Abstract
Yarrowia lipolytica strain is a promising cell factory for the conversion of lignocellulose to biofuels and bioproducts. Despite the inherent robustness of this strain, further improvements to lignocellulose-derived inhibitors toxicity tolerance of Y. lipolytica are also required to achieve industrial application. Here, adaptive laboratory evolution was employed with increasing concentrations of ferulic acid. The adaptive laboratory evolution experiments led to evolve Y. lipolytica strain yl-XYL + *FA*4 with increased tolerance to ferulic acid as compared to the parental strain. Specifically, the evolved strain could tolerate 1.5 g/L ferulic acid, whereas 0.5 g/L ferulic acid could cause about 90% lethality of the parental strain. Transcriptome analysis of the evolved strain revealed several targets underlying toxicity tolerance enhancements. YALI0_E25201g, YALI0_F05984g, YALI0_B18854g, and YALI0_F16731g were among the highest upregulated genes, and the beneficial contributions of these genes were verified via reverse engineering. Recombinant strains with overexpressing each of these four genes obtained enhanced tolerance to ferulic acid as compared to the control strain. Fortunately, recombinant strains with overexpression of YALI0_E25201g, YALI0_B18854g, and YALI0_F16731g individually also obtained enhanced tolerance to vanillic acid. Overall, this work demonstrated a whole strain improvement cycle by “non-rational” metabolic engineering and presented new targets to modify Y. lipolytica for microbial lignocellulose valorization.
Key points
• Adaptive evolution improved the ferulic acid tolerance of Yarrowia lipolytica
• Transcriptome sequence was applied to analyze the ferulic acid tolerate strain
• Three genes were demonstrated for both ferulic acid and vanillic acid tolerance
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Data availability
The datasets of RNA sequencing raw data generated in this study have been submitted in Genbank with an accession number of PRJNA 675399 (https://dataview.ncbi.nlm.nih.gov/object/PRJNA675399).
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Acknowledgements
We would like to thank Dr. Rodrigo Ledesma-Amaro for providing Y. lipolytica yl-XYL+.
Funding
This work was supported by “Natural Science Foundation of Jiangsu Province,” Grant No. BK20170037 and BK20170829; “National Key R&D Program of China,” Grant No. 2016YFE0105400; “National Natural Science Foundation of China,” Grant Nos. 21606132 and 21706133.
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JM and WZ conceived and designed research. WZ, ZL, WZ, ZY, LM, and ZH performed the experiments; WZ, ZL, XZ, and WZ analyzed the data; JM, XZ, and WZ coordinated and supervised this study; WZ drafted the manuscript. ZL, XZ, and JM revised the manuscript.
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Wang, Z., Zhou, L., Lu, M. et al. Adaptive laboratory evolution of Yarrowia lipolytica improves ferulic acid tolerance. Appl Microbiol Biotechnol 105, 1745–1758 (2021). https://doi.org/10.1007/s00253-021-11130-3
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DOI: https://doi.org/10.1007/s00253-021-11130-3