Biodegradation Mechanisms of Patulin in Candida guilliermondii: An iTRAQ-Based Proteomic Analysis

What are the 100 most cited fungal genera?

The global diversity of fungi has been estimated between 2 to 11 million species, of which only about 155 000 have been named. Most fungi are invisible to the unaided eye, but they represent a major component of biodiversity on our planet, and play essential ecological roles, supporting life as we know it. Although approximately 20 000 fungal genera are presently recognised, the ecology of most remains undetermined. Despite all this diversity, the mycological community actively researches some fungal genera more commonly than others. This poses an interesting question: why have some fungal genera impacted mycology and related fields more than others? To address this issue, we conducted a bibliometric analysis to identify the top 100 most cited fungal genera. A thorough database search of the Web of Science, Google Scholar, and PubMed was performed to establish which genera are most cited. The most cited 10 genera are Saccharomyces, Candida, Aspergillus, Fusarium, Penicillium, Trichoderma, Botrytis, Pichia, Cryptococcus and Alternaria. Case studies are presented for the 100 most cited genera with general background, notes on their ecology and economic significance and important research advances. This paper provides a historic overview of scientific research of these genera and the prospect for further research. Citation: Bhunjun CS, Chen YJ, Phukhamsakda C, Boekhout T, Groenewald JZ, McKenzie EHC, Francisco EC, Frisvad JC, Groenewald M, Hurdeal VG, Luangsa-ard J, Perrone G, Visagie CM, Bai FY, Błaszkowski J, Braun U, de Souza FA, de Queiroz MB, Dutta AK, Gonkhom D, Goto BT, Guarnaccia V, Hagen F, Houbraken J, Lachance MA, Li JJ, Luo KY, Magurno F, Mongkolsamrit S, Robert V, Roy N, Tibpromma S, Wanasinghe DN, Wang DQ, Wei DP, Zhao CL, Aiphuk W, Ajayi-Oyetunde O, Arantes TD, Araujo JC, Begerow D, Bakhshi M, Barbosa RN, Behrens FH, Bensch K, Bezerra JDP, Bilański P, Bradley CA, Bubner B, Burgess TI, Buyck B, Čadež N, Cai L, Calaça FJS, Campbell LJ, Chaverri P, Chen YY, Chethana KWT, Coetzee B, Costa MM, Chen Q, Custódio FA, Dai YC, Damm U, de Azevedo Santiago ALCM, De Miccolis Angelini RM, Dijksterhuis J, Dissanayake AJ, Doilom M, Dong W, Alvarez-Duarte E, Fischer M, Gajanayake AJ, Gené J, Gomdola D, Gomes AAM, Hausner G, He MQ, Hou L, Iturrieta-González I, Jami F, Jankowiak R, Jayawardena RS, Kandemir H, Kiss L, Kobmoo N, Kowalski T, Landi L, Lin CG, Liu JK, Liu XB, Loizides M, Luangharn T, Maharachchikumbura SSN, Makhathini Mkhwanazi GJ, Manawasinghe IS, Marin-Felix Y, McTaggart AR, Moreau PA, Morozova OV, Mostert L, Osiewacz HD, Pem D, Phookamsak R, Pollastro S, Pordel A, Poyntner C, Phillips AJL, Phonemany M, Promputtha I, Rathnayaka AR, Rodrigues AM, Romanazzi G, Rothmann L, Salgado-Salazar C, Sandoval-Denis M, Saupe SJ, Scholler M, Scott P, Shivas RG, Silar P, Souza-Motta CM, Silva-Filho AGS, Spies CFJ, Stchigel AM, Sterflinger K, Summerbell RC, Svetasheva TY, Takamatsu S, Theelen B, Theodoro RC, Thines M, Thongklang N, Torres R, Turchetti B, van den Brule T, Wang XW, Wartchow F, Welti S, Wijesinghe SN, Wu F, Xu R, Yang ZL, Yilmaz N, Yurkov A, Zhao L, Zhao RL, Zhou N, Hyde KD, Crous PW (2024). What are the 100 most cited fungal genera? Studies in Mycology 108: 1-411. doi: 10.3114/sim.2024.108.01.

Natural feed additives and bioactive supplements versus chemical additives as a safe and practical approach to combat foodborne mycotoxicoses

This review highlights the possible hazard of mycotoxins occurrence in foods and feeds in regards to foodborne diseases. The possible management of the risk of contamination of foods and feeds with mycotoxins by using natural feed additives, protecting against deleterious effects of mycotoxins or inhibiting the growth of fungi and mycotoxin production, is deeply investigated in the available literature and some effective measures for safe utilization of mycotoxin contaminated feed/food are proposed. The biological methods of decontamination, degradation or biotransformation of mycotoxins are deeply analyzed and discussed. Some natural antagonists against target fungi are also reviewed and a comparison is made with conventional fungicides for ensuring a safe prevention of mycotoxin contamination. The most common and useful chemical methods of mycotoxins decontamination of agricultural commodities or raw materials are also investigated, e.g., chemical additives inactivating or destroying and/or adsorbing mycotoxins as well as chemical additives inhibiting the growth of fungi and mycotoxin production. The practical use and safety of various kind of feed/food additives or herbal/biological supplements as possible approach for ameliorating the adverse effects of some dangerous mycotoxins is deeply investigated and some suggestions are given. Various possibilities for decreasing mycotoxins toxicity, e.g., by clarifying the mechanisms of their toxicity and using some target antidotes and vitamins as supplements to the diet, are also studied in the literature and appropriate discussions or suggestions are made in this regard. Some studies on animal diets such as low carbohydrate intake, increased protein content, calorie restriction or the importance of dietary fats are also investigated in the available literature for possible amelioration of the ailments associated with mycotoxins exposure. It could be concluded that natural feed additives and bioactive supplements would be more safe and practical approach to combat foodborne mycotoxicoses as compared to chemical additives.

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

Global warming has increased the contamination of mycotoxins. Patulin (PAT) is a harmful contaminant that poses a serious threat to food safety and human health. Saccharomyces cerevisiae biodegrades PAT by its enzymes during fermentation, which is a safe and efficient method of detoxification. However, the key degradation enzymes remain unclear. In this study, the proteomic differences of Saccharomyces cerevisiae under PAT stress were investigated. The results showed that the proteins involved in redox reactions and defense mechanisms were significantly up-regulated to resist PAT stress. Subsequently, molecular docking was used to virtual screen for degrading enzymes. Among 18 proteins, YKL069W showed the highest binding affinity to PAT and was then expressed in Escherichia coli, where the purified YKL069W completely degraded 10 μg/mL PAT at 48 h. YKL069W was demonstrated to be able to degrade PAT into E-ascladiol. Molecular dynamics simulations confirmed that YKL069W was stable in catalyzing PAT degradation with a binding free energy of - 7.5 kcal/mol. Furthermore, it was hypothesized that CYS125 and CYS101 were the key amino acid residues for degradation. This study offers new insights for the rapid screening and development of PAT degrading enzymes and provides a theoretical basis for the detoxification of mycotoxins.

Infiltration of porcine pancreatic lipase into magnetic hierarchical mesoporous UiO-66-NH2 metal-organic frameworks for efficient detoxification of patulin from apple juice

Patulin (PAT) is a mycotoxin known to globally contaminate fruits. The economic losses and health hazards caused by PAT desires a safe and efficient strategy for detoxifying PAT. Here, a magnetic core-shell hierarchical mesoporous metal-organic framework (Fe3O4@HMUiO-66-NH2) was synthesized via a salt-assisted nanoemulsion guided assembly method. This mesoporous structure (centered at 4.25 nm) allowed porcine pancreatic lipase (PPL) to infiltrate into the MOF shell at an immobilized amount of 255 mg/g, providing protection for PPL and enabling rapid separation and recovery. Compared with free PPL, PPL/Fe3O4@HMUiO-66-NH2 at 70 °C possessed 4.7 folds improved thermal stability in terms of half-life. The detoxification rates of immobilized enzyme for PAT in neutral water, acidic water, and apple juice were 99.6%, 60.9%, and 52.6%, respectively. Moreover, the so designed PPL/Fe3O4@HMUiO-66-NH2 showed extraordinary storage stability, reusability, and biocompatibility. Crucially, the quality of apple juice did not change significantly after PPL/Fe3O4@HMUiO-66-NH2 treatment, which facilitated its application in apple juice. The magnetic core-shell mesoporous structure along with the revealed mechanism of immobilized enzyme detoxification of PAT provide tremendous opportunity for designing a safe and efficient PAT detoxification method.

Molecular Response of Meyerozyma guilliermondii to Patulin: Transcriptomic-Based Analysis

Patulin (PAT), mainly produced by Penicillium expansum, is a potential threat to health. In recent years, PAT removal using antagonistic yeasts has become a hot research topic. Meyerozyma guilliermondii, isolated by our group, produced antagonistic effects against the postharvest diseases of pears and could degrade PAT in vivo or in vitro. However, the molecular responses of M. guilliermondii over PAT exposure and its detoxification enzymes are not apparent. In this study, transcriptomics is used to unveil the molecular responses of M. guilliermondii on PAT exposure and the enzymes involved in PAT degradation. The functional enrichment of differentially expressed genes indicated that the molecular response mainly includes the up-regulated expression of genes related to resistance and drug-resistance, intracellular transport, growth and reproduction, transcription, DNA damage repair, antioxidant stress to avoid cell damage, and PAT detoxification genes such as short-chain dehydrogenase/reductases. This study elucidates the possible molecular responses and PAT detoxification mechanism of M. guilliermondii, which could be helpful to further accelerate the commercial application of antagonistic yeast toward mycotoxin decontamination.

Immobilized short-chain dehydrogenase/reductase on Fe3O4 particles acts as a magnetically recoverable biocatalyst component in patulin bio-detoxification system

Patulin is one of the most important mycotoxins that contaminates fruit-derived products and causes acute or chronic toxicity in humans. In the present study, a novel patulin-degrading enzyme preparation was developed by taking a short-chain dehydrogenase/reductase and covalently linking it to dopamine/polyethyleneimine co-deposited magnetic Fe₃O₄ particles. Optimum immobilization provided 63% immobilization efficiency and 62% activity recovery. Moreover, the immobilization protocol substantially improved thermal and storage stabilities, proteolysis resistance, and reusability. Using reduced nicotinamide adenine dinucleotide phosphate as a cofactor, the immobilized enzyme exhibited a detoxification rate of 100% in phosphate-buffered saline and a detoxification rate of more than 80% in apple juice. The immobilized enzyme did not cause adverse effects on juice quality and could be magnetically separated quickly after detoxification to ensure convenient recycling. Moreover, it did not exhibit cytotoxicity against a human gastric mucosal epithelial cell line at a concentration of 100 mg/L. Consequently, the immobilized enzyme as a biocatalyst had the characteristics of high efficiency, stability, safety, and easy separation, establishing the first step in building a bio-detoxification system to control patulin contamination in juice and beverage products.

Overexpression of the SDR gene improves the ability of Meyerozyma guilliermondii to degrade patulin in pears and juices

The intracellular enzymes of antagonistic yeast are effective in controlling patulin (PAT) contamination. However, countless enzymes that have been revealed remain functionally uncharacterized. The study built on previous transcriptomic data obtained by our research group to amplify and express a gene encoding a short-chain dehydrogenase/reductase (SDR) in Meyerozyma guilliermondii. Overexpression of SDR increased the tolerance of M. guilliermondii to PAT and the ability to degrade PAT of the intracellular enzymes. Furthermore, MgSDR-overexpressed M. guilliermondii showed higher PAT degradation in juices (apple and peach) and controlled the blue mold of pears at 20 °C and 4 °C while significantly reduced the content of PAT and the biomass of Penicillium expansum in decayed tissues than wild-type M. guilliermondii. This study provides theoretical references for the subsequent heterologous expression, formulation, and application of the SDR protein from M. guilliermondii and contributes to elucidating the PAT degradation mechanism of antagonistic yeasts.

Efficient Biodegradation of Patulin by Aspergillus niger FS10 and Metabolic Response of Degrading Strain

Patulin, a mycotoxin commonly found in fruits and derived products, causes serious health problems for humans and animals worldwide. Several microbial strains have been observed to possess the ability to effectively remove patulin. However, these methods are presently associated with disadvantages such as low degradation efficiency and an unclear biodegradation mechanism. In the current study, the characteristics of patulin degradation via Aspergillus niger FS10 were evaluated, and the mechanisms involved were analyzed using metabolomics technologies. The results showed that the suspension of A. niger FS10 could degrade 94.72% of patulin within 36 h. The moment concentration pf patulin was 0.116 μg/mL, and the detection limit value was 0.01 μg/mL. In addition, the patulin content was reduced to levels below the detection limit within 48 h. A. niger FS10 mainly degrades patulin by producing intracellular enzymes, which can convert patulin into ascladiol. This degradation method can effectively reduce the damage caused by patulin to HepG2 cells. In addition, the patulin treatment significantly affects the pentose phosphate pathway and the glutathione pathway. These two metabolic pathways are speculated to be closely related to patulin degradation via A. niger FS10. The incubation of A. niger FS10 with patulin-contaminated apple pomace can not only eliminate patulin but also increase the utilization of apple pomace. Therefore, our research results provide a new method for addressing patulin contamination in the food and feed industries.

Microbial Enzymes Involved in the Biotransformation of Major Mycotoxins

Mycotoxins, the most researched biological toxins, can contaminate food and feed, resulting in severe health implications for humans and animals. Physical, chemical, and biological techniques are used to mitigate mycotoxin contamination. The biotransformation method using whole microbial cells or isolated enzymes is the best choice to mitigate mycotoxins. Using specific enzymes may avoid the disadvantages of utilizing a full microbe, such as accidental harm to the product's organoleptic characteristics and hazardous safety features. Moreover, the degradation rates of the isolated enzymes are higher than those of the whole-cell reactions, and they are substrate-specific. Their specificity is comprehensive and is shown at the positional and/or chiral center in many circumstances. Currently, only a few enzymes of microbial origin are commercially available. Therefore, there is a need to identify more novel enzymes of microbial origin that can mitigate mycotoxins. In this review, we conducted an in-depth summary of the microbial enzymes involved in the biotransformation of mycotoxins.

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.

Ultrasensitive detection of patulin based on a Ag+-driven one-step dual signal amplification

Due to improper storage, the presence of patulin in fruits poses a threat to food safety. Herein, a one-step dual amplification strategy-based electrochemical aptasensor was proposed for patulin detection. Silver-palladium nanoparticles (AgPdNPs) with a hollow and branched structure were used as a supporting material for thionine to provide numerous attachment sites. AuNFs/g-C₃N₄ was employed as an electrode modification material, which has been demonstrated to facilitate electron transport and improve signal label loading capacity. Ag⁺ ions were released in the presence of patulin, activating the Ag⁺-DNAzyme on the electrode surface. The formed Ag⁺-DNAzymes further cyclically cleaved the substrate DNA, and the released sequences were used as a new trigger to mediate the secondary recirculation. This one-step dual amplification strategy enabled double target recycling without additional procedures. The signal cascade amplification through dual target recycling, was thus available for trace detection of patulin. Under the optimal conditions, the electrochemical aptasensor achieved a satisfactory linear range from 5.0 × 10^-6 μg L^-1 to 50 μg L^-1 with a detection limit of 0.92 fg·mL^-1 for the determination of patulin. In addition, the aptasensor exhibited favorable selectivity, reproducibility, repeatability and long-term stability, and thus can be employed for patulin detection in apple juice samples, providing excellent choice for the detection of trace patulin.

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.

Highly efficient removal of patulin using immobilized enzymes of Pseudomonas aeruginosa TF-06 entrapped in calcium alginate beads

Patulin is a toxic secondary metabolite produced by several moulds, which contaminates fruits and their products posing serious threats to human health. Though several microorganisms and enzymes have been reported to effectively degrade patulin, separation of them from fruit juice challenges the commercial applications. Here, a Pseudomonas aeruginosa strain TF-06 was isolated, its patulin degradation mechanism and optimum conditions for enzyme immobilization were investigated. The results indicated that TF-06 could degrade patulin into non-cytotoxic E/Z-ascladiol mainly by the activity of intracellular enzymes. For easy separation of enzymes, calcium alginate was selected for immobilization of intracellular enzymes from TF-06. The immobilized enzyme beads were effective in detoxification of patulin in apple juice. The mitigation rate was reached 95%, while there was no negative effect on juice quality. The study provides a promising way to resolve the issue of enzyme separation during mycotoxin biological detoxification in fruit juice.

Reduction of the Fusarium Mycotoxins: Deoxynivalenol, Nivalenol and Zearalenone by Selected Non-Conventional Yeast Strains in Wheat Grains and Bread

Mycotoxins, toxic secondary metabolites produced by fungi, are important contaminants in food and agricultural industries around the world. These toxins have a multidirectional toxic effect on living organisms, causing damage to the kidneys and liver, and disrupting the functions of the digestive tract and the immune system. In recent years, much attention has been paid to the biological control of pathogens and the mycotoxins they produce. In this study, selected yeasts were used to reduce the occurrence of deoxynivalenol (DON), nivalenol (NIV), and zearalenone (ZEA) produced by Fusarium culmorum, F. graminearum, and F. poae on wheat grain and bread. In a laboratory experiment, an effective reduction in the content of DON, NIV, and ZEA was observed in bread prepared by baking with the addition of an inoculum of the test yeast, ranging from 16.4% to 33.4%, 18.5% to 36.2% and 14.3% to 35.4%, respectively. These results indicate that the selected yeast isolates can be used in practice as efficient mycotoxin decontamination agents in the food industry.

Microbiological Decontamination of Mycotoxins: Opportunities and Limitations

The contamination of food and feeds with mycotoxins poses a global health risk to humans and animals, with major economic consequences. Good agricultural and manufacturing practices can help control mycotoxin contamination. Since these actions are not always effective, several methods of decontamination have also been developed, including physical, chemical, and biological methods. Biological decontamination using microorganisms has revealed new opportunities. However, these biological methods require legal regulations and more research before they can be used in food production. Currently, only selected biological methods are acceptable for the decontamination of feed. This review discusses the literature on the use of microorganisms to remove mycotoxins and presents their possible mechanisms of action. Special attention is given to Saccharomyces cerevisiae yeast and lactic acid bacteria, and the use of yeast cell wall derivatives.

Patulin in food: A mycotoxin concern for human health and its management strategies

The mycotoxin patulin is primarily produced as a secondary metabolite by numerous fungal species and predominantly by Aspergillus, Byssochlamys, and Penicillium species. It is generally associated with fungal infected food materials. Penicillium expansum is considered the only fungal species liable for patulin contamination in pome fruits, especially in apples and apple-based products. This toxin in food poses serious health concerns and economic threat, which has aroused the need to adopt effective detection and mitigation strategies. Understanding its origin sources and biosynthetic mechanism stands essential for efficiently designing a management strategy against this fungal contamination. This review aims to present an updated outline of the sources of patulin occurrence in different foods and their biosynthetic mechanisms. It further provides information regarding the detrimental effects of patulin on human and agriculture as well as its effective detection, management, and control strategies.

Microbiome Status of Cider-Apples, from Orchard to Processing, with a Special Focus on Penicillium expansum Occurrence and Patulin Contamination

Patulin is a secondary metabolite produced primarily by the fungus Penicillium expansum, responsible for the blue mold disease on apples. It is found in apple products including apple cider when apple juice is added after fermentation. In the present study, two hundred and twenty-five cider-apples of the variety “Bedan”, cultivated in Brittany in France, were sampled from the orchard during harvesting until the storage step, right before processing. The patulin analysis on these samples reported a low contamination at the orchard and a significantly higher-level of contamination in the cider-apples starting from the transporting bin. The percentage of positive samples increased from 6% to 47% after 12 h in the harvesting bin before transporting and reached 95% after 24 h of transporting, decreasing then to 69% at the end of the storage. Penicillium expansum was quantified on the surface of apples using real-time PCR and was observed to be mostly consistent between the harvest and post-harvest steps. It was detected on average, on the surface of 85% of all sampled apples with a mean value around 2.35 × 10⁶Penicillium expansum DNA/g of apple. Moreover, the changes in the fungal and bacterial epiphytic microbiota in the different steps were studied using a metabarcoding approach. The alpha and beta diversity analysis revealed the presence of unique and more diverse bacterial and fungal communities on the surface of apples picked from the orchard compared to the rest of the sampling steps. Potential indigenous biological control agents were identified on the surface of sampled apples. Future perspective includes developing actions of prevention and control of the contamination by Penicillium expansum during the harvest and along the various critical post-harvest stages before transformation in a sustainable development concern.

Patulin and Trichothecene: characteristics, occurrence, toxic effects and detection capabilities via clinical, analytical and nanostructured electrochemical sensing/biosensing assays in foodstuffs

Patulin and Trichothecene as the main groups of mycotoxins in significant quantities can cause health risks from allergic reactions to death on both humans and animals. Accordingly, rapid and highly sensitive determination of these toxics agents is of great importance. This review starts with a comprehensive outlook regarding the characteristics, occurrence and toxic effects of Patulin and Trichothecene. In the following, numerous clinical and analytical approaches have been extensively discussed. The main emphasis of this review is placed on the utilization of novel nanomaterial based electrochemical sensing/biosensing tools for highly sensitive determination of Patulin and Trichothecene. Furthermore, a detailed and comprehensive comparison has been performed between clinical, analytical and sensing methods. Subsequently, the nanomaterial based electrochemical sensing platforms have been approved as reliable tools for on-site analysis of Patulin and Trichothecene in food processing and manufacturing industries. Different nanomaterials in improving the performance of detecting assays were investigated and have various benefits toward clinical and analytical methods. This paper would address the limitations in the current developments as well as the future challenges involved in the successful construction of sensing approaches with the functionalized nanomaterials and also allow exploring into core-research works regarding this area.

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.

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.

Antagonistic Yeasts: A Promising Alternative to Chemical Fungicides for Controlling Postharvest Decay of Fruit

Fruit plays an important role in human diet. Whereas, fungal pathogens cause huge losses of fruit during storage and transportation, abuse of chemical fungicides leads to serious environmental pollution and endangers human health. Antagonistic yeasts (also known as biocontrol yeasts) are promising substitutes for chemical fungicides in the control of postharvest decay owing to their widespread distribution, antagonistic ability, environmentally friendly nature, and safety for humans. Over the past few decades, the biocontrol mechanisms of antagonistic yeasts have been extensively studied, such as nutrition and space competition, mycoparasitism, and induction of host resistance. Moreover, combination of antagonistic yeasts with other agents or treatments were developed to improve the biocontrol efficacy. Several antagonistic yeasts are used commercially. In this review, the application of antagonistic yeasts for postharvest decay control is summarized, including the antagonistic yeast species and sources, antagonistic mechanisms, commercial applications, and efficacy improvement. Issues requiring further study are also discussed.

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.

Ribonucleoside Diphosphate Reductase Plays an Important Role in Patulin Degradation by Enterobacter cloacae subsp. dissolvens

Patulin contamination is a worldwide concern due to its significant impact on human health. Several yeast strains have been screened for patulin biodegradation; however, little information is available on bacterial strains and their mechanism of degradation. In the present study, we isolated a bacterial strain TT-09 and identified it as Enterobacter cloacae subsp. dissolvens based on the BioLog system and 16S rDNA phylogenetic analysis. The strain was demonstrated to be able to transform patulin into E-ascladiol. Isobaric tags for relative and absolute quantitation and reverse transcription quantitative polymerase chain reaction analyses provided evidence that ribonucleoside diphosphate reductase (NrdA), an important enzyme involved in DNA biosynthesis, plays a crucial role in patulin degradation. Deletion of nrdA resulted in a total loss in the ability to degrade patulin in TT-09. These results indicate a new function for NrdA in mycotoxin biodegradation. The present study provides evidence for understanding a new mechanism of patulin degradation and information that can be used to develop new approaches for managing patulin contamination.

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.

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 pH-responsive PacC transcription factor plays pivotal roles in virulence and patulin biosynthesis in Penicillium expansum

The PacC (loss or reduction in phosphatase activity at acid but not at alkaline pH [Pac]) transcription factor regulates environmental adaptation, secondary metabolism and virulence in many fungal pathogens. Here, we report the functions of PacC in Penicillium expansum, a postharvest pathogenic fungus in horticultural crops, and ascertain that the gene expression and proteolytic processing of PePacC are strictly pH-dependent. Loss of PePacC resulted in an obvious decrease in growth and conidiation of P. expansum cultured in both acidic and alkaline conditions. The ΔPePacC mutant lost the ability of patulin production at pH values above 6.0 because expressions of all the genes in patulin cluster were significantly down-regulated. Additionally, virulence of the ΔPePacC mutant was obviously reduced in pear and apple fruits. Proteome analysis revealed that PePacC could function as an activator or repressor for different target proteins, including calreticulin (PeCRT) and sulfate adenylyltransferase (PeSAT), which were further proved to be involved in virulence of P. expansum. Our results demonstrate important roles for PePacC in patulin biosynthesis via limiting expressions of the genes in the cluster, and in pathogenesis via mediating a known virulence factor glucose oxidase (PeGOD) and new virulence factors, such as PeCRT and PeSAT.

Enzymes for Detoxification of Various Mycotoxins: Origins and Mechanisms of Catalytic Action

Mycotoxins are highly dangerous natural compounds produced by various fungi. Enzymatic transformation seems to be the most promising method for detoxification of mycotoxins. This review summarizes current information on enzymes of different classes to convert various mycotoxins. An in-depth analysis of 11 key enzyme mechanisms towards dozens of major mycotoxins was realized. Additionally, molecular docking of mycotoxins to enzymes' active centers was carried out to clarify some of these catalytic mechanisms. Analyzing protein homologues from various organisms (plants, animals, fungi, and bacteria), the prevalence and availability of natural sources of active biocatalysts with a high practical potential is discussed. The importance of multifunctional enzyme combinations for detoxification of mycotoxins is posed.

Effects of ascorbic acid on patulin in aqueous solution and in cloudy apple juice

Degradation of the mycotoxin patulin (PAT) and the generation of (less toxic) breakdown products, such as (E/Z)-ascladiol (ASC-E/Z) and desoxypatulinic acid (D-PAT), can occur due to chemical, physical and biological treatments. Our study focused on the chemical degradation of PAT in the presence of ascorbic acid (AA) both for pure PAT standard in acidified aqueous solution and for PAT-contaminated cloudy apple juice (CAJ) (obtained via addition of apple mash produced from apples inoculated with Penicillium expansum). Within this framework, different concentrations of AA were evaluated, as well as the presence/absence of oxygen and different storage temperatures. In order to do so, an in-house methodology allowing a good separation of PAT from its reaction and breakdown products was optimized first. The highest PAT reduction (60%) in CAJ with an initial PAT concentration of 100 μg/kg and 0.25% (w/v) AA was achieved after 6 days of incubation at 22 °C in the presence of oxygen. It was also found that the treatment by AA resulted in the generation of degradation products less toxic than PAT (such as (E/Z)-ASC). In conclusion, AA used to improve numerous product quality aspects (e.g. colour (less browning), nutritional value, etc.) and considered as a safe food additive (Food and Drug Administration (FDA) (1999)) has an effect on PAT degradation. It was shown that such degradation generated less toxic compounds in the presence of oxygen. In view of consumers' safety, fortification of apple juice (and possibly apple-based products) with AA could be helpful within an integrated system to ensure products with low levels of patulin. The optimum conditions for such an approach within a legal and practical point of view need to be further explored.

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.

Proteomic profiling and integrated analysis with transcriptomic data bring new insights in the stress responses of Kluyveromyces marxianus after an arrest during high-temperature ethanol fermentation

BACKGROUND

The thermotolerant yeast Kluyveromyces marxianus is a potential candidate for high-temperature fermentation. When K. marxianus was used for high-temperature ethanol fermentation, a fermentation arrest was observed during the late fermentation stage and the stress responses have been investigated based on the integration of RNA-Seq and metabolite data. In order to bring new insights into the cellular responses of K. marxianus after the fermentation arrest during high-temperature ethanol fermentation, quantitative proteomic profiling and integrated analysis with transcriptomic data were performed in this study.

RESULTS

Samples collected at 14, 16, 18, 20 and 22 h during high-temperature fermentation were subjected to isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic profiling and integrated analysis with transcriptomic data. The correlations between transcripts and proteins for the comparative group 16 h vs 14 h accounted for only 4.20% quantified proteins and 3.23% differentially expressed proteins (DEPs), respectively, much higher percentages of correlations (30.56%-59.11%) were found for other comparative groups (i.e., 18 h vs 14 h, 20 h vs 14 h, and 22 h vs 14 h). According to Spearman correlation tests between transcriptome and proteome (the absolute value of a correlation coefficient between 0.5 and 1 indicates a strong correlation), poor correlations were found for all quantified proteins (R = - 0.0355 to 0.0138), DEPs (R = - 0.0079 to 0.0233) and the DEPs with opposite expression trends to corresponding differentially expressed genes (DEGs) (R = - 0.0478 to 0.0636), whereas stronger correlations were observed in terms of the DEPs with the same expression trends as the correlated DEGs (R = 0.5593 to 0.7080). The results of multiple reaction monitoring (MRM) verification indicate that the iTRAQ results were reliable. After the fermentation arrest, a number of proteins involved in transcription, translation, oxidative phosphorylation and fatty acid metabolism were down-regulated, some molecular chaperones and proteasome proteins were up-regulated, the ATPase activity significantly decreased, and the total fatty acids gradually accumulated. In addition, the contents of palmitic acid, oleic acid, C16, C18, C22 and C24 fatty acids increased by 16.77%, 28.49%, 14.14%, 26.88%, 628.57% and 125.29%, respectively.

CONCLUSIONS

This study confirmed some biochemical and enzymatic alterations provoked by the stress conditions in the specific case of K. marxianus: such as decreases in transcription, translation and oxidative phosphorylation, alterations in cellular fatty acid composition, and increases in the abundance of molecular chaperones and proteasome proteins. These findings provide potential targets for further metabolic engineering towards improvement of the stress tolerance in K. marxianus.

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).

Effective Biodegradation of Aflatoxin B1 Using the Bacillus licheniformis (BL010) Strain

Aflatoxin B1 (AFB1), a pollutant of agricultural products, has attracted considerable attention in recent years, due to its potential impact on health. In the present study, Bacillus licheniformis (BL010) was demonstrated to efficiently degrade AFB1, reducing over 89.1% of the toxin content within 120 h. A crude enzyme solution of BL010 exhibited the highest degradation level (97.3%) after three induction periods. However, uninduced BL010 bacteria was not capable of reducing AFB1. Furthermore, high performance liquid chromatography (HPLC) analysis showed that while a cell-free extract caused a significant decrease in AFB1 content (93.6%, p < 0.05), cell culture fluid treatment did not significantly degrade AFB1. The biotransformation products of AFB1 were detected and further identified by quadrupole time-of-flight liquid chromatography⁻mass spectrometry (LC-Q-TOF/MS); these corresponded to a molecular formula of C12H14O₄. A sequence analysis of whole BL010 genes with a bioinformatics approach identified the secondary structures of two degrading enzymes (Chia010 and Lac010), providing an important basis for subsequent homology modeling and functional predictions.

Patulin Induces Autophagy-Dependent Apoptosis through Lysosomal-Mitochondrial Axis and Impaired Mitophagy in HepG2 Cells

Patulin (PAT) is a compound produced by fungi including those of the Aspergillus, Penicillium, and Byssochlamys species. PAT has been linked with negative outcomes in certain microorganisms and animal species, but how it causes hepatotoxicity is poorly understood. In this study, we determined that, by treating HepG2 cells using PAT, these cells could be induced to rapidly undergo autophagy, and this was followed within 12 h of treatment by lysosomal membrane permeabilization (LMP) and cathepsin B release. We were able to block these outcomes if cells were treated with 3-methyladenine (3MA), an inhibitor of autophagy, prior to PAT treatment. Moreover, PAT-induced collapse of mitochondrial membrane potential (ΔΨm) depended both on cathepsin B and autophagy. 3MA was further able to reduce the induction of apoptosis in response to PAT, suggesting that autophagy is a driving mechanism for this apoptotic induction. Inhibiting cathepsin B using CA-074 Me further reduced PAT-induced collapses of ΔΨm, mitochondiral cytochrome c release, and apoptosis. We also found that extended treatment of HepG2 cells using PAT over a period of 24 h led to the impairment of mitophagy such that morphologically swollen mitochondria accumulated within cells, and PINK1 failed to colocalize with LC3. Together these data reveal that PAT treatment can promote the induction of apoptosis in HepG2 cells in a manner dependent upon autophagy that progresses via the lysosomal-mitochondrial axis. This study thereby affords new insights into the mechanisms by which PAT drives hepatotoxicity.

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.

Current Strategies for the Detoxification of Jatropha curcas Seed Cake: A Review

Jatropha curcas is an important oilseed plant, with considerable potential in the development of biodiesel. Although Jatropha seed cake, the byproduct of oil extraction, is a residue rich in nitrogen, phosphorus, potassium, and carbon, with high protein content suitable for application in animal feed, the presence of toxic phorbol esters limits its application in feed supplements and fertilizers. This review summarizes the current methods available for detoxification of this residue, based upon chemical, physical, biological, or combined processes. The advantages and disadvantages of each process are discussed, and future directions involving genomic and proteomic approaches for advancing our understanding of biodegradation processes involving microorganisms are highlighted.

[Yeasts from the CTG clade (Candida clade): Biology, impact in human health, and biotechnological applications]

Among the subdivision of Saccharomycotina (ascomycetes budding yeasts), the CTG clade (formerly the Candida clade) includes species that display a particular genetic code. In these yeasts, the CTG codon is predominantly translated as a serine instead of a leucine residue. It is now well-known that some CTG clade species have a major impact on human and its activities. Some of them are recognized as opportunistic agents of fungal infections termed candidiasis. In addition, another series of species belonging to the CTG clade draws the attention of some research groups because they exhibit a strong potential in various areas of biotechnology such as biological control, bioremediation, but also in the production of valuable biocompounds (biofuel, vitamins, sweeteners, industrial enzymes). Here we provide an overview of recent advances concerning the biology, clinical relevance, and currently tested biotechnological applications of species of the CTG clade. Future directions for scientific research on these particular yeasts are also discussed.

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.