Improving ethanol tolerance of Saccharomyces cerevisiae through adaptive laboratory evolution using high ethanol concentrations as a selective pressure

Where Biology Meets Engineering: Scaling Up Microbial Nutraceuticals to Bridge Nutrition, Therapeutics, and Global Impact

The global nutraceutical industry is experiencing a paradigm shift, driven by an increasing demand for functional foods and dietary supplements that address malnutrition and chronic diseases such as obesity, diabetes, cardiovascular conditions, and cancer. Traditional plant- and animal-derived nutraceuticals face limitations in scalability, cost, and environmental impact, paving the way for microbial biotechnology as a sustainable alternative. Microbial cells act as bio-factories, converting nutrients like glucose and amino acids into valuable nutraceutical products such as polyunsaturated fatty acids (PUFAs), peptides, and other bioactive compounds. By harnessing their natural metabolic capabilities, microorganisms efficiently synthesize these bioactive compounds, making microbial production a sustainable and effective approach for nutraceutical development. This review explores the transformative role of microbial platforms in the production of nutraceuticals, emphasizing advanced fermentation techniques, synthetic biology, and metabolic engineering. It addresses the challenges of optimizing microbial strains, ensuring product quality, and scaling production while navigating regulatory frameworks. Furthermore, the review highlights cutting-edge technologies such as CRISPR/Cas9 for genome editing, adaptive evolution for strain enhancement, and bioreactor innovations to enhance yield and efficiency. With a focus on sustainability and precision, microbial production is positioned as a game-changer in the nutraceutical industry, offering eco-friendly and scalable solutions to meet global health needs. The integration of omics technologies and the exploration of novel microbial sources hold the potential to revolutionize this field, aligning with the growing consumer demand for innovative and functional bioactive products.

Adaptive Laboratory Evolution Uncovers Potential Role of a DNA Helicase Mutation in Torulaspora delbrueckii Increased Sulphite Resistance

Wine industry has faced pressure to innovate its products. Saccharomyces cerevisiae has been the traditional yeast for producing alcoholic beverages, but interest has shifted from the conventional S. cerevisiae to non-Saccharomyces yeasts for their biotechnological potential. Among these, Torulaspora delbrueckii is particularly notable for its ability to enrich wine with novel flavours. During winemaking, sulphites are added to suppress spoilage microorganisms, making sulphite tolerance a valuable characteristic of wine yeasts. Adaptive laboratory evolution in liquid and solid media improved sulphite resistance in two T. delbrueckii strains, achieving, in the best case, a fourfold increase from 0.50 to 2.00 mM of sodium metabisulphite, highlighting the potential of these evolve strains for winemaking applications. Genomic analysis revealed SNPs/InDels in all the strains, including a novel unique missense mutation common to the four evolved isolates, but absent from the parental strains, located in chromosome VIII (protein TDEL0H03170, homologue of S. cerevisiae MPH1). These genes code for a protein catalogued as an ATP-dependent DNA helicase, known for its role in maintaining genome stability by participating in DNA repair pathways. We propose that this valine-to-serine mutation, common to all the evolved isolates, helps the evolved strains repair sulphite-induced DNA damage more effectively.

Adaptive evolution and mechanism elucidation for ethanol tolerant Saccharomyces cerevisiae used in starch based biorefinery

Ethanol tolerant Saccharomyces cerevisiae is compulsory for ethanol production in starch based biorefinery, especially during high-gravity fermentation. In this study, adaptive evolution with increased initial ethanol concentrations as a driving force was harnessed for achieving ethanol tolerant S. cerevisiae. After evolution, an outstanding ethanol tolerant strain was screened, which contributed to significant improvements in glucose consumption and ethanol production in scenarios of 300 g/L initial glucose, high solid loadings (30 wt%, 33 wt%, 35 wt% and 40 wt%) of corn, and high solid loadings (30 wt% and 33 wt%) of cassava, compared with the original strain. Genome re-sequencing was applied for the evolved strain, and 504 sense mutations in 205 genes were detected, among which PAM1 gene was demonstrated related to the elevated ethanol tolerance. In sum, this study provided a practical approach for obtaining ethanol tolerant strain and the identified PAM1 gene enhanced our understanding on ethanol tolerant mechanism, as well as provided a target basis for rational metabolic engineering.

Alternative Solvents for Life: Framework for Evaluation, Current Status, and Future Research

Life is a complex, dynamic chemical system that requires a dense fluid solvent in which to take place. A common assumption is that the most likely solvent for life is liquid water, and some researchers argue that water is the only plausible solvent. However, a persistent theme in astrobiological research postulates that other liquids might be cosmically common and could be solvents for the chemistry of life. In this article, we present a new framework for the analysis of candidate solvents for life, and we deploy this framework to review substances that have been suggested as solvent candidates. We categorize each solvent candidate through the following four criteria: occurrence, solvation, solute stability, and solvent chemical functionality. Our semiquantitative approach addresses all the requirements for a solvent not only from the point of view of its chemical properties but also from the standpoint of its biochemical function. Only the protonating solvents fulfill all the chemical requirements to be a solvent for life, and of those only water and concentrated sulfuric acid are also likely to be abundant in a rocky planetary context. Among the nonprotonating solvents, liquid CO2 stands out as a planetary solvent, and its potential as a solvent for life should be explored. We conclude with a discussion of whether it is possible for a biochemistry to change solvents as an adaptation to radical changes in a planet's environment. Our analysis provides the basis for prioritizing future experimental work to explore potential complex chemistry on other planets. Key Words: Habitability-Alternative solvents for life-Alternative biochemistry. Astrobiology 24, 1231-1256.

Adaptive laboratory evolution for improved tolerance of vitamin K in Bacillus subtilis

Menaquinone-7 (MK-7), a subtype of vitamin K2 (VK2), assumes crucial roles in coagulation function, calcium homeostasis, and respiratory chain transmission. The production of MK-7 via microbial fermentation boasts mild technological conditions and high biocompatibility. Nevertheless, the redox activity of MK-7 imposes constraints on its excessive accumulation in microorganisms. To address this predicament, an adaptive laboratory evolution (ALE) protocol was implemented in Bacillus subtilis BS011, utilizing vitamin K3 (VK3) as a structural analog of MK-7. The resulting strain, BS012, exhibited heightened tolerance to high VK3 concentrations and demonstrated substantial enhancements in biofilm formation and total antioxidant capacity (T-AOC) when compared to BS011. Furthermore, MK-7 production in BS012 exceeded that of BS011 by 76% and 22% under static and shaking cultivation conditions, respectively. The molecular basis underlying the superior performance of BS012 was elucidated through genome and transcriptome analyses, encompassing observations of alterations in cell morphology, variations in central carbon and nitrogen metabolism, spore formation, and antioxidant systems. In summation, ALE technology can notably enhance the tolerance of B. subtilis to VK and increase MK-7 production, thus offering a theoretical framework for the microbial fermentation production of other VK2 subtypes. Additionally, the evolved strain BS012 can be developed for integration into probiotic formulations within the food industry to maintain intestinal flora homeostasis, mitigate osteoporosis risk, and reduce the incidence of cardiovascular disease. KEY POINTS: • Bacillus subtilis was evolved for improved vitamin K tolerance and menaquinone-7 (MK-7) production • Evolved strains formed wrinkled biofilms and elongated almost twofold in length • Evolved strains induced sporulation to improve tolerance when carbon was limited.

Evolutionary engineering and molecular characterization of cobalt-resistant Rhodobacter sphaeroides

With its versatile metabolism including aerobic and anaerobic respiration, photosynthesis, photo-fermentation and nitrogen fixation, Rhodobacter sphaeroides can adapt to diverse environmental and nutritional conditions, including the presence of various stressors such as heavy metals. Thus, it is an important microorganism to study the molecular mechanisms of bacterial stress response and resistance, and to be used as a microbial cell factory for biotechnological applications or bioremediation. In this study, a highly cobalt-resistant and genetically stable R. sphaeroides strain was obtained by evolutionary engineering, also known as adaptive laboratory evolution (ALE), a powerful strategy to improve and characterize genetically complex, desired microbial phenotypes, such as stress resistance. For this purpose, successive batch selection was performed in the presence of gradually increased cobalt stress levels between 0.1-15 mM CoCl2 for 64 passages and without any mutagenesis of the initial population prior to selection. The mutant individuals were randomly chosen from the last population and analyzed in detail. Among these, a highly cobalt-resistant and genetically stable evolved strain called G7 showed significant cross-resistance against various stressors such as iron, magnesium, nickel, aluminum, and NaCl. Growth profiles and flame atomic absorption spectrometry analysis results revealed that in the presence of 4 mM CoCl2 that significantly inhibited growth of the reference strain, the growth of the evolved strain was unaffected, and higher levels of cobalt ions were associated with G7 cells than the reference strain. This may imply that cobalt ions accumulated in or on G7 cells, indicating the potential of G7 for cobalt bioremediation. Whole genome sequencing of the evolved strain identified 23 single nucleotide polymorphisms in various genes that are associated with transcriptional regulators, NifB family-FeMo cofactor biosynthesis, putative virulence factors, TRAP-T family transporter, sodium/proton antiporter, and also in genes with unknown functions, which may have a potential role in the cobalt resistance of R. sphaeroides.

Histidine modified Fe3O4 nanoparticles improving the ethanol yield and tolerance of Saccharomyces cerevisiae

Saccharomyces cerevisiae, the primary microorganism involved in ethanol production, is hindered by the accumulation of ethanol, leading to reduced ethanol production. In this study, we employed histidine-modified Fe3O4 nanoparticles (His-Fe3O4) for the first time, to the best of our knowledge, as a method to enhance ethanol yield during the S. cerevisiae fermentation process. The results demonstrated that exposing S. cerevisiae cells to Fe3O4 nanoparticles (Fe3O4 NPs) led to increased cell proliferation and glucose consumption. Moreover, the introduction of His-Fe3O4 significantly boosted ethanol content by 17.3% (p < 0.05) during fermentation. Subsequent findings indicated that the increase in ethanol content was associated with enhanced ethanol tolerance and improved electron transport efficiency. This study provided evidence for the positive effects of His-Fe3O4 on S. cerevisiae cells and proposed a straightforward approach to enhance ethanol production in S. cerevisiae fermentation. The mediation of improved ethanol tolerance offers significant potential in the fermentation and bioenergy sectors.

Optimal trade-off between boosted tolerance and growth fitness during adaptive evolution of yeast to ethanol shocks

BACKGROUND

The selection of Saccharomyces cerevisiae strains with higher alcohol tolerance can potentially increase the industrial production of ethanol fuel. However, the design of selection protocols to obtain bioethanol yeasts with higher alcohol tolerance poses the challenge of improving industrial strains that are already robust to high ethanol levels. Furthermore, yeasts subjected to mutagenesis and selection, or laboratory evolution, often present adaptation trade-offs wherein higher stress tolerance is attained at the expense of growth and fermentation performance. Although these undesirable side effects are often associated with acute selection regimes, the utility of using harsh ethanol treatments to obtain robust ethanologenic yeasts still has not been fully investigated.

RESULTS

We conducted an adaptive laboratory evolution by challenging four populations (P1-P4) of the Brazilian bioethanol yeast, Saccharomyces cerevisiae PE-2_H4, through 68-82 cycles of 2-h ethanol shocks (19-30% v/v) and outgrowths. Colonies isolated from the final evolved populations (P1c-P4c) were subjected to whole-genome sequencing, revealing mutations in genes enriched for the cAMP/PKA and trehalose degradation pathways. Fitness analyses of the isolated clones P1c-P3c and reverse-engineered strains demonstrated that mutations were primarily selected for cell viability under ethanol stress, at the cost of decreased growth rates in cultures with or without ethanol. Under this selection regime for stress survival, the population P4 evolved a protective snowflake phenotype resulting from BUD3 disruption. Despite marked adaptation trade-offs, the combination of reverse-engineered mutations cyr1A1474T/usv1Δ conferred 5.46% higher fitness than the parental PE-2_H4 for propagation in 8% (v/v) ethanol, with only a 1.07% fitness cost in a culture medium without alcohol. The cyr1A1474T/usv1Δ strain and evolved P1c displayed robust fermentations of sugarcane molasses using cell recycling and sulfuric acid treatments, mimicking Brazilian bioethanol production.

CONCLUSIONS

Our study combined genomic, mutational, and fitness analyses to understand the genetic underpinnings of yeast evolution to ethanol shocks. Although fitness analyses revealed that most evolved mutations impose a cost for cell propagation, combination of key mutations cyr1A1474T/usv1Δ endowed yeasts with higher tolerance for growth in the presence of ethanol. Moreover, alleles selected for acute stress survival comprising the P1c genotype conferred stress tolerance and optimal performance under conditions simulating the Brazilian industrial ethanol production.

From Saccharomyces cerevisiae to Ethanol: Unlocking the Power of Evolutionary Engineering in Metabolic Engineering Applications

Increased human population and the rapid decline of fossil fuels resulted in a global tendency to look for alternative fuel sources. Environmental concerns about fossil fuel combustion led to a sharp move towards renewable and environmentally friendly biofuels. Ethanol has been the primary fossil fuel alternative due to its low carbon emission rates, high octane content and comparatively facile microbial production processes. In parallel to the increased use of bioethanol in various fields such as transportation, heating and power generation, improvements in ethanol production processes turned out to be a global hot topic. Ethanol is by far the leading yeast output amongst a broad spectrum of bio-based industries. Thus, as a well-known platform microorganism and native ethanol producer, baker's yeast Saccharomyces cerevisiae has been the primary subject of interest for both academic and industrial perspectives in terms of enhanced ethanol production processes. Metabolic engineering strategies have been primarily adopted for direct manipulation of genes of interest responsible in mainstreams of ethanol metabolism. To overcome limitations of rational metabolic engineering, an alternative bottom-up strategy called inverse metabolic engineering has been widely used. In this context, evolutionary engineering, also known as adaptive laboratory evolution (ALE), which is based on random mutagenesis and systematic selection, is a powerful strategy to improve bioethanol production of S. cerevisiae. In this review, we focus on key examples of metabolic and evolutionary engineering for improved first- and second-generation S. cerevisiae bioethanol production processes. We delve into the current state of the field and show that metabolic and evolutionary engineering strategies are intertwined and many metabolically engineered strains for bioethanol production can be further improved by powerful evolutionary engineering strategies. We also discuss potential future directions that involve recent advancements in directed genome evolution, including CRISPR-Cas9 technology.