Characterization of the largest effector gene cluster of Ustilago maydis

Plant-endophyte communication: Scaling from molecular mechanisms to ecological outcomes

Diverse communities of fungal endophytes reside in plant tissues, where they affect and are affected by plant physiology and ecology. For these intimate interactions to form and persist, endophytes and their host plants engage in intricate systems of communication. The conversation between fungal endophytes and plant hosts ultimately dictates endophyte community composition and function and has cascading effects on plant health and plant interactions. In this review, we synthesize our current knowledge on the mechanisms and strategies of communication used by endophytic fungi and their plant hosts. We discuss the molecular mechanisms of communication that lead to organ specificity of endophytic communities and distinguish endophytes, pathogens, and saprotrophs. We conclude by offering emerging perspectives on the relevance of plant-endophyte communication to microbial community ecology and plant health and function.

Novel Secreted Effectors Conserved Among Smut Fungi Contribute to the Virulence of Ustilago maydis

Fungal pathogens deploy a set of molecules (proteins, specialized metabolites, and sRNAs), so-called effectors, to aid the infection process. In comparison to other plant pathogens, smut fungi have small genomes and secretomes of 20 Mb and around 500 proteins, respectively. Previous comparative genomic studies have shown that many secreted effector proteins without known domains, i.e., novel, are conserved only in the Ustilaginaceae family. By analyzing the secretomes of 11 species within Ustilaginaceae, we identified 53 core homologous groups commonly present in this lineage. By collecting existing mutants and generating additional ones, we gathered 44 Ustilago maydis strains lacking single core effectors as well as 9 strains containing multiple deletions of core effector gene families. Pathogenicity assays revealed that 20 of these 53 mutant strains were affected in virulence. Among the 33 mutants that had no obvious phenotypic changes, 13 carried additional, sequence-divergent, structurally similar paralogs. We report a virulence contribution of seven previously uncharacterized single core effectors and of one effector family. Our results help to prioritize effectors for understanding U. maydis virulence and provide genetic resources for further characterization. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Surface frustration re-patterning underlies the structural landscape and evolvability of fungal orphan candidate effectors

Pathogens secrete effector proteins to subvert host physiology and cause disease. Effectors are engaged in a molecular arms race with the host resulting in conflicting evolutionary constraints to manipulate host cells without triggering immune responses. The molecular mechanisms allowing effectors to be at the same time robust and evolvable remain largely enigmatic. Here, we show that 62 conserved structure-related families encompass the majority of fungal orphan effector candidates in the Pezizomycotina subphylum. These effectors diversified through changes in patterns of thermodynamic frustration at surface residues. The underlying mutations tended to increase the robustness of the overall effector protein structure while switching potential binding interfaces. This mechanism could explain how conserved effector families maintained biological activity over long evolutionary timespans in different host environments and provides a model for the emergence of sequence-unrelated effector families with conserved structures.

The nuclear effector MoHTR3 of Magnaporthe oryzae modulates host defence signalling in the biotrophic stage of rice infection

Fungal effectors play a pivotal role in suppressing the host defence system, and their evolution is highly dynamic. By comparative sequence analysis of plant-pathogenic fungi and Magnaporthe oryzae, we identified the small secreted C₂ H₂ zinc finger protein MoHTR3. MoHTR3 exhibited high conservation in M. oryzae strains but low conservation among other plant-pathogenic fungi, suggesting an emerging evolutionary selection process. MoHTR3 is exclusively expressed in the biotrophic stage of fungal invasion, and the encoded protein localizes to the biotrophic interfacial complex (BIC) and the host cell nucleus. The signal peptide crucial for MoHTR3' secretion to the BIC and the protein section required for its translocation to the nucleus were both identified by a functional protein domain study. The host-nuclear localization of MoHTR3 suggests a function as a transcriptional modulator of host defence gene induction. After ΔMohtr3 infection, the expression of jasmonic acid- and ethylene-associated genes was diminished in rice, in contrast to when the MoHTR3-overexpressing strain (MoHTR3ox) was applied. The transcript levels of salicylic acid- and defence-related genes were also affected after ΔMohtr3 and MoHTR3ox application. In pathogenicity assays, ΔMohtr3 was indistinguishable from the wild type. However, MoHTR3ox-infected plants showed diminished lesion formation and hydrogen peroxide accumulation, accompanied by a decrease in susceptibility, suggesting that the MoHTR3-induced manipulation of host cells affects host-pathogen interaction. MoHTR3 emphasizes the role of the host nucleus as a critical target for the pathogen-driven manipulation of host defence mechanisms and underscores the ongoing evolution of rice blast's arms race.

Progress in pathogenesis research of Ustilago maydis, and the metabolites involved along with their biosynthesis

Ustilago maydis is a pathogenic fungus that causes corn smut. Because of its easy cultivation and genetic transformation, U. maydis has become an important model organism for plant-pathogenic basidiomycetes. U. maydis is able to infect maize by producing effectors and secreted proteins as well as surfactant-like metabolites. In addition, the production of melanin and iron carriers is also associated with its pathogenicity. Here, advances in our understanding of the pathogenicity of U. maydis, the metabolites involved in the pathogenic process, and the biosynthesis of these metabolites, are reviewed and discussed. This summary will provide new insights into the pathogenicity of U. maydis and the functions of associated metabolites, as well as new clues for deciphering the biosynthesis of metabolites.

Functional Clustering of Metabolically Related Genes Is Conserved across Dikarya

Transcriptional regulation is vital for organismal survival, with many layers and mechanisms collaborating to balance gene expression. One layer of this regulation is genome organization, specifically the clustering of functionally related, co-expressed genes along the chromosomes. Spatial organization allows for position effects to stabilize RNA expression and balance transcription, which can be advantageous for a number of reasons, including reductions in stochastic influences between the gene products. The organization of co-regulated gene families into functional clusters occurs extensively in Ascomycota fungi. However, this is less characterized within the related Basidiomycota fungi despite the many uses and applications for the species within this clade. This review will provide insight into the prevalence, purpose, and significance of the clustering of functionally related genes across Dikarya, including foundational studies from Ascomycetes and the current state of our understanding throughout representative Basidiomycete species.

Systematic characterization of Ustilago maydis sirtuins shows Sir2 as a modulator of pathogenic gene expression

Phytopathogenic fungi must adapt to the different environmental conditions found during infection and avoid the immune response of the plant. For these adaptations, fungi must tightly control gene expression, allowing sequential changes in transcriptional programs. In addition to transcription factors, chromatin modification is used by eukaryotic cells as a different layer of transcriptional control. Specifically, the acetylation of histones is one of the chromatin modifications with a strong impact on gene expression. Hyperacetylated regions usually correlate with high transcription and hypoacetylated areas with low transcription. Thus, histone deacetylases (HDACs) commonly act as repressors of transcription. One member of the family of HDACs is represented by sirtuins, which are deacetylases dependent on NAD+, and, thus, their activity is considered to be related to the physiological stage of the cells. This property makes sirtuins good regulators during environmental changes. However, only a few examples exist, and with differences in the extent of the implication of the role of sirtuins during fungal phytopathogenesis. In this work, we have performed a systematic study of sirtuins in the maize pathogen Ustilago maydis, finding Sir2 to be involved in the dimorphic switch from yeast cell to filament and pathogenic development. Specifically, the deletion of sir2 promotes filamentation, whereas its overexpression highly reduces tumor formation in the plant. Moreover, transcriptomic analysis revealed that Sir2 represses genes that are expressed during biotrophism development. Interestingly, our results suggest that this repressive effect is not through histone deacetylation, indicating a different target of Sir2 in this fungus.

The nuclear effector ArPEC25 from the necrotrophic fungus Ascochyta rabiei targets the chickpea transcription factor CaβLIM1a and negatively modulates lignin biosynthesis, increasing host susceptibility

Fungal pathogens deploy a barrage of secreted effectors to subvert host immunity, often by evading, disrupting, or altering key components of transcription, defense signaling, and metabolic pathways. However, the underlying mechanisms of effectors and their host targets are largely unexplored in necrotrophic fungal pathogens. Here, we describe the effector protein Ascochyta rabiei PEXEL-like Effector Candidate 25 (ArPEC25), which is secreted by the necrotroph A. rabiei, the causal agent of Ascochyta blight disease in chickpea (Cicer arietinum), and is indispensable for virulence. After entering host cells, ArPEC25 localizes to the nucleus and targets the host LIM transcription factor CaβLIM1a. CaβLIM1a is a transcriptional regulator of CaPAL1, which encodes phenylalanine ammonia lyase (PAL), the regulatory, gatekeeping enzyme of the phenylpropanoid pathway. ArPEC25 inhibits the transactivation of CaβLIM1a by interfering with its DNA-binding ability, resulting in negative regulation of the phenylpropanoid pathway and decreased levels of intermediates of lignin biosynthesis, thereby suppressing lignin production. Our findings illustrate the role of fungal effectors in enhancing virulence by targeting a key defense pathway that leads to the biosynthesis of various secondary metabolites and antifungal compounds. This study provides a template for the study of less explored necrotrophic effectors and their host target functions.

Prediction of effector protein structures from fungal phytopathogens enables evolutionary analyses

Elucidating the similarity and diversity of pathogen effectors is critical to understand their evolution across fungal phytopathogens. However, rapid divergence that diminishes sequence similarities between putatively homologous effectors has largely concealed the roots of effector evolution. Here we modelled the structures of 26,653 secreted proteins from 14 agriculturally important fungal phytopathogens, six non-pathogenic fungi and one oomycete with AlphaFold 2. With 18,000 successfully predicted folds, we performed structure-guided comparative analyses on two aspects of effector evolution: uniquely expanded sequence-unrelated structurally similar (SUSS) effector families and common folds present across the fungal species. Extreme expansion of lineage-specific SUSS effector families was found only in several obligate biotrophs, Blumeria graminis and Puccinia graminis. The highly expanded effector families were the source of conserved sequence motifs, such as the Y/F/WxC motif. We identified new classes of SUSS effector families that include known virulence factors, such as AvrSr35, AvrSr50 and Tin2. Structural comparisons revealed that the expanded structural folds further diversify through domain duplications and fusion with disordered stretches. Putatively sub- and neo-functionalized SUSS effectors could reconverge on regulation, expanding the functional pools of effectors in the pathogen infection cycle. We also found evidence that many effector families could have originated from ancestral folds conserved across fungi. Collectively, our study highlights diverse effector evolution mechanisms and supports divergent evolution as a major force in driving SUSS effector evolution from ancestral proteins.

Virulence and pathogenicity determinants in whole genome sequence of Fusarium udum causing wilt of pigeon pea

The present study deals with whole genome analysis of Fusarium udum, a wilt causing pathogen of pigeon pea. The de novo assembly identified a total of 16,179 protein-coding genes, of which 11,892 genes (73.50%) were annotated using BlastP and 8,928 genes (55.18%) from KOG annotation. In addition, 5,134 unique InterPro domains were detected in the annotated genes. Apart from this, we also analyzed genome sequence for key pathogenic genes involved in virulence, and identified 1,060 genes (6.55%) as virulence genes as per the PHI-BASE database. The secretome profiling of these virulence genes indicated the presence of 1,439 secretory proteins. Of those, an annotation of 506 predicted secretory proteins through CAZyme database indicated maximum abundance of Glycosyl hydrolase (GH, 45%) family proteins followed by auxiliary activity (AA) family proteins. Interestingly, the presence of effectors for cell wall degradation, pectin degradation, and host cell death was found. The genome comprised approximately 895,132 bp of repetitive elements, which includes 128 long terminal repeats (LTRs), and 4,921 simple sequence repeats (SSRs) of 80,875 bp length. The comparative mining of effector genes among different Fusarium species revealed five common and two specific effectors in F. udum that are related to host cell death. Furthermore, wet lab experiment validated the presence of effector genes like SIX (for Secreted in Xylem). We conclude that deciphering the whole genome of F. udum would be instrumental in understanding evolution, virulence determinants, host-pathogen interaction, possible control strategies, ecological behavior, and many other complexities of the pathogen.

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

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

The Sporisorium reilianum Effector Vag2 Promotes Head Smut Disease via Suppression of Plant Defense Responses

Genome comparison between the maize pathogens Ustilago maydis and Sporisorium reilianum revealed a large diversity region (19-1) containing nearly 30 effector gene candidates, whose deletion severely hampers virulence of both fungi. Dissection of the S. reilianum gene cluster resulted in the identification of one major contributor to virulence, virulence-associated gene 2 (vag2; sr10050). Quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) experiments revealed high expression of vag2 during biotrophic growth of S. reilianum. Using the yeast secretion trap assay, we confirmed the existence of a functional signal peptide allowing protein secretion via the conventional secretory pathway. We identified the cytoplasmic maize chorismate mutase ZmCM2 by yeast two-hybrid screening as a possible interaction partner of Vag2. Interaction of the two proteins in planta was confirmed by bimolecular fluorescence complementation. qRT-PCR experiments revealed vag2-dependent downregulation of salicylic acid (SA)-induced genes, which correlated with higher SA levels in plant tissues colonized by Δvag2 deletion strains relative to S. reilianum wildtype strains. Metabolite analysis suggested rewiring of pathogen-induced SA biosynthesis by preferential conversion of the SA precursor chorismate into the aromatic amino acid precursor prephenate by ZmCM2 in the presence of Vag2. Possibly, the binding of Vag2 to ZmCM2 inhibits the back reaction of the ZmCM2-catalyzed interconversion of chorismate and prephenate, thus contributing to fungal virulence by lowering the plant SA-induced defenses.

An Improved Assembly of the Albugo candida Ac2V Genome Reveals the Expansion of the "CCG" Class of Effectors

Albugo candida is an obligate oomycete pathogen that infects many plants in the Brassicaceae family. We resequenced the genome of isolate Ac2V using PacBio long reads and constructed an assembly augmented by Illumina reads. The Ac2VPB genome assembly is 10% larger and more contiguous compared with a previous version. Our annotation of the new assembly, aided by RNA-sequencing information, revealed a 175% expansion (40 to 110) in the CHxC effector class, which we redefined as "CCG" based on motif analysis. This class of effectors consist of arrays of phylogenetically related paralogs residing in gene sparse regions, and shows signatures of positive selection and presence/absence polymorphism. This work provides a resource that allows the dissection of the genomic components underlying A. candida adaptation and, particularly, the role of CCG effectors in virulence and avirulence on different hosts.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

A sugarcane smut fungus effector simulates the host endogenous elicitor peptide to suppress plant immunity

The smut fungus Sporisorium scitamineum causes the most prevalent disease on sugarcane. The mechanism of its pathogenesis, especially the functions and host targets of its effector proteins, are unknown. In order to identify putative effectors involving in S. scitamineum infection, a weighted gene co-expression network analysis was conducted based on the transcriptome profiles of both smut fungus and sugarcane using a customized microarray. A smut effector gene, termed SsPele1, showed strong co-expression with sugarcane PLANT ELICITOR PEPTIDE RECEPTOR1 (ScPEPR1), which encodes a receptor like kinase for perception of plant elicitor peptide1 (ScPep1). The relationship between SsPele1 and ScPEPR1, and the biological function of SsPele1 were characterized in this study. The SsPele1 C-terminus contains a plant elicitor peptide-like motif, by which SsPele1 interacts strongly with ScPEPR1. Strikingly, the perception of ScPep1 on ScPEPR1 is competed by SsPele1 association, leading to the suppression of ScPEPR1-mediated immune responses. Moreover, the Ustilago maydis effector UmPele1, an ortholog of SsPele1, promotes fungal virulence using the same strategy. This study reveals a novel strategy by which a fungal effector can mimic the plant elicitor peptide to complete its perception and attenuate receptor-activated immunity.

Identification and Severity Monitoring of Maize Dwarf Mosaic Virus Infection Based on Hyperspectral Measurements

Prompt monitoring of maize dwarf mosaic virus (MDMV) is critical for the prevention and control of disease and to ensure high crop yield and quality. Here, we first analyzed the spectral differences between MDMV-infected red leaves and healthy leaves and constructed a sensitive index (SI) for measurements. Next, based on the characteristic bands (Rλ) associated with leaf anthocyanins (Anth), we determined vegetation indices (VIs) commonly used in plant physiological and biochemical parameter inversion and established a vegetation index (VIc) by utilizing the combination of two arbitrary bands following the construction principles of NDVI, DVI, RVI, and SAVI. Furthermore, we developed classification models based on linear discriminant analysis (LDA) and support vector machine (SVM) in order to distinguish the red leaves from healthy leaves. Finally, we performed UR, MLR, PLSR, PCR, and SVM simulations on Anth based on Rλ, VIs, VIc, and Rλ + VIs + VIc and indirectly estimated the severity of MDMV infection based on the relationship between the reflection spectra and Anth. Distinct from those of the normal leaves, the spectra of red leaves showed strong reflectance characteristics at 640 nm, and SI increased with increasing Anth. Moreover, the accuracy of the two VIc-based classification models was 100%, which is significantly higher than that of the VIs and Rλ-based models. Among the Anth regression models, the accuracy of the MLR model based on Rλ + VIs + VIc was the highest (R2c = 0.85; R2v = 0.74). The developed models could accurately identify MDMV and estimate the severity of its infection, laying the theoretical foundation for large-scale remote sensing-based monitoring of this virus in the future.

Pathogens pulling the strings: Effectors manipulating salicylic acid and phenylpropanoid biosynthesis in plants

During evolution, plants have developed sophisticated ways to cope with different biotic and abiotic stresses. Phytohormones and secondary metabolites are known to play pivotal roles in defence responses against invading pathogens. One of the key hormones involved in plant immunity is salicylic acid (SA), of which the role in plant defence is well established and documented. Plants produce an array of secondary metabolites categorized in different classes, with the phenylpropanoids as major players in plant immunity. Both SA and phenylpropanoids are needed for an effective immune response by the plant. To successfully infect the host, pathogens secrete proteins, called effectors, into the plant tissue to lower defence. Secreted effectors can interfere with several metabolic or signalling pathways in the host to facilitate infection. In this review, we will focus on the different strategies pathogens have developed to affect the levels of SA and phenylpropanoids to increase plant susceptibility.

The small-secreted cysteine-rich protein CyrA is a virulence factor participating in the attack of Caenorhabditis elegans by Duddingtonia flagrans

Nematode-trapping fungi (NTF) are a diverse and intriguing group of fungi that live saprotrophically but can switch to a predatory lifestyle when starving and in the presence of nematodes. NTF like Arthrobotrys oligospora or Duddingtonia flagrans produce adhesive trapping networks to catch and immobilize nematodes. After penetration of the cuticle, hyphae grow and develop inside the worm and secrete large amounts of hydrolytic enzymes for digestion. In many microbial pathogenic interactions small-secreted proteins (SSPs) are used to manipulate the host. The genome of D. flagrans encodes more than 100 of such putative SSPs one of which is the cysteine-rich protein CyrA. We have chosen this gene for further analysis because it is only found in NTF and appeared to be upregulated during the interaction. We show that the cyrA gene was transcriptionally induced in trap cells, and the protein accumulated at the inner rim of the hyphal ring before Caenorhabditis elegans capture. After worm penetration, the protein appeared at the fungal infection bulb, where it is likely to be secreted with the help of the exocyst complex. A cyrA-deletion strain was less virulent, and the time from worm capture to paralysis was extended. Heterologous expression of CyrA in C. elegans reduced its lifespan. CyrA accumulated in C. elegans in coelomocytes where the protein possibly is inactivated. This is the first example that SSPs may be important in predatory microbial interactions.

Cross-species analysis between the maize smut fungi Ustilago maydis and Sporisorium reilianum highlights the role of transcriptional change of effector orthologs for virulence and disease

The constitution and regulation of effector repertoires shape host-microbe interactions. Ustilago maydis and Sporisorium reilianum are two closely related smut fungi, which both infect maize but cause distinct disease symptoms. Understanding how effector orthologs are regulated in these two pathogens can therefore provide insights into the evolution of different infection strategies. We tracked the infection progress of U. maydis and S. reilianum in maize leaves and used two distinct infection stages for cross-species RNA-sequencing analyses. We identified 207 of 335 one-to-one effector orthologs as differentially regulated during host colonization, which might reflect the distinct disease development strategies. Using CRISPR-Cas9-mediated gene conversion, we identified two differentially expressed effector orthologs with conserved function between two pathogens. Thus, differential expression of functionally conserved genes might contribute to species-specific adaptation and symptom development. Interestingly, another differentially expressed orthogroup (UMAG_05318/Sr10075) showed divergent protein function, providing a possible case for neofunctionalization. Collectively, we demonstrated that the diversification of effector genes in related pathogens can be caused both by alteration on the transcriptional level and through functional diversification of the encoded effector proteins.

Tactics of host manipulation by intracellular effectors from plant pathogenic fungi

Fungal pathogens can secrete hundreds of effectors, some of which are known to promote host susceptibility. This biological complexity, together with the lack of genetic tools in some fungi, presents a substantial challenge to develop a broad picture of the mechanisms these pathogens use for host manipulation. Nevertheless, recent advances in understanding individual effector functions are beginning to flesh out our view of fungal pathogenesis. This review discusses some of the latest findings that illustrate how effectors from diverse species use similar strategies to modulate plant physiology to their advantage. We also summarize recent breakthroughs in the identification of effectors from challenging systems, like obligate biotrophs, and emerging concepts such as the 'iceberg model' to explain how the activation of plant immunity can be turned off by effectors with suppressive activity.

Nuclear status and leaf tumor formation in the Ustilago maydis-maize pathosystem

Ustilago maydis is a biotrophic fungus causing smut disease in corn. The infectious forms are dikaryotic hyphae. Here we analyze mutants lacking the nlt1 transcription factor and investigate why these mutants are unable to induce leaf tumors. The study involved reverse genetics, complementation, epistasis analysis, microscopy, gene expression analysis by quantitative reverse transcriptase PCR and virulence assays. We show that nlt1 mutants colonize maize leaves efficiently but fail to undergo karyogamy and are attenuated in late proliferation. Nlt1 activates transcription of ros1, a transcription factor controlling karyogamy, and represses see1, an effector previously shown to contribute to leaf tumor induction. In mononuclate solopathogenic strains, nlt1 mutants cause attenuated leaf tumor formation. In actively dividing maize organs, nlt1 mutants undergo karyogamy and induce tumor formation. Sporisorium reilianum, a smut fungus unable to induce leaf tumors, possesses an ortholog of nlt1 that controls the fusion of dikaryotic nuclei late in infection during cob colonization. Our results have established a regulatory connection between nlt1, ros1 and see1 and suggest the existence of two stages contributing to leaf tumor formation, one before nuclear fusion and involving nlt1 and one after karyogamy that is nlt1 independent.

A small Ustilago maydis effector acts as a novel adhesin for hyphal aggregation in plant tumors

The biotrophic basidiomycete fungus Ustilago maydis causes smut disease in maize. Hallmarks of the disease are characteristic large tumors in which dark pigmented spores are formed. Here, we functionally characterized a novel core effector lep1 (late effector protein 1) which is highly expressed during tumor formation and contributes to virulence. We characterize lep1 mutants, localize the protein, determine phenotypic consequences upon deletion as well as constitutive expression, and analyze relationships with the repellent protein Rep1 and hydrophobins. In tumors, lep1 mutants show attenuated hyphal aggregation, fail to undergo massive late proliferation and produce only a few spores. Upon constitutive expression, cell aggregation is induced and the surface of filamentous colonies displays enhanced hydrophobicity. Lep1 is bound to the cell wall of biotrophic hyphae and associates with Rep1 when constitutively expressed in hyphae. We conclude that Lep1 acts as a novel kind of cell adhesin which functions together with other surface-active proteins to allow proliferation of diploid hyphae as well as for induction of the morphological changes associated with spore formation.

Population Genomics of the Maize Pathogen Ustilago maydis: Demographic History and Role of Virulence Clusters in Adaptation

The tight interaction between pathogens and their hosts results in reciprocal selective forces that impact the genetic diversity of the interacting species. The footprints of this selection differ between pathosystems because of distinct life-history traits, demographic histories, or genome architectures. Here, we studied the genome-wide patterns of genetic diversity of 22 isolates of the causative agent of the corn smut disease, Ustilago maydis, originating from five locations in Mexico, the presumed center of origin of this species. In this species, many genes encoding secreted effector proteins reside in so-called virulence clusters in the genome, an arrangement that is so far not found in other filamentous plant pathogens. Using a combination of population genomic statistical analyses, we assessed the geographical, historical, and genome-wide variation of genetic diversity in this fungal pathogen. We report evidence of two partially admixed subpopulations that are only loosely associated with geographic origin. Using the multiple sequentially Markov coalescent model, we inferred the demographic history of the two pathogen subpopulations over the last 0.5 Myr. We show that both populations experienced a recent strong bottleneck starting around 10,000 years ago, coinciding with the assumed time of maize domestication. Although the genome average genetic diversity is low compared with other fungal pathogens, we estimated that the rate of nonsynonymous adaptive substitutions is three times higher in genes located within virulence clusters compared with nonclustered genes, including nonclustered effector genes. These results highlight the role that these singular genomic regions play in the evolution of this pathogen.

A fungal member of the Arabidopsis thaliana phyllosphere antagonizes Albugo laibachii via a GH25 lysozyme

Plants are not only challenged by pathogenic organisms but also colonized by commensal microbes. The network of interactions these microbes establish with their host and among each other is suggested to contribute to the immune responses of plants against pathogens. In wild Arabidopsis thaliana populations, the oomycete pathogen Albugo laibachii plays an influential role in structuring the leaf phyllosphere. We show that the epiphytic yeast Moesziomyces bullatus ex Albugo on Arabidopsis, a close relative of pathogenic smut fungi, is an antagonistic member of the A. thaliana phyllosphere, which reduces infection of A. thaliana by A. laibachii. Combination of transcriptomics, reverse genetics, and protein characterization identified a GH25 hydrolase with lysozyme activity as a major effector of this microbial antagonism. Our findings broaden the understanding of microbial interactions within the phyllosphere, provide insights into the evolution of epiphytic basidiomycete yeasts, and pave the way for novel biocontrol strategies.

Effectors with Different Gears: Divergence of Ustilago maydis Effector Genes Is Associated with Their Temporal Expression Pattern during Plant Infection

Plant pathogens secrete a variety of effector proteins that enable host colonization but are also typical pathogen detection targets for the host immune system. Consequently, effector genes encounter high selection pressures, which typically makes them fast evolving. The corn smut pathogen Ustilago maydis has an effector gene repertoire with a dynamic expression across the different disease stages. We determined the amino acid divergence of U. maydis effector candidates with Sporisorium reilianum orthologs, a close relative of U. maydis. Intriguingly, there are two distinct groups of effector candidates, ones with a respective conserved and diverged protein evolution. Conservatively evolving effector genes especially have their peak expression during the (pre-)penetration stages of the disease cycle. In contrast, expression of divergently evolving effector genes generally peaks during fungal proliferation within the host. To test if this interspecific effector diversity corresponds to intraspecific diversity, we sampled and sequenced a diverse collection of U. maydis strains from the most important maize breeding and production regions in China. Effector candidates with a diverged interspecific evolution had more intraspecific amino acid variation than candidates with a conserved evolution. In conclusion, we highlight diversity in evolution within the U. maydis effector repertoire with dynamically and conservatively evolving members.

Understanding Ustilago maydis Infection of Multiple Maize Organs

Ustilago maydis is a smut fungus that infects all aerial maize organs, namely, seedling leaves, tassels, and ears. In all organs, tumors are formed by inducing hypertrophy and hyperplasia in actively dividing cells; however, the vast differences in cell types and developmental stages for different parts of the plant requires that U. maydis have both general and organ-specific strategies for infecting maize. In this review, we summarize how the maize–U. maydis interaction can be studied using mutant U. maydis strains to better understand how individual effectors contribute to this interaction, either through general or specific expression in a cell type, tissue, or organ. We also examine how male sterile maize mutants that do not support tumor formation can be used to explore key features of the maize anthers that are required for successful infection. Finally, we discuss key unanswered questions about the maize–U. maydis interaction and how new technologies can potentially be used to answer them.

Carbamoyl phosphate synthetase subunit Cpa1 interacting with Dut1, controls development, arginine biosynthesis, and pathogenicity of Colletotrichum gloeosporioides

Carbamoyl phosphate synthetase is involved in arginine biosynthesis in many organisms. In this study, we investigate the biological function of Cpa1, a small subunit of carbamoyl phosphate synthetase of Colletotrichum gloeosporioides. The deletion of the CPA1 gene affected vegetative growth, arginine biosynthesis, and fungal pathogenicity. Genetic complementation with native CPA1 fully recovered all these defective phenotypes. We observed that Cpa1-RFP fusion protein is localized at the mitochondria, which is consistent with Cpa2, a large subunit of carbamoyl phosphate synthetase. We identified the proteins that interact with Cpa1 by using the two-hybrid screen approach, and we showed that Dut1 interacts with Cpa1 but without Cpa2 in vivo. Dut1 is dispensable for hyphal growth, appressorial formation, and fungal pathogenicity. Interestingly, the Dut1-Cpa1 complex is localized at the mitochondria. Further studies showed that Dut1 regulates Cpa1-Cpa2 interaction in response to arginine. In summary, our studies provide new insights into how Cpa1 interacts with its partner proteins to mediate arginine synthesis.

Engineering Smut Resistance in Maize by Site-Directed Mutagenesis of LIPOXYGENASE 3

Biotic stresses caused by microbial pathogens impair crop yield and quality if not restricted by expensive and often ecologically problematic pesticides. For a sustainable agriculture of tomorrow, breeding or engineering of pathogen-resistant crop varieties is therefore a major cornerstone. Maize is one of the four most important cereal crops in the world. The biotrophic fungal pathogen Ustilago maydis causes galls on all aerial parts of the maize plant. Biotrophic pathogens like U. maydis co-evolved with their host plant and depend during their life cycle on successful manipulation of the host's cellular machinery. Therefore, removing or altering plant susceptibility genes is an effective and usually durable way to obtain resistance in plants. Transcriptional time course experiments in U. maydis-infected maize revealed numerous maize genes being upregulated upon establishment of biotrophy. Among these genes is the maize LIPOXYGENASE 3 (LOX3) previously shown to be a susceptibility factor for other fungal genera as well. Aiming to engineer durable resistance in maize against U. maydis and possibly other pathogens, we took a Cas endonuclease technology approach to generate loss of function mutations in LOX3. lox3 maize mutant plants react with an enhanced PAMP-triggered ROS burst implicating an enhanced defense response. Based on visual assessment of disease symptoms and quantification of relative fungal biomass, homozygous lox3 mutant plants exposed to U. maydis show significantly decreased susceptibility. U. maydis infection assays using a transposon mutant lox3 maize line further substantiated that LOX3 is a susceptibility factor for this important maize pathogen.

Proteinaceous effector discovery and characterization in filamentous plant pathogens

The complicated interplay of plant-pathogen interactions occurs on multiple levels as pathogens evolve to constantly evade the immune responses of their hosts. Many economically important crops fall victim to filamentous pathogens that produce small proteins called effectors to manipulate the host and aid infection/colonization. Understanding the effector repertoires of pathogens is facilitating an increased understanding of the molecular mechanisms underlying virulence as well as guiding the development of disease control strategies. The purpose of this review is to give a chronological perspective on the evolution of the methodologies used in effector discovery from physical isolation and in silico predictions, to functional characterization of the effectors of filamentous plant pathogens and identification of their host targets.

UhAVR1, an HR-Triggering Avirulence Effector of Ustilago hordei, Is Secreted via the ER-Golgi Pathway, Localizes to the Cytosol of Barley Cells during in Planta-Expression, and Contributes to Virulence Early in Infection

The basidiomycete Ustilago hordei causes covered smut disease of barley and oats. Virulence effectors promoting infection and supporting pathogen lifestyle have been described for this fungus. Genetically, six avirulence genes are known and one codes for UhAVR1, the only proven avirulence effector identified in smuts to date that triggers complete immunity in barley cultivars carrying resistance gene Ruh1. A prerequisite for resistance breeding is understanding the host targets and molecular function of UhAVR1. Analysis of this effector upon natural infection of barley coleoptiles using teliospores showed that UhAVR1 is expressed during the early stages of fungal infection where it leads to HR triggering in resistant cultivars or performs its virulence function in susceptible cultivars. Fungal secretion of UhAVR1 is directed by its signal peptide and occurs via the BrefeldinA-sensitive ER-Golgi pathway in cell culture away from its host. Transient in planta expression of UhAVR1 in barley and a nonhost, Nicotiana benthamiana, supports a cytosolic localization. Delivery of UhAVR1 via foxtail mosaic virus or Pseudomonas species in both barley and N. benthamiana reveals a role in suppressing components common to both plant systems of Effector- and Pattern-Triggered Immunity, including necrosis triggered by Agrobacterium-delivered cell death inducers.

Smut fungi as a stratagem to characterize rust effectors: opportunities and challenges

The rust pathogens are one of the most complex fungi in the Basidiomycetes. The development of genomic resources for rust and other plant pathogens has opened the opportunities for functional genomics of fungal genes. Despite significant progress in the field of fungal genomics, functional characterization of the genome components has lacked, especially for the rust pathogens. Their obligate nature and lack of standard stable transformation protocol are the primary reasons for rusts to be one of the least explored genera despite its significance. In the recently sequenced rust genomes, a vast catalogue of predicted effectors and pathogenicity genes have been reported. However, most of these candidate genes remained unexplored due to the lack of suitable characterization methods. The heterologous expression of putative effectors in Nicotiana benthamiana and Arabidopsis thaliana has proved to be a rapid screening method for identifying the role of these effectors in virulence. However, no fungal system has been used for the functional validation of these candidate genes. The smuts, from the evolutionary point of view, are closely related to the rust pathogens. Moreover, they have been widely studied and hence could be a suitable model system for expressing rust fungal genes heterologously. The genetic manipulation methods for smuts are also well standardized. Complementation assays can be used for functional validation of the homologous genes present in rust and smut fungal pathogens, while the species-specific proteins can be expressed in the mutant strains of smut pathogens having reduced or no virulence for virulence analysis. We propose that smuts, especially Ustilago maydis, may prove to be a good model system to characterize rust effector proteins in the absence of methods to manipulate the rust genomes directly.

Effector Biology of Biotrophic Plant Fungal Pathogens: Current Advances and Future Prospects

The interaction of fungal pathogens with their host requires a novel invading mechanism and the presence of various virulence-associated components responsible for promoting the infection. The small secretory proteins, explicitly known as effector proteins, are one of the prime mechanisms of host manipulation utilized by the pathogen to disarm the host. Several effector proteins are known to translocate from fungus to the plant cell for host manipulation. Many fungal effectors have been identified using genomic, transcriptomic, and bioinformatics approaches. Most of the effector proteins are devoid of any conserved signatures, and their prediction based on sequence homology is very challenging, therefore by combining the sequence consensus based upon machine learning features, multiple tools have also been developed for predicting apoplastic and cytoplasmic effectors. Various post-genomics approaches like transcriptomics of virulent isolates have also been utilized for identifying active consortia of effectors. Significant progress has been made in understanding biotrophic effectors; however, most of it is underway due to their complex interaction with host and complicated recognition and signaling networks. This review discusses advances, and challenges in effector identification and highlighted various features of the potential effector proteins and approaches for understanding their genetics and strategies for regulation.

Ultraviolet Mutagenesis Coupled with Next-Generation Sequencing as a Method for Functional Interrogation of Powdery Mildew Genomes

Powdery mildews are obligate biotrophic fungal pathogens causing important diseases of plants worldwide. Very little is known about the requirements for their pathogenicity at the molecular level. This is largely due to the inability to culture these organisms in vitro or to modify them genetically. Here, we describe a mutagenesis procedure based on ultraviolet (UV) irradiation to accumulate mutations in the haploid genome of the barley powdery mildew pathogen Blumeria graminis f. sp. hordei. Exposure of B. graminis f. sp. hordei conidia to different durations of UV-C radiation (10 s to 12 min) resulted in a reduced number of macroscopically visible fungal colonies. B. graminis f. sp. hordei colony number was negatively correlated with exposure time and the total number of consecutive cycles of UV irradiation. Dark incubation following UV exposure further reduced fungal viability, implying that photoreactivation is an important component of DNA repair in B. graminis f. sp. hordei. After several rounds of UV mutagenesis, we selected two mutant isolates in addition to the parental B. graminis f. sp. hordei K1 isolate for whole-genome resequencing. By combining automated prediction of sequence variants and their manual validation, we identified unique UV-induced mutations in the genomes of the two isolates. Most of these mutations were in the up- or downstream regions of genes or in the intergenic space. Some of the variants detected in genes led to predicted missense mutations. As an additional insight, our bioinformatic analyses revealed a complex population structure within supposedly clonal B. graminis f. sp. hordei isolates.

The functionally conserved effector Sta1 is a fungal cell wall protein required for virulence in Ustilago maydis

The biotrophic fungus Ustilago maydis causes the smut disease of maize. The interaction with its host and induction of characteristic tumors are governed largely by secreted effectors whose function is mostly unknown. To identify effectors with a prominent role in virulence, we used RNA sequencing and found that the gene sta1 is upregulated during early stages of infection. We characterized Sta1 by comparative genomics, reverse genetics, protein localization, stress assays, and microscopy. sta1 mutants show a dramatic reduction of virulence and show altered colonization of tissue neighboring the vascular bundles. Functional orthologues of Sta1 are found in related smut pathogens infecting monocot and dicot plants. Sta1 is secreted by budding cells but is attached to the cell wall of filamentous hyphae. Upon constitutive expression of Sta1, fungal filaments become susceptible to Congo red, β-glucanase, and chitinase, suggesting that Sta1 alters the structure of the fungal cell wall. Constitutive or delayed expression of sta1 during plant colonization negatively impacts on virulence. Our results suggest that Sta1 is a novel kind of effector, which needs to modify the hyphal cell wall to allow hyphae to be accommodated in tissue next to the vascular bundles.

Bioinformatic Detection of Positive Selection Pressure in Plant Pathogens: The Neutral Theory of Molecular Sequence Evolution in Action

The genomes of plant pathogenic fungi and oomycetes are often exposed to strong positive selection pressure. During speciation, shifts in host range and preference can lead to major adaptive changes. Furthermore, evolution of total host resistance to most isolates can force rapid evolutionary changes in host-specific pathogens. Crop pathogens are subjected to particularly intense selective pressures from monocultures and fungicides. Detection of the footprints of positive selection in plant pathogen genomes is a worthwhile endeavor as it aids understanding of the fundamental biology of these important organisms. There are two main classes of test for detection of positively selected alleles. Tests based on the ratio of non-synonymous to synonymous substitutions per site detect the footprints of multiple fixation events between divergent lineages. Thus, they are well-suited to the study of ancient adaptation events spanning speciations. On the other hand, tests that scan genomes for local fluctuations in allelic diversity within populations are suitable for detection of recent positive selection in populations. In this review, I briefly describe some of the more widely used tests of positive selection and the theory underlying them. I then discuss various examples of their application to plant pathogen genomes, emphasizing the types of genes that are associated with signatures of positive selection. I conclude with a discussion of the practicality of such tests for identification of pathogen genes of interest and the important features of pathogen ecology that must be taken into account for accurate interpretation.

Smut fungal strategies for the successful infection

The smut fungi include a large number of plant pathogens that establish obligate biotrophic relationships with their host. Throughout the whole life inside plant tissue, smut fungi keep plant cells alive and acquire nutrients via biotrophic interfaces. This mini-review mainly summarizes the interactions between smut fungi and their host plants during the infection process. Despite various strategies recruited by plants to defense invading pathogens, smut fungi successfully evolved an arsenal for colonization. Mating of two compatible haploids gives rise to parasitic mycelium, which can sense plant surface cues such as fatty acids and hydrophobic surface, and induce the formation of appressoria for surface penetration. Plants can recognize fungal invading and activate defense response, including callose and lignin deposition, programmed cell death, and SA signaling pathway. To suppress plant immunity and alter the metabolic pathway of host plants, a cocktail of effectors is secreted by smut fungi depending on the plant organ and cell type that is infected.

N-glycosylation of the protein disulfide isomerase Pdi1 ensures full Ustilago maydis virulence

Fungal pathogenesis depends on accurate secretion and location of virulence factors which drive host colonization. Protein glycosylation is a common posttranslational modification of cell wall components and other secreted factors, typically required for correct protein localization, secretion and function. Thus, the absence of glycosylation is associated with animal and plant pathogen avirulence. While the relevance of protein glycosylation for pathogenesis has been well established, the main glycoproteins responsible for the loss of virulence observed in glycosylation-defective fungi have not been identified. Here, we devise a proteomics approach to identify such proteins and use it to demonstrate a role for the highly conserved protein disulfide isomerase Pdi1 in virulence. We show that efficient Pdi1 N-glycosylation, which promotes folding into the correct protein conformation, is required for full pathogenic development of the corn smut fungus Ustilago maydis. Remarkably, the observed virulence defects are reminiscent of those seen in glycosylation-defective cells suggesting that the N-glycosylation of Pdi1 is necessary for the full secretion of virulence factors. All these observations, together with the fact that Pdi1 protein and RNA expression levels rise upon virulence program induction, suggest that Pdi1 glycosylation is important for normal pathogenic development in U. maydis. Our results provide new insights into the role of glycosylation in fungal pathogenesis.

A unique life-strategy of an endophytic yeast Rhodotorula mucilaginosa JGTA-S1-a comparative genomics viewpoint

Endophytic yeasts of genus Rhodotorula are gaining importance for their ability to improve plant growth. The nature of their interaction with plants, however, remains unknown. Rhodotorula mucilaginosa JGTA-S1 was isolated as an endophyte of Typha angustifolia and promoted growth in the host. To investigate the life-strategy of the yeast from a genomics perspective, we used Illumina and Oxford Nanopore reads to generate a high-quality annotated draft assembly of JGTA-S1 and compared its genome to three other Rhodotorula yeasts and the close relative Rhodosporidium toruloides. JGTA-S1 is a haploid yeast possessing several genes potentially facilitating its endophytic lifestyle such as those responsible for solubilizing phosphate and producing phytohormones. An intact mating-locus in JGTA-S1 raised the possibility of a yet unknown sexual reproductive cycle in Rhodotorula yeasts. Additionally, JGTA-S1 had functional anti-freezing genes and was also unique in lacking a functional nitrate-assimilation pathway—a feature that is associated with obligate biotrophs. Nitrogen-fixing endobacteria were found within JGTA-S1 that may circumvent this defective N-metabolism. JGTA-S1 genome data coupled with experimental evidence give us an insight into the nature of its beneficial interaction with plants.

The Farnesyltransferase β-Subunit Ram1 Regulates Sporisorium scitamineum Mating, Pathogenicity and Cell Wall Integrity

The basidiomycetous fungus Sporisorium scitamineum causes a serious sugarcane smut disease in major sugarcane growing areas. Sexual mating is essential for infection to the host; however, its underlying molecular mechanism has not been fully studied. In this study, we identified a conserved farnesyltransferase (FTase) β subunit Ram1 in S. scitamineum. The ram1Δ mutant displayed significantly reduced mating/filamentation, thus of weak pathogenicity to the host cane. The ram1Δ mutant sporidia showed more tolerant toward cell wall stressor Congo red compared to that of the wild-type. Transcriptional profiling showed that Congo red treatment resulted in notable up-regulation of the core genes involving in cell wall integrity pathway in ram1Δ sporidia compared with that of WT, indicating that Ram1 may be involved in cell wall integrity regulation. In yeast the heterodimeric FTase is responsible for post-translational modification of Ras (small G protein) and a-factor (pheromone). We also identified and characterized two conserved Ras proteins, Ras1 and Ras2, respectively, and a MAT-1 pheromone precursor Mfa1. The ras1Δ, ras2Δ and mfa1Δ mutants all displayed reduced mating/filamentation similar as the ram1Δ mutant. However, both ras1Δ and ras2Δ mutants were hypersensitive to Congo red while the mfa1Δ mutant was the same as wild-type. Overall our study displayed that RAM1 plays an essential role in S. scitamineum mating/filamentation, pathogenicity, and cell wall stability.

A small cysteine-rich protein from two kingdoms of microbes is recognized as a novel pathogen-associated molecular pattern

Pathogen-associated molecular patterns (PAMPs) are conserved molecules that are crucial for normal life cycle of microorganisms. However, the diversity of microbial PAMPs is little known. During screening of cell-death-inducing factors from the necrotrophic fungus Valsa mali, we identified a novel PAMP VmE02 that is widely spread in oomycetes and fungi. Agrobacterium tumefaciens-mediated transient expression or infiltration of recombinant protein produced by Escherichia coli was performed to assay elicitor activity of the proteins tested. Virus-induced gene silencing in Nicotiana benthamiana was used to determine the components involved in VmE02-triggered cell death. The role of VmE02 in virulence and conidiation of V. mali were characterized by gene deletion and complementation. We found that VmE02, together with some of its homologues from both oomycete and fungal species, exhibited cell-death-inducing activity in N. benthamiana. VmE02-triggered cell death was shown to be dependent on BRI1-ASSOCIATED KINASE-1, SUPPRESSOR OF BIR1-1, HSP90 and SGT1 in N. benthamiana. Deletion of VmE02 in V. mali greatly attenuated pathogen conidiation but not virulence, and treatment of N. benthamiana with VmE02 enhances plant resistance to Sclerotinia sclerotiorum and Phytophthora capsici. We conclude that VmE02 is a novel cross-kingdom PAMP produced by several fungi and oomycetes.

Analysis of Epichloë festucae small secreted proteins in the interaction with Lolium perenne

Epichloë festucae is an endophyte of the agriculturally important perennial ryegrass. This species systemically colonises the aerial tissues of this host where its growth is tightly regulated thereby maintaining a mutualistic symbiotic interaction. Recent studies have suggested that small secreted proteins, termed effectors, play a vital role in the suppression of host defence responses. To date only a few effectors with important roles in mutualistic interactions have been described. Here we make use of the fully assembled E. festucae genome and EffectorP to generate a suite of 141 effector candidates. These were analysed with respect to their genome location and expression profiles in planta and in several symbiosis-defective mutants. We found an association between effector candidates and a class of transposable elements known as MITEs, but no correlation with other dynamic features of the E. festucae genome, such as transposable element-rich regions. Three effector candidates and a small GPI-anchored protein were chosen for functional analysis based on their high expression in planta compared to in culture and their differential regulation in symbiosis defective E. festucae mutants. All three candidate effector proteins were shown to possess a functional signal peptide and two could be detected in the extracellular medium by western blotting. Localization of the effector candidates in planta suggests that they are not translocated into the plant cell, but rather, are localized in the apoplastic space or are attached to the cell wall. Deletion and overexpression of the effector candidates, as well as the putative GPI-anchored protein, did not affect the plant growth phenotype or restrict growth of E. festucae mutants in planta. These results indicate that these proteins are either not required for the interaction at the observed life stages or that there is redundancy between effectors expressed by E. festucae.

Sporisorium reilianum possesses a pool of effector proteins that modulate virulence on maize

The biotrophic maize head smut fungus Sporisorium reilianum is a close relative of the tumour-inducing maize smut fungus Ustilago maydis with a distinct disease aetiology. Maize infection with S. reilianum occurs at the seedling stage, but spores first form in inflorescences after a long endophytic growth phase. To identify S. reilianum-specific virulence effectors, we defined two gene sets by genome comparison with U. maydis and with the barley smut fungus Ustilago hordei. We tested virulence function by individual and cluster deletion analysis of 66 genes and by using a sensitive assay for virulence evaluation that considers both disease incidence (number of plants with a particular symptom) and disease severity (number and strength of symptoms displayed on any individual plant). Multiple deletion strains of S. reilianum lacking genes of either of the two sets (sr10057, sr10059, sr10079, sr10703, sr11815, sr14797 and clusters uni5-1, uni6-1, A1A2, A1, A2) were affected in virulence on the maize cultivar 'Gaspe Flint', but each of the individual gene deletions had only a modest impact on virulence. This indicates that the virulence of S. reilianum is determined by a complex repertoire of different effectors which each contribute incrementally to the aggressiveness of the pathogen.

Neofunctionalization of the secreted Tin2 effector in the fungal pathogen Ustilago maydis

Plant-pathogenic fungi hijack their hosts by secreting effector proteins. Effectors serve to suppress plant immune responses and modulate the host metabolism to benefit the pathogen. Smut fungi are biotrophic pathogens that also parasitize important cereals, including maize¹. Symptom development is usually restricted to the plant inflorescences. Ustilago maydis is an exception in its ability to cause tumours in both inflorescences and leaves of maize, and in inducing anthocyanin biosynthesis through the secreted Tin2 effector^2,3. How the unique lifestyle of U. maydis has evolved remains to be elucidated. Here we show that Tin2 in U. maydis has been neofunctionalized. We functionally compared Tin2 effectors of U. maydis and the related smut Sporisorium reilianum, which results in symptoms only in the inflorescences of maize and fails to induce anthocyanin. We show that Tin2 effectors from both fungi target distinct paralogues of a maize protein kinase, leading to stabilization and inhibition, respectively. An ancestral Tin2 effector functionally replaced the virulence function of S. reilianum Tin2 but failed to induce anthocyanin, and was unable to substitute for Tin2 in U. maydis. This shows that Tin2 in U. maydis has acquired a specialized function, probably connected to the distinct pathogenic lifestyle of this fungus.

Virulence function of the Ustilago maydis sterol carrier protein 2

The peroxisomal sterol carrier protein 2 (Scp2) of the biotrophic maize pathogen Ustilago maydis was detected in apoplastic fluid, suggesting that it might function as a secreted effector protein. Here we analyze the role of the scp2 gene during plant colonization. We used reverse genetics approaches to delete the scp2 gene, determined stress sensitivity and fatty acid utilization of mutants, demonstrated secretion of Scp2, used quantitative reverse transcription polymerase chain reaction for expression analysis and expressed GFP-Scp2 fusion proteins for protein localization. scp2 mutants were strongly attenuated in virulence and this defect manifested itself during penetration. Scp2 localized to peroxisomes and peroxisomal targeting was necessary for its virulence function. Deletion of scp2 in U. maydis interfered neither with growth nor with peroxisomal β-oxidation. Conventionally secreted Scp2 protein could not rescue the virulence defect. scp2 mutants displayed an altered localization of peroxisomes. Our results show a virulence function for Scp2 during penetration that is probably carried out by Scp2 in peroxisomes. We speculate that Scp2 affects the lipid composition of membranes and in this way ensures the even cellular distribution of peroxisomes.

Comparative whole-genome analysis reveals artificial selection effects on Ustilago esculenta genome

Ustilago esculenta, infects Zizania latifolia, and induced host stem swollen to be a popular vegetable called Jiaobai in China. It is the long-standing artificial selection that maximizes the occurrence of favourable Jiaobai, and thus maintaining the plant-fungi interaction and modulating the fungus evolving from plant pathogen to entophyte. In this study, whole genome of U. esculenta was sequenced and transcriptomes of the fungi and its host were analysed. The 20.2 Mb U. esculenta draft genome of 6,654 predicted genes including mating, primary metabolism, secreted proteins, shared a high similarity to related Smut fungi. But U. esculenta prefers RNA silencing not repeat-induced point in defence and has more introns per gene, indicating relatively slow evolution rate. The fungus also lacks some genes in amino acid biosynthesis pathway which were filled by up-regulated host genes and developed distinct amino acid response mechanism to balance the infection-resistance interaction. Besides, U. esculenta lost some surface sensors, important virulence factors and host range-related effectors to maintain the economic endophytic life. The elucidation of the U. esculenta genomic information as well as expression profiles can not only contribute to more comprehensive insights into the molecular mechanism underlying artificial selection but also into smut fungi-host interactions.

Combined analysis of genome-wide expression profiling of maize (Zea mays L.) leaves infected with Ustilago maydis

Although many gene expression profiling studies of maize leaves infected with Ustilago maydis have been published, heterogeneity of the results, caused by various data processing methods and pathogenic strains in different data sets, remains strong. Hence, we conducted a combined analysis of six genome-wide expression data sets of maize leaves infected with five different U. maydis strains by using the same pre-processing and quality control procedures. Six data sets were regrouped into five groups according to pathogenic strain used. Subsequently, each group of data set was processed by Multi-array Average for pre-processing and by pair-wise Pearson correlation for quality control. The differentially expressed genes were calculated by a standard linear mixed-effect model and then validated by various sensitivity analysis and multiple evidences. Finally, 44 unique differentially expressed genes were identified. Pathway enrichment analysis indicated that these genes related to response to fungus, oxidation-reduction, transferase activity, and several carbohydrate metabolic and catabolic processes. In addition, the hub genes within protein-protein interaction networks showed high relevance with the basic pathogenesis. We report a highly credible differentially expressed list, and the genes with multiple validations may denote a common signature of U. maydis in maize, which provides a new window for disease-resistant protection of maize plants.

Fungal effectors at the crossroads of phytohormone signaling

Phytohormone networks are crucial for maintaining the delicate balance between growth and biotic stress responses in plants. Jasmonic acid, salicylic acid, ethylene, and the associated signaling crosstalk are important for pathogen defense; whereas gibberellin and cytokinin function in growth and development in plants. Plant pathogenic fungi have evolved remarkable strategies to manipulate and/or hijack such phytohormone signaling cascades for their own benefit, thus leading to susceptibility and disease in host plants. Interestingly, these hormones are also targeted by fungal endosymbionts and mutualists during beneficial interactions with plants. We highlight current advances in our understanding of the role of fungal effectors in such antagonistic manipulation of phytohormones during pathogenic as well as symbiotic association with plant hosts. In addition to the aforementioned effector-based control, certain phytohormone mimics have recently emerged as a powerful molecular language in fungal manipulation of defense responses and innate immunity in plants.

Ustilago maydis effectors and their impact on virulence

Biotrophic fungal plant pathogens establish an intimate relationship with their host to support the infection process. Central to this strategy is the secretion of a range of protein effectors that enable the pathogen to evade plant immune defences and modulate host metabolism to meet its needs. In this Review, using the smut fungus Ustilago maydis as an example, we discuss new insights into the effector repertoire of smut fungi that have been gained from comparative genomics and discuss the molecular mechanisms by which U. maydis effectors change processes in the plant host. Finally, we examine how the expression of effector genes and effector secretion are coordinated with fungal development in the host.

Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression

Background

Biotrophic fungal plant pathogens cause billions of dollars in losses to North American crops annually. The model for functional investigation of these fungi is Ustilago maydis. Its 20.5 Mb annotated genome sequence has been an excellent resource for investigating biotrophic plant pathogenesis. Expressed-sequence tag libraries and microarray hybridizations have provided insight regarding the type of transcripts produced by U. maydis but these analyses were not comprehensive and there were insufficient data for transcriptome comparison to other smut fungi. To improve transcriptome annotation and enable comparative analyses, comprehensive strand-specific RNA-seq was performed on cell-types of three related smut species: U. maydis (common smut of corn), Ustilago hordei (covered smut of barley), and Sporisorium reilianum (head smut of corn).

Results

In total, >1 billion paired-end sequence reads were obtained from haploid cell, dikaryon and teliospore RNA of U. maydis, haploid cell RNA of U. hordei, and haploid and dikaryon cell RNA of S. reilianum. The sequences were assembled into transfrags using Trinity, and updated gene models were created using PASA and categorized with Cufflinks Cuffcompare. Representative genes that were predicted for the first time with these RNA-seq analyses and genes with novel annotation features were independently assessed by reverse transcriptase PCR. The analyses indicate hundreds more predicted proteins, relative to the previous genome annotation, could be produced by U. maydis from altered transcript forms, and that the number of non-coding RNAs produced, including transcribed intergenic sequences and natural antisense transcripts, approximately equals the number of mRNAs. This high representation of non-coding RNAs appears to be a conserved feature of the smut fungi regardless of whether they have RNA interference machinery. Approximately 50% of the identified NATs were conserved among the smut fungi.

Conclusions

Overall, these analyses revealed: 1) smut genomes encode a number of transcriptional units that is twice the number of annotated protein-coding genes, 2) a small number of intergenic transcripts may encode proteins with characteristics of fungal effectors, 3) the vast majority of intergenic and antisense transcripts do not contain ORFs, 4) a large proportion of the identified antisense transcripts were detected at orthologous loci among the smut fungi, and 5) there is an enrichment of functional categories among orthologous loci that suggests antisense RNAs could have a genome-wide, non-RNAi-mediated, influence on gene expression in smut fungi.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3720-8) contains supplementary material, which is available to authorized users.

Cross-talk of the biotrophic pathogen Claviceps purpurea and its host Secale cereale

BACKGROUND

The economically important Ergot fungus Claviceps purpurea is an interesting biotrophic model system because of its strict organ specificity (grass ovaries) and the lack of any detectable plant defense reactions. Though several virulence factors were identified, the exact infection mechanisms are unknown, e.g. how the fungus masks its attack and if the host detects the infection at all.

RESULTS

We present a first dual transcriptome analysis using an RNA-Seq approach. We studied both, fungal and plant gene expression in young ovaries infected by the wild-type and two virulence-attenuated mutants. We can show that the plant recognizes the fungus, since defense related genes are upregulated, especially several phytohormone genes. We present a survey of in planta expressed fungal genes, among them several confirmed virulence genes. Interestingly, the set of most highly expressed genes includes a high proportion of genes encoding putative effectors, small secreted proteins which might be involved in masking the fungal attack or interfering with host defense reactions. As known from several other phytopathogens, the C. purpurea genome contains more than 400 of such genes, many of them clustered and probably highly redundant. Since the lack of effective defense reactions in spite of recognition of the fungus could very well be achieved by effectors, we started a functional analysis of some of the most highly expressed candidates. However, the redundancy of the system made the identification of a drastic effect of a single gene most unlikely. We can show that at least one candidate accumulates in the plant apoplast. Deletion of some candidates led to a reduced virulence of C. purpurea on rye, indicating a role of the respective proteins during the infection process.

CONCLUSIONS

We show for the first time that- despite the absence of effective plant defense reactions- the biotrophic pathogen C. purpurea is detected by its host. This points to a role of effectors in modulation of the effective plant response. Indeed, several putative effector genes are among the highest expressed genes in planta.