Molecular Engineering of Bacillus paralicheniformis Acid Urease To Degrade Urea and Ethyl Carbamate in Model Chinese Rice Wine

Mechanism of Polygonum hydropiper reducing ethyl carbamate in Chinese rice wine (Huangjiu) brewing

Polygonum hydropiper (PH) is a rich source of active compounds and serves as a pivotal ingredient in Chinese rice wine (Huangjiu) production. This study investigates the impact of PH and Polygonum hydropiper extract (PHE) on ethyl carbamate (EC) production during Huangjiu fermentation. Our findings reveal that PH enhances the relative abundance of Bacillus subtilis in Huangjiu fermentation, thereby facilitating its interaction with Saccharomyces cerevisiae. Furthermore, PH modulates the urea metabolism of S. cerevisiae. In the PH-B. subtilis-S. cerevisiae fermentation system, the expression of DUR1,2 and DUR3 genes in S. cerevisiae is upregulated. This augmentation leads to increased urea uptake and metabolism by S. cerevisiae in the fermentation broth, subsequently reducing the urea concentration in the fermentation medium (The EC content in the CK group was approximately 355.55 % and 356.05 % higher than those in the PH and PHE groups, respectively). Consequently, PH demonstrates promise in reducing the EC concentration of Huangjiu, offering a novel approach to enhance the safety of Huangjiu consumption.

Characterization of urease active calcite-producing strain YX-3 combined with the whole genome

Urease found in a wide range of microorganisms plays a vital role in ureolytic induced calcite precipitation (UICP). However, the genomic information on urease-producing strains is limited, and there is a need for further in-depth studies on aspects such as the regulation of urease activity by nickel ligand residues. The present study delved into the elucidation of urease activity in a newly isolated strain YX-3 coupled with nickel-ligand residues by employing the genetic architecture of biomineralization-controlled growth, molecular docking, molecular dynamics simulation (MDS), and site-directed mutagenesis. Genome-wide sequencing showed the presence of urease gene clusters, comprising structural genes ureA, ureB, and ureC, alongside auxiliary genes ureD, ureE, ureF, and ureG. RT-qPCR analysis showed that the addition of NiCl2 resulted in a significant up-regulation of ureC expression. His267, His294, and Gly325 in the domain of UreC were further proved to coordinate with nickel ions and urea simultaneously through homology modeling and molecular docking, and molecular dynamics simulations (MDS) showed the urease-urea docking complexes exhibited degressive binding stability by four metrics including root mean square deviations (RMSD) when those residues were mutated into alanine respectively. Western blotting exhibited that mutations of H267A, H294A, and G325A led to a reduction in the relative expression of urease, wherein urease activity was about 62%, 45%, and 20% times that of the wild type (WT), respectively. The overexpression results further confirmed the importance of these residues for urease activity and CaCO3 precipitation. These results would help to deepen the understanding of urease-producing strains at a molecular level and expand the theoretical basis for modulating urease activity.

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.

Application of Strain Selection Technology in Alcoholic Beverages: A Review

The diversity of alcohol beverage microorganisms is of great significance for improving the brewing process and the quality of alcohol beverage products. During the process of making alcoholic beverages, a group of microorganisms, represented by yeast and lactic acid bacteria, conducts fermentation. These microorganisms have complex synergistic or competitive relationships, and the participation of different microorganisms has a major impact on the fermentation process and the flavor and aroma of the product. Strain selection is one of the key steps. Utilizing scientific breeding technology, the relationship between strains can be managed, the composition of the alcoholic beverage microbial community can be improved, and the quality and flavor of the alcoholic beverage products can be increased. Currently, research on the microbial diversity of alcohol beverages has received extensive attention. However, the selection technology for dominant bacteria in alcohol beverages has not yet been systematically summarized. To breed better-quality alcohol beverage strains and improve the quality and characteristics of wine, this paper introduces the microbial diversity characteristics of the world's three major brewing alcohols: beer, wine, and yellow wine, as well as the breeding technologies of related strains. The application of culture selection technology in the study of microbial diversity of brewed wine was reviewed and analyzed. The strain selection technology and alcohol beverage process should be combined to explore the potential application of a diverse array of alcohol beverage strains, thereby boosting the quality and flavor of the alcohol beverage and driving the sustainable development of the alcoholic beverage industry.

Mitigation of microbial nitrogen-derived metabolic hazards as a driver for safer alcoholic beverage choices: An evidence-based review and future perspectives

Alcoholic beverages have been enjoyed worldwide as hedonistic commodities for thousands of years. The unique quality and flavor are attributed to the rich microbiota and nutritional materials involved in fermentation. However, the metabolism of these microbiota can also introduce toxic compounds into foods. Nitrogen-derived metabolic hazards (NMH) are toxic metabolic hazards produced by microorganisms metabolizing nitrogen sources that can contaminate alcoholic beverages during fermentation and processing. NMH contamination poses a risk to dietary safety and human health without effective preventive strategies. Existing literature has primarily focused on investigating the causes of NMH formation, detection methods, and abatement techniques for NMH in fermentation end-products. Devising effective process regulation strategies represents a major challenge for the alcoholic beverage industry considering our current lack of understanding regarding the processes whereby NMH are generated, real-time and online detection, and the high degradation rate after NMH formation. This review summarizes the types and mechanisms of nitrogenous hazard contamination, the potential risk points, and the analytical techniques to detect NMH contamination. We discussed the changing patterns of NMH contamination and effective strategies to prevent contamination at different stages in the production of alcoholic beverages. Moreover, we also discussed the advanced technologies and methods to control NMH contamination in alcoholic beverages based on intelligent monitoring, synthetic ecology, and computational assistance. Overall, this review highlights the risks of NMH contamination during alcoholic beverage production and proposes promising strategies that could be adopted to eliminate the risk of NMH contamination.

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.

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.

Genetic Engineering Production of Ethyl Carbamate Hydrolase and Its Application in Degrading Ethyl Carbamate in Chinese Liquor

Ethyl carbamate (EC), classified as a Group 2A carcinogen, is most abundant in the fermented foods, such as Cachaca, Shaoxing wine, and Chinese liquor (baijiu). Although biodegradation can reduce its concentration, a high ethanol concentration and acidic environment often limit its degradation. In the present study, a novel ethyl carbamate hydrolase (ECH) with high specificity to EC was isolated from Acinetobacter calcoaceticus, and its enzymatic properties and EC degradability were investigated. ECH was immobilized to resist extreme environmental conditions, and the flavor substance changes were explored by gas chromatography-mass spectrometry (GC/MS). The specific enzymatic activity of ECH was 68.31 U/mg. Notably, ECH exhibited excellent thermal stability and tolerance to sodium chloride and high ethanol concentration (remaining at 40% activity in 60% (v/v) ethanol, 1 h). The treatment of immobilized ECH for 12 h decreased the EC concentration in liquor by 71.6 μg/L. Furthermore, the immobilized ECH exerted less effect on its activity and on the flavor substances, which could be easily filtrated during industrial production.

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

Origin, Succession, and Control of Biotoxin in Wine

Wine is a worldwide alcoholic beverage with antioxidant active substances and complex flavors. Moderate drinking of wine has been proven to be beneficial to health. However, wine has some negative components, such as residual pesticides, heavy metals, and biotoxins. Of these, biotoxins from microorganisms were characterized as the most important toxins in wine. Wine fermentation mainly involves alcoholic fermentation, malolactic fermentation, and aging, which endue wine with complex flavors and even produce some undesirable metabolites. These metabolites cause potential safety risks that are not thoroughly understood. This review aimed to investigate the origin, evolution, and control technology of undesirable metabolites (e.g., ochratoxin A, ethyl carbamate, and biogenic amines) in wine. It also highlighted current wine industry practices of minimizing the number of biotoxins in wine.

Biodegradation of polystyrene by deep-sea Bacillus paralicheniformis G1 and genome analysis

Polystyrene (PS) films were subjected to in vitro biodegradation by Bacillus paralicheniformis G1 (MN720578) isolated from 3538 m depth sediments of the Arabian Sea. The growth of the isolate was most favourable at pH 7.5, 30 °C and 4% salinity. A series of batch experiments were conducted to investigate the degradation of PS films up to 60 days. The results of this study indicated that the strain degraded 34% of PS film within 60 days of incubation. The complete genome sequence consists of 4,281,959 bp with 45.88% GC content and encodes 4213 protein coding genes. A high number of genes encoding monooxygenase, dioxygenase, peroxidase, esterase and hydrolase involved in the degradation of synthetic polymers were identified. Also genes associated with flagellum dependent motility, chemotaxis, biofilm formation and siderophores biosynthesis were identified in this deep-sea strain G1. This study suggests that B. paralicheniformis G1 could be a potential species for degradation of PS and its genome analysis provides insight into the molecular basis of biodegradation.

Inhibition of ethyl carbamate accumulation in soy sauce by adding quercetin and ornithine during thermal process

Ethyl carbamate (EC), a genotoxic and carcinogenic compound in soy sauce accumulated during thermal processes, has raised public health concern for its multipoint potential carcinogenic risk to human. In this work, based on the analysis of EC accumulation during thermal processes of soy sauce, ornithine and quercetin were added before thermal processes to reduce EC accumulation. A reduction rate of 23.7-63.8% in simulated solution was founded. Kinetic studies indicated that ornithine was a byproduct of alcoholysis reaction when EC formed, while quercetin could compete with the precursor ethanol and react with carbamyl compounds, which therefore preventedEC accumulation. A maximum of 47.2% decrease of EC in soy sauce was achieved, and no remarkable changes in volatile compounds profile and color of soy sauce were found. In conclusion, the addition of quercetin and ornithine before thermal processes may be preferable for the controlling of EC content in soy sauce.

Improving activity and stabilization of urease by crosslinking to nanoaggregate forms for herbicide degradation

Bioremediation is the most effective green protocol for degradation of environmental contaminants. Present study involves carrier free urease immobilization with synthesis of its new crosslinked aggregates using two different crosslinkers, divinyl benzene (DVB) and tripropyleneglycol dimethacrylate (TPGDA) via free radical mechanism. Resulting crosslinked ureases were further converted to nanoform (CLUNAs) using solvent evaporation technique. The activity of free and the crosslinked ureases was studied as a function of operational parameters viz. temperature (20-80), pH (2-11) and substrate concentration (5-20 mM) using urea as substrate at contact time of 10 min. Storability study of the pristine urease and CLUNAs was carried out for 40 days, and the CLUNAs were reused in 10 repeat cycles to assess their reusability. Isoproturone degradation was studied under the above-cited range of pH and temperature and results were recorded after 24 h.

New urethanase from the yeast Candida parapsilosis

Urethanase (EC 3.5.1.75) is an effective enzyme for removing ethyl carbamate (EC) present in alcoholic beverages. However, urethanase is not well studied and has not yet been developed for practical use. In this study, we report a new urethanase (CPUTNase) from the yeast Candida parapsilosis. Because C. parapsilosis can assimilate EC as its sole nitrogen source, the enzyme was extracted from yeast cells and purified using ion-exchange chromatography. The CPUTNase was estimated as a homotetramer comprising four units of a 61.7 kDa protein. In a 20% ethanol solution, CPUTNase had 73% activity compared with a solution without ethanol. Residual activity after 18 h indicated that CPUTNase was stable in 0%-40% ethanol solutions. The optimum temperature of CPUTNase was 43°C. This enzyme showed urethanase activity at pH 5.5-10.0 and exhibited its highest activity at pH 10. The gene of CPUTNase was identified, and a recombinant enzyme was expressed in the yeast Saccharomyces cerevisiae. Characteristics of recombinant CPUTNase were identical to the native enzyme. The putative amino acid sequence indicated that CPUTNase was an amidase family protein. Further, substrate specificity supported this sequence analysis because CPUTNase showed higher activities toward amide compounds. These results suggest that amidase could be a candidate for urethanase. We discovered a new enzyme and investigated its enzymatic characteristics, sequence, and recombinant CPUTNase expression. These results contribute to a further understanding of urethanase.

Self-assembled nano-aggregates of fluorinases demonstrate enhanced enzymatic activity, thermostability and reusability

Three SAP (self-assembling peptide)-tagged fluorinases (FLAs), namely, FLA-ELK16, FLA-L6KD and FLA-18A (named after the SAP used for tagging FLA) were successfully engineered. All three SAP-tagged FLAs could be highly over-expressed using engineered E. coli host cells despite being in the form of aggregates (inclusion bodies). It was noted that all three SAP-tagged FLAs exhibited enzymatic activity. It was also observed that all three SAP-tagged FLAs were capable of self-assembly to form nano-sized particles with different dimensions in aqueous solutions. Strikingly, one of the SAP-tagged FLA (FLA-L6KD) displayed improved enzyme activity, thermostability and reusability, which is potentially ideal for bio-transformation. FLA is an exotic enzyme that is capable of catalysing the formation of C-F bonds using inorganic fluorine ions as substrates. This significant feature enables it to incorporate [18F]-fluoride into different small molecules to generate radiopharmaceuticals in PET (positron emission tomography) labeling. In addition, fluorinase is greatly valuable in synthetic biology for incorporating the fluorine element into building blocks to produce non-natural organofluorines or as a biocatalyst for transforming non-native substrates. Our method would be a further step in making FLA-based biocatalysis even 'greener' by enhancing the enzymatic activity, thermostability and reusability of FLA through the introduction of nano-sized aggregates. Enzymes are such nontrivial biomaterials, which can be manifested in different scenarios. Our research expands their reach and tunes their properties by tagging SAP partners. Thus, this methodology can be put into the 'toolbox' of enzymologists, which can be further explored and generalised for others.