Searching for genes responsible for patulin degradation in a biocontrol yeast provides insight into the basis for resistance to this mycotoxin

Identification and Application of Novel Patulin-Degrading Enzymes from Bacillus subtilis 168

Patulin (PAT), a toxic secondary metabolite produced mainly by Penicillium species that frequently contaminates fruit and fruit-derived products, poses serious health risks to humans and animals. In the present study, three short-chain dehydrogenases/reductases (SDRs) with PAT-degrading ability, designated BsSDR1, BsSDR2, and BsSDR3, were identified from the genome of Bacillus subtilis 168. BsSDR1 and BsSDR2 showed powerful PAT elimination abilities, which can completely convert PAT to nontoxic E-ascladiol. Moreover, BsSDR1, BsSDR2, and BsSDR3 shared the highest sequence identity of 36.03% with the reported PAT-degrading enzymes, indicating that they are novel PAT-degrading enzymes. BsSDR1, BsSDR2, and BsSDR3 exhibited the highest activity against PAT at 40, 40, and 35 °C, respectively. Additionally, BsSDR1, BsSDR2, and BsSDR3 displayed remarkable thermostability, retaining 32.50, 24.63, and 46.74% residual activity, respectively, after incubation at 50 °C for 1 h. Three-dimensional (3D) simulation and site-directed mutagenesis indicated that the catalytic triad formed by the residues (Ser, Tyr, and Lys) was the key for SDR activity, and this conserved catalytic mechanism was followed in the catalytic process of novel PAT-degrading enzymes BsSDR1, BsSDR2, and BsSDR3. More importantly, BsSDR1, BsSDR2, and BsSDR3 can degrade PAT in apple juice at rates of 86.90, 90.17, and 61.57%, respectively. The identification of BsSDR1, BsSDR2, and BsSDR3 enriched the PAT-degrading enzyme libraries, providing promising candidates for PAT decontamination in the food industry.

Dual Role of Yeasts and Filamentous Fungi in Fermented Sausages

This contribution aims to review the presence and the potential double role-positive or beneficial and negative or harmful-of fungi in fermented sausages as well as their use as starter cultures. Traditionally, studies have been focused on lactic acid bacteria; however, over the years, interest in the study of fungi has increased. The important contribution of yeasts and filamentous fungi to the quality and safety of fermented sausages has emerged from reviewing the literature regarding these fermented products. In conclusion, this review contributes to the existing literature by considering the double role of filamentous fungi and yeasts, the global fermented sausage market size, the role and use of starters, and the starters mainly present in the worldwide market, as well as the main factors to take into account to optimize production. Finally, some suggestions for future broadening of the sector are discussed.

Structural switching aptamer-based electrochemical sensor for mycotoxin patulin detection

In this study, an electrochemical and aptamer-based aptasensor was developed for the sensitive detection of patulin, a mycotoxin commonly found in fruits and fruit-based products. The aptasensor used an innovative structural switching signal-off platform for detecting patulin. The aptamer immobilization on screen-printed carbon electrodes was achieved through Au electrodeposition and thiol group (-SH) route. Response surface methodology was used to determine the optimal incubation times for the aptamer, blocking agent, and target molecule, which were found to be 180 min, 40 min, and 89 min, respectively. The response of the aptamer to different concentrations of patulin was measured using square wave voltammetry by exploiting the structural switching mechanism. The sensor response was determined by quantifying differences in the aptasensor's background current. The aptasensor exhibited a linear working range of 1-25 μM and a low detection limit of 3.56 ng/mL for patulin. The aptasensor's relative standard deviation and accuracy were determined to be 0.067 and 94.4%, respectively. A non-specific interaction was observed at low concentrations of two other mycotoxins, ochratoxin A and zearalenone. The interference from ochratoxin A in the measurements was below 10%. In real sample tests using apple juice, interference, particularly at low concentrations, had changed the recovery of patulin negatively with a significant effect on the structural switching behavior. Nevertheless, at a concentration of 25 ng/mL, the interference effect was eliminated, and the recovery standard deviation improved to 6.6%. The aptasensor's stability was evaluated over 10 days, and it demonstrated good performance, retaining 13.12% of its initial response. These findings demonstrate the potential of the developed electrochemical aptasensor for the sensitive detection of patulin in fruit-based products, with prospects for application in food safety and quality control.

A Predictive Assessment of Ochratoxin A's Effects on Oxidative Stress Parameters and the Fermentation Ability of Yeasts Using Neural Networks

The aim of this paper was to examine the effect of different OTA concentrations on the parameters of oxidative stress (glutathione (GSH) and malondialdehyde (MDA) concentrations) and glucose utilization in ethanol production by wine yeasts. In addition to the above, artificial neural networks (ANN) were used to predict the effects of different OTA concentrations on the fermentation ability of yeasts and oxidative stress parameters. The obtained results indicate a negative influence of OTA (4 µg mL-1) on ethanol production after 12 h. For example, K. marxianus produced 1.320 mg mL-1 of ethanol, while in the control sample 1.603 µg mL-1 of ethanol was detected. However, after 24 h, OTA had no negative effect on ethanol production, since it was higher (7.490 and 3.845 mg mL-1) in comparison to control samples. Even low concentrations of OTA affect GSH concentrations, with the highest being detected after 12 and 24 h (up to 16.54 µM), while MDA concentrations are affected by higher OTA concentrations, with the highest being detected at 24 h (1.19 µM). The obtained results with the use of ANNs showed their potential for quantification purposes based on experimental data, while the results of ANN prediction models have shown to be useful for predictions of what outcomes different concentrations of OTA that were not part of experiment will have on the fermentation capacity and oxidative stress parameters of yeasts.

Exploring yeast-based microbial interactions: The next frontier in postharvest biocontrol

Fresh fruits and vegetables are susceptible to a large variety of spoilage agents before and after harvest. Among these, fungi are mostly responsible for the microbiological deteriorations that lead to economically significant losses of fresh produce. Today, synthetic fungicides represent the first approach for controlling postharvest spoilage in fruits and vegetables worldwide. However, the emergence of fungicide-resistant pathogen biotypes and the increasing awareness of consumers toward the health implications of hazardous chemicals imposed an urgent need to reduce the use of synthetic fungicides in the food supply; this phenomenon strengthened the search for alternative biocontrol strategies that are more effective, safer, nontoxic, low-residue, environment friendly, and cost-effective. In the last decade, biocontrol with antagonistic yeasts became a promising strategy to reduce chemical compounds during fruit and vegetable postharvest, and several yeast-based biocontrol products have been commercialized. Biocontrol is a multipartite system that includes different microbial groups (spoilage mold, yeast, bacteria, and nonspoilage resident microorganisms), host fruit, vegetables, or plants, and the environment. The majority of biocontrol studies focused on yeast-mold mechanisms, with little consideration for yeast-bacteria and yeast-yeast interactions. The current review focused mainly on the unexplored yeast-based interactions and the mechanisms of actions in biocontrol systems as well as on the importance and advantages of using yeasts as biocontrol agents, improving antagonist efficiency, the commercialization process and associated challenges, and future perspectives.

Microbial detoxification of mycotoxins in food

Mycotoxins are toxic secondary metabolites produced by certain genera of fungi including but not limited to Fusarium, Aspergillus, and Penicillium. Their persistence in agricultural commodities poses a significant food safety issue owing to their carcinogenic, teratogenic, and immunosuppressive effects. Due to their inherent stability, mycotoxin levels in contaminated food often exceed the prescribed regulatory thresholds posing a risk to both humans and livestock. Although physical and chemical methods have been applied to remove mycotoxins, these approaches may reduce the nutrient quality and organoleptic properties of food. Microbial transformation of mycotoxins is a promising alternative for mycotoxin detoxification as it is more specific and environmentally friendly compared to physical/chemical methods. Here we review the biological detoxification of the major mycotoxins with a focus on microbial enzymes.

Structure-based rational design of a short-chain dehydrogenase/reductase for improving activity toward mycotoxin patulin

Patulin is a fatal mycotoxin that is widely detected in drinking water and fruit-derived products contaminated by diverse filamentous fungi. CgSDR from Candida guilliermondii represents the first NADPH-dependent short-chain dehydrogenase/reductase that catalyzes the reduction of patulin to the nontoxic E-ascladiol. To elucidate the catalytic mechanism of CgSDR, we solved its crystal structure in complex with cofactor and substrate. Structural analyses indicate that patulin is situated in a hydrophobic pocket adjacent to the cofactor, with the hemiacetal ring orienting toward the nicotinamide moiety of NADPH. In addition, we conducted structure-guided engineering to modify substrate-binding residue V187 and obtained variant V187F, V187K and V187W, whose catalytic activity was elevated by 3.9-, 2.2- and 1.7-fold, respectively. The crystal structures of CgSDR variants suggest that introducing additional aromatic stacking or hydrogen-bonding interactions to bind the lactone ring of patulin might account for the observed enhanced activity. These results illustrate the catalytic mechanism of SDR-mediated patulin detoxification for the first time and provide the upgraded variants that exhibit tremendous potentials in industrial applications.

Unveiling ochratoxin a controlling and biodetoxification molecular mechanisms: Opportunities to secure foodstuffs from OTA contamination

Anarchic growth of ochratoxin A (OTA) producing fungi during crop production, prolonged storage, and processing results in OTA contamination in foodstuffs. OTA in food exacerbates the risk of health and economic problems for consumers and farmers worldwide. Although the toxic effects of OTA on human health have not been well established, comprehensive preventive and remedial measures will be essential to eliminate OTA from foodstuffs. Strict regulations, controlling OTA at pre- or post-harvest stage, and decontamination of OTA have been adopted to prevent human and animal OTA exposure. Biological control of OTA and bio-decontamination are the most promising strategies due to their safety, specificity and nutritional value. This review addresses the current understanding of OTA biodegradation mechanisms and recent developments in OTA control and bio-decontamination strategies. Additionally, this review analyses the strength and weaknesses of different OTA control methods and the contemporary approaches to enhance the efficiency of biocontrol agents. Overall, this review will support the implementation of new strategies to effectively control OTA in food sectors. Further studies on efficacy-related issues, production issues and cost-effectiveness of OTA biocontrol are to be carried out to improve the knowledge, develop improved delivery technologies and safeguard the durability of OTA biocontrol approaches.

Structure-function characterization of an aldo-keto reductase involved in detoxification of the mycotoxin, deoxynivalenol

Deoxynivalenol (DON) is a mycotoxin, produced by filamentous fungi such as Fusarium graminearum, that causes significant yield losses of cereal grain crops worldwide. One of the most promising methods to detoxify this mycotoxin involves its enzymatic epimerization to 3-epi-DON. DepB plays a critical role in this process by reducing 3-keto-DON, an intermediate in the epimerization process, to 3-epi-DON. DepB_Rleg from Rhizobium leguminosarum is a member of the new aldo-keto reductase family, AKR18, and it has the unusual ability to utilize both NADH and NADPH as coenzymes, albeit with a 40-fold higher catalytic efficiency with NADPH compared to NADH. Structural analysis of DepB_Rleg revealed the putative roles of Lys-217, Arg-290, and Gln-294 in NADPH specificity. Replacement of these residues by site-specific mutagenesis to negatively charged amino acids compromised NADPH binding with minimal effects on NADH binding. The substrate-binding site of DepB_Rleg is larger than its closest structural homolog, AKR6A2, likely contributing to its ability to utilize a wide range of aldehydes and ketones, including the mycotoxin, patulin, as substrates. The structure of DepB_Rleg also suggests that 3-keto-DON can adopt two binding modes to facilitate 4-pro-R hydride transfer to either the re- or si-face of the C3 ketone providing a possible explanation for the enzyme's ability to convert 3-keto-DON to 3-epi-DON and DON in diastereomeric ratios of 67.2% and 32.8% respectively.

Modulation of extracellular Penicillium expansum-driven acidification by Papiliotrema terrestris affects biosynthesis of patulin and has a possible role in biocontrol activity

The active regulation of extracellular pH is critical for the virulence of fungal pathogens. Penicillium expansum is the causal agent of green-blue mold on stored pome fruits and during its infection process acidifies the host tissues by secreting organic acids. P. expansum is also the main producer of patulin (PAT), a mycotoxin found in pome fruit-based products and that represents a serious health hazard for its potential carcinogenicity. While it is known that PAT biosynthesis in P. expansum is regulated by nutritional factors such as carbon and nitrogen and by the pH, the mechanistic effects of biocontrol on PAT production by P. expansum are not known. In this work, we assessed how optimal and suboptimal concentrations of the biocontrol agent (BCA) Papiliotrema terrestris LS28 affect both extracellular pH and PAT biosynthesis in P. expansum. In wounded apples, the optimal and suboptimal concentrations of the BCA provided almost complete and partial protection from P. expansum infection, respectively, and reduced PAT contamination in both cases. However, the suboptimal concentration of the BCA increased the specific mycotoxigenic activity by P. expansum. In vitro, the rate of PAT biosynthesis was strictly related to the extracellular pH, with the highest amount of PAT detected in the pH range 4–7, whereas only traces were detectable at pH 3. Moreover, both in vitro and in apple wounds the BCA counteracted the extracellular P. expansum-driven acidification maintaining extracellular pH around 4, which is within the pH range that is optimal for PAT biosynthesis. Conversely, in the absence of LS28 the pathogen-driven acidification led to rapidly achieving acidic pH values (<3) that lie outside of the optimal pH range for PAT biosynthesis. Taken together, these results suggest that pH modulation by LS28 is important to counteract the host tissue acidification and, therefore, the virulence of P. expansum. On the other hand, the buffering of P. expansum-driven acidification provided by the BCA increases the specific rate of PAT biosynthesis through the extension of the time interval at which the pH value lies within the optimal range for PAT biosynthesis. Nevertheless, the antagonistic effect provided by the BCA greatly reduced the total amount of PAT.

Characterization of Two Dehydrogenases from Gluconobacter oxydans Involved in the Transformation of Patulin to Ascladiol

Patulin is a mycotoxin that primarily contaminate apples and apple products. Whole cell or cell-free extracts of Gluconobacter oxydans ATCC 621 were able to transform patulin to E-ascladiol. Proteins from cell-free extracts were separated by anion exchange chromatography and fractions with patulin transformation activity were subjected to peptide mass fingerprinting, enabling the identification of two NADPH dependent short chain dehydrogenases, GOX0525 and GOX1899, with the requisite activity. The genes encoding these enzymes were expressed in E. coli and purified. Kinetic parameters for patulin reduction, as well as pH profiles and thermostability were established to provide further insight on the potential application of these enzymes for patulin detoxification.

Reduction the contamination of patulin during the brewing of apple cider and its characteristics

Patulin is one of the most significant food safety problems in fruit and derived products. The reduction of patulin contamination in food processing has always been the focus of research. In this study, nine yeast strains were applied for the brewing of apple cider and the fate of patulin was determined. In this process, the patulin contamination can be decreased by adsorption onto and degradation of yeast cells in the main fermentation (20.8-49.1%), as well as the adsorption removal during clarification (18.7-58%), inverted cans (21.3-31.4%) and aging (1.0-5.8%). Saccharomyces cerevisiae (1027) was selected to reveal the elimination mechanism of patulin in main fermentation. The decrease of patulin content was mainly due to degradation and the intracellular enzymes played a more important role than extracellular ones. In addition, the synthesis of enzymes was related to the induction of patulin. Furthermore, the degradation product of patulin in the main fermentation was identified as E-ascladiol, which is less toxic than patulin. Based on the representative strain of S. cerevisiae 1027, patulin contamination can be effectively eliminated during apple cider brewing. This study provides a new insight into eliminating patulin contamination in the brewing of apple cider.

More than a Virulence Factor: Patulin Is a Non-Host-Specific Toxin that Inhibits Postharvest Phytopathogens and Requires Efflux for Penicillium Tolerance

Mycotoxin contamination is a leading cause of food spoilage and waste on a global scale. Patulin, a mycotoxin produced by Penicillium spp. during postharvest pome fruit decay, causes acute and chronic effects in humans, withstands pasteurization, and is not eliminated by fermentation. While much is known about the impact of patulin on human health, there are significant knowledge gaps concerning the effect of patulin during postharvest fruit-pathogen interactions. Application of patulin on six apple cultivars reproduced some blue mold symptoms that were cultivar-independent and dose-dependent. Identical symptoms were also observed in pear and mandarin orange. Six Penicillium isolates exposed to exogenous patulin exhibited delayed germination after 24 h, yet all produced viable colonies in 7 days. However, four common postharvest phytopathogenic fungi were completely inhibited by patulin during conidial germination and growth, suggesting the toxin is important for Penicillium to dominate the postharvest niche. Using clorgyline, a broad-spectrum efflux pump inhibitor, we demonstrated that efflux plays a role in Penicillium auto-resistance to patulin during conidial germination. The work presented here contributes new knowledge of patulin auto-resistance, its mode of action, and inhibitory role in fungal-fungal interactions. Our findings provide a solid foundation to develop toxin and decay mitigation approaches.

Biological Detoxification of Mycotoxins: Current Status and Future Advances

Mycotoxins are highly toxic metabolites produced by fungi that pose a huge threat to human and animal health. Contamination of food and feed with mycotoxins is a worldwide issue, which leads to huge financial losses, annually. Decades of research have developed various approaches to degrade mycotoxins, among which the biological methods have been proved to have great potential and advantages. This review provides an overview on the important advances in the biological removal of mycotoxins over the last decade. Here, we provided further insight into the chemical structures and the toxicity of the main mycotoxins. The innovative strategies including mycotoxin degradation by novel probiotics are summarized in an in-depth discussion on potentialities and limitations. We prospected the promising future for the development of multifunctional approaches using recombinant enzymes and microbial consortia for the simultaneous removal of multiple mycotoxins.

Control of Penicillium expansum by an Epiphytic Basidiomycetous Yeast

Postharvest biocontrol agents are considered a viable alternative to the use of synthetic chemicals as demonstrated by extensive research conducted by scientists and companies worldwide. In the present investigation, the biocontrol potential of a carotenoid-producing basidiomycetous yeast isolated from table grape flowers was analyzed. The strain RY1 proved to be Sporobolomyces roseus. In vitro and in vivo tests were conducted to assess its efficacy against Penicillium expansum, one of the most important postharvest pathogens and producer of the mycotoxin patulin. The yeast proved to control both fungal growth and patulin production, and, in addition, to greatly affect disease incidence and severity on apples. Its mode of action is presumably related both to the competition for nutrients and the production of antifungal volatiles. As such, although further large-scale trials are needed, our S. roseus strain represents a potential interesting biocontrol agent to be applied after harvest.

Bacterial Quorum-Quenching Lactonase Hydrolyzes Fungal Mycotoxin and Reduces Pathogenicity of Penicillium expansum-Suggesting a Mechanism of Bacterial Antagonism

Penicillium expansum is a necrotrophic wound fungal pathogen that secrets virulence factors to kill host cells including cell wall degrading enzymes (CWDEs), proteases, and mycotoxins such as patulin. During the interaction between P. expansum and its fruit host, these virulence factors are strictly modulated by intrinsic regulators and extrinsic environmental factors. In recent years, there has been a rapid increase in research on the molecular mechanisms of pathogenicity in P. expansum; however, less is known regarding the bacteria–fungal communication in the fruit environment that may affect pathogenicity. Many bacterial species use quorum-sensing (QS), a population density-dependent regulatory mechanism, to modulate the secretion of quorum-sensing signaling molecules (QSMs) as a method to control pathogenicity. N-acyl homoserine lactones (AHLs) are Gram-negative QSMs. Therefore, QS is considered an antivirulence target, and enzymes degrading these QSMs, named quorum-quenching enzymes, have potential antimicrobial properties. Here, we demonstrate that a bacterial AHL lactonase can also efficiently degrade a fungal mycotoxin. The mycotoxin is a lactone, patulin secreted by fungi such as P. expansum. The bacterial lactonase hydrolyzed patulin at high catalytic efficiency, with a k_cat value of 0.724 ± 0.077 s⁻¹ and K_M value of 116 ± 33.98 μM. The calculated specific activity (k_cat/K_M) showed a value of 6.21 × 10³ s⁻¹M⁻¹. While the incubation of P. expansum spores with the purified lactonase did not inhibit spore germination, it inhibited colonization by the pathogen in apples. Furthermore, adding the purified enzyme to P. expansum culture before infecting apples resulted in reduced expression of genes involved in patulin biosynthesis and fungal cell wall biosynthesis. Some AHL-secreting bacteria also express AHL lactonase. Here, phylogenetic and structural analysis was used to identify putative lactonase in P. expansum. Furthermore, following recombinant expression and purification of the newly identified fungal enzyme, its activity with patulin was verified. These results indicate a possible role for patulin and lactonases in inter-kingdom communication between fungi and bacteria involved in fungal colonization and antagonism and suggest that QQ lactonases can be used as potential antifungal post-harvest treatment.

Analysis of Stored Wheat Grain-Associated Microbiota Reveals Biocontrol Activity among Microorganisms against Mycotoxigenic Fungi

Wheat grains are colonized by complex microbial communities that have the potential to affect seed quality and susceptibility to disease. Some of the beneficial microbes in these communities have been shown to protect plants against pathogens through antagonism. We evaluated the role of the microbiome in seed health: in particular, against mycotoxin-producing fungi. Amplicon sequencing was used to characterize the seed microbiome and determine if epiphytes and endophytes differ in their fungal and bacterial diversity and community composition. We then isolated culturable fungal and bacterial species and evaluated their antagonistic activity against mycotoxigenic fungi. The most prevalent taxa were found to be shared between the epiphytic and endophytic microbiota of stored wheat seeds. Among the isolated bacteria, Bacillus strains exhibited strong antagonistic properties against fungal pathogens with noteworthy fungal load reduction in wheat grain samples of up to a 3.59 log₁₀ CFU/g compared to untreated controls. We also found that a strain of the yeast, Rhodotorula glutinis, isolated from wheat grains, degrades and/or metabolizes aflatoxin B₁, one of the most dangerous mycotoxins that negatively affects physiological processes in animals and humans. The mycotoxin level in grain samples was significantly reduced up to 65% in the presence of the yeast strain, compared to the untreated control. Our study demonstrates that stored wheat grains are a rich source of bacterial and yeast antagonists with strong inhibitory and biodegradation potential against mycotoxigenic fungi and the mycotoxins they produce, respectively. Utilization of these antagonistic microorganisms may help reduce fungal and mycotoxin contamination, and potentially replace traditionally used synthetic chemicals.

Characterization of a short-chain dehydrogenase/reductase and its function in patulin biodegradation in apple juice

Biodegradation based on microbial enzymes is considered to be one of the promising ways for controlling patulin contamination. However, few patulin degrading enzymes have been isolated and characterized until now. Here, a short-chain dehydrogenase/reductase (SDR) gene, CgSDR, was cloned from a yeast strain Candida guilliermondii, and expressed in Escherichia coli. The expression of CgSDR conferred a strong patulin tolerance and degradation ability to E. coli, and purified CgSDR could transform patulin into E-ascladiol in vitro with NADPH as a coenzyme. Moreover, addition of CgSDR at 150 μg/mL could reduce 80% of patulin in apple juice and the biodegradation process did not affect the quality of the apple juice. A molecular docking analysis and site-directed mutagenesis indicated that CgSDR might interact with patulin via VAL188 as an active binding sites. The findings provide new insights for developing enzymic formulations for mycotoxin detoxification in fruit derived products.

Effect of ascorbic acid, oxygen and storage duration on patulin in cloudy apple juice produced on a semi-industrial scale

Patulin (PAT), a mycotoxin mainly produced by Penicillium expansum, is of high concern with regard to human food safety. This study examined the stability of PAT in artificially contaminated cloudy apple juice (CAJ) produced on a semi-industrial scale using an innovative technology allowing degassing and pressing under low-oxygen conditions (VaculIQ 1000). The effects of adding ascorbic acid (AA), degassing during production and storing in the dark at 20 °C on the PAT concentration were studied, as well as possible degradation and reaction products formed. The highest PAT degradation (50%) was observed for flash-pasteurised juice with AA added, produced under low-oxygen conditions and degassed and stored for 14 days at 20 °C in the dark in aluminium laminate aseptic bags. Juices produced showed no significant differences in the quality parameters measured and did not show significant formation of reaction products. Further research needs to be focused on the fate of PAT in CAJ produced on an industrial level with and without addition of AA.

The characteristics of patulin detoxification by Lactobacillus plantarum 13M5

Patulin (PAT) is a widespread mycotoxin that harms the health of both humans and animals. In this study, among the 17 tested Lactobacillus plantarum strains, L. plantarum 13M5, isolated from traditional Chinese fermented foods, showed the highest PAT degradation rate of up to 43.8% (PAT 5 mg/L). Evaluation of the living and dead 13M5 cells revealed that only the living cells had the ability to remove PAT and degrade it into E-ascladiol. A cell-based assay revealed that L. plantarum 13M5 administration alleviated PAT-induced injuries in Caco-2 cells, including cytotoxicity, oxidative stress, and tight junction disruption. Our results suggest that L. plantarum 13M5 has the potential to reduce PAT toxicity and can thus be used as a probiotic supplement to reduce or eliminate the toxicity of PAT ingested from diet.

Mycotoxins: Biotransformation and Bioavailability Assessment Using Caco-2 Cell Monolayer

The determination of mycotoxins content in food is not sufficient for the prediction of their potential in vivo cytotoxicity because it does not reflect their bioavailability and mutual interactions within complex matrices, which may significantly alter the toxic effects. Moreover, many mycotoxins undergo biotransformation and metabolization during the intestinal absorption process. Biotransformation is predominantly the conversion of mycotoxins meditated by cytochrome P450 and other enzymes. This should transform the toxins to nontoxic metabolites but it may possibly result in unexpectedly high toxicity. Therefore, the verification of biotransformation and bioavailability provides valuable information to correctly interpret occurrence data and biomonitoring results. Among all of the methods available, the in vitro models using monolayer formed by epithelial cells from the human colon (Caco-2 cell) have been extensively used for evaluating the permeability, bioavailability, intestinal transport, and metabolism of toxic and biologically active compounds. Here, the strengths and limitations of both in vivo and in vitro techniques used to determine bioavailability are reviewed, along with current detailed data about biotransformation of mycotoxins. Furthermore, the molecular mechanism of mycotoxin effects is also discussed regarding the disorder of intestinal barrier integrity induced by mycotoxins.

Protection of Citrus Fruits from Postharvest Infection with Penicillium digitatum and Degradation of Patulin by Biocontrol Yeast Clavispora lusitaniae 146

Fungal rots are one of the main causes of large economic losses and deterioration in the quality and nutrient composition of fruits during the postharvest stage. The yeast Clavispora lusitaniae 146 has previously been shown to efficiently protect lemons from green mold caused by Penicillium digitatum. In this work, the effect of yeast concentration and exposure time on biocontrol efficiency was assessed; the protection of various citrus fruits against P. digitatum by C. lusitaniae 146 was evaluated; the ability of strain 146 to degrade mycotoxin patulin was tested; and the effect of the treatment on the sensory properties of fruits was determined. An efficient protection of lemons was achieved after minimum exposure to a relatively low yeast cell concentration. Apart from lemons, the yeast prevented green mold in grapefruits, mandarins, oranges, and tangerines, implying that it can be used as a broad-range biocontrol agent in citrus. The ability to degrade patulin indicated that strain 146 may be suitable for the control of further Penicillium species. Yeast treatment did not alter the sensory perception of the aroma of fruits. These results corroborate the potential of C. lusitaniae 146 for the control of postharvest diseases of citrus fruits and indicate its suitability for industrial-scale fruit processing.

Recent trends in detecting, controlling, and detoxifying of patulin mycotoxin using biotechnology methods

Patulin (PAT) is a mycotoxin that can contaminate many foods and especially fruits and fruit-based products. Therefore, accurate and effective testing is necessary to enable producers to comply with regulations and promote food safety. Traditional approaches involving the use of chemical compounds or physical treatments in food have provided practical methods that have been used to date. However, growing concerns about environmental and health problems associated with these approaches call for new alternatives. In contrast, recent advances in biotechnology have revolutionized the understanding of living organisms and brought more effective biological tools. This review, therefore, focuses on the study of biotechnology approaches for the detection, control, and mitigation of PAT in food. Future aspects of biotechnology development to overcome the food safety problem posed by PAT were also examined. We find that biotechnology advances offer novel, more effective, and environmental friendly approaches for the control and elimination of PAT in food compared to traditional methods. Biosensors represent the future of PAT detection and use biological tools such as aptamer, enzyme, and antibody. PAT prevention strategies include microbial biocontrol, the use of antifungal biomolecules, and the use of microorganisms in combination with antifungal molecules. PAT detoxification aims at the breakdown and removal of PAT in food by using enzymes, microorganisms, and various adsorbent biopolymers. Finally, biotechnology advances will be dependent on the understanding of fundamental biology of living organisms regarding PAT synthesis and resistance mechanisms.

Microbiological Detoxification of Mycotoxins: Focus on Mechanisms and Advances

Some fungal species of the genera Aspergillus, Penicillium, and Fusarium secretes toxic metabolites known as mycotoxins, have become a global concern that is toxic to different species of animals and humans. Biological mycotoxins detoxification has been studied by researchers around the world as a new strategy for mycotoxin removal. Bacteria, fungi, yeast, molds, and protozoa are the main living organisms appropriate for the mycotoxin detoxification. Enzymatic and degradation sorptions are the main mechanisms involved in microbiological detoxification of mycotoxins. Regardless of the method used, proper management tools that consist of before-harvest prevention and after-harvest detoxification are required. Here, in this review, we focus on the microbiological detoxification and mechanisms involved in the decontamination of mycotoxins.

Biological Control of Fruit Rot and Anthracnose of Postharvest Mango by Antagonistic Yeasts from Economic Crops Leaves

To select antagonistic yeasts for the control of fruit rot caused by Lasiodiplodiatheobromae and anthracnose caused by Colletotrichum gloeosporioides in postharvest mango fruit, 307 yeast strains isolated from plant leaves were evaluated for their antagonistic activities against these two fungal pathogens in vitro. Torulaspora indica DMKU-RP31, T. indica DMKU-RP35 and Pseudozyma hubeiensis YE-21 were found to inhibit the growth of L. theobromae whereas only Papiliotrema aspenensis DMKU-SP67 inhibited the growth of C. gloeosporioides. Antagonistic mechanisms of these four antagonistic yeasts in vitro consisted of the production of antifungal volatile organic compounds (VOCs), biofilm formation and siderophore production. T. indica DMKU-RP35 was the most effective strain in controlling fruit rot on postharvest mango fruits. Its action was comparable to that of the fungicide, benomyl, reducing the disease severity by 82.4%, whereas benomyl revealed 87.5% reduction. P. aspenensis DMKU-SP67 reduced anthracnose severity by 94.1%, which was comparable to that of using benomyl (93.9%). The antifungal VOCs produced by these yeast strains also reduced the severity of these diseases on postharvest mango fruits but at lower rates than using yeast cells. Therefore, these antagonistic yeasts have the potential for use as biological control agents for the control of fruit rot and anthracnose diseases.

Detoxification of Mycotoxins through Biotransformation

Mycotoxins are toxic fungal secondary metabolites that pose a major threat to the safety of food and feed. Mycotoxins are usually converted into less toxic or non-toxic metabolites through biotransformation that are often made by living organisms as well as the isolated enzymes. The conversions mainly include hydroxylation, oxidation, hydrogenation, de-epoxidation, methylation, glycosylation and glucuronidation, esterification, hydrolysis, sulfation, demethylation and deamination. Biotransformations of some notorious mycotoxins such as alfatoxins, alternariol, citrinin, fomannoxin, ochratoxins, patulin, trichothecenes and zearalenone analogues are reviewed in detail. The recent development and applications of mycotoxins detoxification through biotransformation are also discussed.

The Aspergilli and Their Mycotoxins: Metabolic Interactions With Plants and the Soil Biota

Species of the highly diverse fungal genus Aspergillus are well-known agricultural pests, and, most importantly, producers of various mycotoxins threatening food safety worldwide. Mycotoxins are studied predominantly from the perspectives of human and livestock health. Meanwhile, their roles are far less known in nature. However, to understand the factors behind mycotoxin production, the roles of the toxins of Aspergilli must be understood from a complex ecological perspective, taking mold-plant, mold-microbe, and mold-animal interactions into account. The Aspergilli may switch between saprophytic and pathogenic lifestyles, and the production of secondary metabolites, such as mycotoxins, may vary according to these fungal ways of life. Recent studies highlighted the complex ecological network of soil microbiotas determining the niches that Aspergilli can fill in. Interactions with the soil microbiota and soil macro-organisms determine the role of secondary metabolite production to a great extent. While, upon infection of plants, metabolic communication including fungal secondary metabolites like aflatoxins, gliotoxin, patulin, cyclopiazonic acid, and ochratoxin, influences the fate of both the invader and the host. In this review, the role of mycotoxin producing Aspergillus species and their interactions in the ecosystem are discussed. We intend to highlight the complexity of the roles of the main toxic secondary metabolites as well as their fate in natural environments and agriculture, a field that still has important knowledge gaps.

Diversity and phylogeny of basidiomycetous yeasts from plant leaves and soil: Proposal of two new orders, three new families, eight new genera and one hundred and seven new species

Nearly 500 basidiomycetous yeast species were accepted in the latest edition of The Yeasts: A Taxonomic Study published in 2011. However, this number presents only the tip of the iceberg of yeast species diversity in nature. Possibly more than 99 % of yeast species, as is true for many groups of fungi, are yet unknown and await discovery. Over the past two decades nearly 200 unidentified isolates were obtained during a series of environmental surveys of yeasts in phyllosphere and soils, mainly from China. Among these isolates, 107 new species were identified based on the phylogenetic analyses of nuclear ribosomal DNA (rDNA) [D1/D2 domains of the large subunit (LSU), the small subunit (SSU), and the internal transcribed spacer region including the 5.8S rDNA (ITS)] and protein-coding genes [both subunits of DNA polymerase II (RPB1 and RPB2), the translation elongation factor 1-α (TEF1) and the mitochondrial gene cytochrome b (CYTB)], and physiological comparisons. Forty-six of these belong to 16 genera in the Tremellomycetes (Agaricomycotina). The other 61 are distributed in 26 genera in the Pucciniomycotina. Here we circumscribe eight new genera, three new families and two new orders based on the multi-locus phylogenetic analyses combined with the clustering optimisation analysis and the predicted similarity thresholds for yeasts and filamentous fungal delimitation at genus and higher ranks. Additionally, as a result of these analyses, three new combinations are proposed and 66 taxa are validated.

S-Adenosylmethionine-Dependent Methyltransferase Helps Pichia caribbica Degrade Patulin

Patulin contamination not only is a menace to human health but also causes serious environmental problems worldwide due to the synthetic fungicides that are used to control it. This study focused on investigating the patulin degradation mechanism in Pichia caribbica at the molecular level. According to the results, P. caribbica (2 × 10⁶ cells/mL) was able to degrade patulin from 20 μg/mL to an undetectable level in 72 h. The RNA-seq data showed patulin-induced oxidative stress and responses in P. caribbica. The deletion of PcCRG1 led to a significant decrease in patulin degradation by P. caribbica, whereas the overexpression of PcCRG1 accelerated the degradation of patulin. The study identified that PcCRG1 protein had the ability to degrade patulin in vitro. Overall, we demonstrated that the patulin degradation process in P. caribbica was more than one way; PcCRG1 was an S-adenosylmethionine-dependent methyltransferase and played an important role in the patulin degradation process in P. caribbica.

The presence of ochratoxin A does not influence Saccharomyces cerevisiae growth kinetics but leads to the formation of modified ochratoxins

Yeasts are able to reduce the levels of ochratoxin A in fermentative processes; and, through their enzymatic complex, these micro-organisms are also capable of forming modified mycotoxins. These mycotoxins are often underreported, and may increase health risks after ingestion of contaminated food. In this sense, this study aims to evaluate whether the presence of ochratoxin A influences yeast growth kinetic parameters and to elucidate the formation of modified ochratoxin by Saccharomyces cerevisiae strains during fermentation. Three S. cerevisiae strains (12 M, 01 PP, 41 PP) were exposed to OTA at the concentrations of 10, 20 and 30 μg/L. The Baranyi model was fitted to the growth data (Log CFU/mL), and the identification of modified ochratoxins was performed through High Resolution Mass Spectrometry. The presence of ochratoxin A did not influence the growth of S. cerevisiae strains. Four pathways were proposed for the metabolization of OTA: dechlorination, hydrolysis, hydroxylation, and conjugation. Among the elected targets, the following were identified: ochratoxin α, ochratoxin β, ochratoxin α methyl ester, ochratoxin B methyl ester, ethylamide ochratoxin A, ochratoxin C, hydroxy-ochratoxin A, hydroxy-ochratoxin A methyl ester, and ochratoxin A cellobiose ester. These derivatives formed from yeast metabolism may contribute to the occurrence of underreporting levels of total mycotoxin in fermented products.

Mycotoxin patulin in food matrices: occurrence and its biological degradation strategies

Patulin is a mycotoxin produced by a number of filamentous fungal species. It is a polyketide secondary metabolite which can gravely cause human health problems and food safety issues. This review deals with the occurrence of patulin in major food commodities from 2008 to date, including historical aspects, source, occurrence, regulatory limits and its toxicity. Most importantly, an overview of the recent research progress about the biodegradation strategies for contaminated food matrices is provided. The physical and chemical approaches have some drawbacks such as safety issues, possible losses in the nutritional quality, chemical hazards, limited efficacy, and high cost. The biological decontamination based on elimination or degradation of patulin using yeast, bacteria, and fungi has shown good results and it seems to be attractive since it works under mild and environment-friendly conditions. Further studies are needed to make clear the detoxification pathways by available potential biosorbents and to determine the practical applications of these methods at a commercial level to remove patulin from food products with special reference to their effects on sensory characteristics of foods.

Isotopic Labeling Studies Reveal the Patulin Detoxification Pathway by the Biocontrol Yeast Rhodotorula kratochvilovae LS11

Patulin (1) is a mycotoxin contaminant in fruit and vegetable products worldwide. Biocontrol agents, such as the yeast Rhodotorula kratochvilovae strain LS11, can reduce patulin (1) contamination in food. R. kratochvilovae LS11 converts patulin (1) into desoxypatulinic acid (DPA) (5), which is less cytotoxic than the mycotoxin (1) to in vitro human lymphocytes. In the present study, we report our investigations into the pathway of degradation of patulin (1) to DPA (5) by R. kratochvilovae. Isotopic labeling experiments revealed that 5 derives from patulin (1) through the hydrolysis of the γ-lactone ring and subsequent enzymatic modifications. The ability of patulin (1) and DPA (5) to cause genetic damage was also investigated by the cytokinesis-block micronucleus cytome assay on in vitro human lymphocytes. Patulin (1) was demonstrated to cause much higher chromosomal damage than DPA (5).

Patulin in Apples and Apple-Based Food Products: The Burdens and the Mitigation Strategies

Apples and apple-based products are among the most popular foods around the world for their delightful flavors and health benefits. However, the commonly found mold, Penicillium expansum invades wounded apples, causing the blue mold decay and ensuing the production of patulin, a mycotoxin that negatively affects human health. Patulin contamination in apple products has been a worldwide problem without a satisfactory solution yet. A comprehensive understanding of the factors and challenges associated with patulin accumulation in apples is essential for finding such a solution. This review will discuss the effects of the pathogenicity of Penicillium species, quality traits of apple cultivars, and environmental conditions on the severity of apple blue mold and patulin contamination. Moreover, beyond the complicated interactions of the three aforementioned factors, patulin control is also challenged by the lack of reliable detection methods in food matrices, as well as unclear degradation mechanisms and limited knowledge about the toxicities of the metabolites resulting from the degradations. As apple-based products are mainly produced with stored apples, pre- and post-harvest strategies are equally important for patulin mitigation. Before storage, disease-resistance breeding, orchard-management, and elicitor(s) application help control the patulin level by improving the storage qualities of apples and lowering fruit rot severity. From storage to processing, patulin mitigation strategies could benefit from the optimization of apple storage conditions, the elimination of rotten apples, and the safe and effective detoxification or biodegradation of patulin.

An analysis of codon bias in six red yeast species

Red yeasts, primarily species of Rhodotorula, Sporobolomyces, and other genera of Pucciniomycotina, are traditionally considered proficient systems for lipid and terpene production, and only recently have also gained consideration for the production of a wider range of molecules of biotechnological potential. Improvements of transgene delivery protocols and regulated gene expression systems have been proposed, but a dearth of information on compositional and/or structural features of genes has prevented transgene sequence optimization efforts for high expression levels. Here, the codon compositional features of genes in six red yeast species were characterized, and the impact that evolutionary forces may have played in shaping this compositional bias was dissected by using several computational approaches. Results obtained are compatible with the hypothesis that mutational bias, although playing a significant role, cannot alone explain synonymous codon usage bias of genes. Nevertheless, several lines of evidences indicated a role for translational selection in driving the synonymous codons that allow high expression efficiency. These optimal synonymous codons are identified for each of the six species analyzed. Moreover, the presence of intragenic patterns of codon usage, which are thought to facilitate polyribosome formation, was highlighted. The information presented should be taken into consideration for transgene design for optimal expression in red yeast species.

Complete Genome Sequence of the Biocontrol Agent Yeast Rhodotorula kratochvilovae Strain LS11

Rhodotorula kratochvilovae strain LS11 is a biocontrol agent (BCA) selected for its antagonistic activity against several plant pathogens both in the field and postharvest. Genome assembly includes 62 contigs for a total of 22.56 Mbp and a G+C content of 66.6%. Genome annotation predicts 7,642 protein-encoding genes.

Properties and Fermentation Activity of Industrial Yeasts Saccharomyces cerevisiae, S. uvarum, Candida utilis and Kluyveromyces marxianus Exposed to AFB1, OTA and ZEA

In this paper the effect of aflatoxin B₁, ochratoxin A and zearalenon on morphology, growth parameters and metabolic activity of yeasts Saccharomyces cerevisiae, Saccharomyces uvarum, Candida utilis and Kluyveromyces marxianus was determined. The results showed that the three mycotoxins affected the morphology of all these yeasts, primarily the cell diameter, but not their final cell count. Fourier transform infrared spectroscopy showed that the yeast membranes bound the mycotoxins, C. utilis in particular. The cell membranes of most yeasts underwent denaturation, except S. uvarum exposed to ochratoxin A and zearalenone. In the early stage of fermentation, all mycotoxin-exposed yeasts had lower metabolic activity and biomass growth than controls, but fermentation products and biomass concentrations reached the control levels by the end of the fermentation, except for C. utilis exposed to 20 µg/mL of zearalenone. The adaptive response to mycotoxins suggests that certain yeasts could be used to control mycotoxin concentrations in the production of fermented food and beverages.

Wild Grape-Associated Yeasts as Promising Biocontrol Agents against Vitis vinifera Fungal Pathogens

The increasing level of hazardous residues in the environment and food chains has led the European Union to restrict the use of chemical fungicides. Thus, exploiting new natural antagonistic microorganisms against fungal diseases could serve the agricultural production to reduce pre- and post-harvest losses, to boost safer practices for workers and to protect the consumers' health. The main aim of this work was to evaluate the antagonistic potential of epiphytic yeasts against Botrytis cinerea, Aspergillus carbonarius, and Penicillium expansum pathogen species. In particular, yeast isolation was carried out from grape berries of Vitis vinifera ssp sylvestris populations, of the Eurasian area, and V. vinifera ssp vinifera cultivars from three different farming systems (organic, biodynamic, and conventional). Strains able to inhibit or slow the growth of pathogens were selected by in vitro and in vivo experiments. The most effective antagonist yeast strains were subsequently assayed for their capability to colonize the grape berries. Finally, possible modes of action, such as nutrients and space competition, iron depletion, cell wall degrading enzymes, diffusible and volatile antimicrobial compounds, and biofilm formation, were investigated as well. Two hundred and thirty-one yeast strains belonging to 26 different species were isolated; 20 of them, ascribed to eight species, showed antagonistic action against all molds. Yeasts isolated from V. vinifera ssp sylvestris were more effective (up to 50%) against B. cinerea rather than those isolated from V. vinifera ssp vinifera. Six strains, all isolated from wild vines, belonging to four species (Meyerozyma guilliermondii, Hanseniaspora uvarum, Hanseniaspora clermontiae, and Pichia kluyveri) revealed one or more phenotypical characteristics associated to the analyzed modes of antagonistic action.

Crosstalk between proteins expression and lysine acetylation in response to patulin stress in Rhodotorula mucilaginosa

The proteomic and lysine acetylation (Kac) changes, accompanying degradation of patulin in Rhodotorula mucilaginosa were analyzed using tandem mass tagging and N6-acetyllysine affinity enrichment followed by LC-MS/MS. Proteomic results showed that expression level of short-chain reductase protein and glutathione S-transferase involved in detoxification was significantly up-regulated. In addition, the expression levels of zinc-binding oxidoreductase and quinone oxidoreductase that are involved in antioxidant process, ABC transport and MFS transport responsible for chemical transport were activated when treated with patulin. The quantitative real time PCR (qRT-PCR) result also indicated these genes expression levels were increased when treated with patulin. Kac changes accompanying degradation of patulin in R. mucilaginosa were also observed. Totally, 130 Kac sites in 103 proteins were differentially expressed under patulin stress. The differentially up expressed modified proteins were mainly involved in tricarboxylic acid cycle and nuclear acid biosynthesis. The differentially down expressed Kac proteins were mainly classified to ribosome, oxidative phosphorylation, protein synthesis and defense to stress process. Our results suggest that patulin exposure prompt R. mucilaginosa to produce a series of actions to resist or degrade patulin, including Kac. In addition, the Kac information in R. mucilaginosa and Kac in response to patulin stress was firstly revealed.

A silver bullet in a golden age of functional genomics: the impact of Agrobacterium-mediated transformation of fungi

The implementation of Agrobacterium tumefaciens as a transformation tool revolutionized approaches to discover and understand gene functions in a large number of fungal species. A. tumefaciens mediated transformation (AtMT) is one of the most transformative technologies for research on fungi developed in the last 20 years, a development arguably only surpassed by the impact of genomics. AtMT has been widely applied in forward genetics, whereby generation of strain libraries using random T-DNA insertional mutagenesis, combined with phenotypic screening, has enabled the genetic basis of many processes to be elucidated. Alternatively, AtMT has been fundamental for reverse genetics, where mutant isolates are generated with targeted gene deletions or disruptions, enabling gene functional roles to be determined. When combined with concomitant advances in genomics, both forward and reverse approaches using AtMT have enabled complex fungal phenotypes to be dissected at the molecular and genetic level. Additionally, in several cases AtMT has paved the way for the development of new species to act as models for specific areas of fungal biology, particularly in plant pathogenic ascomycetes and in a number of basidiomycete species. Despite its impact, the implementation of AtMT has been uneven in the fungi. This review provides insight into the dynamics of expansion of new research tools into a large research community and across multiple organisms. As such, AtMT in the fungi, beyond the demonstrated and continuing power for gene discovery and as a facile transformation tool, provides a model to understand how other technologies that are just being pioneered, e.g. CRISPR/Cas, may play roles in fungi and other eukaryotic species.

Patulin Degradation by the Biocontrol Yeast Sporobolomyces sp. Is an Inducible Process

Patulin is a mycotoxin produced by Penicillium expansum and a common contaminant of pome fruits and their derived products worldwide. It is considered to be mutagenic, genotoxic, immunotoxic, teratogenic and cytotoxic, and the development of strategies to reduce this contamination is an active field of research. We previously reported that Sporobolomyces sp. is able to degrade patulin and convert it into the breakdown products desoxypatulinic acid and ascladiol, both of which were found to be less toxic than patulin. The specific aim of this study was the evaluation of the triggering of the mechanisms involved in patulin resistance and degradation by Sporobolomyces sp. Cells pre-incubated in the presence of a low patulin concentration showed a higher resistance to patulin toxicity and a faster kinetics of degradation. Similarly, patulin degradation was faster when crude intracellular protein extracts of Sporobolomyces sp. were prepared from cells pre-treated with the mycotoxin, indicating the induction of the mechanisms involved in the resistance and degradation of the mycotoxin by Sporobolomyces sp. This study contributes to the understanding of the mechanisms of patulin resistance and degradation by Sporobolomyces sp., which is an essential prerequisite for developing an industrial approach aiming at the production of patulin-free products.