Adaptive strategies and genomic rewiring underlying polyphenol tolerance in Yarrowia lipolytica

Polyphenols are bioactive compounds used in food, beverages, cosmetics, and medicine. Despite their expanding use, the mechanisms of polyphenol toxicity in microbial polyphenol producers and the adaptive strategies that confer tolerance, remain poorly characterized. Here, we integrated adaptive laboratory evolution, morphological characterization, and omics approaches to systematically investigate critical regulators and transcriptional dynamics in response to polyphenol stress adaptation in the yeast Yarrowia lipolytica. Our findings primarily identified mutations in six genes and large segment duplications on chromosome E in evolved strains showing improved tolerance to high-concentration polyphenols, resveratrol, naringenin, and curcumin. MHY1 (YALI1_B28150g) was identified as the critical regulator, with functional validation confirming that both knockout and point mutations (F240L, C153) confer tolerance by locking cells in yeast morphology and reprogramming stress response pathways. Transcriptomic profiling detected a significant cellular shift, with proteostatic and redox defense systems upregulated, and core metabolic processes downregulated, demonstrating a transcriptional diversion of resources from growth-related metabolism to survival and stress-induced damage. While proving allele-specific toxicity toward endoplasmic reticulum function and autophagic processes, MHY1 also broadly regulates morphogenetic signaling, membrane assembly, and stress response pathways. Our findings show a regulatory network of complex transcriptional phenotypes enabling polyphenol stress adaptation in Y. lipolytica, emphasizing the role of transcription factors in creating diverse adaptive strategies.