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Versatile biomanufacturing through stimulus-responsive cell–material feedback

Nature Chemical Biology volume 15, pages 1017–1024 (2019)Cite this article

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Abstract

Small-scale production of biologics has great potential for enhancing the accessibility of biomanufacturing. By exploiting cell–material feedback, we have designed a concise platform to achieve versatile production, analysis and purification of diverse proteins and protein complexes. The core of our technology is a microbial swarmbot, which consists of a stimulus-sensitive polymeric microcapsule encapsulating engineered bacteria. By sensing the confinement, the bacteria undergo programmed partial lysis at a high local density. Conversely, the encapsulating material shrinks responding to the changing chemical environment caused by cell growth, squeezing out the protein products released by bacterial lysis. This platform is then integrated with downstream modules to enable quantification of enzymatic kinetics, purification of diverse proteins, quantitative control of protein interactions and assembly of functional protein complexes and multienzyme metabolic pathways. Our work demonstrates the use of the cell–material feedback to engineer a modular and flexible platform with sophisticated yet well-defined programmed functions.

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Fig. 1: Programmable cell–material feedback for versatile protein production.
Fig. 2: Sustained synthesis and quantification of BlaM.
Fig. 3: Integrated protein production and purification.
Fig. 4: Composition control and DOL using MSBs.
Fig. 5: One-pot reconstruction of the multienzyme metabolic pathway underlying FAS.

Data availability

All data generated or analyzed during the current study are available from the corresponding author on reasonable request.

Code availability

All code used in this study is available from the author upon reasonable request.

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Acknowledgements

We thank M. Lynch for plasmid constructs, insightful comments and suggestions; D.A. Tirrell, Y. Zhang and F. Sun for plasmid constructs; K. Zhu and K. Luginbuhl for insightful suggestions; J. Decker for useful suggestions; and P. Li, B. Chen, Q. Hu, X. Peng and Y. Zhang for assistance in revision. This study was partially supported by the U.S. Army Research Office under grant W911NF-14-1-0490 (to L.Y.), the National Institutes of Health (grant R01-GM098642 to L.Y. and grant R35GM127042 to A.C.), the Office of Naval Research (grant N00014-12-1-0631 to L.Y.), Beijing Municipal Natural Science Foundation (grant 5182017 to Z.L.) and a David and Lucile Packard Fellowship to L.Y.

Author information

Author notes

  1. Zhuojun Dai

    Present address: Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China

Authors and Affiliations

  1. Department of Biomedical Engineering, Duke University, Durham, NC, USA

    Zhuojun Dai, Anna J. Lee, Stefan Roberts, Tatyana A. Sysoeva, Michael Dzuricky, Ashutosh Chilkoti & Lingchong You

  2. Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China

    Shuqiang Huang & Xi Zhang

  3. School of Life Sciences, Peking University, Beijing, China

    Xiaoyu Yang

  4. College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China

    Zihe Liu

  5. Center for Genomic and Computational Biology, Duke University, Durham, NC, USA

    Lingchong You

  6. Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA

    Lingchong You

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Contributions

Z.D. conceived the research, designed and performed experiments, interpreted the results, assisted in the model development and wrote the manuscript. A.J.L. developed the model and assisted in experimental setup, data interpretation and manuscript revisions. S.R. assisted in performing experiments, data analysis and manuscript revisions. T.A.S. and S.H. assisted in experimental setup, data interpretation and manuscript revisions. M.D. and X.Y. assisted in performing experiments, data interpretation and manuscript revisions. X.Z. and Z.L. assisted in performing experiments during the manuscript revisions. A.C. assisted in research design, experimental setup, data interpretation and manuscript revisions. L.Y. conceived the research and assisted in research design, modeling, data interpretation and manuscript writing.

Corresponding author

Correspondence to Lingchong You.

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Supplementary information

Supplementary information

Supplementary Tables 1–3 and Supplementary Figures 1–18

Reporting Summary

Supplementary Video 1

Oscillatory behavior of engineered cells was observed on the microfluidic device.

Supplementary Video 2

Capsules carrying engineered bacteria shrunk with cell growth.

Supplementary Video 3

Capsules carrying engineered bacteria swelled slightly before shrinking with cell growth.

Supplementary Video 4

Oscillations of the capsule size in the culture chamber were observed under microscopy.

Supplementary Video 5

Periodic accumulation of fluorescence in the assay chamber were observed under microscopy.

Supplementary Video 6

Response of chitosan capsules to periodic change in pH.

Supplementary Video 7

Alginate capsules maintain the same size at varied chemical conditions.

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Dai, Z., Lee, A.J., Roberts, S. et al. Versatile biomanufacturing through stimulus-responsive cell–material feedback. Nat Chem Biol 15, 1017–1024 (2019). https://doi.org/10.1038/s41589-019-0357-8

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