Metabolic Engineering 12

Systems Metabolic Engineering for Superior Bio-Production

The Westin Grand Munich, Munich, Germany

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Dynamic metabolic engineering harnessing synthetic biological tools and metabolomic analysis

◯ Yuki Soma1,2, Yuri Fujiwara1, Kohsuke Hata1,2, Yoshihiro Izumi1,2, Takeshi Bamba1,2, Taizo Hanai2

1 1Division of Metabolomics, Research Center for Transomics Medicine, Medical institute of Bioregulation (MiB), Kyushu University,

2 Laboratory for Bioinformatics, Graduate School of Systems Lifesciences, Kyushu University

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Supplementary Information

Materials and methods

Construction of metabolic toggle switches

• pZ vectors

• MTS

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Construction of Calibration-Curve-Locking Database

• Agilent G1676AA Fiehn GC/MS Metabolomics RTL Library Method

• Agilent DFTPP tuning method

• EPA Method 625

• ​GL sciences Metabolomcis standard mixture

• ​NIST SRM 1950, Metabolites in Human Plasma

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References

 Dynamic Metabolic Engineering, Reviews

1. Holtz, W. J., & Keasling, J. D. (2010). Engineering static and dynamic control of synthetic pathways. Cell, 140(1), 19-23.

2. Venayak, N., Anesiadis, N., Cluett, W. R., & Mahadevan, R. (2015). Engineering metabolism through dynamic control. Current opinion in biotechnology, 34, 142-152.

3. Brockman, I. M., & Prather, K. L. (2015). Dynamic metabolic engineering: new strategies for developing responsive cell factories. Biotechnology journal, 10(9), 1360-1369.

4. Xu, P. (2018). Production of chemicals using dynamic control of metabolic fluxes. Current opinion in biotechnology, 53, 12-19

5. Qian, S., & Cirino, P. C. (2016). Using metabolite-responsive gene regulators to improve microbial biosynthesis. Current Opinion in Chemical Engineering, 14, 93-102.

6. Lalwani, M. A., Zhao, E. M., & Avalos, J. L. (2018). Current and future modalities of dynamic control in metabolic engineering. Current opinion in biotechnology, 52, 56-65.

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 Dynamic Metabolic Engineering, Research Papers

1. Farmer, W. R., & Liao, J. C. (2000). Improving lycopene production in Escherichia coli by engineering metabolic control. Nature biotechnology, 18(5), 533.

2. Zhang, F., Carothers, J. M., & Keasling, J. D. (2012). Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nature biotechnology, 30(4), 354.

3. Solomon, K. V., Sanders, T. M., & Prather, K. L. (2012). A dynamic metabolite valve for the control of central carbon metabolism. Metabolic engineering, 14(6), 661-671.

4. Chou, H. H., & Keasling, J. D. (2013). Programming adaptive control to evolve increased metabolite production. Nature communications, 4, 2595.

5. Torella, J. P., Ford, T. J., Kim, S. N., Chen, A. M., Way, J. C., & Silver, P. A. (2013). Tailored fatty acid synthesis via dynamic control of fatty acid elongation. Proceedings of the National Academy of Sciences, 110(28), 11290-11295.

6. Soma, Y., Tsuruno, K., Wada, M., Yokota, A., & Hanai, T. (2014). Metabolic flux redirection from a central metabolic pathway toward a synthetic pathway using a metabolic toggle switch. Metabolic engineering, 23, 175-184.

7. Xu, P., Li, L., Zhang, F., Stephanopoulos, G., & Koffas, M. (2014). Improving fatty acids production by engineering dynamic pathway regulation and metabolic control. Proceedings of the National Academy of Sciences, 111(31), 11299-11304.

8. Soma, Y., & Hanai, T. (2015). Self-induced metabolic state switching by a tunable cell density sensor for microbial isopropanol production. Metabolic engineering, 30, 7-15.

9. Brockman, I. M., & Prather, K. L. (2015). Dynamic knockdown of E. coli central metabolism for redirecting fluxes of primary metabolites. Metabolic engineering, 28, 104-113.

10. Soma, Y., Yamaji, T., Matsuda, F., & Hanai, T. (2017). Synthetic metabolic bypass for a metabolic toggle switch enhances acetyl-CoA supply for isopropanol production by Escherichia coli. Journal of bioscience and bioengineering, 123(5), 625-633.

11. Soma, Y., Fujiwara, Y., Nakagawa, T., Tsuruno, K., & Hanai, T. (2017). Reconstruction of a metabolic regulatory network in Escherichia coli for purposeful switching from cell growth mode to production mode in direct GABA fermentation from glucose. Metabolic engineering, 43, 54-63.

12. Pandit, A. V., Srinivasan, S., & Mahadevan, R. (2017). Redesigning metabolism based on orthogonality principles. Nature communications, 8, 15188.

13. Gupta, A., Reizman, I. M. B., Reisch, C. R., & Prather, K. L. (2017). Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit. Nature biotechnology, 35(3), 273.

14. Bothfeld, W., Kapov, G., & Tyo, K. E. (2017). A glucose-sensing toggle switch for autonomous, high productivity genetic control. ACS synthetic biology, 6(7), 1296-1304.

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 Other information: coming soon