Comparative transcriptome profiling analyses during the lag phase uncover YAP1, PDR1, PDR3, RPN4, and HSF1 as key regulatory genes in genomic adaptation to the lignocellulose derived inhibitor HMF for Saccharomyces cerevisiae

Abstract

BackgroundThe yeast Saccharomyces cerevisiae is able to adapt and in situ detoxify lignocellulose derived inhibitors such as furfural and HMF. The length of lag phase for cell growth in response to the inhibitor challenge has been used to measure tolerance of strain performance. Mechanisms of yeast tolerance at the genome level remain unknown. Using systems biology approach, this study investigated comparative transcriptome profiling, metabolic profiling, cell growth response, and gene regulatory interactions of yeast strains and selective gene deletion mutations in response to HMF challenges during the lag phase of growth.ResultsWe identified 365 candidate genes and found at least 3 significant components involving some of these genes that enable yeast adaptation and tolerance to HMF in yeast. First, functional enzyme coding genes such as ARI1, ADH6, ADH7, and OYE3, as well as gene interactions involved in the biotransformation and inhibitor detoxification were the direct driving force to reduce HMF damages in cells. Expressions of these genes were regulated by YAP1 and its closely related regulons. Second, a large number of PDR genes, mainly regulated by PDR1 and PDR3, were induced during the lag phase and the PDR gene family-centered functions, including specific and multiple functions involving cellular transport such as TPO1, TPO4, RSB1, PDR5, PDR15, YOR1, and SNQ2, promoted cellular adaptation and survival in order to cope with the inhibitor stress. Third, expressed genes involving degradation of damaged proteins and protein modifications such as SHP1 and SSA4, regulated by RPN4, HSF1, and other co-regulators, were necessary for yeast cells to survive and adapt the HMF stress. A deletion mutation strain Δrpn4 was unable to recover the growth in the presence of HMF.ConclusionsComplex gene interactions and regulatory networks as well as co-regulations exist in yeast adaptation and tolerance to the lignocellulose derived inhibitor HMF. Both induced and repressed genes involving diversified functional categories are accountable for adaptation and energy rebalancing in yeast to survive and adapt the HMF stress during the lag phase of growth. Transcription factor genes YAP1, PDR1, PDR3, RPN4, and HSF1 appeared to play key regulatory rules for global adaptation in the yeast S. cerevisiae.

Roles of the Yap1 Transcription Factor and Antioxidants in Saccharomyces cerevisiae's Tolerance to Furfural and 5-Hydroxymethylfurfural, Which Function as Thiol-Reactive Electrophiles Generating Oxidative Stress

“…However, induction of stress-responsive genes was commonly observed when cells were treated with either furfural or HMF. Especially, Yap1, a major oxidative stress regulator, was identified as one of the key regulators involved in genomic adaptation to HMF in S. cerevisiae, suggesting that HMF might elicit oxidative stress (17,18). In agreement with the role for Yap1 in adaptation to HMF, the overexpression of YAP1 has been shown to increase tolerance to HMF and dilute acid spruce hydrolysates (18).…”

“…Previous DNA microarray experiments have revealed that Yap1 is one of the key regulators involved in genomic adaptation to HMF in S. cerevisiae (17). Yap1 is activated by H 2 O 2 and thiolreactive electrophiles through different mechanisms (27).…”

“…Since both furfural and HMF act as thiol-reactive electrophiles which can induce oxidative stress, the overexpression of YAP1 might confer resistance to furfural and HMF by activation of genes involved in resistance to oxidative stress and reduction of furan aldehydes (17,31). Indeed, overexpression of YAP1 has been shown to convey resistance to HMF, although the detailed mechanisms have not been investigated (18).…”

“…Genome-wide transcriptome analyses have revealed a wide range of cellular functions regulated by furfural and HMF in yeast (16,17). Because different yeast strains and conditions were used for these previous experiments, little overlap exists among the genes identified to be upregulated by furfural and HMF.…”

Increased Furfural Tolerance Due to Overexpression of NADH-Dependent Oxidoreductase FucO in Escherichia coli Strains Engineered for the Production of Ethanol and Lactate

“…Several genes encoding oxidoreductases that reduce furfural and 5-hydroxymethylfurfural (5-HMF) (a dehydration product of hexose sugars) have been implicated in furan tolerance in Saccharomyces cerevisiae (2,20,21,22,23) and in Escherichia coli (29)(30)(31)38). Gene array studies identified more than 365 genes that changed in expression level during an HMF challenge, and these changes are proposed to be mediated by at least 5 different regulatory genes (24).…”