Prioritized Expression of BDH2 under Bulk Translational Repression and Its Contribution to Tolerance to Severe Vanillin Stress in Saccharomyces cerevisiae

How adaptive laboratory evolution can boost yeast tolerance to lignocellulosic hydrolyses

The yeast Saccharomyces cerevisiae is an excellent candidate for establishing cell factories to convert lignocellulosic biomass into chemicals and fuels. To enable this technology, yeast robustness must be improved to withstand the fermentation inhibitors (e.g., weak organic acids, phenols, and furan aldehydes) resulting from biomass pretreatment and hydrolysis. Here, we discuss how evolution experiments performed in the lab, a method commonly known as adaptive laboratory evolution (ALE), may contribute to lifting yeast tolerance against the inhibitors of lignocellulosic hydrolysates (LCHs). The key is that, through the combination of whole-genome sequencing and reverse engineering, ALE provides a robust platform for discovering and testing adaptive alleles, allowing to explore the genetic underpinnings of yeast responses to LCHs. We review the insights gained from past evolution experiments with S. cerevisiae in LCH inhibitors and propose experimental designs to optimise the discovery of genetic variants adaptive to biomass toxicity. The knowledge gathered through ALE projects is envisaged as a roadmap to engineer superior yeast strains for biomass-based bioprocesses.

Response mechanisms of Saccharomyces cerevisiae to the stress factors present in lignocellulose hydrolysate and strategies for constructing robust strains

Bioconversion of lignocellulosic biomass to biofuels such as bioethanol and high value-added products has attracted great interest in recent decades due to the carbon neutral nature of biomass feedstock. However, there are still many key technical difficulties for the industrial application of biomass bioconversion processes. One of the challenges associated with the microorganism Saccharomyces cerevisiae that is usually used for bioethanol production refers to the inhibition of the yeast by various stress factors. These inhibitive effects seriously restrict the growth and fermentation performance of the strains, resulting in reduced bioethanol production efficiency. Therefore, improving the stress response ability of the strains is of great significance for industrial production of bioethanol. In this article, the response mechanisms of S. cerevisiae to various hydrolysate-derived stress factors including organic acids, furan aldehydes, and phenolic compounds have been reviewed. Organic acids mainly stimulate cells to induce intracellular acidification, furan aldehydes mainly break the intracellular redox balance, and phenolic compounds have a greater effect on membrane homeostasis. These damages lead to inadequate intracellular energy supply and dysregulation of transcription and translation processes, and then activate a series of stress responses. The regulation mechanisms of S. cerevisiae in response to these stress factors are discussed with regard to the cell wall/membrane, energy, amino acids, transcriptional and translational, and redox regulation. The reported key target genes and transcription factors that contribute to the improvement of the strain performance are summarized. Furthermore, the genetic engineering strategies of constructing multilevel defense and eliminating stress effects are discussed in order to provide technical strategies for robust strain construction. It is recommended that robust S. cerevisiae can be constructed with the intervention of metabolic regulation based on the specific stress responses. Rational design with multilevel gene control and intensification of key enzymes can provide good strategies for construction of robust strains.

Biosynthesis of vanillin by different microorganisms: a review

Vanillin is a popular flavoring agent widely used around the world. Vanillin is generated by natural extraction, chemical synthesis, or tissue culture technology, but these production methods no longer meet the increasing worldwide demand for vanillin. Accordingly, a biotechnological approach may provide an effective replacement route to obtaining vanillin. Processes for environmentally friendly production of vanillin in microorganisms from different carbon sources, such as eugenol, isoeugenol, lignin, ferulic acid, sugars, and waste residues, with high productivity and yield have been developed. However, challenges remain for optimizing the vanillin biosynthesis process and further improving production titer and yield. In this review, successful and applicable strategies for increasing vanillin titer and yield in different microorganisms are summarized. Additionally, perspectives for further optimizing the production of vanillin are discussed.

Increasing Yield of 2,3,5,6-Tetramethylpyrazine in Baijiu Through Saccharomyces cerevisiae Metabolic Engineering

Baijiu is a traditional distilled beverage in China with a rich variety of aroma substances. 2,3,5,6-tetramethylpyrazine (TTMP) is an important component in Baijiu and has the function of promoting cardiovascular and cerebrovascular health. During the brewing of Baijiu, the microorganisms in jiuqu produce acetoin and then synthesize TTMP, but the yield of TTMP is very low. In this work, 2,3-butanediol dehydrogenase (BDH) coding gene BDH1 and another BDH2 gene were deleted or overexpressed to evaluate the effect on the content of acetoin and TTMP in Saccharomyces cerevisiae. The results showed that the acetoin synthesis of strain α5-D1B2 was significantly enhanced by disrupting BDH1 and overexpressing BDH2, leading to a 2.6-fold increase of TTMP production up to 10.55 mg/L. To further improve the production level of TTMP, the α-acetolactate synthase (ALS) of the pyruvate decomposition pathway was overexpressed to enhance the synthesis of diacetyl. However, replacing the promoter of the ILV2 gene with a strong promoter (PGK1p) to increase the expression level of the ILV2 gene did not result in further increased diacetyl, acetoin and TTMP production. Based on these evidences, we constructed the diploid strains AY-SB1 (ΔBDH1:loxP/ΔBDH1:loxP) and AY-SD1B2 (ΔBDH1:loxP-PGK1p-BDH2-PGK1t/ΔBDH1:loxP-PGK1p-BDH2-PGK1t) to ensure the fermentation performance of the strain is more stable in Baijiu brewing. The concentration of TTMP in AY-SB1 and AY-SD1B2 was 7.58 and 9.47 mg/L, respectively, which represented a 2.3- and 2.87-fold increase compared to the parental strain. This work provides an example for increasing TTMP production in S. cerevisiae by genetic engineering, and highlight a novel method to improve the quality and beneficial health attributes of Baijiu.

Newly identified genes contribute to vanillin tolerance in Saccharomyces cerevisiae

Exploring the mechanisms of tolerance in microorganisms to vanillin, which is derived from lignin, will benefit the design of robust cell factories that produce biofuels and chemicals using lignocellulosic materials. Our objective was to identify the genes related to vanillin tolerance in Saccharomyces cerevisiae. We investigated the effects on vanillin tolerance of several genes that have site mutations in the highly vanillin‐tolerant strain EMV‐8 compared to its parental line NAN‐27. The results showed that overexpression of GCY1, a gene that encodes an aldo‐keto reductase that also has mRNA‐binding activity, YPR1, a paralog of GCY1 that encodes an aldo‐keto reductase, PEX5, a gene that encodes a peroxisomal membrane signal receptor and MBF1, a gene that encodes a multiprotein bridging factor increase the specific growth rates (μ) by 49%, 41%, 44% and 48 %, respectively, in medium containing 6 mmol l⁻¹ vanillin. Among these gene products, Gcy1p and Ypr1p showed NADPH‐dependent and NAD(P)H‐dependent vanillin reductase activity, respectively. The reductase‐inactive mutant Gcy1p^Y56F also increased vanillin tolerance in S. cerevisiae, suggesting that other mechanisms exist. Although TRS85 and PEX5, genes for which the mRNAs are binding targets of Gcy1p, were shown to be related to vanillin tolerance, both the mRNA and protein levels of these genes were not changed by overexpression of GCY1. The relationship between the mRNA‐binding activity of Gcy1p and its positive effect on vanillin tolerance is still not clear. Finally, we found that the point mutation D112A in Mbf1p, which disrupts the binding of Mbf1p and the TATA element‐binding protein (TBP), did not decrease the positive effect of Mbf1p on vanillin tolerance. This indicates that the binding of Mbf1p and TBP is not necessary for the positive effect on vanillin tolerance mediated by Mbf1p. We have successfully identified new genes related to vanillin tolerance and provided novel targets that can be used to improve the vanillin tolerance of S. cerevisiae. Moreover, we have extended our understanding of the proteins encoded by these genes.

New insights into two yeast BDHs from the PDH subfamily as aldehyde reductases in context of detoxification of lignocellulosic aldehyde inhibitors

At least 24 aldehyde reductases from Saccharomyces cerevisiae have been characterized and most function in in situ detoxification of lignocellulosic aldehyde inhibitors, but none is classified into the polyol dehydrogenase (PDH) subfamily of the medium-chain dehydrogenase/reductase (MDR) superfamily. This study confirmed that two (2R,3R)-2,3-butanediol dehydrogenases (BDHs) from industrial (denoted Y)/laboratory (denoted B) strains of S. cerevisiae, Bdh1p(Y)/Bdh1p(B) and Bdh2p(Y)/Bdh2p(B), were members of the PDH subfamily with an NAD(P)H binding domain and a catalytic zinc binding domain, and exhibited reductive activities towards lignocellulosic aldehyde inhibitors, such as acetaldehyde, glycolaldehyde, and furfural. Especially, the highest enzyme activity towards acetaldehyde by Bdh2p(Y) was 117.95 U/mg with cofactor nicotinamide adenine dinucleotide reduced (NADH). Based on the comparative kinetic property analysis, Bdh2p(Y)/Bdh2p(B) possessed higher specific activity, substrate affinity, and catalytic efficiency towards glycolaldehyde than Bdh1p(Y)/Bdh1p(B). This was speculated to be related to their 49% sequence differences and five nonsynonymous substitutions (Ser41Thr, Glu173Gln, Ile270Leu, Ile316Met, and Gly317Cys) occurred in their conserved NAD(P)H binding domains. Compared with BDHs from a laboratory strain, Bdh1p(Y) and Bdh2p(Y) from an industrial strain displayed five nonsynonymous mutations (Thr¹², Asn⁶¹, Glu¹⁶⁸, Val²²², and Ala²³⁵) and three nonsynonymous mutations (Ala³⁴, Ile⁹⁶, and Ala³⁶⁹), respectively. From a first analysis with selected aldehydes, their reductase activities were different from BDHs of laboratory strain, and their catalytic efficiency was higher towards glycolaldehyde and lower towards acetaldehyde. Comparative investigation of kinetic properties of BDHs from S. cerevisiae as aldehyde reductases provides a guideline for their practical applications in in situ detoxification of aldehyde inhibitors during lignocellulose bioconversion.Key Points• Two yeast BDHs have enzyme activities for reduction of aldehydes.• Overexpression of BDHs slightly improves yeast tolerance to acetaldehyde and glycolaldehyde.• Bdh1p and Bdh2p differ in enzyme kinetic properties.• BDHs from strains with different genetic backgrounds differ in enzyme kinetic properties.

Protein synthesis of Btn2 under pronounced translation repression during the process of alcoholic fermentation and wine-making in yeast

Acute high-concentration ethanol (> 9% v/v) has adverse effects on Saccharomyces cerevisiae, including the remarkable repression of bulk mRNA translation. Therefore, increased mRNA levels do not necessarily lead to an increase in the corresponding protein levels in yeast cells under severe ethanol stress. We previously identified that synthesis of Btn2 protein was efficiently induced even under the pronounced translation repression caused by acute severe ethanol stress under laboratory conditions. However, it remains to be clarified whether the translational activity is also repressed and whether the synthesis of Btn2 protein is induced during the process of alcoholic fermentation, in which the ethanol concentration increases gradually to reach high levels. In this study, we revealed that the pronounced translation repression and the translation of BTN2 are induced by high ethanol concentrations that form gradually during alcoholic fermentation using a wine yeast strain EC1118. Furthermore, we confirmed the induced expression of non-native genes driven by the BTN2 promoter during the later stage of the wine-making process. Our findings provide new information on the translation activity in yeast cells during alcoholic fermentation and suggest the utility of the BTN2 promoter for sustaining the fermentation efficiency and quality modification of alcoholic beverages.

Prioritized Expression of BTN2 of Saccharomyces cerevisiae under Pronounced Translation Repression Induced by Severe Ethanol Stress

Severe ethanol stress (>9% ethanol, v/v) as well as glucose deprivation rapidly induces a pronounced repression of overall protein synthesis in budding yeast Saccharomyces cerevisiae. Therefore, transcriptional activation in yeast cells under severe ethanol stress does not always indicate the production of expected protein levels. Messenger RNAs of genes containing heat shock elements can be intensively translated under glucose deprivation, suggesting that some mRNAs are preferentially translated even under severe ethanol stress. In the present study, we tried to identify the mRNA that can be preferentially translated under severe ethanol stress. BTN2 encodes a v-SNARE binding protein, and its null mutant shows hypersensitivity to ethanol. We found that BTN2 mRNA was efficiently translated under severe ethanol stress but not under mild ethanol stress. Moreover, the increased Btn2 protein levels caused by severe ethanol stress were smoothly decreased with the elimination of ethanol stress. These findings suggested that severe ethanol stress extensively induced BTN2 expression. Further, the BTN2 promoter induced protein synthesis of non-native genes such as CUR1, GIC2, and YUR1 in the presence of high ethanol concentrations, indicating that this promoter overcame severe ethanol stress-induced translation repression. Thus, our findings provide an important clue about yeast response to severe ethanol stress and suggest that the BTN2 promoter can be used to improve the efficiency of ethanol production and stress tolerance of yeast cells by modifying gene expression in the presence of high ethanol concentration.