Genomic analysis ofFusarium verticillioides

The autophagy-related proteins FvAtg4 and FvAtg8 are involved in virulence and fumonisin biosynthesis in Fusarium verticillioides

Autophagy is the main intracellular degradation system by which cytoplasmic materials are transported to and degraded in the vacuole/lysosome of eukaryotic cells, and it also controls cellular differentiation and virulence in a variety of filamentous fungi. However, the contribution of the autophagic pathway to fungal development and pathogenicity in the important maize pathogen and mycotoxigenic fungus Fusarium verticillioides is still unknown. In this study, we characterized two autophagy-related proteins, FvAtg4 and FvAtg8. The F. verticillioides deletion mutants ΔFvAtg4 and ΔFvAtg8 were impaired in autophagosome formation, aerial hyphal formation, sexual growth, lipid turnover, pigmentation and fungal virulence. Interestingly, ΔFvAtg4 and ΔFvAtg8 were defective in fumonisin B1 (FB1) synthesis, which may have resulted from decreased intracellular levels of alanine in the mutants. Our results indicate that FvAtg4 and FvAtg8 contribute to F. verticillioides pathogenicity by regulating the autophagic pathway to control lipid turnover, fumonisin biosynthesis, and pigmentation during its infectious cycle.

Carbon sources to enhance the biosynthesis of useful secondary metabolites in Fusarium verticillioides submerged cultures

Fusarium verticillioides is a prolific producer of useful secondary metabolites such as naphthoquinone pigments, monoterpenes, and sesquiterpenes, as well as the harmful mycotoxins fumonisins. A strategy to increase their production includes creating a proper nutritional environment that enables the fungus to produce the compounds of interest. The aim of the present work was to study the effect of different carbon sources (glucose, fructose, xylose, sucrose, and lactose) on secondary metabolites biosynthesis in F. verticillioides submerged cultures. The production of volatile terpenes was evaluated through gas chromatography coupled to mass spectrometry. The quantification and identification of pigments was conducted using a UV/VIS spectrophotometer and NMR spectrometer, respectively. The quantification of fumonisin B₁ and fumonisin B₂ was performed by high-performance liquid chromatography. Our results showed that the biosynthesis of naphthoquinone pigments, monoterpenes, and sesquiterpenes was highest in cultures with fructose (13.00 ± 0.71 mmol/g), lactose [564.52 × 10^-11 ± 11.50 × 10^-11 μg/g dry weight (DW)], and xylose (54.41 × 10^-11 ± 1.55 × 10^-11 μg/g DW), respectively, with fumonisin being absent or present in trace amounts in the presence of these carbon sources. The highest biosynthesis of fumonisins occurred in sucrose-containing medium (fumonisin B₁: 7.85 × 10³ ± 0.25 × 10³ μg/g DW and fumonisin B₂: 0.38 × 10³ ± 0.03 × 10³ μg/g DW). These results are encouraging since we were able to enhance the production of useful fungal metabolites without co-production with harmful mycotoxins by controlling the carbon source provided in the culture medium.

Potato dry rot disease: current status, pathogenomics and management

Potato dry rot disease caused by Fusarium species is a major threat to global potato production. The soil and seed-borne diseases influence the crop stand by inhibiting the development of potato sprouts and cause severe rots in seed tubers, table and processing purpose potatoes in cold stores. The symptoms of the dry rot include sunken and wrinkled brown to black tissue patches on tubers having less dry matter and shriveled flesh. Fungal infection accompanied by toxin development in the rotten tubers raises more concern for consumer health. The widespread dry rot causing fungal species (Fusarium graminearum) is reported to have a hemibiotrophic lifestyle. A cascade of enzymes, toxins and small secreted proteins are involved in the pathogenesis of these hemibiotrophs. With the availability of the genome sequence of the most devastating species Fusarium sambucinum, it is important to identify the potential pathogenicity factors and small secreted proteins that will help in designing management strategies. Limited resistant cultivars and the emergence of fungicide-resistant strains have made it more threatening for potato cultivation and trade. Several novel fungicide molecules (Azoxystrobin, chlorothalonil and fludioxonil), are found very effective as tuber treatment chemicals. Besides, many beneficial bioagents and safer chemicals have shown antibiosis and mycoparasitism against this pathogen. Germplasm screening for dry rot resistance is important to assist the resistance breeding program for the development of resistant cultivars. This review aims to draw attention to the symptomatology, infection process, pathogenomics, the role of toxins and management approaches for potato dry rot disease, which is very much critical in designing better management strategies.

FvSet2 regulates fungal growth, pathogenicity, and secondary metabolism in Fusarium verticillioides

Histone H3 lysine 36 methylation (H3K36me) is generally associated with activation of gene expression in most eukaryotic cells. However, the function of H3K36me in filamentous fungi is largely unknown. Set2 is the sole lysine histone methyltransferase (KHMTase) enzyme responsible for the methylation of H3K36 in Saccharomyces cerevisiae. In the current study, we identified a single ortholog of S. cerevisiae Set2 in Fusarium verticillioides. We report that FvSet2 is responsible for the trimethylation of H3K36 (H3K36me3). The FvSET2 deletion mutant (ΔFvSet2) showed significant defects in vegetative growth, FB₁ biosynthesis, pigmentation, and fungal virulence. Furthermore, trimethylation of H3K36 was found to be important for active transcription of genes involved in FB₁ and bikaverin biosyntheses. These data indicate that FvSet2 plays an important role in the regulation of secondary metabolism, vegetative growth and fungal virulence in F. verticillioides.

Candidate gene based association mapping in Fusarium culmorum for field quantitative pathogenicity and mycotoxin production in wheat

Background

Quantitative traits are common in nature, but quantitative pathogenicity has received only little attention in phytopathology. In this study, we used 100 Fusarium culmorum isolates collected from natural field environments to assess their variation for two quantitative traits, aggressiveness and deoxynivalenol (DON) production on wheat plants grown in four different field environments (location-year combinations). Seventeen Fusarium graminearum pathogenicity candidate genes were assessed for their effect on the aggressiveness and DON production of F. culmorum under field conditions.

Results

For both traits, genotypic variance among isolates was high and significant while the isolate-by-environment interaction was also significant, amounting to approximately half of the genotypic variance. Among the studied candidate genes, the mitogen-activated protein kinase (MAPK) HOG1 was found to be significantly associated with aggressiveness and deoxynivalenol (DON) production, explaining 10.29 and 6.05% of the genotypic variance, respectively.

Conclusions

To the best of our knowledge, this is the first report of a protein kinase regulator explaining differences in field aggressiveness and mycotoxin production among individuals from natural populations of a plant pathogen.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-017-0511-9) contains supplementary material, which is available to authorized users.

Transcriptional changes in developing maize kernels in response to fumonisin-producing and nonproducing strains of Fusarium verticillioides

Fusarium verticillioides infects maize producing ear rot, yield loss and the accumulation of fumonisins. In the present study, a transcriptomic approach was employed to investigate the molecular aspects of the interaction of susceptible/resistant maize genotypes with fumonisin-producing/nonproducing strains of F. verticillioides over a time course of 4 days after inoculation. The fumonisin-nonproducing strain led transcription in susceptible maize kernels, starting from 48h post inoculation, with a peak of differentially expressed genes at 72h after inoculation. Pathogen attack altered the mRNA levels of approximately 1.0% of the total number of maize genes assayed, with 15% encoding proteins having potential functions in signal transduction mechanisms, and 9% in the category of transcription factors. These findings indicate that signalling and regulation pathways were prominent in the earlier phases of kernel colonization, inducing the following expression of defense genes. In the resistant maize genotype, the fum1 mutant of F. verticillioides, impaired in this polyketide synthase gene (PKS), provoked a delayed and weakened activation of defense and oxidative stress-related genes, compared to the wild-type strain. The inability to infect resistant kernels may be related to the lack of PKS activity and its association with the lipoxygenase pathway. Plant and fungal 9-lipoxygenases had greater expression after fum1 mutant inoculation, suggesting that PKS plays an indirect effect on pathogen colonization by interfering with the lipid mediated cross-talk between host and pathogen.

RNA-Seq analysis reveals new gene models and alternative splicing in the fungal pathogen Fusarium graminearum

Background

The genome of Fusarium graminearum has been sequenced and annotated previously, but correct gene annotation remains a challenge. In addition, posttranscriptional regulations, such as alternative splicing and RNA editing, are poorly understood in F. graminearum. Here we took advantage of RNA-Seq to improve gene annotations and to identify alternative splicing and RNA editing in F. graminearum.

Results

We identified and revised 655 incorrectly predicted gene models, including revisions of intron predictions, intron splice sites and prediction of novel introns. 231 genes were identified with two or more alternative splice variants, mostly due to intron retention. Interestingly, the expression ratios between different transcript isoforms appeared to be developmentally regulated. Surprisingly, no RNA editing was identified in F. graminearum. Moreover, 2459 novel transcriptionally active regions (nTARs) were identified and our analysis indicates that many of these could be missed genes. Finally, we identified the 5′ UTR and/or 3′ UTR sequences of 7666 genes. A number of representative novel gene models and alternatively spliced genes were validated by reverse transcription polymerase chain reaction and sequencing of the generated amplicons.

Conclusions

We have developed novel and efficient strategies to identify alternatively spliced genes and incorrect gene models based on RNA-Seq data. Our study identified hundreds of alternatively spliced genes in F. graminearum and for the first time indicated that alternative splicing is developmentally regulated in filamentous fungi. In addition, hundreds of incorrect predicted gene models were identified and revised and thousands of nTARs were discovered in our study, which will be helpful for the future genomic and transcriptomic studies in F. graminearum.

FUM and BIK gene expression contribute to describe fumonisin and bikaverin synthesis in Fusarium verticillioides

Fusarium verticillioides is a maize pathogen that produces toxic secondary metabolites, including fumonisins and bikaverin. The regulation of biosynthetic gene expression and the production of these metabolites are not fully understood and in this study we investigated the influence of water activity (0.955 and 0.990) on the expression of 5 genes (FUM3-FUM8-FUM13-FUM14 and BIK1) in F. verticillioides strains after 14 and 21days incubation. Fumonisin production and biosynthetic gene expression were greatest at a(w)=0.990, and the same trend was observed for bikaverin production, and BIK1 expression. FUM3 and FUM14 were the most highly expressed genes and were positively correlated with the production of FB(1), FB(2) and FB(3). When FUM14 is more highly expressed than FUM3 the amount of FB(3) quantified is higher with respect to FB(1); this could be explained by the role of FUM3 in the hydroxylation of FB(3) to FB(1).

Lae1 regulates expression of multiple secondary metabolite gene clusters in Fusarium verticillioides

The filamentous fungus Fusarium verticillioides can cause disease of maize and is capable of producing fumonisins, a family of toxic secondary metabolites linked to esophageal cancer and neural tube defects in humans and lung edema in swine and leukoencephalomalacia in equines. The expression of fumonisin biosynthetic genes is influenced by broad-domain transcription factors (global regulators) and Fum21, a pathway-specific transcription factor. LaeA is a global regulator that in Aspergillus nidulans, affects the expression of multiple secondary metabolite gene clusters by modifying heterochromatin structure. Here, we employed gene deletion analysis to assess the effect of loss of a F. verticillioides laeA orthologue, LAE1, on genome-wide gene expression and secondary metabolite production. Loss of Lae1 resulted in reduced expression of gene clusters responsible for synthesis of the secondary metabolites bikaverin, fumonisins, fusaric acid and fusarins as well as two clusters for which the corresponding secondary metabolite is unknown. Analysis of secondary metabolites revealed that, in contrast to a previously described Fusarium fujikuroi lae1 mutant, bikaverin production is reduced. Fumonisin production is unchanged in the F. verticillioides lae1 mutant. Complementation of the F. verticillioides mutant resulted in increased fumonisin production.

Identification of gene clusters associated with fusaric acid, fusarin, and perithecial pigment production in Fusarium verticillioides

The genus Fusarium is of concern to agricultural production and food/feed safety because of its ability to cause crop disease and to produce mycotoxins. Understanding the genetic basis for production of mycotoxins and other secondary metabolites (SMs) has the potential to limit crop disease and mycotoxin contamination. In fungi, SM biosynthetic genes are typically located adjacent to one another in clusters of co-expressed genes. Such clusters typically include a core gene, responsible for synthesis of an initial chemical, and several genes responsible for chemical modifications, transport, and/or regulation. Fusarium verticillioides is one of the most common pathogens of maize and produces a variety of SMs of concern. Here, we employed whole genome expression analysis and utilized existing knowledge of polyketide synthase (PKS) genes, a common cluster core gene, to identify three novel clusters of co-expressed genes in F. verticillioides. Functional analysis of the PKS genes linked the clusters to production of three known Fusarium SMs, a violet pigment in sexual fruiting bodies (perithecia) and the mycotoxins fusarin C and fusaric acid. The results indicate that microarray analysis of RNA derived from culture conditions that induce differential gene expression can be an effective tool for identifying SM biosynthetic gene clusters.

Phylogenomic and functional domain analysis of polyketide synthases in Fusarium

Fusarium species are ubiquitous in nature, cause a range of plant diseases, and produce a variety of chemicals often referred to as secondary metabolites. Although some fungal secondary metabolites affect plant growth or protect plants from other fungi and bacteria, their presence in grain-based food and feed is more often associated with a variety of diseases in plants and in animals. Many of these structurally diverse metabolites are derived from a family of related enzymes called polyketide synthases (PKSs). A search of genomic sequence of Fusarium verticillioides, Fusarium graminearum, Fusarium oxysporum, and Fusarium solani identified a total of 58 PKS genes. To gain insight into how this gene family evolved and to guide future studies, we conducted phylogenomic and functional domain analyses. The resulting geneaology suggested that Fusarium PKSs represent 34 different groups responsible for synthesis of different core metabolites. The analyses indicate that variation in the Fusarium PKS gene family is due to gene duplication and loss events as well as enzyme gain-of-function due to the acquisition of new domains or of loss-of-function due to nucleotide mutations. Transcriptional analysis indicates that the 16 F. verticillioides PKS genes are expressed under a range of conditions, further evidence that they are functional genes that confer the ability to produce secondary metabolites.

Transgenic approaches for pre-harvest control of mycotoxin contamination in crop plants

Mycotoxins are fungal metabolites that can contaminate food and feed crops worldwide and are responsible for toxic effects in animals and humans that consume contaminated commodities. Regulatory guidelines and limits for mycotoxins have been set by the US Food and Drug Administration (FDA) and food safety agencies of other countries for both import and export of affected commodities. Mycotoxin contamination of foods and feeds can also cause serious economic hardships to producers, processors, and the consumer. Therefore, there has been a concerted effort by researchers worldwide to develop strategies for the effective control of mycotoxin contamination of crops, particularly at the pre-harvest stage. Strategies currently being utilised to combat pre-harvest mycotoxin contamination include: (1) use of non-toxigenic biocontrol strains; (2) improved agricultural practices; (3) application of agrochemicals; (4) plant breeding for resistance; and (5) genetic engineering of resistance genes into crop plants. This article highlights research on the genetic engineering of plants for resistance to invasion by mycotoxigenic fungi as well as detoxification of mycotoxins. Emphasis is placed on the most economically relevant fungi and the mycotoxins they produce. These include aflatoxins produced mainly by Aspergillus flavus and A. parasiticus, trichothecenes produced mainly by Fusarium graminearum, and to a lesser extent, fumonisins produced by F. verticillioides. Information is also presented on the use of genomics and proteomics technologies as a means of identifying genes and proteins that can be utilised in transgenic approaches to control the growth of mycotoxigenic fungi and the mycotoxins that they produce in food and feed crops.

Cross-species hybridization with Fusarium verticillioides microarrays reveals new insights into Fusarium fujikuroi nitrogen regulation and the role of AreA and NMR

In filamentous fungi, the GATA-type transcription factor AreA plays a major role in the transcriptional activation of genes needed to utilize poor nitrogen sources. In Fusarium fujikuroi, AreA also controls genes involved in the biosynthesis of gibberellins, a family of diterpenoid plant hormones. To identify more genes responding to nitrogen limitation or sufficiency in an AreA-dependent or -independent manner, we examined changes in gene expression of F. fujikuroi wild-type and DeltaareA strains by use of a Fusarium verticillioides microarray representing approximately 9,300 genes. Analysis of the array data revealed sets of genes significantly down- and upregulated in the areA mutant under both N starvation and N-sufficient conditions. Among the downregulated genes are those involved in nitrogen metabolism, e.g., those encoding glutamine synthetase and nitrogen permeases, but also those involved in secondary metabolism. Besides AreA-dependent genes, we found an even larger set of genes responding to N starvation and N-sufficient conditions in an AreA-independent manner. To study the impact of NMR on AreA activity, we examined the expression of several AreA target genes in the wild type and in areA and nmr deletion and overexpression mutants. We show that NMR interacts with AreA as expected but affects gene expression only in early growth stages. This is the first report on genome-wide expression studies examining the influence of AreA on nitrogen-responsive gene expression in a genome-wide manner in filamentous fungi.