Adaptive responses of yeast strains tolerant to acidic pH, acetate, and supraoptimal temperature

Evaluation of Stress Tolerance and Fermentation Performance in Commercial Yeast Strains for Industrial Applications

This study evaluates the stress tolerance and metabolic adaptability of twelve yeast strains, including eleven commercial strains from Wyeast Laboratories and one prototrophic laboratory strain, under industrially relevant conditions. Yeast strains were assessed for their fermentation performance and stress responses under glucose limitation, osmotic stress, acid stress, elevated ethanol concentrations, and temperature fluctuations. Results revealed significant variability in glucose consumption, ethanol production, and stress tolerance across strains. ACY34 and ACY84 demonstrated the highest fermentation efficiency, while ACY19 exhibited exceptional stress resilience, excelling under multiple stress conditions such as osmotic and ethanol stress. The findings highlight strain-specific performance, with some strains suited for high-yield fermentation and others excelling under challenging environmental conditions. These results provide critical insights for selecting and optimizing yeast strains tailored to specific industrial fermentation processes, contributing to improved productivity and product quality in food and beverage production.

Effective removal of Pb from industrial wastewater: A new approach to remove Pb from wastewater based on engineered yeast

The use of synthetic biology to construct engineered strains has provided new perspectives for addressing Pb contamination; however, the large-scale treatment of contaminants is still limited by high operating costs and technological constraints. This study introduces a novel technique for applying engineered yeast in the removal of heavy metals, offering a solution to the cost and process scale challenges associated with utilizing engineered yeast. Hydrogen sulfide-producing engineered yeast strains were constructed based on existing strategies by knocking out the gene encoding the O-acetyl-L-homoserine mercapturic enzyme, which plays a role in sulfate assimilation. To facilitate the transition of engineered yeast from laboratory settings to industrial applications while reducing operating costs and addressing process scale-up issues, we proposes a new operational technology for engineered yeast based on their mechanistic understanding and a response surface optimization approach. The development and application of low-cost engineered media provide important guidance for utilizing engineered yeast to tackle Pb-contaminated wastewater and for the production of PbS crystalline nanomaterials. The industrial culture system was designed using economical materials and, through the response surface methodology, achieved removal rates of 99.02 ± 0.06 % and 80.95 ± 9.68 % of Pb²⁺ from Pb acid electrolyte and industrial Pb wastewater, respectively. This study presents a new technological solution for cost control and process scale-up based on the bioregulatory mechanisms of engineered yeast, laying the groundwork for their industrial application. Furthermore, it offers essential parameters and theoretical support for the industrial applications of engineered yeast in Pb wastewater treatment.

Saccharomyces cerevisiae strains performing similarly during fermentation of lignocellulosic hydrolysates show pronounced differences in transcriptional stress responses

Improving our understanding of the transcriptional changes of Saccharomyces cerevisiae during fermentation of lignocellulosic hydrolysates is crucial for the creation of more efficient strains to be used in biorefineries. We performed RNA sequencing of a CEN.PK laboratory strain, two industrial strains (KE6-12 and Ethanol Red), and two wild-type isolates of the LBCM collection when cultivated anaerobically in wheat straw hydrolysate. Many of the differently expressed genes identified among the strains have previously been reported to be important for tolerance to lignocellulosic hydrolysates or inhibitors therein. Our study demonstrates that stress responses typically identified during aerobic conditions such as glutathione metabolism, osmotolerance, and detoxification processes also are important for anaerobic processes. Overall, the transcriptomic responses were largely strain dependent, and we focused our study on similarities and differences in the transcriptomes of the LBCM strains. The expression of sugar transporter-encoding genes was higher in LBCM31 compared with LBCM109 that showed high expression of genes involved in iron metabolism and genes promoting the accumulation of sphingolipids, phospholipids, and ergosterol. These results highlight different evolutionary adaptations enabling S. cerevisiae to strive in lignocellulosic hydrolysates and suggest novel gene targets for improving fermentation performance and robustness.

IMPORTANCE

The need for sustainable alternatives to oil-based production of biochemicals and biofuels is undisputable. Saccharomyces cerevisiae is the most commonly used industrial fermentation workhorse. The fermentation of lignocellulosic hydrolysates, second-generation biomass unsuited for food and feed, is still hampered by lowered productivities as the raw material is inhibitory for the cells. In order to map the genetic responses of different S. cerevisiae strains, we performed RNA sequencing of a CEN.PK laboratory strain, two industrial strains (KE6-12 and Ethanol Red), and two wild-type isolates of the LBCM collection when cultivated anaerobically in wheat straw hydrolysate. While the response to inhibitors of S. cerevisiae has been studied earlier, this has in previous studies been done in aerobic conditions. The transcriptomic analysis highlights different evolutionary adaptations among the different S. cerevisiae strains and suggests novel gene targets for improving fermentation performance and robustness.

Adaptive responses of erythritol-producing Yarrowia lipolytica to thermal stress after evolution

Elucidation of the thermotolerance mechanism of erythritol-producing Yarrowia lipolytica is of great significance to breed robust industrial strains and reduce cost. This study aimed to breed thermotolerant Y. lipolytica and investigate the mechanism underlying the thermotolerant phenotype. Yarrowia lipolytica HT34, Yarrowia lipolytica HT36, and Yarrowia lipolytica HT385 that were capable of growing at 34 °C, 36 °C, and 38.5 °C, respectively, were obtained within 150 days (352 generations) by adaptive laboratory evolution (ALE) integrated with 60Co-γ radiation and ultraviolet ray radiation. Comparative genomics analysis showed that genes involved in signal transduction, transcription, and translation regulation were mutated during adaptive evolution. Further, we demonstrated that thermal stress increased the expression of genes related to DNA replication and repair, ceramide and steroid synthesis, and the degradation of branched amino acid (BCAA) and free fatty acid (FFA), while inhibiting the expression of genes involved in glycolysis and the citrate cycle. Erythritol production in thermotolerant strains was remarkably inhibited, which might result from the differential expression of genes involved in erythritol metabolism. Exogenous addition of BCAA and soybean oil promoted the growth of HT385, highlighting the importance of BCAA and FFA in thermal stress response. Additionally, overexpression of 11 out of the 18 upregulated genes individually enabled Yarrowia lipolytica CA20 to grow at 34 °C, of which genes A000121, A003183, and A005690 had a better effect. Collectively, this study provides novel insights into the adaptation mechanism of Y. lipolytica to thermal stress, which will be conducive to the construction of thermotolerant erythritol-producing strains. KEY POINTS: • ALE combined with mutagenesis is efficient for breeding thermotolerant Y. lipolytica • Genes encoding global regulators are mutated during thermal adaptive evolution • Ceramide and BCAA are critical molecules for cells to tolerate thermal stress.

The Hrk1 kinase is a determinant of acetic acid tolerance in yeast by modulating H+ and K+ homeostasis

Acetic acid-induced stress is a common challenge in natural environments and industrial bioprocesses, significantly affecting the growth and metabolic performance of Saccharomyces cerevisiae. The adaptive response and tolerance to this stress involves the activation of a complex network of molecular pathways. This study aims to delve deeper into these mechanisms in S. cerevisiae, particularly focusing on the role of the Hrk1 kinase. Hrk1 is a key determinant of acetic acid tolerance, belonging to the NPR/Hal family, whose members are implicated in the modulation of the activity of plasma membrane transporters that orchestrate nutrient uptake and ion homeostasis. The influence of Hrk1 on S. cerevisiae adaptation to acetic acid-induced stress was explored by employing a physiological approach based on previous phosphoproteomics analyses. The results from this study reflect the multifunctional roles of Hrk1 in maintaining proton and potassium homeostasis during different phases of acetic acid-stressed cultivation. Hrk1 is shown to play a role in the activation of plasma membrane H+-ATPase, maintaining pH homeostasis, and in the modulation of plasma membrane potential under acetic acid stressed cultivation. Potassium (K+) supplementation of the growth medium, particularly when provided at limiting concentrations, led to a notable improvement in acetic acid stress tolerance of the hrk1Δ strain. Moreover, abrogation of this kinase expression is shown to confer a physiological advantage to growth under K+ limitation also in the absence of acetic acid stress. The involvement of the alkali metal cation/H+ exchanger Nha1, another proposed molecular target of Hrk1, in improving yeast growth under K+ limitation or acetic acid stress, is proposed.