Genetic characterization and modification of a bioethanol-producing yeast strain

Multi-omics network model reveals key genes associated with p-coumaric acid stress response in an industrial yeast strain

The production of ethanol from lignocellulosic sources presents increasingly difficult issues for the global biofuel scenario, leading to increased production costs of current second-generation (2G) ethanol when compared to first-generation (1G) plants. Among the setbacks encountered in industrial processes, the presence of chemical inhibitors from pre-treatment processes severely hinders the potential of yeasts in producing ethanol at peak efficiency. However, some industrial yeast strains have, either naturally or artificially, higher tolerance levels to these compounds. Such is the case of S. cerevisiae SA-1, a Brazilian fuel ethanol industrial strain that has shown high resistance to inhibitors produced by the pre-treatment of cellulosic complexes. Our study focuses on the characterization of the transcriptomic and physiological impact of an inhibitor of this type, p-coumaric acid (pCA), on this strain under chemostat cultivation via RNAseq and quantitative physiological data. It was found that strain SA-1 tend to increase ethanol yield and production rate while decreasing biomass yield when exposed to pCA, in contrast to pCA-susceptible strains, which tend to decrease their ethanol yield and fermentation efficiency when exposed to this substance. This suggests increased metabolic activity linked to mitochondrial and peroxisomal processes. The transcriptomic analysis also revealed a plethora of differentially expressed genes located in co-expressed clusters that are associated with changes in biological pathways linked to biosynthetic and energetical processes. Furthermore, it was also identified 20 genes that act as interaction hubs for these clusters, while also having association with altered pathways and changes in metabolic outputs, potentially leading to the discovery of novel targets for metabolic engineering toward a more robust industrial yeast strain.

Global Analysis of Furfural-Induced Genomic Instability Using a Yeast Model

Furfural is an important renewable precursor for multiple commercial chemicals and fuels; a main inhibitor existing in cellulosic hydrolysate, which is used for bioethanol fermentation; and a potential carcinogen, as well. Using a genetic system in Saccharomyces cerevisiae that allows detection of crossover events, we observed that the frequency of mitotic recombination was elevated by 1.5- to 40-fold when cells were treated with 0.1 g/liter to 20 g/liter furfural. Analysis of the gene conversion tracts associated with crossover events suggested that most furfural-induced recombination resulted from repair of DNA double-strand breaks (DSBs) that occurred in the G₁ phase. Furfural was incapable of breaking DNA directly in vitro but could trigger DSBs in vivo related to reactive oxygen species accumulation. By whole-genome single nucleotide polymorphism (SNP) microarray and sequencing, furfural-induced genomic alterations that range from single base substitutions, loss of heterozygosity, and chromosomal rearrangements to aneuploidy were explored. At the whole-genome level, furfural-induced events were evenly distributed across 16 chromosomes but were enriched in high-GC-content regions. Point mutations, particularly the C-to-T/G-to-A transitions, were significantly elevated in furfural-treated cells compared to wild-type cells. This study provided multiple novel insights into the global effects of furfural on genomic stability.IMPORTANCE Whether and how furfural affects genome integrity have not been clarified. Using a Saccharomyces cerevisiae model, we found that furfural exposure leads to in vivo DSBs and elevation in mitotic recombination by orders of magnitude. Gross chromosomal rearrangements and aneuploidy events also occurred at a higher frequency in furfural-treated cells. In a genome-wide analysis, we show that the patterns of mitotic recombination and point mutations differed dramatically in furfural-treated cells and wild-type cells.

Hydrogen peroxide, a potent inducer of global genomic instability

Oxidative stress has been implicated in a variety of human diseases. One plausible mechanism is that reactive active species can induce DNA damages and jeopardize genome integrity. To explore how oxidative stress results in global genomic instability in cells, our current study examined the genomic alterations caused by H₂O₂ exposure at the whole genome level in yeast. Using SNP microarrays and genome sequencing, we mapped H₂O₂-induced genomic alterations in the yeast genome ranging from point mutations and mitotic recombination to chromosomal aneuploidy. Our results suggested most H₂O₂-induced mitotic recombination events were the result of DNA double-stand breaks generated by hydroxyl radicals. Moreover, the mutagenic effect of H₂O₂ was shown to be largely dependent on DNA polymerase ζ. Lastly, we showed that H₂O₂ exposure allows rapid phenotypic evolution in yeast strains. Our findings indicate DNA lesions resulting from H₂O₂ may be general factors that drive genome instability and phenotypic evolution in organisms.

Using drug-loaded pH-responsive poly(4-vinylpyridine) microspheres as a new strategy for intelligent controlling of Lactobacillus plantarum contamination in bioethanol fermentation

Bioethanol fermentation is usually contaminated by bacteria, especially lactic acid bacteria (LAB), thereby leading to decrease of bioethanol yield and serious economic losses. Nisin is safer for controlling of bacterial contamination than antibiotics that are widely applied in industry. Moreover, in LAB contaminative bioethanol fermentation system, consistently decreased pH value provides opportunity to realize pH value responsive material-based release of anti-bacteria substances for intelligent and persistent controlling of bacterial contamination. In this study, nisin was embedded into pH-sensitive poly(4-vinylpyridine) (P4VP) microspheres synthesized by suspension polymerization to realize intelligent controlling of Lactobacillus plantarum contamination in bioethanol fermentation. Chloramphenicol with the highest antimicrobial activity and excellent stability was chosen as the model drug to be embedded into P4VP microspheres to test the drug release behavior. The drug release curve of chloramphenicol-loaded P4VP microspheres showed sustained and pH-responsive release properties. The diameters of the microspheres ranged from 40 to 100 µm. The encapsulation efficiency of nisin into P4VP microspheres was 47.67% and the drug-loading capacity of nisin was 2.5%. Nisin-loaded P4VP microspheres were added into the simulated contaminative fermentation system, and successfully reversed the decline of bioethanol yield secondary to L. plantarum contamination. The results in this study indicated that L. plantarum contamination in bioethanol fermentation could be effectively controlled by nisin-loaded P4VP microspheres.