Transcriptomic analysis of synchrony and productivity in self-cycling fermentation of engineered yeast producing shikimic acid.
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ABSTRACT:
SUBMITTER: Tan Y
PROVIDER: S-EPMC8660916 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The cellulosic ethanol industry has developed efficient strategies for converting sugars obtained from various cellulosic feedstocks to bioethanol. However, any further major improvements in ethanol productivity will require development of novel and innovative fermentation strategies that enhance incumbent technologies in a cost-effective manner. The present study investigates the feasibility of applying self-cycling fermentation (SCF) to cellulosic ethanol production to elevate productivity. SCF is a semi-continuous cycling process that employs the following strategy: once the onset of stationary phase is detected, half of the broth volume is automatically harvested and replaced with fresh medium to initiate the next cycle. SCF has been shown to increase product yield and/or productivity in many types of microbial cultivation. To test whether this cycling process could increase productivity during ethanol fermentations, we mimicked the process by manually cycling the fermentation for five cycles in shake flasks, and then compared the results to batch operation.Mimicking SCF for five cycles resulted in regular patterns with regards to glucose consumption, ethanol titer, pH, and biomass production. Compared to batch fermentation, our cycling strategy displayed improved ethanol volumetric productivity (the titer of ethanol produced in a given cycle per corresponding cycle time) and specific productivity (the amount of ethanol produced per cellular biomass) by 43.1 ± 11.6 and 42.7 ± 9.8%, respectively. Five successive cycles contributed to an improvement of overall productivity (the aggregate amount of ethanol produced at the end of a given cycle per total processing time) and the estimated annual ethanol productivity (the amount of ethanol produced per year) by 64.4 ± 3.3 and 33.1 ± 7.2%, respectively.This study provides proof of concept that applying SCF to ethanol production could significantly increase productivities, which will help strengthen the cellulosic ethanol industry.
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Project description:BackgroundThe growth of the cellulosic ethanol industry is currently impeded by high production costs. One possible solution is to improve the performance of fermentation itself, which has great potential to improve the economics of the entire production process. Here, we demonstrated significantly improved productivity through application of an advanced fermentation approach, named self-cycling fermentation (SCF), for cellulosic ethanol production.ResultsThe flow rate of outlet gas from the fermenter was used as a real-time monitoring parameter to drive the cycling of the ethanol fermentation process. Then, long-term operation of SCF under anaerobic conditions was improved by the addition of ergosterol and fatty acids, which stabilized operation and reduced fermentation time. Finally, an automated SCF system was successfully operated for 21 cycles, with robust behavior and stable ethanol production. SCF maintained similar ethanol titers to batch operation while significantly reducing fermentation and down times. This led to significant improvements in ethanol volumetric productivity (the amount of ethanol produced by a cycle per working volume per cycle time)-ranging from 37.5 to 75.3%, depending on the cycle number, and in annual ethanol productivity (the amount of ethanol that can be produced each year at large scale)-reaching 75.8 ± 2.9%. Improved flocculation, with potential advantages for biomass removal and reduction in downstream costs, was also observed.ConclusionOur successful demonstration of SCF could help reduce production costs for the cellulosic ethanol industry through improved productivity and automated operation.
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Project description:Hydrogen, the most abundant and lightest element in the universe, has much potential as a future energy source. Hydrogenases catalyse one of the simplest chemical reactions, 2H(+) + 2e(-) ? H(2), yet their structure is very complex. Biologically, hydrogen can be produced via photosynthetic or fermentative routes. This review provides an overview of microbial production of hydrogen by fermentation (currently the more favourable route) and focuses on biochemical pathways, theoretical hydrogen yields and hydrogenase structure. In addition, several examples of metabolic engineering to enhance fermentative hydrogen production are presented along with some examples of expression of heterologous hydrogenases for enhanced hydrogen production.
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Project description:The economic feasibility and waste treatment problem are challenges to the industrialization of lycopene production from Saccharomyces cerevisiae. In this study, fermentation wastewater, biomass residue, and residual D-galactose are recycled for lycopene production. Results show that when fresh water is totally replaced by wastewater, lycopene titer attains 1.21 ± 0.02 g/L, which is 14.2% higher than the fresh water group (P < 0.05). An 80% replacement ratio of yeast extract by biomass residue causes no significant difference to lycopene production while 100% replacement ratio significantly lowers lycopene titer compared with the yeast extract group. Then, a novel fermentation medium containing wastewater and biomass residue with supplementing 3 g/L yeast extract and D-galactose is used for lycopene production. Lycopene titer increases 22.4% than the traditional fermentation in shake flasks (P < 0.05). Continuous self-cycling strategy using wastewater and biomass residue was tested in shake flasks. The mean lycopene titer of the first five recycles shows no significant difference with the start batch. Scaling up to 70 L fermenter, the mean lycopene titer attains 5.88 ± 0.15 g/L in three recycles, which is 22.25% higher than the start batch (P < 0.05). Economic analysis shows that the lowest unite product cost is achieved when four recycles are accomplished, which is 29.6% lower than the traditional fermentation while the chemical oxygen demand decreases 64.0%. Our study shows that continuous self-cycling fermentation process for lycopene production is feasible for the first time. The comprehensive utilization of wastewater and biomass residue from lycopene production by S. cerevisiae and achievement of high lycopene titer will hopefully accelerate industrialization of microbial production of lycopene.
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Project description:Ammonia is an essential substance for agriculture and the chemical industry. The intracellular production of ammonia in yeast (Saccharomyces cerevisiae) by metabolic engineering is difficult because yeast strongly assimilates ammonia, and the knockout of genes enabling this assimilation is lethal. Therefore, we attempted to produce ammonia outside the yeast cells by displaying a glutaminase (YbaS) from Escherichia coli on the yeast cell surface. YbaS-displaying yeast successfully produced 3.34 g/L ammonia from 32.6 g/L glutamine (83.2% conversion rate), providing it at a higher yield than in previous studies. Next, using YbaS-displaying yeast, we also succeeded in producing ammonia from glutamine in soybean residues (okara) produced as food waste from tofu production. Therefore, ammonia production outside cells by displaying ammonia-lyase on the cell surface is a promising strategy for producing ammonia from food waste as a novel energy resource, thereby preventing food loss.
| S-EPMC7158961 | biostudies-literature
Project description:Dekkera bruxellensis is a non-conventional Crabtree-positive yeast with a good ethanol production capability. Compared to Saccharomyces cerevisiae, its tolerance to acidic pH and its utilization of alternative carbon sources make it a promising organism for producing biofuel. In this study, we developed an auxotrophic transformation system and an expression vector, which enabled the manipulation of D. bruxellensis, thereby improving its fermentative performance. Its gene ADH3, coding for alcohol dehydrogenase, was cloned and overexpressed under the control of the strong and constitutive promoter TEF1. Our recombinant D. bruxellensis strain displayed 1.4 and 1.7 times faster specific glucose consumption rate during aerobic and anaerobic glucose fermentations, respectively; it yielded 1.2 times and 1.5 times more ethanol than did the parental strain under aerobic and anaerobic conditions, respectively. The overexpression of ADH3 in D. bruxellensis also reduced the inhibition of fermentation by anaerobiosis, the "Custer effect". Thus, the fermentative capacity of D. bruxellensis could be further improved by metabolic engineering.
| S-EPMC4786601 | biostudies-literature
Project description:BackgroundEfficient production of SA in Escherichia coli has been achieved by modifying key genes of the central carbon metabolism and SA pathway, resulting in overproducing strains grown in batch- or fed-batch-fermentor cultures using a complex broth including glucose and YE. In this study, we performed a GTA to identify those genes significantly upregulated in an engineered E. coli strain, PB12.SA22, in mid EXP (5 h), early STA (STA1, 9 h), and late STA (STA2, 44 h) phases, grown in complex fermentation broth in batch-fermentor cultures.ResultsGrowth of E. coli PB12.SA22 in complex fermentation broth for SA production resulted in an EXP growth during the first 9 h of cultivation depending of supernatant available aromatic amino acids provided by YE because, when tryptophan was totally consumed, cells entered into a second, low-growth phase (even in the presence of glucose) until 26 h of cultivation. At this point, glucose was completely consumed but SA production continued until the end of the fermentation (50 h) achieving the highest accumulation (7.63 g/L of SA). GTA between EXP/STA1, EXP/STA2 and STA1/STA2 comparisons showed no significant differences in the regulation of genes encoding enzymes of central carbon metabolism as in SA pathway, but those genes encoding enzymes involved in sugar, amino acid, nucleotide/nucleoside, iron and sulfur transport; amino acid catabolism and biosynthesis; nucleotide/nucleoside salvage; acid stress response and modification of IM and OM were upregulated between comparisons.ConclusionsGTA during SA production in batch-fermentor cultures of strain PB12.SA22 grown in complex fermentation broth during the EXP, STA1 and STA2 phases was studied. Significantly, upregulated genes during the EXP and STA1 phases were associated with transport, amino acid catabolism, biosynthesis, and nucleotide/nucleoside salvage. In STA2, upregulation of genes encoding transporters and enzymes involved in the synthesis and catabolism of Arg suggests that this amino acid could have a key role in the fuelling of carbon toward SA synthesis, whereas upregulation of genes involved in pH stress response, such as membrane modifications, suggests a possible response to environmental conditions imposed on the cell at the end of the fermentation.
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Project description:Commercial wine yeast strains of the species Saccharomyces cerevisiae have been selected to satisfy many different, and sometimes highly specific, oenological requirements. As a consequence, more than 200 different strains with significantly diverging phenotypic traits are produced globally. This genetic resource has been rather neglected by the scientific community because industrial strains are less easily manipulated than the limited number of laboratory strains that have been successfully employed to investigate fundamental aspects of cellular biology. However, laboratory strains are unsuitable for the study of many phenotypes that are of significant scientific and industrial interest. Here, we investigate whether a comparative transcriptomics and phenomics approach, based on the analysis of five phenotypically diverging industrial wine yeast strains, can provide insights into the molecular networks that are responsible for the expression of such phenotypes. For this purpose, some oenologically relevant phenotypes, including resistance to various stresses, cell wall properties, and metabolite production of these strains were evaluated and aligned with transcriptomic data collected during alcoholic fermentation. The data reveal significant differences in gene regulation between the five strains. While the genetic complexity underlying the various successive stress responses in a dynamic system such as wine fermentation reveals the limits of the approach, many of the relevant differences in gene expression can be linked to specific phenotypic differences between the strains. This is, in particular, the case for many aspects of metabolic regulation. The comparative approach therefore opens new possibilities to investigate complex phenotypic traits on a molecular level.
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Project description:Quinoa, a nutritional grain, can be used as an ingredient in gluten-free sourdoughs. This study characterizes quinoa flour spontaneous fermentation with emphasis in the isolation of exopolysaccharide (EPS) producer bacteria. Real, red and black grains were studied. Dough yield, microbiota composition and fermentation biochemistry were determined for a total of 36 quinoa flour fermentations. The fermentation biochemistry was monitored by high-performance liquid chromatography (HPLC) analysis, pH measurement and titratable acidity. Changes in the microbiota were monitored by plating on deMann Rogosa and Sharp 5 agar (MRS5) and yeast and mold agar (YMA) plates and with metagenetic analysis. The ability to produce exopolysaccharides was screened in selected lactic acid bacteria (LAB) isolates. Production of organic acids in the spontaneous fermentation dropped the pH to 4.0 ± 0.3. The community of presumptive LAB reached 8.37 ± 0.01 log colony forming units (CFU)/mL by day 8 of back-slopped fermentations. The microbiota was composed of Lactobacillus, Enterococcus, Leuconostoc, Lactococcus, Pediococcus and Weissella. P. pentosaceous,L. citreum and W. cibaria were able to produce EPS in a starch-rich medium. P. pentosaceous showed higher exopolysaccharide yield, rapid acidifying kinetics and was able to drop the dough broth pH to values below 4.0 and a positive fermentation quotient after 24 h of incubation. Therefore, the bacterium might be a potential candidate for quinoa sourdough production.
| S-EPMC7142942 | biostudies-literature
Project description:Comparison between two commercial wine yeast strains (UCD522 and P29) differing in their production of H2S during wine fermentation.
2009-12-03 | GSE16215 | GEO