New insights into searching patulin degrading enzymes in Saccharomyces cerevisiae through proteomic and molecular docking analysis

Identification and characterization of aldo-keto reductase responsible for patulin degradation in Saccharomyces cerevisiae

Patulin (PAT) is a hazardous mycotoxin that contaminates fruits and their products, causing significant economic losses. An aldo-keto reductase from Saccharomyces cerevisiae (ScAKR) was expressed in Escherichia coli in this study. The purified ScAKR converted PAT to E-ascladiol with NADPH as a cofactor. The ScAKR exhibited a strong degradation activity on PAT and the optimal degradation conditions were pH 7 and 37 °C. Molecular docking and site-specific mutagenesis indicated that the amino acids in ScAKR interacting with PAT aldehyde affected the degradation effect, and the mutation of Trp298 showed the most significant effect on the degradation rate. Furthermore, ScAKR also showed a strong degradation effect on 3-keto-deoxynivalenol, a metabolite of another mycotoxin, deoxynivalenol (DON). The findings offer new insights on the detoxification mechanism of PAT by S. cerevisiae and for the development and application of bioenzymes with broad-spectrum mycotoxin degradation properties.

Elucidation of molecular mechanisms underlying degradation of nicosulfuron and its derivative by Klebsiella jilinsis 2N3 using multiomic analysis

Nicosulfuron is a herbicide used in agricultural production. Its prolonged application causes significant ecological risks to soil and water environment. In this study, the molecular mechanisms underlying degradation of nicosulfuron and its derivative by Klebsiella jilinsis 2N3 was determined. Strain 2N3 degraded nicosulfuron primarily via cleavage of the sulfonylurea bridge and deamination and demethoxylation of its derivative, 2-amino-4,6-dimethoxypyrimidine (ADMP). Multiomic analysis indicated significant alterations in genes and proteins predominantly associated with glycolysis, tricarboxylic acid cycle, quorum sensing, signal transduction, energy metabolism, and nucleotide synthesis. Heterologous expression and gene knockout confirmed that degradation of the sulfonylurea bridge in nicosulfuron by strain 2N3 was accompanied by a hydrolysis process, in which arginine hydrolase Kj-CY657_RS10725 participated in nicosulfuron degradation Deletion of its gene decreased the biodegradation rate of nicosulfuron by 11.04 % in 24 h. Moreover, our study demonstrated that nicosulfuron derivative ADMP can effectively dock within the active site of the Kj-CY657_RS01600 protein, forming hydrogen bonds that enhanced the catalytic activity. Kj-CY657_RS01600 could degrade 10 mg mL-1 ADMP by 43.08 % within 30 min, resulting in the formation of 4,6-dimethoxypyrimidine as a byproduct. Additionally, after Kj-CY657_RS01600 knockout, the ability of strain 2N3 to biodegrade ADMP decreased by 52.48 %. This study provided molecular mechanism for comprehensive understanding the biodegradation of nicosulfuron and its derivative ADMP by strain 2N3.

Identification and Application of a Novel Patulin Degrading Enzyme From Meyerozyma guilliermondii

Patulin (PAT), a highly toxic mycotoxin, poses significant health risks due to its contamination of fruits and their derived products. Recent biological strategies for eliminating PAT mainly focus on elucidating the molecular detoxification processes of antagonistic microorganisms using omics technologies. However, there is still a scarcity of research on the rapid screening and catalytic mechanisms of bio-enzymes. In this study, a short-chain dehydrogenase/reductase (MgSDR1) capable of degrading PAT is rapidly identified from Meyerozyma guilliermondii by integrating transcriptomics with molecular docking. MgSDR1 completely degrades PAT into E-ascladiol within 2 h within the presence of reduced nicotinamide adenine dinucleotide phosphate (NADPH). Biodegradation efficiency is influenced by temperature, pH, enzyme/substrate concentrations, metal ions, and organic reagents. Notably, MgSDR1 shows efficient PAT degradation ability in fresh pear juice while maintaining key quality parameters, such as color parameters, pH, polyphenol oxidase activity, the contents of vitamin C, total phenols, titratable acidity, and soluble solids. The degradation process enhances the antioxidant capacity and enriches the aromatic compounds of the juice. Furthermore, site-directed mutagenesis reveals the essential role of the catalytic triad (Ser174-Tyr188-Lys192) in MgSDR1 activity. This study provides an efficient methodology for screening PAT-degrading enzymes and lays a theoretical foundation for the removal of mycotoxins in the food industry.

Patulin-degrading enzymes sources, structures, and mechanisms: A review

Patulin (PAT), a fungal secondary metabolite with multiple toxicities, is an unavoidable contaminant in fruit and vegetable processing, posing potential health risks to consumers and causing significant economic losses to the global food industry. Traditional control strategies, such as physical and chemical methods, face several challenges, including low efficiency, high costs, and unverified safety. In contrast, microbial degradation of patulin is considered a more efficient and environmentally friendly approach, which has become a popular research focus. However, there is still insufficient research on the key degradation enzymes involved in microorganisms. Therefore, this review comprehensively summarizes recent research progress on the biological degradation of patulin, with a focus on microbial species capable of degrading patulin, the degradation enzymes they express, potential degradation mechanisms, and the toxicity of degradation products, while providing prospects for future research. It offers valuable insights for controlling patulin in food and stimulates further investigation. Ultimately, this review aims to promote the development of efficient and eco-friendly methods to mitigate patulin contamination in fruits and vegetables.

Integrated omics analyses elucidate acetaminophen biodegradation by Enterobacter sp. APAP_BS8

Acetaminophen (APAP) is an extensively consumed over-the-counter and prescribed medication and a constituent of many active pharmaceutical compounds as well as personal care products. Its wide-scale prevalence in the environment due to inefficient treatment technologies has classified APAP as a contaminant of emerging concern. Thus, it is imperative to explore efficient and sustainable methods for remediation of contaminated environments. Considering the need for potent microbial resources, the present study deals with the evaluation of Enterobacter sp. APAP_BS8, degrading ∼88% of APAP (300 mg kg-1) in 16 days in microcosms, and accomplishes the mechanistic perspectives of degradation through in-depth insights into genomics, proteomics, and metabolomics. Whole genome analysis of the 4.9 Mbp genome sequence revealed deaminated glutathione amidase, glucosamine-6-phosphate deaminase, LLM class flavin-dependent oxidoreductase, and oxidoreductase genes can mediate the degradation. Increased expression of proteins corresponding to these genes was observed in proteome analysis. Molecular docking and simulations presented operative interaction and binding of the degradation pathway intermediates at the catalytic site of the identified enzymes. Analysis of the metabolome identified hydroxyquinol, 4-aminophenol, and 3-hydroxy-cis, cis-muconate as intermediates. The outcomes revealed that Enterobacter sp. APAP_BS8 exhibits potential enzymatic machinery for APAP degradation, thus providing scope for formulating sustainable bioremediation technologies.

Efficient Expression and Activity Optimization of Manganese Peroxidase for the Simultaneous Degradation of Aflatoxins AFB1, AFB2, AFG1, and AFG2

Aflatoxins (AFs), notorious mycotoxins that pose significant risks to human and animal health, make biodegradation extremely crucial as they offer a promising approach to managing and reducing their harmful impacts. In this study, we identified a manganese peroxidase from Punctularia strigosozonata (PsMnp) through protein similarity analysis, which has the capability to degrade four AFs (AFB1, AFB2, AFG1, and AFG2) simultaneously. The gene encoding this enzyme was subject to codon optimization, followed by cold shock induction expression using the pColdII vector, leading to the soluble expression of manganese peroxidase (Mnp) in Escherichia coli. This study tackled the problem of inclusion body formation that often occurs during Mnp expression in E. coli. After optimizing the degradation conditions, the degradation rates for AFB1, AFB2, AFG1, and AFG2 were 87.9, 72.8, 77.3, and 85.6%, respectively. Molecular docking and molecular dynamics simulations indicated that PsMnp facilitated the degradation of AFs through hydrophobic and polar interactions among various amino acid residues. This research offers novel insights into the rapid discovery of enzymes capable of degrading AFs and establishes a theoretical foundation for the efficient expression of mycotoxin detoxification enzymes.

Omics-centric evidences of fipronil biodegradation by Rhodococcus sp. FIP_B3

The widespread use of the pesticide fipronil in domestic and agriculture sectors has resulted in its accumulation across the environment. Its use to assure food security has inadvertently affected soil microbiome composition, fertility and, ultimately, human health. Degradation of residual fipronil present in the environment using specific microbial species is a promising strategy for its removal. The present study delves into the omics approach for fipronil biodegradation using the native bacterium Rhodococcus sp. FIP_B3. It has been observed that within 40 days, nearly 84% of the insecticide gets degraded. The biodegradation follows a pseudo-first-order kinetics (k = 0.0197/d with a half-life of ∼11 days). Whole genome analysis revealed Cytochrome P450 monooxygenase, peroxidase-related enzyme, haloalkane dehalogenase, 2-nitropropane dioxygenase, and aconitate hydratase are involved in the degradation process. Fipronil-sulfone, 5-amino-1-(2-chloro-4-(trifluoromethyl)phenyl)-4- ((trifluoromethyl)sulfonyl)-1H-pyrazole-3-carbonitrile, (E)-5-chloro-2-oxo-3- (trifluoromethyl)pent-4-enoic acid, 4,4,4-trifluoro-2-oxobutanoic acid, and 3,3,3- trifluoropropanoic acid were identified as the major metabolites that support the bacterial degradation of fipronil. In-silico molecular docking and molecular dynamic simulation-based analyses of degradation pathway intermediates with their respective enzymes have indicated stable interactions with significant binding energies (-5.9 to -9.7 kcal/mol). These results have provided the mechanistic cause of the elevated potential of Rhodococcus sp. FIP_B3 for fipronil degradation and will be advantageous in framing appropriate strategies for the bioremediation of fipronil-contaminated environment.

Current insights into yeast application for reduction of patulin contamination in foods: A comprehensive review

Patulin, a fungal secondary metabolite with multiple toxicities, is widely existed in a variety of fruits and their products. This not only causes significant economic losses to the agricultural and food industries but also poses a serious threat to human health. Conventional techniques mainly involved physical and chemical methods present several challenges include incomplete patulin degradation, high technical cost, and fruit quality decline. In comparison, removal of mycotoxin through biodegradation is regarded as a greener and safer strategy which has become popular research. Among them, yeast has a unique advantage in detoxification effect and application, which has attracted our attention. Therefore, this review provides a comprehensive account of the yeast species that can degrade patulin, degradation mechanism, current application status, and future challenges. Yeasts can efficiently convert patulin into nontoxic or low-toxic substances through biodegradation. Alternatively, it can use physical adsorption, which has the advantages of safety, high efficiency, and environmental friendliness. Nevertheless, due to the inherent complexity of the production environment, the sole utilization of yeast as a control agent remains inherently unstable and challenging to implement on a large scale in a practical manner. Integration control, enhancement of yeast resilience, improvement of yeast cell wall adsorption capacity, and research on additional patulin-degrading enzymes will facilitate the practical application of this approach. Furthermore, we analyzed the feasibility of the yeast commercial application in patulin reduction and provided suggestions on how to enhance its commercial value, which is of great significance for the control of mycotoxins in food products.

New insights into mechanism of ellagic acid alleviating arsenic-induced oxidative stress through MAPK/keap1-Nrf2 signaling pathway response, molecular docking and metabolomics analysis in HepG2 cells

The increase of oxidative stress level is one of the vital mechanisms of liver toxicity induced by arsenic (As). Ellagic acid (EA) is widely known due to its excellent antioxidation. Nevertheless, whether EA could alleviate As-induced oxidative stress and the underlying mechanisms remain unknown. Herein, As (2 and 4 μM) and EA (25 and 50 μM) were selected for alone and combined exposure of HepG2 cells to investigate the effects of EA on As-induced oxidative stress. Results indicated that EA could alleviate the oxidative stress caused by As via decreasing intracellular ROS level and MDA content, as well as improving SOD, CAT and GSH-PX activities. qRT-PCR showed that EA might enhance the expression levels of antioxidant enzymes NQO1, CAT and GPX1 by activating MAPK (JNK, p38 and ERK)/keap1-Nrf2 signaling pathway. EA was found to promote dissociation from keap1 and nuclear translocation of Nrf2 by competing with Nrf2 at ARG-380 and ARG-415 sites on keap1 to exert antioxidation using molecular docking. Moreover, metabolomics revealed that EA might maintain the redox balance of HepG2 cells by modulating or reversing disorders of carbon, amino acid, lipid and other metabolisms caused by As. This study provides diversified new insights for the removal of liver toxicity of As and the application of EA.

Unraveling the effective inhibition of α-terpinol and terpene-4-ol against Aspergillus carbonarius: Antifungal mechanism, ochratoxin A biosynthesis inhibition and degradation perspectives

Aspergillus carbonarius, a common food-contaminating fungus, produces ochratoxin A (OTA) and poses a risk to human health. This study aimed to assess the inhibitory activity of tea tree essential oil and its main components, Terpene-4-ol (T4), α-terpineol (αS), and 3-carene (3C) against A. carbonarius. The study showed αS and T4 were the main antifungal components of tea tree essential oil, which primarily inhibit A. carbonarius growth through cell membrane disruption, reducing antioxidant enzyme activities (catalase, peroxidase, superoxide dismutase) and interrupting the tricarboxylic acid cycle. Furthermore, αS and T4 interacted with enzymes related to OTA biosynthesis. Molecular docking and molecular dynamics show that they bound mainly to P450 with a minimum binding energy of -7.232 kcal/mol, we infered that blocking the synthesis of OTA precursor OTβ. Our hypothesis was preliminarily verified by the detection of key substances in the OTA synthesis pathway. The results of UHPLC-QTOF-MS2 analysis demonstrated that T4 achieved a degradation rate of 43 % for OTA, while αS reached 29.6 %, resulting in final breakdown products such as OTα and phenylalanine. These results indicated that α-terpinol and Terpene-4-ol have the potential to be used as naturally safe and efficient preservatives or active packaging to prevent OTA contamination.

Insights into the biodegradation of fipronil through soil microcosm-omics analyses of Pseudomonas sp. FIP_ A4

Fipronil, a phenylpyrazole insecticide, is used to kill insects resistant to conventional insecticides. Though its regular and widespread use has substantially reduced agricultural losses, it has also caused its accumulation in various environmental niches. The biodegradation is an effective natural process that helps in reducing the amount of residual insecticides. This study deals with an in-depth investigation of fipronil degradation kinetics and pathways in Pseudomonas sp. FIP_A4 using multi-omics approaches. Soil-microcosm results revealed ∼87% degradation within 40 days. The whole genome of strain FIP_A4 comprises 4.09 Mbp with 64.6% GC content. Cytochrome P450 monooxygenase and enoyl-CoA hydratase-related protein, having 30% identity with dehalogenase detected in the genome, can mediate the initial degradation process. Proteome analysis revealed differential enzyme expression of dioxygenases, decarboxylase, and hydratase responsible for subsequent degradation. Metabolome analysis displayed fipronil metabolites in the presence of the bacterium, supporting the proposed degradation pathway. Molecular docking and dynamic simulation of each identified enzyme in complex with the specific metabolite disclosed adequate binding and high stability in the enzyme-metabolite complex. This study provides in-depth insight into genes and their encoded enzymes involved in the fipronil degradation and formation of different metabolites during pollutant degradation. The outcome of this study can contribute immensely to developing efficient technologies for the bioremediation of fipronil-contaminated soils.

Expression of a novel hydrolase MhpC in Brevibacillus parabrevis BCP-09 and its characteristics for degrading synthetic pyrethroids

Synthetic pyrethroids are widely used insecticides which may cause chronic diseases in non-target organisms upon long-term exposure. Microbial degradation offers a reliable method to remove them from the environment. This study focused on Brevibacillus parabrevis BCP-09 and its enzymes for degrading pyrethroids. The predicted deltamethrin-degrading genes phnA and mhpC were used to construct recombinant plasmids. These plasmids, introduced into Escherichia coli BL21(DE3) cells and induced with L-arabinose. The results indicated that the intracellular crude enzyme efficiently degraded deltamethrin by 98.8 %, β-cypermethrin by 94.84 %, and cyfluthrin by 73.52 % within 24 h. The hydrolytic enzyme MhpC possesses a catalytic triad Ser/His/Asp and a typical "Gly-X-Ser-X-Gly" conservative sequence of the esterase family. Co-cultivation of induced E. coli PhnA and E. coli MhpC resulted in degradation rates of 41.44 ± 3.55 % and 60.30 ± 4.55 %, respectively, for deltamethrin after 7 d. This study states that the degrading enzymes from B. parabrevis BCP-09 are an effective method for the degradation of pyrethroids, providing available enzyme resources for food safety and environmental protection.

Biodegradation Characteristics and Mechanism of Aflatoxin B1 by Bacillus amyloliquefaciens from Enzymatic and Multiomics Perspectives

Aflatoxin B1 (AFB1), a mycotoxin and natural carcinogen, commonly contaminates cereals and animal feeds, posing serious health risks to human and animal. In this study, Bacillus amyloliquefaciens ZG08 isolated from kimchi could effectively remove 80.93% of AFB1 within 72 h at 37 °C and pH 7.0. Metabolome and transcriptome analysis showed that metabolic processes including glycerophospholipid metabolism and amino acid metabolism were most affected in B. amyloliquefaciens ZG08 exposed to AFB1. The adaptation mechanism likely involved activation of the thioredoxin system to restore intracellular redox equilibrium. The key genes, tpx and gldA, overexpressed in Escherichia coli BL21, achieved degradation rates of 60.15% and 47.16% for 100 μg/kg AFB1 under optimal conditions of 37 °C and pH 8.0 and 45 °C and pH 7.0, respectively. The degradation products, identified as AFD1, were less cytotoxic than AFB1 in HepG2 cells. These findings suggest potential strategies for utilizing probiotics and engineered enzymes in AFB1 detoxification.

Drug repurposing for diabetes mellitus: In silico and in vitro investigation of DrugBank database for α-glucosidase inhibitors

The process of developing novel compounds/drugs is arduous, time-intensive, and financially burdensome, characterized by a notably low success rate and relatively high attrition rates. To alleviate these challenges, compound/drug repositioning strategies are employed to predict potential therapeutic effects for DrugBank-approved compounds across various diseases. In this study, we devised a computational and enzyme inhibitory mechanistic approach to identify promising compounds from the pool of DrugBank-approved substances targeting Diabetes Mellitus (DM). Molecular docking analyses were employed to validate the binding interaction patterns and conformations of the screened compounds within the active site of α-glucosidase. Notably, Asp352 and Glu277 participated in interactions within the α-glucosidase-ligand complexes, mediated by conventional hydrogen bonding and van der Waals forces, respectively. The stability of the docked complexes (α-glucosidase-compounds) was scrutinized through Molecular Dynamics (MD) simulations. Subsequent in vitro analyses assessed the therapeutic potential of the repositioned compounds against α-glucosidase. Kinetic studies revealed that "Forodesine" exhibited a lower IC50 (0.24 ± 0.04 mM) compared to the control, and its inhibitory pattern corresponds to that of competitive inhibitors. In-depth in silico secondary structure content analysis detailed the interactions between Forodesine and α-glucosidase, unveiling significant alterations in enzyme conformation upon binding, impacting its catalytic activity. Overall, our findings underscore the potential of Forodesine as a promising candidate for DM treatment through α-glucosidase inhibition. Further validation through in vitro and in vivo studies is imperative to confirm the therapeutic benefits of Forodesine in conformational diseases such as DM.

Regulation and mechanism of organic selenium on quorum sensing, biofilm, and antioxidant effects of Lactobacillus paracasei

Different organic compounds can have varying degrees of impact on the activity of Lactobacillus paracasei. The study focused on the impact and action mechanism of different organic selenium products on the bioactivity of two strains of L. paracasei. The growth, antioxidant activity, extracellular polysaccharide secretion, quorum sensing (QS), and biofilm formation of the strains before and after the addition of organic selenium crude products and three organic selenium standard were evaluated. The results showed that the addition of crude organic selenium promoted the various activities of the strain. l-selenocysteine had the strongest regulatory effect, with maximum GIM1.80 biofilm formation when it reached a critical concentration of 0.4 μg/mL; l-selenomethionine resulted in the highest activity of the signal molecule Auto inducer-2 of GDMCC1.155, when it reached a critical concentration of 0.4 μg/mL. The results of scanning electron microscopy demonstrated that the addition of organic selenium effectively improved the morphological structure of the two bacterial cells. Molecular docking revealed that the mechanism by which organic selenium regulates QS in Lactobacillus was achieved by binding two crucial receptor proteins (histidine protein kinase HKP and periplasmic binding protein LuxP) from specific sites. Furthermore, organic selenium products have a beneficial regulatory effect on the biological activity of L. paracasei. Overall, these findings provide a new alternative (organic selenium) for regulating the viability and beneficial activity of L. paracasei.

Recent advances in biosynthesis of mycotoxin-degrading enzymes and their applications in food and feed

Mycotoxins are secondary metabolites produced by fungi in food and feed, which can cause serious health problems. Bioenzymatic degradation is gaining increasing popularity due to its high specificity, gentle degradation conditions, and environmental friendliness. We reviewed recently reported biosynthetic mycotoxin-degrading enzymes, traditional and novel expression systems, enzyme optimization strategies, food and feed applications, safety evaluation of both degrading enzymes and degradation products, and commercialization potentials. Special emphasis is given to the novel expression systems, advanced optimization strategies, and safety considerations for industrial use. Over ten types of recombinases such as oxidoreductase and hydrolase have been studied in the enzymatic hydrolysis of mycotoxins. Besides traditional expression system of Escherichia coli and yeasts, these enzymes can also be expressed in novel systems such as Bacillus subtilis and lactic acid bacteria. To meet the requirements of industrial applications in terms of degradation efficacy and stability, genetic engineering and computational tools are used to optimize enzymatic expression. Currently, registration and technical difficulties have restricted commercial application of mycotoxin-degrading enzymes. To overcome these obstacles, systematic safety evaluation of both biosynthetic enzymes and their degradation products, in-depth understanding of degradation mechanisms and a comprehensive evaluation of their impact on food and feed quality are urgently needed.