Cryo-EM structure and rational engineering of a superefficient ochratoxin A-detoxifying amidohydrolase

A thermostable OTA-detoxifying hydrolase from Thermonema rossianum: identification, characterization, structure, catalytic mechanism, and application

Ochratoxin A (OTA) is highly toxic and widely distributed, posing serious threats to human and animal health. Searching for effective OTA-detoxifying enzyme is crucial for the prevention and control of OTA contaminations. Here, a new OTA-detoxifying enzyme, TrADH from Thermonema rossianum is identified, which exhibits highest temperature tolerance among OTA-detoxifying enzymes. TrADH maintains good activity in the range of 45-85 °C and retains about 50 % activity after heating at 70 °C for 30 min. Based on the solved crystal structures, the catalytic mechanism is proposed, and protein engineering of catalytic-related residues is performed to obtain a 2.1-fold upgraded variant TrADHS67E with the specific enzyme activity of 3990 U/mg, which is more efficient than the reported OTA-detoxifying enzymes. The efficient degradation of OTA in rum and walnut reveals the prospect of TrADH in food applications. The results indicate that TrADH has the potential in OTA bio-detoxification in food and feed industry.

Metarhizium spp. encode an ochratoxin cluster and a high efficiency ochratoxin-degrading amidohydrolase revealed by genomic analysis

INTRODUCTION

Ochratoxins (OTs) are worldwide regulated mycotoxins contaminating a variety of food-environment and agro-environment. Several Aspergillus and Pencillium species synthesize OTs from a six-gene biosynthetic gene cluster (BGC) to produce the highly toxic final product OTA. Although many studies on OTA-degrading enzymes were performed, high efficiency enzymes with strong stability are extremely needed, and the OTA degrading mechanism is poorly understood.

OBJECTIVES

The study aimed to explore the OT-degradation enzyme and investigate its degradation mechanisms in Metarhizium, which contain an OT biosynthetic gene cluster.

METHODS

Phylogenomic relationship combined with RNA expression analysis were used to explore the distribution of OT BGC in fungi. Bioactivity-guided isolation and protein mass spectrometry were conducted to trace the degrading enzymes in Metarhizium spp., and the enzymes were heterologously expressed in E. coli and verified by in vitro assays. Structure prediction and point mutation were performed to reveal the catalytic mechanism of MbAmh1.

RESULTS

Beyond Aspergillus and Pencillium species, three species of the distant phylogenetic taxon Metarhizium contain an expressed OT-like BGC but lack an otaD gene. Unexpectedly, no OT BGC products were found in some Metarhizium species. Instead, Metarhizium metabolized both OTA and OTB to their non-toxic degradation products. This activity of M. brunneum was attributed to an intracellular hydrolase MbAmh1, which was tracked by bioactivity-guided proteomic analysis combined with in vitro reaction. Recombinant MbAmh1 (5 μg/mL) completely degraded 1 μg/mL OTA within 3 min, demonstrating a strong degrading ability towards OTA. Additionally, MbAmh1 showed considerable temperature adaptability ranging from 30 to 70 °C and acidic pH stability ranging from 4.0 to 7.0. Identification of active sites supported the crucial role of metal iron for this enzymatic reaction.

CONCLUSION

These findings reveal different patterns of OT synthesis in fungi and provide a potential OTA degrading enzyme for industrial applications.

Molecular insights into ochratoxin A biodegradation

Most of the agricultural products can potentially be exposed to mycotoxins-especially to ochratoxin A (OTA)-, which may cause foodborne diseases such as renal toxicity and notable economic losses worldwide. Biological detoxification is the most promising method to control OTA contamination. To provide a comprehensive understanding, this review summarizes the biodegradation pathways of OTA and discusses microbes capable of degrading OTA and their detoxification strategies. A detailed analysis of potentially useful enzymes for food and feed detoxification will be reported, highlighting specific enzymatic strategies identified in scientific literature. A comparative analysis of the functional capabilities of different OTA hydrolases demonstrates significant variation in degradation efficiency, thus the optimization of these enzymes is essential for the development of effective detoxification strategies. This review underscores the potential of harnessing these microorganisms and their enzymes for mitigating the toxic effects of OTA in contaminated environment and examining the essential requirements that must be met for the successful application of OTA degrading enzyme technology for promoting public health and food safety.

Analysis of the subtype I amidohydrolase responsible for Ochratoxin A degradation in the Sphingomonas genus

Ochratoxin A (OTA) is a mycotoxin that contaminates the agricultural environment, food and feed, leading to substantial economic losses. Among the alpha-proteobacteria, certain strains from the Sphingomonas genus are known to degrade a wide range of naturally occurring and synthetic compounds, including OTA. In this work, type strains for 17 Sphingomonas species were tested for their ability to detoxify OTA in culture. Most of them demonstrated OTA-detoxification capabilities. We observed that all OTA-degrading strains possessed an amidohydrolase homologous to others identified in gamma-proteobacteria. Conversely, strains that did not degrade OTA lacked this enzyme. This strong correlation suggests that the OTA-degrading phenotype exhibited by Sphingomonas cultures is directly linked to the presence of this enzyme. A PCR-based detection method was designed to identify strains possessing the amidohydrolase-encoding gene, marking them as potential OTA-degrading strains. Additionally, the OTA-transforming amidohydrolase from S. dokdonensis DSM 21029T (SdOTA) was identified and biochemically characterized. In silico prediction of the SdOTA structure with AlphaFold, combined with molecular docking simulations, revealed the structural basis of the substrate specificity and insights into the mycotoxin-binding mechanism. The ability Sphingomonas strains to detoxify OTA, coupled with the collection of genes enabling bioremediation, positions them as highly versatile bacteria for pollutant detoxification.

Mechanism of patulin biodegradation by a reductase from Saccharomyces cerevisiae and its potential application to apple juice

Bioenzymatic degradation exhibits great potential for mycotoxins removal. So far, little is known about patulin (PAT) degrading enzymes from Saccharomyces cerevisiae. Here, the degradation mechanism of PAT by a free methionine-R-sulfoxide reductase (FRMSR) from S. cerevisiae was investigated. The results showed that purified FRMSR had high degradability without cofactor and displayed strong substrate specificity. The optimal degradation conditions in aqueous solution were 37 °C and pH 7.0. Isothermal titration calorimetry and molecular docking suggested that the PAT degradation by FRMSR was related to the hydrogen bonds formed between amino acids with PAT. Site-specific mutagenesis indicated that the mutation of Asp151 had the most significant effect on the degradation rate. Furthermore, the addition of FRMSR successfully degraded 88.16 % of PAT in apple juice without affecting its soluble solids content, pH value, titrable acidity and total phenols. These findings could provide valuable insights into the development of PAT-degrading enzymes in apple products and their industrial applications.

Brevibacterium enzymes as biological tools for ochratoxin A detoxification in dairy foods

The origin of ochratoxin A (OTA) in cheeses is mainly due to mould growth during the ripening process, and to a lesser extent, to the use of OTA-contaminated milk in cheese production. Bacterial smear-ripened cheeses developed a smear microbiota on their rind during ripening that greatly contributes to its typical aroma and texture. Bacteria from the Brevibacterium genus belong to the typical smear microbiota of cheeses. Type strains from Brevibacterium species frequently isolated from cheese and milk products were able to transform OTA into much less toxic ochratoxin α (OTα) and L-phenylalanine. Protein searches allowed the identification of a protein annotated as amidohydrolase in these OTA-degrader Brevibacterium strains. The OTA-hydrolytic activity of the identified amidohydrolase was demonstrated by the heterologous production of this protein from B. linens DSM 20425T (BlOTA). In vitro assays revealed that BlOTA transformed OTA into less toxic OTα, as well as ochratoxin B. When compared with other previously described OTA-degrading amidohydrolases, BlOTA exhibited optimal activity at a higher pH (8.0), while showing similar high temperature for optimal activity (55 °C) and thermostability; in addition, a clear preference for substrates with Phe, Tyr or Leu amino acid residues at the C-terminal position was clearly observed. BlOTA efficiently detoxifies OTA-contaminated bovine milk, without provoking changes on its free amino acid composition. Moreover, in silico predictions revealed that BlOTA is a non-allergenic, non-antigenic, and poorly immunogenic protein. Therefore, the QPS status possessed by cheese-Brevibacterium species, as well as the characteristics exhibited by BlOTA, make them suitable tools for the biological detoxification of OTA in dairy and food products.

Automated identification of small molecules in cryo-electron microscopy data with density- and energy-guided evaluation

Methodological improvements in cryo-electron microscopy (cryoEM) have made it a useful tool in ligand-bound structure determination for biology and drug design. However, determining the conformation and identity of bound ligands is still challenging at the resolutions typical for cryoEM. Automated methods can aid in ligand conformational modeling, but current ligand identification tools - developed for X-ray crystallography data - perform poorly at resolutions common for cryoEM. Here, we present EMERALD-ID, a method capable of docking and evaluating small molecule conformations for ligand identification. EMERALD-ID identifies 43% of common ligands exactly and identifies closely related ligands in 66% of cases. We then use this tool to discover possible ligand identification errors, as well as previously unidentified ligands. Furthermore, we show EMERALD-ID is capable of identifying ligands from custom ligand libraries of various small molecule types, including human metabolites and drug fragments. Our method provides a valuable addition to cryoEM modeling tools to improve small molecule model accuracy and quality.

Mechanisms of efficient polyacrylamide degradation: From multi-omics analysis to structural characterization of two amidohydrolases

Polyacrylamide (PAM) is a high molecular weight polymer with extensive applications. However, inefficient natural degradation of PAM results in its environmental accumulation. Here, using multi-omics analysis, we constructed the PAM biodegradation pathway in Klebsiella sp. PCX, an efficient PAM-degrading bacterium. Subsequently, two unclassified amidohydrolases (PCX00451 and PCX04581) were identified as key factors for rapid PAM biodegradation, both of which possessed much higher hydrolysis efficiency for PAM than for small molecule amide compounds. Besides, crystal structures of PCX00451 and PCX04581 were solved. Both two amidohydrolases were consisted with a twisted triosephosphateisomerase (TIM)-barrel and a smaller β-sandwich domain. And their binding pockets were in the conserved metal center of TIM-barrel domain. Moreover, Asp267 of PCX00451 and Asp282 of PCX04581 were examined as active sites for acid/base catalysis. Our research characterized the molecular mechanisms of two efficient amidohydrolases, providing theoretical basis and valuable tools for PAM bioremediation.

Functional characterization and structural basis of an efficient ochratoxin A-degrading amidohydrolase

Ochratoxin A (OTA) contamination in various agro-products poses a serious threat to the global food safety and human health, leading to enormous economic losses. Enzyme-mediated OTA degradation is an appealing strategy, and the search for more efficient enzymes is a prerequisite for achieving this goal. Here, a novel amidohydrolase, termed PwADH, was demonstrated to exhibit 7.3-fold higher activity than that of the most efficient OTA-degrading ADH3 previously reported. Cryo-electron microscopy structure analysis indicated that additional hydrogen-bond interactions among OTA and the adjacent residue H163, the more compact substrate-binding pocket, and the wider entry to the substrate-access cavity might account for the more efficient OTA-degrading activity of PwADH compared with that of ADH3. We conducted a structure-guided rational design of PwADH and obtained an upgraded variant, G88D, whose OTA-degrading activity was elevated by 1.2-fold. In addition, PwADH and the upgraded G88D were successfully expressed in the industrial yeast Pichia pastoris, and their catalytic activities were compared to those of their counterparts produced in E. coli, revealing the feasibility of producing PwADH and its variants in industrial yeast strains. These results illustrate the structural basis of a novel, efficient OTA-degrading amidohydrolase and will be beneficial for the development of high-efficiency OTA-degrading approaches.

Aspergillus niger Ochratoxinase Is a Highly Specific, Metal-Dependent Amidohydrolase Suitable for OTA Biodetoxification in Food and Feed

Microbial enzymes can be used as processing aids or additives in food and feed industries. Enzymatic detoxification of ochratoxin A (OTA) is a promising method to reduce OTA content. Here, we characterize the full-length enzyme ochratoxinase (AnOTA), an amidohydrolase from Aspergillus niger. AnOTA hydrolyzes OTA and ochratoxin B (OTB) mycotoxins efficiently and also other substrates containing phenylalanine, alanine, or leucine residues at their C-terminal position, revealing a narrow specificity profile. AnOTA lacks endopeptidase or aminoacylase activities. The structural basis of the molecular recognition by AnOTA of OTA, OTB, and a wide array of model substrates has been investigated by molecular docking simulation. AnOTA shows maximal hydrolytic activity at neutral pH and high temperature (65 °C) and retained high activity after prolonged incubation at 45 °C. The reduction of OTA levels in food products by AnOTA has been investigated using several commercial plant-based beverages. The results showed complete degradation of OTA with no detectable modification of beverage proteins. Therefore, the addition of AnOTA seems to be a useful procedure to eliminate OTA in plant-based beverages. Moreover, computational predictions of in vivo characteristics indicated that AnOTA is neither an allergenic nor antigenic protein. All characteristics found for AnOTA supported the suitability of its use for OTA detoxification in food and feed.

Bioenzymatic detoxification of mycotoxins

Mycotoxins are secondary metabolites produced during the growth, storage, and transportation of crops contaminated by fungi and are physiologically toxic to humans and animals. Aflatoxin, zearalenone, deoxynivalenol, ochratoxin, patulin, and fumonisin are the most common mycotoxins and can cause liver and nervous system damage, immune system suppression, and produce carcinogenic effects in humans and animals that have consumed contaminated food. Physical, chemical, and biological methods are generally used to detoxify mycotoxins. Although physical methods, such as heat treatment, irradiation, and adsorption, are fast and simple, they have associated problems including incomplete detoxification, limited applicability, and cause changes in food characteristics (e.g., nutritive value, organoleptic properties, and palatability). Chemical detoxification methods, such as ammonification, ozonation, and peroxidation, pollute the environment and produce food safety risks. In contrast, bioenzymatic methods are advantageous as they achieve selective detoxification and are environmentally friendly and reusable; thus, these methods are the most promising options for the detoxification of mycotoxins. This paper reviews recent research progress on common mycotoxins and the enzymatic principles and mechanisms for their detoxification, analyzes the toxicity of the degradation products and describes the challenges faced by researchers in carrying out enzymatic detoxification. In addition, the application of enzymatic detoxification in food and feed is discussed and future directions for the development of enzymatic detoxification methods are proposed for future in-depth study of enzymatic detoxification methods.

Isolation, identification, degradation mechanism and exploration of active enzymes in the ochratoxin A degrading strain Acinetobacter pittii AP19

Ochratoxin A (OTA) is a polyketide mycotoxin that commonly contaminates agricultural products and causes significant economic losses. In this study, the efficient OTA-degrading strain AP19 was isolated from vineyard soil and was identified as Acinetobacter pittii. Compared with growth in nutrient broth supplemented with OTA (OTA-NB), strain AP19 grew faster in nutrient broth (NB), but the ability of the resulting cell lysates to remove OTA was weaker. After cultivation in NB, the cell lysate of strain AP19 was able to remove 100% of 1 mg/L OTA within 18 h. The cell lysate fraction > 30 kDa degraded 100% of OTA within 12 h, while the fractions < 30 kDa were practically unable to degrade OTA. Further anion exchange chromatography of the > 30 kDa fraction yielded two peaks exhibiting significant OTA degradation activity. The degradation product was identified as OTα. Amino acid metabolism exhibited major transcriptional trends in the response of AP19 to OTA. The dacC gene encoding carboxypeptidase was identified as one of the contributors to OTA degradation. Soil samples inoculated with strain AP19 showed significant OTA degradation. These results provide significant insights into the discovery of novel functions in A. pittii, as well as its potential as an OTA decomposer.

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.