A polyketide synthase gene required for ochratoxin A biosynthesis in Aspergillus ochraceus

Survey of knowledge, and attitudes to storage practices preempting the occurrence of filamentous fungi and mycotoxins in some Ghanaian staple foods and processed products

Mycotoxigenic fungi can infect and produce potent mycotoxins in foodstuffs prior to harvest, during harvest (field fungi), and in storage after harvest (storage fungi), which when ingested, can result in adverse health effects. This study was aimed at assessing the knowledge, attitudes, and practices adopted by the Ghanaian populace to help mitigate the occurrence of molds and mycotoxins in foods. A cross-sectional survey involving a structured questionnaire was conducted with 642 respondents from twelve regions of Ghana. Descriptive statistics and analyses of variance were calculated. Correct Classification Rate (CCR) was measured to assess the utility of a logistic regression model. The results of the study showed that the majority of 299 (46.6%) of the respondents were between the ages of 18-25. Age and educational level were related to knowledge about the occurrence of fungi and mycotoxins in foods (p < 0.05). More than half the respondents, 50% indicated that they knew of aflatoxins as a major mycotoxin present in food. Higher education directly influenced on the knowledge of mycotoxicosis and the management of stored food to present intoxication by fungal metabolites. 502 (32.9%) knew that consuming foods with toxins could cause stomach aches. The most commonly consumed food commodity despite the presence of visible growth of fungi was bread (35.3%). The average KAP score for knowledge showed that, out of 100%, there was adequate knowledge (63.8%) among the members of the Ghanaian populace. Favorable environmental conditions of high humidity (> 85% ERH) and temperature (> 28-32 °C) enhance the proliferation of fungi in most foods and the attendant production of mycotoxins such as aflatoxins, ochratoxins, and fumonisins are associated with several severe human and animal health conditions; mycotoxicosis was associated with high fever, pain, vomiting, suppression of immunity, cancer, etc. when these foods are consumed on regular basis for a prolonged length of time. Future examination of the food items used for the School Feeding Programme in Ghana will offer opportunities to examine the risks of feeding youth with fungal-contaminated food preparations from providers.

Current status of secondary metabolite pathways linked to their related biosynthetic gene clusters in Aspergillus section Nigri

Covering: up to the end of 2021Aspergilli are biosynthetically 'talented' micro-organisms and therefore the natural products community has continually been interested in the wealth of biosynthetic gene clusters (BGCs) encoding numerous secondary metabolites related to these fungi. With the rapid increase in sequenced fungal genomes combined with the continuous development of bioinformatics tools such as antiSMASH, linking new structures to unknown BGCs has become much easier when taking retro-biosynthetic considerations into account. On the other hand, in most cases it is not as straightforward to prove proposed biosynthetic pathways due to the lack of implemented genetic tools in a given fungal species. As a result, very few secondary metabolite biosynthetic pathways have been characterized even amongst some of the most well studied Aspergillus spp., section Nigri (black aspergilli). This review will cover all known biosynthetic compound families and their structural diversity known from black aspergilli. We have logically divided this into sub-sections describing major biosynthetic classes (polyketides, non-ribosomal peptides, terpenoids, meroterpenoids and hybrid biosynthesis). Importantly, we will focus the review on metabolites which have been firmly linked to their corresponding BGCs.

Dietary assessment of ochratoxin A in Chinese dark tea and inhibitory effects of tea polyphenols on ochratoxigenic Aspergillus niger

In recent years, there has been an increasingly heated debate on whether Chinese dark tea is contaminated with mycotoxins and whether it poses health risks to consumers. In this study, a rapid method based on high-performance liquid chromatography was used to detect ochratoxin A (OTA) in Chinese dark tea samples from different regions of China and different years. Of the 228 Chinese dark tea samples tested, 21 were detected for OTA contamination, with a concentration ranging from 2.51 ± 0.16 to 12.62 ± 0.72 μg/kg. Subsequently, a dark tea drinking risk assessment was conducted, and the hazard quotient for each group was far below the acceptable level of 1.0. Of the 12 Aspergillus spp. strains isolated, one strain of Aspergillus niger had the ability to produce OTA. We also found that tea polyphenols and epigallocatechin gallate inhibited the growth of ochratoxin-producing Aspergillus niger and the expression of non-ribosomal peptide synthetase (NRPS), a key gene for ochratoxin synthesis. Thus, OTA contamination of dark tea is at an acceptable risk level, and the inhibition of ochratoxigenic Aspergillus niger by polyphenols provides new insights into the safety of dark tea consumption.

Control of toxigenic Aspergillus spp. in dried figs by volatile organic compounds (VOCs) from antagonistic yeasts

Aspergillus flavus and Aspergillus niger are fungi which can contaminate dried figs before and after harvest and consequently produce aflatoxins (AFs) and ochratoxin A (OTA). Many approaches have been applied to minimise the growth of these filamentous fungi, mainly involving the use of synthetic fungicides which are limited due to their negative impact on human health and the environment. In this context, biocontrol is a recent approach that needs to be explored. This study evaluated the potential of three volatile organic compounds (VOCs), octanoic acid (OA), 2-phenylethyl acetate (2PEA) and furfuryl acetate (FA), produced by Hanseniaspora uvarum and Hanseniaspora opuntiae yeasts on the growth, germination, gene expression and production of AFs and OTA by A. flavus M144 and A. niger M185 on dried fig-based agar and the incidence rates in dried figs. Two of the three VOCs evaluated (2PEA and FA) effectively controlled A. flavus M144 and A. niger M185 by using at least amounts of 50 μL (715 μL/L in the headspace) for FA and 100 μL (1430 μL/L in the headspace) for 2PEA in dried figs. One of the mode of actions of both compounds consists in early repressing the expression of genes involved in the biosynthesis of AFs (aflR) and OTA (pks) of A. flavus and A. niger, respectively. The results of this study support the application of 2PEA and FA at the early post-harvest stages of dried figs to control mycotoxin accumulation.

Detection, Contamination, Toxicity, and Prevention Methods of Ochratoxins: An Update Review

Ochratoxins (OTs) with nephrotoxic, immunosuppressive, teratogenic, and carcinogenic properties are thermostable fungal subordinate metabolites. OTs contamination can occur before or after harvesting, during the processing, packing, distribution, and storage of food. Mold development and mycotoxin contamination can occur in any crop or cereal that has not been stored properly for long periods of time and is subjected to high levels of humidity and temperature. Ochratoxin A (OTA) presents a significant health threat to creatures and individuals. There is also a concern of how human interaction with OTA will also express the remains of OTA from feedstuffs into animal-derived items. Numerous approaches have been studied for the reduction of the OTA content in agronomic products. These methods can be classified into two major classes: inhibition of OTA adulteration and decontamination or detoxification of food. A description of the various mycotoxins, the organism responsible for the development of mycotoxins, and their adverse effects are given. In the current paper, the incidence of OTA in various fodder and food materials is discussed, which is accompanied by a brief overview of the OTA mode of synthesis, physicochemical properties, toxic effects of various types of ochratoxins, and OTA decontamination adaptation methods. To our knowledge, we are the first to report on the structure of many naturally accessible OTAs and OTA metabolism. Finally, this paper seeks to be insightful and draw attention to dangerous OTA, which is too frequently neglected and overlooked in farm duplication from the list of discrepancy studies.

Molecular and HPLC-based approaches for detection of aflatoxin B1 and ochratoxin A released from toxigenic Aspergillus species in processed meat

BACKGROUND

Meat-products are considered an enriched media for mycotoxins. This study aimed to investigate the prevalence of toxigenic Aspergillus species in processed meat samples, HPLC-quantitative measurement of aflatoxin B1 and ochratoxin A residues, and molecular sequencing of aflR1 and pks genes. One hundred and twenty processed beef meat specimens (basterma, sausage, and minced meat; n = 40 for each) were collected from Ismailia Province, Egypt. Samples were prepared for total mold count, isolation, and identification of Aspergillus species. All samples were analyzed for the production of both Aflatoxin B1 and Ochratoxin A mycotoxins by HPLC. Molecular identification of Aspergillus flavus and Aspergillus ochraceus was performed using PCR amplification of the internal transcribed spacer (ITS) region; furthermore, the aflR1 and pks genes were sequenced.

RESULTS

The total mold count obtained from sausage samples was the highest one, followed by minced meat samples. The prevalence of A. flavus was (15%), (7.5%), and (10%), while the prevalence of A. ochraceus was (2.5%), (10%), and (0%) in the examined basterma, sausage, and minced meat samples, respectively. Using PCR, the ITS region was successfully amplified in all the tested A. flavus and A. ochraceus strains. Aflatoxin B1 was detected in six basterma samples (15%). Moreover, the ochratoxin A was detected only in four sausage samples (10%). The aflR1 and pks genes were amplified and sequenced successfully and deposited in the GenBank with accession numbers MF694264 and MF694264, respectively.

CONCLUSIONS

To the best of our knowledge, this is the first report concerning the HPLC-Molecular-based approaches for the detection of aflatoxin B1 and ochratoxin A in processed beef meat in Egypt. The production of aflatoxin B1 and ochratoxin A in processed meat constitutes a public health threat. Aflatoxin B1 is commonly associated with basterma samples. Moreover, ochratoxin A was detected frequently in sausage samples. The routine inspection of mycotoxins in processed meat products is essential to protect human consumers.

Colorimetric and chemiluminescence based enzyme linked apta-sorbent assay (ELASA) for ochratoxin A detection

Ochratoxin A (OTA) is one of the most widespread mycotoxin found to contaminate various food products such as cereals, spices, groundnuts, coffee, wine, beer etc. It is also carried over from contaminated feed and fodder to milk, blood, meat, kidney and liver of animals consuming it. Enzyme-linked to biorecognition molecules like antibodies or aptamers are very popular due to their ability to be used as labels or tags in biosensing formats. In this work, OTA aptamer based colorimetric and chemiluminescence biosensing formats were evaluated for the detection of OTA. The colorimetric enzyme linked apta-sorbent assay (Co-ELASA) and chemiluminescence enzyme linked apta-sorbent assay (Cl-ELASA) showed a linear detection range from 1 pg/mL to 1 μg/mL with a limit of detection (LOD) of 0.84 pg/mL for Co-ELASA (limit of quantification (LOQ) = 2.54 pg/mL) and 1.29 pg/mL for Cl-ELASA (LOQ = 3.94 pg/mL) under optimized buffer conditions. Comparison of ELASA methods with sandwich ELISA indicated that the developed techniques had sensitivity similar to the conventional technique which indicated a LOD of 1.13 pg/mL and LOQ of 3.41 pg/mL. Studies in simulated contaminated food samples by spiking OTA in groundnut and coffee bean at concentrations of 0.1, 1 and 10 ppb, indicated recoveries in the range of 50.21 to 113.27% for Co-ELASA, 90.47 to 107.72% for Cl-ELASA and 76.23 to 141.49% for ELISA. Results of the study indicate that Co-ELASA and Cl-ELASA assays could be an alternate approach for ultrasensitive detection of OTA in food samples, which can also be adapted for biosensor development.

AuNanostar@4-MBA@Au Core-Shell Nanostructure Coupled with Exonuclease III-Assisted Cycling Amplification for Ultrasensitive SERS Detection of Ochratoxin A

The "turn-on" mode surface-enhanced Raman scattering (SERS) aptasensor for ultrasensitive ochratoxin A (OTA) detection was developed based on the SERS "hot spots" of AuNanostar@4-MBA@Au core-shell nanostructures (AuNS@4-MBA@Au) and exonuclease III (Exo III)-assisted target cycle amplification strategy. Compared with conventional gold nanoparticles, AuNS@4-MBA@Au provides a much higher SERS enhancement factor because AuNS exhibits a larger surface roughness and the lightning rod effect, as well as an excellent electromagnetic field between the AuNS core and the Au shell, which contribute to the superstrong SERS signal. Meanwhile, Exo III-assisted target cycle amplification can be used as an effective method for the further amplified detection of OTA. Additionally, the utilization of streptavidin magnesphere paramagnetic particles offers a green, economical, and facile technology for the accumulation and separation of the signal probe AuNS@4-MBA@Au from solution. All these factors lead to a significant enhancement of detectable signals and superhigh sensitivity. As a result, the limit of detection as low as 0.25 fg mL^-1 could be achieved, which was lower than that in the other reported literatures on SERS methods for OTA detection as we know. The developed SERS aptasensor also provides a promising tool for foodstuff detection.

Occurrence and bioacessibility of mycotoxins in fish feed

In this study Aflatoxin B₁ (AFB₁), ochratoxin A (OTA) and zearalenone (ZEN) occurrence in fish feed, regarding its chemical composition, were investigated. Besides, AFB₁ bioaccessibility to fish was evaluated by in vitro digestion. Mycotoxins were extracted by QuEChERS and quantified by HPLC-FLD. Results showed that 93.3% of the samples were contaminated at maximum levels of 16.5, 31.6, and 322 µg/kg in the cases of AFB₁, OTA, and ZEN, respectively. A positive correlation between OTA, ZEN contamination, and lipid content was observed. Risk estimation of feed consumption by fish at the highest levels of AFB₁, OTA, and ZEN shows that the younger the fish, the higher the risk of exposure to mycotoxins. The AFB₁ bioaccessibility assay showed that 85% of this mycotoxin may be absorbed by fish. Therefore, establishing maximum levels in the fishing sector is fundamental to contribute to feed quality and nutritional safety of fish species.

Transition-transversion mutations in the polyketide synthase gene of Aspergillus section Nigri

This study determined the transition-transversion mutation in the pks gene of Aspergillus section Nigri in order to gain insight into the patterns of nucleotide base substitution and the process of molecular evolution using standard recommended techniques. Results obtained depict frequent occurrence of transition (23 ± 0.96) than transversion (11.37 ± 1.38) (p < 0.05) with C/T being the most frequently observed transitional base substitution and C/A the most frequently occurring transversional base change. The number of single base insertions (56 ± 1.00) were significantly higher than the observed single base deletions (38 ± 2.00) (p < 0.05) while varying degrees of two or more base deletions and insertions were also observed both inside and outside the open reading frame. The maximum likelihood value estimated for the pks gene was calculated to be -9458.80 in 423 positions of the final dataset while the transition-transversion ratio was estimated to be 0.50. The Tajima's neutrality test approaches seven (7) with the nucleotide diversity estimated to be approximately 65%. Evolutionary test depicts positive selection as ratio of non synonymous to synonymous divergence was found to be greater than ratio of the number of non synonymous to synonymous polymorphisms. The proportion of substitution driven by positive selection was calculated to be approximately 96.2%. This research therefore provides an insight into the understanding of pks gene mutation patterns as some of the observed indels resulted in frame shift mutations.

A Consensus Ochratoxin A Biosynthetic Pathway: Insights from the Genome Sequence of Aspergillus ochraceus and a Comparative Genomic Analysis

Ochratoxin A (OTA) is a toxic secondary metabolite produced by Aspergillus and Penicillium species that widely contaminates food and feed. We sequenced and assembled the complete ∼37-Mb genome of Aspergillusochraceus fc-1, a well-known producer of OTA. Key genes of the OTA biosynthetic pathway were identified by comparative genomic analyses with five other sequenced OTA-producing fungi: A. carbonarius, A. niger, A. steynii, A. westerdijkiae, and Penicillium nordicum OTA production was completely inhibited in the deletion mutants (ΔotaA, ΔotaB, ΔotaC, ΔotaD, and ΔotaR1), and OTA biosynthesis was restored by feeding a postblock substrate to the corresponding mutant. The OTA biosynthetic pathway was unblocked in the ΔotaD mutant by the addition of heterologously expressed halogenase. OTA biosynthesis begins with a polyketide synthase (PKS), OtaA, utilizing acetyl coenzyme A (acetyl-CoA) and malonyl-CoA to synthesize 7-methylmellein, which is oxidized to OTβ by cytochrome P450 monooxygenase (OtaC). OTβ and l-β-phenylalanine are combined by a nonribosomal peptide synthetase (NRPS), OtaB, to form an amide bond to synthesize OTB. Finally, OTB is chlorinated by a halogenase (OtaD) to OTA. The otaABCD genes were expressed at low levels in the ΔotaR1 mutant. A second regulator, otaR2, which is adjacent to the biosynthetic gene, could modulate only the expression of otaA, otaB, and otaD Thus, we have identified a consensus OTA biosynthetic pathway that can be used to prevent and control OTA synthesis and will help us understand the variation and production of the intermediate components in the biosynthetic pathway.IMPORTANCE Ochratoxin A (OTA) is a significant mycotoxin that contaminates cereal products, coffee, grapes, wine, cheese, and meat. OTA is nephrotoxic, carcinogenic, teratogenic, and immunotoxic. OTA contamination is a serious threat to food safety, endangers human health, and can cause huge economic losses. At present, >20 species of the genera Aspergillus and Penicillium are known to produce OTA. Here we demonstrate that a consensus OTA biosynthetic pathway exists in all OTA-producing fungi and is encoded by a gene cluster containing four highly conserved biosynthetic genes and a bZIP transcription factor.

Differentiation and quantification of the ochratoxin A producers Aspergillus ochraceus and Aspergillus westerdijkiae using PCR-DGGE

Ochratoxin A (OTA) is a nephrotoxic, teratogenic, immunotoxic, and carcinogenic mycotoxin which is produced in tropical zones mainly by Aspergillus carbonarius, A. niger, A. ochraceus, and A. westerdijkiae. A. ochraceus and A. westerdijkiae species are phenotypically and genomically very close but A. westerdijkiae produce OTA at a very higher level than A. ochraceus. These species have been differentiated recently. The DNA primer pairs which were drawn so far are not specific and a genomic region of the same size is amplified for both species or they are too specific, and in this case, the DNA of a single species is amplified. To help preventing OTA contamination of foodstuffs, the PCR-DGGE (Denaturing Gradient Gel Electrophoresis) method was used to discriminate between A. ochraceus and A. westerdijkiae DNA fragments of the same size but with different sequences and thus faster access to a diagnosis of the toxigenic potential of the fungal microflora. The proposed methodology was able to differentiate A. westerdijkiae from A. ochraceus with only one primer pairs in a single run. A calibration based on initial DNA content was obtained from image analysis of the DGGE gels and a method of quantification of the two strains was proposed.

Genomic diversity in ochratoxigenic and non ochratoxigenic strains of Aspergillus carbonarius

Ochratoxin A (OTA) is a mycotoxin with nephrotoxic effects on animals and humans. Aspergillus carbonarius is the main responsible for OTA contamination of grapes and derived products. We present the genome resequencing of four A. carbonarius strains, one OTA producer and three atypical and unique non-OTA producing strains. These strains were sequenced using Illumina technology and compared with a reference genome of this species. We performed some specific bioinformatics analyses in genes involved in OTA biosynthesis. Data obtained in this study revealed the high genomic diversity within A. carbonarius strains. Although some gaps of more than 1,000 bp were identified in non-ochratoxigenic strains, no large deletions in functional genes related with OTA production were found. Moreover, the expression of five genes of the putative OTA biosynthetic cluster was down regulated under OTA-inducing conditions in the non-ochratoxigenic strains. Knowledge of the regulatory mechanisms involved in OTA biosynthesis will provide a deeper understanding of these non-ochratoxigenic strains.

Description of an orthologous cluster of ochratoxin A biosynthetic genes in Aspergillus and Penicillium species. A comparative analysis

Ochratoxin A (OTA) is one of the most important mycotoxins due to its toxic properties and worldwide distribution which is produced by several Aspergillus and Penicillium species. The knowledge of OTA biosynthetic genes and understanding of the mechanisms involved in their regulation are essential. In this work, we obtained a clear picture of biosynthetic genes organization in the main OTA-producing Aspergillus and Penicillium species (A. steynii, A. westerdijkiae, A. niger, A. carbonarius and P. nordicum) using complete genome sequences obtained in this work or previously available on databases. The results revealed a region containing five ORFs which predicted five proteins: halogenase, bZIP transcription factor, cytochrome P450 monooxygenase, non-ribosomal peptide synthetase and polyketide synthase in all the five species. Genetic synteny was conserved in both Penicillium and Aspergillus species although genomic location seemed to be different since the clusters presented different flanking regions (except for A. steynii and A. westerdijkiae); these observations support the hypothesis of the orthology of this genomic region and that it might have been acquired by horizontal transfer. New real-time RT-PCR assays for quantification of the expression of these OTA biosynthetic genes were developed. In all species, the five genes were consistently expressed in OTA-producing strains in permissive conditions. These protocols might favour futures studies on the regulation of biosynthetic genes in order to develop new efficient control methods to avoid OTA entering the food chain.

Diversity, Application, and Synthetic Biology of Industrially Important Aspergillus Fungi

The filamentous fungal genus Aspergillus consists of over 340 officially recognized species. A handful of these Aspergillus fungi are predominantly used for food fermentation and large-scale production of enzymes, organic acids, and bioactive compounds. These industrially important Aspergilli primarily belong to the two major Aspergillus sections, Nigri and Flavi. Aspergillus oryzae (section Flavi) is the most commonly used mold for the fermentation of soybeans, rice, grains, and potatoes. Aspergillus niger (section Nigri) is used in the industrial production of various enzymes and organic acids, including 99% (1.4 million tons per year) of citric acid produced worldwide. Better understanding of the genomes and the signaling mechanisms of key Aspergillus species can help identify novel approaches to enhance these commercially significant strains. This review summarizes the diversity, current applications, key products, and synthetic biology of Aspergillus fungi commonly used in industry.

Integration of transcriptome and proteome data reveals ochratoxin A biosynthesis regulated by pH in Penicillium citrinum

Proteomics and transcriptomics of P. citrinum under pH 5 (highest OTA-production) and pH 3 (not produce OTA) were analyzed to reveal the possible mechanism of OTA biosynthesis in P. citrinum.

Targeting Ochratoxin Biosynthetic Genes

The pathway of ochratoxin A (OTA) biosynthesis has not yet been completely elucidated. Essentially, two kind of genes have been demonstrated to be involved in the biosynthesis of OTA. One of them is the nrps gene encoding a non-ribosomal peptide synthetase (NRPS) which catalyzes the ligation between the isocoumarin group, constituting the polyketide group of OTA molecule, and the amino acid phenylalanine.Here we describe a conventional PCR method developed for the detection of OTA-producing molds belonging to Penicillium and Aspergillus genera by Luque et al. (Food Control 29:270-278, 2013). This method is based on the OTA nrps gene of Penicillium nordicum. It produces a specific amplicon of 459 bp and its functionality in naturally infected samples was also demonstrated.

Use of functional genomics to assess the climate change impact on Aspergillus flavus and aflatoxin production

Aspergillus flavus is an opportunistic and pathogenic fungus that infects several crops of agricultural importance and under certain conditions may produce carcinogenic mycotoxins. Rising global temperatures, disrupted precipitation patterns and increased CO2 levels that are associated with future climate conditions are expected to impact the growth and toxigenic potential of A. flavus. Both laboratory and real world observations have demonstrated this potential, especially when examining the effects of water availability and temperature. Recent experiments have also established that CO2 may also be affecting toxin production. The application of current technologies in the field of functional genomics, including genomic sequencing, RNA-seq, microarray technologies and proteomics have revealed climate change-related, abiotic regulation of the aflatoxin cluster and influence on the plant-fungus interaction. Furthermore, elevated CO2 levels have been shown to impact expression of the aflatoxin biosynthetic regulatory gene aflR. The use of functional genomics will allow researchers to better understand the underlying transcriptomic response within the fungus to climate change, with a view towards predicting changes in fungal infection and toxin production associated with climate change.

Complete Genome Sequence of the Filamentous Fungus Aspergillus westerdijkiae Reveals the Putative Biosynthetic Gene Cluster of Ochratoxin A

Ochratoxin A (OTA) is a common mycotoxin that contaminates food and agricultural products. Sequencing of the complete genome of Aspergillus westerdijkiae, a major producer of OTA, reveals more than 50 biosynthetic gene clusters, including a putative OTA biosynthetic gene cluster that encodes a dozen of enzymes, transporters, and regulatory proteins.

Sequencing and functional annotation of the whole genome of the filamentous fungus Aspergillus westerdijkiae

BACKGROUND

Aspergillus westerdijkiae produces ochratoxin A (OTA) in Aspergillus section Circumdati. It is responsible for the contamination of agricultural crops, fruits, and food commodities, as its secondary metabolite OTA poses a potential threat to animals and humans. As a member of the filamentous fungi family, its capacity for enzymatic catalysis and secondary metabolite production is valuable in industrial production and medicine. To understand the genetic factors underlying its pathogenicity, enzymatic degradation, and secondary metabolism, we analysed the whole genome of A. westerdijkiae and compared it with eight other sequenced Aspergillus species.

RESULTS

We sequenced the complete genome of A. westerdijkiae and assembled approximately 36 Mb of its genomic DNA, in which we identified 10,861 putative protein-coding genes. We constructed a phylogenetic tree of A. westerdijkiae and eight other sequenced Aspergillus species and found that the sister group of A. westerdijkiae was the A. oryzae - A. flavus clade. By searching the associated databases, we identified 716 cytochrome P450 enzymes, 633 carbohydrate-active enzymes, and 377 proteases. By combining comparative analysis with Kyoto Encyclopaedia of Genes and Genomes (KEGG), Conserved Domains Database (CDD), and Pfam annotations, we predicted 228 potential carbohydrate-active enzymes related to plant polysaccharide degradation (PPD). We found a large number of secondary biosynthetic gene clusters, which suggested that A. westerdijkiae had a remarkable capacity to produce secondary metabolites. Furthermore, we obtained two more reliable and integrated gene sequences containing the reported portions of OTA biosynthesis and identified their respective secondary metabolite clusters. We also systematically annotated these two hybrid t1pks-nrps gene clusters involved in OTA biosynthesis. These two clusters were separate in the genome, and one of them encoded a couple of GH3 and AA3 enzyme genes involved in sucrose and glucose metabolism.

CONCLUSIONS

The genomic information obtained in this study is valuable for understanding the life cycle and pathogenicity of A. westerdijkiae. We identified numerous enzyme genes that are potentially involved in host invasion and pathogenicity, and we provided a preliminary prediction for each putative secondary metabolite (SM) gene cluster. In particular, for the OTA-related SM gene clusters, we delivered their components with domain and pathway annotations. This study sets the stage for experimental verification of the biosynthetic and regulatory mechanisms of OTA and for the discovery of new secondary metabolites.

Ochratoxin A production by Penicillium thymicola

Ochratoxin A (OTA) is a mycotoxin produced by some Aspergillus and Penicillium species that grow on economically important agricultural crops and food products. OTA is classified as Group 2B carcinogen and is potently nephrotoxic, which is the basis for its regulation in some jurisdictions. Using high resolution mass spectroscopy, OTA and ochratoxin B (OTB) were detected in liquid culture extracts of Penicillium thymicola DAOMC 180753 isolated from Canadian cheddar cheese. The genome of this strain was sequenced, assembled and annotated to probe for putative genes involved in OTA biosynthesis. Known OTA biosynthetic genes from Penicillium verrucosum or Penicillium nordicum, two related Penicillium species that produce OTA, were not found in P. thymicola. However, a gene cluster containing a polyketide synthase (PKS) and PKS-nonribosomal peptide synthase (NRPS) hybrid encoding genes were located in the P. thymicola genome that showed a high degree of similarity to OTA biosynthetic enzymes of Aspergillus carbonarius and Aspergillus ochraceus. This is the first report of ochratoxin from P. thymicola and a new record of the species in Canada.

RNA-Seq Reveals OTA-Related Gene Transcriptional Changes in Aspergillus carbonarius

Ochratoxin A (OTA) is a mycotoxin harmful for animals and humans. Aspergillus carbonarius is the main responsible for OTA contamination of grapes and derived products. Gene transcriptional profiling of 4 A. carbonarius strains was carried out by RNA-Seq analysis to study transcriptome changes associated with OTA production. By comparing OTA inducing (OTAI) vs. non-inducing (OTAN) cultural conditions, a total of 3,705 differentially expressed genes (DEGs) (fold change > |2| and FDR ≤ 0.05) were identified. Several genes involved in primary metabolic processes, with particular regard to carbohydrate and amino acid metabolisms, secondary metabolic processes, transport, response to stress and sporulation were up-regulated by OTAI conditions at all the analysed sampling times (4, 6 and 8 DAI) or starting from 6 DAI. Highly up-regulated DEGs encoding enzymes involved in biosynthesis of secondary metabolites, oxidoreductases, transporters and transcription factors were examined for their potential involvement in OTA biosynthesis and related metabolic pathways. Differential expression of genes encoding polyketide synthases (pks), non-ribosomal peptide synthetases (nrps) and chloroperoxidase (cpo) was validated by RT-qPCR. Among clusters of co-regulated genes involved in SM biosynthesis, one putative OTA-gene cluster, including both pks and nrps genes, was detected in the A. carbonarius genome.

Genome sequence of Valsa canker pathogens uncovers a potential adaptation of colonization of woody bark

Canker caused by ascomycetous Valsa species are among the most destructive diseases of woody plants worldwide. These pathogens are distinct from other pathogens because they only effectively attack tree bark in the field. To unravel the potential adaptation mechanism of bark colonization, we examined the genomes of Valsa mali and Valsa pyri that preferentially infect apple and pear, respectively. We reported the 44.7 and 35.7 Mb genomes of V. mali and V. pyri, respectively. We also identified the potential genomic determinants of wood colonization by comparing them with related cereal pathogens. Both genomes encode a plethora of pathogenicity-related genes involved in plant cell wall degradation and secondary metabolite biosynthesis. In order to adapt to the nutrient limitation and low pH environment in bark, they seem to employ membrane transporters associated with nitrogen uptake and secrete proteases predominantly with acidic pH optima. Remarkably, both Valsa genomes are especially suited for pectin decomposition, but are limited in lignocellulose and cutin degradation. Besides many similarities, the two genomes show distinct variations in many secondary metabolism gene clusters. Our results show a potential adaptation of Valsa canker pathogens to colonize woody bark. Secondary metabolism gene clusters are probably responsible for this host specificity.

Comparative Ochratoxin Toxicity: A Review of the Available Data

Ochratoxins are a group of mycotoxins produced by a variety of moulds. Ochratoxin A (OTA), the most prominent member of this toxin family, was first described by van der Merwe et al. in Nature in 1965. Dietary exposure to OTA represents a serious health issue and has been associated with several human and animal diseases including poultry ochratoxicosis, porcine nephropathy, human endemic nephropathies and urinary tract tumours in humans. More than 30 years ago, OTA was shown to be carcinogenic in rodents and since then extensive research has been performed in order to investigate its mode of action, however, this is still under debate. OTA is regarded as the most toxic family member, however, other ochratoxins or their metabolites and, in particular, ochratoxin mixtures or combinations with other mycotoxins may represent serious threats to human and animal health. This review summarises and evaluates current knowledge about the differential and comparative toxicity of the ochratoxin group.

RNA sequencing of an nsdC mutant reveals global regulation of secondary metabolic gene clusters in Aspergillus flavus

The filamentous fungus, Aspergillus flavus (A. flavus) is an opportunistic pathogen capable of invading a number of crops and contaminating them with toxic secondary metabolites such as aflatoxins. Characterizing the molecular mechanisms governing growth and development of this organism is vital for developing safe and effective strategies for reducing crop contamination. The transcription factor nsdC has been identified as being required for normal asexual development and aflatoxin production in A. flavus. Building on a previous study using a large (L)-sclerotial morphotype A. flavus nsdC mutant we observed alterations in conidiophore development and loss of sclerotial and aflatoxin production using a nsdC mutant of a small (S)-sclerotial morphotype, that normally produces aflatoxin and sclerotia in quantities much higher than the L-morphotype. RNA sequencing analysis of the nsdC knockout mutant and isogenic control strain identified a number of differentially expressed genes related to development and production of secondary metabolites, including aflatoxin, penicillin and aflatrem. Further, RNA-seq data indicating down regulation of aflatrem biosynthetic gene expression in the nsdC mutant correlated with HPLC analyses showing a decrease in aflatrem levels. The current study expands the role of nsdC as a globally acting transcription factor that is a critical regulator of both asexual reproduction and secondary metabolism in A. flavus.

Clustered array of ochratoxin A biosynthetic genes in Aspergillus steynii and their expression patterns in permissive conditions

Aspergillus steynii is probably the most relevant species of section Circumdati producing ochratoxin A (OTA). This mycotoxin contaminates a wide number of commodities and it is highly toxic for humans and animals. Little is known on the biosynthetic genes and their regulation in Aspergillus species. In this work, we identified and analysed three contiguous genes in A. steynii using 5'-RACE and genome walking approaches which predicted a cytochrome P450 monooxygenase (p450ste), a non-ribosomal peptide synthetase (nrpsste) and a polyketide synthase (pksste). These three genes were contiguous within a 20742 bp long genomic DNA fragment. Their corresponding cDNA were sequenced and their expression was analysed in three A. steynii strains using real time RT-PCR specific assays in permissive conditions in in vitro cultures. OTA was also analysed in these cultures. Comparative analyses of predicted genomic, cDNA and amino acid sequences were performed with sequences of similar gene functions. All the results obtained in these analyses were consistent and point out the involvement of these three genes in OTA biosynthesis by A. steynii and showed a co-ordinated expression pattern. This is the first time that a clustered organization OTA biosynthetic genes has been reported in Aspergillus genus. The results also suggested that this situation might be common in Aspergillus OTA-producing species and distinct to the one described for Penicillium species.

Rapid genome resequencing of an atoxigenic strain of Aspergillus carbonarius

In microorganisms, Ion Torrent sequencing technology has been proved to be useful in whole-genome sequencing of bacterial genomes (5 Mbp). In our study, for the first time we used this technology to perform a resequencing approach in a whole fungal genome (36 Mbp), a non-ochratoxin A producing strain of Aspergillus carbonarius. Ochratoxin A (OTA) is a potent nephrotoxin which is found mainly in cereals and their products, but it also occurs in a variety of common foods and beverages. Due to the fact that this strain does not produce OTA, we focused some of the bioinformatics analyses in genes involved in OTA biosynthesis, using a reference genome of an OTA producing strain of the same species. This study revealed that in the atoxigenic strain there is a high accumulation of nonsense and missense mutations in several genes. Importantly, a two fold increase in gene mutation ratio was observed in PKS and NRPS encoding genes which are suggested to be involved in OTA biosynthesis.

Next-generation sequencing approach for connecting secondary metabolites to biosynthetic gene clusters in fungi

Genomics has revolutionized the research on fungal secondary metabolite (SM) biosynthesis. To elucidate the molecular and enzymatic mechanisms underlying the biosynthesis of a specific SM compound, the important first step is often to find the genes that responsible for its synthesis. The accessibility to fungal genome sequences allows the bypass of the cumbersome traditional library construction and screening approach. The advance in next-generation sequencing (NGS) technologies have further improved the speed and reduced the cost of microbial genome sequencing in the past few years, which has accelerated the research in this field. Here, we will present an example work flow for identifying the gene cluster encoding the biosynthesis of SMs of interest using an NGS approach. We will also review the different strategies that can be employed to pinpoint the targeted gene clusters rapidly by giving several examples stemming from our work.

Reliable and simple detection of ochratoxin and fumonisin production in black Aspergillus

To date, edible fungi such as black Aspergillus (Aspergillus niger aggregates) have been considered as safe. However, it has recently been reported that some strains have a mycotoxin biosynthetic capability, and this capability must be evaluated to determine the safety of edible fungi. In this study, we assessed the ability of mycotoxin production in A. niger aggregates isolated from various Korean foods using multiplex PCR and high-performance liquid chromatography (HPLC) analyses. Multiplex PCR and HPLC analyses of 32 A. niger aggregates showed that ochratoxin and fumonisin were produced only by strains exhibiting positive PCR patterns with ochratoxin and fumonisin biosynthesis genes. However, several strains did not produce mycotoxins, even though they contained mycotoxin biosynthesis genes. Using multiplex PCR pattern and HPLC analyses, we selected Aspergillus strains that do not produce mycotoxins, which will contribute to the development of safer fermented foods.

A molecular and bioinformatic study on the ochratoxin A (OTA)-producing Aspergillus affinis (section Circumdati)

Aspergillus affinis (section Circumdati) is a novel ochratoxin A (OTA)-producing species found in submerged riparian decomposing leaves. However, very little is known about its role on the breakdown of plant debris and its ability to degrade carbohydrate polymers. Moreover, its OTA biosynthetic pathway has not yet been explored. In the present paper, we investigated the gene encoding the extracellular alpha-amylase (amyAa) of A. affinis within the evolution of the Aspergillus lineages in relation to the possible use of this enzyme in starch processing. The novel amyAa, despite being related to branches of the Aspergillus species of the sections Terrei and Flavi, formed a distinct phylogenetic branch, which may be of outstanding importance from a biotechnological point of view. Moreover, we identified the polyketide synthase gene (pks) putatively required for the first step of OTA biosynthesis in A. affinis. This otapks was examined in relation to a limited number of orthologous genes available from Aspergillus species of the sections Circumdati and Nigri. Our study highlights the importance of otapks as target genes in the treatment of ochratoxigenic Aspergillus species on a more comprehensive evolutionary basis.

Identification and characterization of the polyketide synthase involved in ochratoxin A biosynthesis in Aspergillus carbonarius

Ochratoxin A (OTA) is a potent mycotoxin produced by Aspergillus and Penicillium species and is a common contaminant of a wide variety of food commodities, with Aspergillus carbonarius being the main producer of OTA contamination in grapes and wine. The molecular structure of OTA comprises a dihydroisocoumarin ring linked to phenylalanine and, as shown in different producing fungal species, a polyketide synthase (PKS) is a component of the OTA biosynthetic pathway. Similar to observations in other filamentous ascomycetes, the genome sequence of A. carbonarius contains a large number of genes predicted to encode PKSs. In this work a pks gene identified within the putative OTA cluster of A. carbonarius, designated as AcOTApks, was inactivated and the resulting mutant strain was unable to produce OTA, confirming the role of AcOTApks in this biosynthetic pathway. AcOTApks protein is characteristic of the highly reduced (HR)-PKS family, and also contains a putative methyltransferase domain likely responsible for the addition of the methyl group to the OTA polyketide structure. AcOTApks is different from the ACpks protein that we previously described in A. carbonarius, which showed an expression profile compatible with OTA production. We performed phylogenetic analyses of the β-ketosynthase and acyl-transferase domains of the OTA PKSs that had been identified and characterized in different OTA producing fungal species. The phylogenetic results were similar for both domains analyzed and showed that OTA PKS of A. carbonarius, Aspergillus niger and Aspergillus ochraceus clustered in a monophyletic group with 100% bootstrap support suggesting a common origin, while the other OTA PKSs analyzed were phylogenetically distant. A quantitative RT-PCR assay monitored AcOTApks expression during fungal growth and concomitant production of OTA by A. carbonarius in synthetic grape medium. A clear correlation between the expression profile of AcOTApks and kinetics of OTA production was observed, with AcOTApks reaching its maximum level of transcription before OTA accumulation in mycelium reached its highest level, confirming the fact that gene transcription always precedes phenotypic production.

The polyketide synthase gene pks4 of Trichoderma reesei provides pigmentation and stress resistance

Species of the fungal genus Trichoderma (Hypocreales, Ascomycota) are well-known for their production of various secondary metabolites. Nonribosomal peptides and polyketides represent a major portion of these products. In a recent phylogenomic investigation of Trichoderma polyketide synthase (PKS)-encoding genes, the pks4 from T. reesei was shown to be an orthologue of pigment-forming PKSs involved in synthesis of aurofusarin and bikaverin in Fusarium spp. In this study, we show that deletion of this gene in T. reesei results in loss of green conidial pigmentation and in pigmentation alteration of teleomorph structures. It also has an impact on conidial cell wall stability and the antagonistic abilities of T. reesei against other fungi, including formation of inhibitory metabolites. In addition, deletion of pks4 significantly influences the expression of other PKS-encoding genes of T. reesei. To our knowledge, this is the first indication that a low-molecular-weight pigment-forming PKS is involved in defense, mechanical stability, and stress resistance in fungi.

Non-Botrytis grape-rotting fungi responsible for earthy and moldy off-flavors and mycotoxins

The grape microflora is complex and includes filamentous fungi, yeasts and bacteria with different physiological characteristics and effects on wine production. Most studies have focused on the wine microbiota, but a few studies have reported the ecology of grape microorganisms. Some of these organisms - such as non-Botrytis bunch rotting fungi, which greatly influence the safety or sensory quality of wine, due to the production of mycotoxins and off-flavors, respectively - are considered to be spoilage agents. We review here the diversity of filamentous fungi on grapes and the factors influencing their development, such as grape ripening stage, environmental factors (climate, rain and cultivation practices), grape variety and grape health status. We also discuss the pathways by which mycotoxins and off-flavors are produced, the control of the population, the metabolites responsible for wine spoilage and the methods for detecting and characterizing the microorganisms involved.

Effect of Kluyveromyces thermotolerans on polyketide synthase gene expression and ochratoxin accumulation by Penicillium and Aspergillus

In a previous study, it was demonstrated that Kluyveromyces thermotolerans strains can reduce both growth and ochratoxin A (OTA) accumulation by Aspergillus section Nigri strains. There is no information about the mechanisms related to this reduction. A viable hypothesis can be that the presence of biocontrol agents can affect OTA biosynthesis by influencing the transcriptional activity of the polyketide synthase (pks) gene, one of the key enzymes in the OTA biosynthetic pathway. The aims of this work were to determine the effect of two selected strains of K. thermotolerans as potential biocontrol agents and to evaluate if their presence can affect the otapks gene expression of ochratoxigenic Aspergillus and Penicillium species. Growth, OTA and ochratoxin B (OTB) biosynthesis by the fungal strains at the phenotypic and molecular levels were monitored. The results obtained showed that both K. thermotolerans strains evaluated had a strong influence on growth, OTA and OTB biosynthesis, and expression of the mycotoxin biosynthesis genes. However, no direct correlation between the influence of the biocontrol yeasts on pks gene expression, OTA and OTB production could be found. These results could indicate an inhibitory mechanism by the yeasts, which apparently involve a post-transcriptional mechanism. The data obtained could imply that the production of mycotoxins can be regarded as a kind of adaptation mechanism to environmental stress conditions by these mycotoxigenic species.

Microbial detoxification of mycotoxins

Mycotoxins are fungal natural products that are toxic to vertebrate animals including humans. Microbes have been identified that enzymatically convert aflatoxin, zearalenone, ochratoxin, patulin, fumonisin, deoxynivalenol, and T-2 toxin to less toxic products. Mycotoxin-degrading fungi and bacteria have been isolated from agricultural soil, infested plant material, and animal digestive tracts. Biotransformation reactions include acetylation, glucosylation, ring cleavage, hydrolysis, deamination, and decarboxylation. Microbial mycotoxin degrading enzymes can be used as feed additives or to decontaminate agricultural commodities. Some detoxification genes have been expressed in plants to limit the pre-harvest mycotoxin production and to protect crop plants from the phytotoxic effects of mycotoxins. Toxin-deficient mutants may be useful in assessing the role of mycotoxins in the ecology of the microorganisms.

A gene cluster of the ochratoxin A biosynthetic genes inPenicillium

A putative ochratoxin A (OTA) biosynthetic gene cluster inP. nordicum has been identified. The first part of the gene cluster is located on a DNA fragment of 10 kb in length and harbours three genes. A gene with high homology to an alkaline serine protease gene (accession number AY557343), which represents the upstream border of the cluster. Furthermore the fragment carries a large part (about 2 kb) of the 5' end of a polyketide synthase (otapksPN, accession number AY196315) and a complete non-ribosomal peptide synthetase (otanpsPN, accession number AY534879). The second part of the cluster is located on a 4.3 kb fragment that harbours three open reading frames (ORFs) encoding putative OTA biosynthetic proteins: one incomplete ORF at the 5' end of the fragment demonstrated homology to an organic anion transporter from rat kidneys (otatraPN). This transporter has been described to be responsible for the transport of toxic OTA out of the cell. One complete ORF of 951 nucleotides is also located on this fragment. This gene has limited homology to a chloroperoxidase fromGluconobacter oxidans. At the 3' end of this DNA fragment is an incomplete open reading frame of a potential nitrate transporter. The transcription of all putative OTA biosynthetic genes is increased under OTA conducive conditions. The expression kinetics of the genes resembles that of secondary metabolite biosynthetic genes, in which these genes are co-ordinately expressed during the late growth phase.PCR analysis demonstrated that the gene cluster is only present in the two ochratoxin A producingPenicillium species,P. verrucosum andP. nordicum. P. nalgiovense, a species occurring in the same habitat asP. nordicum carries inactive homologues of the genes. All other species proved to be negative for the genes. This was also true for OTA producing Aspergilli.

Genetic background of ochratoxin A production inPenicillium

A part of the gene cluster responsible for the production of ochratoxin A inP. nordicum has been characterised recently. The analysed DNA region contains three putative genes: an alcaline proteinase (aspPN), a non-ribosomal peptide synthetase (npsPN) and an polyketide synthase (otapksPN). The last two genes are putative genes of the ochratoxin A biosynthetic pathway. Interestingly theotapksPN gene is present in this form only inP. nordicum but not inP. verrucosum indicating genetic differences between both ochratoxin A producingPenicillium species. The genes in ochratoxin A producingAspergillus species seems to be completely different. It has been demonstrated that thenpsPN gene is actively transcribed inP. nordicum under ochratoxin A producing conditions, indicating that this gene is involved in ochratoxin A biosynthesis.

Identification of Genes Differentially Expressed Between Ochratoxin-Producing and Non-Producing Strains of Aspergillus westerdijkiae

Approximately 70 % of Aspergillus westerdijkiae strains are able to produce ochratoxin A (OTA), a nephrotoxic and carcinogenic mycotoxin which have been found in cereal and food commodities. Despite of its importance there is, up to now, no information available about which genes are differentially expressed between A. westerdijkiae ochratoxin-producing and non-producing strains. Using cDNA RDA approach we successfully sequenced 231 raw ESTs expected to be enriched in the ochratoxin-producing strain. BLASTX searches against the public databases showed that of these, 205 ESTs (79 %) exhibited significant similarities with proteins of known functions, 28 ESTs (11 %) had matches to hypothetical proteins, and the remaining 27 ESTs (10 %) had no significant hits. EST alignment resulted in a total of 14 non-redundant consensus sequences. Three putative genes encoding oxidoreductases were validated as up-expressed in the OTA producer strain using RT-qPCR approach. The expression of the putative genes encoding a cytochrome P450 family protein, 3-hydroxyphenylacetate-6-hydroxylase, and endoplasmic reticulum oxidoreductin were higher (32-, 2.8- and 20-fold respectively) in the OTA producer strain compared to the non-producer strain.

Phylogenetic study of polyketide synthases and nonribosomal peptide synthetases involved in the biosynthesis of mycotoxins

Polyketide synthase (PKSs) and nonribosomal peptide synthetase (NRPSs) are large multimodular enzymes involved in biosynthesis of polyketide and peptide toxins produced by fungi. Furthermore, hybrid enzymes, in which a reducing PKS region is fused to a single NRPS module, are also responsible of the synthesis of peptide-polyketide metabolites in fungi. The genes encoding for PKSs and NRPSs have been exposed to complex evolutionary mechanisms, which have determined the great number and diversity of metabolites. In this study, we considered the most important polyketide and peptide mycotoxins and, for the first time, a phylogenetic analysis of both PKSs and NRPSs involved in their biosynthesis was assessed using two domains for each enzyme: β-ketosynthase (KS) and acyl-transferase (AT) for PKSs; adenylation (A) and condensation (C) for NRPSs. The analysis of both KS and AT domains confirmed the differentiation of the three classes of highly, partially and non-reducing PKSs. Hybrid PKS-NRPSs involved in mycotoxins biosynthesis grouped together in the phylogenetic trees of all the domains analyzed. For most mycotoxins, the corresponding biosynthetic enzymes from distinct fungal species grouped together, except for PKS and NRPS involved in ochratoxin A biosynthesis, for which an unlike process of evolution could be hypothesized in different species.