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ePathBrick: A Synthetic Biology Platform for Engineering Metabolic Pathways in E. coli
Abstract
Harnessing cell factories for producing biofuel and pharmaceutical molecules has stimulated efforts to develop novel synthetic biology tools customized for modular pathway engineering and optimization. Here we report the development of a set of vectors compatible with BioBrick standards and its application in metabolic engineering. The engineered ePathBrick vectors comprise four compatible restriction enzyme sites allocated on strategic positions so that different regulatory control signals can be reused and manipulation of expression cassette can be streamlined. Specifically, these vectors allow for fine-tuning gene expression by integrating multiple transcriptional activation or repression signals into the operator region. At the same time, ePathBrick vectors support the modular assembly of pathway components and combinatorial generation of pathway diversities with three distinct configurations. We also demonstrated the functionality of a seven-gene pathway (~9 Kb) assembled on one single ePathBrick vector. The ePathBrick vectors presented here provide a versatile platform for rapid design and optimization of metabolic pathways in E. coli.
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Cites
Enzymatic assembly of DNA molecules up to several hundred kilobases
Gibson, D. G., Young, L., Chuang, R.-Y., Venter, J. C., Hutchison, C. A., & Smith, H. O. (2009) · Nature Methods · doi:10.1038/nmeth.1318 · Cited by 9,996
Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels
Atsumi, S., Hanai, T., & Liao, J. C. (2008) · Nature · doi:10.1038/nature06450 · Cited by 1,945
Automated design of synthetic ribosome binding sites to control protein expression
Salis, H. M., Mirsky, E. A., & Voigt, C. A. (2009) · Nature Biotechnology · doi:10.1038/nbt.1568 · Cited by 1,844
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
Synthetic protein scaffolds provide modular control over metabolic flux
Dueber, J. E., Wu, G. C., Malmirchegini, G. R., Moon, T. S., Petzold, C. J., Ullal, A. V., Prather, K. L. J., & Keasling, J. D. (2009) · Nature Biotechnology · doi:10.1038/nbt.1557 · Cited by 1,242
Synthetic biology: new engineering rules for an emerging discipline
Andrianantoandro, E., Basu, S., Karig, D. K., & Weiss, R. (2006) · Molecular Systems Biology · doi:10.1038/msb4100073 · Cited by 1,081
Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC
Li, M. Z., & Elledge, S. J. (2007) · Nature Methods · doi:10.1038/nmeth1010 · Cited by 953
Tuning genetic control through promoter engineering
Alper, H., Fischer, C., Nevoigt, E., & Stephanopoulos, G. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504604102 · Cited by 893
Engineering BioBrick vectors from BioBrick parts
Shetty, R. P., Endy, D., & Knight, T. F. (2008) · Journal of Biological Engineering · doi:10.1186/1754-1611-2-5 · Cited by 760
Refinement and standardization of synthetic biological parts and devices
Canton, B., Labno, A., & Endy, D. (2008) · Nature Biotechnology · doi:10.1038/nbt1413 · Cited by 753
An engineered microbial platform for direct biofuel production from brown macroalgae
Wargacki, A. J., Leonard, E., Win, M. N., Regitsky, D. D., Santos, C. N. S., Kim, P. B., Cooper, S. R., Raisner, R. M., Herman, A., Sivitz, A. B., et al. (2012) · Science · doi:10.1126/science.1214547 · Cited by 734
Westfall, P. J., Pitera, D. J., Lenihan, J. R., Eng, D., Woolard, F. X., Regentin, R., Horning, T., Tsuruta, H., Melis, D. J., Owens, A., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1110740109 · Cited by 722
DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways
Shao, Z., Zhao, H., & Zhao, H. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn991 · Cited by 678
Identification and microbial production of a terpene-based advanced biofuel
Peralta-Yahya, P. P., Ouellet, M., Chan, R., Mukhopadhyay, A., Keasling, J. D., & Lee, T. S. (2011) · Nature Communications · doi:10.1038/ncomms1494 · Cited by 637
Driving Forces Enable High-Titer Anaerobic 1-Butanol Synthesis in Escherichia coli
Shen, C. R., Lan, E. I., Dekishima, Y., Baez, A., Cho, K. M., & Liao, J. C. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.03034-10 · Cited by 623
Davis, M. S., Solbiati, J., & Cronan, J. E. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m004756200 · Cited by 479
BglBrick vectors and datasheets: A synthetic biology platform for gene expression
Lee, T. S., Krupa, R. A., Zhang, F., Hajimorad, M., Holtz, W. J., Prasad, N., Lee, S. K., & Keasling, J. D. (2011) · Journal of Biological Engineering · doi:10.1186/1754-1611-5-12 · Cited by 476
BglBricks: A flexible standard for biological part assembly
Anderson, J. C., Dueber, J. E., Leguia, M., Wu, G. C., Goler, J. A., Arkin, A. P., & Keasling, J. D. (2010) · Journal of Biological Engineering · doi:10.1186/1754-1611-4-1 · Cited by 429
Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology
Wang, B., Kitney, R. I., Joly, N., & Buck, M. (2011) · Nature Communications · doi:10.1038/ncomms1516 · Cited by 425
Zhou, Y. J., Gao, W., Rong, Q., Jin, G., Chu, H., Liu, W., Yang, W., Zhu, Z., Li, G., Zhu, G., et al. (2012) · Journal of the American Chemical Society · doi:10.1021/ja2114486 · Cited by 401
Idempotent Vector Design for Standard Assembly of Biobricks
Knight, T. (2003) · doi:10.21236/ada457791 · Cited by 388
Engineering alternative butanol production platforms in heterologous bacteria
Nielsen, D. R., Leonard, E., Yoon, S.-H., Tseng, H.-C., Yuan, C., & Prather, K. L. J. (2009) · Metabolic Engineering · doi:10.1016/j.ymben.2009.05.003 · Cited by 373
Tsuruta, H., Paddon, C. J., Eng, D., Lenihan, J. R., Horning, T., Anthony, L. C., Regentin, R., Keasling, J. D., Renninger, N. S., & Newman, J. D. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004489 · Cited by 363
Programming gene expression with combinatorial promoters
Cox, R. S., Surette, M. G., & Elowitz, M. B. (2007) · Molecular Systems Biology · doi:10.1038/msb4100187 · Cited by 363
Bokinsky, G., Peralta-Yahya, P. P., George, A., Holmes, B. M., Steen, E. J., Dietrich, J., Soon Lee, T., Tullman-Ercek, D., Voigt, C. A., Simmons, B. A., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1106958108 · Cited by 361
Xu, P., Ranganathan, S., Fowler, Z. L., Maranas, C. D., & Koffas, M. A. G. (2011) · Metabolic Engineering · doi:10.1016/j.ymben.2011.06.008 · Cited by 346
Self-citationThe future of metabolic engineering and synthetic biology: Towards a systematic practice
Yadav, V. G., De Mey, M., Giaw Lim, C., Kumaran Ajikumar, P., & Stephanopoulos, G. (2012) · Metabolic Engineering · doi:10.1016/j.ymben.2012.02.001 · Cited by 322
Tuning Gene Expression in Yarrowia lipolytica by a Hybrid Promoter Approach
Blazeck, J., Liu, L., Redden, H., & Alper, H. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.05763-11 · Cited by 318
Promoter library designed for fine-tuned gene expression in Pichia pastoris
Hartner, F. S., Ruth, C., Langenegger, D., Johnson, S. N., Hyka, P., Lin-Cereghino, G. P., Lin-Cereghino, J., Kovar, K., Cregg, J. M., & Glieder, A. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn369 · Cited by 310
DNA assembly for synthetic biology: from parts to pathways and beyond
Ellis, T., Adie, T., & Baldwin, G. S. (2011) · Integrative Biology · doi:10.1039/c0ib00070a · Cited by 305
Anthony, J. R., Anthony, L. C., Nowroozi, F., Kwon, G., Newman, J. D., & Keasling, J. D. (2009) · Metabolic Engineering · doi:10.1016/j.ymben.2008.07.007 · Cited by 292
Modular Engineering of l -Tyrosine Production in Escherichia coli
Juminaga, D., Baidoo, E. E. K., Redding-Johanson, A. M., Batth, T. S., Burd, H., Mukhopadhyay, A., Petzold, C. J., & Keasling, J. D. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.06017-11 · Cited by 273
High-Yield Resveratrol Production in Engineered Escherichia coli
Lim, C. G., Fowler, Z. L., Hueller, T., Schaffer, S., & Koffas, M. A. G. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.02186-10 · Cited by 269
Self-citationImproving cellular malonyl-CoA level in Escherichia coli via metabolic engineering
Zha, W., Rubin-Pitel, S. B., Shao, Z., & Zhao, H. (2009) · Metabolic Engineering · doi:10.1016/j.ymben.2009.01.005 · Cited by 263
Engineering Central Metabolic Pathways for High-Level Flavonoid Production in Escherichia coli
Leonard, E., Lim, K.-H., Saw, P.-N., & Koffas, M. A. G. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.00200-07 · Cited by 262
Self-citationStrategies for protein coexpression in Escherichia coli
Tolia, N. H., & Joshua‐Tor, L. (2005) · Nature Methods · doi:10.1038/nmeth0106-55 · Cited by 246
Combinatorial transcriptional control of the lactose operon of Escherichia coli
Kuhlman, T., Zhang, Z., Saier, M. H., & Hwa, T. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0606717104 · Cited by 240
Fundamental relationship between operon organization and gene expression
Lim, H. N., Lee, Y., & Hussein, R. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1105692108 · Cited by 214
Morrone, D., Lowry, L., Determan, M. K., Hershey, D. M., Xu, M., & Peters, R. J. (2010) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-009-2219-x · Cited by 211
Michener, J. K., Thodey, K., Liang, J. C., & Smolke, C. D. (2011) · Metabolic Engineering · doi:10.1016/j.ymben.2011.09.004 · Cited by 147
Parts plus pipes: Synthetic biology approaches to metabolic engineering
Boyle, P. M., & Silver, P. A. (2011) · Metabolic Engineering · doi:10.1016/j.ymben.2011.10.003 · Cited by 131
Tseng, H.-C., Martin, C. H., Nielsen, D. R., & Prather, K. L. J. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.02667-08 · Cited by 120
Structural basis of lipid biosynthesis regulation in Gram‐positive bacteria
Schujman, G. E., Guerin, M. E., Buschiazzo, A., Schaeffer, F., Llarrull, L. I., Reh, G., Vila, A. J., Alzari, P. M., & de Mendoza, D. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7601284 · Cited by 118
Reiterative Recombination for the in vivo assembly of libraries of multigene pathways
Wingler, L. M., & Cornish, V. W. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1100507108 · Cited by 111
Nawabi, P., Bauer, Š., Kyrpides, N. C., & Lykidis, A. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.05046-11 · Cited by 106
Rapid characterization and engineering of natural product biosynthetic pathways via DNA assembler
Shao, Z., Luo, Y., & Zhao, H. (2011) · Molecular BioSystems · doi:10.1039/c0mb00338g · Cited by 90
Optimized compatible set of BioBrick™ vectors for metabolic pathway engineering
Vick, J. E., Johnson, E. T., Choudhary, S., Bloch, S. E., López‐Gallego, F., Srivastava, P., Tikh, I. B., Wawrzyn, G. T., & Schmidt‐Dannert, C. (2011) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-011-3633-4 · Cited by 64
Okuda, S., Kawashima, S., Kobayashi, K., Ogasawara, N., Kanehisa, M. I., & Goto, S. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-48 · Cited by 59
Re-engineering multicloning sites for function and convenience
Crook, N., Freeman, E. S., & Alper, H. S. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr346 · Cited by 47
Metabolic engineering ofEscherichia colifor biofuel production
Xu, P., & Koffas, M. A. G. (2010) · Biofuels · doi:10.4155/bfs.10.13 · Cited by 37
Self-citationKrøll, J., Steinle, A., Reichelt, R., Ewering, C., & Steinbüchel, A. (2009) · Metabolic Engineering · doi:10.1016/j.ymben.2009.01.007 · Cited by 34
Norville, J. E., Derda, R., Gupta, S., Drinkwater, K. A., Belcher, A. M., Leschziner, A. E., & Knight, T. F. (2010) · Journal of Biological Engineering · doi:10.1186/1754-1611-4-17 · Cited by 29
Construction of a genetic AND gate under a new standard for assembly of genetic parts
Ayukawa, S., Kobayashi, A., Nakashima, Y., Takagi, H., Hamada, S., Uchiyama, M., Yugi, K., Murata, S., Sakakibara, Y., Hagiya, M., et al. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-s4-s16 · Cited by 22
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Metadata
- Authors
- Xu, P., Vansiri, A., Bhan, N., & Koffas, M. A. G.
- Venue
- ACS Synthetic Biology
- Publisher
- American Chemical Society (ACS)
- Published
- 2012-05-04
- Volume
- 1
- Issue
- 7
- Pages
- 256-266
- ISSN
- 2161-5063 (ISSN-L)
- OpenAlex
- W2037630877
- Cited by
- 255
- References
- 53
- FWCI
- 6.27
- Type
- journal article
- Language
- en
- Open access
- closed
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