Tailored UPRE2 variants for dynamic gene regulation in yeast.

Genetic elements are foundational in synthetic biology serving as vital building blocks. They enable programming host cells for efficient production of valuable chemicals and recombinant proteins. The unfolded protein response (UPR) is a stress pathway in which the transcription factor Hac1 interacts with the upstream unfolded protein response element (UPRE) of the promoter to restore endoplasmic reticulum (ER) homeostasis. Here, we created a UPRE2 mutant (UPRE2m) library. Several rounds of screening identified many elements with enhanced responsiveness and a wider dynamic range. The most active element m84 displayed a response activity 3.72 times higher than the native UPRE2. These potent elements are versatile and compatible with various promoters. Overexpression of HAC1 enhanced stress signal transduction, expanding the signal output range of UPRE2m. Through molecular modeling and site-directed mutagenesis, we pinpointed the DNA-binding residue Lys60 in Hac1(Hac1-K60). We also confirmed that UPRE2m exhibited a higher binding affinity to Hac1. This shed light on the mechanism underlying the Hac1-UPRE2m interaction. Importantly, applying UPRE2m for target gene regulation effectively increased both recombinant protein production and natural product synthesis. These genetic elements provide valuable tools for dynamically regulating gene expression in yeast cell factories.

Overexpression of genes by stress-responsive promoters increases protein secretion in Saccharomyces cerevisiae.

Recombinant proteins produced by cell factories are now widely used in various fields. Many efforts have been made to improve the secretion capacity of cell factories to meet the increasing demand for recombinant proteins. Recombinant protein production usually causes cell stress in the endoplasmic reticulum (ER). The overexpression of key genes possibly removes limitations in protein secretion. However, inappropriate gene expression may have negative effects. There is a need for dynamic control of genes adapted to cellular status. In this study, we constructed and characterized synthetic promoters that were inducible under ER stress conditions in Saccharomyces cerevisiae. The unfolded protein response element UPRE2, responding to stress with a wide dynamic range, was assembled with various promoter core regions, resulting in UPR-responsive promoters. Synthetic responsive promoters regulated gene expression by responding to stress level, which reflected the cellular status. The engineered strain using synthetic responsive promoters P4UPRE2 - TDH3 and P4UPRE2 - TEF1 for co-expression of ERO1 and SLY1 had 95% higher α-amylase production compared with the strain using the native promoters PTDH3 and PTEF1. This work showed that UPR-responsive promoters were useful in the metabolic engineering of yeast strains for tuning genes to support efficient protein production.

Biosensor-assisted evolution for high-level production of 4-hydroxyphenylacetic acid in Escherichia coli.

4-Hydroxyphenylacetic acid (4HPAA) is an important building block for synthesizing drugs, agrochemicals, and biochemicals, and requires sustainable production to meet increasing demand. Here, we use a 4HPAA biosensor to overcome the difficulty of conventional library screening in identification of preferred mutants. Strains with higher 4HPAA production and tolerance are successfully obtained by atmospheric and room temperature plasma (ARTP) mutagenesis coupled with adaptive laboratory evolution using this biosensor. Genome shuffling integrates preferred properties in the strain GS-2-4, which produces 25.42 g/L 4HPAA. Chromosomal mutations of the strain GS-2-4 are identified by whole genome sequencing. Through comprehensive analysis and experimental validation, important genes, pathways and regulations are revealed. The best gene combination in inverse engineering, acrD-aroG, increases 4HPAA production of strain GS-2-4 by 37% further. These results emphasize precursor supply and stress resistance are keys to efficient 4HPAA biosynthesis. Our work shows the power of biosensor-assisted screening of mutants from libraries. The methods developed here can be easily adapted to construct cell factories for the production of other aromatic chemicals. Our work also provides many valuable target genes to build cell factories for efficient 4HPAA production in the future.

Exploring core functional microbiota responsible for the production of volatile flavour during the traditional brewing of Wuyi Hong Qu glutinous rice wine.

The objective of this study was to explore the core functional microbiota for the production of volatile flavour during the traditional brewing of Wuyi Hong Qu glutinous rice wine, one of the most typical representatives of rice wine in China. Microbiological analysis based on high-throughput sequencing (HTS) technology demonstrated that bacteria of Lactobacillus, Bacillus, Leuconostoc, Lactococcus, Raoultella, Staphylococcus, Pediococcus, and Weissella, and fungi of Saccharomyces, Saccharomycopsis, Rhizopus, Monascus, Pichia, Wickerhamomyces, Candida, and Aspergillus were the predominant genera during the traditional fermentation process. Principal component analysis (PCA) based on the relative abundance showed that both of bacterial and fungal communities varied significantly in different fermentation phases. Some predominant microbial species or genera (including bacteria of Bacillus spp., Staphylococcus spp., Weissella spp., and P. acidilactici, and fungi of M. purpureus, R. oryzae, R. arrhizus var. arrhizus, and A. niger) were detected at the initial brewing stage, and their populations decreased as the fermentation progressed, while those of Lactobacillus, Gluconacetobacter, Leuconostoc, Pichia, Wickerhamomyces, and Saccharomyces increased to become the predominant genera at the final stage. A total of 79 volatile compounds were identified in traditional fermentation starters and during the traditional brewing process, mainly including esters, alcohols, acids, aldehydes, ketones, and phenols. Heatmaps and PCA also revealed the significant variances in the composition of volatile compounds among different samples. Furthermore, the potential correlations between microbiota succession and volatile flavour dynamics were explored through bidirectional orthogonal partial least squares (O2PLS) based correlation analysis. Three bacterial genera, namely, Gluconacetobacter, Lactobacillus, Lactococcus, and three fungal genera of Pichia, Wickerhamomyces, and Saccharomyces, were determined as the core functional microbiota for production of main volatile compounds in Wuyi Hong Qu glutinous rice wine. To conclude, information provided by this study is valuable to the development of effective strategies for the selection of beneficial bacterial and fungal strains to improve the quality of Wuyi Hong Qu glutinous rice wine.

[Discharge characteristic and spectrum measurement of a new type of single filament in a dielectric barrier discharge].

A new type of single filament was observed in a dielectric barrier discharge (DBD) system for the first time. It was formed with a larger discharge gap (d=3. 8 mm) and a smaller discharge area (S= 1 cm x 1 cm) in an air/argon gas mixture. Compared with the single filament observed by other experimental groups, the new type of single filament is composed of volume discharge (VD) and surface discharge (SD). In addition, the single filament has excellent discharge stability and sustainability. In order to study more about the discharge characteristic of the new type of single filament in a half-cycle of the applied voltage and the plasma state in different positions of the discharge column in the side view of the new type of single filament, both a high speed framing camera (HSFC) and a spectrograph were used in the experiment. The instantaneous images of end and side view of the new type of single filament were taken by the HSFC with different exposure time, and the discharge characteristic of the new type of single filament in a half-cycle of the applied voltage was compared with that of glow discharge. The spectral lines of Ar I 763. 26 nm (2P6-->1S5) and Ar I 772.13 nm (2P2-->IS3) in different positions of the discharge column of the new type of single filament were measured by using optical emission spectra, and chosen to estimate the corresponding electron excitation temperature by the relative intensity ratio method. It was found that the new type of single filament is composed of VD and SD, and SD produces a dendritic discharge around VD. The discharge characteristic of the new type of single filament in a half-cycle of the applied voltage is similar to that of glow discharge, and a funnel-shaped discharge emerges at the instantaneous cathode. The spectral line intensity and the corresponding electron excitation temperature all decrease with the distance away from the electrodes, indicating that the plasma state in different positions of the discharge column in the side view of the new type of single filament is different.

De Novo Pterostilbene Production from Glucose Using Modular Coculture Engineering in Escherichia coli.

Pterostilbene, a derivative of resveratrol, is of increasing interest due to its increased bioavailability and potential health benefits. Sustainable production of pterostilbene is important, especially given the challenges of traditional plant extraction and chemical synthesis methods. While engineered microbial cell factories provide a potential alternative for pterostilbene production, most approaches necessitate feeding intermediate compounds. To address these limitations, we adopted a modular coculture engineering strategy, dividing the pterostilbene biosynthetic pathway between two engineered E. coli strains. Using a combination of gene knockout, atmospheric and room-temperature plasma mutagenesis, and error-prone PCR-based whole genome shuffling to engineer strains for the coculture system, we achieved a pterostilbene production titer of 134.84 ± 9.28 mg/L from glucose using a 1:3 inoculation ratio and 0.1% dimethyl sulfoxide supplementation. This represents the highest reported de novo production titer. Our results underscore the potential of coculture systems and metabolic balance in microbial biosynthesis.

ER stress-induced transcriptional response reveals tolerance genes in yeast.

Saccharomyces cerevisiae is important for protein secretion studies, yet the complexities of protein synthesis and secretion under endoplasmic reticulum (ER) stress conditions remain not fully understood. ER stress, triggered by alterations in the ER protein folding environment, poses substantial challenges to cells, especially during heterologous protein production. In this study, we used RNA-seq to analyze the transcriptional responses of yeast strains to ER stress induced by reagents such as tunicamycin (Tm) or dithiothreitol (DTT). Our gene expression analysis revealed several crucial genes, such as HMO1 and BIO5, that are involved in ER-stress tolerance. Through metabolic engineering, the best engineered strain R23 with HMO1 overexpression and BIO5 deletion, showed enhanced ER stress tolerance and improved protein folding efficiency, leading to a 2.14-fold increase in α-amylase production under Tm treatment and a 2.04-fold increase in cell density under DTT treatment. Our findings contribute to the understanding of cellular responses to ER stress and provide a basis for further investigations into the mechanisms of ER stress at the cellular level.

Optimizing the Biosynthesis of Dihydroquercetin from Naringenin in Saccharomyces cerevisiae.

Dihydroquercetin (DHQ), known for its varied physiological benefits, is widely used in the food, chemical, and pharmaceutical industries. However, the efficiency of the DHQ synthesis is significantly limited by the substantial accumulation of intermediates during DHQ biosynthesis. In this study, DHQ production was achieved by integrating genes from various organisms into the yeast chromosome for the expression of flavanone-3-hydroxylase (F3H), flavonoid-3'-hydroxylase, and cytochrome P450 reductase. A computer-aided protein design approach led to the development of optimal F3H mutant P221A, resulting in a 1.67-fold increase in DHQ yield from naringenin (NAR) compared with the control. Subsequently, by analysis of the enzyme reaction and optimization of the culture medium composition, 637.29 ± 20.35 mg/L DHQ was synthesized from 800 mg/L NAR. This corresponds to a remarkable conversion rate of 71.26%, one of the highest reported values for DHQ synthesis from NAR to date.

Concentrated Solar Light Photoelectrochemical Water Splitting for Stable and High-Yield Hydrogen Production.

Photoelectrochemical water splitting is a promising technique for converting solar energy into low-cost and eco-friendly H2 fuel. However, the production rate of H2 is limited by the insufficient number of photogenerated charge carriers in the conventional photoelectrodes under 1 sun (100 mW cm-2 ) light. Concentrated solar light irradiation can overcome the issue of low yield, but it leads to a new challenge of stability because the accelerated reaction alters the surface chemical composition of photoelectrodes. Here, it is demonstrated that loading Pt nanoparticles (NPs) on single crystalline GaN nanowires (NWs) grown on n+ -p Si photoelectrode operates efficiently and stably under concentrated solar light. Although a large number of Pt NPs detach during the initial reaction due to H2 gas bubbling, some Pt NPs which have an epitaxial relation with GaN NWs remain stably anchored. In addition, the stability of the photoelectrode further improves by redepositing Pt NPs on the reacted Pt/GaN surface, which results in maintaining onset potential >0.5 V versus reversible hydrogen electrode and photocurrent density >60 mA cm-2 for over 1500 h. The heterointerface between Pt cocatalysts and single crystalline GaN nanostructures shows great potential in designing an efficient and stable photoelectrode for high-yield solar to H2 conversion.

[Spectra line profile and vibrational temperature of dot and line discharge in a dielectric barrier discharge].

The emission spectrum line shift and vibrational temperature of dot and line discharges, which coexist in argon/air dielectric barrier discharge, were measured and compared. Emission spectral lines of ArI (2P2 --> 1S5) and the N2 second positive band system (C 3pi(u) --> B 3pi(g)) were used to measure the spectrum line shift and the vibrational temperature respectively. It was found that the spectrum line shift of the dot discharge channel is larger than that of the line discharge channel, indicating that the former has high electron density compared to the latter. While the vibrational temperature of the dot discharge channel is lower than that of the line discharge channel.

Comprehensive Analysis of Signal Peptides in Saccharomyces cerevisiae Reveals Features for Efficient Secretion.

Signal peptides (SPs) are N-terminus sequences on the nascent polypeptide for protein export or localization delivery, which are essential for maintaining cell function. SPs are also employed as a key element for industrial production of secreted recombinant proteins. Yet, detailed information and rules about SPs and their cellular interactions are still not well understood. Here, systematic bioinformatics analysis and secretion capacity measurement of genome-wide SPs from the model organism Saccharomyces cerevisiae is performed. Several key features of SPs, including region properties, consensus motifs, evolutionary relationships, codon bias, e.g., are successfully revealed. Diverse cell metabolism can be trigged by using different SPs for heterologous protein secretion. Influences on SPs with different properties by chaperones can cause different secretory efficiencies. Protein secretion by the SP NCW2 in SEC72 deletion strain is 10 times than the control. These findings provide insights into the properties and functions of SPs and contribute to both fundamental research and industrial application.

Optimization of Protein Folding for Improved Secretion of Human Serum Albumin Fusion Proteins in Saccharomyces cerevisiae.

The successful expression and secretion of recombinant proteins in cell factories significantly depend on the correct folding of nascent peptides, primarily achieved through disulfide bond formation. Thus, optimizing cellular protein folding is crucial, especially for proteins with complex spatial structures. In this study, protein disulfide isomerases (PDIs) from various species were introduced into Saccharomyces cerevisiae to facilitate proper disulfide bond formation and enhance recombinant protein secretion. The impacts of these PDIs on recombinant protein production and yeast growth metabolism were evaluated by substituting the endogenous PDI1. Heterologous PDIs cannot fully compensate the endogenous PDI. Furthermore, protein folding mediators, PDI and ER oxidoreductase 1 (Ero1), from different species were used to increase the production of complex human serum albumin (HSA) fusion proteins. The validated folding mediators were then introduced into unfolded protein response (UPR)-optimized strains, resulting in a 7.8-fold increase in amylase-HSA and an 18.2-fold increase in albiglutide compared with the control strain. These findings provide valuable insights for optimizing protein folding and expressing HSA-based drugs.

Renewable formate from sunlight, biomass and carbon dioxide in a photoelectrochemical cell.

The sustainable production of chemicals and fuels from abundant solar energy and renewable carbon sources provides a promising route to reduce climate-changing CO2 emissions and our dependence on fossil resources. Here, we demonstrate solar-powered formate production from readily available biomass wastes and CO2 feedstocks via photoelectrochemistry. Non-precious NiOOH/α-Fe2O3 and Bi/GaN/Si wafer were used as photoanode and photocathode, respectively. Concurrent photoanodic biomass oxidation and photocathodic CO2 reduction towards formate with high Faradaic efficiencies over 85% were achieved at both photoelectrodes. The integrated biomass-CO2 photoelectrolysis system reduces the cell voltage by 32% due to the thermodynamically favorable biomass oxidation over conventional water oxidation. Moreover, we show solar-driven formate production with a record-high yield of 23.3 µmol cm-2 h-1 as well as high robustness using the hybrid photoelectrode system. The present work opens opportunities for sustainable chemical and fuel production using abundant and renewable resources on earth-sunlight, biomass and CO2.

Effects of alkaloid-rich extracts obtained from Grifola frondosa on gut microbiota and glucose homeostasis in rats.

Grifola frondosa (GF), also known as maitake (a type of mushroom), has been widely used as a food item and it exhibits various health-beneficial hypoglycemic activities. Rats fed with a fat/high-sucrose-based diet were used to determine the hypoglycemic activity of 95% and 55% GF ethanol extracts (labeled as GF95 and GF55, respectively). The activity was determined by monitoring the fasting blood glucose level. Oral glucose tolerance tests were conducted, and the levels of alanine aminotransferase and aspartate aminotransferase were studied to study the hypoglycemic activity. The HPLC-ESI-TOF-MS technique was used to analyze the samples, and the results revealed that alkaloids were present in abundance in GF95 and GF55. It was also observed that GF55 contained some organic acids and GF95 contained extra small amounts of phenoloid. The levels of intestinal microbiota were analyzed, and the results from transcriptome analysis indicated that GF55 reduced the relative abundance of Romboutsia and affected RT-Db1, thereby improving the extent of glucose metabolism achieved. GF95 downregulated the mRNA level of Socs1 by increasing the levels of Oscillibacter, Butyricimonas, Barnesiella, Turicibacter, Methanosphaera, Asaccharobacter, Globicatella, Bifidobacterium, Allobaculum, and Romboutsia. The expression of Pik3rl was upregulated when the levels of Ruminococcus and Saccharibacteria increased. The hypoglycemic activity was induced under these conditions. The obtained data indicated that the efficiency of GF95 to control glucose levels was higher than the efficiency of GF55. This suggested that GF95 can be potentially used to protect against hyperglycemia.

Anti-fatigue property of the oyster polypeptide fraction and its effect on gut microbiota in mice.

We aimed to evaluate the anti-fatigue effects of the oyster polypeptide (OP) fraction and its regulatory effect on the gut microbiota in mice. Our exhaustive swimming experiment showed that the swimming time of the low-, middle- and high-dose groups of the OP fraction was increased by 1.82, 2.18 and 2.44 times compared with the control group, respectively. Besides, the liver glycogen levels of the three groups were increased by 19.3%, 42.02% and 65.07%, while the lactate levels were decreased by 18.85%, 21.18% and 28.74%, respectively. Moreover, administration of the OP fraction upregulated the expressions of PEPCK and AMPK, but downregulated the TNF-α expression. Correlation analysis between the gut microbiota and fatigue-related biochemical indicators showed that Faecalibacterium, Desulfovibri and Intestinibacter were negatively correlated with the swimming time, blood lactate, blood urea nitrogen, liver glycogen and muscle glycogen, while Yaniella and Romboutsia were positively correlated. Therefore, the OP fraction had anti-fatigue effects, and could regulate the abundance of gut microbiota and maintain its balance.

Regulatory effect of Grifola frondosa extract rich in polysaccharides and organic acids on glycolipid metabolism and gut microbiota in rats.

The present study investigated the composition of water extract of Grifola frondosa (GFWE) and its regulatory effects on glycolipid metabolism and gut microbiota in rats. Structural characteristics of GFWE were detected by high performance liquid chromatography and ultra-high-performance liquid chromatography with mass spectrometry. The hypoglycemic and hypolipidemic activities of GFWE were obtained by inhibition of weight gain, recovery of serum glucose and lipid, and reverse of liver tissue damage. GFWE has up-regulated the relative mRNA and protein expression levels of adenine monophosphate activated protein kinase-α, peroxisome proliferator-activated receptors-α, and glucokinase, while down-regulated sterol regulatory element-binding transcription factor-1c and acetyl CoA carboxylase. Moreover, GFWE increased the abundances of caecal bacteria Oscillibacter and Barnesiella, which showed a significant negative correlation with serum glucose and lipid parameters. And GFWE enhanced the levels of total bile acids and short-chain fatty acids in the cecum. These results indicated that GFWE could be provided as a potential candidate to regulate glycolipid metabolism and gut microbiota.

Hypoglycemic and hypolipidemic activities of Grifola frondosa polysaccharides and their relationships with the modulation of intestinal microflora in diabetic mice induced by high-fat diet and streptozotocin.

This study aimed to investigate the hypoglycemic and hypolipidemic activities of polysaccharides from Grifola frondosa (GFP) in diabetic mice induced by high-fat diet (HFD) and streptozotocin (STZ). Results showed that oral administration of GFP markedly reduced the serum levels of fasting blood glucose (FBG), oral glucose tolerance (OGT), cholesterol (TC), triglyceride (TG) and low-density lipoprotein cholesterol (LDL-C), and significantly decreased the hepatic levels of TC, TG and free fatty acids (FFA). Meanwhile, high-dose of GFP supplementation (900 mg/kg day) also showed powerful effects on moderating the composition of intestinal microflora in diabetic mice, especially altering the functionally relevant intestinal microbial phylotypes. Spearman's correlation network analysis revealed that key microbial phylotypes responding to GFP intervention were strongly correlated with the glucose and lipid metabolic disorders associated parameters. Moreover, GFP treatment regulated mRNA expression levels of the genes responsible for hepatic glucose and lipid metabolism. It is noteworthy that GFP treatment markedly increased mRNA expression of cholesterol 7α-hydroxylase (CYP7A1) and bile salt export pump (BSEP), suggesting an enhancement of bile acids (BAs) synthesis and excretion in liver. These findings demonstrated that GFP could prevent hyperglycemia and hyperlipidemia in diabetic mice by altering gut microbiota and regulating hepatic glycolipid metabolism related genes, and therefore could be used as potential functional food ingredients for the prevention or treatment of hyperglycemia and hyperlipidemia.

Formation of kagome-white-eye-honeycomb hexagonal superlattice pattern in dielectric barrier discharge.

A kagome-white-eye-honeycomb hexagonal superlattice pattern is observed in dielectric barrier discharge and studied by two photomultipliers, an intensified charge-coupled device, and a spectrograph. It consists of four sublattices, which are kagome structure, halos of white-eye hexagon, honeycomb frame, and central spots hexagon. As an unconventional symmetry sublattice, the kagome structure results in amazing sublattice discharge order. Based on the consideration that any discharge is related to all previous discharges, a mapping matrix which governs self-organization of the pattern is proposed. These results will promote the development of the pattern dynamics.

Polyunsaturated fatty acids from microalgae Spirulina platensis modulates lipid metabolism disorders and gut microbiota in high-fat diet rats.

Effects of Spirulina platensis 55% ethanol extract (SPL55) on lipid metabolism in high-fat diet-induced hyperlipidaemic rats were investigated. Ultra performance liquid chromatography-quadrupole time-of-flight mass spectrometry indicated that SPL55 was enriched with polyunsaturated fatty acids. Meanwhile, serum and liver lipid levels, including total triglyceride, total cholesterol, and low-density-lipoprotein cholesterol, were significantly decreased in hyperlipidaemic rats of SPL55. Analysis of tissue sections showed that SPL55 treatment could markedly inhibit hepatic lipid accumulation and steatosis. Moreover, SPL55 regulated the mRNA and protein expression levels of SREBP-1c, HMG-CoA, PEPCK, ACC, and AMPK genes involved in lipid metabolism. Furthermore, SPL55 led to decrease the abundances of Turicibacter, Clostridium_XlVa, and Romboutsia, which were positive correlation with lipid metabolism indicators, and has also enriched Alloprevotella, Prevotella, Porphyromonadaceae, and Barnesiella. These results provided evidence that SPL55 might be developed as a functional food to ameliorate lipid metabolic disorders and hyperlipidaemia.

A complex pattern with hexagonal lattice and white-eye stripe in dielectric barrier discharge.

A novel type of white-eye pattern in a dielectric barrier discharge system has been investigated in this paper. It is a superposition of a hexagonal lattice and a white-eye stripe in appearance and evolves from a white-eye square grid state with the applied voltage increasing. Its spatio-temporal dynamics obtained by an intensified charge-coupled device shows that it consists of three transient rectangular sublattices. The spatiotemporally resolved evolutions of the molecular vibrational temperature and electron density of the pattern are measured by optical emission spectra. The evolution of surface charge distribution is given and its effect on the self-organized pattern formation is discussed.