Identification of an urethanase from Lysinibacillus fusiformis for degrading ethyl carbamate in fermented foods

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.

Bioremediation potential of the consortium of indigenous microbial isolates in degrading multiwall carbon nanotube (MWCNT) present in contaminated water

MWCNT is being explored in various sectors like medical healthcare, electronics, aerospace, defence research, and many more leading to the continuous generation of waste discharged into water sources. Once introduced into the environment it may adversely affect flora and fauna. It is high time MWCNT should be recovered, treated, and degraded from wastewater. Bio-degradation is one of the popular sustainable techniques for the remediation of hazardous contaminants. This work evaluated indigenous microbes Bacillus nitratireducens SW_NMI_TSB1, Comamonas denitrificans SW_NMI_TSB2, and Lysinibacillus fusiformis SW_NMI_TSB3 isolated from the nanomaterial manufacturing industry from India for their competence in degrading MWCNT. The microbes in this study showed survivability in the nutrient medium devoid of carbon but containing MWCNT (100 and 400 mg/L). The bacterial strain exhibited proliferation for up to 50 days. Degradation of MWCNT can be observed through TEM images which displayed the distorted morphology, XRD, and RAMAN spectroscopy revealed that treated MWCNT exhibit a loss of structural integrity. SEM images and colony forming unit (CFU) counts show a good survival rate of the three isolates independently and in the consortium. LCMS detected intermediates generated during MWCNT degradation. The microbes isolated in this study can survive in the presence of MWCNT and exhibit degradation of MWCNT. The three isolates could biodegrade the MWCNT however their consortium showed the highest potential. The prospects of this study lie in utilizing the consortium of these strains for large-scale MWCNT degradation, improving water treatment systems, and advancing sustainable nanomaterial management practices.

PUR-GEN: A web server for automated generation of polyurethane fragment libraries

The biodegradation of synthetic polymers offers a promising solution for sustainable plastic recycling. Polyurethanes (PUR) stand out among these polymers due to their susceptibility to enzymatic hydrolysis. However, the intricate 3D structures formed by PUR chains present challenges for biodegradation studies, both computational and experimental. To facilitate in silico research, we introduce PUR-GEN, a web server tailored for the automated generation of PUR fragment libraries. PUR-GEN allows users to input isocyanate and alcohol structural units, facilitating the creation of combinatorial oligomer libraries enriched with conformers and compound property tables. PUR-GEN can serve as a valuable tool for designing PUR fragments to mimic PUR structure interactions with proteins, as well as characterising simplistic PUR models. To illustrate an application of the web server, we present a case study on selected four cutinases and three urethanases with experimentally confirmed PUR-degrading activity or ability to hydrolyse carbamates. The use of PUR-GEN in molecular docking of 414 generated oligomers provides an example of the pipeline for initiation of the PUR degrading enzymes discovery.

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.

Recent Applications and Prospects of Enzymes in Quality and Safety Control of Fermented Foods

Fermented foods have gained global attention for their unique flavor and immense health benefits. These flavor compounds and nutrients result from the metabolic activities of microorganism during fermentation. However, some unpleasant sensory characteristics and biohazard substances could also be generated in fermentation process. These quality and safety issues in fermented foods could be addressed by endogenous enzymes. In this review, the applications of enzymes in quality control of fermented foods, including texture improvement, appearance stability, aroma enhancement, and debittering, are discussed. Furthermore, the enzymes employed in eliminating biohazard compounds such as ethyl carbamate, biogenic amines, and nitrites, formed during fermentation, are reviewed. Advanced biological methods used for enhancing the enzymatic activity and stability are also summarized. This review focused on the applications and future prospects of enzymes in the improvement quality and safety qualities of fermented foods.

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.

The latest advances on soy sauce research in the past decade: Emphasis on the advances in China

As an indispensable soybean-fermented condiment, soy sauce is extensively utilized in catering, daily cooking and food industry in East Asia and Southeast Asia and is becoming popular in the whole world. In the past decade, researchers began to pay great importance to the scientific research of soy sauce, which remarkably promoted the advances on fermentation strains, quality, safety, function and other aspects of soy sauce. Of them, the screening and reconstruction of Aspergillus oryzae with high-yield of salt and acid-tolerant proteases, mechanism of soy sauce flavor formation, improvement of soy sauce quality through the combination of novel physical processing technique and microbial/enzyme, separation and identification of soy sauce functional components are attracting more attention of researchers, and related achievements have been reported continually. Meanwhile, we pointed out the drawbacks of the above research and the future research directions based on published literature and our knowledge. We believe that this review can provide an insightful reference for international related researchers to understand the advances on soy sauce research.

Ethyl Carbamate in Fermented Food Products: Sources of Appearance, Hazards and Methods for Reducing Its Content

Ethyl carbamate, the ethyl ester of carbamic acid, has been identified in fermented foods and alcoholic beverages. Since ethyl carbamate is a probable human carcinogen, reduction of its content is important for food safety and human health. In alcoholic beverages, ethyl carbamate is mostly formed from the reaction of ethanol with urea, citrulline and carbamyl phosphate during fermentation and storage. These precursors are generated from arginine metabolism by wine yeasts and lactic acid bacteria. This review summarizes the mechanisms of ethyl carbamate formation, its impact on human health and methods used in winemaking to minimize its content. These approaches include genetic modification of Saccharomyces cerevisiae wine strains targeting pathways of arginine transport and metabolism, the use of lactic acid bacteria to consume arginine, direct degradation of ethyl carbamate by enzymes and microorganisms, and different technological methods of grape cultivation, alcoholic fermentation, wine aging, temperature and duration of storage and transportation.

Research Progress on Flavor and Quality of Chinese Rice Wine in the Brewing Process

Chinese rice wine (CRW) is a traditional and unique alcoholic beverage in China, favored by many consumers for its rich aroma, unique taste, and complex ingredients. Its flavor is primarily composed of volatile and nonvolatile compounds. These flavor compounds are partly derived from grains and starters (Qu), while the other part is produced by microbial metabolism and chemical reactions during the brewing process. Additionally, ethyl carbamate (EC) in CRW, a hazardous chemical, necessitates controlling its concentration during brewing. In recent years, numerous new brewing techniques for CRW have emerged. Therefore, this paper aims to collect aroma descriptions and thresholds of flavor compounds in CRW, summarize the relationship between the brewing process of CRW and flavor formation, outline methods for reducing the concentration of EC in the brewing process of CRW, and summarize the four stages (pretreatment of grains, fermentation, sterilization, and aging process) of new techniques. Furthermore, we will compare the advantages and disadvantages of different approaches, with the expectation of providing a valuable reference for improving the quality of CRW.

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.

Improving ethanol tolerance of ethyl carbamate hydrolase by diphasic high pressure molecular dynamic simulations

Ethyl carbamate (EC) is mainly found in fermented foods and fermented alcoholic beverages, which could cause carcinogenic potential to humans. Reducing EC is one of the key research priorities to address security of fermented foods. Enzymatic degradation of EC with EC hydrolase in food is the most reliable and efficient method. However, poor tolerance to ethanol severely hinders application of EC hydrolase. In this study, the mutants of EC hydrolase were screened by diphasic high pressure molecular dynamic simulations (dHP-MD). The best variant with remarkable improvement in specific activity and was H68A/K70R/S325N, whose specific activity was approximately 3.42-fold higher than WT, and relative enzyme activity under 20% (v/v) was 5.02-fold higher than WT. Moreover, the triple mutant increased its stability by acquiring more hydration shell and forming extra hydrogen bonds. Furthermore, the ability of degrading EC of the immobilized triple mutant was both detected in mock wine and under certain reaction conditions. The stability of immobilized triple mutant and WT were both improved, and immobilized triple mutant degraded nearly twice as much EC as that of immobilized WT. Overall, dHP-MD was proved to effectively improve enzyme activity and ethanol tolerance for extent application at industrial scale.

Research progress on the application of different controlling strategies to minimizing ethyl carbamate in grape wine

Ethyl carbamate (EC) is a probable carcinogenic compound commonly found in fermented foods and alcoholic beverages and has been classified as a category 2A carcinogen by the International Agency for Research on Cancer (IARC). Alcoholic beverages are one of the main sources of EC intake by humans. Therefore, many countries have introduced a standard EC limit in alcoholic beverages. Wine is the second largest alcoholic beverage in the world after beer and is loved by consumers for its rich taste. However, different survey results showed that the detection rate of EC in wine was almost 100%, while the maximum content was as high as 100 μg/L, necessitating EC content regulation in wine. The existing methods for controlling the EC level in wine mainly include optimizing raw fermentation materials and processes, using genetically engineered strains, and enzymatic methods (urease or urethanase). This review focused on introducing and comparing the advantages, disadvantages, and applicability of methods for controlling EC, and proposes two possible new techniques, that is, changing the fermentation strain and exogenously adding phenolic compounds. In the future, it is hoped that the feasibility of this prospect will be verified by pilot-scale or large-scale application to provide new insight into the regulation of EC during wine production. The formation mechanism and influencing factors of EC in wine were also introduced and the analytical methods of EC were summarized.

Microbial elimination of carbamate pesticides: specific strains and promising enzymes

Carbamate pesticides are widely used in the environment, and compared with other pesticides in nature, they are easier to decompose and have less durability. However, due to the improper use of carbamate pesticides, some nontarget organisms still may be harmed. To this end, it is necessary to investigate effective removal or elimination methods for carbamate pesticides. Current effective elimination methods could be divided into four categories: physical removal, chemical reaction, biological degradation, and enzymatic degradation. Physical removal primarily includes elution, adsorption, and supercritical fluid extraction. The chemical reaction includes Fenton oxidation, photo-radiation, and net electron reduction. Biological degradation is an environmental-friendly manner, which achieves degradation by the metabolism of microorganisms. Enzymatic degradation is more promising due to its high substrate specificity and catalytic efficacy. All in all, this review primarily summarizes the property of carbamate pesticides and the traditional degradation methods as well as the promising biological elimination. KEY POINTS: • The occurrence and toxicity of carbamate pesticides were shown. • Biological degradation strains against carbamate pesticides were presented. • Promising enzymes responsible for the degradation of carbamates were discussed.

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.

Occurrence of Ethyl Carbamate in Foods and Beverages: Review of the Formation Mechanisms, Advances in Analytical Methods, and Mitigation Strategies

ABSTRACT

Ethyl carbamate (EC) is a process contaminant that can be formed as a by-product during fermentation and processing of foods and beverages. Elevated EC concentrations are primarily associated with distilled spirits, but this compound has also been found at lower concentrations in foods and beverages, including breads, soy sauce, and wine. Evidence from animal studies suggests that EC is a probable human carcinogen. Consequently, several governmental institutions have established allowable limits for EC in the food supply. This review includes EC formation mechanisms, occurrence of EC in the food supply, and EC dietary exposure assessments. Current analytical methods used to detect EC will be covered, in addition to emerging technologies, such as nanosensors and surface-enhanced Raman spectroscopy. Various mitigation methods have been used to maintain EC concentrations below allowable limits, including distillation, enzymatic treatments, and genetic engineering of yeast. More research in this field is needed to refine mitigation strategies and develop methods to rapidly detect EC in the food supply.

HIGHLIGHTS

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.