Ferulic acid  tolerance mechanisms in a vanillin-producing Komagataella phaffii
The bioconversion of lignocellulosic derivatives into high-value fine chemicals demonstrates immense potential for balancing sustainable utilization and value-added processing of renewable feedstock. Ferulic acid (FA), a lignocellulosic derivative abundant in plant cell walls, is a major bioavailable aromatic monomer, serves as a promising precursor for the biosynthesis of high-value aromatic products such as vanillin. However, the inherent toxicity of high-concentration of FA significantly inhibits cell growth, posing a major challenge in the development of efficient cell factories for the industrial production of high-value compounds from FA. In this study, we conducted a comprehensive transcriptome analysis of a vanillin-producing Komagataella phaffii cell factory under 20 mM FA stress, to investigate the molecular mechanisms underlying the strain's ability to withstand high-concentrations of FA. The data revealed that differentially expressed genes (DEGs) involved in cell membrane/wall defense, redox regulation, central carbon metabolism (CCM), oxidative phosphorylation, amino acid metabolism, and transcription and translation pathways were closely associated with the FA tolerance of the engineered K. phaffii. Protein interaction analysis and gene overexpression validation further identified KGD1, CIT1, SOD2, and TRP5 as key genes in the FA-stress tolerance regulation. This study offers an in-depth understanding of the FA tolerance mechanisms and metabolic engineering target genes of the K. phaffii cell factory, which could significantly contribute to the development of more efficient and robust cell factories for the biosynthesis of high-value compounds from FA using K. phaffii as a potent chassis cell.