Khanijou, J. K., Hee, Y. T., Scipion, C. P. M., Chen, X., & Selvarajoo, K. (2024). Systems biology approach for enhancing limonene yield by re-engineering Escherichia coli. Npj Systems Biology and Applications, 10(1). https://doi.org/10.1038/s41540-024-00440-7
Abstract:
Engineered microorganisms have emerged as viable alternatives for limonene production. However, issues such as low enzyme abundance or activities, and regulatory feedback/forward inhibition may reduce yields. To understand the underlying metabolism, we adopted a systems biology approach for an engineered limonene producing Escherichia coli strain K-12 MG1655. Firstly, we generated time-series metabolomics data and, secondly, developed a dynamic model based on enzyme dynamics to track the native metabolic networks and the engineered mevalonate pathway. After several iterations of model fitting with experimental profiles, which also included 13C tracer studies, we performed in silico knockouts (KOs) of all enzymes to identify bottleneck(s) for optimal limonene yields. The simulations indicated that ALDH/ADH (aldehyde dehydrogenase/alcohol dehydrogenase) and LDH (lactate dehydrogenase) suppression, and HK (hexokinase) enhancement would increase limonene yields. Experimental confirmation was achieved, where ALDH-ADH and LDH KOs, and HK overexpression improved limonene yield by 8- to 11-folds. Our systems biology approach can guide microbial strain re-engineering for optimal target production.
License type:
Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)
Funding Info:
This research / project is supported by the National Research Foundation - Intra-create Thematic Grant “Cities”
Grant Reference no. : NRF2019-THE001-0007