J. A.; Saucerman, J. J. (2011). Whole-genome metabolic network reconstruction and constraint-based modeling. Methods in Enzymology, 500, 411-433.
24. Chavali, A. K.; D'Auria, K. M.; Hewlett, E. L. (2012). A metabolic network approach for the identification and prioritization of antimicrobial drug targets. Trends in Microbiology, 20, 113-123.
25. Stephanopoulos, G.; Simpson, T. W. (1997). Flux amplification in complex metabolic networks. Chemical Engineering Science, 52, 2607-2627.
26. Stephanopoulos, G.; Valino, J. J. (1991). Network rigidity and metabolic engineering in metabolite overproduction. Science, 252, 1675-1681.
27. Kacser, H.; Burns, J. A. (1973). The control of flux. Symposia of the Society for Experimental Biology, 27, 65-104.
28. Lee, J. M.; Gianchandani, E. P.; Papin, J. A. (2006). Flux balance analysis in the era of metabolomics. Briefings in Bioinformatics, 7, 140-150.
29. Chang, M. C.; Keasling, J. D. (2006). Production of isoprenoid pharmaceuticals by engineered microbes. Nature Chemical Biology, 2, 674-681.
30. Palsson, B. (2006). Systems biology: properties of reconstructed networks. Cambridge University Press.
31. Delgado, J.; Liao, J. C. (1992). Metabolic control analysis from transient metabolite concentrations. Biochemical Journal, 282, 919-927.
32. Nielsen, J.; Jorgensen, H. S. (1995). Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates. Biochemical Journal, 321, 133-138.
33. Pissarra, P. N.; Nielsen, J.; Bazin, M. J. (1996). Pathway kinetics and metabolic control analysis of high yielding strain of Penicillium chrysogenum during fed-batch cultivation. Biotechnology and Bioengineering, 51, 168-176.
34. Petterson, G. (1996). Errors associated with experimental determination of enzyme flux control coefficients. Journal of Theoretical Biology, 179, 191-197.
35. Rivera, S. J. B.; Bennett, G. N.; San, K. Y. (2001). The effect of increasing NADH availability on the redistribution of metabolic fluxes in E. coli. Chemostat Cultures. Metabolic Engineering, 4, 230-237.
36. Yang, Y. T.; Bennett, G. N.; San, K. Y. (1998). Genetic and metabolic engineering. Electronic Journal of Biotechnology, 1, 3.
37. Gillespie, D. T. (1976). A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. Journal of Computational Physics, 22, 403-434.
38. Mavelli, F. (2012). Stochastic simulations of minimal cells: the Rivocell models. BMC Bioinformatics, 13, S10.
39. Carletti, T.; Filisetti, A. (2012). The stochastic evolution of a protocell: the Gillespie algorithm in a dynamically varying volume. Computational and Mathematical Methods in Medicine, 20, 423627.
40. Huang, D.; Jia, X.; Wen, J.; Wang, G.; Yu, G.; Caiyin, Q.; Chen, Y. (2011). Metabolic flux analysis and principal nodes identification for daptomycin production improvement by Streptomyces roseosporus. Applied Biochemistry and Biotechnology, 7-8, 1725-1739.
41. Schuetz, R.; Zamboni, N.; Zampieri, M.; Heinemann, M.; Sauer, U. (2012). Multidimensional optimality of microbial metabolism. Science, 6081, 601-604.
42. Ay, F.; Dang, M.; Kahveci, T. (2012). Metabolic network alignment in large scale by network compression (13): Suppl 3:S2.
43. Kern, A.; Tilley, E.; Hunter, I. S.; Legisa, M.; Glieder, A. (2007). Engineering primary metabolic pathways of industrial microorganisms. J. Biotech, 1, 6-29.
44. Orman, M. A.; Berthiaume, F.; Androulakis, I. P.; Lerapetritou, M. G. (2011). Advanced stoichiometric analysis of metabolic networks of mammalian systems. Critical Reviews in Biomedical Engineering, 6, 511-534.
45. Wahrheit, J.; Nicolae, A.; Heinzle, E. (2011). Eukaryotic metabolism: measuring compartment fluxes. Biotechnology Journal, 9, 1071-1085.
46. Nookaew, I.; Olivares-Hernandez, R.; Bhumiratana, S.; Nielsen, J. (2011). Genome-scale metabolic models of S. cerevisiae. Methods in Molecular Biology, 759, 445-463.
47. Noh, K.; Wiechert, W. (2011). The benefit of being transient: isotope-based metabolic flux analysis at the short time scale. Applied Microbiology and Biotechnology, 5, 1247-1265.
48. Price, N. D.; Kim, P. J. (2010). Macroscopic kinetic effect of cell to cell variation in biochemical reactions. Physical Review Letters, 104, 148103.
49. Kravchenko-Balasha, N.; Levitzki, A.; Goldstein, A.; Rotter, V.; Gross, A.; Remacle, R.; Levine, R. D. (2012). On the fundamental structure of gene networks in living cells. Proceedings of the National Academy of Sciences USA, 12, 4702-4707.
50. Kravchenko-Balasha, N.; LRemacle, F.; Gross, A.; Rotter, V.; Levitzki, A.; Levine, R. D. (2011). Convergence of logic of cellular regulation in different premalignant cells by an information theoretical approach. BMC Systems Biology, 5, 42.
51. Han, M. J.; Lee, S. Y.; Koh, S. T.; Noh, S. G.; Han, W. H. (2010). Biotechnological applications of microbial proteomes. Journal of Biotechnology, 4, 314-319.
52. Jensen, P.R.; Hammer, K. (1998). Artificial promoters for metabolic optimization (2-3):191-5.
53. Weeks, A. M.; Chang, M. C. (2011). Constructing de novo biosynthetic pathways for chemical synthesis inside living cells. Biochemistry, 24, 5404-5418.
54. Chemlet, J. A.; Koffas, M. A. (2008). Metabolic engineering for plant natural product biosynthesis in microbes. Current Opinion in Biotechnology, 6, 597-605.
55. Mitchell, W. (2011). Natural products from synthetic biology. (4):505-15.
56. White, N. J. (2008). Qinghaosu (Artemisinin): the price of success. Science, 18, 330-334.
57. Madduri, K.; Kennedy, J.; Rivola, G.; Inventi-Solari, A.; Fillippini, S. (1998). Production of the antitumor drug epirubicin (4′-epidoxorubicin) and its precursor by a genetically engineered strain of S. peucetius. Nature Biotechnology, 16, 69-74.
58. Nicolaou, K.C.; Yang, Z.; Liu, J.J.; Ueno, H. (1994). Total synthesis of taxol (367):630-634.
59. McDaniel, R.; Ebert-Khosla, S.; Hopwood, D. A.; Khosla, C. (1993). Engineering biosynthesis of novel polyketides. Science, 262, 1547-1550.
60. Pitera, D. J.; Paddon, C. J.; Newman, C. J.; Keasling, J. D. (2007). Balancing a heterologous mevalonate pathway for improved isoprenoid production in E. Coli. Metabolic Engineering, 9, 193-207.
61. Martin, V. J.; Pitera, D. J.; Withers, S. T.; Newman, J. D.; Keasling, J. D. (2003). Engineering a mevalonate pathway in E. coli for production of terpenoids. Nature Biotechnology, 21, 796-802.
62. Leonard, E.; Koffas, M. A. (2007). Engineering of artificial plant cytochrome P450 enzymes for synthesis of isoflavones by E. Coli. Applied and Environmental Microbiology, 73, 7246-7251.
63. Jung, W. S.; Lee, S. K.; Hong, J. S. J.; Park, S. R.; Jeong, S. J.; Han, A. R.; Sohng, J. K.; Kim, B. G.; Choi, C. Y.; Sherman, D. H. (2006). Heterologous expression of tylosin polyketide synthase and production of a hybrid bioactive macrolide in Streptomyces venezuelae. Applied Genetics and Molecular Biotechnology, 72, 763-769.
64. Lum, A. M.; Huang, J.; Hutchinson, C. R.; Kao, C. M. (2004). Reverse engineering of industrial pharmaceutical-producing actinomycete strains using DNA microarrays. Metabolic Engineering, 3, 186-196.
65. Butler, A. R.; Cundliffe, E. (2001). Influence of dimethylsulfoxide on tylosin production in Streptomyces fradiae. Journal of Industrial Microbiology and Biotechnology, 27, 46-51.
66. Shang, K.; Hu, Y.; Zhu, C.; Zhu, B. (2008). Production of 4′-epidaunorubicun by metabolic engineering of Streptomyces coeruleorubidus strain SIPI-1482. World Journal of Microbiology and Biotechnology, 24, 1107-1113.
67. Pfiefer, B. A.; Admiraal, S. J.; Gramajo, H.; Cane, D. E.; Khosla, C. (2001). Biosynthesis of complex polyketides in a metabolically engineered strain of E. coli. Science, 291, 1790-1792.
68. Vadali, R. V.; Bennett, G. N.; San, K. Y. (2004). Cofactor engineering of intracellular CoA/acetyl-CoA and its effect on metabolic flux redistribution in E. coli. Metabolic Engineering, 2, 133-139.
69. Kinoshita, S.; Nakayama, K.; Kitada, S. (1958). l-Lysine production using microbial auxotroph. J. Gen. Appl. Microbiol.
70. Dikshit, K. L.; Webster, D. A. (1988). Cloning, characterization and expression of the bacterial globin gene from Vitreoscilla in E. Coli. Gene, 70, 377-386.
71. Brabetz, W.; Liebl, W.; Schleifer, K. H. (1991). Studies on the utilization of lactose by Corynebacterium glutamicum, bearing the lactose operon of Escherichia coli. Archives of Microbiology, 155, 607-612.
72. Cameron, D. C.; Altaras, N. E.; Hoffman, M. L.; Shaw, A. J. (1998). Metabolic engineering of propanediol pathways. Biotechnology Progress, 14, 116-125.
73. Fussenegger, M.; Schlatter, S.; Datwyler, D.; Mazur, X.; Bailey, J. (1998). Controlled proliferation by multi-gene metabolic engineering enhances the productivity of Chinese hamster ovary cells. Nature Biotechnology, 16, 468-472.
74. Dunlop, M. J.; Keasling, J. D.; Mukhopadhyay, A. (2010). A model for improving microbial biofuel production using a synthetic feedback loop. Systems and Synthetic Biology, 2, 95-104.
75. Salas, J. A.; Mendez, C. (1998). Genetic manipulation of antitumor-agent biosynthesis to produce novel drugs. Trends in Biotechnology, 16, 475-482.
76. Zadran, S.; Qin, Q.; Bi, X.; Zadran, H.; Kim, Y.; Foy, M. R.; Thompson, R.; Baudry, M. (2009). 17-Beta-estradiol increases neuronal excitability through MAP kinase-induced calpain activation. Proceedings of the National Academy of Sciences of the United States of America, 106(51), 21936-21941.