The future of metabolic engineering and synthetic biology: Towards a systematic practice

Metabolic Engineering

Volumn 14, Issue 3, 2012, Pages 233-241

  Yadav, Vikramaditya G ^a   De Mey, Marjan ^a,b   Giaw Lim, Chin ^a   Kumaran Ajikumar, Parayil ^a,c   Stephanopoulos, Gregory ^a  

^a Massachusetts Institute of Technology Cambridge   (United States)

^b GHENT UNIVERSITY   (Belgium)

^c Manus Biosynthesis   (United States)

Author keywords

Metabolic engineering; Modularization; Multivariate analysis; Natural products; Secondary metabolic pathways; Synthetic biology; Terpenoids

Indexed keywords

METABOLIC PATHWAYS; MODULARIZATIONS; MULTI VARIATE ANALYSIS; NATURAL PRODUCTS; SYNTHETIC BIOLOGY; TERPENOIDS;

BIOINFORMATICS; ESCHERICHIA COLI; METABOLISM; METABOLITES; MODULAR CONSTRUCTION;

METABOLIC ENGINEERING;

ARTICLE; BIOINFORMATICS; BIOSYNTHESIS; CATALYSIS; CELL METABOLISM; CHEMICAL REACTION; DATA ANALYSIS; ESCHERICHIA COLI; GENE SYNTHESIS; METABOLIC ENGINEERING; METABOLIC REGULATION; METABOLITE; MICROBIAL METABOLISM; MULTIVARIATE MODULAR METABOLIC ENGINEERING; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SYNTHETIC BIOLOGY;

ESCHERICHIA COLI; METABOLIC ENGINEERING; SACCHAROMYCES CEREVISIAE; SYNTHETIC BIOLOGY;

EID: 84859776222     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2012.02.001     Document Type: Article

References (53)

1. Ajikumar P.K., et al. Terpenoids: opportunities for biosynthesis of natural product drugs using engineered microorganisms. Mol. Pharm. 2008, 5:167-190.
2. Ajikumar P.K., et al. Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. Science 2010, 330:70-74.
3. Alper H., et al. Tuning genetic control through promoter engineering. PNAS 2005, 102:12678-12683.
4. Alper H., et al. Tuning genetic control through promoter engineering. Proc. Natl. Acad. Sci. USA 2005, 102:12678.
5. Alper H., et al. Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets. Nat. Biotechnol. 2005, 23:612-616.
6. Alper H., et al. Engineering yeast transcription machinery for improved ethanol tolerance and production. Science 2006, 314:1565-1568.
7. Alper H., Stephanopoulos G. Global transcription machinery engineering: a new approach for improving cellular phenotype. Metab. Eng. 2007, 9:258-267.
8. Alper H., Stephanopoulos G. Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential?. Nat. Rev. Microbiol. 2009, 7:715-723.
9. Anthony J.R., et al. Optimization of the mevalonate-based isoprenoid biosynthetic pathway in Escherichia coli for production of the anti-malarial drug precursor amorpha-4,11-diene. Metab. Eng. 2009, 11:13-19.
10. Bailey J.E., et al. Inverse metabolic engineering: a strategy for directed genetic engineering of useful phenotypes. Biotechnol. Bioeng. 1996, 52:109-121.
11. Bentley W.E., et al. Plasmid-encoded protein: the principal factor in the "metabolic burden" associated with recombinant bacteria. Biotechnol. Bioeng. 1990, 35:668-681.
12. Blazeck J., Alper H. Systems metabolic engineering: genome-scale models and beyond. Biotechnol. J. 2010, 5:647-659.
13. Bond-Watts B.B., et al. Enzyme mechanism as a kinetic control element for designing synthetic biofuel pathways. Nat. Chem. Biol. 2011, 7:222-227.
14. Chemler J.A., Koffas M.A.G. Metabolic engineering for plant natural product biosynthesis in microbes. Curr. Opin. Biotechnol. 2008, 19:597-605.
15. De Mey M., et al. Construction and model-based analysis of a promoter library for E. coli: an indispensable tool for metabolic engineering. BMC Biotechnol. 2007, 7:34.
16. Dueber J.E., et al. Synthetic protein scaffolds provide modular control over metabolic flux. Nat. Biotechnol. 2009, 27:753-759.
17. Dugar D., Stephanopoulos G. Relative potential of biosynthetic pathways for biofuels and bio-based products. Nat. Biotechnol. 2011, 29:1074-1078.
18. Farmer W.R., Liao J.C. Improving lycopene production in Escherichia coli by engineering metabolic control. Nat. Biotechnol. 2000, 18:533-537.
19. Gershenzon J., Dudareva N. The function of terpene natural products in the natural world. Nat. Chem. Biol. 2007, 3:408-414.
20. Jones C.G., Firn R.D. On the evolution of plant secondary chemical diversity. Philos. Trans. R. Soc. London B (Biol. Sci.) 1991, 333:273-280.
21. Jones K.L., et al. Low-copy plasmids can perform as well as or better than high-copy plasmids for metabolic engineering of bacteria. Metab. Eng. 2000, 2:328-338.
22. Kamm B., Kamm M. Principles of biorefineries. Appl. Microbiol. Biotechnol. 2004, 64:137-145.
23. Keasling J.D. Synthetic biology for synthetic chemistry. ACS Chem. Biol. 2008, 3:64-76.
24. Keasling J.D. Manufacturing molecules through metabolic engineering. Science 2010, 330:1355-1358.
25. Kholodenko B.N., Westerhoff H.V. Metabolic Engineering in the Post Genomic Era 2004, Horizon Bioscience, Norfolk.
26. Kirby J., Keasling J.D. Biosynthesis of plant isoprenoids: perspectives for microbial engineering. Annu. Rev. Plant Biol. 2009, 60:335-355.
27. Klein-Marcuschamer D., et al. Engineering microbial cell factories for biosynthesis of isoprenoid molecules: beyond lycopene. Trends Biotechnol. 2007, 25:417-424.
28. Lee J.Y., et al. Engineering butanol-tolerance in Escherichia coli with artificial transcription factor libraries. Biotechnol. Bioeng. 2011, 108:742-749.
29. Leonard E., et al. Combining metabolic and protein engineering of a terpenoid biosynthetic pathway for overproduction and selectivity control. Proc. Natl. Acad. Sci. USA 2010, 107:13654-13659.
30. Martin V.J.J., et al. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol. 2003, 21:796-802.
31. Martin V.J.J., et al. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol. 2003, 796-802.
32. Muntendam R., et al. Perspectives and limits of engineering the isoprenoid metabolism in heterologous hosts. Appl. Microbiol. Biotechnol. 2009, 84:1003-1019.
33. Newman J.D., et al. High-level production of amorpha-4,11-diene in a two-phase partitioning bioreactor of metabolically engineered Escherichia coli. Biotechnol. Bioeng. 2006, 95:684-691.
34. Nishizaki T., et al. Metabolic engineering of carotenoid biosynthesis in Escherichia coli by ordered gene assembly in Bacillus subtilis. Appl. Environ. Microbiol. 2007, 73:1355-1361.
35. Noack D., et al. Maintenance and genetic stability of vector plasmids pBR322 and pBR325 in Escherichia coli K12 strains grown in a chemostat. Mol. Gen. Genet. 1981, 184:121-124.
36. Park J.H., Lee S.Y. Towards systems metabolic engineering of microorganisms for amino acid production. Curr. Opin. Biotechnol. 2008, 19:454-460.
37. Pfleger B.F., et al. Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat. Biotechnol. 2006, 24:1027-1032.
38. Pitera D.J., et al. Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli. Metab. Eng. 2007, 9:193-207.
39. Salis H.M., et al. Automated design of synthetic ribosome binding sites to control protein expression. Nat. Biotechnol. 2009, 27:946-950.
40. Santos C.N.S., Stephanopoulos G. Combinatorial engineering of microbes for optimizing cellular phenotype. Curr. Opin. Chem. Biol. 2008, 12:168-176.
41. Shen C.R., et al. Driving forces enable high-titer anaerobic 1-butanol synthesis in Escherichia coli. Appl. Environ. Microbiol. 2011, 77:2905-2915.
42. Shetty R.P., et al. Engineering BioBrick vectors from BioBrick parts. J. Biol. Eng. 2008, 2.
43. Stafford D.E., Stephanopoulos G. Metabolic engineering as an integrating platform for strain development. Curr. Opin. Microbiol. 2001, 4:336-340.
44. Stephanopoulos G. Challenges in engineering microbes for biofuels production. Science 2007, 315:801.
45. Stephanopoulos G., et al. Exploiting biological complexity for strain improvement through systems biology. Nat. Biotechnol. 2004, 22:1261-1267.
46. Stephanopoulos G., Sinskey A.J. Metabolic engineering-methodologies and future prospects. Trends Biotechnol. 1993, 11:392-396.
47. Tyo K.E., et al. Stabilized gene duplication enables long-term selection-free heterologous pathway expression. Nat. Biotechnol. 2009, 27:760-765.
48. Tyo K.E., et al. Expanding the metabolic engineering toolbox: more options to engineer cells. Trends Biotechnol. 2007, 25:132-137.
49. Tyo K.E.J., et al. Toward design-based engineering of industrial microbes. Curr. Opin. Microbiol. 2010, 13:255-262.
50. Wang H.H., et al. Programming cells by multiplex genome engineering and accelerated evolution. Nature 2009, 460:894-898.
51. Yadav V.G., Stephanopoulos G. Reevaluating synthesis by biology. Curr. Opin. Microbiol. 2010, 13:371-376.
52. Yoon S.H., et al. Combinatorial expression of bacterial whole mevalonate pathway for the production of beta-carotene in E. coli. J. Biotechnol. 2009, 140:218-226.
53. Yuan L.Z., et al. Chromosomal promoter replacement of the isoprenoid pathway for enhancing carotenoid production in E. coli. Metab. Eng. 2006, 8:79-90.