Creation of an ethanol-tolerant Saccharomyces cerevisiae strain by 266 nm laser radiation and repetitive cultivation

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.

Evolutionary Adaptation by Repetitive Long-Term Cultivation with Gradual Increase in Temperature for Acquiring Multi-Stress Tolerance and High Ethanol Productivity in Kluyveromyces marxianus DMKU 3-1042

During ethanol fermentation, yeast cells are exposed to various stresses that have negative effects on cell growth, cell survival, and fermentation ability. This study, therefore, aims to develop Kluyveromyces marxianus-adapted strains that are multi-stress tolerant and to increase ethanol production at high temperatures through a novel evolutionary adaptation procedure. K. marxianus DMKU 3-1042 was subjected to repetitive long-term cultivation with gradual increases in temperature (RLCGT), which exposed cells to various stresses, including high temperatures. In each cultivation step, 1% of the previous culture was inoculated into a medium containing 1% yeast extract, 2% peptone, and 2% glucose, and cultivation was performed under a shaking condition. Four adapted strains showed increased tolerance to ethanol, furfural, hydroxymethylfurfural, and vanillin, and they also showed higher production of ethanol in a medium containing 16% glucose at high temperatures. One showed stronger ethanol tolerance. Others had similar phenotypes, including acetic acid tolerance, though genome analysis revealed that they had different mutations. Based on genome and transcriptome analyses, we discuss possible mechanisms of stress tolerance in adapted strains. All adapted strains gained a useful capacity for ethanol fermentation at high temperatures and improved tolerance to multi-stress. This suggests that RLCGT is a simple and efficient procedure for the development of robust strains.

Harnessing the Keratinolytic Activity of Bacillus licheniformis Through Random Mutagenesis Using Ultraviolet and Laser Irradiations

Keratinase is one of the important proteases, which is widely used for converting keratin of the keratinaceous materials into various value-added products. In this study, a popular keratinase producer, Bacillus licheniformis PWD-1, was exposed to ultraviolet (UV) and He-Ne laser irradiations to develop high keratinase-producing mutants. Laser irradiation showed a higher lethality of cells (94%) than UV treatment (92%), whereas laser treatment required a longer time (75 min) than UV treatment (20 min). A total of 58 mutants were selected from 176 isolates to study protein and keratinase production capability of the mutants. The highest keratin-to-casein (K:C) ratio (1.43) was exhibited by LU11 mutant, which was obtained from the combined laser and UV irradiations. The purified keratinase (65 kDa) of LU11 showed 40% yield 1.7-fold purity, while the respective value for wild enzyme was 29% and 1.3-fold. Both enzymes showed optimal activity at 55 ℃ and pH 8, with a Z value of 15.78 ℃ for LU11 and 19.72 ℃ for wild strain. The V_max and specific constant (K_cat/K_m) of the mutant enzyme were 357.17 U/ml and 33.11 min^-1 mM^-1, respectively, which were significantly higher than the respective values of wild enzyme (102.04 U/ml and 28.36 min^-1 mM^-1).

Adaptive laboratory evolution principles and applications in industrial biotechnology

Adaptive laboratory evolution (ALE) is an innovative approach for the generation of evolved microbial strains with desired characteristics, by implementing the rules of natural selection as presented in the Darwinian Theory, on the laboratory bench. New as it might be, it has already been used by several researchers for the amelioration of a variety of characteristics of widely used microorganisms in biotechnology. ALE is used as a tool for the deeper understanding of the genetic and/or metabolic pathways of evolution. Another important field targeted by ALE is the manufacturing of products of (high) added value, such as ethanol, butanol and lipids. In the current review, we discuss the basic principles and techniques of ALE, and then we focus on studies where it has been applied to bacteria, fungi and microalgae, aiming to improve their performance to biotechnological procedures and/or inspect the genetic background of evolution. We conclude that ALE is a promising and efficacious method that has already led to the acquisition of useful new microbiological strains in biotechnology and could possibly offer even more interesting results in the future.

Laser Mutagenesis of Phellinus igniarius Protoplasts for the Selective Breeding of Strains with High Laccase Activity

Phellinus igniarius is a medicinal fungus that utilizes lignin as a nutrient substrate. This fungus has a weak lignin degradation ability and, as a result, a slow growth rate. Laccases are crucial enzymes for lignin degradation in P. igniarius, and thus, the cultivation of strains with high laccase activity is expected to increase the growth rate of P. igniarius. To generate P. igniarius strains with high laccase activity, we performed laser mutagenesis of P. igniarius protoplasts and screened for mutants with high laccase activity. Our results showed that the laser power density and P. igniarius protoplast survival rate exhibited a power-function relationship. The power density threshold value between lethality and growth promotion was 0.24 mW/mm². Mutagenesis was carried out using a laser beam diameter of 3 mm and an irradiation period of 40 min. After five generations of selection, we identified a high laccase activity strain, termed SJZ2. The laccase activity in SJZ2 during 4 h of fermentation was increased by 36.84% in comparison with the control and ranged from 0.20216 to 0.27664 U. The Km and Vmax of the laccase produced by SJZ2 were 0.21 mmol/mL and 0.53 mmol/L/min, respectively. This study demonstrated the feasibility of laser mutagenesis of P. igniarius protoplasts for the selection of high laccase activity. This study characterized the key factors in the laser mutagenesis process of P. igniarius protoplasts and provided a reference for the application of lasers in biological mutagenesis. Future studies should evaluate the bioactive functionality and stability of this novel strain of P. igniarius, particularly the organoleptic and medical characteristics of the fruiting bodies.

Selection of thermotolerant Saccharomyces cerevisiae for high temperature ethanol production from molasses and increasing ethanol production by strain improvement

A thermotolerant ethanol fermenting yeast strain is a key requirement for effective ethanol production at high temperature. This work aimed to select a thermotolerant yeast producing a high ethanol concentration from molasses and increasing its ethanol production by mutagenesis. Saccharomyces cerevisiae DMKU 3-S087 was selected from 168 ethanol producing strains because it produced the highest ethanol concentration from molasses at 40 °C. Optimization of molasses broth composition was performed by the response surface method using Box-Behnken design. In molasses broth containing optimal total fermentable sugars (TFS) of 200 g/L and optimal (NH₄)₂SO₄ of 1 g/L, with an initial pH of 5.5 by shaking flask cultivation at 40 °C ethanol, productivity and yield were 58.4 ± 0.24 g/L, 1.39 g/L/h and 0.29 g/g, respectively. Batch fermentation in a 5 L stirred-tank fermenter with 3 L optimized molasses broth adjusted to an initial pH of 5.5 and fermentation controlled at 40 °C and 300 rpm agitation resulted in 72.4 g/L ethanol, 1.21 g/L/h productivity and 0.36 g/g yield at 60 h. Strain DMKU 3-S087 improvement was performed by mutagenesis using ultraviolet radiation and ethyl methane sulfonate (EMS). Six EMS mutants produced higher ethanol (65.2 ± 0.48-73.0 ± 0.54 g/L) in molasses broth containing 200 g/L TFS and 1 g/L (NH₄)₂SO₄ by shake flask fermentation at 37 °C than the wild type (59.8 ± 0.25 g/L). Among these mutants, only mutant S087E100-265 produced higher ethanol (62.5 ± 0.26 g/L) than the wild type (59.5 ± 0.02 g/L) at 40 °C. In addition, mutant S087E100-265 showed better tolerance to high sugar concentration, furfural, hydroxymethylfurfural and acetic acid than the wild type.

Eu3+-Doped Y3−xNdxAl3O12 garnet: synthesis and structural investigation

Nd³⁺-doped yttrium aluminium garnet and Eu³⁺–Nd³⁺-co-Doped yttrium aluminium garnet were synthesized using an environmentally friendly sol–gel method at low temperatures.