Metabolic Competition Reshapes the Performance of Engineered Polyketide Synthases
5 affiliations
- 1Department of Chemistry
- 2the University of Texas at Austin
- 3DOE Center for Advanced Bioenergy and Bioproducts Innovation
- 4University of Illinois at Urbana-Champaign
- 5Department of Molecular Biosciences
Abstract
Directed evolution is widely used to enhance enzymatic performance and evolve new-to-nature reactivities, typically in vitro or in model microbial systems. However, variants selected in a model host may not retain their relative performance in the intended production organism. Here, we engineered a single 2-pyrone synthase (2PS) scaffold by directed evolution in Escherichia coli ( E. coli ) and evaluated the resulting variants in both E. coli and planta. In E. coli, engineered 2PS variants showed distinct chemoselectivities, giving access to precursors for kavalactones and raspberry ketone from one protein scaffold. The best variant achieved >98% conversion of p -coumaric acid to >200 µg/mL bisnoryangonin. In planta, however, variant performance was reordered: the top-performing microbial variant was outperformed 2.7-fold by one with lower activity in E. coli . We traced this host-dependent shift to competition for the shared p -coumaroyl-CoA pool and identified cinnamoyl-CoA reductase from Nicotiana benthamiana ( Nb CCR) as a key competing enzyme. Introducing Nb CCR into E. coli recapitulated the variant rank order observed in planta, demonstrating that metabolic competition can reshape the performance of engineered enzymes across hosts. These results also suggest that reconstructing key competing pathways of the target host in a tractable microbial system can provide a practical strategy for engineering enzymes for otherwise difficult-to-evolve production hosts. Finally, 2PS variants enabled the chemoenzymatic synthesis of natural and fluorinated kavalactones with up to 64% isolated yield over two steps.
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BibTeX
@misc{zhou2026metabolic,
title = {{Metabolic Competition Reshapes the Performance of Engineered Polyketide Synthases}},
author = {Yu Zhou and Zhengyao Shao and Xueyi Xue and Li-Qing Chen and Hong Qiao and Yi Lu},
howpublished = {ChemRxiv},
year = {2026},
month = sep,
doi = {10.26434/chemrxiv.15007623/v2},
url = {https://chemrxiv.org/doi/full/10.26434/chemrxiv.15007623/v2},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Metabolic Competition Reshapes the Performance of Engineered Polyketide Synthases
AU - Yu Zhou
AU - Zhengyao Shao
AU - Xueyi Xue
AU - Li-Qing Chen
AU - Hong Qiao
AU - Yi Lu
PY - 2026
DA - 2026/09/15
PB - ChemRxiv
DO - 10.26434/chemrxiv.15007623/v2
UR - https://chemrxiv.org/doi/full/10.26434/chemrxiv.15007623/v2
AB - Directed evolution is widely used to enhance enzymatic performance and evolve new-to-nature reactivities, typically in vitro or in model microbial systems. However, variants selected in a model host may not retain their relative performance in the intended production organism. Here, we engineered a single 2-pyrone synthase (2PS) scaffold by directed evolution in Escherichia coli ( E. coli ) and evaluated the resulting variants in both E. coli and planta. In E. coli, engineered 2PS variants showed distinct chemoselectivities, giving access to precursors for kavalactones and raspberry ketone from one protein scaffold. The best variant achieved >98% conversion of p -coumaric acid to >200 µg/mL bisnoryangonin. In planta, however, variant performance was reordered: the top-performing microbial variant was outperformed 2.7-fold by one with lower activity in E. coli . We traced this host-dependent shift to competition for the shared p -coumaroyl-CoA pool and identified cinnamoyl-CoA reductase from Nicotiana benthamiana ( Nb CCR) as a key competing enzyme. Introducing Nb CCR into E. coli recapitulated the variant rank order observed in planta, demonstrating that metabolic competition can reshape the performance of engineered enzymes across hosts. These results also suggest that reconstructing key competing pathways of the target host in a tractable microbial system can provide a practical strategy for engineering enzymes for otherwise difficult-to-evolve production hosts. Finally, 2PS variants enabled the chemoenzymatic synthesis of natural and fluorinated kavalactones with up to 64% isolated yield over two steps.
ER -