| Summary: | <i>Pichia kudriavzevii</i> is one of the major non-<i>Saccharomyces cerevisiae</i> yeasts in Chinese <i>baijiu</i> brewing, which has shown a substantially higher tolerance to acid, heat, and ethanol. Exploring the mechanism of <i>P. kudriavzevii</i> could have a positive effect on the artificially controlled production of <i>baijiu</i>. In this study, an efficient acetic-acid-tolerant <i>P. kudriavzevii</i> strain, Y2, was isolated from the yellow water of strong-flavored <i>baijiu</i> brewing waste, and its molecular mechanism of acetic acid tolerance was investigated through a comparative transcriptomic analysis. The strain Y2 could tolerate 12 g/L of acetic acid. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, differentially expressed genes (DEGs) were mainly enriched in oxidative phosphorylation, the citrate cycle, glycolysis/gluconeogenesis, and carbon metabolism under low (AL group) and high (AH group) concentrations of acetic acid. However, the DEG enrichment was more profound in the AH group when compared to the control. Compared with the AL group, the expression of genes related to oxidative phosphorylation was more significantly upregulated, while in terms of the TCA cycle, phosphoenolpyruvate carboxykinase was significantly upregulated in both the AH and AL groups and was positively correlated with tolerance to acetic acid. This was followed by citrate synthase, isocitrate dehydrogenase, malate dehydrogenase, and succinate dehydrogenase. These results illustrated a possible mechanism of acid tolerance by regulating the metabolism-related pathways in <i>P. kudriavzevii</i> and provided a basis for the further investigation of the acid tolerance mechanism.
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