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Exploiting nongenetic cell-to-cell variation for enhanced biosynthesis

Nature Chemical Biology volume 12, pages 339–344 (2016)Cite this article

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Abstract

Biosynthesis enables renewable production of manifold compounds, yet often biosynthetic performance must be improved for it to be economically feasible. Nongenetic, cell-to-cell variations in protein and metabolite concentrations are naturally inherent, suggesting the existence of both high- and low-performance variants in all cultures. Although having an intrinsic source of low performers might cause suboptimal ensemble biosynthesis, the existence of high performers suggests an avenue for performance enhancement. Here we develop in vivo population quality control (PopQC) to continuously select for high-performing, nongenetic variants. We apply PopQC to two biosynthetic pathways using two alternative design principles and demonstrate threefold enhanced production of both free fatty acid (FFA) and tyrosine. We confirm that PopQC improves ensemble biosynthesis by selecting for nongenetic high performers. Additionally, we use PopQC in fed-batch FFA production and achieve 21.5 g l−1 titer and 0.5 g l−1 h−1 productivity. Given the ubiquity of nongenetic variation, PopQC should be applicable to a variety of metabolic pathways for enhanced biosynthesis.

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Figure 1: Cell-to-cell variation in biosynthetic performance of the FFA pathway within an isoclonal population.
Figure 2: Design principle of PopQC.
Figure 3: PopQC improves FFA overproduction.
Figure 4: Expanding the applicability of PopQC.

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Acknowledgements

The authors acknowledge D. Liu at Harvard University for the GFP reporter gene. The authors would like to thank K. Naegle, C. Immethun, A. Hoynes-O'Connor, D. Giblin, F.-F. Hsu and E. Lantelme for technical assistance and the Genome Technology Access Center in the Department of Genetics at Washington University School of Medicine for helping with genomic analysis. This work was supported by a start-up package from Washington University, the Defense Advanced Research Projects Agency (D13AP00038 to F.Z.), the National Science Foundation (MCB1453147 and MCB1331194, both to F.Z.), the Human Frontier Science Program (RGY0076/2015 to F.Z.) and the International Center for Advanced Renewable Energy and Sustainability (I-CARES).

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Authors and Affiliations

  1. Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA

    Yi Xiao, Christopher H Bowen, Di Liu & Fuzhong Zhang

  2. Division of Biological and Biomedical Sciences, Washington University in St. Louis, St. Louis, Missouri, USA

    Fuzhong Zhang

  3. Institute of Materials Science and Engineering, Washington University in St. Louis, St. Louis, Missouri, USA

    Fuzhong Zhang

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  1. Yi Xiao
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Contributions

F.Z. conceived the project. F.Z., Y.X. and C.H.B. designed the experiments. Y.X. and C.H.B. performed the experiments. F.Z., Y.X., C.H.B. and D.L. analyzed the data and wrote the paper.

Corresponding author

Correspondence to Fuzhong Zhang.

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Competing interests

Y.X. and F.Z. have filed a patent application ("A Genetically-Encoded Quality Control System for Improving the Microbial Production of Chemicals, Pharmaceuticals and Fuels," US Provisional Patent Application Ser. No. #62/214,248) on the basis of this contribution.

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Supplementary Results, Supplementary Figures 1–12, Supplementary Tables 1–4 and Supplementary Note. (PDF 2137 kb)

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Xiao, Y., Bowen, C., Liu, D. et al. Exploiting nongenetic cell-to-cell variation for enhanced biosynthesis. Nat Chem Biol 12, 339–344 (2016). https://doi.org/10.1038/nchembio.2046

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