Team:NUS Singapore-A/Results
CONNECT WITH US
Not content with simple fermentation to produce our target compounds, we sought to address the gaps in current biomanufacturing and incorporated various features into Coup Dy'état. Our system was designed with three main principles in mind: commercial viability, eco-friendliness, and emerging technology adoption (Figure 1).
In our project, we set out to demonstrate the possibility of converting waste to dyes in E. coli via dynamic and stress regulation, achieved using computer-assisted optogenetic control. The illustration below encapsulates how all the features are integrated together to complete the bioproduction process.
The various parts of our system are designed to be modular; they can be incorporated into another system and be expected to work. With the advent of more biomanufacturing technologies, additional features can be assimilated seamlessly. Coup Dy'état is thus a technological platform where microbial production of any chemicals can be optimized.
With Coup Dy'état, we hope to set the standard for biomanufacturing.
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References
[1] Goodacre, D. (2018). Faking Flavours. Lateral Magazine, Physical Science (28). Retrieved from http://www.lateralmag.com/articles/issue-28/faking-flavours
[2] Geddes, C. C., Nieves, I. U., & Ingram, L. O. (2011). Advances in ethanol production. Current opinion in biotechnology, 22(3), 312-319.
[3] World Wildlife Fund. (2015). Sugarcane Farming's Toll on the Environment. World Wildlife Magazine, Summer 2015. Retrieved from https://www.worldwildlife.org/magazine/issues/summer-2015/articles/sugarcane-farming-s-toll-on-the-environment
[4] Sudiyani, Y., Styarini, D., Triwahyuni, E., Sembiring, K. C., Aristiawan, Y., Abimanyu, H., & Han, M. H. (2013). Utilization of biomass waste empty fruit bunch fiber of palm oil for bioethanol production using pilot–scale unit. Energy Procedia, 32, 31-38.
[5] Sievert, C., Nieves, L. M., Panyon, L. A., Loeffler, T., Morris, C., Cartwright, R. A., & Wang, X. (2017). Experimental evolution reveals an effective avenue to release catabolite repression via mutations in XylR. Proceedings of the National Academy of Sciences, 114(28), 7349-7354.
[6] Zhang, W., Liu, H., Li, X., Liu, D., Dong, X. T., Li, F. F., ... & Yuan, Y. J. (2017). Production of naringenin from D‐xylose with co‐culture of E. coli and S. cerevisiae. Engineering in Life Sciences, 17(9), 1021-1029.
[7] Marín, L., Gutiérrez-del-Río, I., Yagüe, P., Manteca, Á., Villar, C. J., & Lombó, F. (2017). De novo biosynthesis of apigenin, luteolin, and eriodictyol in the actinomycete Streptomyces albus and production improvement by feeding and spore conditioning. Frontiers in microbiology, 8, 921.
[8] Ganesan, V., Li, Z., Wang, X., & Zhang, H. (2017). Heterologous biosynthesis of natural product naringenin by co-culture engineering. Synthetic and systems biotechnology, 2(3), 236-242.
[9] Yeong, C. J. (2012). Discovery and development of novel anti-microbial therapeutics (Doctoral dissertation).
[10] Grovier, K. (2018). The murky history of the colour yellow. BBC. Retrieved from http://www.bbc.com/culture/story/20180906-did-animal-cruelty-create-indian-yellow
[11] Vorkamp, K. (2016). An overlooked environmental issue? A review of the inadvertent formation of PCB-11 and other PCB congeners and their occurrence in consumer products and in the environment. Science of the Total Environment, 541, 1463-1476.
[12] Singh, H. B., & Kumar, A. B. (2014). Handbook of natural dyes and pigments. Woodhead Publishing India Pvt Limited.
[13] Marín, L., Gutiérrez-del-Río, I., Yagüe, P., Manteca, Á., Villar, C. J., & Lombó, F. (2017). De novo biosynthesis of apigenin, luteolin, and eriodictyol in the actinomycete Streptomyces albus and production improvement by feeding and spore conditioning. Frontiers in microbiology, 8, 921.
[14] Lopez, P. J., Marchand, I., Joyce, S. A., & Dreyfus, M. (1999). The C‐terminal half of RNase E, which organizes the Escherichia coli degradosome, participates in mRNA degradation but not rRNA processing in vivo. Molecular microbiology, 33(1), 188-199.
[15] Leonard, E., Yan, Y., Fowler, Z. L., Li, Z., Lim, C. G., Lim, K. H., & Koffas, M. A. (2008). Strain improvement of recombinant Escherichia coli for efficient production of plant flavonoids. Molecular pharmaceutics, 5(2), 257-265.
[16] Zuo, J., & Chua, N. (2000). Chemical-inducible systems for regulated expression of plant genes. Current Opinion In Biotechnology, 11(2), 146-151.
[17] Dvorak, P., Chrast, L., Nikel, P. I., Fedr, R., Soucek, K., Sedlackova, M., . . . Damborsky, J. (2015). Exacerbation of substrate toxicity by IPTG in escherichia coli BL21(DE3) carrying a synthetic metabolic pathway. Microbial Cell Factories, 14(1), 201-201.
18] Politi, N., Pasotti, L., Zucca, S., Casanova, M., Micoli, G., Cusella De Angelis, Maria Gabriella, & Magni, P. (2014). Half-life measurements of chemical inducers for recombinant gene expression. Journal of Biological Engineering, 8(1), 5-5.
[19] Tischer, D., & Weiner, O. D. (2014). Illuminating cell signalling with optogenetic tools. Nature Reviews. Molecular Cell Biology, 15(8), 551-558.
[20] Zhang, K., & Cui, B. (2015). Optogenetic control of intracellular signaling pathways. Trends in biotechnology, 33(2), 92-100.
[21] Jayaraman, P., Devarajan, K., Chua, T. K., Zhang, H., Gunawan, E., & Poh, C. L. (2016). Blue light-mediated transcriptional activation and repression of gene expression in bacteria. Nucleic acids research, 44(14), 6994-7005.
[22] Zhao, E. M., Zhang, Y., Mehl, J., Park, H., Lalwani, M. A., Toettcher, J. E., & Avalos, J. L. (2018). Optogenetic regulation of engineered cellular metabolism for microbial chemical production. Nature, 555(7698), 683.
[23] Henzler, H. J., Schügerl, K., Kretzmer, G., Kieran, P. M., MacLoughlin, P. F., Malone, D. M., ... & Yim, S. S. (Eds.). (2000). Influence of stress on cell growth and product formation (Vol. 67). Springer Science & Business Media.
[24] Gasser, B., Saloheimo, M., Rinas, U., Dragosits, M., Rodríguez-Carmona, E., Baumann, K., ... & Porro, D. (2008). Protein folding and conformational stress in microbial cells producing recombinant proteins: a host comparative overview. Microbial cell factories, 7(1), 11.
[25] Ceroni, F., Boo, A., Furini, S., Gorochowski, T. E., Borkowski, O., Ladak, Y. N., ... & Ellis, T. (2018). Burden-driven feedback control of gene expression. Nature methods, 15(5), 387.
[26] 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.
[27] Lo, T. M., Chng, S. H., Teo, W. S., Cho, H. S., & Chang, M. W. (2016). A two-layer gene circuit for decoupling cell growth from metabolite production. Cell systems, 3(2), 133-143.
[28] Milias-Argeitis, A., Rullan, M., Aoki, S. K., Buchmann, P., & Khammash, M. (2016). Automated optogenetic feedback control for precise and robust regulation of gene expression and cell growth. Nature communications, 7, 12546.
[29] Chen, S., Harrigan, P., Heineike, B., Stewart-Ornstein, J., & El-Samad, H. (2013). Building robust functionality in synthetic circuits using engineered feedback regulation. Current opinion in biotechnology, 24(4), 790-796.
[2] Geddes, C. C., Nieves, I. U., & Ingram, L. O. (2011). Advances in ethanol production. Current opinion in biotechnology, 22(3), 312-319.
[3] World Wildlife Fund. (2015). Sugarcane Farming's Toll on the Environment. World Wildlife Magazine, Summer 2015. Retrieved from https://www.worldwildlife.org/magazine/issues/summer-2015/articles/sugarcane-farming-s-toll-on-the-environment
[4] Sudiyani, Y., Styarini, D., Triwahyuni, E., Sembiring, K. C., Aristiawan, Y., Abimanyu, H., & Han, M. H. (2013). Utilization of biomass waste empty fruit bunch fiber of palm oil for bioethanol production using pilot–scale unit. Energy Procedia, 32, 31-38.
[5] Sievert, C., Nieves, L. M., Panyon, L. A., Loeffler, T., Morris, C., Cartwright, R. A., & Wang, X. (2017). Experimental evolution reveals an effective avenue to release catabolite repression via mutations in XylR. Proceedings of the National Academy of Sciences, 114(28), 7349-7354.
[6] Zhang, W., Liu, H., Li, X., Liu, D., Dong, X. T., Li, F. F., ... & Yuan, Y. J. (2017). Production of naringenin from D‐xylose with co‐culture of E. coli and S. cerevisiae. Engineering in Life Sciences, 17(9), 1021-1029.
[7] Marín, L., Gutiérrez-del-Río, I., Yagüe, P., Manteca, Á., Villar, C. J., & Lombó, F. (2017). De novo biosynthesis of apigenin, luteolin, and eriodictyol in the actinomycete Streptomyces albus and production improvement by feeding and spore conditioning. Frontiers in microbiology, 8, 921.
[8] Ganesan, V., Li, Z., Wang, X., & Zhang, H. (2017). Heterologous biosynthesis of natural product naringenin by co-culture engineering. Synthetic and systems biotechnology, 2(3), 236-242.
[9] Yeong, C. J. (2012). Discovery and development of novel anti-microbial therapeutics (Doctoral dissertation).
[10] Grovier, K. (2018). The murky history of the colour yellow. BBC. Retrieved from http://www.bbc.com/culture/story/20180906-did-animal-cruelty-create-indian-yellow
[11] Vorkamp, K. (2016). An overlooked environmental issue? A review of the inadvertent formation of PCB-11 and other PCB congeners and their occurrence in consumer products and in the environment. Science of the Total Environment, 541, 1463-1476.
[12] Singh, H. B., & Kumar, A. B. (2014). Handbook of natural dyes and pigments. Woodhead Publishing India Pvt Limited.
[13] Marín, L., Gutiérrez-del-Río, I., Yagüe, P., Manteca, Á., Villar, C. J., & Lombó, F. (2017). De novo biosynthesis of apigenin, luteolin, and eriodictyol in the actinomycete Streptomyces albus and production improvement by feeding and spore conditioning. Frontiers in microbiology, 8, 921.
[14] Lopez, P. J., Marchand, I., Joyce, S. A., & Dreyfus, M. (1999). The C‐terminal half of RNase E, which organizes the Escherichia coli degradosome, participates in mRNA degradation but not rRNA processing in vivo. Molecular microbiology, 33(1), 188-199.
[15] Leonard, E., Yan, Y., Fowler, Z. L., Li, Z., Lim, C. G., Lim, K. H., & Koffas, M. A. (2008). Strain improvement of recombinant Escherichia coli for efficient production of plant flavonoids. Molecular pharmaceutics, 5(2), 257-265.
[16] Zuo, J., & Chua, N. (2000). Chemical-inducible systems for regulated expression of plant genes. Current Opinion In Biotechnology, 11(2), 146-151.
[17] Dvorak, P., Chrast, L., Nikel, P. I., Fedr, R., Soucek, K., Sedlackova, M., . . . Damborsky, J. (2015). Exacerbation of substrate toxicity by IPTG in escherichia coli BL21(DE3) carrying a synthetic metabolic pathway. Microbial Cell Factories, 14(1), 201-201.
18] Politi, N., Pasotti, L., Zucca, S., Casanova, M., Micoli, G., Cusella De Angelis, Maria Gabriella, & Magni, P. (2014). Half-life measurements of chemical inducers for recombinant gene expression. Journal of Biological Engineering, 8(1), 5-5.
[19] Tischer, D., & Weiner, O. D. (2014). Illuminating cell signalling with optogenetic tools. Nature Reviews. Molecular Cell Biology, 15(8), 551-558.
[20] Zhang, K., & Cui, B. (2015). Optogenetic control of intracellular signaling pathways. Trends in biotechnology, 33(2), 92-100.
[21] Jayaraman, P., Devarajan, K., Chua, T. K., Zhang, H., Gunawan, E., & Poh, C. L. (2016). Blue light-mediated transcriptional activation and repression of gene expression in bacteria. Nucleic acids research, 44(14), 6994-7005.
[22] Zhao, E. M., Zhang, Y., Mehl, J., Park, H., Lalwani, M. A., Toettcher, J. E., & Avalos, J. L. (2018). Optogenetic regulation of engineered cellular metabolism for microbial chemical production. Nature, 555(7698), 683.
[23] Henzler, H. J., Schügerl, K., Kretzmer, G., Kieran, P. M., MacLoughlin, P. F., Malone, D. M., ... & Yim, S. S. (Eds.). (2000). Influence of stress on cell growth and product formation (Vol. 67). Springer Science & Business Media.
[24] Gasser, B., Saloheimo, M., Rinas, U., Dragosits, M., Rodríguez-Carmona, E., Baumann, K., ... & Porro, D. (2008). Protein folding and conformational stress in microbial cells producing recombinant proteins: a host comparative overview. Microbial cell factories, 7(1), 11.
[25] Ceroni, F., Boo, A., Furini, S., Gorochowski, T. E., Borkowski, O., Ladak, Y. N., ... & Ellis, T. (2018). Burden-driven feedback control of gene expression. Nature methods, 15(5), 387.
[26] 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.
[27] Lo, T. M., Chng, S. H., Teo, W. S., Cho, H. S., & Chang, M. W. (2016). A two-layer gene circuit for decoupling cell growth from metabolite production. Cell systems, 3(2), 133-143.
[28] Milias-Argeitis, A., Rullan, M., Aoki, S. K., Buchmann, P., & Khammash, M. (2016). Automated optogenetic feedback control for precise and robust regulation of gene expression and cell growth. Nature communications, 7, 12546.
[29] Chen, S., Harrigan, P., Heineike, B., Stewart-Ornstein, J., & El-Samad, H. (2013). Building robust functionality in synthetic circuits using engineered feedback regulation. Current opinion in biotechnology, 24(4), 790-796.
HEAR OUR STORY
We’re using synthetic biology to change the way the world thinks and functions.
We’re a little disruptive, dangerous and maybe a tad too bold. But the world needs some shaking up every now and then, and we think we’re just the right people for that.
Together we’re going to engineer biology and create something awesome.
CONTACT US
nusigem@gmail.com21 Lower Kent Ridge Rd, Singapore 119077