Diversity of polyketide synthase gene sequences in Aspergillus species

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.

Profiling of secondary metabolite gene clusters regulated by LaeA in Aspergillus niger FGSC A1279 based on genome sequencing and transcriptome analysis

The global regulator LaeA controls the production of many fungal secondary metabolites, possibly via chromatin remodeling. Here we aimed to survey the secondary metabolite profile regulated by LaeA in Aspergillus niger FGSC A1279 by genome sequencing and comparative transcriptomics between the laeA deletion (ΔlaeA) and overexpressing (OE-laeA) mutants. Genome sequencing revealed four putative polyketide synthase genes specific to FGSC A1279, suggesting that the corresponding polyketide compounds might be unique to FGSC A1279. RNA-seq data revealed 281 putative secondary metabolite genes upregulated in the OE-laeA mutants, including 22 secondary metabolite backbone genes. LC-MS chemical profiling illustrated that many secondary metabolites were produced in OE-laeA mutants compared to wild type and ΔlaeA mutants, providing potential resources for drug discovery. KEGG analysis annotated 16 secondary metabolite clusters putatively linked to metabolic pathways. Furthermore, 34 of 61 Zn₂Cys₆ transcription factors located in secondary metabolite clusters were differentially expressed between ΔlaeA and OE-laeA mutants. Three secondary metabolite clusters (cluster 18, 30 and 33) containing Zn₂Cys₆ transcription factors that were upregulated in OE-laeA mutants were putatively linked to KEGG pathways, suggesting that Zn₂Cys₆ transcription factors might play an important role in synthesizing secondary metabolites regulated by LaeA. Taken together, LaeA dramatically influences the secondary metabolite profile in FGSC A1279.

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.

Phylogenomic and domain analysis of iterative polyketide synthases in Aspergillus species

Aspergillus species are industrially and agriculturally important as fermentors and as producers of various secondary metabolites. Among them, fungal polyketides such as lovastatin and melanin are considered a gold mine for bioactive compounds. We used a phylogenomic approach to investigate the distribution of iterative polyketide synthases (PKS) in eight sequenced Aspergilli and classified over 250 fungal genes. Their genealogy by the conserved ketosynthase (KS) domain revealed three large groups of nonreducing PKS, one group inside bacterial PKS, and more than 9 small groups of reducing PKS. Polyphyly of nonribosomal peptide synthase (NRPS)-PKS genes raised questions regarding the recruitment of the elegant conjugation machinery. High rates of gene duplication and divergence were frequent. All data are accessible through our web database at http://metabolomics.jp/wiki/Category:PK.

Cladosporium cladosporioides LPSC 1088 produces the 1,8-dihydroxynaphthalene-melanin-like compound and carries a putative pks gene

Cladosporium cladosporioides is a dematiaceous fungus with coloured mycelia and conidia due to the presence of dark pigments. The purpose of this study was to characterize the dark pigments synthetized by Cladosporium sp. LPSC no. 1088 and also to identify the putative polyketide synthase (pks) gene that might be involved in the pigment biosynthesis. Morphological as well as molecular features like the ITS sequence confirmed that LPSC 1088 is Cladosporium cladosporioides. UV-visible, Fourier Transform Infrared (FTIR) and Electron Spin Resonance (ESR) spectroscopy analysis as well as melanin inhibitors suggest that the main dark pigment of the isolate was 1,8 dihydroxynaphthalene (DHN)-melanin-type compound. Two commercial fungicides, Difenoconazole and Chlorothalonil, inhibited fungal growth as well as increased pigmentation of the colonies suggesting that melanin might protect the fungus against chemical stress. The pigment is most probably synthetized by means of a pentaketide pathway since the sequence of a 651 bp fragment, coding for a putative polyketide synthase, is highly homologous to pks sequences from other fungi.

Polyketide synthase gene aolc35-12 controls the differential expression of ochratoxin A gene aoks1 in Aspergillus westerdijkiae

Ochratoxine A (OTA), a potential human carcinogen is produced by several species of Aspergillus and Penicillium, including Aspergillus westerdijkiae. In this study a putative polyketide synthase gene aolc35-12 has been partially cloned from A. westerdijkiae. The predicted amino acid sequence of the 3.22 kb clone was found to have a high degree of similarity to other previously identified polyketide synthase genes from various OTA-producing fungi including Aspergillus ochraceus, Aspergillus niger, Aspergillus carbonarius and Penicillium nordicum. The aolc35-12 gene was disrupted and inactivated by insertion of Escherichia coli hygromycin B phosphotransferase gene, which resulted in an OTA negative mutant aoΔlc35-12. Genetic complementation confirmed aolc35-12 as OTA-polyketide synthase gene. Furthermore, study of the differential expression of aolc35-12 and a previously identified OTA-polyketide synthase gene, i.e. aoks1, in the wild-type A. westerdijkiae and aoΔlc35-12 mutant revealed that aolc35-12 could code for a certain polyketide compound complementary for the expression of aoks1 and hence for the activation of OTA biosynthesis system in A. westerdijkiae.

The diversity of polyketide synthase genes from sugarcane-derived fungi

The chemical ecology and biotechnological potential of metabolites from endophytic and rhizosphere fungi are receiving much attention. A collection of 17 sugarcane-derived fungi were identified and assessed by PCR for the presence of polyketide synthase (PKS) genes. The fungi were all various genera of ascomycetes, the genomes of which encoded 36 putative PKS sequences, 26 shared sequence homology with β-ketoacyl synthase domains, while 10 sequences showed homology to known fungal C-methyltransferase domains. A neighbour-joining phylogenetic analysis of the translated sequences could group the domains into previously established chemistry-based clades that represented non-reducing, partially reducing and highly reducing fungal PKSs. We observed that, in many cases, the membership of each clade also reflected the taxonomy of the fungal isolates. The functional assignment of the domains was further confirmed by in silico secondary and tertiary protein structure predictions. This genome mining study reveals, for the first time, the genetic potential of specific taxonomic groups of sugarcane-derived fungi to produce specific types of polyketides. Future work will focus on isolating these compounds with a view to understanding their chemical ecology and likely biotechnological potential.

Ochratoxin a: general overview and actual molecular status

Ochratoxin A (OTA) is a mycotoxin produced by several species of Aspergillus and Penicillium fungi that structurally consists of a para-chlorophenolic group containing a dihydroisocoumarin moiety that is amide-linked to L-phenylalanine. OTA is detected worldwide in various food and feed sources. Studies show that this molecule can have several toxicological effects such as nephrotoxic, hepatotoxic, neurotoxic, teratogenic and immunotoxic. A role in the etiology of Balkan endemic nephropathy and its association to urinary tract tumors has been also proved. In this review, we will explore the general aspect of OTA: physico-chemical properties, toxicological profile, OTA producing fungi, contaminated food, regulation, legislation and analytical methods. Due to lack of sufficient information related to the molecular background, this paper will discuss in detail the recent advances in molecular biology of OTA biosynthesis, based on information and on new data about identification and characterization of ochratoxin biosynthetic genes in both Penicillium and Aspergillus species. This review will also cover the development of the molecular methods for the detection and quantification of OTA producing fungi in various foodstuffs.

Phylogenetic methods in natural product research

Natural products researchers are increasingly employing evolutionary analyses of genes and gene products that rely on phylogenetic trees. The field of phylogenetic inference and of evolutionary analyses based on phylogenies is growing at an amazing rate, making it difficult to keep up with the latest methodologies. Here, we summarize phylogenetic applications in natural products research, and review methods and software useful for carrying out analyses inferring or using phylogenetic trees. We include an updated overview of available alignment methods and programs, as well as a selection of some useful phylogenetic analysis tools. This review covers primarily the period 2000-2009 for applications of phylogenetic methods in natural product research, and 1990-2009 for phylogenetic methods, with some references going back to the 1960s.

Acyl Transferase Domains of Putative Polyketide Synthase (PKS) Genes in Aspergillus and Penicillium Producers of Ochratoxin A and the Evaluation of PCR Primers to Amplify PKS Sequences in Black Aspergillus Species

Fungal polyketide synthases (PKS) are responsible for the biosynthesis of several mycotoxins and other secondary metabolites. PKS genes in ochratoxin producing species from Aspergillus and Penicillum genera have been identified using a degenerate primer pair developed for the acyl transferase (AT) domain of fungal PKSs. Sequences of AT domains were aligned and analyzed using phylogenetic methods. The AT domain sequences appeared to be specific for a particular type of fungal PKSs and were related to PKSs involved in different mycotoxin biosynthesis pathways, including ochratoxin A. We have also developed primers suitable for amplifying AT domain sequences in strains belonging to the A. niger aggregate. DNA from most of the black Aspergillus species currently recognized was tested. Primers showed general applicability and other Aspergillus species belonging to section Nigri were successfully amplified.

Characterisation of a pks gene which is expressed during ochratoxin A production by Aspergillus carbonarius

Aspergillus carbonarius is considered the main fungus responsible for ochratoxin A (OTA) contamination in grapes. OTA is a potent nephrotoxin and a possible human carcinogen with a polyketide derived structure. Fungal polyketide synthases (PKSs) have recently been demonstrated to be involved in OTA biosynthesis in both Penicillium and Aspergillus species. We report here on the identification and characterisation of part of a novel polyketide synthase gene, ACpks from A. carbonarius. The sequence appears to encode conserved ketosynthase and acyl transferase domains, which are characteristic of previously characterised PKS enzymes. Expression of the ACpks gene is differentially regulated, with transcription being observed when the fungus was grown on synthetic grape medium and on OTA permissive medium (MM) whereas no transcription was detected when the fungus was grown on OTA restrictive medium (YES). ACpks expression was also observed when A. carbonarius was grown at low pH, with concomitant increases in OTA production. This correlation between ACpks gene expression and OTA production suggests the likely involvement for the product of this gene in ochratoxin A biosynthesis in the fungus. From a preliminary screening of Aspergillus isolates with ACpks specific primers, ACpks gene homologues appear to be present in A. sclerotioniger and A. ibericus, two species of section Nigri which are closely related to A. carbonarius.

Occurrence of ochratoxin A and ochratoxigenic mycoflora in corn and corn based foods and feeds in some South American countries

Cereals and cereal- derived products constitute the base of human and animal feeding in South American countries. This review attempts to give an overview of the ochratoxin A (OTA) occurrence and potential sources of OTA contamination in those products. The environmental conditions as humidity and temperature in the colonization of the substrates by Aspergillus section Nigri isolated from corn kernels were also discussed. The available information on the ochratoxigenic mycoflora and OTA presence in corn, corn based food and feed is limited. Only few surveys have been carried out in Argentina, Ecuador and Brazil; which showed that Aspergillus niger aggregate and A. ochraceus species would be the main source of OTA. It's possible to emphasize that, the species A. carbonarius has not been isolated from these substrates and Penicillium verrucosum was isolated only from pig feeds of Argentinean samples in low percentage. Studies about the ecophysiology of ochratoxigenic fungi and OTA occurrence are in progress in Latin America to reduce the impact of this toxin in the food chain.

Exploring the diversity of marine-derived fungal polyketide synthases

Using an approach based on polymerase chain reaction (PCR), we examined the diversity of polyketide synthase (PKS) genes present in 160 marine fungal isolates, representing 142 species. We obtained ketosynthase (KS) domain PCR products from 99 fungal isolates, representing Dothideomycetes, Sordariomycetes, Eurotiomycetes, and incertae sedis. Sequence similarity searches and phylogenetic analysis of 29 marine partial-KS-encoding sequences revealed domains predicted to encode reducing, nonreducing, and 6-methylsalicylic acid PKSs. Bioinformatic analysis of an alignment of the KS sequences from marine-derived fungi revealed no unique motifs in this region. However, several specificity-determining positions were apparent between fungal 6-methylsalicylic acid PKSs as compared with either reducing or nonreducing PKSs. Evaluation of these positions in the context of a modelled three-dimensional protein structure highlighted their potential use as PKS classification markers. Evaluating primer-binding sites was necessary to obtain KS domain fragments from putative PKSs while maintaining a level of sequence information adequate to properly classify and characterize them.

Amplification and diversity analysis of ketosynthase domains of putative polyketide synthase genes inAspergillus ochraceus andAspergillus carbonarius producers of ochratoxin A

The diversity of polyketide synthase (PKS) genes in Aspergillus ochraceus NRRL 3174 and Aspergillus carbonarius 2Mu134 has been investigated using different primer pairs previously developed for the ketosynthase (KS) domain of fungal PKSs. Nine different KS domain sequences in A. ochraceus NRRL 3174 as well as five different KS domain sequences in A. carbonarius 2Mu134 have been identified. The identified KS fragments were distributed in five different clusters on the phylogenetic tree, indicating that they most probably represent PKSs responsible for different functions.

Diversity of type I polyketide synthase genes in the wood-decay fungus Xylaria sp. BCC 1067

Fungal type I polyketide (PK) compounds are highly valuable for medical treatment and extremely diverse in structure, partly because of the enzymatic activities of reducing domains in polyketide synthases (PKSs). We have cloned several PKS genes from the fungus Xylaria sp. BCC 1067, which produces two polyketides: depudecin (reduced PK) and 19,20-epoxycytochalasin Q (PK-nonribosomal peptide (NRP) hybrid). Two new degenerate primer sets, KA-series and XKS, were designed to amplify reducing PKS and PKS-NRP synthetase hybrid genes, respectively. Five putative PKS genes were amplified in Xylaria using KA-series primers and two more with the XKS primers. All seven are predicted to encode proteins homologous to highly reduced (HR)-type PKSs. Previously designed primers in LC-, KS-, and MT-series identified four additional PKS gene fragments. Selected PKS fragments were used as probes to identify PKS genes from the genomic library of this fungus. Full-length sequences for five PKS genes were obtained: pks12, pks3, pksKA1, pksMT, and pksX1. They are structurally diverse with 1-9 putative introns and products ranging from 2162 to 3654 amino acids in length. The finding of 11 distinct PKS genes solely by means of PCR cloning supports that PKS genes are highly diverse in fungi. It also indicates that our KA-series primers can serve as powerful tools to reveal the genetic potential of fungi in production of multiple types of HR PKs, which the conventional compound screening could underestimate.

Ochratoxin A biosynthetic genes in Aspergillus ochraceus are differentially regulated by pH and nutritional stimuli

Expression of the polyketide synthase (pks) gene which is involved in ochratoxin A (OTA) biosynthesis in Aspergillus ochraceus is linked to production of the mycotoxin, with high levels of pks mRNA accumulation occurring in cultures producing OTA, as assessed by real-time reverse transcription (RT)-PCR. OTA production is regulated by nutrient availability, with supplementation of OTA restrictive potato dextrose broth with yeast extract resulting in a 39-fold increase in production of the mycotoxin. This effect appears to be mediated at the level of gene transcription as there is a concomitant increase in pks mRNA accumulation. OTA production is also strongly influenced by culture pH with large amounts of OTA being produced at pH values <7.0 with reduced amounts being produced at higher pH values. pks transcript levels again mirrored the OTA production profile observed at the different pH values. The transcription of two putative p450 type monooxygenase genes, namely p450-H11 and p450-B03 genes closely mirrored that of the pks gene under all growth conditions tested, suggesting their involvement together with the pks in OTA biosynthesis. The expression profile of the p450-B03 gene in particular is very similar to that of the pks gene, indicating that this gene may be clustered with the pks as part of the OTA biosynthetic gene cluster.

Nonribosomal peptide synthetase genes in the genome of Fusarium graminearum, causative agent of wheat head blight

Fungal nonribosomal peptide synthetases (NRPSs) are responsible for the biosynthesis of numerous metabolites which serve as virulence factors in several plant-pathogen interactions. The aim of our work was to investigate the diversity of these genes in a Fusarium graminearum sequence database using bioinformatic techniques. Our search identified 15 NRPS sequences, among which two were found to be closely related to peptide synthetases of various fungi taking part in ferrichrome biosynthesis. Another peptide synthetase gene was similar to that identified in Aspergillus oryzae which is possibly responsible for the biosynthesis of fusarinine, an extracellular iron-chelating siderophore. To our knowledge, this is the first report on the identification of a putative NRPS gene possibly responsible for the biosynthesis of fusarinine-type siderophores. The other NRPSs were found to be related to peptide synthetases taking part in the biosynthesis of various peptides in other fungi. Transcription factors carrying ankyrin repeats were observed in the vicinity of four of the identified peptide synthetase genes. Additionally, NRPS related genes similar to putative long-chain fatty acid CoA ligases, acyl CoA ligases, ABC transport proteins, a highly conserved putative transmembrane protein of Aspergillus nidulans, and alpha-aminoadipate reductases have also been identified. Further studies are in progress to clarify the role of some of the identified NRPS genes in plant pathogenesis.

Discovery of a novel superfamily of type III polyketide synthases in Aspergillus oryzae

Identification of genes encoding type III polyketide synthase (PKS) superfamily members in the industrially useful filamentous fungus, Aspergillus oryzae, revealed that their distribution is not specific to plants or bacteria. Among other Aspergilli (Aspergillus nidulans and Aspergillus fumigatus), A. oryzae was unique in possessing four chalcone synthase (CHS)-like genes (csyA, csyB, csyC, and csyD). Expression of csyA, csyB, and csyD genes was confirmed by RT-PCR. Comparative genome analyses revealed single putative type III PKS in Neurospora crassa and Fusarium graminearum, two each in Magnaporthe grisea and Podospora anserina, and three in Phenarocheate chrysosporium, with a phylogenic distinction from bacteria and plants. Conservation of catalytic residues in the CHSs across species implicated enzymatically active nature of these newly discovered homologs.

Legioliulin, a new isocoumarin compound responsible for blue-white autofluorescence in Legionella (Fluoribacter) dumoffii under long-wavelength UV light

Legionella dumoffii is one of the causative agents of Legionnaires' disease. There are 50 species in the genus Legionella, of which 10 species including L. dumoffii are known to exhibit uncharacterized blue-white autofluorescence. We constructed an L. dumoffii strain that exhibited a high intensity blue-white fluorescence, isolated a fluorescent pigment from the strain, and determined its molecular formula to be C(19)H(14)O(3) by high-resolution mass spectrometry. An NMR analysis revealed that this was a new isocoumarin compound, which was named legioliulin.