In-Depth Two-Stage Transcriptional Reprogramming and Evolutionary Engineering of Saccharomyces cerevisiae for Efficient Bioethanol Production from Xylose with Acetate

Dual assistance of surfactants in glycerol organosolv pretreatment and enzymatic hydrolysis of lignocellulosic biomass for bioethanol production

This study investigated an innovative strategy of incorporating surfactants into alkaline-catalyzed glycerol pretreatment and enzymatic hydrolysis to improve lignocellulosic biomass (LCB) conversion efficiency. Results revealed that adding 40 mg/g PEG 4000 to the pretreatment at 195 °C obtained the highest glucose yield (84.6%). This yield was comparable to that achieved without surfactants at a higher temperature (240 °C), indicating a reduction of 18.8% in the required heat input. Subsequently, Triton X-100 addition during enzymatic hydrolysis of PEG 4000-assisted pretreated substrate increased glucose yields to 92.1% at 6 FPU/g enzyme loading. High-solid fed-batch semi-simultaneous saccharification and co-fermentation using this dual surfactant strategy gave 56.4 g/L ethanol and a positive net energy gain of 1.4 MJ/kg. Significantly, dual assistance with surfactants rendered 56.3% enzyme cost savings compared to controls without surfactants. Therefore, the proposed surfactant dual-assisted promising approach opens the gateway to economically viable enzyme-mediated LCB biorefinery.

Metabolic engineering of Saccharomyces cerevisiae for the synthesis of valuable chemicals

In the twenty first century, biotechnology offers great opportunities and solutions to climate change mitigation, energy and food security and resource efficiency. The use of metabolic engineering to modify microorganisms for producing industrially significant chemicals is developing and becoming a trend. As a famous, generally recognized as a safe (GRAS) model microorganism, Saccharomyces cerevisiae is widely used due to its excellent operational convenience and high fermentation efficiency. This review summarizes recent advancements in the field of using metabolic engineering strategies to construct engineered S. cerevisiae over the past ten years. Five different types of compounds are classified by their metabolites, and the modified metabolic pathways and strategies are summarized and discussed independently. This review may provide guidance for future metabolic engineering efforts toward such compounds and analogues. Additionally, the limitations of S. cerevisiae as a cell factory and its future trends are comprehensively discussed.

High titer (>100 g/L) ethanol production from pretreated corn stover hydrolysate by modified yeast strains

Developing a reliable lignocellulose pretreatment method to extract mixed sugars and engineering efficient strains capable of utilizing xylose are crucial for advancing cellulosic ethanol production. In this study, chemical and characterization analyses revealed that alkali cooking can significantly remove lignin from lignocellulose crops. The highest amount of mixed sugar was obtained from corn stover hydrolysates with a 15 % solid loading. Our genetically engineered yeast strain ΔsnR4, derived from a well-staged WXY70, demonstrated excellent performance in low 10 % solids loading corn stover hydrolysate, producing a high ethanol yield of 0.485 g/g total sugars. When a combined NaOH-ball milling pretreatment strategy was applied at high solids loading, ΔsnR4 exhibited the maximum ethanol titer of 110.9 g/L within 36 h, achieving an ethanol yield of 92.9 % theoretical maximum. Therefore, ΔsnR4 is highly compatible with high solid loading NaOH-ball milling pretreatment, making it a potential candidate for industrial cellulosic ethanol.

An outlook to sophisticated technologies and novel developments for metabolic regulation in the Saccharomyces cerevisiae expression system

Saccharomyces cerevisiae is one of the most extensively used biosynthetic systems for the production of diverse bioproducts, especially biotherapeutics and recombinant proteins. Because the expression and insertion of foreign genes are always impaired by the endogenous factors of Saccharomyces cerevisiae and nonproductive procedures, various technologies have been developed to enhance the strength and efficiency of transcription and facilitate gene editing procedures. Thus, the limitations that block heterologous protein secretion have been overcome. Highly efficient promoters responsible for the initiation of transcription and the accurate regulation of expression have been developed that can be precisely regulated with synthetic promoters and double promoter expression systems. Appropriate codon optimization and harmonization for adaption to the genomic codon abundance of S. cerevisiae are expected to further improve the transcription and translation efficiency. Efficient and accurate translocation can be achieved by fusing a specifically designed signal peptide to an upstream foreign gene to facilitate the secretion of newly synthesized proteins. In addition to the widely applied promoter engineering technology and the clear mechanism of the endoplasmic reticulum secretory pathway, the innovative genome editing technique CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated system) and its derivative tools allow for more precise and efficient gene disruption, site-directed mutation, and foreign gene insertion. This review focuses on sophisticated engineering techniques and emerging genetic technologies developed for the accurate metabolic regulation of the S. cerevisiae expression system.

Developing high-dimensional machine learning models to improve generalization ability and overcome data insufficiency for mixed sugar fermentation simulation

Biorefinery can be promoted by building accurate machine learning models. This work proposed a strategy to enhance model's generalization ability and overcome insufficient data conditions for mixed sugar fermentation simulation. Multiple inputs single output models, using initial glucose, initial xylose, and time together as inputs, have higher generalization ability than single input single output models with time as sole input in predicting glucose, xylose, ethanol, or biomass separately. Multiple inputs multiple outputs models, integrating outputs, enhanced model accuracy and resulted in an average R² at 0.99. To overcome data insufficiency conditions, consensus yeast (CY) model, through consolidating data from 4 yeasts, obtained R² at 0.90. By adjusting the pretrained CY model, the model can save more than 50% data and get R² at 0.95 and 0.93 for yeast and bacterial fermentation simulation. The strategy can expand the application range and save costs of data curation for ANN models.

Rewiring of metabolic pathways in yeasts for sustainable production of biofuels

The ever-increasing global energy demand has led world towards negative repercussions such as depletion of fossil fuels, pollution, global warming and climate change. Designing microbial cell factories for the sustainable production of biofuels is therefore an active area of research. Different yeast cells have been successfully engineered using synthetic biology and metabolic engineering approaches for the production of various biofuels. In the present article, recent advancements in genetic engineering strategies for production of bioalcohols, isoprenoid-based biofuels and biodiesels in different yeast chassis designs are reviewed, along with challenges that must be overcome for efficient and high titre production of biofuels.

Overexpressing GRE3 in Saccharomyces cerevisiae enables high ethanol production from different lignocellulose hydrolysates

The efficiently renewable bioethanol can help to alleviate energy crisis and environmental pollution. Genetically modified strains for efficient use of xylose and developing lignocellulosic hydrolysates play an essential role in facilitating cellulosic ethanol production. Here we present a promising strain GRE3^OE via GRE3 overexpressed in a previously reported Saccharomyces cerevisiae strain WXY70. A comprehensive evaluation of the fermentation level of GRE3^OE in alkaline-distilled sweet sorghum bagasse, sorghum straw and xylose mother liquor hydrolysate. Under simulated corn stover hydrolysate, GRE3^OE produced 53.39 g/L ethanol within 48 h. GRE3^OE produced about 0.498 g/g total sugar in sorghum straw hydrolysate solution. Moreover, GRE3^OE consumed more xylose than WXY70 in the high-concentration xylose mother liquor. Taken together, GRE3^OE could be a candidate strain for industrial ethanol development, which is due to its remarkable fermentation efficiency during different lignocellulosic hydrolysates.

Metabolic and Evolutionary Engineering of Diploid Yeast for the Production of First- and Second-Generation Ethanol

Despite a growing preference for second-generation (2G) ethanol in industries, its application is severely restricted owing to a major obstacle of developing a suitable yeast strain for fermentation using feedstock biomasses. In this study, a yeast strain, Saccharomyces cerevisiae A31Z, for 2G bioethanol production was developed from an industrial strain, Angel, using metabolic engineering by the incorporation of gene clusters involved in the xylose metabolism combined with adaptive evolution for evolving its anti-inhibitory properties. This strain outcompeted its ancestors in xylose utilization and subsequent ethanol production and manifested higher tolerance against common inhibitors from lignocellulosic hydrolysates, and also it lowered the production of glycerol by-product. Furthermore, A31Z outperformed in ethanol production using industrial hydrolysate from dried distillers grains with solubles and whole corn. Overall, this study provided a promising path for improving 2G bioethanol production in industries using S. cerevisiae.

Transcriptomic evaluation on methyl bromide-induced phytotoxicity in Arabidopsis thaliana and its mode of phytotoxic action via the occurrence of reactive oxygen species and uneven distribution of auxin hormones

The increase in worldwide trade has caused the quality maintenance of commercialized agriproducts to be crucial in keeping its economic value. In recent years, methyl bromide (MB) has been used dominantly during quarantine and pre-shipment, despite it being an environmental hazard with global repercussions. Through this study, it was shown that Arabidopsis thaliana's 2 h exposure to the MB treatment displayed no signs of phytotoxicity, whereas its 4 h exposure significantly interfered with growth. The transcriptomic analysis found the molecular modifications in A. thaliana after the MB fumigation with the up-regulation of genes specifically relative to the abiotic and oxidative stress, and the down-regulation of auxin transporter genes. Some important gene expressions were verified by RT-qPCR and their expression patterns were similar. Oxidative stresses via the reactive oxygen species (ROS) in relation to MB phytotoxicity were confirmed with the increased malondialdehyde in MB-4h-treated A. thaliana. Uneven distribution of auxins via lower expression of auxin transporter genes was also determined using UPLC-ESI-QqQ MS. Application of two ROS scavengers such as N-acetyl-cysteine and L-glutathione minimized MB phytotoxic effect in A. thaliana. Therefore, MB caused severe oxidative stress, and alternatives regarding the use of MB should be considered.

Overexpressing CCW12 in Saccharomyces cerevisiae enables highly efficient ethanol production from lignocellulose hydrolysates

A Saccharomyces cerevisiae strain CCW12^OE was constructed by overexpressing CCW12 in a previously reported strain WXY70 harboring six xylose utilization genes. CCW12^OE produced an optimal ethanol yield of 98.8% theoretical value within 48 h in a simulated corn stover hydrolysate. CCW12^OEwas comprehensively evaluated for ethanol production in Miscanthus, maize and corncob hydrolysates, among which a 96.1% theoretical value was achieved within 12 h in corncob hydrolysates. Under normal growth conditions, CCW12^OE did not display altered cell morphology; however, in the presence of acetate, CCW12^OE maintained relatively intact cell structure and increased cell wall thickness by nearly 50%, while WXY70 had abnormal cell morphology and reduced cell wall thickness by nearly 50%. Besides, CCW12^OE had higher fermentation capacity than that of WXY70 in undetoxified and detoxified hydrolysates with both aerobic and anaerobic conditions, demonstrating that CCW12 overexpression alone exhibits improved stress resistance and better fermentation performance.

Minimize the Xylitol Production in Saccharomyces cerevisiae by Balancing the Xylose Redox Metabolic Pathway

Xylose is the second most abundant sugar in lignocellulose, but it cannot be used as carbon source by budding yeast Saccharomyces cerevisiae. Rational promoter elements engineering approaches were taken for efficient xylose fermentation in budding yeast. Among promoters surveyed, HXT7 exhibited the best performance. The HXT7 promoter is suppressed in the presence of glucose and derepressed by xylose, making it a promising candidate to drive xylose metabolism. However, simple ectopic expression of both key xylose metabolic genes XYL1 and XYL2 by the HXT7 promoter resulted in massive accumulation of the xylose metabolic byproduct xylitol. Through the HXT7-driven expression of a reported redox variant, XYL1-K270R, along with optimized expression of XYL2 and the downstream pentose phosphate pathway genes, a balanced xylose metabolism toward ethanol formation was achieved. Fermented in a culture medium containing 50 g/L xylose as the sole carbon source, xylose is nearly consumed, with less than 3 g/L xylitol, and more than 16 g/L ethanol production. Hence, the combination of an inducible promoter and redox balance of the xylose utilization pathway is an attractive approach to optimizing fuel production from lignocellulose.

Overexpression of SFA1 in engineered Saccharomyces cerevisiae to increase xylose utilization and ethanol production from different lignocellulose hydrolysates

Here, an engineered Saccharomyces cerevisiae strain SFA1^OE was constructed by overexpressing SFA1 in a reported WXY70 with effective six-gene clusters. Under simulated maize hydrolysate, SFA1^OE produced an ethanol yield of 0.492 g/g totalsugars within 48 h. The productivity of SFA1^OE was comprehensively evaluated in typical hydrolysates from stalks of maize, sweet sorghum, wheat and Miscanthus. Within 48 h, SFA1^OE achieved an ethanol yield of 0.489 g/g totalsugars in the optimized hydrolysate of alkaline-distilled sweet sorghum bagasse derived from Advanced Solid-State Fermentation process. By crossing SFA1^OE with a DQ1-derived haploid strain, we obtained an evolved diploid strain SQ-2, exhibiting improved ethanol production and thermotolerance. This study demonstrates that overexpressing SFA1 enables efficient fermentation performance in different lignocellulosic hydrolysates, especially in the hydrolysate of alkaline-distilled sweet sorghum bagasse. The increased cellulosic bioethanol production of SFA1^OE provides a promising platform for efficient biorefineries.