New urethanase from the yeast Candida parapsilosis

A highly thermostable ethyl carbamate-degrading urethanase from Thermoflavimicrobium dichotomicum

The carcinogen ethyl carbamate (EC) in food is a potential threat to health. Available urethanases cannot efficiently degrade EC because of their instability or low activity under acidic conditions. Here, a novel thermostable urethanase was identified in Thermoflavimicrobium dichotomicum using a database-mining approach. The enzyme displayed exceptional thermotolerance, with an optimum temperature of 75 °C, and exhibited 58.6 % of its maximum activity at 90 °C. After incubation at temperatures below 70 °C for 30 min, 100 % activity was maintained. Following treatment at 4 °C for 6 h, it retained 59-87 % of its activity at pH 4.0-5.0, demonstrating the highest acid stability reported so far. This enzyme showed good ethanol tolerance. 80.4 % of its activity was retained after incubation in 10 % (v/v) ethanol solution at 37 °C for 1 h. The enzyme exhibited the highest EC affinity (Km, 3.545 mM), and catalytic efficiency (kcat/Km, 46.75 ± 2.34 s-1·mM-1) at pH 4.5. After reacting with 200 U/L purified enzyme at 30 °C for 5 h, 62.4 % and 9.7 % of EC were degraded from rice wine samples with pH 6.0 and 4.5, respectively. Furthermore, the enzyme exhibited significant hydrolytic activity against the 2A carcinogen acrylamide. These findings suggest that this urethanase is a promising industrial enzyme.

A comprehensive review of recombinant technology in the food industry: Exploring expression systems, application, and future challenges

Biotechnology has significantly advanced the production of recombinant proteins (RPs). This review examines the latest advancements in protein production technologies, including CRISPR, genetic engineering, vector integration, and fermentation, and their implications for the food industry. This review delineates the merits and shortcomings of prevailing host systems for RP production, underscoring molecular and process strategies pivotal for amplifying yields and purity. It traverses the spectrum of RP applications, challenges, and burgeoning trends, highlighting the imperative of employing robust hosts and cutting-edge genetic engineering to secure high-quality, high-yield outputs while circumventing protein aggregation and ensuring correct folding for enhanced activity. Recombinant technology has paved the way for the food industry to produce alternative proteins like leghemoglobin and cytokines, along with enzyme preparations such as proteases and lipases, and to modify microbial pathways for synthesizing beneficial compounds, including pigments, terpenes, flavonoids, and functional sugars. However, scaling microbial production to industrial scales presents economic, efficiency, and environmental challenges that demand innovative solutions, including high-throughput screening and CRISPR/Cas9 systems, to bolster protein yield and quality. Although recombinant technology holds much promise, it must navigate high costs and scalability to satisfy the escalating global demand for RPs in therapeutics and food. The variability in ethical and regulatory hurdles across regions further complicates market acceptance, underscoring an urgent need for robust regulatory frameworks for genetically modified organisms. These frameworks are essential for safeguarding the production process, ensuring product safety, and upholding the efficacy of RPs in industrial applications.

An overview on polyurethane-degrading enzymes

Polyurethanes (PUR) are durable synthetic polymers widely used in various industries, contributing significantly to global plastic consumption. PUR pose unique challenges in terms of degradability and recyclability, as they are characterised by intricate compositions and diverse formulations. Additives and proprietary structures used in commercial PUR formulations further complicate recycling efforts, making the effective management of PUR waste a daunting task. In this review, we delve into the complex challenge of enzymatic degradation of PUR, focusing on the structural and functional attributes of both enzymes and PUR. We also present documented native enzymes with reported efficacy in hydrolysing specific bonds within PUR, analysis of these enzyme structures, reaction mechanisms, substrate specificity, and binding site architecture. Furthermore, we propose essential features for the future redesign of enzymes to optimise PUR biodegradation efficiency. By outlining prospective research directions aimed at advancing the field of enzymatic biodegradation of PUR, we aim to contribute to the development of sustainable solutions for managing PUR waste and reducing environmental pollution.

Decoding the Formation and Elimination Mechanism of Ethyl Carbamate in Strong-Aroma Baijiu

In the present study, changes in the physicochemical indices, ethyl carbamate (EC) precursor and EC contents, and microbial communities of fermented grains under different fermentation patterns during strong-aroma Baijiu (SAB) fermentation and changes in EC precursor and EC contents during distillation were investigated to study EC formation during these processes. In detail, the amounts of sorghum added in protocols C and D were half those added in protocols A and B (the normal SAB-producing technology). When fermented for about 30 to 35 days, the fermented grains of protocols A and C were, respectively, remixed with Daqu and second-distilled SAB (so-called "Huijiu jiaqu", HJJQ) and fermented for about 30 to 40 days. The results showed that the acidities of the final fermented grains of protocols A (2.43 ± 0.09 mmol/10 g) and C (3.18 ± 0.08 mmol/10 g) were lower than those of protocols B (3.71 ± 0.07 mmol/10 g) and D (4.66 ± 0.10 mmol/10 g), while the alcohol contents in the final fermented grains of protocols A (18.33 ± 0.76%) and C (15.33 ± 1.08%) were higher than those of protocols B (5.10 ± 0.85%) and D (1.85 ± 0.62%). No significant differences were observed in the other physicochemical indices among the samples. The HJJQ operation significantly increases the alcohol content and reduces the acidity of the fermented grains but has little influence on the other physicochemical indices during SAB fermentation. Excluding the influence of the HJJQ operation and a half input of sorghum on the EC precursor and EC contents for the fermented grains of protocol B, the linear relationships between the EC content and alcohol (R2: 0.4465), citrulline (R2: 0.6962), urea (R2: 0.4705), and HCN (R2: 0.6324) contents were good (all the confidence levels were at 0.05), indicating that these compounds were the dominant EC precursors during SAB fermentation. HJJQ also facilitated the reaction between alcohol and other EC precursors, decreasing EC precursor content and increasing the EC content. KEGG pathway analysis demonstrated that EC precursors were mainly synthesized by alcohol and arginine metabolism. HCN (R2: 0.3875 to 0.8198) and alcohol (R2: 0.4642 to 0.8423) were the dominant EC precursors during SAB distillation. Overall, the HJJQ operation, especially in protocol C, could significantly reduce the content of EC in base SAB, and the base SAB obtained was of good quality. This, therefore, may be an alternative and effective way to reduce the EC content in base Baijiu.

Crystal structure of urethanase from Candida parapsilosis and insights into the substrate-binding through in silico mutagenesis and improves the catalytic activity and stability

Ethyl carbamate (EC) is classified as a Class 2A carcinogen, and is present in various fermented foods, posing a threat to human health. Urethanase (EC 3.5.1.75) can catalyze EC to produce ethanol, CO2 and NH3. The urethanase (cpUH) from Candida parapsilosis can hydrolyze EC, but its low affinity and poor stability hinder its application. Here, the structure of cpUH from Candida parapsilosis was determined with a resolution of 2.66 Å. Through sequence alignment and site-directed mutagenesis, it was confirmed that cpUH contained the catalytic triad Ser-cisSer-Lys of the amidase family. Then, the structure-oriented engineering mutant N194V of urethanase was obtained. Its urethanase activity increased by 6.12 %, the catalytic efficiency (kcat/Km) increased by 21.04 %, and the enzyme stability was also enhanced. Modeling and molecular docking analysis showed that the variant N194V changed the number of hydrogen bonds between the substrate and the catalytic residue, resulting in enhanced catalytic ability. MD simulation also demonstrated that the introduction of hydrophobic amino acid Val reduced the RMSD value and increased protein stability. The findings of this study suggest that the N194V variant exhibits significant potential for industrial applications due to its enhanced affinity for substrate binding, improved catalytic efficiency, and increased enzyme stability.

High Salt-Resistant Urethanase Degrades Ethyl Carbamate in Soy Sauce

Urethanase is a promising biocatalyst for degrading carcinogen ethyl carbamate (EC) in fermented foods. However, their vulnerability to high ethanol and/or salt and acidic conditions severely limits their applications. In this study, a novel urethanase from Alicyclobacillus pomorum (ApUH) was successfully discovered using a database search. ApUH shares 49.4% sequence identity with the reported amino acid sequences. It belongs to the Amidase Signature family and has a conserved "K-S-S" catalytic triad and the characteristic "GGSS" motif. The purified enzyme overexpressed in Escherichia coli exhibits a high EC affinity (Km, 0.306 mM) and broad pH tolerance (pH 4.0-9.0), with an optimum pH 7.0. Enzyme activity remained at 58% in 12% (w/v) NaCl, and 80% in 10% (v/v) ethanol or after 1 h treatment with the same ethanol solution at 37 °C. ApUH has no hydrolytic activity toward urea. Under 30 °C, the purified enzyme (200 U/L) degraded about 15.4 and 43.1% of the EC in soy sauce samples (pH 5.0, 6.0), respectively, in 5 h. Furthermore, the enzyme also showed high activity toward the class 2A carcinogen acrylamide in foods. These attractive properties indicate their potential applications in the food industry.

Structure-guided engineered urethanase from Candida parapsilosis with pH and ethanol tolerance to efficiently degrade ethyl carbamate in Chinese rice wine

Urethane hydrolase can degrade the carcinogen ethyl carbamate (EC) in fermented food, but its stability and activity limit its application. In this study, a mutant G246A and a double mutant N194V/G246A with improved cpUH activity and stability of Candida parapsilosis were obtained by site-directed mutagenesis. The catalytic efficiency (Kcat/Km) of mutant G246A and double mutant N194V/G246A are 1.95 times and 1.88 times higher than that of WT, respectively. In addition, compared with WT, the thermal stability and pH stability of mutant G246A and double mutant N194V/G246A were enhanced. The ability of mutant G246A and double mutant N194V/G246A to degrade EC in rice wine was also stronger than that of WT. The mutation increased the stability of the enzyme, as evidenced by decreased root mean square deviation (RMSD) and increased hydrogen bonds between the enzyme and substrate by molecular dynamics simulation and molecular docking analysis. The molecule modification of new cpUH promotes the industrial process of EC degradation.

Advancements in Fermented Beverage Safety: Isolation and Application of Clavispora lusitaniae Cl-p for Ethyl Carbamate Degradation and Enhanced Flavor Profile

Ethyl carbamate (EC) is a natural by-product in the production of fermented food and alcoholic beverages and is carcinogenic and genotoxic, posing a significant food safety concern. In this study, Clavispora lusitaniae Cl-p with a strong EC degradation ability was isolated from Daqu rich in microorganisms by using EC as the sole nitrogen source. When 2.5 g/L of EC was added to the fermentation medium, the strain decomposed 47.69% of ethyl carbamate after five days of fermentation. It was unexpectedly found that the strain had the ability to produce aroma and ester, and the esterification power reached 30.78 mg/(g·100 h). When the strain was added to rice wine fermentation, compared with the control group, the EC content decreased by 41.82%, and flavor substances such as ethyl acetate and β-phenylethanol were added. The EC degradation rate of the immobilized crude enzyme in the finished yellow rice wine reached 31.01%, and the flavor substances of yellow rice wine were not affected. The strain is expected to be used in the fermented food industry to reduce EC residue and improve the safety of fermented food.

The Screening and Isolation of Ethyl-Carbamate-Degrading Strains from Fermented Grains and Their Application in the Degradation of Ethyl Carbamate in Chinese Baijiu

Ethyl carbamate (EC), a 2A carcinogen produced during the fermentation of foods and beverages, primarily occurs in distilled spirits. Currently, most studies focus on strategies for EC mitigation. In the present research, we aimed to screen strains that can degrade EC directly. Here, we report two Candida ethanolica strains (J1 and J116), isolated from fermented grains, which can reduce EC concentrations directly. These two yeasts were grown using EC as the sole carbon source, and they grew well on different carbon sources. Notably, after immobilization with chitosan, the two strains degraded EC in Chinese Baijiu by 42.27% and 27.91% in 24 h (from 253.03 ± 9.89 to 146.07 ± 1.67 and 182.42 ± 5.05 μg/L, respectively), which was better than the performance of the non-immobilized strains. Furthermore, the volatile organic compound content, investigated using gas chromatography-mass spectrometry, did not affect the main flavor substances in Chinese Baijiu. Thus, the yeasts J1 and J116 may be potentially used for the treatment and commercialization of Chinese Baijiu.

Sequence and Structure-Guided Engineering of Urethanase from Agrobacterium tumefaciens d3 for Improved Catalytic Activity

The amidase from Agrobacterium tumefaciens d3 (AmdA) degrades the carcinogenic ethyl carbamate (EC) in alcoholic beverages. However, its limited catalytic activity hinders practical applications. Here, multiple sequence alignment was first used to predict single variants with improved activity. Afterward, AlphaFold 2 was applied to predict the three-dimensional structure of AmdA and 21 amino acids near the catalytic triad were randomized by saturation mutagenesis. Each of the mutation libraries was then screened, and the improved single variants were combined to obtain the best double variant I97L/G195A that showed a 3.1-fold increase in the urethanase activity and a 1.5-fold increase in ethanol tolerance. MD simulations revealed that the mutations shortened the distance between catalytic residues and the substrate and enhanced the occurrence of a critical hydrogen bond in the catalytic pocket. This study displayed a useful strategy to engineer an amidase for the improvement of urethanase activity, and the variant obtained provided a good candidate for applications in the food industry.

Features and application potential of microbial urethanases

Urethanase (EC 3.5.1.75) can reduce ethyl carbamate (EC), a group 2A carcinogen found in foods and liquor. However, it is not yet commercially available. Urethanase has been detected as an intracellular enzyme from yeast, filamentous fungi, and bacteria. Based on the most recent progress in the sequence analysis of this enzyme, it was observed that amidase-type enzyme can degrade EC. All five enzymes had highly conserved sequences of amidase signature family, and their molecular masses were in the range of 52-62 kDa. The enzymes of Candida parapsilosis and Aspergillus oryzae formed a homotetramer, and that of Rhodococcus equi strain TB-60 existed as a monomer. Most urethanases exhibited amidase activity, and those of C. parapsilosis and A. oryzae also demonstrated high activity against acrylamide, which is a group 2A carcinogen. It was recently reported that urease and esterase also exhibited urethanase activity. Although research on the enzymatic degradation of EC has been very limited, recently some sequences of EC-degrading enzyme have been elucidated, and it is anticipated that new enzymes would be developed and applied into practical use. KEY POINTS: • Recently, some urethanase sequences have been elucidated • The amino acid residues that formed the catalytic triad were conserved • Urethanase shows amidase activity and can also degrade acrylamide.

A Genome-Scale Metabolic Model for the Human Pathogen Candida Parapsilosis and Early Identification of Putative Novel Antifungal Drug Targets

Candida parapsilosis is an emerging human pathogen whose incidence is rising worldwide, while an increasing number of clinical isolates display resistance to first-line antifungals, demanding alternative therapeutics. Genome-Scale Metabolic Models (GSMMs) have emerged as a powerful in silico tool for understanding pathogenesis due to their systems view of metabolism, but also to their drug target predictive capacity. This study presents the construction of the first validated GSMM for C. parapsilosis—iDC1003—comprising 1003 genes, 1804 reactions, and 1278 metabolites across four compartments and an intercompartment. In silico growth parameters, as well as predicted utilisation of several metabolites as sole carbon or nitrogen sources, were experimentally validated. Finally, iDC1003 was exploited as a platform for predicting 147 essential enzymes in mimicked host conditions, in which 56 are also predicted to be essential in C. albicans and C. glabrata. These promising drug targets include, besides those already used as targets for clinical antifungals, several others that seem to be entirely new and worthy of further scrutiny. The obtained results strengthen the notion that GSMMs are promising platforms for drug target discovery and guide the design of novel antifungal therapies.

Expression, isolation, and identification of an ethanol-resistant ethyl carbamate-degrading amidase from Agrobacterium tumefaciens d3

Ethyl carbamate (EC), widely found in alcoholic beverages, has been revealed to be a probable carcinogen in humans. Urethanase (EC 3.5.1.75) is an effective enzyme for the degradation of EC; however, the previously identified urethanases exhibited insufficient acid and alcohol resistance. In this study, an enantioselective amidase (AmdA) screened from Agrobacterium tumefaciens d₃ exhibited urethanase activity with excellent alcohol resistance. AmdA was first overexpressed in Escherichia coli; however, the recombinant protein was primarily located in inclusion bodies, and thus, co-expression of molecular chaperones was used. The activity of AmdA increased 3.1 fold to 307 U/L, and the specific activity of urethanase with C-terminal His-tags reached 0.62 U/mg after purification through a Ni-NTA column. Subsequently, the enzymatic properties and kinetic constants of AmdA were investigated. The optimum temperature for AmdA was 55 °C, it showed the highest activity at pH 7.5, and the K_m was 0.964 mM. Moreover, after 1 h of heat treatment at 37 °C in a 5-20% (v/v) ethanol solution, the residual urethanase activity was higher than 91%, considerably more than that reported thus far.