Expression profile analysis of wild-type and fcc1 mutant strains of Fusarium verticillioides during fumonisin biosynthesis

Proteomics analysis of Fusarium proliferatum under various initial pH during fumonisin production

Fusarium proliferatum as a fungal pathogen can produce fumonisin which causes a great threat to animal and human health. Proteomic approach was a useful tool for investigation into mycotoxin biosynthesis in fungal pathogens. In this study, we analyzed the fumonisin content and mycelium proteins of Fusarium proliferatum cultivated under the initial pH5 and 10. Fumonisin production after 10days was significantly induced in culture condition at pH10 than pH5. Ninety nine significantly differently accumulated protein spots under the two pH conditions were detected using two dimensional polyacrylamide gel electrophoresis and 89 of these proteins were successfully identified by MALDI-TOF/TOF and LC-ESI-MS/MS analysis. Among these 89 proteins, 45 were up-regulated at pH10 while 44 were up-accumulated at pH5. At pH10, these proteins were found to involve in the modification of fumonisin backbone including up-regulated polyketide synthase, cytochrome P450, S-adenosylmethionine synthase and O-methyltransferase, which might contribute to the induction of fumonisin production. At pH5, these up-regulated proteins such as l-amino-acid oxidase, isocitrate dehydrogenase and citrate lyase might inhibit the condensation of fumonisin backbone, resulting in reduced production of fumonisins. These results may help us to understand the molecular mechanism of the fumonisin synthesis in F. proliferatum.

BIOLOGICAL SIGNIFICANCE

To extend our understanding of the mechanism of the fumonisin biosynthesis of F. proliferatum, we reported the fumonisin production in relation to the differential proteins of F. proliferatum mycelium under two pH culture conditions. Among these 89 identified spots, 45 were up-accumulated at pH10 while 44 were up-accumulated at pH5. Our results revealed that increased fumonisin production at pH10 might be related to the induction of fumonisin biosynthesis caused by up-regulation of polyketide synthase, cytochrome P450, S-adenosylmethionine synthase and O-methyltransferase. Meanwhile, the up-regulation of l-amino-acid oxidase, isocitrate dehydrogenase and citrate lyase at pH5 might be related to the inhibition of the condensation of fumonisin backbone, resulting in reduced production of fumonisin. These results may help us to understand better the molecular mechanism of the fumonisin synthesis in F. proliferatum and then broaden the current knowledge of the mechanism of the fumonisin biosynthesis.

Detection of Transcriptionally Active Mycotoxin Gene Clusters: DNA Microarray

Various bioanalytical tools including DNA microarrays are frequently used to map global transcriptional changes in mycotoxin producer filamentous fungi. This effective hybridization-based transcriptomics technology helps researchers to identify genes of secondary metabolite gene clusters and record concomitant gene expression changes in these clusters initiated by versatile environmental conditions and/or gene deletions. Such transcriptional data are of great value when future mycotoxin control technologies are considered and elaborated. Giving the readers insights into RNA extraction and DNA microarray hybridization steps routinely used in our laboratories and also into the normalization and evaluation of primary gene expression data, we would like to contribute to the interlaboratory standardization of DNA microarray based transcriptomics studies being carried out in many laboratories worldwide in this important field of fungal biology.

Integrating gene expression, ecology and mycotoxin production by Fusarium and Aspergillus species in relation to interacting environmental factors

Environmental factors, such as water availability (water activity, aw), temperature and their interactions, have a significant impact on the life cycle of mycotoxigenic fungi. Growth and mycotoxin production are influenced by these interacting factors resulting in a broader range of aw × temperature conditions for germination, than growth or mycotoxin production. The biosynthetic genes are mostly clustered together and by using microarrays with sub-arrays for specific mycotoxins, such as trichothecenes, fumonisins and aflatoxins it has been possible to examine the relationship between interacting aw × temperature conditions on growth, toxin gene cluster expression and relate these to phenotypic toxin production. The data for groups of biosynthetic genes (Fusarium culmorum/Fusarium graminearum; Fusarium verticillioides; Aspergillus flavus) were integrated with data on growth and mycotoxin production under different aw × temperature conditions using a mixed growth model. This was used to correlate these factors and predict toxin levels which may be produced under different abiotic stress conditions. Indeed, the relative importance of the different genes could be examined using ternary diagrams of the relative expression of 3 genes at a time in relation to aw, temperature and mycotoxin production to identify the most important relationships. The effect of three-way interacting environmental factors representative of climate change (CC) scenarios (water stress × temperature (+2-4 °C) × elevated CO2 (350-400 vs 650 and 1000 ppm) on growth and mycotoxin production by A. flavus and by species of the Aspergillus section Circumdati and section Nigri have been determined. These studies on maize grain and coffee, respectively, suggest that while growth may not be significantly affected, mycotoxin production may be stimulated by CC factors. This approach to integrate such data sets and model the relationships could be a powerful tool for predicting the relative toxin production under extreme stress conditions, including CC scenarios.

Aflatoxins, fumonisins, and trichothecenes: a convergence of knowledge

Plant pathogenic fungi Aspergillus flavus, Fusarium verticillioides, and Fusarium graminearum infect seeds of the most important food and feed crops, including maize, wheat, and barley. More importantly, these fungi produce aflatoxins, fumonisins, and trichothecenes, respectively, which threaten health and food security worldwide. In this review, we examine the molecular mechanisms and environmental factors that regulate mycotoxin biosynthesis in each fungus, and discuss the similarities and differences in the collective body of knowledge. Whole-genome sequences are available for these fungi, providing reference databases for genomic, transcriptomic, and proteomic analyses. It is well recognized that genes responsible for mycotoxin biosynthesis are organized in clusters. However, recent research has documented the intricate transcriptional and epigenetic regulation that affects these gene clusters. Significantly, molecular networks that respond to environmental factors, namely nitrogen, carbon, and pH, are connected to components regulating mycotoxin production. Furthermore, the developmental status of seeds and specific tissue types exert conditional influences during fungal colonization. A comparison of the three distinct mycotoxin groups provides insight into new areas for research collaborations that will lead to innovative strategies to control mycotoxin contamination of grain.

Proteome analysis of the fungus Aspergillus carbonarius under ochratoxin A producing conditions

Aspergillus carbonarius is an important ochratoxin A producing fungus that is responsible for mycotoxin contamination of grapes and wine. In this study, the proteomes of highly (W04-40) and weakly (W04-46) OTA-producing A. carbonarius strains were compared to identify proteins that may be involved in OTA biosynthesis. Protein samples were extracted from two biological replicates and subjected to two dimensional gel electrophoresis analysis and mass spectrometry. Expression profile comparison (PDQuest software), revealed 21 differential spots that were statistically significant and showed a two-fold change in expression, or greater. Among these, nine protein spots were identified by MALDI-MS/MS and MASCOT database and twelve remain unidentified. Of the identified proteins, seven showed a higher expression in strain W04-40 (high OTA producer) and two in strain W04-46 (low OTA producer). Some of the identified amino acid sequences shared homology with proteins involved in regulation, amino acid metabolism, oxidative stress and sporulation. It is worth noting the presence of a protein with 126.5 fold higher abundance in strain W04-40 showing homology with protein CipC, a protein with unknown function related with pathogenesis and mycotoxin production by some authors. Variations in protein expression were also further investigated at the mRNA level by real-time PCR analysis. The mRNA expression levels from three identified proteins including CipC showed correlation with protein expression levels. This study represents the first proteomic analysis for a comparison of two A. carbonarius strains with different OTA production and will contribute to a better understanding of the molecular events involved in OTA biosynthesis.

Gene encoding a c-type cyclin in Mycosphaerella graminicola is involved in aerial mycelium formation, filamentous growth, hyphal swelling, melanin biosynthesis, stress response, and pathogenicity

Mycosphaerella graminicola is an important wheat pathogen causing Septoria tritici blotch. To date, an efficient strategy to control M. graminicola has not been developed. More significantly, we have a limited understanding of the molecular mechanisms of M. graminicola pathogenicity. In this study, we attempted to characterize an MCC1-encoding c-type cyclin, a gene homologous to FCC1 in Fusarium verticillioides. Four independent MCC1 knock-out mutants were generated via Agrobacterium tumefaciens-mediated transformation. All of the MCC1 mutants showed consistent multiple phenotypes. Significant reductions in radial growth on potato dextrose agar (PDA) were observed in all of the MCC1 mutants. In addition, MCC1 gene-deletion mutants produced less aerial mycelium on PDA, showed delayed filamentous growth, had unusual hyphal swellings, produced more melanin, showed an increase in their stress tolerance response, and were reduced significantly in pathogenicity. These results indicate that the MCC1 gene is involved in multiple signaling pathways, including those involved in pathogenicity in M. graminicola.

Fusarium verticillioides GAP1, a gene encoding a putative glycolipid-anchored surface protein, participates in conidiation and cell wall structure but not virulence

Fusarium verticillioides is an important pathogen of maize that causes ear rot and produces the mycotoxins known as fumonisins. To date, knowledge of pathogenicity and the regulation of fumonisin biosynthesis in F. verticillioides is limited. Here, the molecular characterization of GAP1, a gene encoding a putative 540 aa protein that belongs to a glycolipid-anchored surface (GAS) protein family, is presented. F. verticillioides GAP1 was identified as an expressed sequence tag (EST) upregulated in a culture condition conducive to conidiation and fumonisin B(1) (FB(1)) production. GAP1 null mutants GAM126 (Deltagap1 : : HYG) and GAG8 (Deltagap1 : : GEN) exhibited restricted growth, with more aerial hyphae than their wild-type progenitor on solid media. No defect in mycelial mass or filamentous growth was observed when the GAM126 and GAG8 strains were grown in liquid media under shaking conditions. When grown in suspended conditions, GAM126 and GAG8 strains produced significantly fewer conidia and produced comparatively densely branched hyphae. Concanavalin A staining indicated that the GAP1 deletion altered the cell wall carbohydrate composition/deposition process. Deletion of GAP1 did not affect the production level of FB(1) or F. verticillioides virulence on maize seedlings and stalks. Complementation of GAM126 with the wild-type GAP1 gene restored growth, conidiation and cell wall abnormality phenotypes. The results suggest that GAP1 is associated with growth, development and conidiation in F. verticillioides, but not with pathogenicity or regulation of FB(1).

The first fifty microarray studies in filamentous fungi

Microarray studies have examined global gene expression in over 20 species of filamentous fungi encompassing a wide variety of research areas. The majority have addressed aspects of metabolism or pathogenicity. Metabolic studies have revealed important differences in the transcriptional regulation of genes for primary metabolic pathways between filamentous fungi and yeast. Transcriptional profiles for genes involved in secondary metabolism have also been established. Genes required for the biosynthesis of both useful and detrimental secondary metabolites have been identified. Due to the economic, ecological and medical implications, it is not surprising that many studies have used microarray analysis to examine gene expression in pathogenic filamentous fungi. Genes involved in various stages of pathogenicity have been identified, including those thought to be important for adaptation to the host environment. While most of the studies have simulated pathogenic conditions in vitro, a small number have also reported fungal gene expression within their plant hosts. This review summarizes the first 50 microarray studies in filamentous fungi and highlights areas for future investigation.

Interaction of water activity and bicarbonate salts in the inhibition of growth and mycotoxin production by Fusarium and Aspergillus species of importance to corn

The combined effects of water activity (a(w)) and ammonium/sodium bicarbonate on growth and mycotoxin production in corn by Fusarium and Aspergillus species were investigated. Interaction was observed between the salts and a(w) on the colony growth rates and lag phase durations of all isolates. Growth stimulation at low salt levels was observed only for the Fusarium isolates as the fastest growth of F. verticillioides and F. proliferatum occurred at levels of 0.1-0.2 and 0.5% ammonium and sodium bicarbonate, respectively. Although the complete inhibition of the growth of the Fusarium and Aspergillus isolates investigated took place at a level of 1% ammonium bicarbonate as much as 4% sodium bicarbonate failed to completely inhibit the growth of the Aspergillus isolates. Increase in concentration of either salt generally resulted in large reductions of both fumonisin B(1) and aflatoxin B(1) production. According to the sensorial analysis performed, corn treated with up to 1% ammonium bicarbonate was still acceptable for consumption, whereas corn treated with at least 2% sodium bicarbonate was determined to be sensorially unsuitable. Ammonium bicarbonate can be concluded to be more suitable for protecting stored corn from fungal contamination as it was capable of completely inhibiting both growth and mycotoxin production of the Fusarium and Aspergillus isolates of most importance to corn at levels that were still sensorially acceptable. Therefore ammonium bicarbonate could possibly be applied as a cheap and easy to apply treatment for use in resource limited developing countries.

Fusarium genomic resources: tools to limit crop diseases and mycotoxin contamination

It has been almost 10 years since Joan Bennett suggested that fungal biologists create a "wish list" for fungal genome sequences (Bennett JW. White paper: Genomics for filamentous fungi. Fungal Genet Biol 1997; 21: 3-7). The availability of over 200 review papers concerning fungal genomics is a reflection of significant progress with a diversity of fungal species. Although much progress has been made, the use of genomic data to study mycotoxin synthesis and function, pathogenesis and other aspects of fungal biology is in its infancy. Here, we briefly present the status of publicly available genomic resources for Fusarium, a genus of important plant pathogenic and mycotoxin-producing fungi of worldwide concern. Preliminary examination of microarray data collected from F. verticillioides liquid cultures provides evidence of widespread differential gene expression over time.

The putative monomeric G-protein GBP1 is negatively associated with fumonisin B production in Fusarium verticillioides

SUMMARY Fumonisin B(1) (FB(1)) is a mycotoxin produced by Fusarium verticillioides that contaminates maize. FB(1) has been linked to a number of human and animal mycotoxicoses worldwide. Despite its significance, our understanding of the FB(1) biosynthesis regulatory mechanisms is limited. Here, we describe F. verticillioides GBP1, encoding a monomeric G-protein, and its role in FB(1) biosynthesis. GBP1 was discovered as an expressed sequence tag (EST) up-regulated in the F. verticillioides fcc1 mutant that showed reduced conidiation and no FB(1) biosynthesis when grown on maize kernels. Sequence analysis showed that GBP1 encodes a putative 368-amino-acid protein with similarity to DRG and Obg subclasses of G-proteins that are involved in development and stress responses. A GBP1 knockout mutant (Deltagbp1) exhibited normal growth, but increased FB(1) production (> 58%) compared with the wild-type when grown on corn kernels. Complementation of Deltagbp1 with the wild-type GBP1 gene restored FB(1) production levels to that of the wild-type. Our data indicate that GBP1 is negatively associated with FB(1) biosynthesis but not with conidiation in F. verticillioides. The deletion of GBP1 led to up-regulation of key FB(1) biosynthetic genes, FUM1 and FUM8, suggesting that the increased FB(1) production in Deltagbp1 is due to over-expression of FUM genes.

FSR1 is essential for virulence and female fertility in Fusarium verticillioides and F. graminearum

Fusarium verticillioides (teleomorph Gibberella moniliformis) and F. graminearum (teleomorph G. zeae) are well known to cause devastating diseases on cereal crops. Despite their importance, our understanding of the molecular mechanisms involved in these host-pathogen interactions is limited. The FSR1 locus in F. verticillioides was identified by screening REMI mutants for loss of virulence in maize stalk rot inoculation studies. FSR1 encodes an 823-codon open reading frame interrupted by two introns. The Fsr1 protein shares 60% sequence identity with the Sordaria macrospora Pro11, a multimodular protein with four putative protein-protein binding domains (caveolin-binding domain, coiled-coil structure, calmodulin-binding motif, and seven-WD40 repeats), which plays a regulatory role in cell differentiation and ascocarp development. Our data demonstrate that FSR1 is essential for female fertility and virulence in F. verticillioides. Significantly, targeted disruption of the FSR1 ortholog in F. graminearum (FgFSR1) reduced virulence on barley and deterred perithecia formation. Cross-complementation experiments demonstrated that the gene function is conserved in the two Fusarium species. FSR1 is expressed constitutively, and we hypothesize that Fsr1 regulates virulence by acting as a scaffold for a signal transduction pathway. A survey of available genome databases indicates Fsr1 homologs are present in a number of filamentous fungi and animal systems but not in budding yeast or plants. A maximum likelihood analysis of this gene family reveals well-supported monophyletic clades associated with fungi and animals.

Development of a Fusarium graminearum Affymetrix GeneChip for profiling fungal gene expression in vitro and in planta

Recently the genome sequences of several filamentous fungi have become available, providing the opportunity for large-scale functional analysis including genome-wide expression analysis. We report the design and validation of the first Affymetrix GeneChip microarray based on the entire genome of a filamentous fungus, the ascomycetous plant pathogen Fusarium graminearum. To maximize the likelihood of representing all putative genes (approximately 14,000) on the array, two distinct sets of automatically predicted gene calls were used and integrated into the online F. graminearum Genome DataBase. From these gene sets, a subset of calls was manually annotated and a non-redundant extract of all calls together with additional EST sequences and controls were submitted for GeneChip design. Experiments were conducted to test the performance of the F. graminearum GeneChip. Hybridization experiments using genomic DNA demonstrated the usefulness of the array for experimentation with F. graminearum and at least four additional pathogenic Fusarium species. Differential transcript accumulation was detected using the F. graminearum GeneChip with treatments derived from the fungus grown in culture under three nutritional regimes and in comparison with fungal growth in infected barley. The ability to detect fungal genes in planta is surprisingly sensitive even without efforts to enrich for fungal transcripts. The Plant Expression Database (PLEXdb, http://www.plexdb.org) will be used as a public repository for raw and normalized expression data from the F. graminearum GeneChip. The F. graminearum GeneChip will help to accelerate exploration of the pathogen-host pathways that may involve interactions between pathogenicity genes in the fungus and disease response in the plant.

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.

Fck1, a C-type cyclin-dependent kinase, interacts with Fcc1 to regulate development and secondary metabolism in Fusarium verticillioides

In Fusarium verticillioides, the C-type cyclin Fcc1 is a global regulator of gene expression. In Saccharomyces cerevisiae and other organisms, C-type cyclins regulate the activity of specific cyclin-dependent kinases through physical association. We identified FCK1, a gene encoding a cyclin-dependent kinase in F. verticillioides. The Fck1 protein is predicted to contain a cyclin-binding motif and a serine-threonine protein kinase domain homologous to previously described cyclin-dependent kinases. Disruption of FCK1 resulted in pleiotropic morphological defects including reduced growth, conidiation, fumonisin B(1) (FB(1)) production, and enhanced pigmentation. Two-hybrid analysis indicated a strong physical interaction between Fcc1 and Fck1. This study presents the first description of the interaction between a C-type cyclin and a cyclin-dependent kinase in a filamentous fungus and provides new insight regarding a molecular mechanism that regulates aspects of maize kernel colonization by F. verticillioides.

The dawn of fungal pathogen genomics

Recent advances in sequencing technologies have led to a remarkable increase in the number of sequenced fungal genomes. Several important plant pathogenic fungi are among those that have been sequenced or are being sequenced. Additional fungal pathogens are likely to be sequenced in the near future. Analysis of the available genomes has provided useful information about genes that may be important for plant infection and colonization. Genome features, such as repetitive sequences, telomeres, conserved syntenic blocks, and expansion of pathogenicity-related genes, are discussed in detail with Magnaporthe oryzae (M. grisea) and Fusarium graminearum as examples. Functional and comparative genomic studies in plant pathogenic fungi, although still in the early stages and limited to a few pathogens, have enormous potential to improve our understanding of the molecular mechanisms involved in host-pathogen interactions. Development of advanced genomics tools and infrastructure is critical for efficient utilization of the vast wealth of available genome sequence information and will form a solid foundation for systems biology studies of plant pathogenic fungi.

Cross-species microarray hybridization to identify developmentally regulated genes in the filamentous fungus Sordaria macrospora

The filamentous fungus Sordaria macrospora forms complex three-dimensional fruiting bodies that protect the developing ascospores and ensure their proper discharge. Several regulatory genes essential for fruiting body development were previously isolated by complementation of the sterile mutants pro1, pro11 and pro22. To establish the genetic relationships between these genes and to identify downstream targets, we have conducted cross-species microarray hybridizations using cDNA arrays derived from the closely related fungus Neurospora crassa and RNA probes prepared from wild-type S. macrospora and the three developmental mutants. Of the 1,420 genes which gave a signal with the probes from all the strains used, 172 (12%) were regulated differently in at least one of the three mutants compared to the wild type, and 17 (1.2%) were regulated differently in all three mutant strains. Microarray data were verified by Northern analysis or quantitative real time PCR. Among the genes that are up- or down-regulated in the mutant strains are genes encoding the pheromone precursors, enzymes involved in melanin biosynthesis and a lectin-like protein. Analysis of gene expression in double mutants revealed a complex network of interaction between the pro gene products.

Recent advances in the characterization of ambient pH regulation of gene expression in filamentous fungi and yeasts

All microorganisms must adapt to the pH of their environment. One aspect of this adaptation, particularly important for organisms that grow over a wide pH range, is the ability to express appropriately genes whose roles ultimately involve functions at the cell surface or in the environment. Genes encoding permeases, secreted enzymes, enzymes involved in synthesis of exported metabolites such as toxins and antibiotics, and probably enzymes modifying secreted proteins posttranslationally all fall into this category. Here we discuss the most recent findings on the transcriptional regulatory system in fungi that enables such genes to be expressed only when the ambient pH is conducive to their ultimate functions. The intriguing issue of how pH is sensed and how the resulting signal is transmitted to the transcription factor involves at least one late endosome component. Proper functioning of the regulatory system responding to ambient pH is essential for fungal pathogenicity of both animals and plants.