Clathrin-mediated endocytosis facilitates the internalization of Magnaporthe oryzae effectors into rice cells

The Magnaporthe oryzae effector Pwl2 alters HIPP43 localization to suppress host immunity

The rice blast fungus Magnaporthe oryzae secretes a battery of effector proteins to facilitate host infection. Among these effectors, pathogenicity toward weeping lovegrass 2 (Pwl2) was originally identified as a host specificity determinant for the infection of weeping lovegrass (Eragrostis curvula) and is also recognized by the barley (Hordeum vulgare) Mla3 resistance protein. However, the biological activity of Pwl2 remains unknown. Here, we showed that the Pmk1 MAP kinase regulates PWL2 expression during the cell-to-cell movement of M. oryzae at plasmodesmata-containing pit fields. Consistent with this finding, we provided evidence that Pwl2 binds to the barley heavy metal-binding isoprenylated protein HIPP43, which results in HIPP43 displacement from plasmodesmata. Transgenic barley lines overexpressing PWL2 or HIPP43 exhibit attenuated immune responses and increased disease susceptibility. In contrast, a Pwl2SNDEYWY variant that does not interact with HIPP43 fails to alter the plasmodesmata localization of HIPP43. Targeted deletion of 3 PWL2 copies in M. oryzae resulted in a Δpwl2 mutant showing gain of virulence toward weeping lovegrass and barley Mla3 lines, but reduced blast disease severity on susceptible host plants. Taken together, our results provide evidence that Pwl2 is a virulence factor that suppresses host immunity by perturbing the plasmodesmatal deployment of HIPP43.

Ergosterol-induced immune response in barley involves phosphorylation of phosphatidylinositol phosphate metabolic enzymes and activation of diterpene biosynthesis

Lipids play crucial roles in plant-microbe interactions, functioning as structural components, signaling molecules, and microbe-associated molecular patterns (MAMPs). However, the mechanisms underlying lipid perception and signaling in plants remain largely unknown. Here, we investigate the immune responses activated in barley (Hordeum vulgare) by lipid extracts from the beneficial root endophytic fungus Serendipita indica and compare them to responses elicited by chitohexaose and the fungal sterol ergosterol. We demonstrate that S. indica lipid extract induces hallmarks of pattern-triggered immunity (PTI) in barley. Ergosterol emerged as the primary immunogenic component and was detected in the apoplastic fluid of S. indica-colonized barley roots. Notably, S. indica colonization suppresses the ergosterol-induced burst of reactive oxygen species (ROS) in barley. By employing a multi-omics approach, which integrates transcriptomics, phosphoproteomics, and metabolomics, we provide evidence for the phosphorylation of phosphatidylinositol phosphate (PIP) metabolic enzymes and activation of diterpene biosynthesis upon exposure to fungal lipids. Furthermore, we show that phosphatidic acid (PA) enhances lipid-mediated apoplastic ROS production in barley. These findings indicate that plant lipids facilitate immune responses to fungal lipids in barley, providing new insights into lipid-based signaling mechanisms in plant-microbe interactions.

Rice extracellular vesicles send defense proteins into fungus Rhizoctonia solani to reduce disease

The exchange of molecular information across kingdoms is crucial for the survival of both plants and their pathogens. Recent research has identified that plants transfer their small RNAs and microRNAs into fungal pathogens to suppress infection. However, whether and how plants send defense proteins into pathogens remains unknown. Here, we report that rice (Oryza sativa) plants package defense proteins into extracellular vesicles (EVs) and deliver them to the fungal pathogen Rhizoctonia solani. These EVs, enriched with host defense proteins, are internalized by the fungal cells. Reducing the transfer of host defense proteins via EVs results in increased disease susceptibility. Furthermore, the overexpression of host defense proteins in either rice plants or the fungal cells reduced the infection. Therefore, plants use EVs to send defense proteins into fungal pathogens, thereby combating infection. This mechanism represents a form of protein exchange between plants and pathogens, which contributes to reducing crop diseases.

A Novel Effector FoUpe9 Enhances the Virulence of Fusarium oxysporum f. sp. cubense Tropical Race 4 by Inhibiting Plant Immunity

Fusarium wilt caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) is the most destructive disease of the banana. Effectors play a crucial role in Foc TR4-banana interaction; however, only a few effectors have been functionally characterized. Our previous secretome studies on Foc TR4 highlighted an uncharacterized protein without any conserved domains (named FoUpe9), which was predicted to be a candidate effector. Herein, bioinformatics analysis showed that FoUpe9 was highly conserved among Fusarium species. FoUpe9 was highly induced during the early infection stages in the banana. A yeast signal sequence trap assay showed that FoUpe9 is a secretory protein. FoUpe9 could inhibit cell death and ROS accumulation triggered by BAX through the Agrobacterium-mediated Nicotiana benthamiana expression system. Subcellular location showed that FoUpe9 was located in the nucleus and cytoplasm of N. benthamiana cells. Deletion of the FoUpe9 gene did not affect mycelial growth, conidiation, sensitivity to cell-wall integrity, or osmotic and oxidative stress, but significantly attenuated fungal virulence. FoUpe9 deletion diminished fungal colonization and induced ROS production and expression of SA-related defense genes in banana plants. These results suggest that FoUpe9 enhances Foc TR4 virulence by inhibiting host immune responses and provide new insights into the functions of the uncharacterized proteins, further enhancing our understanding of effector-mediated Foc TR4 pathogenesis.

Plant salicylic acid signaling is inhibited by a cooperative strategy of two powdery mildew effectors

Powdery mildew is a global threat to crops and economically valuable plants. Salicylic acid (SA) signaling plays a significant role in plant resistance to biotrophic parasites; however, the mechanisms behind how powdery mildew fungi circumvent SA-mediated resistance remain unclear. Many phytopathogenic microbes deliver effectors into the host to sustain infection. In this study, we showed that the rubber tree powdery mildew fungus Erysiphe quercicola inhibits host SA biosynthesis by employing two effector proteins, EqCmu and EqPdt. These effector proteins can be delivered into plant cells to hydrolyze chorismate, the main precursor of SA, through their enzymatic activities. Notably, EqCmu and EqPdt can interact with each other, providing mutual protection against protein degradation mediated by the plant ubiquitin-proteasome system. This interaction enhances their activities in the hydrolysis of chorismate. Our study reveals a new pathogenic strategy by which two powdery mildew effector proteins cooperate to evade recognition by dampening the host immune system.

IMPORTANCE

Powdery mildew fungi may develop diverse strategies to disturb salicylic acid (SA) signaling in plants, which plays an important role in activating immunity, and little is known about these strategies. Our results suggest that the Erysiphe quercicola effector protein EqCmu can be translocated into host cells and inhibit host SA levels during the infection stage; however, it is targeted by the plant ubiquitin-proteasome system (UPS) and ubiquitinated, which induces EqCmu degradation. To evade the UPS, EqCmu interacts with EqPdt, another E. quercicola effector protein, to prevent that ubiquitination. EqPdt also inhibits host SA biosynthesis through its prephenate dehydratase activity. Taken together, these two powdery mildew effector proteins cause a synergistic effect in disturbing host SA signaling. Our study also suggests that enhancing SA signaling is required for boosting immunity against powdery mildew fungus.

Dynamic Gene-for-Gene Interactions Undermine Durable Resistance

Harold Flor's gene-for-gene model explained boom-bust cycles in which resistance (R) genes are deployed in farmers' fields, only to have pathogens overcome resistance by modifying or losing corresponding active avirulence (AVR) genes. Flor understood that host R genes with corresponding low rates of virulence mutation in the pathogen should maintain resistance for longer periods of time. This review focuses on AVR gene dynamics of the haploid Ascomycete fungus Pyricularia oryzae, which causes rice blast disease, a gene-for-gene system with a complex race structure and a very rapid boom-bust cycle due to high rates of AVR gene mutation. Highly mutable blast AVR genes are often characterized by deletion and by movement to new chromosomal locations, implying a loss/regain mechanism in response to R gene deployment. Beyond rice blast, the recent emergence of two serious new blast diseases on wheat and Lolium ryegrasses highlighted the role of AVR genes that act at the host genus level and serve as infection barriers that separate host genus-specialized P. oryzae subpopulations. Wheat and ryegrass blast diseases apparently evolved through sexual crosses involving fungal individuals from five host-adapted subpopulations, with the host jump enabled by the introduction of virulence alleles of key host-specificity AVR genes. Despite identification of wheat AVR/R gene interactions operating at the host genus specificity level, the paucity of effective R genes identified thus far limits control of wheat blast disease. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Design of a pseudo-color-assisted biocompatible supramolecular sensing probe for "lighting up" endogenous salicylic acid in plants

The widely recognized phytohormone, salicylic acid (SA), serves not only as an exogenous additive for fruits and vegetables but, more crucially, as an in vivo regulator of the entire plant growth process. Consequently, it is essential to achieve both in vitro detection and in vivo imaging analysis of the plant hormone SA. In this study, a biocompatible supramolecular probe was crafted using a "label-free" SA aptamer as the host for an aggregation-induced emission (AIE) organic small molecule. Upon recognizing the target SA, the aptamer is not readily digested by the exonuclease (Exo.I), which permits the aptamer sequence to be largely preserved. Under these conditions, the aptamer can be further integrated with the AIE organic small molecule, thereby enabling it to produce fluorescence emission due to restricted intramolecular motion. The probe can efficiently accomplish in vitro detection of SA within a linear range of 0.3-70 μM, with a detection limit reaching 0.09 μM. Most importantly, building on the achievement of fluorescence imaging monitoring of SA in plants, this work has developed a fluorescence image processing program utilizing the Java algorithm. This program facilitates the one-click conversion of monochrome images to pseudo-color in conventional fluorescence imaging, thereby enhancing the ability of the naked eye to discern image details.

Live cell imaging of plant infection provides new insight into the biology of pathogenesis by the rice blast fungus Magnaporthe oryzae

Magnaporthe oryzae is the causal agent of rice blast, one of the most serious diseases affecting rice cultivation around the world. During plant infection, M. oryzae forms a specialised infection structure called an appressorium. The appressorium forms in response to the hydrophobic leaf surface and relies on multiple signalling pathways, including a MAP kinase phosphorelay and cAMP-dependent signalling, integrated with cell cycle control and autophagic cell death of the conidium. Together, these pathways regulate appressorium morphogenesis.The appressorium generates enormous turgor, applied as mechanical force to breach the rice cuticle. Re-polarisation of the appressorium requires a turgor-dependent sensor kinase which senses when a critical threshold of turgor has been reached to initiate septin-dependent re-polarisation of the appressorium and plant infection. Invasive growth then requires differential expression and secretion of a large repertoire of effector proteins secreted by distinct secretory pathways depending on their destination, which is also governed by codon usage and tRNA thiolation. Cytoplasmic effectors require an unconventional Golgi-independent secretory pathway and evidence suggests that clathrin-mediated endocytosis is necessary for their delivery into plant cells. The blast fungus then develops a transpressorium, a specific invasion structure used to move from cell-to-cell using pit field sites containing plasmodesmata, to facilitate its spread in plant tissue. This is controlled by the same MAP kinase signalling pathway as appressorium development and requires septin-dependent hyphal constriction. Recent progress in understanding the mechanisms of rice infection by this devastating pathogen using live cell imaging procedures are presented.

Plant pathogenic fungi hijack phosphate signaling with conserved enzymatic effectors

Inorganic phosphate (Pi) is essential for life, and plant cells monitor Pi availability by sensing inositol pyrophosphate (PP-InsP) levels. In this work, we describe the hijacking of plant phosphate sensing by a conserved family of Nudix hydrolase effectors from pathogenic Magnaporthe and Colletotrichum fungi. Structural and enzymatic analyses of the Nudix effector family demonstrate that they selectively hydrolyze PP-InsP. Gene deletion experiments of Nudix effectors in Magnaporthe oryzae, Colletotrichum higginsianum, and Colletotrichum graminicola indicate that PP-InsP hydrolysis substantially enhances disease symptoms in diverse pathosystems. Further, we show that this conserved effector family induces phosphate starvation signaling in plants. Our study elucidates a molecular mechanism, used by multiple phytopathogenic fungi, that manipulates the highly conserved plant phosphate sensing pathway to exacerbate disease.

Piecing together oomycete effector processing and host translocation

This article is a Commentary on Xu et al. (2025), 245: 1640–1654.

Proteolytic processing of both RXLR and EER motifs in oomycete effectors

Arg-any amino acid-Leu-Arg (RXLR) effectors are central oomycete virulence factors that suppress plant immunity. Relatively little is known about how they are processed post-translationally before delivery into host cells. A range of molecular, cell and biochemical processes were used to investigate proteolytic processing of RXLR and Glu-Glu-Arg (EER) motifs in Phytophthora infestans effectors. Proteolytic cleavage at the RXLR motif occurred before secretion in all effectors tested, suggesting it is a general rule. Cleavage occurred between the leucine and the second arginine. There was no cleavage of a naturally occurring second RXLR motif in a structured region of Pi21388/AvrBlb1, or one introduced at a similar position in effector Pi04314, in keeping with the motif being positionally constrained, potentially to disordered regions closely following the signal peptide. Remarkably, independent proteolytic cleavage of the EER motif, often found immediately after the RXLR, was also observed, occurring immediately after the arginine. Full-length effectors expressed in host plant Nicotiana benthamiana revealed that, although secreted, they were poorly processed, suggesting that RXLR and EER cleavage does not occur in all eukaryotic cells. We conclude that, whether possessing both RXLR and EER, or either motif alone, these effectors are likely generally proteolytically processed before secretion.

Immunoisolation of Plant Endosomal Vesicles to Explore Uptake of Pathogen Effector Proteins During Infection of Nicotiana benthamiana

Endocytosis is an essential cellular process that uptakes substances into cells at the plasma membrane from the extracellular space and plays a major role in plant development and responses to environmental stimuli. Research has shown that plant membrane-resident proteins are endocytosed and transported into plant endosomes in response to pathogen-secreted elicitors. However, there is no conclusive experimental evidence demonstrating how secreted cytoplasmic effectors from oomycetes and fungi enter host cells during infection. The adapted protocol in this chapter describes endosome isolation using immunopurification with the aim to co-capture Phytophthora infestans RXLR effectors during infection. This protocol can be widely used in the isolation and purification of different subtypes of endosomal vesicles that uptake extracellular molecules during pathogen infection and in response to environmental stimuli.

A pharmacological approach to investigating effector translocation in rice-Magnaporthe oryzae interactions

Fungal pathogens deliver effector proteins into living plant cells to suppress plant immunity and control plant processes that are needed for infection. During plant infection, the devastating rice blast fungus, Magnaporthe oryzae, forms the specialized biotrophic interfacial complex (BIC), which is essential for effector translocation. Cytoplasmic effectors are first focally secreted into BICs, and subsequently packaged into dynamic membranous effector compartments (MECs), then translocated via clathrin-mediated endocytosis (CME) into the host cytoplasm. This study demonstrates that clathrin-heavy chain inhibitors endosidin-9 (ES9) and endosidin-9-17 (ES9-17) blocked the internalization of the fluorescently labeled effectors Bas1 and Pwl2 in rice cells, leading to swollen BICs lacking MECs. In contrast, ES9-17 treatment had no impact on the localization pattern of the apoplastic effector Bas4. This study provides further evidence that cytoplasmic effector translocation occurs by CME in BICs, suggesting a potential role for M. oryzae effectors in co-opting plant endocytosis.

Nuclear localization sequence of MoHTR1, a Magnaporthe oryzae effector, for transcriptional reprogramming of immunity genes in rice

Plant pathogens secrete nuclear effectors into the host nuclei to modulate the host immune system. Although several nuclear effectors of fungal pathogens have been recently reported, the molecular mechanism of NLS-associated transport vehicles of nuclear effectors and the roles of NLS in transcriptional reprogramming of host immunity genes remain enigmatic. We previously reported the MoHTR1, a nuclear effector of the rice blast fungus, Magnaporthe oryzae. MoHTR1 is translocated to rice nuclei but not in fungal nuclei. Here, we identify the core NLS (RxKK) responsible for MoHTR1's nuclear localization. MoHTR1 is translocated in the host nucleus through interaction with rice importin α. MoHTR1 NLS empowers it to translocate the cytoplasmic effectors of M. oryzae into rice nuclei. Furthermore, other nuclear effector candidates of the blast pathogen and rice proteins which have RxKK also exhibit nuclear localization, highlighting the crucial role of RxKK in this process. We also unveil the importance of SUMOylation in the stability of MoHTR1 and translocation of MoHTR1 to host nuclei. Moreover, MoHTR1 NLS is essential for the pathogenicity of M. oryzae by reprogramming immunity-associated genes in the host. Our findings provide insights into the significance of plant-specific NLS on fungal nuclear effectors and its role in plant-pathogen interactions.

Roadmap to Success: How Oomycete Plant Pathogens Invade Tissues and Deliver Effectors

Filamentous plant pathogens threaten global food security and ecosystem resilience. In recent decades, significant strides have been made in deciphering the molecular basis of plant-pathogen interactions, especially the interplay between pathogens' molecular weaponry and hosts' defense machinery. Stemming from interdisciplinary investigations into the infection cell biology of filamentous plant pathogens, recent breakthrough discoveries have provided a new impetus to the field. These advances include the biophysical characterization of a novel invasion mechanism (i.e., naifu invasion) and the unraveling of novel effector secretion routes. On the plant side, progress includes the identification of components of cellular networks involved in the uptake of intracellular effectors. This exciting body of research underscores the pivotal role of logistics management by the pathogen throughout the infection cycle, encompassing the precolonization stages up to tissue invasion. More insight into these logistics opens new avenues for developing environmentally friendly crop protection strategies in an era marked by an imperative to reduce the use of agrochemicals.

Transformation-based gene silencing and functional characterization of an ISC effector reveal how a powdery mildew fungus disturbs salicylic acid biosynthesis and immune response in the plant

Obligate biotrophic powdery mildew fungi infect a wide range of economically important plants. These fungi often deliver effector proteins into the host tissues to suppress plant immunity and sustain infection. The phytohormone salicylic acid (SA) is one of the most important signals that activate plant immunity against pathogens. However, how powdery mildew effectors interact with host SA signalling is poorly understood. Isochorismatase (ISC) effectors from two other filamentous pathogens have been found to inhibit host SA biosynthesis by hydrolysing isochorismate, the main SA precursor in the plant cytosol. Here, we identified an ISC effector, named EqIsc1, from the rubber tree powdery mildew fungus Erysiphe quercicola. In ISC enzyme assays, EqIsc1 displayed ISC activity by transferring isochorismate to 2,3-dihydro-2,3-dihydroxybenzoate in vitro and in transgenic Nicotiana benthamiana plants. In EqIsc1-expressing transgenic Arabidopsis thaliana, SA biosynthesis and SA-mediated immune response were significantly inhibited. In addition, we developed an electroporation-mediated transformation method for the genetic manipulation of E. quercicola. Inoculation of rubber tree leaves with EqIsc1-silenced E. quercicola strain induced SA-mediated immunity. We also detected the translocation of EqIsc1 into the plant cytosol during the interaction between E. quercicola and its host. Taken together, our results suggest that a powdery mildew effector functions as an ISC enzyme to hydrolyse isochorismate in the host cytosol, altering the SA biosynthesis and immune response.

Membrane fluidity control by the Magnaporthe oryzae acyl-CoA binding protein sets the thermal range for host rice cell colonization

Following leaf cuticle penetration by specialized appressorial cells, the devastating blast fungus Magnaporthe oryzae grows as invasive hyphae (IH) in living rice cells. IH are separated from host cytoplasm by plant-derived membranes forming an apoplastic compartment and a punctate biotrophic interfacial complex (BIC) that mediate the molecular host-pathogen interaction. What molecular and cellular processes determine the temperature range for this biotrophic growth stage is an unanswered question pertinent to a broader understanding of how phytopathogens may cope with environmental stresses arising under climate change. Here, we shed light on thermal adaptation in M. oryzae by disrupting the ACB1 gene encoding the single acyl-CoA-binding protein, an intracellular transporter of long-chain acyl-CoA esters. Loss of ACB1 affected fatty acid desaturation levels and abolished pathogenicity at optimal (26°C) and low (22°C) but not elevated (29°C) infection temperatures (the latter following post-penetration shifts from 26°C). Relative to wild type, the Δacb1 mutant strain exhibited poor vegetative growth and impaired membrane trafficking at 22°C and 26°C, but not at 29°C. In planta, Δacb1 biotrophic growth was inhibited at 26°C-which was accompanied by a multi-BIC phenotype-but not at 29°C, where BIC formation was normal. Underpinning the Δacb1 phenotype was impaired membrane fluidity at 22°C and 26°C but not at elevated temperatures, indicating Acb1 suppresses membrane rigidity at optimal- and suboptimal- but not supraoptimal temperatures. Deducing a temperature-dependent role for Acb1 in maintaining membrane fluidity homeostasis reveals how the thermal range for rice blast disease is both mechanistically determined and wider than hitherto appreciated.

The roles of Magnaporthe oryzae avirulence effectors involved in blast resistance/susceptibility

Phytopathogens represent an ongoing threat to crop production and a significant impediment to global food security. During the infection process, these pathogens spatiotemporally deploy a large array of effectors to sabotage host defense machinery and/or manipulate cellular pathways, thereby facilitating colonization and infection. However, besides their pivotal roles in pathogenesis, certain effectors, known as avirulence (AVR) effectors, can be directly or indirectly perceived by plant resistance (R) proteins, leading to race-specific resistance. An in-depth understanding of the intricate AVR-R interactions is instrumental for genetic improvement of crops and safeguarding them from diseases. Magnaporthe oryzae (M. oryzae), the causative agent of rice blast disease, is an exceptionally virulent and devastating fungal pathogen that induces blast disease on over 50 monocot plant species, including economically important crops. Rice-M. oryzae pathosystem serves as a prime model for functional dissection of AVR effectors and their interactions with R proteins and other target proteins in rice due to its scientific advantages and economic importance. Significant progress has been made in elucidating the potential roles of AVR effectors in the interaction between rice and M. oryzae over the past two decades. This review comprehensively discusses recent advancements in the field of M. oryzae AVR effectors, with a specific focus on their multifaceted roles through interactions with corresponding R/target proteins in rice during infection. Furthermore, we deliberated on the emerging strategies for engineering R proteins by leveraging the structural insights gained from M. oryzae AVR effectors.

Fungal effectors: past, present, and future

Fungal effector proteins function at the interfaces of diverse interactions between fungi and their plant and animal hosts, facilitating interactions that are pathogenic or mutualistic. Recent advancements in protein structure prediction have significantly accelerated the identification and functional predictions of these rapidly evolving effector proteins. This development enables scientists to generate testable hypotheses for functional validation using experimental approaches. Research frontiers in effector biology include understanding pathways through which effector proteins are secreted or translocated into host cells, their roles in manipulating host microbiomes, and their contribution to interacting with host immunity. Comparative effector repertoires among different fungal-host interactions can highlight unique adaptations, providing insights for the development of novel antifungal therapies and biocontrol strategies.

The Transcriptional Landscape of Berry Skin in Red and White PIWI ("Pilzwiderstandsfähig") Grapevines Possessing QTLs for Partial Resistance to Downy and Powdery Mildews

PIWI, from the German word Pilzwiderstandsfähig, meaning "fungus-resistant", refers to grapevine cultivars bred for resistance to fungal pathogens such as Erysiphe necator (the causal agent of powdery mildew) and Plasmopara viticola (the causal agent of downy mildew), two major diseases in viticulture. These varieties are typically developed through traditional breeding, often crossbreeding European Vitis vinifera with American or Asian species that carry natural disease resistance. This study investigates the transcriptional profiles of exocarp tissues in mature berries from four PIWI grapevine varieties compared to their elite parental counterparts using RNA-seq analysis. We performed RNA-seq on four PIWI varieties (two red and two white) and their noble parents to identify differential gene expression patterns. Comprehensive analyses, including Differential Gene Expression (DEGs), Gene Set Enrichment Analysis (GSEA), Weighted Gene Co-expression Network Analysis (WGCNA), and tau analysis, revealed distinct gene clusters and individual genes characterizing the transcriptional landscape of PIWI varieties. Differentially expressed genes indicated significant changes in pathways related to organic acid metabolism and membrane transport, potentially contributing to enhanced resilience. WGCNA and k-means clustering highlighted co-expression modules linked to PIWI genotypes and their unique tolerance profiles. Tau analysis identified genes uniquely expressed in specific genotypes, with several already known for their defense roles. These findings offer insights into the molecular mechanisms underlying grapevine resistance and suggest promising avenues for breeding strategies to enhance disease resistance and overall grape quality in viticulture.

Antagonistic Mechanism Analysis of Bacillus velezensis JLU-1, a Biocontrol Agent of Rice Pathogen Magnaporthe oryzae

Magnaporthe oryzae, the causal agent of rice blast, is a fungal disease pathogen. Bacillus spp. have emerged as the most promising biological control agent alternative to chemical fungicides. In this study, the bacterial strain JLU-1 with significant antagonistic activity isolated from the rhizosphere soil of rice was identified as Bacillus velezensis through whole-genome sequencing, average nucleotide identity analysis, and 16S rRNA gene sequencing. Twelve gene clusters for secondary metabolite synthesis were identified in JLU-1. Furthermore, 3 secondary metabolites were identified in JLU-1, and the antagonistic effect of secondary metabolites against fungal pathogens was confirmed. Exposure to JLU-1 reduced the virulence of M. oryzae, and JLU-1 has the ability to induce the reactive oxygen species production of rice and improve the salt tolerance of rice. All of these results indicated that JLU-1 and its secondary metabolites have the promising potential to be developed into a biocontrol agent to control fungal diseases.

Paths of Least Resistance: Unconventional Effector Secretion by Fungal and Oomycete Plant Pathogens

Effector secretion by different routes mediates the molecular interplay between host plant and pathogen, but mechanistic details in eukaryotes are sparse. This may limit the discovery of new effectors that could be utilized for improving host plant disease resistance. In fungi and oomycetes, apoplastic effectors are secreted via the conventional endoplasmic reticulum (ER)-Golgi pathway, while cytoplasmic effectors are packaged into vesicles that bypass Golgi in an unconventional protein secretion (UPS) pathway. In Magnaporthe oryzae, the Golgi bypass UPS pathway incorporates components of the exocyst complex and a t-SNARE, presumably to fuse Golgi bypass vesicles to the fungal plasma membrane. Upstream, cytoplasmic effector mRNA translation in M. oryzae requires the efficient decoding of AA-ending codons. This involves the modification of wobble uridines in the anticodon loop of cognate tRNAs and fine-tunes cytoplasmic effector translation and secretion rates to maintain biotrophic interfacial complex integrity and permit host infection. Thus, plant-fungal interface integrity is intimately tied to effector codon usage, which is a surprising constraint on pathogenicity. Here, we discuss these findings within the context of fungal and oomycete effector discovery, delivery, and function in host cells. We show how cracking the codon code for unconventional cytoplasmic effector secretion in M. oryzae has revealed AA-ending codon usage bias in cytoplasmic effector mRNAs across kingdoms, including within the RxLR-dEER motif-encoding sequence of a bona fide Phytophthora infestans cytoplasmic effector, suggesting its subjection to translational speed control. By focusing on recent developments in understanding unconventional effector secretion, we draw attention to this important but understudied area of host-pathogen interactions. [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.

The cysteine-rich virulence factor NipA of Arthrobotrys flagrans interferes with cuticle integrity of Caenorhabditis elegans

Animals protect themself from microbial attacks by robust skins or a cuticle as in Caenorhabditis elegans. Nematode-trapping fungi, like Arthrobotrys flagrans, overcome the cuticle barrier and colonize the nematode body. While lytic enzymes are important for infection, small-secreted proteins (SSPs) without enzymatic activity, emerge as crucial virulence factors. Here, we characterized NipA (nematode induced protein) which A. flagrans secretes at the penetration site. In the absence of NipA, A. flagrans required more time to penetrate C. elegans. Heterologous expression of the fungal protein in the epidermis of C. elegans led to blister formation. NipA contains 13 cysteines, 12 of which are likely to form disulfide bridges, and the remaining cysteine was crucial for blister formation. We hypothesize that NipA interferes with cuticle integrity to facilitate fungal entry. Genome-wide expression analyses of C. elegans expressing NipA revealed mis-regulation of genes associated with extracellular matrix (ECM) maintenance and innate immunity.

An Efficient Method for Screening Rice Breeding Lines Against Races of Magnaporthe oryzae

Rice blast, caused by Magnaporthe oryzae, is the most destructive rice disease worldwide. The disease symptoms are usually expressed on the leaf and panicle. The leaf disease intensity in controlled environmental conditions is frequently quantified using a 0 to 5 scale, where 0 represents the absence of symptoms, and 5 represents large eyespot lesions. However, this scale restricts the qualitative classification of the varieties into intermediate resistant and susceptible categories. Here, we develop a 0 to 6 scale for blast disease that allows proper assignment of rice breeding lines and varieties into six resistance levels (highly resistant, resistant, moderately resistant, moderately susceptible, susceptible, and highly susceptible). We evaluated 40 common rice varieties against four major blast races (IB1, IB17, IB49, and IE1-K). Varieties carrying the Pi-ta gene were either highly resistant, resistant, or moderately resistant to IB17. The IE1-K race was able to break Pi-ta-mediated resistance of the rice varieties. The Pi-z gene conferred resistance to the IB17 and IE1-K races. The varieties M201, Cheniere, and Frontier were highly susceptible (score 6; 100% disease) to the race IE1-K. Moreover, varieties that were resistant or susceptible to all four blast races also showed similar levels of resistance/susceptibility to blast disease in the field. Taken together, our data proved that the 0 to 6 blast scale can efficiently determine the resistance levels of rice varieties against major blast races. This robust method will assist rice breeding programs to incorporate durable resistance against major and emerging blast races.[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.

The plant immune system: From discovery to deployment

Plant diseases cause famines, drive human migration, and present challenges to agricultural sustainability as pathogen ranges shift under climate change. Plant breeders discovered Mendelian genetic loci conferring disease resistance to specific pathogen isolates over 100 years ago. Subsequent breeding for disease resistance underpins modern agriculture and, along with the emergence and focus on model plants for genetics and genomics research, has provided rich resources for molecular biological exploration over the last 50 years. These studies led to the identification of extracellular and intracellular receptors that convert recognition of extracellular microbe-encoded molecular patterns or intracellular pathogen-delivered virulence effectors into defense activation. These receptor systems, and downstream responses, define plant immune systems that have evolved since the migration of plants to land ∼500 million years ago. Our current understanding of plant immune systems provides the platform for development of rational resistance enhancement to control the many diseases that continue to plague crop production.

Phytoalexin sakuranetin attenuates endocytosis and enhances resistance to rice blast

Phytoalexin sakuranetin functions in resistance against rice blast. However, the mechanisms underlying the effects of sakuranetin remains elusive. Here, we report that rice lines expressing resistance (R) genes were found to contain high levels of sakuranetin, which correlates with attenuated endocytic trafficking of plasma membrane (PM) proteins. Exogenous and endogenous sakuranetin attenuates the endocytosis of various PM proteins and the fungal effector PWL2. Moreover, accumulation of the avirulence protein AvrCO39, resulting from uptake into rice cells by Magnaporthe oryzae, was reduced following treatment with sakuranetin. Pharmacological manipulation of clathrin-mediated endocytic (CME) suggests that this pathway is targeted by sakuranetin. Indeed, attenuation of CME by sakuranetin is sufficient to convey resistance against rice blast. Our data reveals a mechanism of rice against M. oryzae by increasing sakuranetin levels and repressing the CME of pathogen effectors, which is distinct from the action of many R genes that mainly function by modulating transcription.

The emerging roles of clathrin-mediated endocytosis in plant development and stress responses

Clathrin-mediated endocytosis (CME) is a highly conserved pathway that plays a crucial role in the endocytosis of plasma membrane proteins in eukaryotic cells. The pathway is initiated when the adaptor protein complex 2 (AP2) and TPLATE complex (TPC) work together to recognize cargo proteins and recruit clathrin. This review provides a concise overview of the functions of each subunit of AP2 and TPC, and highlights the involvement of CME in various biological processes, such as pollen development, root development, nutrient transport, extracellular signal transduction, auxin polar transport, hyperosmotic stress, salinity stress, high ammonium stress, and disease resistance. Additionally, the review explores the regulation of CME by phytohormones, clathrin-mediated exocytosis (CMX), and AP2M phosphorylation. It also suggests potential future research directions for CME.

Pyricularia oryzae: Lab star and field scourge

Pyricularia oryzae (syn. Magnaporthe oryzae), is a filamentous ascomycete that causes a major disease called blast on cereal crops, as well as on a wide variety of wild and cultivated grasses. Blast diseases have a tremendous impact worldwide particularly on rice and on wheat, where the disease emerged in South America in the 1980s, before spreading to Asia and Africa. Its economic importance, coupled with its amenability to molecular and genetic manipulation, have inspired extensive research efforts aiming at understanding its biology and evolution. In the past 40 years, this plant-pathogenic fungus has emerged as a major model in molecular plant-microbe interactions. In this review, we focus on the clarification of the taxonomy and genetic structure of the species and its host range determinants. We also discuss recent molecular studies deciphering its lifecycle.

TAXONOMY

Kingdom: Fungi, phylum: Ascomycota, sub-phylum: Pezizomycotina, class: Sordariomycetes, order: Magnaporthales, family: Pyriculariaceae, genus: Pyricularia.

HOST RANGE

P. oryzae has the ability to infect a wide range of Poaceae. It is structured into different host-specialized lineages that are each associated with a few host plant genera. The fungus is best known to cause tremendous damage to rice crops, but it can also attack other economically important crops such as wheat, maize, barley, and finger millet.

DISEASE SYMPTOMS

P. oryzae can cause necrotic lesions or bleaching on all aerial parts of its host plants, including leaf blades, sheaths, and inflorescences (panicles, spikes, and seeds). Characteristic symptoms on leaves are diamond-shaped silver lesions that often have a brown margin and whose appearance is influenced by numerous factors such as the plant genotype and environmental conditions. USEFUL WEBSITES Resources URL Genomic data repositories http://genome.jouy.inra.fr/gemo/ Genomic data repositories http://openriceblast.org/ Genomic data repositories http://openwheatblast.net/ Genome browser for fungi (including P. oryzae) http://fungi.ensembl.org/index.html Comparative genomics database https://mycocosm.jgi.doe.gov/mycocosm/home T-DNA mutant database http://atmt.snu.kr/ T-DNA mutant database http://www.phi-base.org/ SNP and expression data https://fungidb.org/fungidb/app/.

Border Control: Manipulation of the Host-Pathogen Interface by Perihaustorial Oomycete Effectors

Filamentous plant pathogens, including fungi and oomycetes, cause some of the most devastating plant diseases. These organisms serve as ideal models for understanding the intricate molecular interplay between plants and the invading pathogens. Filamentous pathogens secrete effector proteins via haustoria, specialized structures for infection and nutrient uptake, to suppress the plant immune response and to reprogram plant metabolism. Recent advances in cell biology have provided crucial insights into the biogenesis of the extrahaustorial membrane and the redirection of host endomembrane trafficking toward this interface. Functional studies have shown that an increasing number of oomycete effectors accumulate at the perihaustorial interface to subvert plant focal immune responses, with a particular convergence on targets involved in host endomembrane trafficking. In this review, we summarize the diverse mechanisms of perihaustorial effectors from oomycetes and pinpoint pressing questions regarding their role in manipulating host defense and metabolism at the haustorial interface. [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.

Effector-triggered susceptibility by the rice blast fungus Magnaporthe oryzae

Rice blast, the most destructive disease of cultivated rice world-wide, is caused by the filamentous fungus Magnaporthe oryzae. To cause disease in plants, M. oryzae secretes a diverse range of effector proteins to suppress plant defense responses, modulate cellular processes, and support pathogen growth. Some effectors can be secreted by appressoria even before host penetration, while others accumulate in the apoplast, or enter living plant cells where they target specific plant subcellular compartments. During plant infection, the blast fungus induces the formation of a specialized plant structure known as the biotrophic interfacial complex (BIC), which appears to be crucial for effector delivery into plant cells. Here, we review recent advances in the cell biology of M. oryzae-host interactions and show how new breakthroughs in disease control have stemmed from an increased understanding of effector proteins of M. oryzae are deployed and delivered into plant cells to enable pathogen invasion and host susceptibility.

RxLR Effectors: Master Modulators, Modifiers and Manipulators

Cytoplasmic effectors with an Arg-any amino acid-Arg-Leu (RxLR) motif are encoded by hundreds of genes within the genomes of oomycete Phytophthora spp. and downy mildew pathogens. There has been a dramatic increase in our understanding of the evolution, function, and recognition of these effectors. Host proteins with a wide range of subcellular localizations and functions are targeted by RxLR effectors. Many processes are manipulated, including transcription, post-translational modifications, such as phosphorylation and ubiquitination, secretion, and intracellular trafficking. This involves an array of RxLR effector modes-of-action, including stabilization or destabilization of protein targets, altering or disrupting protein complexes, inhibition or utility of target enzyme activities, and changing the location of protein targets. Interestingly, approximately 50% of identified host proteins targeted by RxLR effectors are negative regulators of immunity. Avirulence RxLR effectors may be directly or indirectly detected by nucleotide-binding leucine-rich repeat resistance (NLR) proteins. Direct recognition by a single NLR of RxLR effector orthologues conserved across multiple Phytophthora pathogens may provide wide protection of diverse crops. Failure of RxLR effectors to interact with or appropriately manipulate target proteins in nonhost plants has been shown to restrict host range. This knowledge can potentially be exploited to alter host targets to prevent effector interaction, providing a barrier to host infection. Finally, recent evidence suggests that RxLR effectors, like cytoplasmic effectors from fungal pathogen Magnaporthe oryzae, may enter host cells via clathrin-mediated endocytosis. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Effector translocation and rational design of disease resistance

The effector repertoire of a pathogen is dynamically evolving. However, the effector translocation mechanism, partly elucidated recently, may be conserved. By targeting the effector translocation machinery, rather than the individual evolving effector, rational design of durable and broad-spectrum disease resistance can be achieved, facilitated by genome-editing and artificial intelligence-enabling technologies.

Filamentous pathogen effectors enter plant cells via endocytosis

Recent findings demonstrate that cytoplasmic effectors from fungal and oomycete pathogens enter plant cells via clathrin-mediated endocytosis (CME). This raises several questions: Does effector secretion pathway facilitate host uptake? How is CME triggered in host cells? How are the effectors released from endosomal compartments to reach diverse subcellular destinations?

A transcriptional activator effector of Ustilago maydis regulates hyperplasia in maize during pathogen-induced tumor formation

Ustilago maydis causes common smut in maize, which is characterized by tumor formation in aerial parts of maize. Tumors result from the de novo cell division of highly developed bundle sheath and subsequent cell enlargement. However, the molecular mechanisms underlying tumorigenesis are still largely unknown. Here, we characterize the U. maydis effector Sts2 (Small tumor on seedlings 2), which promotes the division of hyperplasia tumor cells. Upon infection, Sts2 is translocated into the maize cell nucleus, where it acts as a transcriptional activator, and the transactivation activity is crucial for its virulence function. Sts2 interacts with ZmNECAP1, a yet undescribed plant transcriptional activator, and it activates the expression of several leaf developmental regulators to potentiate tumor formation. On the contrary, fusion of a suppressive SRDX-motif to Sts2 causes dominant negative inhibition of tumor formation, underpinning the central role of Sts2 for tumorigenesis. Our results not only disclose the virulence mechanism of a tumorigenic effector, but also reveal the essential role of leaf developmental regulators in pathogen-induced tumor formation.

Extracellular RNAs released by plant-associated fungi: from fundamental mechanisms to biotechnological applications

Extracellular RNAs are an emerging research topic in fungal-plant interactions. Fungal plant pathogens and symbionts release small RNAs that enter host cells to manipulate plant physiology and immunity. This communication via extracellular RNAs between fungi and plants is bidirectional. On the one hand, plants release RNAs encapsulated inside extracellular vesicles as a defense response as well as for intercellular and inter-organismal communication. On the other hand, recent reports suggest that also full-length mRNAs are transported within fungal EVs into plants, and these fungal mRNAs might get translated inside host cells. In this review article, we summarize the current views and fundamental concepts of extracellular RNAs released by plant-associated fungi, and we discuss new strategies to apply extracellular RNAs in crop protection against fungal pathogens. KEY POINTS: • Extracellular RNAs are an emerging topic in plant-fungal communication. • Fungi utilize RNAs to manipulate host plants for colonization. • Extracellular RNAs can be engineered to protect plants against fungal pathogens.

Vesicle trafficking in rice: too little is known

The vesicle trafficking apparatus is a fundamental machinery to maintain the homeostasis of membrane-enclosed organelles in eukaryotic cells. Thus, it is broadly conserved in eukaryotes including plants. Intensive studies in the model organisms have produced a comprehensive picture of vesicle trafficking in yeast and human. However, with respect to the vesicle trafficking of plants including rice, our understanding of the components and their coordinated regulation is very limited. At present, several vesicle trafficking apparatus components and cargo proteins have been identified and characterized in rice, but there still remain large unknowns concerning the organization and function of the rice vesicle trafficking system. In this review, we outline the main vesicle trafficking pathways of rice based on knowledge obtained in model organisms, and summarize current advances of rice vesicle trafficking. We also propose to develop methodologies applicable to rice and even other crops for further exploring the mysteries of vesicle trafficking in plants.

Fungal small RNAs ride in extracellular vesicles to enter plant cells through clathrin-mediated endocytosis

Small RNAs (sRNAs) of the fungal pathogen Botrytis cinerea can enter plant cells and hijack host Argonaute protein 1 (AGO1) to silence host immunity genes. However, the mechanism by which these fungal sRNAs are secreted and enter host cells remains unclear. Here, we demonstrate that B. cinerea utilizes extracellular vesicles (EVs) to secrete Bc-sRNAs, which are then internalized by plant cells through clathrin-mediated endocytosis (CME). The B. cinerea tetraspanin protein, Punchless 1 (BcPLS1), serves as an EV biomarker and plays an essential role in fungal pathogenicity. We observe numerous Arabidopsis clathrin-coated vesicles (CCVs) around B. cinerea infection sites and the colocalization of B. cinerea EV marker BcPLS1 and Arabidopsis CLATHRIN LIGHT CHAIN 1, one of the core components of CCV. Meanwhile, BcPLS1 and the B. cinerea-secreted sRNAs are detected in purified CCVs after infection. Arabidopsis knockout mutants and inducible dominant-negative mutants of key components of the CME pathway exhibit increased resistance to B. cinerea infection. Furthermore, Bc-sRNA loading into Arabidopsis AGO1 and host target gene suppression are attenuated in those CME mutants. Together, our results demonstrate that fungi secrete sRNAs via EVs, which then enter host plant cells mainly through CME.

Genome editing enables defense-yield balance in rice

This brief article highlights the key findings of the study conducted by Sha et al. (Nature, doi:10.1038/s41586-023-06205-2, 2023), focusing on the cloning of the RBL1 gene from rice, which is associated with lesion mimic mutant (LMM) traits. The RBL1 gene encodes a cytidine diphosphate diacylglycerol (CDP-DAG) synthase and plays a crucial role in regulating cell death and immunity by controlling phosphatidylinositol biosynthesis. The rbl1 mutant shows autoimmunity with multi-pathogen resistance but with severe yield penalty. Using genome editing techniques, the research team successfully generated an elite allele of RBL1 that not only restores rice yield but also provides broad-spectrum resistance against both bacterial and fungal pathogens. These findings demonstrate the potential of utilizing genome editing to enhance crop productivity and pathogen resistance.

Fungal small RNAs ride in extracellular vesicles to enter plant cells through clathrin-mediated endocytosis

Small RNAs (sRNAs) of the fungal pathogen Botrytis cinerea can enter plant cells and hijack host Argonaute protein 1 (AGO1) to silence host immunity genes. However, the mechanism by which these fungal sRNAs are secreted and enter host cells remains unclear. Here, we demonstrate that B. cinerea utilizes extracellular vesicles (EVs) to secrete Bc-sRNAs, which are then internalized by plant cells through clathrin-mediated endocytosis (CME). The B. cinerea tetraspanin protein, Punchless 1 (BcPLS1), serves as an EV biomarker and plays an essential role in fungal pathogenicity. We observe numerous Arabidopsis clathrin-coated vesicles (CCVs) around B. cinerea infection sites and the colocalization of B. cinerea EV marker BcPLS1 and Arabidopsis CLATHRIN LIGHT CHAIN 1, one of the core components of CCV. Meanwhile, BcPLS1 and the B. cinerea-secreted sRNAs are detected in purified CCVs after infection. Arabidopsis knockout mutants and inducible dominant-negative mutants of key components of CME pathway exhibit increased resistance to B. cinerea infection. Furthermore, Bc-sRNA loading into Arabidopsis AGO1 and host target gene suppression are attenuated in those CME mutants. Together, our results demonstrate that fungi secrete sRNAs via EVs, which then enter host plant cells mainly through CME.