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Synthetic Biology and Metabolic Engineering
Abstract
Metabolic engineering emerged 20 years ago as the discipline occupied with the directed modification of metabolic pathways for the microbial synthesis of various products. As such, it deals with the engineering (design, construction, and optimization) of native as well as non-natural routes of product synthesis, aided in this task by the availability of synthetic DNA, the core enabling technology of synthetic biology. The two fields, however, only partially overlap in their interest in pathway engineering. While fabrication of biobricks, synthetic cells, genetic circuits, and nonlinear cell dynamics, along with pathway engineering, have occupied researchers in the field of synthetic biology, the sum total of these areas does not constitute a coherent definition of synthetic biology with a distinct intellectual foundation and well-defined areas of application. This paper reviews the origins of the two fields and advances two distinct paradigms for each of them: that of unit operations for metabolic engineering and electronic circuits for synthetic biology. In this context, metabolic engineering is about engineering cell factories for the biological manufacturing of chemical and pharmaceutical products, whereas the main focus of synthetic biology is fundamental biological research facilitated by the use of synthetic DNA and genetic circuits.
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Citations
Cites
A synthetic oscillatory network of transcriptional regulators
Elowitz, M. B., & Leibler, S. (2000) · Nature · doi:10.1038/35002125 · Cited by 4,630
Construction of a genetic toggle switch in Escherichia coli
Gardner, T. S., Cantor, C. R., & Collins, J. J. (2000) · Nature · doi:10.1038/35002131 · Cited by 4,268
Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome
Gibson, D. G., Glass, J. I., Lartigue, C., Noskov, V. N., Chuang, R.-Y., Algire, M. A., Benders, G. A., Montague, M. G., Ma, L., Moodie, M. M., et al. (2010) · Science · doi:10.1126/science.1190719 · Cited by 2,638
Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli
Ajikumar, P. K., Xiao, W.-H., Tyo, K. E. J., Wang, Y., Simeon, F., Leonard, E., Mucha, O., Phon, T. H., Pfeifer, B., & Stephanopoulos, G. (2010) · Science · doi:10.1126/science.1191652 · Cited by 1,677
Self-citationFeist, A. M., Henry, C. S., Reed, J. L., Krummenacker, M., Joyce, A. R., Karp, P. D., Broadbelt, L. J., Hatzimanikatis, V., & Palsson, B. Ø. (2007) · Molecular Systems Biology · doi:10.1038/msb4100155 · Cited by 1,383
Burgard, A. P., Pharkya, P., & Maranas, C. D. (2003) · Biotechnology and Bioengineering · doi:10.1002/bit.10803 · Cited by 1,256
Toward a Science of Metabolic Engineering
Bailey, J. E. (1991) · Science · doi:10.1126/science.2047876 · Cited by 1,165
Gene Regulation at the Single-Cell Level
Rosenfeld, N., Young, J. W., Alon, U., Swain, P. S., & Elowitz, M. B. (2005) · Science · doi:10.1126/science.1106914 · Cited by 1,104
Varma, A., & Palsson, B. O. (1994) · Applied and Environmental Microbiology · doi:10.1128/aem.60.10.3724-3731.1994 · Cited by 1,051
Scaffold Proteins: Hubs for Controlling the Flow of Cellular Information
Good, M. C., Zalatan, J. G., & Lim, W. A. (2011) · Science · doi:10.1126/science.1198701 · Cited by 885
Zhang, F., Carothers, J. M., & Keasling, J. D. (2012) · Nature Biotechnology · doi:10.1038/nbt.2149 · Cited by 816
Metabolic control analysis: a survey of its theoretical and experimental development
Fell, D. A. (1992) · Biochemical Journal · doi:10.1042/bj2860313 · Cited by 782
Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’
Tamsir, A., Tabor, J. J., & Voigt, C. A. (2011) · Nature · doi:10.1038/nature09565 · Cited by 770
Schuster, S. (1999) · Trends in Biotechnology · doi:10.1016/s0167-7799(98)01290-6 · Cited by 672
Smith, H. O., Hutchison, C. A., Pfannkoch, C., & Venter, J. C. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2237126100 · Cited by 611
Network Rigidity and Metabolic Engineering in Metabolite Overproduction
Stephanopoulos, G., & Vallino, J. J. (1991) · Science · doi:10.1126/science.1904627 · Cited by 594
Self-citationMetabolic Fluxes and Metabolic Engineering
Stephanopoulos, G. (1999) · Metabolic Engineering · doi:10.1006/mben.1998.0101 · Cited by 572
Self-citationElementary metabolite units (EMU): A novel framework for modeling isotopic distributions
Antoniewicz, M. R., Kelleher, J. K., & Stephanopoulos, G. (2007) · Metabolic Engineering · doi:10.1016/j.ymben.2006.09.001 · Cited by 538
Self-citationIdentifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli
Alper, H., Jin, Y.-S., Moxley, J. F., & Stephanopoulos, G. (2005) · Metabolic Engineering · doi:10.1016/j.ymben.2004.12.003 · Cited by 450
Self-citationDetermination of confidence intervals of metabolic fluxes estimated from stable isotope measurements
Antoniewicz, M. R., Kelleher, J. K., & Stephanopoulos, G. (2006) · Metabolic Engineering · doi:10.1016/j.ymben.2006.01.004 · Cited by 449
Self-citationProduction of Complex Human Glycoproteins in Yeast
Hamilton, S. R., Bobrowicz, P., Bobrowicz, B., Davidson, R. C., Li, H., Mitchell, T., Nett, J. H., Rausch, S., Stadheim, T. A., Wischnewski, H., et al. (2003) · Science · doi:10.1126/science.1088166 · Cited by 407
A synthetic gene–metabolic oscillator
Fung, E., Wong, W. W., Suen, J. K., Bulter, T., Lee, S.-G., & Liao, J. C. (2005) · Nature · doi:10.1038/nature03508 · Cited by 382
Leonard, E., Ajikumar, P. K., Thayer, K., Xiao, W.-H., Mo, J. D., Tidor, B., Stephanopoulos, G., & Prather, K. L. J. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1006138107 · Cited by 350
Self-citationExploring the diversity of complex metabolic networks
Hatzimanikatis, V., Li, C., Ionita, J. A., Henry, C. S., Jankowski, M. D., & Broadbelt, L. J. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti213 · Cited by 349
Synthetic biology—putting engineering into biology
Heinemann, M., & Panke, S. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl469 · Cited by 343
The Theory of Oscillating Reactions - Kinetics Symposium
Higgins, J. (1967) · Industrial & Engineering Chemistry · doi:10.1021/ie50689a006 · Cited by 305
Trinh, C. T., Wlaschin, A., & Srienc, F. (2009) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-008-1770-1 · Cited by 294
Styrene biosynthesis from glucose by engineered E. coli
McKenna, R., & Nielsen, D. R. (2011) · Metabolic Engineering · doi:10.1016/j.ymben.2011.06.005 · Cited by 264
Nonlinear Differential Equations of Chemically Reacting Systems
Gavalas, G. R. (1968) · Springer Tracts in Natural Philosophy · doi:10.1007/978-3-642-87643-1 · Cited by 253
Computational tools for the synthetic design of biochemical pathways
Medema, M. H., van Raaphorst, R., Takano, E., & Breitling, R. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2717 · Cited by 226
Metabolic Engineering of Propanediol Pathways
Cameron, D. C., Altaras, N. E., Hoffman, M. L., & Shaw, A. J. (1998) · Biotechnology Progress · doi:10.1021/bp9701325 · Cited by 199
Control analysis of metabolic systems
Burns, J. A., Cornish-Bowden, A., Groen, A. K., Heinrich, R., Kacser, H., Porteous, J. W., Rapoport, S. M., Rapoport, T. A., Stucki, J. W., Tager, J. M., et al. (1985) · Trends in Biochemical Sciences · doi:10.1016/0968-0004(85)90008-8 · Cited by 185
Santos, C. N. S., Xiao, W., & Stephanopoulos, G. N. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1206346109 · Cited by 146
Self-citationBiochemical systems theory and metabolic control theory: 1. fundamental similarities and differences
Savageau, M. A., Voit, E. O., & Irvine, D. H. (1987) · Mathematical Biosciences · doi:10.1016/0025-5564(87)90007-1 · Cited by 122
Cellular and metabolic engineering
Cameron, D. C., & Tong, I.-T. (1993) · Applied Biochemistry and Biotechnology · doi:10.1007/bf02916416 · Cited by 111
Melanin-Based High-Throughput Screen for l -Tyrosine Production in Escherichia coli
Santos, C. N. S., & Stephanopoulos, G. N. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.02448-07 · Cited by 94
Self-citationSchill, N. A., van Gulik, W. M., Voisard, D., & von Stockar, U. (2000) · Biotechnology and Bioengineering · doi:10.1002/(sici)1097-0290(19960920)51:6<725::aid-bit12>3.0.co;2-c · Cited by 86
Inhibition as a Factor in the Maintenance of the Diversity of Microbial Ecosystems
Freitas, M. J. D., & Fredrickson, A. G. (1978) · Journal of General Microbiology · doi:10.1099/00221287-106-2-307 · Cited by 79
Majors, B. S., Betenbaugh, M. J., Pederson, N. E., & Chiang, G. G. (2008) · Biotechnology and Bioengineering · doi:10.1002/bit.21917 · Cited by 73
Dong, H., Tao, W., Zhang, Y., & Li, Y. (2012) · Metabolic Engineering · doi:10.1016/j.ymben.2011.10.004 · Cited by 65
A modeling framework for the study of protein glycosylation
Shelikoff, M., Sinskey, A. J., & Stephanopoulos, G. N. (1996) · Biotechnology and Bioengineering · doi:10.1002/(sici)1097-0290(19960405)50:1<73::aid-bit9>3.0.co;2-z · Cited by 60
Self-citationThe impact of synthetic biology on drug discovery
Weber, W., & Fussenegger, M. (2009) · Drug Discovery Today · doi:10.1016/j.drudis.2009.06.010 · Cited by 47
Probabilistic pathway construction
Yousofshahi, M., Lee, K., & Hassoun, S. (2011) · Metabolic Engineering · doi:10.1016/j.ymben.2011.01.006 · Cited by 40
Permeability of alginate microcapsules to secretory recombinant gene products
Awrey, D. E., Tse, M., Hortelano, G., & Chang, P. L. (1996) · Biotechnology and Bioengineering · doi:10.1002/(sici)1097-0290(19961120)52:4<485::aid-bit4>3.0.co;2-l · Cited by 40
Synthesis of biochemical production routes
Mavrovouniotis, M. L., Stephanopoulos, G., Stephanopoulos, G. N., et al. (1992) · Computers & Chemical Engineering · doi:10.1016/0098-1354(92)80071-g · Cited by 34
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Sheldon, R. A., & Woodley, J. M. (2018) · Chemical Reviews · doi:10.1021/acs.chemrev.7b00203 · Cited by 1,755
Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development
Paddon, C. J., & Keasling, J. D. (2014) · Nature Reviews Microbiology · doi:10.1038/nrmicro3240 · Cited by 675
Biocatalysis engineering: the big picture
Sheldon, R. A., & Pereira, P. C. (2017) · Chemical Society Reviews · doi:10.1039/c6cs00854b · Cited by 353
New applications of synthetic biology tools for cyanobacterial metabolic engineering
Santos-Merino, M., Singh, A. K., & Ducat, D. C. (2019) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2019.00033 · Cited by 222
Zhang, J., Kang, Z., Chen, J., & Du, G. (2015) · Scientific Reports · doi:10.1038/srep08584 · Cited by 148
Metadata
- Authors
- Stephanopoulos, G.
- Venue
- ACS Synthetic Biology
- Publisher
- American Chemical Society (ACS)
- Published
- 2012-11-01
- Volume
- 1
- Issue
- 11
- Pages
- 514-525
- ISSN
- 2161-5063 (ISSN-L)
- OpenAlex
- W2059128096
- Cited by
- 274
- References
- 45
- FWCI
- 6.62
- Type
- journal article
- Language
- en
- Open access
- closed
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