The receptor kinase FER is a RALF-regulated scaffold controlling plant immune signaling

In plants, perception of invading pathogens involves cell-surface immune receptor kinases. Here, we report that the Arabidopsis SITE-1 PROTEASE (S1P) cleaves endogenous RAPID ALKALINIZATION FACTOR (RALF) propeptides to inhibit plant immunity. This inhibition is mediated by the malectin-like receptor kinase FERONIA (FER), which otherwise facilitates the ligand-induced complex formation of the immune receptor kinases EF-TU RECEPTOR (EFR) and FLAGELLIN-SENSING 2 (FLS2) with their co-receptor BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED KINASE 1 (BAK1) to initiate immune signaling. We show that FER acts as a RALF-regulated scaffold modulating receptor kinase complex assembly. A similar scaffolding mechanism may underlie RALF function in other signalling pathways

A highly polymorphic effector protein promotes fungal virulence through suppression of plant-associated Actinobacteria

Plant pathogens secrete effector proteins to support host colonization through a wide range of molecular mechanisms, while plant immune systems evolved receptors to recognize effectors or their activities to mount immune responses to halt pathogens. Importantly, plants do not act as single organisms, but rather as holobionts that actively shape their microbiota as a determinant of health. The soil-borne fungal pathogen Verticillium dahliae was recently demonstrated to exploit the VdAve1 effector to manipulate the host microbiota to promote vascular wilt disease in the absence of the corresponding immune receptor Ve1. We identify a multiallelic V. dahliae gene displaying c. 65% sequence similarity to VdAve1, named VdAve1-like (VdAve1L), which shows extreme sequence variation, including alleles that encode dysfunctional proteins, indicative of selection pressure to overcome host recognition. We show that the orphan cell surface receptor Ve2, encoded at the Ve locus, does not recognize VdAve1L. Additionally, we demonstrate that the full-length variant VdAve1L2 possesses antimicrobial activity, like VdAve1, yet with a divergent activity spectrum, that is exploited by V. dahliae to mediate tomato colonization through the direct suppression of antagonistic Actinobacteria in the host microbiota. Our findings open up strategies for more targeted biocontrol against microbial plant pathogens

Microbiota manipulation through the secretion of effector proteins is fundamental to the wealth of lifestyles in the fungal kingdom

Fungi are well-known decomposers of organic matter that thrive in virtually any environment on Earth where they encounter wealths of other microbes. Some fungi evolved symbiotic lifestyles, including pathogens and mutualists, that have mostly been studied in binary interactions with their hosts. However, we now appreciate that such interactions are greatly influenced by the ecological context in which they take place. While establishing their symbioses, fungi not only interact with their hosts but also with the host-associated microbiota. Thus, they target the host and its associated microbiota as a single holobiont. Recent studies have shown that fungal pathogens manipulate the host microbiota by means of secreted effector proteins with selective antimicrobial activity to stimulate disease development. In this review, we discuss the ecological contexts in which such effector-mediated microbiota manipulation is relevant for the fungal lifestyle and argue that this is not only relevant for pathogens of plants and animals but also beneficial in virtually any niche where fungi occur. Moreover, we reason that effector-mediated microbiota manipulation likely evolved already in fungal ancestors that encountered microbial competition long before symbiosis with land plants and mammalian animals evolved. Thus, we claim that effector-mediated microbiota manipulation is fundamental to fungal biology. Recent findings show that fungal pathogens secrete effector molecules to manipulate the host microbiota to stimulate disease development; here, we argue that fungal effector-mediated microbiota manipulation occurs beyond plant pathogens, is likely widespread in the fungal kingdom and occurs in many contexts

MLO Differentially Regulates Barley Root Colonization by Beneficial Endophytic and Mycorrhizal Fungi

Loss-of-function alleles of MLO (Mildew Resistance Locus O) confer broad-spectrum resistance to foliar infections by powdery mildew pathogens. Like pathogens, microbes that establish mutually beneficial relationships with their plant hosts, trigger the induction of some defense responses. Initially, barley colonization by the root endophyte Serendipita indica (syn. Piriformospora indica) is associated with enhanced defense gene expression and the formation of papillae at sites of hyphal penetration attempts. This phenotype is reminiscent of mlo-conditioned immunity in barley leaf tissue and raises the question whether MLO plays a regulatory role in the establishment of beneficial interactions. Here we show that S. indica colonization was significantly reduced in plants carrying mlo mutations compared to wild type controls. The reduction in fungal biomass was associated with the enhanced formation of papillae. Moreover, epidermal cells of S. indica-treated mlo plants displayed an early accumulation of iron in the epidermal layer suggesting increased basal defense activation in the barley mutant background. Correspondingly, the induction of host cell death during later colonization stages was impaired in mlo colonized plants, highlighting the importance of the early biotrophic growth phase for S. indica root colonization. In contrast, the arbuscular mycorrhizal fungus Funneliformis mosseae displayed a similar colonization morphology on mutant and wild type plants. However, the frequency of mycorrhization and number of arbuscules was higher in mlo-5 mutants. These findings suggest that MLO differentially regulates root colonization by endophytic and AM fungi

Plant species-specific recognition of long and short beta-1,3-linked glucans is mediated by different receptor systems

Plants survey their environment for the presence of potentially harmful or beneficial microbes. During colonization, cell surface receptors perceive microbe-derived or modified-self ligands and initiate appropriate responses. The recognition of fungal chitin oligomers and the subsequent activation of plant immunity are well described. In contrast, the mechanisms underlying beta-glucan recognition and signaling activation remain largely unexplored. Here, we systematically tested immune responses towards different beta-glucan structures and show that responses vary between plant species. While leaves of the monocots Hordeum vulgare and Brachypodium distachyon can recognize longer (laminarin) and shorter (laminarihexaose) beta-1,3-glucans with responses of varying intensity, duration and timing, leaves of the dicot Nicotiana benthamiana activate immunity in response to long beta-1,3-glucans, whereas Arabidopsis thaliana and Capsella rubella perceive short beta-1,3-glucans. Hydrolysis of the beta-1,6 side-branches of laminarin demonstrated that not the glycosidic decoration but rather the degree of polymerization plays a pivotal role in the recognition of long-chain beta-glucans. Moreover, in contrast to the recognition of short beta-1,3-glucans in A. thaliana, perception of long beta-1,3-glucans in N. benthamiana and rice is independent of CERK1, indicating that beta-glucan recognition may be mediated by multiple beta-glucan receptor systems

Long-Read Annotation: Automated Eukaryotic Genome Annotation Based on Long-Read cDNA Sequencing

Single-molecule full-length complementary DNA (cDNA) sequencing can aid genome annotation by revealing transcript structure and alternative splice forms, yet current annotation pipelines do not incorporate such information. Here we present long-read annotation (LoReAn) software, an automated annotation pipeline utilizing short-and long-read cDNA sequencing, protein evidence, and ab initio prediction to generate accurate genome annotations. Based on annotations of two fungal genomes (Verticillium dahliae and Plicaturopsis crispa) and two plant genomes (Arabidopsis [Arabidopsis thaliana] and Oryza sativa), we show that LoReAn outperforms popular annotation pipelines by integrating single-molecule cDNA-sequencing data generated from either the Pacific Biosciences or MinION sequencing platforms, correctly predicting gene structure, and capturing genes missed by other annotation pipelines

The inconspicuous gatekeeper: endophytic Serendipita vermifera acts as extended plant protection barrier in the rhizosphere

In nature, beneficial and pathogenic fungi often simultaneously colonise plants. Despite substantial efforts to understand the composition of natural plant-microbe communities, the mechanisms driving such multipartite interactions remain largely unknown. Here we address how the interaction between the beneficial root endophyte Serendipita vermifera and the pathogen Bipolaris sorokiniana affects fungal behaviour and determines barley host responses using a gnotobiotic soil-based split-root system. Fungal confrontation in soil resulted in induction of B. sorokiniana genes involved in secondary metabolism and a significant repression of genes encoding putative effectors. In S. vermifera, genes encoding hydrolytic enzymes were strongly induced. This antagonistic response was not activated during the tripartite interaction in barley roots. Instead, we observed a specific induction of S. vermifera genes involved in detoxification and redox homeostasis. Pathogen infection but not endophyte colonisation resulted in substantial host transcriptional reprogramming and activation of defence. In the presence of S. vermifera, pathogen infection and disease symptoms were significantly reduced despite no marked alterations of the plant transcriptional response. The activation of stress response genes and concomitant repression of putative effector gene expression in B. sorokiniana during confrontation with the endophyte suggest a reduction of the pathogen's virulence potential before host plant infection

Microbiome manipulation by a soil-borne fungal plant pathogen using effector proteins

During colonization of their hosts, pathogens secrete effector proteins to promote disease development through various mechanisms. Increasing evidence shows that the host microbiome plays a crucial role in health, and that hosts actively shape their microbiomes to suppress disease. We proposed that pathogens evolved to manipulate host microbiomes to their advantage in turn. Here, we show that the previously identified virulence effector VdAve1, secreted by the fungal plant pathogen Verticillium dahliae, displays antimicrobial activity and facilitates colonization of tomato and cotton through the manipulation of their microbiomes by suppressing antagonistic bacteria. Moreover, we show that VdAve1, and also the newly identified antimicrobial effector VdAMP2, are exploited for microbiome manipulation in the soil environment, where the fungus resides in absence of a host. In conclusion, we demonstrate that a fungal plant pathogen uses effector proteins to modulate microbiome compositions inside and outside the host, and propose that pathogen effector catalogues represent an untapped resource for new antibiotics