An Ustilago maydis gene involved in H2O2 detoxification is required for virulence

Response to environmental stresses, cell-wall integrity, and virulence are orchestrated through the calcineurin pathway in Ustilago hordei

In eukaryotes, several biological processes are regulated through calcium signaling. Calcineurin is a calcium-calmodulin-regulated serine/threonine phosphatase consisting of catalytic subunit A and regulatory subunit B. Phosphatase activity resides in the catalytic subunit, which activates by dephosphorylation downstream components such as transcription factor Crz1. The importance of this pathway to respond to environmental stress has been explored in several fungal pathogens. The basidiomycete Ustilago hordei causes covered smut of barley. We addressed the role of the Ca(2+)-calcineurin activated pathway by deleting UhCna1 and UhCnb1. These genes were not essential in U. hordei but the corresponding mutants displayed a variety of phenotypes when applying environmental stress such as sensitivity to pH, temperature, H₂O₂, mono- and divalent cations; and to genotoxic, acid, or oxidative stresses. Cell-wall integrity was compromised and mutants displayed altered cell morphologies. Mating was delayed but not abolished, and combined sensitivities likely explained a severely reduced virulence toward barley plants. Expression analyses revealed that response to salt stress involved the induction of membrane ATPase genes UhEna1 and UhEna2, which were regulated through the calcineurin pathway. Upregulation of UhFKS1, a 1,3-β-d-glucan synthase gene, correlated with the increased amount of 1,3-β-d-glucan in the calcineurin mutants grown under salt stress.

The role of catalase-peroxidase secreted by Magnaporthe oryzae during early infection of rice cells

The biological role of a secretory catalase of the rice blast fungus Magnaporthe oryzae was studied. The internal amino acid sequences of the partially purified catalase in the culture filtrate enabled us to identify its encoding gene as a catalase-peroxidase gene, CPXB, among four putative genes for catalase or catalase-peroxidase in M. oryzae. Knockout of the gene drastically reduced the level of catalase activity in the culture filtrate and supernatant of conidial suspension (SCS), and increased the sensitivity to exogenously added H₂O₂ compared with control strains, suggesting that CPXB is the major gene encoding the secretory catalase and confers resistance to H₂O₂ in hyphae. In the mutant, the rate of appressoria that induced accumulation of H₂O₂ in epidermal cells of the leaf sheath increased and infection at early stages was delayed; however, the formation of lesions in the leaf blade was not affected compared with the control strain. These phenotypes were complimented by reintroducing the putative coding regions of CPXB driven by a constitutive promoter. These results suggest that CPXB plays a role in fungal defense against H₂O₂ accumulated in epidermal cells of rice at the early stage of infection but not in pathogenicity of M. oryzae.

Reactive oxygen species in phytopathogenic fungi: signaling, development, and disease

Reactive oxygen species (ROS) play a major role in pathogen-plant interactions: recognition of a pathogen by the plant rapidly triggers the oxidative burst, which is necessary for further defense reactions. The specific role of ROS in pathogen defense is still unclear. Studies on the pathogen so far have focused on the importance of the oxidative stress response (OSR) systems to overcome the oxidative burst or of its avoidance by effectors. This review focuses on the role of ROS for fungal virulence and development. In the recent years, it has become obvious that (a) fungal OSR systems might not have the predicted crucial role in pathogenicity, (b) fungal pathogens, especially necrotrophs, can actively contribute to the ROS level in planta and even take advantage of the host's response, (c) fungi possess superoxide-generating NADPH oxidases similar to mammalian Nox complexes that are important for pathogenicity; however, recent data indicate that they are not directly involved in pathogen-host communication but in fungal differentiation processes that are necessary for virulence.

A novel transcriptional factor important for pathogenesis and ascosporogenesis in Fusarium graminearum

Fusarium head blight or scab caused by Fusarium graminearum is an important disease of wheat and barley. The pathogen not only causes severe yield losses but also contaminates infested grains with mycotoxins. In a previous study, we identified several pathogenicity mutants by random insertional mutagenesis. One of these mutants was disrupted in the ZIF1 gene, which encodes a b-ZIP transcription factor unique to filamentous ascomycetes. The Δzif1 mutant generated by gene replacement was significantly reduced in deoxynivalenol (DON) production and virulence on flowering wheat heads. It was defective in spreading from inoculated florets to the rachis and other spikelets. Deletion of the ZIF1 ortholog MoZIF1 in the rice blast fungus also caused reductions in virulence and in invasive growth. In addition, the Δzif1 mutant is defective in sexual reproduction. Although it had normal male fertility, when selfed or mated as the female in outcrosess, the Δzif1 mutant produced small, pigmented perithecia that were sterile (lack of asci and ascospores), suggesting a female-specific role for ZIF1 during fertilization or ascus development. Similar female-specific defects in sexual reproduction were observed in the ΔMozif1 mutant. When mated as the female, the ΔMozif1 perithecia failed to develop long necks and asci or ascospores. The ZIF1 gene is well conserved in filamentous ascomycetes, particularly in the b-ZIP domain, which is essential for its function. Expression of ZIF1 in Magnaporthe oryzae complemented the defects of the ΔMozif1 mutant. These results indicate that this b-ZIP transcription factor is functionally conserved in these two fungal pathogens for plant infection and sexual reproduction.

The fungal pathogen Cochliobolus heterostrophus responds to maize phenolics: novel small molecule signals in a plant-fungal interaction

The transcription factor ChAP1 of the fungal pathogen of maize, Cochliobolus heterostrophus, responds to oxidative stress by migration to the nucleus and activation of antioxidant genes. Phenolic and related compounds found naturally in the host also trigger nuclear localization of ChAP1, but only slight upregulation of some antioxidant genes. ChAP1 thus senses phenolic compounds without triggering a strong antioxidant response. We therefore searched for genes whose expression is regulated by phenolic compounds and/or ChAP1. The C. heterostrophus genome contains a cluster of genes for metabolism of phenolics. One such gene, catechol dioxygenase CCHD1, was induced at least 10-fold by caffeic and coumaric acids. At high phenolic concentrations (≥ 1.6 mM), ChAP1 is needed for maximum CCHD1 expression. At micromolar levels of phenolics CCHD1 is as strongly induced in chap1 mutants as in the wild type. The pathogen thus detects phenolics by at least two signalling pathways: one causing nuclear retention of ChAP1, and another triggering induction of CCHD1 expression. The low concentrations required for induction of CCHD1 indicate fungal receptors for plant phenolics. Symbiotic and pathogenic bacteria are known to detect phenolics, and our findings generalize this to a eukaryotic pathogen. Phenolics and related compounds thus provide a ubiquitous plant-derived signal.

Regulation of Candida glabrata oxidative stress resistance is adapted to host environment

The human fungal pathogen Candida glabrata is related to Saccharomyces cerevisiae but has developed high resistance against reactive oxygen species. We find that induction of conserved genes encoding antioxidant functions is dependent on the transcription factors CgYap1 and CgSkn7 which cooperate for promoter recognition. Superoxide stress resistance of C. glabrata is provided by superoxide dismutase CgSod1, which is not dependent on CgYap1/Skn7. Only double mutants lacking both CgSod1 and CgYap1 were efficiently killed by primary mouse macrophages. Our results suggest that in C. glabrata the regulation of key genes providing stress protection is adopted to meet a host-pathogen situation.

Peroxiredoxins from the plant parasitic root-knot nematode, Meloidogyne incognita, are required for successful development within the host

Root-knot nematodes, Meloidogyne spp., are sedentary biotrophic parasites which are able to infest > 2000 plant species. After root invasion they settle sedentarily inside the vascular cylinder and maintain a compatible interaction for up to 8 weeks. Plant cells respond to pathogen attacks by producing reactive oxygen species (ROS). These ROS, in particular hydroperoxides, are important regulators of host-parasite interactions and partly govern the success or failure of disease. ROS producing and ROS scavenging enzymes from both the pathogen and the host finely tune the redox state at the host-pathogen interface. We have analysed the gene structure and organization of peroxiredoxins (prx) in Meloidogyne incognita and analysed their role in the establishment of the nematode in its host. Meloidogyne incognita has seven prx genes that can be grouped with other nematode prx into three clades. Clade B prx genes are more actively transcribed in parasitic stages compared with free-living pre-parasitic juveniles. We confirmed in vitro the activity of one of these, Mi-prx2.1, on hydrogen peroxide and butylhydroperoxide. We showed by ultrastructural immunocytochemistry the expression of clade B PRX proteins in the hypodermis and pseudocoelum beneath the tissues directly in contact with the environment, both in free-living and parasitic stages. Finally, knock-down of clade B prx genes led to a significant reduction in the ability of the nematodes to complete their life cycle in the host. The expression of clade B PRX proteins in the tissues in close contact with plant cells during parasitism and the impaired development of nematodes inside the host after clade B prx knock-down suggest an important role for these genes during infection.

Life without putrescine: disruption of the gene-encoding polyamine oxidase in Ustilago maydis odc mutants

In previous communications the essential role of spermidine in Ustilago maydis was demonstrated by means of the disruption of the genes encoding ornithine decarboxylase (ODC) and spermidine synthase (SPE). However, the assignation of specific roles to each polyamine in different cellular functions was not possible because the spermidine added to satisfy the auxotrophic requirement of odc/spe double mutants is partly back converted into putrescine. In this study, we have approached this problem through the disruption of the gene-encoding polyamine oxidase (PAO), required for the conversion of spermidine into putrescine, and the construction of odc/pao double mutants that were unable to synthesize putrescine by either ornithine decarboxylation or retroconversion from spermidine. Phenotypic analysis of the mutants provided evidence that putrescine is only an intermediary in spermidine biosynthesis, and has no direct role in cell growth, dimorphic transition, or any other vital function of U. maydis. Nevertheless, our results show that putrescine may play a role in the protection of U. maydis against salt and osmotic stress, and possibly virulence. Evidence was also obtained that the retroconversion of spermidine into putrescine is not essential for U. maydis growth but may be important for its survival under natural conditions.

R-SNARE homolog MoSec22 is required for conidiogenesis, cell wall integrity, and pathogenesis of Magnaporthe oryzae

Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins mediate intracellular vesicle fusion, which is an essential cellular process of the eukaryotic cells. To investigate the role of SNARE proteins in the rice blast fungus Magnaporthe oryzae, MoSec22, an ortholog of Saccharomyces cerevisiae SNARE protein Sec22, was identified and the MoSEC22 gene disrupted. MoSec22 restored a S. cerevisiae sec22 mutant in resistance to cell wall perturbing agents, and the ΔMosec22 mutant also exhibited defects in mycelial growth, conidial production, and infection of the host plant. Treatment with oxidative stress inducers indicated a breach in cell wall integrity, and staining and quantification assays suggested abnormal chitin deposition on the lateral walls of hyphae of the ΔMosec22 mutant. Furthermore, hypersensitivity to the oxidative stress correlates with the reduced expression of the extracellular enzymes peroxidases and laccases. Our study thus provides new evidence on the conserved function of Sec22 among fungal organisms and indicates that MoSec22 has a role in maintaining cell wall integrity affecting the growth, morphogenesis, and virulence of M. oryzae.

The use of FLP-mediated recombination for the functional analysis of an effector gene family in the biotrophic smut fungus Ustilago maydis

*In the Ustilago maydis genome, several novel secreted effector proteins are encoded by gene families. Because of the limited number of selectable markers, the ability to carry out sequential gene deletions has limited the analysis of effector gene families that may have redundant functions. *Here, we established an inducible FLP-mediated recombination system in U. maydis that allows repeated rounds of gene deletion using a single selectable marker (Hyg(R)). To avoid genome rearrangements via FRT sites remaining in the genome after excision, different mutated FRT sites were introduced. *The FLP-mediated selectable marker-removal technique was successfully applied to delete a family of 11 effector genes (eff1) using five sequential rounds of recombination. We showed that expression of all 11 genes is up-regulated during the biotrophic phase. Strains carrying deletions of 9 or all 11 genes showed a significant reduction in virulence, and this phenotype could be partially complemented by the introduction of different members from the gene family, demonstrating redundancy. *The establishment of the FLP/FRT system in a plant pathogenic fungus paves the way for analyzing multigene families with redundant functions.

The Ustilago maydis forkhead transcription factor Fox1 is involved in the regulation of genes required for the attenuation of plant defenses during pathogenic development

Ustilago maydis is a plant-pathogenic fungus that establishes a biotrophic relationship with its host plant, Zea mays. The pathogenic stage of U. maydis is initiated by the fusion of two haploid cells, resulting in the formation of a dikaryotic hypha that invades the plant cell. The switch from saprophytic, yeast-like cells to the biotrophic hyphae requires the complex regulation of a multitude of biological processes to constitute the compatible host-fungus interaction. Transcriptional regulators involved in the establishment of the infectious dikaryon and penetration of the host tissue have been identified; however, regulators required during the post-penetration stages remained to be elucidated. In this study, we report the identification of a U. maydis forkhead transcription factor, Fox1, which is exclusively expressed during biotrophic development. Deletion of fox1 results in reduced virulence and impaired tumor development. The Deltafox1 hyphae induce the accumulation of H(2)O(2) in and around infected cells and a maize defense response phenotypically represented by the encasement of proliferating hyphae in a cellulose-containing matrix. The phenotype can be attributed to the fox1-dependent deregulation of several effector genes that are linked to pathogenic development and host defense suppression.

The basic leucine zipper transcription factor Moatf1 mediates oxidative stress responses and is necessary for full virulence of the rice blast fungus Magnaporthe oryzae

Magnaporthe oryzae is the causal agent of rice blast disease, leading to enormous losses of rice production. Here, we characterized a basic leucine zipper (bZIP) transcription factor, Moatf1, in M. oryzae, a homolog of Schizosaccharomyces pombe ATF/CREB that regulates the oxidative stress response. Moatf1 deletion caused retarded vegetative growth of mycelia, and the Moatf1 mutant exhibited higher sensitivity to hydrogen peroxide (H(2)O(2)) than did the wild-type strain. The mutant showed severely reduced activity of extracellular enzymes and transcription level of laccases and peroxidases and exhibited significantly reduced virulence on rice cultivar CO-39. On rice leaf sheath, most of the infectious hyphae of the mutant became swollen and displayed restricted growth in primary infected cells. Defense response was strongly activated in plants infected by the mutant. Diamino benzidine staining revealed an accumulation of H(2)O(2) around Moatf1 mutant appressoria and rice cells with Moatf1 hyphae that was absent in the wild type. Inhibition of the plant NADPH oxidase by diphenyleneiodonium prevented host-derived H(2)O(2) accumulation and restored infectious hyphal growth of the mutant in rice cells. Thus, we conclude that Moatf1 is necessary for full virulence of M. oryzae by regulating the transcription of laccases and peroxidases to impair reactive oxygen species-mediated plant defense.

The myosin motor domain of fungal chitin synthase V is dispensable for vesicle motility but required for virulence of the maize pathogen Ustilago maydis

Class V chitin synthases are fungal virulence factors required for plant infection. They consist of a myosin motor domain fused to a membrane-spanning chitin synthase region that participates in fungal cell wall formation. The function of the motor domain is unknown, but it might deliver the myosin chitin synthase-attached vesicles to the growth region. Here, we analyze the importance of both domains in Mcs1, the chitin synthase V of the maize smut fungus Ustilago maydis. By quantitative analysis of disease symptoms, tissue colonization, and single-cell morphogenic parameters, we demonstrate that both domains are required for fungal virulence. Fungi carrying mutations in the chitin synthase domain are rapidly recognized and killed by the plant, whereas fungi carrying a deletion of the motor domain show alterations in cell wall composition but can invade host tissue and cause a moderate plant response. We also show that Mcs1-bound vesicles exhibit long-range movement for up to 20 microm at a velocity of approximately 1.75 microm/s. Apical Mcs1 localization depends on F-actin and the motor domain, whereas Mcs1 motility requires microtubules and persists when the Mcs1 motor domain is deleted. Our results suggest that the myosin motor domain of ChsV supports exocytosis but not long-range delivery of transport vesicles.

ROS in biotic interactions

Production of reactive oxygen species (ROS) is a hallmark of successful recognition of infection and activation of plant defenses. ROS play multifaceted signaling functions mediating the establishment of multiple responses and can act as local toxins. Controversy surrounds the origin of these ROS. Several enzymatic mechanisms, among them a plasma membrane NADPH oxidase and cell wall peroxidases, can be responsible for the ROS detected in the apoplast. However, high levels of ROS from metabolic origins and/or from downregulation of ROS-scavenging systems can also accumulate in different compartments of the plant cell. This compartmentalization could contribute to the specific functions attributed to ROS. Additionally, ROS interact with other signals and phytohormones, which could explain the variety of different scenarios where ROS signaling plays an important part. Interestingly, pathogens have developed ways to alter ROS accumulation or signaling to modify plant defenses. Although ROS have been mainly associated with pathogen attack, ROS are also detected in other biotic interactions including beneficial symbiotic interactions with bacteria or mycorrhiza, suggesting that ROS production is a common feature of different biotic interactions. Here, we present a comprehensive review describing the newer views in ROS signaling and function during biotic stress.

TmpL, a transmembrane protein required for intracellular redox homeostasis and virulence in a plant and an animal fungal pathogen

The regulation of intracellular levels of reactive oxygen species (ROS) is critical for developmental differentiation and virulence of many pathogenic fungi. In this report we demonstrate that a novel transmembrane protein, TmpL, is necessary for regulation of intracellular ROS levels and tolerance to external ROS, and is required for infection of plants by the necrotroph Alternaria brassicicola and for infection of mammals by the human pathogen Aspergillus fumigatus. In both fungi, tmpL encodes a predicted hybrid membrane protein containing an AMP-binding domain, six putative transmembrane domains, and an experimentally-validated FAD/NAD(P)-binding domain. Localization and gene expression analyses in A. brassicicola indicated that TmpL is associated with the Woronin body, a specialized peroxisome, and strongly expressed during conidiation and initial invasive growth in planta. A. brassicicola and A. fumigatus ΔtmpL strains exhibited abnormal conidiogenesis, accelerated aging, enhanced oxidative burst during conidiation, and hypersensitivity to oxidative stress when compared to wild-type or reconstituted strains. Moreover, A. brassicicola ΔtmpL strains, although capable of initial penetration, exhibited dramatically reduced invasive growth on Brassicas and Arabidopsis. Similarly, an A. fumigatus ΔtmpL mutant was dramatically less virulent than the wild-type and reconstituted strains in a murine model of invasive aspergillosis. Constitutive expression of the A. brassicicola yap1 ortholog in an A. brassicicola ΔtmpL strain resulted in high expression levels of genes associated with oxidative stress tolerance. Overexpression of yap1 in the ΔtmpL background complemented the majority of observed developmental phenotypic changes and partially restored virulence on plants. Yap1-GFP fusion strains utilizing the native yap1 promoter exhibited constitutive nuclear localization in the A. brassicicola ΔtmpL background. Collectively, we have discovered a novel protein involved in the virulence of both plant and animal fungal pathogens. Our results strongly suggest that dysregulation of oxidative stress homeostasis in the absence of TmpL is the underpinning cause of the developmental and virulence defects observed in these studies.

The critical roles of reactive oxygen species (ROS) in fungal development and virulence have been well established over the past half a century since the first experimental detection of hydrogen peroxide in fungal cells by Bach (1950). In the cell, ROS act as signaling molecules regulating physiological responses and developmental processes and are also involved in sophisticated virulence processes for many pathogenic fungi. Therefore, uncovering the biological roles of cellular ROS appears to be very important in understanding fungal development and virulence. Currently we have limited knowledge of how intracellular ROS are generated by fungal cells and which cellular ROS regulatory mechanisms are involved in establishing homeostasis. In this study we describe a novel protein, TmpL, involved in development and virulence in both plant and animal pathogenic fungi. In the absence of TmpL, dysregulation of oxidative stress homeostasis in both fungi caused developmental and virulence defects. Therefore, elucidating the role of TmpL presents an opportunity to uncover a common pathogenicity mechanism employed by both plant and animal pathogens and to develop efficient and novel therapeutics for both plant and animal fungal disease. Our findings provide new insights into mechanisms underlying the complex web of interactions between ROS and cell differentiation and the involvement of ROS for both plant and animal fungal pathogenesis.

GintPDX1 encodes a protein involved in vitamin B6 biosynthesis that is up-regulated by oxidative stress in the arbuscular mycorrhizal fungus Glomus intraradices

Vitamin B6 is an essential metabolite that has recently been implicated in defense against cellular oxidative stress. In fungi, the de novo biosynthetic pathway of vitamin B6 involves two genes, PDX1 and PDX2. Here, we report a component of the PDX1/PDX2 vitamin B6 biosynthetic pathway in an arbuscular mycorrhizal (AM) fungus. Using rapid amplification of cDNA ends, we isolated the full-length cDNA of a PDX-like gene, GintPDX1, from Glomus intraradices. GintPDX1 expression was analysed by real-time reverse transcription-polymerase chain reaction (RT-PCR). GintPDX1 activity and function were investigated by heterologous complementation of the yeast strainDeltasnz1, which is deficient in vitamin B6 biosynthesis. Sequence data revealed that GintPDX1 is highly homologous to other identified PDX1 proteins. GintPDX1 restores prototrophy to the vitamin B6 auxotrophic yeast mutant and reverts its superoxide sensitivity. GintPDX1 is expressed throughout the fungal life cycle, with the highest transcription levels found in the intraradical fungal structures. GintPDX1 expression was induced in response to hydrogen peroxide, paraquat and copper. The results demonstrate that AM fungi possess at least one component of the machinery necessary for vitamin B6 biosynthesis. Transcriptional regulation of GintPDX1 suggests a role for vitamin B6 as an antioxidant and modulator of reactive oxygen species in G. intraradices.

The O-mannosyltransferase PMT4 is essential for normal appressorium formation and penetration in Ustilago maydis

In Saccharomyces cerevisiae, the PMT, KRE2/MNT1, and MNN1 mannosyltransferase protein families catalyze the steps of the O-mannosylation pathway, sequentially adding mannoses to target proteins. We have identified members of all three families and analyzed their roles in pathogenesis of the maize smut fungus Ustilago maydis. Furthermore, we have shown that PMT4, one of the three PMT family members in U. maydis, is essential for tumor formation in Zea mays. Significantly, PMT4 seems to be required only for pathogenesis and is dispensable for other aspects of the U. maydis life cycle. We subsequently show that the deletion of pmt4 results in a strong reduction in the frequency of appressorium formation, with the few appressoria that do form lacking the capacity to penetrate the plant cuticle. Our findings suggest that the O-mannosylation pathway plays a key role in the posttranslational modification of proteins involved in the pathogenic development of U. maydis. The fact that PMT homologs are not found in plants may open new avenues for the development of fungal control strategies. Moreover, the discovery of a highly specific requirement for a single O-mannosyltransferase should aid in the identification of the proteins directly involved in fungal plant penetration, thus leading to a better understanding of plant-fungi interactions.

Effects of catalase on the accumulation of H(2)O(2) in rice cells inoculated with rice blast fungus, Magnaporthe oryzae

Roles of H(2)O(2) in the infection process of Magnaporthe oryzae on rice were investigated. In a leaf sheath assay for up to 48 h post-inoculation, the absence or presence of catalase in the conidia suspension was correlated with the level of accumulated H(2)O(2) in infected leaf cells, as observed by staining with 3',3-diaminobenzidine tetrahydrochloride. In the incompatible interaction, the appearance of autofluorescence or frequency of cell death characterized by granulation (symptoms characteristic of hypersensitive responses) was not significantly affected by the presence of catalase in the conidia suspension. In the leaf blade assay, inoculation of compatible conidia in the presence of catalase produced more severe symptoms than that of conidia in the absence of catalase at 6 days post-inoculation. These results suggest that, in this host-parasite interaction, the primary role of host-produced H(2)O(2) is in limiting hyphal growth after penetration through toxic action. Furthermore, in incompatible interactions, H(2)O(2) is implied not to be a major mediator of hypersensitive cell death.

Assessing the impact of transcriptomics, proteomics and metabolomics on fungal phytopathology

SUMMARY Peer-reviewed literature is today littered with exciting new tools and techniques that are being used in all areas of biology and medicine. Transcriptomics, proteomics and, more recently, metabolomics are three of these techniques that have impacted on fungal plant pathology. Used individually, each of these techniques can generate a plethora of data that could occupy a laboratory for years. When used in combination, they have the potential to comprehensively dissect a system at the transcriptional and translational level. Transcriptomics, or quantitative gene expression profiling, is arguably the most familiar to researchers in the field of fungal plant pathology. Microarrays have been the primary technique for the last decade, but others are now emerging. Proteomics has also been exploited by the fungal phytopathogen community, but perhaps not to its potential. A lack of genome sequence information has frustrated proteomics researchers and has largely contributed to this technique not fulfilling its potential. The coming of the genome sequencing era has partially alleviated this problem. Metabolomics is the most recent of these techniques to emerge and is concerned with the non-targeted profiling of all metabolites in a given system. Metabolomics studies on fungal plant pathogens are only just beginning to appear, although its potential to dissect many facets of the pathogen and disease will see its popularity increase quickly. This review assesses the impact of transcriptomics, proteomics and metabolomics on fungal plant pathology over the last decade and discusses their futures. Each of the techniques is described briefly with further reading recommended. Key examples highlighting the application of these technologies to fungal plant pathogens are also reviewed.

Does botrytis cinerea Ignore H(2)O(2)-induced oxidative stress during infection? Characterization of botrytis activator protein 1

Botrytis cinerea is a phytopathogen infecting a broad range of plants including strawberries and grapevine. During infection, the necrotrophic fungus is exposed to reactive oxygen species (ROS) released by the oxidative burst, an early plant defense reaction. B. cinerea even produces ROS itself in planta. This raises questions about how the pathogen senses and responds to the host defense reaction and which role the pathogen's oxidative stress response systems play. Functional analysis of the AP-1 transcription factor Bap1 confirmed its role as a pivotal regulator of ROS detoxification in vitro. Macroarray analysis revealed 99 H(2)O(2)-induced Bap1 target genes, of which several genes encoded ROS-degrading enzymes as well as other central components of the cellular redox status. However, Bap1 is not essential for pathogenesis. In planta analyses revealed that the Bap1 target genes were not expressed 2 days postinoculation although H(2)O(2) was detectable, proving that the normal virulence of the Deltabap1 mutant is not due to alternative regulation of the major oxidative stress response system in planta. The fungus obviously does not suffer H(2)O(2)-induced oxidative stress in planta, questioning classical ideas about the role of the oxidative burst in the infection process.

The YAP1 homolog-mediated oxidative stress tolerance is crucial for pathogenicity of the necrotrophic fungus Alternaria alternata in citrus

Citrus brown spot disease is caused by the necrotrophic fungus Alternaria alternata. Its pathogenic capability has been thought to depend exclusively on the production of host-selective ACT toxin. However, circumvention of plant defenses is also likely to be important for the disease process. To investigate the fungal response to host-generated reactive oxygen species (ROS), we cloned and characterized the AaAP1 gene of A. alternata, which encodes a polypeptide resembling yeast YAP1-like transcriptional activators implicated in cellular responses to stress. Expression of the AaAP1 gene in a wild-type strain was primarily induced by H(2)O(2) or ROS-generating oxidants. Using a loss-of-function mutation in the AaAP1 gene, we demonstrated an essential requirement for oxidative tolerance during the host invasion step. Mutants lacking AaAP1 showed increased sensitivity to H(2)O(2) and loss of fungal pathogenicity. The DeltaAaAP1 null mutant did not cause any visible necrotic lesions on wounded or unwounded leaves of citrus cv. Minneola. Compared with the wild type, the null mutant displayed lower catalase, peroxidase, and superoxide dismutase activities. All mutant phenotypes were restored to the wild type in fungal strains expressing a functional copy of AaAP1. Upon exposure to H(2)O(2), the AaAP1::sGFP (synthetic green fluorescent protein) fusion protein became localized in the nucleus. Inoculation of the mutant with NADPH oxidase inhibitors partially restored fungal pathogenicity. Our results highlight the global regulatory role of a YAP1 homolog in response to oxidative stress in A. alternata and provide insights into the critical role of ROS detoxification in the pathogenicity of A. alternata.

A novel pathogenicity gene is required in the rice blast fungus to suppress the basal defenses of the host

For successful colonization and further reproduction in host plants, pathogens need to overcome the innate defenses of the plant. We demonstrate that a novel pathogenicity gene, DES1, in Magnaporthe oryzae regulates counter-defenses against host basal resistance. The DES1 gene was identified by screening for pathogenicity-defective mutants in a T-DNA insertional mutant library. Bioinformatic analysis revealed that this gene encodes a serine-rich protein that has unknown biochemical properties, and its homologs are strictly conserved in filamentous Ascomycetes. Targeted gene deletion of DES1 had no apparent effect on developmental morphogenesis, including vegetative growth, conidial germination, appressorium formation, and appressorium-mediated penetration. Conidial size of the mutant became smaller than that of the wild type, but the mutant displayed no defects on cell wall integrity. The Δdes1 mutant was hypersensitive to exogenous oxidative stress and the activity and transcription level of extracellular enzymes including peroxidases and laccases were severely decreased in the mutant. In addition, ferrous ion leakage was observed in the Δdes1 mutant. In the interaction with a susceptible rice cultivar, rice cells inoculated with the Δdes1 mutant exhibited strong defense responses accompanied by brown granules in primary infected cells, the accumulation of reactive oxygen species (ROS), the generation of autofluorescent materials, and PR gene induction in neighboring tissues. The Δdes1 mutant displayed a significant reduction in infectious hyphal extension, which caused a decrease in pathogenicity. Notably, the suppression of ROS generation by treatment with diphenyleneiodonium (DPI), an inhibitor of NADPH oxidases, resulted in a significant reduction in the defense responses in plant tissues challenged with the Δdes1 mutant. Furthermore, the Δdes1 mutant recovered its normal infectious growth in DPI-treated plant tissues. These results suggest that DES1 functions as a novel pathogenicity gene that regulates the activity of fungal proteins, compromising ROS-mediated plant defense.

Coevolution of plants and microbial pathogens leads to interactions that resemble a molecular war. Pathogens generate effector molecules to infect their hosts, and plants produce defense molecules against pathogen attacks. Interactions between these molecules results in plant immunity or disease. Plant disease could be likened to a complex and delicate matter of balance, where a number of molecules are involved in the battlefield. Discovering and understanding the tipping points in the battle are vital for developing disease-free crops. In the interaction of rice and rice blast fungus, a microbe sensor on rice stimulates the generation of reactive oxygen species (ROS) at the site of infection. ROS is known as an antimicrobial material and a stimulator for defense signaling that is important for preparing reinforcement in neighboring tissues. This paper presents the counter-defense mechanism of the fungus against plant-driven ROS. We found that a pathogenicity factor from rice blast fungus, DES1 (Defense Suppressor 1), is involved in overcoming oxidative stress for the counter-defense mechanism, suggesting that this gene is required for fungal pathogenicity.

Pep1, a secreted effector protein of Ustilago maydis, is required for successful invasion of plant cells

The basidiomycete Ustilago maydis causes smut disease in maize. Colonization of the host plant is initiated by direct penetration of cuticle and cell wall of maize epidermis cells. The invading hyphae are surrounded by the plant plasma membrane and proliferate within the plant tissue. We identified a novel secreted protein, termed Pep1, that is essential for penetration. Disruption mutants of pep1 are not affected in saprophytic growth and develop normal infection structures. However, Deltapep1 mutants arrest during penetration of the epidermal cell and elicit a strong plant defense response. Using Affymetrix maize arrays, we identified 116 plant genes which are differentially regulated in Deltapep1 compared to wild type infections. Most of these genes are related to plant defense. By in vivo immunolocalization, live-cell imaging and plasmolysis approaches, we detected Pep1 in the apoplastic space as well as its accumulation at sites of cell-to-cell passages. Site-directed mutagenesis identified two of the four cysteine residues in Pep1 as essential for function, suggesting that the formation of disulfide bridges is crucial for proper protein folding. The barley covered smut fungus Ustilago hordei contains an ortholog of pep1 which is needed for penetration of barley and which is able to complement the U. maydis Deltapep1 mutant. Based on these results, we conclude that Pep1 has a conserved function essential for establishing compatibility that is not restricted to the U. maydis / maize interaction.

Ustilago maydis as a Pathogen

The Ustilago maydis-maize pathosystem has emerged as the current model for plant pathogenic basidiomycetes and as one of the few models for a true biotrophic interaction that persists throughout fungal development inside the host plant. This is based on the highly advanced genetic system for both the pathogen and its host, the ability to propagate U. maydis in axenic culture, and its unique capacity to induce prominent disease symptoms (tumors) on all aerial parts of maize within less than a week. The corn smut pathogen, though economically not threatening, will continue to serve as a model for related obligate biotrophic fungi such as the rusts, but also for closely related smut species that induce symptoms only in the flower organs of their hosts. In this review we describe the most prominent features of the U. maydis-maize pathosystem as well as genes and pathways most relevant to disease. We highlight recent developments that place this system at the forefront of understanding the function of secreted effectors in eukaryotic pathogens and describe the expected spin-offs for closely related species exploiting comparative genomics approaches.

Direct identification of the Meloidogyne incognita secretome reveals proteins with host cell reprogramming potential

The root knot nematode, Meloidogyne incognita, is an obligate parasite that causes significant damage to a broad range of host plants. Infection is associated with secretion of proteins surrounded by proliferating cells. Many parasites are known to secrete effectors that interfere with plant innate immunity, enabling infection to occur; they can also release pathogen-associated molecular patterns (PAMPs, e.g., flagellin) that trigger basal immunity through the nematode stylet into the plant cell. This leads to suppression of innate immunity and reprogramming of plant cells to form a feeding structure containing multinucleate giant cells. Effectors have generally been discovered using genetics or bioinformatics, but M. incognita is non-sexual and its genome sequence has not yet been reported. To partially overcome these limitations, we have used mass spectrometry to directly identify 486 proteins secreted by M. incognita. These proteins contain at least segmental sequence identity to those found in our 3 reference databases (published nematode proteins; unpublished M. incognita ESTs; published plant proteins). Several secreted proteins are homologous to plant proteins, which they may mimic, and they contain domains that suggest known effector functions (e.g., regulating the plant cell cycle or growth). Others have regulatory domains that could reprogram cells. Using in situ hybridization we observed that most secreted proteins were produced by the subventral glands, but we found that phasmids also secreted proteins. We annotated the functions of the secreted proteins and classified them according to roles they may play in the development of root knot disease. Our results show that parasite secretomes can be partially characterized without cognate genomic DNA sequence. We observed that the M. incognita secretome overlaps the reported secretome of mammalian parasitic nematodes (e.g., Brugia malayi), suggesting a common parasitic behavior and a possible conservation of function between metazoan parasites of plants and animals.

Parasitic nematodes are microscopic worms that cause major diseases of plants, animals, and humans. Infection is associated with secretion of proteins by the parasite; these proteins suppress the immune system and cause other changes to host cells that are required for infection. Identification of secreted proteins has been difficult because they are released only in trace amounts. We have developed very sensitive methods that enabled the discovery of 486 proteins secreted by the root knot nematode, Meloidogyne incognita; prior to this, only a handful of secreted proteins were known. Several secreted proteins appear to mimic normal plant proteins, and they may participate in the process by which the nematode hijacks the plant cell for its own purposes. Meloidogyne species infect many crops, including corn, soybean, cotton, rice, tomato, carrots, alfalfa, and tobacco. The discovery of these secreted proteins could lead to new methods for protecting these important crops from nematode damage. We observed that the secretome of the human pathogen, Brugia malayi, overlaps that of M. incognita, suggesting a common parasitic behavior between pathogens of plants and animals.

Genomes, free radicals and plant cell invasion: recent developments in plant pathogenic fungi

This review describes current advances in our understanding of fungal-plant interactions. The widespread application of whole genome sequencing to a diverse range of fungal species has allowed new insight into the evolution of fungal pathogenesis and the definition of the gene inventories associated with important plant pathogens. This has also led to functional genomic approaches to carry out large-scale gene functional analysis. There has also been significant progress in understanding appressorium-mediated plant infection by fungi and its underlying genetic basis. The nature of biotrophic proliferation of fungal pathogens in host tissue has recently revealed new potential mechanisms for cell-to-cell movement by invading pathogens.

Comparison of the thiol-dependent antioxidant systems in the ectomycorrhizal Laccaria bicolor and the saprotrophic Phanerochaete chrysosporium

Sequencing of the Laccaria bicolor and Phanerochaete chrysosporium genomes, together with the availability of many fungal genomes, allow careful comparison to be made of these two basidiomycetes, which possess a different way of life (either symbiotic or saprophytic), with other fungi. Central to the antioxidant systems are superoxide dismutases, catalases and thiol-dependent peroxidases (Tpx). The two reducing systems (thioredoxin (Trx) and glutathione/glutaredoxin (Grx)) are of particular importance against oxidative insults, both for detoxification, through the regeneration of thiol-peroxidases, and for developmental, physiological and signalling processes. Among those thiol-dependent antioxidant systems, special emphasis is given to the redoxin and methionine sulfoxide reductase (Msr) multigenic families. The genes coding for these enzymes were identified in the L. bicolor and P. chrysosporium genomes, were correctly annotated, and the gene content, organization and distribution were compared with other fungi. Expression of the Laccaria genes was also compiled from microarray data. A complete classification, based essentially on gene structure, on phylogenetic and sequence analysis, and on existing experimental data, was proposed. Comparison of the gene content of fungi from all phyla did not show huge differences for multigenic families in the reactive oxygen species (ROS) detoxification network, although some protein subgroups were absent in some fungi.

MAPK signaling regulates nitric oxide and NADPH oxidase-dependent oxidative bursts in Nicotiana benthamiana

Nitric oxide (NO) and reactive oxygen species (ROS) act as signals in innate immunity in plants. The radical burst is induced by INF1 elicitin, produced by the oomycete pathogen Phytophthora infestans. NO ASSOCIATED1 (NOA1) and NADPH oxidase participate in the radical burst. Here, we show that mitogen-activated protein kinase (MAPK) cascades MEK2-SIPK/NTF4 and MEK1-NTF6 participate in the regulation of the radical burst. NO generation was induced by conditional activation of SIPK/NTF4, but not by NTF6, in Nicotiana benthamiana leaves. INF1- and SIPK/NTF4-mediated NO bursts were compromised by the knockdown of NOA1. However, ROS generation was induced by either SIPK/NTF4 or NTF6. INF1- and MAPK-mediated ROS generation was eliminated by silencing Respiratory Burst Oxidase Homolog B (RBOHB), an inducible form of the NADPH oxidase. INF1-induced expression of RBOHB was compromised in SIPK/NTF4/NTF6-silenced leaves. These results indicated that INF1 regulates NOA1-mediated NO and RBOHB-dependent ROS generation through MAPK cascades. NOA1 silencing induced high susceptibility to Colletotrichum orbiculare but not to P. infestans; conversely, RBOHB silencing decreased resistance to P. infestans but not to C. orbiculare. These results indicate that the effects of the radical burst on the defense response appear to be diverse in plant-pathogen interactions.

High resistance to oxidative stress in the fungal pathogen Candida glabrata is mediated by a single catalase, Cta1p, and is controlled by the transcription factors Yap1p, Skn7p, Msn2p, and Msn4p

We characterized the oxidative stress response of Candida glabrata to better understand the virulence of this fungal pathogen. C. glabrata could withstand higher concentrations of H(2)O(2) than Saccharomyces cerevisiae and even Candida albicans. Stationary-phase cells were extremely resistant to oxidative stress, and this resistance was dependent on the concerted roles of stress-related transcription factors Yap1p, Skn7p, and Msn4p. We showed that growing cells of C. glabrata were able to adapt to high levels of H(2)O(2) and that this adaptive response was dependent on Yap1p and Skn7p and partially on the general stress transcription factors Msn2p and Msn4p. C. glabrata has a single catalase gene, CTA1, which was absolutely required for resistance to H(2)O(2) in vitro. However, in a mouse model of systemic infection, a strain lacking CTA1 showed no effect on virulence.

Adaptive value of sex in microbial pathogens

Explaining the adaptive value of sex is one of the great outstanding problems in biology. The challenge comes from the difficulty in identifying the benefits provided by sex, which must outweigh the substantial costs of sex. Here, we consider the adaptive value of sex in viruses, bacteria and fungi, and particularly the information available on the adaptive role of sex in pathogenic microorganisms. Our general theme is that the varied aspects of sex in pathogens illustrate the varied issues surrounding the evolution of sex generally. These include, the benefits of sex (in the short- and long-term), as well as the costs of sex (both to the host and to the pathogen). For the benefits of sex (that is, its adaptive value), we consider three hypotheses: (i) sex provides for effective and efficient recombinational repair of DNA damages, (ii) sex provides DNA for food, and (iii) sex produces variation and reduces genetic associations among alleles under selection. Although the evolution of sex in microbial pathogens illustrates these general issues, our paper is not a general review of theories for the evolution of sex in all organisms. Rather, we focus on the adaptive value of sex in microbial pathogens and conclude that in terms of short-term benefits, the DNA repair hypothesis has the most support and is the most generally applicable hypothesis in this group. In particular, recombinational repair of DNA damages may substantially benefit pathogens when challenged by the oxidative defenses of the host. However, in the long-term, sex may help get rid of mutations, increase the rate of adaptation of the population, and, in pathogens, may infrequently create new infective strains. An additional general issue about sex illustrated by pathogens is that some of the most interesting consequences of sex are not necessarily the reasons for which sex evolved. For example, antibiotic resistance may be transferred by bacterial sex, but this transfer is probably not the reason sex evolved in bacteria.