Tolerance mechanisms of Candida utilis LM-1 in phenolic-rich environments

Lignin-rich process streams contain phenolic inhibitors that often limit yeast performance in lignocellulosic biorefineries. Here, we describe the isolation of Candida utilis LM-1 from a lignin-enriched consortium (LigMet) and use integrated omics analyses (genomics, transcriptomics, and proteomics), supplemented with phenotypic assays, to characterize its response to Kraft lignin and representative lignin-derived phenolics. LM-1 tolerated up to 1.0% (w/v) Kraft lignin on solid medium and can rapidly reduce phenolic aldehydes, converting vanillin to vanillyl alcohol within 4 h at high-cell-density in liquid cultures. Therefore, LM-1 did not show strong expression of typical extracellular lignin-depolymerizing enzymes, such as laccases or peroxidases, under the tested conditions. The primary response to Kraft lignin indicates a tolerance strategy employed by the strain, including increased expression of genes related to transmembrane transporter activity (GO: 0022857; 81 genes; 2.4-fold) and oxidoreductase activity (GO: 0016491; 44 genes). Proteomic analysis of yeast cells cultivated in media containing Kraft lignin identified stress proteins, including alcohol dehydrogenases, peroxiredoxins, glutathione enzymes, and chaperones. Transcriptomics also revealed downregulation of respiratory/TCA pathways in response to Kraft lignin, along with increased redox-cofactor supply (PPP) and alternative redox-balancing routes. Overall, these results suggest that the yeast uses tolerance mechanisms to withstand phenolic stress through barrier and transport defenses and intracellular reductive detoxification, rather than enzymatic lignin degradation. The multi-omics approach described here can guide engineering and process development to create phenolic-tolerant yeasts for lignin-rich biorefineries, enhancing sugar fermentation and enabling aromatic biotransformations through synthetic biology.