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Molecular crowding shapes gene expression in synthetic cellular nanosystems

Nature Nanotechnology volume 8, pages 602–608 (2013)Cite this article

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Abstract

The integration of synthetic and cell-free biology has made tremendous strides towards creating artificial cellular nanosystems using concepts from solution-based chemistry, where only the concentrations of reacting species modulate gene expression rates. However, it is known that macromolecular crowding, a key feature in natural cells, can dramatically influence biochemical kinetics via volume exclusion effects, which reduce diffusion rates and enhance binding rates of macromolecules. Here, we demonstrate that macromolecular crowding can increase the robustness of gene expression by integrating synthetic cellular components of biological circuits and artificial cellular nanosystems. Furthermore, we reveal how ubiquitous cellular modules, including genetic components, a negative feedback loop and the size of the crowding molecules can fine-tune gene circuit response to molecular crowding. By bridging a key gap between artificial and living cells, our work has implications for efficient and robust control of both synthetic and natural cellular circuits.

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Figure 1: Shaping gene expression in artificial cellular systems by molecular crowding.
Figure 2: Molecular crowding modulates dynamics of gene expression.
Figure 3: Molecular crowding increases robustness of gene expression.
Figure 4: Volume-dependent impact of molecular crowding in artificial cells.

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Acknowledgements

The authors thank members of the LeDuc and Schwartz laboratories, the group of the Center for Mechanical Technology and Automation at University of Aveiro in Portugal, Dr. Shuqiang Huang, Dr. Gang Bao, and Dr. Lingchong You for discussions and comments, and R. Murphy, A. Mitchell, B. Armitage, T. Lee, F. Lanni and the Molecular Biosensor and Imaging Center for providing access to equipment. This work was partially supported by a Lane Postdoctoral Fellowship (C.T.), a Society in Science – Branco Weiss Fellowship (C.T.), NIH 1R01GM086237 (M.B. & S.S.), NIH 8U54GM103529 (M.B. & S.S.), NIH 1R01AI076318 (R.S), NIH 1R01CA140214 (R.S), NSF CMMI-1100430 (P.L.), NSF CMMI-0856187 (P.L.), NSF CMMI-1160840 (P.L.), ONR N000140910215 (P.L.), and NSF CPS-1135850 (P.L.).

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Authors and Affiliations

  1. Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, 15213, Pennsylvania, USA

    Cheemeng Tan, Russell Schwartz & Philip LeDuc

  2. Department of Chemistry, Carnegie Mellon University, Pittsburgh, 15213, Pennsylvania, USA

    Saumya Saurabh & Marcel P. Bruchez

  3. Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, 15213, Pennsylvania, USA

    Saumya Saurabh & Marcel P. Bruchez

  4. Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, 15213, Pennsylvania, USA

    Marcel P. Bruchez, Russell Schwartz & Philip LeDuc

  5. Department of Mechanical Engineering and Biomedical Engineering, Carnegie Mellon University, Pittsburgh, 15213, Pennsylvania, USA

    Philip LeDuc

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  1. Cheemeng Tan
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  2. Saumya Saurabh
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Contributions

C.T., S.S., R.S. and P.L. conceived the research and designed the experiments. C.T. and S.S. performed the experiments. C.T. carried out the modelling analysis. C.T., S.S., M.B. and P.L. provided materials and reagents. C.T., R.S. and P.L. interpreted the results and wrote the manuscript, with critical input from S.S. and M.B. All authors approved the manuscript.

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Correspondence to Russell Schwartz or Philip LeDuc.

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The authors declare no competing financial interests.

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Tan, C., Saurabh, S., Bruchez, M. et al. Molecular crowding shapes gene expression in synthetic cellular nanosystems. Nature Nanotech 8, 602–608 (2013). https://doi.org/10.1038/nnano.2013.132

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