Microbial toxins in plant-pathogen interactions: Biosynthesis, resistance mechanisms, and significance

MeJA inhibits fungal growth and DON toxin production by interfering with the cAMP-PKA signaling pathway in the wheat scab fungus Fusarium graminearum

Deoxynivalenol (DON), a mycotoxin primarily produced by Fusarium species, is commonly found in cereal grains and poses risks to human and animal health, as well as global grain trade. This study demonstrates that methyl jasmonate (MeJA), a natural plant hormone, inhibits the growth and conidiation of Fusarium graminearum. Importantly, MeJA significantly reduces DON production by suppressing TRI gene expression and toxisome formation. To explore the molecular mechanism, we identified MeJA-tolerant mutants, including a transcription factor MRT1 and cAMP-PKA pathway-related genes (FgGPA1 and FgSNT1). MeJA treatment reduced PKA activity and intracellular cAMP levels in F. graminearum, suggesting it targets the cAMP-PKA pathway. Notably, the MeJA-resistant mutant FgGPA1R178H enhanced fungal growth, DON production, and cAMP levels in the presence of MeJA. Exogenous cAMP alleviated MeJA's inhibitory effects on DON production, further supporting this pathway's involvement. Interestingly, MeJA had no effect on all three MAP kinase pathways (Mgv1, Gpmk1, and FgHog1). Truncated and phospho-mimicking mutations in Mrt1 or FgSnt1 conferred MeJA resistance, suggesting they may act downstream of the cAMP-PKA pathway. In conclusion, MeJA presents a promising approach to control F. graminearum growth and DON production.IMPORTANCEDeoxynivalenol (DON) poses significant risks to both human and animal health and severely disrupts the global grain trade due to its prevalence as a common contaminant in wheat grains. With rising public concern over food safety, finding effective and sustainable methods to reduce DON contamination becomes increasingly urgent. In our study, we found that methyl jasmonate (MeJA), a natural plant hormone, can effectively inhibit the vegetative growth of F. graminearum and significantly reduce its DON toxin production. To explore the underlying molecular mechanism, we identified the mutations in MeJA-tolerant mutants and revealed that MeJA effectively exerts its antifungal activities by inhibiting the cAMP-PKA signaling pathway in F. graminearum. Our work provides a promising natural solution to reduce DON toxin contamination in cereal grains, enhancing food safety while decreasing the reliance on chemical fungicides and their associated environmental impact.

Targeting of Specialized Metabolites Biosynthetic Enzymes to Membranes and Vesicles by Posttranslational Palmitoylation: A Mechanism of Non-Conventional Traffic and Secretion of Fungal Metabolites

In nature, the formation of specialized (secondary) metabolites is associated with the late stages of fungal development. Enzymes involved in the biosynthesis of secondary metabolites in fungi are located in distinct subcellular compartments including the cytosol, peroxisomes, endosomes, endoplasmic reticulum, different types of vesicles, the plasma membrane and the cell wall space. The enzymes traffic between these subcellular compartments and the secretion through the plasma membrane are still unclear in the biosynthetic processes of most of these metabolites. Recent reports indicate that some of these enzymes initially located in the cytosol are later modified by posttranslational acylation and these modifications may target them to membrane vesicle systems. Many posttranslational modifications play key roles in the enzymatic function of different proteins in the cell. These modifications are very important in the modulation of regulatory proteins, in targeting of proteins, intracellular traffic and metabolites secretion. Particularly interesting are the protein modifications by palmitoylation, prenylation and miristoylation. Palmitoylation is a thiol group-acylation (S-acylation) of proteins by palmitic acid (C16) that is attached to the SH group of a conserved cysteine in proteins. Palmitoylation serves to target acylated proteins to the cytosolic surface of cell membranes, e.g., to the smooth endoplasmic reticulum, whereas the so-called toxisomes are formed in trichothecene biosynthesis. Palmitoylation of the initial enzymes involved in the biosynthesis of melanin serves to target them to endosomes and later to the conidia, whereas other non-palmitoylated laccases are secreted directly by the conventional secretory pathway to the cell wall space where they perform the last step(s) of melanin biosynthesis. Six other enzymes involved in the biosynthesis of endocrosin, gliotoxin and fumitremorgin believed to be cytosolic are also targeted to vesicles, although it is unclear if they are palmitoylated. Bioinformatic analysis suggests that palmitoylation may be frequent in the modification and targeting of polyketide synthetases and non-ribosomal peptide synthetases. The endosomes may integrate other small vesicles with different cargo proteins, forming multivesicular bodies that finally fuse with the plasma membrane during secretion. Another important effect of palmitoylation is that it regulates calcium metabolism by posttranslational modification of the phosphatase calcineurin. Mutants defective in the Akr1 palmitoyl transferase in several fungi are affected in calcium transport and homeostasis, thus impacting on the biosynthesis of calcium-regulated specialized metabolites. The palmitoylation of secondary metabolites biosynthetic enzymes and their temporal distribution respond to the conidiation signaling mechanism. In summary, this posttranslational modification drives the spatial traffic of the biosynthetic enzymes between the subcellular organelles and the plasma membrane. This article reviews the molecular mechanism of palmitoylation and the known fungal palmitoyl transferases. This novel information opens new ways to improve the biosynthesis of the bioactive metabolites and to increase its secretion in fungi.

The unsung roles of microbial secondary metabolite effectors in the plant disease cacophony

Plants counter disease with an array of responses to styme pathogen ingress. In contrast to this cacophony, plant pathogens orchestrate a finely tuned repertoire of virulence mechanisms in their attempt to cause disease. One such example is the production of secondary metabolite effectors (SMEs). Despite many attempts to functionally categorize SMEs, their many roles in plant disease have proven they march to the beat of their producer's drum. Some lesser studied features of SMEs in plant disease include self-resistance (SR) and manipulation of the microbiome to enhance pathogen virulence. SR can be accomplished in three general compositions, with the first being the transport of the SME to a benign location; the second being modification of the SME so it cannot harm the producer; and the third being metabolic regulation of the SME or the producer homolog of the SME target. SMEs may also play an interlude prior to disease by shaping the plant microbial community, allowing producers to better establish themselves. Taken together, SMEs are integral players in the phytopathology canon.

Identification of Candidate Genes Associated with Trichothecene Biosynthesis in Fusarium graminearum Species Complex Combined with Transcriptomic and Proteomic Analysis

The Fusarium graminearum species complex is the main causal agent of wheat head blight worldwide. Trichothecenes produced by the pathogen in infected grains have important food safety implications. Previously reported studies on trichothecene production have all focused on the conditions conducive to mycotoxin production, while the molecular mechanisms of trichothecene biosynthesis in Fusarium strains under normal or non-inducing conditions are still unclear. Here, a global analysis of the fungal gene expression of three strains using the Affymetrix Fusarium GeneChip under non-inducing conditions is reported. Differentially expressed genes were identified among strains with different trichothecene-production ability, and some novel genes associated with trichothecene biosynthesis were found by bioinformatics analysis. To verify the transcriptome results, proteomic analyses of the three strains were conducted under the same culture conditions. In total, 69 unique fungal proteins were identified in 77 protein spots. Combined with transcriptome and proteome analysis, 27 novel genes were predicted to be associated with trichothecene mycotoxin production. A protein, encoded by FGSG_01403, was found to be associated with trichothecene production via proteome analysis. Gene knock-out mutations of FGSG_01403 resulted in mutants with increased production of trichothecenes. Future functional analysis of the candidate genes identified in this study may reveal new insights into the negative regulation of trichothecene production in the Fusarium graminearum species complex.

Comparative genomics reveals low levels of inter- and intraspecies diversity in the causal agents of dwarf and common bunt of wheat and hint at conspecificity of Tilletia caries and T. laevis

Tilletia caries and T. laevis, which are the causal agents of common bunt, as well as T. controversa, which causes dwarf bunt of wheat, threaten especially organic wheat farming. The three closely related fungal species differ in their teliospore morphology and partially in their physiology and infection biology. The gene content as well as intraspecies variation in these species and the genetic basis of their separation is unknown. We sequenced the genome of four T. caries, five T. controversa, and two T. laevis and extended this dataset with five publicly available ones. The genomes of the three species displayed microsynteny with up to 94.3% pairwise aligned regions excluding repetitive regions. The majority of functionally characterized genes involved in pathogenicity, life cycle, and infection of corn smut, Ustilago maydis, were found to be absent or poorly conserved in the draft genomes and the biosynthetic pathway for trimethylamine in Tilletia spp. could be different from bacteria. Overall, 75% of the identified protein-coding genes comprising 84% of the total predicted carbohydrate utilizing enzymes, 72.5% putatively secreted proteins, and 47.4% of effector-like proteins were conserved and shared across all 16 isolates. We predicted nine highly identical secondary metabolite biosynthesis gene clusters comprising in total 62 genes in all species and none were species-specific. Less than 0.1% of the protein-coding genes were species-specific and their function remained mostly unknown. Tilletia controversa had the highest intraspecies genetic variation, followed by T. caries and the lowest in T. laevis. Although the genomes of the three species are very similar, employing 241 single copy genes T. controversa was phylogenetically distinct from T. caries and T. laevis, however these two could not be resolved as individual monophyletic groups. This was in line with the genome-wide number of single nucleotide polymorphisms and small insertions and deletions. Despite the conspicuously different teliospore ornamentation of T. caries and T. laevis, a high degree of genomic identity and scarcity of species-specific genes indicate that the two species could be conspecific.

The plasma membrane H+ -ATPase FgPMA1 regulates the development, pathogenicity, and phenamacril sensitivity of Fusarium graminearum by interacting with FgMyo-5 and FgBmh2

Fusarium graminearum, as the causal agent of Fusarium head blight (FHB), not only causes yield loss, but also contaminates the quality of wheat by producing mycotoxins, such as deoxynivalenol (DON). The plasma membrane H⁺ -ATPases play important roles in many growth stages in plants and yeasts, but their functions and regulation in phytopathogenic fungi remain largely unknown. Here we characterized two plasma membrane H⁺ -ATPases: FgPMA1 and FgPMA2 in F. graminearum. The FgPMA1 deletion mutant (∆FgPMA1), but not FgPMA2 deletion mutant (∆FgPMA2), was impaired in vegetative growth, pathogenicity, and sexual and asexual development. FgPMA1 was localized to the plasma membrane, and ∆FgPMA1 displayed reduced integrity of plasma membrane. ∆FgPMA1 not only impaired the formation of the toxisome, which is a compartment where DON is produced, but also suppressed the expression level of DON biosynthetic enzymes, decreased DON production, and decreased the amount of mycelial invasion, leading to impaired pathogenicity by exclusively developing disease on inoculation sites of wheat ears and coleoptiles. ∆FgPMA1 exhibited decreased sensitivity to some osmotic stresses, a cell wall-damaging agent (Congo red), a cell membrane-damaging agent (sodium dodecyl sulphate), and heat shock stress. FgMyo-5 is the target of phenamacril used for controlling FHB. We found FgPMA1 interacted with FgMyo-5, and ∆FgPMA1 showed an increased expression level of FgMyo-5, resulting in increased sensitivity to phenamacril, but not to other fungicides. Furthermore, co-immunoprecipitation confirmed that FgPMA1, FgMyo-5, and FgBmh2 (a 14-3-3 protein) form a complex to regulate the sensitivity to phenamacril and biological functions. Collectively, this study identified a novel regulating mechanism of FgPMA1 in pathogenicity and phenamacril sensitivity of F. graminearum.

Effective methods for isolation and purification of extracellular vesicles from plants

Plant extracellular vesicles (EVs) play critical roles in the cross-kingdom trafficking of molecules from hosts to interacting microbes, most notably in plant defense responses. However, the isolation of pure, intact EVs from plants remains challenging. A variety of methods have been utilized to isolate plant EVs from apoplastic washing fluid (AWF). Here, we compare published plant EV isolation methods, and provide our recommended method for the isolation and purification of plant EVs. This method includes a detailed protocol for clean AWF collection from Arabidopsis thaliana leaves, followed by EV isolation via differential centrifugation. To further separate and purify specific subclasses of EVs from heterogeneous vesicle populations, density gradient ultracentrifugation and immunoaffinity capture are then utilized. We found that immunoaffinity capture is the most precise method for specific EV subclass isolation when suitable specific EV biomarkers and their corresponding antibodies are available. Overall, this study provides a guide for the selection and optimization of EV isolation methods for desired downstream applications.

Message in a Bubble: Shuttling Small RNAs and Proteins Between Cells and Interacting Organisms Using Extracellular Vesicles

Communication between plant cells and interacting microorganisms requires the secretion and uptake of functional molecules to and from the extracellular environment and is essential for the survival of both plants and their pathogens. Extracellular vesicles (EVs) are lipid bilayer-enclosed spheres that deliver RNA, protein, and metabolite cargos from donor to recipient cells and participate in many cellular processes. Emerging evidencehas shown that both plant and microbial EVs play important roles in cross-kingdom molecular exchange between hosts and interacting microbes to modulate host immunity and pathogen virulence. Recent studies revealed that plant EVs function as a defense system by encasing and delivering small RNAs (sRNAs) into pathogens, thereby mediating cross-species and cross-kingdom RNA interference to silence virulence-related genes. This review focuses on the latest advances in our understanding of plant and microbial EVs and their roles in transporting regulatory molecules, especially sRNAs, between hosts and pathogens. EV biogenesis and secretion are also discussed, as EV function relies on these important processes.

Metabolomics as an Emerging Tool for the Study of Plant-Pathogen Interactions

Plants defend themselves from most microbial attacks via mechanisms including cell wall fortification, production of antimicrobial compounds, and generation of reactive oxygen species. Successful pathogens overcome these host defenses, as well as obtain nutrients from the host. Perturbations of plant metabolism play a central role in determining the outcome of attempted infections. Metabolomic analyses, for example between healthy, newly infected and diseased or resistant plants, have the potential to reveal perturbations to signaling or output pathways with key roles in determining the outcome of a plant-microbe interaction. However, application of this -omic and its tools in plant pathology studies is lagging relative to genomic and transcriptomic methods. Thus, it is imperative to bring the power of metabolomics to bear on the study of plant resistance/susceptibility. This review discusses metabolomics studies that link changes in primary or specialized metabolism to the defense responses of plants against bacterial, fungal, nematode, and viral pathogens. Also examined are cases where metabolomics unveils virulence mechanisms used by pathogens. Finally, how integrating metabolomics with other -omics can advance plant pathology research is discussed.

Impact of Five Succinate Dehydrogenase Inhibitors on DON Biosynthesis of Fusarium asiaticum, Causing Fusarium Head Blight in Wheat

Deoxynivalenol (DON) is a class of mycotoxin produced in cereal crops infected with Fusarium graminearum species complex (FGSC). In China, FGSC mainly includes Fusarium asiaticum and F. graminearum. DON belongs to the trichothecenes and poses a serious threat to the safety and health of humans and animals. Succinate dehydrogenase inhibitors (SDHIs) are a class of fungicides that act on succinate dehydrogenase and inhibit the respiration of pathogenic fungi. In this study, the fungicidal activities of five SDHIs, including fluopyram, flutolanil, boscalid, benzovindiflupyr, and fluxapyroxad, against FGSC were determined based on mycelial growth and spore germination inhibition methods. The five SDHIs exhibited better inhibitory activities in spore germination than mycelial growth. Fluopyram exhibited a higher inhibitory effect in mycelial growth and spore germination in comparison to the other four SDHIs. In addition, the biological characteristics of F. asiaticum as affected by the five SDHIs were determined. We found that these five SDHIs decreased DON, pyruvic acid and acetyl-CoA production, isocitrate dehydrogenase mitochondrial (ICDHm) and SDH activities, and NADH and ATP content of F. asiaticum but increased the citric acid content. In addition, TRI5 gene expression was inhibited, and the formation of toxisomes was disrupted by the five SDHIs, further confirming that SDHIs can decrease DON biosynthesis of F. asiaticum. Thus, we concluded that SDHIs may decrease DON biosynthesis of F. asiaticum by inhibiting glycolysis and the tricarboxylic acid (TCA) cycle. Overall, the findings from the study will provide important references for managing Fusarium head blight (FHB) caused by FGSC and reducing DON contamination in F. asiaticum-infected wheat grains.

Whole-Genome Resequencing and Pan-Transcriptome Reconstruction Highlight the Impact of Genomic Structural Variation on Secondary Metabolite Gene Clusters in the Grapevine Esca Pathogen Phaeoacremonium minimum

The Ascomycete fungus Phaeoacremonium minimum is one of the primary causal agents of Esca, a widespread and damaging grapevine trunk disease. Variation in virulence among Pm. minimum isolates has been reported, but the underlying genetic basis of the phenotypic variability remains unknown. The goal of this study was to characterize intraspecific genetic diversity and explore its potential impact on virulence functions associated with secondary metabolism, cellular transport, and cell wall decomposition. We generated a chromosome-scale genome assembly, using single molecule real-time sequencing, and resequenced the genomes and transcriptomes of multiple isolates to identify sequence and structural polymorphisms. Numerous insertion and deletion events were found for a total of about 1 Mbp in each isolate. Structural variation in this extremely gene dense genome frequently caused presence/absence polymorphisms of multiple adjacent genes, mostly belonging to biosynthetic clusters associated with secondary metabolism. Because of the observed intraspecific diversity in gene content due to structural variation we concluded that a transcriptome reference developed from a single isolate is insufficient to represent the virulence factor repertoire of the species. We therefore compiled a pan-transcriptome reference of Pm. minimum comprising a non-redundant set of 15,245 protein-coding sequences. Using naturally infected field samples expressing Esca symptoms, we demonstrated that mapping of meta-transcriptomics data on a multi-species reference that included the Pm. minimum pan-transcriptome allows the profiling of an expanded set of virulence factors, including variable genes associated with secondary metabolism and cellular transport.

The mitochondrial membrane protein FgLetm1 regulates mitochondrial integrity, production of endogenous reactive oxygen species and mycotoxin biosynthesis in Fusarium graminearum

Deoxynivalenol (DON) is a mycotoxin produced in cereal crops infected with Fusarium graminearum. DON poses a serious threat to human and animal health, and is a critical virulence factor. Various environmental factors, including reactive oxygen species (ROS), have been shown to interfere with DON biosynthesis in this pathogen. The regulatory mechanisms of how ROS trigger DON production have been investigated extensively in F. graminearum. However, the role of the endogenous ROS-generating system in DON biosynthesis is largely unknown. In this study, we genetically analysed the function of leucine zipper-EF-hand-containing transmembrane 1 (LETM1) superfamily proteins and evaluated the role of the mitochondrial-produced ROS in DON biosynthesis. Our results show that there are two Letm1 orthologues, FgLetm1 and FgLetm2, in F. graminearum. FgLetm1 is localized to the mitochondria and is essential for mitochondrial integrity, whereas FgLetm2 plays a minor role in the maintenance of mitochondrial integrity. The ΔFgLetm1 mutant demonstrated a vegetative growth defect, abnormal conidia and increased sensitivity to various stress agents. More importantly, the ΔFgLetm1 mutant showed significantly reduced levels of endogenous ROS, decreased DON biosynthesis and attenuated virulence in planta. To our knowledge, this is the first report showing that mitochondrial integrity and endogenous ROS production by mitochondria are important for DON production and virulence in Fusarium species.

Bioactive Secondary Metabolites Produced by the Fungal Endophytes of Conifers

This is a review of bioactive secondary metabolites isolated from conifer-associated endophytic fungi from 1990-2014. This includes compounds with antimicrobial, anti-inflammatory, anti-proliferative and cytotoxic activity towards human cancer cell lines, and activity against either plant pathogens or plant insect pests. Compounds that were originally reported without associated activity were included if other studies ascribed activity to these compounds. Compounds were not included if they were exclusively phytotoxic or if they were isolated from active extracts but were not determined to be the active component of that extract.

Resistance to gray leaf spot of maize: genetic architecture and mechanisms elucidated through nested association mapping and near-isogenic line analysis

Gray leaf spot (GLS), caused by Cercospora zeae-maydis and Cercospora zeina, is one of the most important diseases of maize worldwide. The pathogen has a necrotrophic lifestyle and no major genes are known for GLS. Quantitative resistance, although poorly understood, is important for GLS management. We used genetic mapping to refine understanding of the genetic architecture of GLS resistance and to develop hypotheses regarding the mechanisms underlying quantitative disease resistance (QDR) loci. Nested association mapping (NAM) was used to identify 16 quantitative trait loci (QTL) for QDR to GLS, including seven novel QTL, each of which demonstrated allelic series with significant effects above and below the magnitude of the B73 reference allele. Alleles at three QTL, qGLS1.04, qGLS2.09, and qGLS4.05, conferred disease reductions of greater than 10%. Interactions between loci were detected for three pairs of loci, including an interaction between iqGLS4.05 and qGLS7.03. Near-isogenic lines (NILs) were developed to confirm and fine-map three of the 16 QTL, and to develop hypotheses regarding mechanisms of resistance. qGLS1.04 was fine-mapped from an interval of 27.0 Mb to two intervals of 6.5 Mb and 5.2 Mb, consistent with the hypothesis that multiple genes underlie highly significant QTL identified by NAM. qGLS2.09, which was also associated with maturity (days to anthesis) and with resistance to southern leaf blight, was narrowed to a 4-Mb interval. The distance between major leaf veins was strongly associated with resistance to GLS at qGLS4.05. NILs for qGLS1.04 were treated with the C. zeae-maydis toxin cercosporin to test the role of host-specific toxin in QDR. Cercosporin exposure increased expression of a putative flavin-monooxygenase (FMO) gene, a candidate detoxification-related gene underlying qGLS1.04. This integrated approach to confirming QTL and characterizing the potential underlying mechanisms advances the understanding of QDR and will facilitate the development of resistant varieties.

Molecular and Genetic Studies ofFusariumTrichothecene Biosynthesis: Pathways, Genes, and Evolution

Trichothecenes are a large family of sesquiterpenoid secondary metabolites of Fusarium species (e.g., F. graminearum) and other molds. They are major mycotoxins that can cause serious problems when consumed via contaminated cereal grains. In the past 20 years, an outline of the trichothecene biosynthetic pathway has been established based on the results of precursor feeding experiments and blocked mutant analyses. Following the isolation of the pathway gene Tri5 encoding the first committed enzyme trichodiene synthase, 10 biosynthesis genes (Tri genes; two regulatory genes, seven pathway genes, and one transporter gene) were functionally identified in the Tri5 gene cluster. At least three pathway genes, Tri101 (separated alone), and Tri1 and Tri16 (located in the Tri1-Tri16 two-gene cluster), were found outside of the Tri5 gene cluster. In this review, we summarize the current understanding of the pathways of biosynthesis, the functions of cloned Tri genes, and the evolution of Tri genes, focusing on Fusarium species.

Examination of Gould's modified S1 (mS1) selective medium and Angle's non-selective medium for describing the diversity of Pseudomonas spp. in soil and root environments

Abstract Studies on the diversity of environmental culturable Pseudomonas populations are dependent on the isolation procedure. This procedure includes the use of selective media which may influence the recovery of strains and thus the diversity described. In this study, we assessed the use of two agar isolation media for describing the diversity of soil- and root-inhabiting Pseudomonas associated with the perennial grass Molinia coerulea. A total of 382 Pseudomonas strains were recovered on either non-selective Angle's medium, or on Gould's modified S1 (mS1) Pseudomonas-selective medium. Their diversity was assessed by restriction analysis of PCR (polymerase chain reaction)-amplified 16S-23S rDNA internal transcript spacer sequences. The comparison of mS1- and Angle-recovered populations showed that the use of mS1 selective medium led to an underestimation of both Pseudomonas counts and diversity, especially in the soil environment.

Pseudomonas syringae self-protection from tabtoxinine-β-lactam by ligase TblF and acetylase Ttr

Plant pathogenic Pseudomonas syringae produce the hydroxy-β-lactam antimetabolite tabtoxinine-β-lactam (TβL) as a time-dependent inactivating glutamine analogue of plant glutamine synthetases. The producing pseudomonads use multiple modes of self-protection, two of which are characterized in this study. The first is the dipeptide ligase TblF which converts tabtoxinine-β-lactam to the TβL-Thr dipeptide known as tabtoxin. The dipeptide is not recognized by glutamine synthetase. This represents a Trojan Horse strategy: the dipeptide is secreted, taken up by dipeptide permeases in neighboring cells, and TβL is released by peptidase action. The second self-protection mode is elaboration by the acetyltransferase Ttr, which acetylates the α-amino group of the proximal inactivator TβL, but not the tabtoxin dipeptide.

Functional categorization of unique expressed sequence tags obtained from the yeast-like growth phase of the elm pathogen Ophiostoma novo-ulmi

Background

The highly aggressive pathogenic fungus Ophiostoma novo-ulmi continues to be a serious threat to the American elm (Ulmus americana) in North America. Extensive studies have been conducted in North America to understand the mechanisms of virulence of this introduced pathogen and its evolving population structure, with a view to identifying potential strategies for the control of Dutch elm disease. As part of a larger study to examine the genomes of economically important Ophiostoma spp. and the genetic basis of virulence, we have constructed an expressed sequence tag (EST) library using total RNA extracted from the yeast-like growth phase of O. novo-ulmi (isolate H327).

Results

A total of 4,386 readable EST sequences were annotated by determining their closest matches to known or theoretical sequences in public databases by BLASTX analysis. Searches matched 2,093 sequences to entries found in Genbank, including 1,761 matches with known proteins and 332 matches with unknown (hypothetical/predicted) proteins. Known proteins included a collection of 880 unique transcripts which were categorized to obtain a functional profile of the transcriptome and to evaluate physiological function. These assignments yielded 20 primary functional categories (FunCat), the largest including Metabolism (FunCat 01, 20.28% of total), Sub-cellular localization (70, 10.23%), Protein synthesis (12, 10.14%), Transcription (11, 8.27%), Biogenesis of cellular components (42, 8.15%), Cellular transport, facilitation and routes (20, 6.08%), Classification unresolved (98, 5.80%), Cell rescue, defence and virulence (32, 5.31%) and the unclassified category, or known sequences of unknown metabolic function (99, 7.5%). A list of specific transcripts of interest was compiled to initiate an evaluation of their impact upon strain virulence in subsequent studies.

Conclusions

This is the first large-scale study of the O. novo-ulmi transcriptome. The expression profile obtained from the yeast-like growth phase of this species will facilitate a multigenic approach to gene expression studies to assess their role in the determination of pathogenicity for this species. The identification and evaluation of gene targets in such studies will be a prerequisite to the development of biological control strategies for this pathogen.

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.

Alignment of genetic and physical maps of Gibberella zeae

We previously published a genetic map of Gibberella zeae (Fusarium graminearum sensu lato) based on a cross between Kansas strain Z-3639 (lineage 7) and Japanese strain R-5470 (lineage 6). In this study, that genetic map was aligned with the third assembly of the genomic sequence of G. zeae strain PH-1 (lineage 7) using seven structural genes and 108 sequenced amplified fragment length polymorphism markers. Several linkage groups were combined based on the alignments, the nine original linkage groups were reduced to six groups, and the total size of the genetic map was reduced from 1,286 to 1,140 centimorgans. Nine supercontigs, comprising 99.2% of the genomic sequence assembly, were anchored to the genetic map. Eight markers (four markers from each parent) were not found in the genome assembly, and four of these markers were closely linked, suggesting that >150 kb of DNA sequence is missing from the PH-1 genome assembly. The alignments of the linkage groups and supercontigs yielded four independent sets, which is consistent with the four chromosomes reported for this fungus. Two proposed heterozygous inversions were confirmed by the alignments; otherwise, the colinearity of the genetic and physical maps was high. Two of four regions with segregation distortion were explained by the two selectable markers employed in making the cross. The average recombination rates for each chromosome were similar to those previously reported for G. zeae. Despite an inferred history of genetic isolation of lineage 6 and lineage 7, the chromosomes of these lineages remain homologous and are capable of recombination along their entire lengths, even within the inversions. This genetic map can now be used in conjunction with the physical sequence to study phenotypes (e.g., fertility and fitness) and genetic features (e.g., centromeres and recombination frequency) that do not have a known molecular signature in the genome.

Genetically engineeredFusariumas a tool to evaluate the effects of environmental factors on initiation of trichothecene biosynthesis

Fusarium graminearum was engineered for expression of enhanced green fluorescent protein gene (egfp) as a reporter regulated in a manner similar to Tri5, a key pathway gene in trichothecene biosynthesis. Using the transgenic fungus, it was found that the reporter gene was induced to express in aerial hyphae developed on trichothecene noninducing medium YG solidified by agar. Unexpectedly, the transcriptional activation of egfp was markedly suppressed by adding NaCl that does not significantly affect fungal growth. As suggested by these findings, wild-type F. graminearum that formed aerial hyphae on YG agar plates produced trichothecenes and the production was effectively suppressed by adding 1% NaCl to the agar. To evaluate the effects of abiotic stress on the expression of trichothecene biosynthesis (Tri) genes, a sensitive plate assay was established using GYEP medium (which very weakly induces trichothecene production) solidified with gellan gum. Using this assay, triazole fungicides were shown to cause transcriptional activation of egfp at sublethal concentrations. Indeed, trichothecene production significantly increased when F. graminearum was grown in rice medium (which moderately induces trichothecene) amended with low doses of tebuconazole. The real-time monitoring system described here may help predict the risks of trichothecene contamination by the fungus under various environmental conditions.

RAS2 regulates growth and pathogenesis in Fusarium graminearum

Fusarium graminearum is a ubiquitous pathogen of cereal crops, including wheat, barley, and maize. Diseases caused by F. graminearum are of particular concern because harvested grains frequently are contaminated with harmful mycotoxins such as deoxynivalenol (DON). In this study, we explored the role of Ras GTPases in pathogenesis. The genome of F. graminearum contains two putative Ras GTPase-encoding genes. The two genes (RAS1 and RAS2) showed different patterns of expression under different conditions of nutrient availability and in various mutant backgrounds. RAS2 was dispensable for survival but, when disrupted, caused a variety of morphological defects, including slower growth on solid media, delayed spore germination, and significant reductions in virulence on wheat heads and maize silks. Intracellular cAMP levels were not affected by deletion of RAS2 and exogenous treatment of the ras2 mutant with cAMP did not affect phenotypic abnormalities, thus indicating that RAS2 plays a minor or no role in cAMP signaling. However, phosphorylation of the mitogen-activated protein (MAP) kinase Gpmk1 and expression of a secreted lipase (FGL1) required for infection were reduced significantly in the ras2 mutant. Based on these observations, we hypothesize that RAS2 regulates growth and virulence in F. graminearum by regulating the Gpmk1 MAP kinase pathway.

Advances in molecular diagnosis of toxigenic Fusarium species: a review

The development of advanced molecular diagnosis for the critical toxigenic Fusarium species is considered in this review. The specific topics discussed are (1) isolation of mating type genes of Gibberella complex, (2) molecular detection of Fusarium-producing fumonisins, (3) molecular detection of Fusarium-producing trichothecenes and enniatins. Particular attention is given to the development of PCR assays for genes involved in the toxin biosynthesis that would permit the early detection of Fusarium species-producing toxins and potentially even reveal which particular toxin may be present within a food or feed product. Most of these data have been obtained within the 'De-Tox Fungi' project supported by the European Commission (QLK1-CT-1998-01380).

Concordant evolution of trichothecene 3-O-acetyltransferase and an rDNA species phylogeny of trichothecene-producing and non-producing fusaria and other ascomycetous fungi

The cereal pathogen Fusarium graminearum species complex (e.g. Fusarium asiaticum, previously referred to as F. graminearum lineage 6) produces the mycotoxin trichothecene in infected grains. The fungus has a gene for self-defence, Tri101, which is responsible for 3-O-acetylation of the trichothecene skeleton in the biosynthetic pathway. Recently, trichothecene non-producers Fusarium oxysporum and Fusarium fujikuroi (teleomorph Gibberella fujikuroi) were shown to have both functional (Tri201) and non-functional (pseudo-Tri101) trichothecene 3-O-acetyltransferase genes in their genome. To gain insight into the evolution of the trichothecene genes in Gibberella species, the authors examined whether or not other (pseudo-)biosynthesis-related genes are found near Tri201. However, sequence analysis of a 12 kb region containing Tri201 did not result in identification of additional trichothecene (pseudo-)genes in F. oxysporum. In a further attempt to find other trichothecene (pseudo-)genes from the non-producer, the authors examined whether or not the non-trichothecene genes flanking the ends of the core trichothecene gene cluster (i.e. the Tri5 cluster) comprise a region of synteny in Gibberella species. However, it was not possible to isolate trichothecene (pseudo-)genes from F. oxysporum (in addition to the previously identified pseudo-Tri101), because synteny was not observed for this region in F. asiaticum and F. oxysporum. In contrast to this unsuccessful identification of additional trichothecene (pseudo-)genes in the non-producer, a functional trichothecene 3-O-acetyltransferase gene could be identified in fusaria other than Gibberella: Fusarium decemcellulare and Fusarium solani; and in an ascomycete from a different fungal genus, Magnaporthe grisea. Together with the recent functional identification of Saccharomyces cerevisiae ScAYT1, these results are suggestive of a different evolutionary origin for the trichothecene 3-O-acetyltransferase gene from other biosynthesis pathway genes. The phylogeny of the 3-O-acetyltransferase was mostly concordant with the rDNA species phylogeny of these ascomycetous fungi.

Plant disease: a threat to global food security

A vast number of plant pathogens from viroids of a few hundred nucleotides to higher plants cause diseases in our crops. Their effects range from mild symptoms to catastrophes in which large areas planted to food crops are destroyed. Catastrophic plant disease exacerbates the current deficit of food supply in which at least 800 million people are inadequately fed. Plant pathogens are difficult to control because their populations are variable in time, space, and genotype. Most insidiously, they evolve, often overcoming the resistance that may have been the hard-won achievement of the plant breeder. In order to combat the losses they cause, it is necessary to define the problem and seek remedies. At the biological level, the requirements are for the speedy and accurate identification of the causal organism, accurate estimates of the severity of disease and its effect on yield, and identification of its virulence mechanisms. Disease may then be minimized by the reduction of the pathogen's inoculum, inhibition of its virulence mechanisms, and promotion of genetic diversity in the crop. Conventional plant breeding for resistance has an important role to play that can now be facilitated by marker-assisted selection. There is also a role for transgenic modification with genes that confer resistance. At the political level, there is a need to acknowledge that plant diseases threaten our food supplies and to devote adequate resources to their control.

Heading for disaster: Fusarium graminearum on cereal crops

SUMMARY The rapid global re-emergence of Fusarium head blight disease of wheat and barley in the last decade along with contamination of grains with mycotoxins attributable to the disease have spurred basic research on the fungal causal agent. As a result, Fusarium graminearum quickly has become one of the most intensively studied fungal plant pathogens. This review briefly summarizes current knowledge on the pathogenicity, population genetics, evolution and genomics of Fusarium graminearum.

TAXONOMY

Based on the sexual state Gibberella zeae (Schwein.) Petch: Superkingdom Eukaryota; Kingdom Fungi; Phylum Ascomycota; Subphylum Pezizomycotina; Class Sordariomycetidae; Subclass Hypocreomycetidae; Order Hypocreales; Family Nectriaceae; Genus Gibberella.

HOST RANGE

The pathogen is capable of causing head blight or 'scab' on wheat (Triticum), barley (Hordeum), rice (Oryza), oats (Avena) and Gibberella stalk and ear rot disease on maize (Zea). The fungus also may infect other plant species without causing disease symptoms. Other host genera cited for Gibberella zeae or F. graminearum sensu lato (see below) are Agropyron, Agrostis, Bromus, Calamagrostis, Cenchrus, Cortaderia, Cucumis, Echinochloa, Glycine, Hierochloe, Lolium, Lycopersicon, Medicago, Phleum, Poa, Schizachyrium, Secale, Setaria, Sorghum, Spartina and Trifolium. Disease symptoms and signs: For wheat, brown, dark purple to black necrotic lesions form on the exterior surface of the florets and glume (Fig. 1). Although these lesion symptoms sometimes are referred to as scab, they are not formally related to the hyperplasia and hypertrophic epidermal growth associated with other scab diseases such as apple scab. Peduncles immediately below the inflorescence may become discoloured brown/purple. With time, tissue of the inflorescence often becomes blighted, appearing bleached and tan, while the grain within atrophies. Awns often become deformed, twisted and curved downward. In barley, infections are not always readily apparent in the field. Infected spikelets may show a browning or water-soaked appearance. Infected barley kernels show a tan to dark brown discolouration that can be similar to that caused by other kernel blighting organisms. During prolonged wet periods, pink to salmon-orange spore masses of the fungus are often seen on infected spikelets, glumes and kernels in both wheat and barley. For maize ear rot, infection occurs by way of colonizing silk and thus symptoms first appear at the ear apex. White mycelium, turning pink to red with time, colonizes kernels and may progress basipetally, covering the entire ear.

USEFUL WEBSITES

http://www.broad.mit.edu/annotation/fungi/fusarium/mips.gsf.de/genre/proj/fusarium/ http://www.cdl.umn.edu/scab/gz-consort.html http://www.scabusa.org/

Patterns of trichothecene production, genetic variability, and virulence to wheat of Fusarium graminearum from smallholder farms in Nepal

Fusarium graminearum causes wheat head blight and contaminates grain with the trichothecenes 4-deoxynivalenol and nivalenol. Sequence analysis of trichothecene genes indicates that nivalenol production is the ancestral trait; however, deoxynivalenol producers occur worldwide and predominate in North and South America and in Europe. Analysis of a large field population (>500 strains) from Nepal identified three groups that were both genetically distinct and polymorphic for trichothecene production: SCAR1 comprising 95% deoxynivalenol producers, SCAR2 comprising 94% nivalenol producers, and SCAR3/5 comprising 34% deoxynivalenol producers/63% nivalenol producers. The ability to cause wheat head blight differed between SCAR groups and trichothecene chemotypes: deoxynivalenol producers were more virulent than nivalenol producers across all three SCAR groups and within the SCAR3/5 genetic background. These data support the hypothesis that production of deoxynivalenol rather than nivalenol confers a selective advantage to this important wheat pathogen.

Use of genes encoding cellobiohydrolase-C and topoisomerase II as targets for phylogenetic analysis and identification of Fusarium

Molecular identification and phylogenetic studies rely to a large extent on rDNA sequence polymorphism. In the field of fungal taxonomy, despite the use of huge amounts of rDNA data available, some species within a given genus remain indistinguishable. Therefore, new target sequences need to be selected and validated. This is the case for Fusarium, which includes numerous species most of which are involved in both animal and plant pathologies. In addition to the rDNA fragment encompassing the internal transcribed spacers ITS1 and ITS2 and the 5.8 S sequence, two newly characterized genes were used as molecular markers for Fusarium species genotyping. The cellobiohydrolase-C (cbh-C) and the topoisomerase II (topII) gene parts were cloned and sequenced for at least one isolate of each of the eleven different species of our collection. Both cbh-C and topII were found to be single copy genes. DNA fragments amplified by PCR in order to establish phylogenetic trees range from 1123 to 1157 bp for rDNA and from 327 to 344 bp for cbh-C (this part contains one intron). The topII gene part encoding the carboxy-terminus of the ATP binding domain of the enzyme is constant in length with a value of 724 bp. PAUP-generated phylogenetic analyses based either on cbh-C or topII data enabled all species to be distinguished, and were more informative than those resulting from rDNA sequences. Furthermore, a combination of the three datasets enhanced the accuracy of the analyses and open up new possibilities for rapid molecular identification and evolution studies within the Fusarium genus.

Repression of phenazine antibiotic production in Pseudomonas aureofaciens strain 30-84 by RpeA

Pseudomonas aureofaciens strain 30-84 is a biological control bacterium that utilizes a two-component GacS/GacA regulatory system interconnected with the PhzR/PhzI quorum sensing system to positively regulate biosynthesis of phenazine antibiotics that contribute to its association with plant hosts. To date, no negative regulators of phenazine production have been identified, nor has the role of repression been studied. Here we describe a novel repressor of secondary metabolism in P. aureofaciens strain 30-84, RpeA, whose deduced amino acid sequence is similar to those of a group of putative two-component regulatory systems of unknown function found in several animal and plant-pathogenic bacteria. In minimal medium where phenazine production is very low, inactivation of the rpeA gene enhanced phenazine biosynthetic gene expression and increased phenazine production but did not increase quorum sensing signal accumulation. Furthermore, RpeA functioned to block phenazine biosynthetic gene transcription in minimal medium even when quorum-sensing signals were at a level that was sufficient for induction of phenazine gene expression in rich medium. Additionally, in the absence of rpeA, the quorum sensor PhzR was not required for phenazine production. Although repression plays a critical role in phenazine regulation, the rpeA mutation could not bypass the requirement for a functional GacS/GacA system, demonstrating that activation is required even in the absence of the RpeA repressor. This study reinforces that multiple signals, including nutrition and population density, are integrated to control the appropriate expression of phenazine antibiotics.

Expression in cereal plants of genes that inactivate Fusarium mycotoxins

Trichothecene 3-O-acetyltransferase (encoded by Tri101) inactivates the virulence factor of the cereal pathogen Fusarium graminearum. Zearalenone hydrolase (encoded by zhd101) detoxifies the oestrogenic mycotoxin produced by the same pathogen. These genes were introduced into a model monocotyledon rice plant to evaluate their usefulness for decontamination of mycotoxins. The strong and constitutive rice Act1 promoter did not cause accumulation of TRI101 protein in transgenic rice plants. In contrast, the same promoter was suitable for transgenic production of ZHD101 protein; so far, five promising T0 plants have been generated. Low transgenic expression of Tri101 was suggested to be increased by addition of an omega enhancer sequence upstream of the start codon.

Trichothecene nonproducer Gibberella species have both functional and nonfunctional 3-O-acetyltransferase genes

The trichothecene 3-O-acetyltransferase gene (FgTri101) required for trichothecene production by Fusarium graminearum is located between the phosphate permease gene (pho5) and the UTP-ammonia ligase gene (ura7). We have cloned and sequenced the pho5-to-ura7 regions from three trichothecene nonproducing Fusarium (i.e., F. oxysporum, F. moniliforme, and Fusarium species IFO 7772) that belong to the teleomorph genus Gibberella. BLASTX analysis of these sequences revealed portions of predicted polypeptides with high similarities to the TRI101 polypeptide. While FspTri101 (Fusarium species Tri101) coded for a functional 3-O-acetyltransferase, FoTri101 (F. oxysporum Tri101) and FmTri101 (F. moniliforme Tri101) were pseudogenes. Nevertheless, F. oxysporum and F. moniliforme were able to acetylate C-3 of trichothecenes, indicating that these nonproducers possess another as yet unidentified 3-O-acetyltransferase gene. By means of cDNA expression cloning using fission yeast, we isolated the responsible FoTri201 gene from F. oxysporum; on the basis of this sequence, FmTri201 has been cloned from F. moniliforme by PCR techniques. Both Tri201 showed only a limited level of nucleotide sequence similarity to FgTri101 and FspTri101. The existence of Tri101 in a trichothecene nonproducer suggests that this gene existed in the fungal genome before the divergence of producers from nonproducers in the evolution of Fusarium species.

A novel lactonohydrolase responsible for the detoxification of zearalenone: enzyme purification and gene cloning

Zearalenone (ZEN) is converted into a far less oestrogenic product by incubation with Clonostachys rosea IFO 7063. An alkaline hydrolase responsible for the detoxification was purified to homogeneity from the fungus by a combination of salt precipitation and column chromatography methods. The purified enzyme was homodimeric with a subunit molecular mass of 30 kDa and contained an intra-subunit disulphide bridge. On the basis of the internal peptide sequences of the purified protein, we cloned the entire coding region of the gene (designated as zhd101) by PCR techniques. The ZEN degradation activity was detected in heterologous hosts (Schizosaccharomyces pombe and Escherichia coli) carrying the cloned gene. Zhd101 could be a promising genetic resource for in planta detoxification of the mycotoxin in important crops.