In vitro prototyping and rapid optimization of biosynthetic enzymes for cellular design

Karim, A. S.; Dudley, Q. M.; Juminaga, A.; Yuan, Y.; Crowe, S. A.; Heggestad, J. T.; Abdalla, T.; Grubbe, W.; Rasor, B.; Coar, D.; Torculas, M.; Krein, M.; Liew, F.; Quattlebaum, A.; Jensen, R. O.; Stuart, J.; Simpson, S. D.; Köpke, M.; Jewett, M. C.

doi:10.1101/685768

bioRxiv · 10.1101/685768

In vitro prototyping and rapid optimization of biosynthetic enzymes for cellular design

Karim, A. S.·Dudley, Q. M.·Juminaga, A.·Yuan, Y.·Crowe, S. A.·Heggestad, J. T.·Abdalla, T.·Grubbe, W.·Rasor, B.·Coar, D.·Torculas, M.·Krein, M.·Liew, F.·Quattlebaum, A.·Jensen, R. O.·Stuart, J.·Simpson, S. D.·Köpke, M.·Jewett, M. C.

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Abstract

Microbial cell factories offer an attractive approach for production of biobased products. Unfortunately, designing, building, and optimizing biosynthetic pathways remains a complex challenge, especially for industrially-relevant, non-model organisms. To address this challenge, we describe a platform for in vitro Prototyping and Rapid Optimization of Biosynthetic Enzymes (iPROBE). In iPROBE, cell lysates are enriched with biosynthetic enzymes by cell-free protein synthesis and then metabolic pathways are assembled in a mix-and-match fashion to assess pathway performance. We demonstrate iPROBE with two examples. First, we tested and ranked 54 different pathways for 3-hydroxybutyrate production, improving in vivo production in Clostridium by 20-fold to 14.63 {+/-} 0.48 g/L and identifying a new biosynthetic route to (S)-(+)-1,3-butanediol. Second, we used iPROBE and data-driven design to optimize a 6-step n-butanol pathway, increasing titers 4-fold across 205 pathways, and showed strong correlation between cell-free and cellular performance. We expect iPROBE to accelerate design-build-test cycles for industrial biotechnology.

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Karim, A. S., Dudley, Q. M., Juminaga, A., Yuan, Y., Crowe, S. A., Heggestad, J. T., Abdalla, T., Grubbe, W., Rasor, B., Coar, D., Torculas, M., Krein, M., Liew, F., Quattlebaum, A., Jensen, R. O., Stuart, J., Simpson, S. D., Köpke, M., Jewett, M. C.. 2019-06-28. In vitro prototyping and rapid optimization of biosynthetic enzymes for cellular design. https://doi.org/10.1101/685768

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