Engineering yeast peroxisome assembly enables the increased production of acetyl-CoA and its derived 5-deoxyflavonoids

Yongxing Li, Bingjie Du, Chun Li () and Xudong Feng ()
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Yongxing Li: Beijing Institute of Technology, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering
Bingjie Du: Beijing Institute of Technology, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering
Chun Li: Tsinghua University, Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering
Xudong Feng: Beijing Institute of Technology, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering

Nature Communications, 2025, vol. 16, issue 1, 1-16

Abstract: Abstract Acetyl-CoA serves as a foundational precursor and energy source for various biosynthesis pathways. The insufficient supply of acetyl-CoA in cytosol is usually a bottleneck for exogenous chemical synthesis in engineered microbes such as yeast. Exportation of acetyl-CoA from peroxisome, an exclusive organelle for fatty acids β-oxidation, may be an effective way to solve this problem. In this study, we develop a peroxin (PEX) engineering strategy to modulate peroxisome assembly in S. cerevisiae. Then, robust peroxisomes are constructed with improved acetyl-CoA supply by up to 98%, which further leads to the increased liquiritigenin titer (1102.4 mg/L). We also demonstrate that the PEX–mediated peroxisome engineering strategy can be extended across yeast species. Hybrid peroxisomes with tailored function are constructed in S. cerevisiae by transplanting selected PEXs from Y. lipolytica. Our study provides mechanistic insights into the “PEXs–peroxisome assembly–acetyl-CoA synthesis” relationship.

Date: 2025
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DOI: 10.1038/s41467-025-65444-1

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