Transcriptomic analysis of formic acid stress response in Saccharomyces cerevisiae

Abstract

Formic acid is a representative small molecule acid cell inhibitor in lignocellulosic hydrolysate, which can inhibit the growth of yeast cells in the process of alcohol fermentation. However, the mechanism of formic acid cytotoxicity remains largely unknown. This study aimed to study the cytotoxicity of formic acid stress to Saccharomyces cerevisiae. We evaluated the effects of formic acid on growth metabolism and cell morphology of yeast cells, and comprehensively and systematically analyzed the molecular mechanism of formic acid stress tolerance through transcriptome technology. The results showed that when the concentration of formic acid was 1.8 g/L, the growth of yeast cells was signi cantly inhibited, the cell surface was wrinkled, and the adhesion between cells was observed, and the cell wall and cell membrane of yeast were destroyed by changing the structure of proteins and carbohydrates, resulting in cell damage. Transcriptome sequencing results showed that formic acid stress inhibited protein biosynthesis, induced oxidative stress, resulted in autophagy, impaired intracellular ATP production and increased consumption, and then impaired normal physiological and metabolic functions of cells. Yeast cells provide su cient ATP by accelerating glucose metabolism, enhancing electron transport and ATP synthesis more energy to resist formic acid stress, and reduce the expression of genes related to energy metabolism such as intracellular amino acids to achieve an energy-saving strategy, In addition, it can also induce sexual reproduction and spore formation to improve cell tolerance to formic acid. This study initially revealed the molecular response mechanism of S. cerevisiae under formic acid stress, and provided a scienti c basis for further research on methods to improve the tolerance of cell inhibitors in lignocellulose hydrolysate.

Mechanisms of Antioxidant Dipeptides Enhancing Ethanol-Oxidation Cross-Stress Tolerance in Lager Yeast: Roles of the Cell Wall and Membrane

“…MDA is the main product of the peroxidation reaction in the plasma membranes . The content of MDA reflects the degree of stress damage to the cell membranes to some extent . The sulfhydryl group is an essential reflection of maintaining the normal conformation of the membrane and protein, and it is usually oxidized by MDA .…”

“…24 The content of MDA reflects the degree of stress damage to the cell membranes to some extent. 39 The sulfhydryl group is an essential reflection of maintaining the normal conformation of the membrane and protein, and it is usually oxidized by MDA. 24 As shown in Figure 4A, lower MDA concentration was found by supplementation with AH, TY, and FC, decreasing by 12.32 ± 0.00, 12.30 ± 0.01, and 11.92 ± respectively, compared with the control.…”

Formate Dehydrogenase Improves the Resistance to Formic Acid and Acetic Acid Simultaneously in Saccharomyces cerevisiae

“…However, the resistance mechanism of formic acid has been rarely investigated to our knowledge. S. cerevisiae GGSF16 grew slowly in the presence of 1.5 g/L formic acid and could hardly grow when the formic acid concentration increased to 1.8 g/L [ 28 ]. For Yarrowia lipolytica , both formic acid and acetic acid inhibited cell growth and lipid production.…”

The cell wall and the response and tolerance to stresses of biotechnological relevance in yeasts

“…This common response is consistent with the important role of CWP in decreasing cell surface porosity and increasing cell wall stability when coping with stress. The upregulation of genes involved in β1,3-glucan synthesis was also reported to be shared by several stresses (heat, ethanol, low and high pH and formic acid stress) and during hyper-osmotic stress in Z. rouxii ( Zhao et al, 1998 ; Viladevall et al, 2004 ; De Melo et al, 2010 ; De Lucena et al, 2012 ; Udom et al, 2019 ; Guo et al, 2020 ; Samakkarn et al, 2021 ; Zeng et al, 2022 ). Genes involved in β1,3-glucan elongation and branching were also found to be upregulated in response to low pH, acetic and lactic acids-induced stresses and under ethanol stress in I. orientalis ( Kawahata et al, 2006 ; De Melo et al, 2010 ; De Lucena et al, 2012 ; Miao et al, 2018 ; Ribeiro et al, 2021 ).…”

“…Under formic acid stress, S. cerevisiae cells exhibited a deformed shape, with collapsed cell wall edges, indicating that the cell wall was damaged, and an FTIR analysis suggested that chitin structure was altered ( Zeng et al, 2022 ). S. cerevisiae genes involved in β1,3-glucan synthesis ( FKS1, ELO2 ), β1,6-glucan synthesis ( TRS65 ), chitin synthesis ( CHS5 ), CWP mannosylation ( PMT2 ), cell wall integrity ( PUN1 ), and CWI pathway regulation ( ROM2 ) are important determinants of formic acid tolerance while FKS3 , encoding an FKS1-2 homolog, is upregulated in response to this acid stress ( Henriques et al, 2017 ; Zeng et al, 2022 ; Figure 3 ). Moreover, the upregulation of EXG2 encoding a major exoglucanase, and PKC1 , encoding a CWI pathway kinase, was reported in an industrial S. cerevisiae strain (S6), engineered to ferment xylose, when grown in a medium with glucose and xylose supplemented with formic acid ( Li et al, 2020 ).…”