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Distributing a metabolic pathway among a microbial consortium enhances production of natural products

Nature Biotechnology volume 33, pages 377–383 (2015)Cite this article

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Abstract

Metabolic engineering of microorganisms such as Escherichia coli and Saccharomyces cerevisiae to produce high-value natural metabolites is often done through functional reconstitution of long metabolic pathways. Problems arise when parts of pathways require specialized environments or compartments for optimal function. Here we solve this problem through co-culture of engineered organisms, each of which contains the part of the pathway that it is best suited to hosting. In one example, we divided the synthetic pathway for the acetylated diol paclitaxel precursor into two modules, expressed in either S. cerevisiae or E. coli, neither of which can produce the paclitaxel precursor on their own. Stable co-culture in the same bioreactor was achieved by designing a mutualistic relationship between the two species in which a metabolic intermediate produced by E. coli was used and functionalized by yeast. This synthetic consortium produced 33 mg/L oxygenated taxanes, including a monoacetylated dioxygenated taxane. The same method was also used to produce tanshinone precursors and functionalized sesquiterpenes.

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Figure 1: A competitive E. coli–S. cerevisiae consortium for production of oxygenated taxanes.
Figure 2: A mutualistic E. coli–S. cerevisiae consortium for production of oxygenated taxanes.
Figure 3: Optimizing the yeast growth and engineering the yeast promoters improved production of the oxygenated taxanes.
Figure 4: Inactivating oxidative phosphorylation in E. coli improved yeast growth and production of oxygenated taxanes.
Figure 5: Production of a monoacetylated dioxygenated taxane by the E. coli–S. cerevisiae co-culture.
Figure 6: Use of the E. coli–S. cerevisiae co-culture for production of other oxygenated isoprenoids.

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Acknowledgements

We acknowledge useful discussions and input from A. Ghaderi, F. Lam, H. Zhang, J. Avalos and W. Wang. This work was supported by National Institutes of Health grant 1-R01-GM085323-01A1 and the Singapore MIT Alliance.

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Authors and Affiliations

  1. Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Kang Zhou, Kangjian Qiao, Steven Edgar & Gregory Stephanopoulos

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  1. Kang Zhou
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  2. Kangjian Qiao
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Contributions

K.Z. and G.S. conceived the project. K.Z., K.Q., S.E. and G.S. designed the experiments, analyzed the results and wrote the manuscript. K.Z., K.Q. and S.E. did all the experiments.

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Correspondence to Gregory Stephanopoulos.

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The authors have filed a patent on the co-culture concept.

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Zhou, K., Qiao, K., Edgar, S. et al. Distributing a metabolic pathway among a microbial consortium enhances production of natural products. Nat Biotechnol 33, 377–383 (2015). https://doi.org/10.1038/nbt.3095

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