RNA-Seq-based transcriptomic and metabolomic analysis reveal stress responses and programmed cell death induced by acetic acid in Saccharomyces cerevisiae

Yachen Dong,Jingjin Hu,Qihe Chen,Linlin Fan

doi:10.1038/srep42659

Abstract

As a typical harmful inhibitor in cellulosic hydrolyzates, acetic acid not only hinders bioethanol production, but also induces cell death in Saccharomyces cerevisiae. Herein, we conducted both transcriptomic and metabolomic analyses to investigate the global responses under acetic acid stress at different stages. There were 295 up-regulated and 427 down-regulated genes identified at more than two time points during acetic acid treatment (150 mM, pH 3.0). These differentially expressed genes (DEGs) were mainly involved in intracellular homeostasis, central metabolic pathway, transcription regulation, protein folding and stabilization, ubiquitin-dependent protein catabolic process, vesicle-mediated transport, protein synthesis, MAPK signaling pathways, cell cycle, programmed cell death, etc. The interaction network of all identified DEGs was constructed to speculate the potential regulatory genes and dominant pathways in response to acetic acid. The transcriptional changes were confirmed by metabolic profiles and phenotypic analysis. Acetic acid resulted in severe acidification in both cytosol and mitochondria, which was different from the effect of extracellular pH. Additionally, the imbalance of intracellular acetylation was shown to aggravate cell death under this stress. Overall, this work provides a novel and comprehensive understanding of stress responses and programmed cell death induced by acetic acid in yeast.

Highlights

Glucose repression in S. cerevisiae[5]
There was no delay in green fluorescent protein (GFP) disappearance in the media without acetic acid at a pH range of 3.0–5.7, but a decrease in GFP-positive cells when the acetic acid concentration was more than 60 mM at pH 3.0 (Fig. 1C,D)
It can be seen that the change of extracellular pH from 6.0 to 3.0 without acetic acid treatment has no significant impact on cell death in S. cerevisiae (P > 0.05, two-tailed t test), but acetic acid induces cell death with the concentration above 30 mM when the culture pH remains at 3.0

Summary

Introduction

Glucose repression in S. cerevisiae[5]. Little is known about the impact of acetate increasingly accumulating in yeast cells upon acetic acid stress. We performed the experiments with 150 mM acetic acid (pH 3.0) for different times in a synthetic complete (SC) medium supplemented with only auxotrophic amino acids and nucleotides Both transcriptomic and metabolomic analyses were used to investigate the global responses of yeast cells under acetic acid stress and identify the regulatory mechanisms for rerouting metabolic fluxes. The imbalance of histone acetylation was analyzed to evaluate the impact on cell death under acetic acid stress These findings suggest new insights into how yeast cells respond to acetic acid stress, and contribute to the exploration of the engineered S. cerevisiae strains with a high inhibitor tolerance for bioethanol production

Methods

Results

Discussion

Conclusion