Differential protein expression in Colletotrichum acutatum: changes associated with reactive oxygen species and nitrogen starvation implicated in pathogenicity on strawberry

Network Analysis of Publicly Available RNA-seq Provides Insights into the Molecular Mechanisms of Plant Defense against Multiple Fungal Pathogens in Arabidopsis thaliana

Fungal pathogens can have devastating effects on global crop production, leading to annual economic losses ranging from 10% to 23%. In light of climate change-related challenges, researchers anticipate an increase in fungal infections as a result of shifting environmental conditions. However, plants have developed intricate molecular mechanisms for effective defense against fungal attacks. Understanding these mechanisms is essential to the development of new strategies for protecting crops from multiple fungi threats. Public omics databases provide valuable resources for research on plant-pathogen interactions; however, integrating data from different studies can be challenging due to experimental variation. In this study, we aimed to identify the core genes that defend against the pathogenic fungi Colletotrichum higginsianum and Botrytis cinerea in Arabidopsis thaliana. Using a custom framework to control batch effects and construct Gene Co-expression Networks in publicly available RNA-seq dataset from infected A. thaliana plants, we successfully identified a gene module that was responsive to both pathogens. We also performed gene annotation to reveal the roles of previously unknown protein-coding genes in plant defenses against fungal infections. This research demonstrates the potential of publicly available RNA-seq data for identifying the core genes involved in defending against multiple fungal pathogens.

Uncovering genetic and metabolite markers associated with resistance against anthracnose fruit rot in northern highbush blueberry

Anthracnose fruit rot (AFR), caused by the fungal pathogen Colletotrichum fioriniae, is among the most destructive and widespread fruit disease of blueberry, impacting both yield and overall fruit quality. Blueberry cultivars have highly variable resistance against AFR. To date, this pathogen is largely controlled by applying various fungicides; thus, a more cost-effective and environmentally conscious solution for AFR is needed. Here we report three quantitative trait loci associated with AFR resistance in northern highbush blueberry (Vaccinium corymbosum). Candidate genes within these genomic regions are associated with the biosynthesis of flavonoids (e.g. anthocyanins) and resistance against pathogens. Furthermore, we examined gene expression changes in fruits following inoculation with Colletotrichum in a resistant cultivar, which revealed an enrichment of significantly differentially expressed genes associated with certain specialized metabolic pathways (e.g. flavonol biosynthesis) and pathogen resistance. Using non-targeted metabolite profiling, we identified a flavonol glycoside with properties consistent with a quercetin rhamnoside as a compound exhibiting significant abundance differences among the most resistant and susceptible individuals from the genetic mapping population. Further analysis revealed that this compound exhibits significant abundance differences among the most resistant and susceptible individuals when analyzed as two groups. However, individuals within each group displayed considerable overlapping variation in this compound, suggesting that its abundance may only be partially associated with resistance against C. fioriniae. These findings should serve as a powerful resource that will enable breeding programs to more easily develop new cultivars with superior resistance to AFR and as the basis of future research studies.

Differential Expression of Cell Wall Remodeling Genes Is Part of the Dynamic Phase-Specific Transcriptional Program of Conidial Germination of Trichoderma asperelloides

The nature of saprophytic and mycoparasitic hyphal growth of Trichoderma spp. has been studied extensively, yet its initiation via conidial germination in this genus is less well understood. Using near-synchronous germinating cultures of Trichoderma asperelloides, we followed the morphological progression from dormant conidia to initial polar growth to germling formation and to evidence for first branching. We found that the stage-specific transcriptional profile of T. asperelloides is one of the most dynamic described to date: transcript abundance of over 5000 genes-comprising approximately half of the annotated genome-was unremittingly reduced in the transition from dormancy to polar growth. Conversely, after the onset of germination, the transcript abundance of approximately a quarter of the genome was unremittingly elevated during the transition from elongation to initial branching. These changes are a testimony to the substantial developmental events that accompany germination. Bayesian network analysis identified several chitinase- and glucanase-encoding genes as active transcriptional hubs during germination. Furthermore, the expression of specific members of the chitin synthase and glucan elongase families was significantly increased during germination in the presence of Rhizoctonia solani-a known host of the mycoparasite-indicating that host recognition can occur during the early stages of mycoparasite development.

In Planta Transcriptome and Proteome Profiles of Spongospora subterranea in Resistant and Susceptible Host Environments Illuminates Regulatory Principles Underlying Host-Pathogen Interaction

Simple Summary

Infections of potato tubers and roots by Spongospora subterranea result in powdery scab and root diseases. Losses due to infections with S. subterranea are substantial in most potato-growing regions of the world with no fully effective treatments available. Understanding the gene regulation of pathogens in their host is dependent on multidimensional datasets. In this study, we profiled the transcriptome and proteome of S. subterranea within the susceptible and resistant host. Enzyme activity and nucleic acid metabolism appear to be important to the virulence of S. subterranea. Our results provide a good resource for future functional studies of powdery scab and might be useful in S. subterranea inoculum management.

Abstract

Spongospora subterranea is an obligate biotrophic pathogen, causing substantial economic loss to potato industries globally. Currently, there are no fully effective management strategies for the control of potato diseases caused by S. subterranea. To further our understanding of S. subterranea biology during infection, we characterized the transcriptome and proteome of the pathogen during the invasion of roots of a susceptible and a resistant potato cultivar. A total of 7650 transcripts from S. subterranea were identified in the transcriptome analysis in which 1377 transcripts were differentially expressed between two cultivars. In proteome analysis, we identified 117 proteins with 42 proteins significantly changed in comparisons between resistant and susceptible cultivars. The functional annotation of transcriptome data indicated that the gene ontology terms related to the transportation and actin processes were induced in the resistant cultivar. The downregulation of enzyme activity and nucleic acid metabolism in the resistant cultivar suggests a probable influence of these processes in the virulence of S. subterranea. The protein analysis results indicated that the majority of differentially expressed proteins were related to the metabolic processes and transporter activity. The present study provides a comprehensive molecular insight into the multiple layers of gene regulation that contribute to S. subterranea infection and development in planta and illuminates the role of host immunity in affecting pathogen responses.

Quantitative proteomics provides an insight into germination-related proteins in the obligate biotrophic plant pathogen Spongospora subterranea

The soil-borne and obligate plant-associated nature of S. subterranea has hindered a detailed study of this pathogen and in particular, the regulatory pathways driving the germination of S. subterranea remain unknown. To better understand the mechanisms that control the transition from dormancy to germination, protein profiles between dormant and germination stimulant-treated resting spores were compared using label-free quantitative proteomics. Among the ~680 proteins identified 20 proteins were found to be differentially expressed during the germination of S. subterranea resting spores. Elongation factor Tu, histones (H2A and H15), proteasome and DJ-1_PfpI, involved in transcription and translation, were upregulated during the germination of resting spores. Downregulation of both actin and beta-tubulin proteins occurred in the germinating spores, indicating that the changes in the cell wall cytoskeleton may be necessary for the morphological changes during the germination of the resting spore in S. subterranea. Our findings provide new approaches for the study of these and similar recalcitrant micro-organisms provide the first insights into the basic protein components of S. subterranea spores. A better understanding of S. subterranea biology may lead to the development of novel approaches for the management of persistent soil inoculum.

GCN4 Regulates Secondary Metabolism through Activation of Antioxidant Gene Expression under Nitrogen Limitation Conditions in Ganoderma lucidum

Nitrogen limitation has been widely reported to affect the growth and development of fungi, and the transcription factor GCN4 (general control nonderepressible 4) is involved in nitrogen restriction. Here, we found that nitrogen limitation highly induced the expression of GCN4 and promoted the synthesis of ganoderic acid (GA), an important secondary metabolite in Ganoderma lucidum. The activated GCN4 is involved in regulating GA biosynthesis. In addition, the accumulation of reactive oxygen species (ROS) also affects the synthesis of GA under nitrogen restrictions. The silencing of the gcn4 gene led to further accumulation of ROS and increased the content of GA. Further studies found that GCN4 activated the transcription of antioxidant enzyme biosynthesis genes gr, gst2, and cat3 (encoding glutathione reductase, glutathione S-transferase, and catalase, respectively) through direct binding to the promoter of these genes to reduce the ROS accumulation. In conclusion, our study found that GCN4 directly interacts with the ROS signaling pathway to negatively regulate GA biosynthesis under nitrogen-limiting conditions. This provides an essential insight into the understanding of GCN4 transcriptional regulation of the ROS signaling pathway and enriches the knowledge of nitrogen regulation mechanisms in fungal secondary metabolism of G. lucidum. IMPORTANCE Nitrogen has been widely reported to regulate secondary metabolism in fungi. Our study assessed the specific nitrogen regulatory mechanisms in Ganoderma lucidum. We found that GCN4 directly interacts with the ROS signaling pathway to negatively regulate GA biosynthesis under nitrogen-limiting conditions. Our research highlights a novel insight that GCN4, the nitrogen utilization regulator, participates in secondary metabolism through ROS signal regulation. In addition, this also provides a theoretical foundation for exploring the regulation of other physiological processes by GCN4 through ROS in fungi.

Comparative response of Metarhizium brunneum to the cuticles of susceptible and resistant hosts

Earlier studies demonstrated that Metarhizium brunneum, usually a broad-host pathogen of arthropods, is unable to complete its pathogenic life cycle when inoculated on the fungus-resistant tick, Hyalomma excavatum engorged females. While the fungus penetrates the cuticle of fungus-susceptible tick, Rhipicephalus annulatus females, it is unable to penetrate the cuticle of fungus-resistant tick, and even perishes on its surface. This is probably due to high concentration of antifungal fatty acids and probably also due to a hypersensitive-like response of the tick. To understand the metabolic pathways occurring in the fungal hyphae upon encountering the cuticles, we compared the response of the fungus to cuticle from susceptible and resistant tick cuticles by 2D-gels. The intracellular proteomes of M. brunneum Mb7 exposed to cuticle of the fungus-susceptible tick, R. annulatus, and to the fungus-resistant tick, H. excavatum engorged females were compared after exposure to either cuticles. By means of liquid chromatography-mass spectrometry/mass spectrometry we identified in both proteomes common proteins involved in biological processes as well as unique proteins identified only in the proteome of fungus exposed to fungus-resistant tick cuticle. These proteins were identified in high probability as heat shock proteins, four key enzymes of the glyoxylate cycle, and proteins associated with hypoxia, and exposure to antifungal drugs. These findings are discussed within the M. brunneum-tick pathosystem in relation to tick resistance and host resistance in general.

Deciphering the Infectious Process of Colletotrichum lupini in Lupin through Transcriptomic and Proteomic Analysis

The fungal phytopathogen Colletotrichum lupini is responsible for lupin anthracnose, resulting in significant yield losses worldwide. The molecular mechanisms underlying this infectious process are yet to be elucidated. This study proposes to evaluate C. lupini gene expression and protein synthesis during lupin infection, using, respectively, an RNAseq-based transcriptomic approach and a mass spectrometry-based proteomic approach. Patterns of differentially-expressed genes in planta were evaluated from 24 to 84 hours post-inoculation, and compared to in vitro cultures. A total of 897 differentially-expressed genes were identified from C. lupini during interaction with white lupin, of which 520 genes were predicted to have a putative function, including carbohydrate active enzyme, effector, protease or transporter-encoding genes, commonly described as pathogenicity factors for other Colletotrichum species during plant infection, and 377 hypothetical proteins. Simultaneously, a total of 304 proteins produced during the interaction were identified and quantified by mass spectrometry. Taken together, the results highlight that the dynamics of symptoms, gene expression and protein synthesis shared similarities to those of hemibiotrophic pathogens. In addition, a few genes with unknown or poorly-described functions were found to be specifically associated with the early or late stages of infection, suggesting that they may be of importance for pathogenicity. This study, conducted for the first time on a species belonging to the Colletotrichum acutatum species complex, presents an opportunity to deepen functional analyses of the genes involved in the pathogenicity of Colletotrichum spp. during the onset of plant infection.

In vitro growth of Colletotrichum gloeosporioides is affected by butyl acetate, a compound produced during the co-culture of Trichoderma sp. and Bacillus subtilis

The co-culture of plant beneficial microbes to stimulate the production of antimicrobial metabolites is gaining ground. Here, the inactivated Colletotrichum gloeosporioides mycelium was used to induce the biosynthesis of antifungal compounds in the co-culture systems of Trichoderma sp. and Bacillus subtilis. The hexanic extracts obtained from the co-culture systems were tested against C. gloeosporioides. Those that inhibited the phytopathogen growth were further fractionated by column and thin-layer chromatography and analyzed by gas chromatography coupled to mass spectrometry (GC-MS). Ethyl butanoate, butyl acetate, acetic acid, 2-butoxyethanol, 3,5-di-tert-butyl-4-hydroxybenzaldehyde, 3,5-di-tert-butyl-4-hydroxybenzyl alcohol, hexadecanoic acid, and octadecanoic acid were identified. Butyl acetate was the most abundant compound, and its application affected the morphology and mycelial development of C. gloeosporioides, thereby inhibiting the radial growth, reducing spore formation, and inducing soft colonies. We conclude that co-culturing Trichoderma sp. and B. subtilis promotes the production of novel diffusible organic compounds with an antifungal effect on C. gloeosporioides.

In vitro antifungal activity of dimethyl trisulfide against Colletotrichum gloeosporioides from mango

Colletotrichum gloeosporioides, one of the main agents of mango anthracnose, causes latent infections in unripe mango, and leads to huge economic losses during storage and transport. Dimethyl trisulfide (DMTS), one of the main volatile compounds produced by some microorganisms or plants, has shown antifungal activity against some phytopathogens in previous studies, but its effects on C. gloeosporioides and mechanisms of action have not been well characterized. In fumigation trials of conidia and mycelia of C. gloeosporioides for 2, 4, 6, 8, or 10 h, at a concentration of 100 μL/L of air space in vitro, DMTS caused serious damage to the integrity of plasma membranes, which significantly reduced the survival rate of spores, and resulted in abnormal hyphal morphology. Moreover, DMTS caused deterioration of subcellular structures of conidia and mycelia, such as cell walls, plasma membranes, Golgi bodies, and mitochondria, and contributed to leakage of protoplasm, thus promoting vacuole formation. In addition, to better understand the molecular mechanisms of the antifungal activity, the global gene expression profiles of isolate C. gloeosporioides TD3 treated in vitro with DMTS at a concentration of 100 μL/L of air for 0 h (Control), 1 h, or 3 h were investigated by RNA sequencing (RNA-seq), and over 62 Gb clean reads were generated from nine samples. Similar expressional patterns for nine differentially expressed genes (DEGs) in both RNA-seq and qRT-PCR assays showed the reliability of the RNA-seq data. In comparison to the non-treated control groups, we found DMTS suppressed expression of β-1, 3-D-glucan, chitin, sterol biosynthesis-related genes, and membrane protein-related genes. These genes related to the formation of fungal cell walls and plasma membranes might be associated with the toxicity of DMTS against C. gloeosporioides. This is the first study demonstrating antifungal activity of DMTS against C. gloeosporioides on mango by direct damage of conidia and hyphae, thus providing a novel tool for postharvest control of mango anthracnose.

Induced expression of the Fragaria × ananassa Rapid alkalinization factor-33-like gene decreases anthracnose ontogenic resistance of unripe strawberry fruit stages

Rapid alkalinization factor (RALF) genes encode for ubiquitous small peptides that stimulate apoplastic alkalinization through interaction with malectin-like receptor kinase. RALF peptides may act as negative regulators of plant immune response, inhibiting the formation of the signal receptor complex for immune activation. Recently RALF homologues were identified in different fungal pathogen genomes contributing to host infection ability. Here, FaRALF-33-like gene expression was evaluated in strawberry fruits inoculated with Colletotrichum acutatum, Botrytis cinerea, or Penicillium expansum after 24 and 48 h post-infection. To investigate the role of FaRALF-33-like in strawberry susceptibility, transient transformation was used to overexpress it in white unripe fruits and silence it in red ripe fruits. Agroinfiltrated fruits were inoculated with C. acutatum and expression, and histological analysis of infection were performed. Silencing of FaRALF-33-like expression in C. acutatum-inoculated red fruits led to a delay in fruit colonization by the fungal pathogen, and infected tissues showed less penetrated infective hyphae than in wild-type fruits. In contrast, C. acutatum-inoculated white unripe fruits overexpressing the FaRALF-33-like gene decreased the ontogenic resistance of these fruits, leading to the appearance of disease symptoms and penetrated subcuticular hyphae, normally absent in white unripe fruits. The different response of transfected strawberry fruits to C. acutatum supports the hypothesis that the FaRALF-33-like gene plays an important role in the susceptibility of fruits to the fungal pathogen C. acutatum.

Csn5 Is Required for the Conidiogenesis and Pathogenesis of the Alternaria alternata Tangerine Pathotype

The COP9 signalosome (CSN) is a highly conserved protein complex involved in the ubiquitin-proteasome system. Its metalloisopeptidase activity resides in subunit 5 (CSN5). Functions of csn5 in phytopathogenic fungi are poorly understood. Here, we knocked out the csn5 ortholog (Aacsn5) in the tangerine pathotype of Alternaria alternata. The ΔAacsn5 mutant showed a moderately reduced growth rate compared to the wildtype strain and was unable to produce conidia. The growth of ΔAacsn5 mutant was not affected in response to oxidative and osmotic stresses. Virulence assays revealed that ΔAacsn5 induced no or significantly reduced necrotic lesions on detached citrus leaves. The defects in hyphal growth, conidial sporulation, and pathogenicity of ΔAacsn5 were restored by genetic complementation of the mutant with wildtype Aacsn5. To explore the molecular mechanisms of conidiation and pathogenesis underlying Aacsn5 regulation, we systematically examined the transcriptomes of both ΔAacsn5 and the wildtype. Generally, 881 genes were overexpressed and 777 were underexpressed in the ΔAacsn5 mutant during conidiation while 694 overexpressed and 993 underexpressed during infection. During asexual development, genes related to the transport processes and nitrogen metabolism were significantly downregulated; the expression of csn1-4 and csn7 in ΔAacsn5 was significantly elevated; secondary metabolism gene clusters were broadly affected; especially, the transcript level of the whole of cluster 28 and 30 was strongly induced. During infection, the expression of the host-specific ACT toxin gene cluster which controls the biosynthesis of the citrus specific toxin was significantly repressed; many other SM clusters with unknown products were also regulated; 86 out of 373 carbohydrate-active enzymes responsible for breaking down the plant dead tissues showed uniquely decreased expression. Taken together, our results expand our understanding of the roles of csn5 on conidiation and pathogenicity in plant pathogenic fungi and provide a foundation for future investigations.

Comparative proteomic analysis between nitrogen supplemented and starved conditions in Magnaporthe oryzae

BACKGROUND

Fungi are constantly exposed to nitrogen limiting environments, and thus the efficient regulation of nitrogen metabolism is essential for their survival, growth, development and pathogenicity. To understand how the rice blast pathogen Magnaporthe oryzae copes with limited nitrogen availability, a global proteome analysis under nitrogen supplemented and nitrogen starved conditions was completed.

METHODS

M. oryzae strain 70-15 was cultivated in liquid minimal media and transferred to media with nitrate or without a nitrogen source. Proteins were isolated and subjected to unfractionated gel-free based liquid chromatography-tandem mass spectrometry (LC-MS/MS). The subcellular localization and function of the identified proteins were predicted using bioinformatics tools.

RESULTS

A total of 5498 M. oryzae proteins were identified. Comparative analysis of protein expression showed 363 proteins and 266 proteins significantly induced or uniquely expressed under nitrogen starved or nitrogen supplemented conditions, respectively. A functional analysis of differentially expressed proteins revealed that during nitrogen starvation nitrogen catabolite repression, melanin biosynthesis, protein degradation and protein translation pathways underwent extensive alterations. In addition, nitrogen starvation induced accumulation of various extracellular proteins including small extracellular proteins consistent with observations of a link between nitrogen starvation and the development of pathogenicity in M. oryzae.

CONCLUSION

The results from this study provide a comprehensive understanding of fungal responses to nitrogen availability.

Irradiation by blue light in the presence of a photoacid confers changes to colony morphology of the plant pathogen Colletotrichum gloeosporioides

We used the photoacid 8-hydroxy-1,3,6-pyrenetrisulfonate (HPTS) that converts blue photons to acidic protons in water, with an efficiency of close to 100%, and determined that this treatment conferred changes to colony morphology of the plant pathogen Colletotrichum gloeosporioides. The time elapsed until hyphal collapse is noticed depends on both the laser intensity in mW/cm², and the concentration of HPTS in the Agar hydrogel. The time elapsed until hyphal collapse is noticed varies by only ±8% at HPTS concentrations of 500μM and at lower concentrations of HPTS the variance increases as the inverse of the concentration. We found that the effect on C. gloeosporioides was photoacid concentration and irradiation dose dependent. In the presence of 500μM of HPTS within the agar hydrogel-based medium, hyphae collapsed after 37±3.5min of irradiation at 405nm at an intensity of 25mW/cm². We propose two mechanisms for such photo-alteration of C. gloeosporioides. One is based on the pH drop in the extracellular environment by the photo-protolytic process that the photoacid molecule undergoes. The second mechanism is based on an intracellular mechanism in which there is an uptake of HPTS into the interior of the fungus. We suggest that both mechanisms for photo-alteration which we found in this study may occur in plants during fungal infection.

Optimization of the HyPer sensor for robust real-time detection of hydrogen peroxide in the rice blast fungus

Reactive oxygen species (ROS) production and breakdown have been studied in detail in plant-pathogenic fungi, including the rice blast fungus, Magnaporthe oryzae; however, the examination of the dynamic process of ROS production in real time has proven to be challenging. We resynthesized an existing ROS sensor, called HyPer, to exhibit optimized codon bias for fungi, specifically Neurospora crassa, and used a combination of microscopy and plate reader assays to determine whether this construct could detect changes in fungal ROS during the plant infection process. Using confocal microscopy, we were able to visualize fluctuating ROS levels during the formation of an appressorium on an artificial hydrophobic surface, as well as during infection on host leaves. Using the plate reader, we were able to ascertain measurements of hydrogen peroxide (H₂ O₂ ) levels in conidia as detected by the MoHyPer sensor. Overall, by the optimization of codon usage for N. crassa and related fungal genomes, the MoHyPer sensor can be used as a robust, dynamic and powerful tool to both monitor and quantify H₂ O₂ dynamics in real time during important stages of the plant infection process.

Transcriptome Profiling of the Phaseolus vulgaris - Colletotrichum lindemuthianum Pathosystem

Bean (Phaseolus vulgaris) anthracnose caused by the hemi-biotrophic pathogen Colletotrichum lindemuthianum is a major factor limiting production worldwide. Although sources of resistance have been identified and characterized, the early molecular events in the host-pathogen interface have not been investigated. In the current study, we conducted a comprehensive transcriptome analysis using Illumina sequencing of two near isogenic lines (NILs) differing for the presence of the Co-1 gene on chromosome Pv01 during a time course following infection with race 73 of C. lindemuthianum. From this, we identified 3,250 significantly differentially expressed genes (DEGs) within and between the NILs over the time course of infection. During the biotrophic phase the majority of DEGs were up regulated in the susceptible NIL, whereas more DEGs were up-regulated in the resistant NIL during the necrotrophic phase. Various defense related genes, such as those encoding PR proteins, peroxidases, lipoxygenases were up regulated in the resistant NIL. Conversely, genes encoding sugar transporters were up-regulated in the susceptible NIL during the later stages of infection. Additionally, numerous transcription factors (TFs) and candidate genes within the vicinity of the Co-1 locus were differentially expressed, suggesting a global reprogramming of gene expression in and around the Co-1 locus. Through this analysis, we reduced the previous number of candidate genes reported at the Co-1 locus from eight to three. These results suggest the dynamic nature of P. vulgaris-C. lindemuthianum interaction at the transcriptomic level and reflect the role of both pathogen and effector triggered immunity on changes in plant gene expression.

Characterization of a Ran gene from Puccinia striiformis f. sp. tritici involved in fungal growth and anti-cell death

Ran, an important family of small GTP-binding proteins, has been shown to regulate a variety of important cellular processes in many eukaryotes. However, little is known about Ran function in pathogenic fungi. In this study, we report the identification and functional analysis of a Ran gene (designated PsRan) from Puccinia striiformis f. sp. tritici (Pst), an important fungal pathogen affecting wheat production worldwide. The PsRan protein contains all conserved domains of Ran GTPases and shares more than 70% identity with Ran proteins from other organisms, indicating that Ran proteins are conserved in different organisms. PsRan shows a low level of intra-species polymorphism and is localized to the nucleus. qRT-PCR analysis showed that transcript level of PsRan was induced in planta during Pst infection. Silencing of PsRan did not alter Pst virulence phenotype but impeded fungal growth of Pst. In addition, heterologous overexpression of PsRan in plant failed to induce cell death but suppressed cell death triggered by a mouse BAX gene or a Pst Ras gene. Our results suggest that PsRan is involved in the regulation of fungal growth and anti-cell death, which provides significant insight into Ran function in pathogenic fungi.

Role of the Colletotrichum acutatum sesquiterpene synthase CaTPS in the biosynthesis of sesquiterpenoids

Colletotrichum acutatum is a major fungal pathogen of fruit crops, which causes severe yield losses in strawberry production. A potential key factor in plant-pathogen interactions is fungal sesquiterpenoids which have mycotoxic and phytotoxic activities. The first committed step in sesquiterpenoid biosynthesis is performed by sesquiterpene synthases (TPS). Only a few TPSs have been functionally characterized from filamentous fungi and none from the genus Colletotrichum. Despite being an important fungal pathogen to agriculture, it is poorly understood at the molecular and chemical levels. The terpenoid biochemistry in Coll. acutatum strain SA 0-1 was studied and one Coll. acutatum TPS (CaTPS) was successfully cloned and characterized in yeast. CaTPS catalyses the biosynthesis of multiple sesquiterpenoids. The two major products are β-caryophyllene and an unidentified sesquiterpenoid along with α-humulene as one of the minor sesquiterpenoid products. These products were also secreted by the fungus in strawberry fruit medium along with several other sesquiterpenoids indicating other TPSs are active during in vitro growth. β-Caryophyllene and α-humulene are known cytotoxic products important for ecological interactions and are produced by SA 0-1. Interestingly, a gene expression analysis using quantitative real-time PCR revealed a significant increase in expression of CaTPS during strawberry fruit infection, thus indicating that it could be involved in fruit infection. This is, we believe, the first characterization of TPS in Colletotrichum spp. and terpenoid profiles of Coll. acutatum, which could facilitate studies on the role of terpenoids in the ecology of Coll. acutatum.

Proteomic and morphometric study of the in vitro interaction between Oncidium sphacelatum Lindl. (Orchidaceae) and Thanatephorus sp. RG26 (Ceratobasidiaceae)

Orchidaceae establish symbiotic relationships with fungi in the Rhizoctonia group, resulting in interactions beneficial to both organisms or in cell destruction in one of them (pathogenicity). Previous studies have focused mostly on terrestrial species with a few, preliminary studies, on epiphytes. To further our understanding of the molecular mechanisms involved in these symbioses, we evaluated the interaction between Oncidium sphacelatum Lindl. and the mycorrhizal fungus Thanatephorus sp. strain RG26 (isolated from a different orchid species) in vitro using morphometric and proteomic analyses. Evidence from the morphometric and microscopic analysis showed that the fungus promoted linear growth and differentiation of orchid protocorms during 98 days interaction. On day 63, protocorm development was evident, so we analyzed the physiological response of both organisms at that moment. Proteome results suggest that orchid development stimulated by the fungus apparently involves cell cycle proteins, purine recycling, ribosome biogenesis, energy metabolism, and secretion that were up-regulated in the orchid; whereas in the fungus, a high expression of proteins implicated in stress response, protein-protein interaction, and saccharides and protein biosynthesis were found in the symbiotic interaction. This is the first work reporting proteins differentially expressed in the epiphytic orchid-fungus interaction and will contribute to the search for molecular markers that will facilitate the study of this symbiosis in both wild orchids and those in danger of extinction.

Comparative Validation of Conventional and RNA-Seq Data-Derived Reference Genes for qPCR Expression Studies of Colletotrichum kahawae

Colletotrichum kahawae is an emergent fungal pathogen causing severe epidemics of Coffee Berry Disease on Arabica coffee crops in Africa. Currently, the molecular mechanisms underlying the Coffea arabica—C. kahawae interaction are still poorly understood, as well as the differences in pathogen aggressiveness, which makes the development of functional studies for this pathosystem a crucial step. Quantitative real time PCR (qPCR) has been one of the most promising approaches to perform gene expression analyses. However, proper data normalization with suitable reference genes is an absolute requirement. In this study, a set of 8 candidate reference genes were selected based on two different approaches (literature and Illumina RNA-seq datasets) to assess the best normalization factor for qPCR expression analysis of C. kahawae samples. The gene expression stability of candidate reference genes was evaluated for four isolates of C. kahawae bearing different aggressiveness patterns (Ang29, Ang67, Zim12 and Que2), at different stages of fungal development and key time points of the plant-fungus interaction process. Gene expression stability was assessed using the pairwise method incorporated in geNorm and the model-based method used by NormFinder software. For C. arabica—C. kahawae interaction samples, the best normalization factor included the combination of PP1, Act and ck34620 genes, while for C. kahawae samples the combination of PP1, Act and ck20430 revealed to be the most appropriate choice. These results suggest that RNA-seq analyses can provide alternative sources of reference genes in addition to classical reference genes. The analysis of expression profiles of bifunctional catalase-peroxidase (cat2) and trihydroxynaphthalene reductase (thr1) genes further enabled the validation of the selected reference genes. This study provides, for the first time, the tools required to conduct accurate qPCR studies in C. kahawae considering its aggressiveness pattern, developmental stage and host interaction.

Comparative analyses of secreted proteins from the phytopathogenic fungus Verticillium dahliae in response to nitrogen starvation

The soilborne fungus Verticillium dahliae is the major pathogen that causes the verticillium wilt disease of plants, which leads to huge economic loss worldwide. At the early stage of infection, growth of the pathogen is subject to the nutrition stress of limited nitrogen. To investigate the secreted pathogenic proteins that play indispensable roles during invasion at this stage, we compared the profiles of secreted proteins of V. dahliae under nitrogen starvation and normal conditions by using in-gel and in-solution digestion combined with liquid chromatography-nano-electrospray ionization tandem mass spectrometry (LC-nanoESI-MS). In total, we identified 212 proteins from the supernatant of liquid medium, including 109 putative secreted proteins. Comparative analysis indicated that the expression of 76 proteins was induced, whereas that of 9 proteins was suppressed under nitrogen starvation. Notably, 24 proteins are constitutively expressed. Further bioinformatic exploration enabled us to classify the stress-induced proteins into seven functional groups: cell wall degradation (10.5%), reactive oxygen species (ROS) scavenging and stress response (11.8%), lipid effectors (5.3%), protein metabolism (21.1%), carbohydrate metabolism (15.8%), electron-proton transport and energy metabolism (14.5%), and other (21.0%). In addition, most stress-suppressed proteins are involved in the cell-wall remodeling. Taken together, our analyses provide insights into the pathogenesis of V. dahliae and might give hints for the development of novel strategy against the verticillium wilt disease.

Differential protein accumulations in isolates of the strawberry wilt pathogen Fusarium oxysporum f. sp. fragariae differing in virulence

This study was conducted to define differences in Fusarium oxysporum f. sp. fragariae (Fof) isolates with different virulence efficiency to strawberry at the proteome level, in combination with their differences in mycelial growth, conidial production and germination. Comparative proteome analyses revealed substantial differences in mycelial proteomes between Fof isolates, where the 54 differentially accumulated protein spots were consistently over-accumulated or exclusively in the highly virulent isolate. These protein spots were identified through MALDI-TOF/TOF mass spectrometry analyses, and the identified proteins were mainly related to primary and protein metabolism, antioxidation, electron transport, cell cycle and transcription based on their putative functions. Proteins of great potential as Fof virulence factors were those involved in ubiquitin/proteasome-mediated protein degradation and reactive oxygen species detoxification; the hydrolysis-related protein haloacid dehalogenase superfamily hydrolase; 3,4-dihydroxy-2-butanone 4-phosphate synthase associated with riboflavin biosynthesis; and those exclusive to the highly virulent isolate. In addition, post-translational modifications may also make an important contribution to Fof virulence.

BIOLOGICAL SIGNIFICANCE

F. oxysporum f. sp. fragariae (Fof), the causal agent of Fusarium wilt in strawberry, is a serious threat to commercial strawberry production worldwide. However, factors and mechanisms contributing to Fof virulence remained unknown. This study provides knowledge of the molecular basis for the differential expression of virulence in Fof, allowing new possibilities towards developing alternative and more effective strategies to manage Fusarium wilt.

Elucidating the fungal stress response by proteomics

Fungal species need to cope with stress, both in the natural environment and during interaction of human- or plant pathogenic fungi with their host. Many regulatory circuits governing the fungal stress response have already been discovered. However, there are still large gaps in the knowledge concerning the changes of the proteome during adaptation to environmental stress conditions. With the application of proteomic methods, particularly 2D-gel and gel-free, LC/MS-based methods, first insights into the composition and dynamic changes of the fungal stress proteome could be obtained. Here, we review the recent proteome data generated for filamentous fungi and yeasts. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.

γ-Glutamyltransferases (GGT) in Colletotrichum graminicola: mRNA and enzyme activity, and evidence that CgGGT1 allows glutathione utilization during nitrogen deficiency

Gamma-glutamyltransferase (GGT, EC 2.3.2.2) cleaves the γ-glutamyl linkage in glutathione (GSH). Three GGTs in the hemibiotrophic plant pathogen Colletotrichum graminicola were identified in silico. GGT mRNA expression was monitored by quantitative reverse-transcriptase PCR. Expression of all three genes was detected in planta during the biotrophic and necrotrophic stages of infection. Of the three GGTs, CgGGT1 mRNA (from gene GLRG_09590) was the most highly expressed. All three GGT mRNAs were up-regulated in wild type nitrogen-starved germlings in comparison to non-starved germlings. CgGGT1 was insertionally mutagenized in C. graminicola, complemented with the wild type form of the gene, and over-expressed. Enzyme assays of two independent CgGGT1 knockouts and the wild type indicated that CgGGT1 is the major GGT and accounts for 86% and 68% of total GGT activity in conidia and mycelia, respectively. The over-expressing strain had 8-fold and 3-fold more enzyme activity in conidia and mycelia, respectively, than the wild type. In an analysis of the GGT knockout, complemented and over-expressing strains, GGT1 transcript levels are highly correlated (r=0.95) with levels of total GGT enzyme activity. CgGGT1 and CgGGT2 genes in strains that had ectopic copies of CgGGT1 were not up-regulated by nitrogen-starvation, in contrast to the wild type. Deletion or over-expression of CgGGT1 had no effect on mRNA expression of CgGGT2 and CgGGT3. In broth in which 3 and 6mM glutathione (GSH) was the nitrogen source, the CgGGT1 over-expressing strain produced significantly (P<0.0001) more biomass than the wild type and complemented strains, whereas the CgGGT1Δ strains produced significantly (P<0.0001) less biomass than the wild type strain. This suggests that CgGGT1 is involved in utilizing GSH as a nitrogen source. However, deletion and over-expression of CgGGT1 had no effect on either virulence in wounded corn leaf sheaths or GSH levels in conidia and mycelia. Thus, the regulation of GSH concentration is apparently independent of CgGGT1 activity.

A bacterial-fungal metaproteomic analysis enlightens an intriguing multicomponent interaction in the rhizosphere of Lactuca sativa

Fusarium oxysporum MSA 35 [wild-type (WT) strain] is an antagonistic isolate that protects plants against pathogenic Fusaria. This strain lives in association with ectosymbiotic bacteria. When cured of the prokaryotic symbionts [cured (CU) form], the fungus is pathogenic, causing wilt symptoms similar to those of F. oxysporum f.sp. lactucae. The aim of this study was to understand if and how the host plant Lactuca sativa contributes to the expression of the antagonistic/pathogenic behaviors of MSA 35 strains. A time-course comparative analysis of the proteomic profiles of WT and CU strains was performed. Fungal proteins expressed during the early stages of plant-fungus interaction were involved in stress defense, energy metabolism, and virulence and were equally induced in both strains. In the late phase of the interkingdom interaction, only CU strain continued the production of virulence- and energy-related proteins. The expression analysis of lettuce genes coding for proteins involved in resistance-related processes corroborated proteomic data by showing that, at the beginning of the interaction, both fungi are perceived by the plant as pathogen. On the contrary, after 8 days, only the CU strain is able to induce plant gene expression. For the first time, it was demonstrated that an antagonistic F. oxysporum behaves initially as pathogen, showing an interesting similarity with other beneficial organisms such as mychorrizae.

Comparative secretome investigation of Magnaporthe oryzae proteins responsive to nitrogen starvation

Magnaporthe oryzae is a fungal pathogen that causes blast disease in rice. During its early infection process, during which starvation of nutrients, including nitrogen, prevails before establishment of successful infection, the fungally secreted proteins play an important role in the pathogenicity and stress response. In this study, M. oryzae-secreted proteins were investigated in an N-deficient minimal medium using two-dimensional gel electrophoresis (2-DGE) coupled with mass spectrometry analysis (MALDI-TOF-MS and μLC-ESI-MS/MS). The 2-DGE analysis of secreted proteins detected 89 differentially expressed protein spots (14 downregulated and 75 upregulated) responsive to N starvation. Eighty five of the protein spots were identified by mass spectrometry analyses. Identified proteins were mainly cell wall hydrolase enzymes (22.4%), protein and lipid hydrolases (24.7%), reactive oxygen species detoxifying proteins (22.4%), and proteins with unknown function (14.1%), suggesting early production of prerequisite proteins for successful infection of the host. SignalP analysis predicted the presence of signal peptides in 67% of the identified proteins, suggesting that in addition to the classical Golgi/endoplasmic reticulum secretory pathway, M. oryzae might possess other, as yet undefined, secretory pathways. Those nonclassical or leaderless secretion proteins accounted for 25.9% of the total identified proteins by TatP and SecretomeP predictions. Semiquantitative reverse transcriptase polymerase chain reaction of seven randomly selected N-responsive secreted proteins also revealed a good correlation between RNA and protein levels. Taken together, the establishment of the M. oryzae secretome that is responsive to N starvation provides the first evidence of the secretion of 60 unreported and 25 previously known proteins. This developed protein inventory could be exploited to improve our understanding of the secretory mechanisms of M. oryzae and its invasive growth process in rice tissue.

Identification of differentially expressed genes in a resistant versus a susceptible blueberry cultivar after infection by Colletotrichum acutatum

Anthracnose fruit rot, caused by the fungus Colletotrichum acutatum, is an important disease of blueberry worldwide. The cultivar Elliott is resistant, severely restricting fungal growth and sporulation relative to the susceptible cultivar Jersey. The objectives of this research were as follows: (i) to analyse pre-penetration events in 'Elliott' and 'Jersey' at different stages of fruit development; (ii) to identify putative defence genes in 'Elliott' fruit; and (iii) to monitor the timing of the oxidative burst in both cultivars. Light microscopy revealed no differences in the pre-penetration activities of C. acutatum on the immature fruit of both cultivars. However, at fruit ripening, conidia germinated and formed appressoria more rapidly on 'Jersey' than on 'Elliott' fruit. Using suppression subtractive hybridization, 37 differentially expressed sequence tags (ESTs) were detected in 'Elliott' versus 'Jersey' upon infection. Several of the ESTs had homology to known plant defence genes, such as a class II chitinase, pathogenesis-related protein 10 (PR10) and β-1,3-glucanase. Two putative genes involved in oxidative stress were identified: a metallothionein-like protein and monodehydroascorbate reductase. ESTs of fungal origin were also detected. Many ESTs had no homology to known genes. Using semi-quantitative and quantitative reverse transcription-polymerase chain reaction (RT-PCR), the expression of most of the candidate genes was detected earlier in 'Elliott' than in 'Jersey', some within 24 h post inoculation (hpi). Monitoring of the oxidative burst showed that the overall H(2) O(2) concentration was two to three times higher in 'Elliott' than in 'Jersey' at 24 hpi. The elucidation of the basis of resistance to C. acutatum in blueberry will facilitate the development of new anthracnose fruit rot-resistant cultivars.

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.

A nitrogen response pathway regulates virulence functions in Fusarium oxysporum via the protein kinase TOR and the bZIP protein MeaB

During infection, fungal pathogens activate virulence mechanisms, such as host adhesion, penetration and invasive growth. In the vascular wilt fungus Fusarium oxysporum, the mitogen-activated protein kinase Fmk1 is required for plant infection and controls processes such as cellophane penetration, vegetative hyphal fusion, or root adhesion. Here, we show that these virulence-related functions are repressed by the preferred nitrogen source ammonium and restored by treatment with l-methionine sulfoximine or rapamycin, two specific inhibitors of Gln synthetase and the protein kinase TOR, respectively. Deletion of the bZIP protein MeaB also resulted in nitrogen source-independent activation of virulence mechanisms. Activation of these functions did not require the global nitrogen regulator AreA, suggesting that MeaB-mediated repression of virulence functions does not act through inhibition of AreA. Tomato plants (Solanum lycopersicum) supplied with ammonium rather than nitrate showed a significant reduction in vascular wilt symptoms when infected with the wild type but not with the DeltameaB strain. Nitrogen source also affected invasive growth in the rice blast fungus Magnaporthe oryzae and the wheat head blight pathogen Fusarium graminearum. We propose that a conserved nitrogen-responsive pathway might operate via TOR and MeaB to control virulence in plant pathogenic fungi.

pH Regulation of ammonia secretion by Colletotrichum gloeosporioides and its effect on appressorium formation and pathogenicity

Host-tissue alkalinization via ammonia accumulation is key to Colletotrichum spp. colonization. Using macroarrays carrying C. gloeosporioides cDNAs, we monitored gene expression during the alkalinization process. A set of genes involved in synthesis and catabolism of ammonia accumulation were identified. Expression of NAD(+)-specific glutamate dehydrogenase (GDH2, encoding ammonia synthesis) and the ammonia exporter AMET were induced at pH 4.0 to 4.5. Conversely, ammonia uptake and transcript activation of the ammonia and glutamate importers (MEP and GLT, respectively) and glutamine synthase (GS1) were higher at pH 6.0 to 7.0. Accumulated ammonia in the wild-type mycelium decreased during ambient alkalinization, concurrent with increased GS1 expression. Deltapac1 mutants of C. gloeosporioides, which are sensitive to alkaline pH changes, showed upregulation of the acid-expressed GDH2 and downregulation of the alkaline-expressed GS1, resulting in 60% higher ammonia accumulation inside the mycelium. Deltagdh2 strains of C. gloeosporioides, impaired in ammonia production, showed 85% inhibition in appressorium formation followed by reduced colonization on avocado fruit (Persea americana cv. Fuerte) pericarp, while exogenic ammonia addition restored appressoria formation. Thus the modulation of genes involved in ammonia metabolism and catabolism by C. gloeosporioides is ambient pH-dependent. Aside from its contribution to necrotrophic stages, ammonia accumulation by germinating spores regulates appressorium formation and determines the initiation of biotrophic stages of avocado-fruit colonization by Colletotrichum spp.

SOD1-targeted gene disruption in the ericoid mycorrhizal fungus Oidiodendron maius reduces conidiation and the capacity for mycorrhization

The genome sequences of mycorrhizal fungi will provide new opportunities for studying the biology and the evolution underlying this symbiotic lifestyle. The generation of null mutants at the wild-type loci is one of the best methods for gene-function assignment in the post-genomic era. To our knowledge, the generation of superoxide dismutase 1 (SOD1)-null mutants in the ericoid mycorrhizal fungus Oidiodendron maius is the first example of a gene-targeted disruption via homologous recombination in a mycorrhizal fungus. The disruption of OmSOD1 by Agrobacterium-mediated transformation resulted in the presence of oxidative stress markers, even in the absence of external superimposed stresses, and an increased sensitivity to reactive oxygen species (ROS)-generating substances, especially to menadione. A reduction in conidiation and in the percentage of mycorrhization of Vaccinium myrtillus roots was also observed. The latter findings establish the pivotal role of SOD1 as an important factor in the relationship between O. maius and its symbiotic partner. The lack of this ROS-scavenger may cause an imbalance in the redox homeostasis during host colonization and an alteration in the delicate dialogue between the fungus and its host plant.

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

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