A Perspective on CRN Proteins in the Genomics Age: Evolution, Classification, Delivery and Function Revisited

Identification of Phytophthora cinnamomi CRN effectors and their roles in manipulating cell death during Persea americana infection

The oomycete Phytophthora cinnamomi is a devastating plant pathogen with a notably broad host range. It is the causal agent of Phytophthora root rot (PRR), arguably the most economically important yield-limiting disease in Persea americana (avocado). Despite this, our understanding of the mechanisms P. cinnamomi employs to infect and successfully colonize avocado remains limited, particularly regarding the pathogen's ability to maintain its biotrophic and necrotrophic lifestyles during infection. The pathogen utilises a large repertoire of effector proteins which function in facilitating and establishing disease in susceptible host plants. Crinkling and necrosis effectors (CRN/Crinklers) are suspected to manipulate cell death to aid in maintenance of the pathogens biotrophic and necrotrophic lifestyles during different stages of infection. The current study identified 25 P. cinnamomi CRN effectors from the GKB4 genome using an HMM profile and assigned putative function to them as either cell death inducers or suppressors. Function was assigned to 10 PcinCRNs by analysing their RNA-seq expression profiles, relatedness to other functionally characterised Phytophthora CRNs and tertiary protein predictions. The full-length coding sequences for these PcinCRNs were confirmed by Sanger sequencing, six of which were found to have two divergent alleles. The presence of alleles indicates that the proteins encoded may perform contradicting functions in cell death manipulation, or function in different host plant species. Overall, this study provides a foundation for future research on P. cinnamomi infection and cell death manipulation mechanisms.

Identification of self- and pathogen-targeted miRNAs from resistant and susceptible Theobroma cacao variety to black pod disease

Cacao (Theobroma cacao) is a highly valuable crop with growing demand in the global market. However, cacao farmers often face challenges posed by black pod disease caused by Phytophthora spp., with P. palmivora being the most dominant. Regulations of various gene expressions influence plant resistance to pathogens. One mechanism involves targeting the mRNA of virulence genes in the invading pathogens, suppressing their infection. However, resistance also could be suppressed by plant-derived miRNAs that target their own defence genes. The objective of this study is to identify differentially expressed miRNAs in black pod-resistant and susceptible cacao varieties and to predict their targets in T. cacao and P. palmivora transcripts. Extracted miRNA from resistant and susceptible varieties of T. Cacao was sequenced, identified, and matched to host and pathogen mRNA. In total, 54 known miRNAs from 40 miRNA families and 67 novel miRNAs were identified. Seventeen miRNAs were differentially expressed in susceptible variety compared to resistant one, with 9 miRNAs upregulated and 8 miRNAs downregulated. In T. cacao transcripts, the upregulated miRNAs were predicted to target several genes, including defence genes. The suppression of these defense genes can lead to a reduction in plant resistance against pathogen infection. In P. palmivora transcripts, the upregulated miRNAs were predicted to target several genes, including P. palmivora effector genes. In the future, limiting expression of miRNAs that target T. cacao's defence genes and applying miRNAs that target P. palmivora effector genes hold promise for enhancing cacao plant resistance against P. palmivora infection.

Phytophthora sojae Effector PsCRN108 Targets CAMTA2 to Suppress HSP40 Expression and ROS Burst

Oomycete pathogens secrete numerous crinkling and necrosis proteins (CRNs) to manipulate plant immunity and promote infection. However, the functional mechanism of CRN effectors is still poorly understood. Previous research has shown that the Phytophthora sojae effector PsCRN108 binds to the promoter of HSP90s and inhibits their expression, resulting in impaired plant immunity. In this study, we found that in addition to HSP90, PsCRN108 also suppressed other Heat Shock Protein (HSP) family genes, including HSP40. Interestingly, PsCRN108 inhibited the expression of NbHSP40 through its promoter, but did not directly bind to its promoter. Instead, PsCRN108 interacted with NbCAMTA2, a negative regulator of plant immunity. NbCAMTA2 was a negative regulator of NbHSP40 expression, and PsCRN108 could promote such inhibition activity of NbCAMTA2. Our results elucidated the multiple roles of PsCRN108 in the suppression of plant immunity and revealed a new mechanism by which the CRN effector hijacked transcription factors to affect immunity. [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.

Seeking the interspecies crosswalk for filamentous microbe effectors

Both pathogenic and symbiotic microorganisms modulate the immune response and physiology of their host to establish a suitable niche. Key players in mediating colonization outcome are microbial effector proteins that act either inside (cytoplasmic) or outside (apoplastic) the plant cells and modify the abundance or activity of host macromolecules. We compile novel insights into the much-disputed processes of effector secretion and translocation of filamentous organisms, namely fungi and oomycetes. We report how recent studies that focus on unconventional secretion and effector structure challenge the long-standing image of effectors as conventionally secreted proteins that are translocated with the aid of primary amino acid sequence motifs. Furthermore, we emphasize the potential of diverse, unbiased, state-of-the-art proteomics approaches in the holistic characterization of fungal and oomycete effectomes.

Genome analysis of Phytophthora cactorum strains associated with crown- and leather-rot in strawberry

Phytophthora cactorum has two distinct pathotypes that cause crown rot and leather rot in strawberry (Fragaria × ananassa). Strains of the crown rot pathotype can infect both the rhizome (crown) and fruit tissues, while strains of the leather rot pathotype can only infect the fruits of strawberry. The genome of a highly virulent crown rot strain, a low virulent crown rot strain, and three leather rot strains were sequenced using PacBio high fidelity (HiFi) long read sequencing. The reads were de novo assembled to 66.4-67.6 megabases genomes in 178-204 contigs, with N50 values ranging from 892 to 1,036 kilobases. The total number of predicted complete genes in the five P. cactorum genomes ranged from 17,286 to 17,398. Orthology analysis identified a core secretome of 8,238 genes. Comparative genomic analysis revealed differences in the composition of potential virulence effectors, such as putative RxLR and Crinklers, between the crown rot and the leather rot pathotypes. Insertions, deletions, and amino acid substitutions were detected in genes encoding putative elicitors such as beta elicitin and cellulose-binding domain proteins from the leather rot strains compared to the highly virulent crown rot strain, suggesting a potential mechanism for the crown rot strain to escape host recognition during compatible interaction with strawberry. The results presented here highlight several effectors that may facilitate the tissue-specific colonization of P. cactorum in strawberry.

EffectorO: Motif-Independent Prediction of Effectors in Oomycete Genomes Using Machine Learning and Lineage Specificity

Oomycete plant pathogens cause a wide variety of diseases, including late blight of potato, sudden oak death, and downy mildews of plants. These pathogens are major contributors to loss in numerous food crops. Oomycetes secrete effector proteins to manipulate their hosts to the advantage of the pathogen. Plants have evolved to recognize effectors, resulting in an evolutionary cycle of defense and counter-defense in plant-microbe interactions. This selective pressure results in highly diverse effector sequences that can be difficult to computationally identify using only sequence similarity. We developed a novel effector prediction tool, EffectorO, that uses two complementary approaches to predict effectors in oomycete pathogen genomes: i) a machine learning-based pipeline that predicts effector probability based on the biochemical properties of the N-terminal amino-acid sequence of a protein and ii) a pipeline based on lineage specificity to find proteins that are unique to one species or genus, a sign of evolutionary divergence due to adaptation to the host. We tested EffectorO on Bremia lactucae, which causes lettuce downy mildew, and Phytophthora infestans, which causes late blight of potato and tomato, and predicted many novel effector candidates while recovering the majority of known effector candidates. EffectorO will be useful for discovering novel families of oomycete effectors without relying on sequence similarity to known effectors. [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 Identification in Plant Pathogens

Effectors play a central role in determining the outcome of plant-pathogen interactions. As key virulence proteins, effectors are collectively indispensable for disease development. By understanding the virulence mechanisms of effectors, fundamental knowledge of microbial pathogenesis and disease resistance have been revealed. Effectors are also considered double-edged swords because some of them activate immunity in disease resistant plants after being recognized by specific immune receptors, which evolved to monitor pathogen presence or activity. Characterization of effector recognition by their cognate immune receptors and the downstream immune signaling pathways is instrumental in implementing resistance. Over the past decades, substantial research effort has focused on effector biology, especially concerning their interactions with virulence targets or immune receptors in plant cells. A foundation of this research is robust identification of the effector repertoire from a given pathogen, which depends heavily on bioinformatic prediction. In this review, we summarize methodologies that have been used for effector mining in various microbial pathogens which use different effector delivery mechanisms. We also discuss current limitations and provide perspectives on how recently developed analytic tools and technologies may facilitate effector identification and hence generation of a more complete vision of host-pathogen interactions. [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.

Phytophthora infestans RxLR Effector PITG06478 Hijacks 14-3-3 to Suppress PMA Activity Leading to Necrotrophic Cell Death

Pathogens often induce cell death for their successful proliferation in the host plant. Plasma membrane H⁺-ATPases (PMAs) are targeted by either pathogens or plant immune receptors in immune response regulation. Although PMAs play pivotal roles in host cell death, the molecular mechanism of effector-mediated regulation of PMA activity has not been described. Here, we report that the Phytophthora infestans RxLR effector PITG06478 can induce cell death in Nicotiana benthamiana but the induced cell death is inhibited by fusicoccin (FC), an irreversible PMA activator. PITG06478, which is localized at the plasma membrane, is not directly associated with the PMA but is associated with Nb14-3-3s, a PMA activator. Immunoblot analyses revealed that the interaction between PITG06478 and Nb14-3-3s was disrupted by FC. PMA activity in PITG06478-expressing plants was eventually inhibited, and cell death likely occurred because the 14-3-3 protein was hijacked. Our results further confirm the significance of PMA activity in host cell death and provide new insight into how pathogens utilize essential host components to sustain their life cycle. [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.

RNA silencing proteins and small RNAs in oomycete plant pathogens and biocontrol agents

Introduction

Oomycetes cause several damaging diseases of plants and animals, and some species also act as biocontrol agents on insects, fungi, and other oomycetes. RNA silencing is increasingly being shown to play a role in the pathogenicity of Phytophthora species, either through trans-boundary movement of small RNAs (sRNAs) or through expression regulation of infection promoting effectors.

Methods

To gain a wider understanding of RNA silencing in oomycete species with more diverse hosts, we mined genome assemblies for Dicer-like (DCL), Argonaute (AGO), and RNA dependent RNA polymerase (RDRP) proteins from Phytophthora plurivora, Ph. cactorum, Ph. colocasiae, Pythium oligandrum, Py. periplocum, and Lagenidium giganteum. Moreover, we sequenced small RNAs from the mycelium stage in each of these species.

Results and discussion

Each of the species possessed a single DCL protein, but they differed in the number and sequence of AGOs and RDRPs. SRNAs of 21nt, 25nt, and 26nt were prevalent in all oomycetes analyzed, but the relative abundance and 5' base preference of these classes differed markedly between genera. Most sRNAs mapped to transposons and other repeats, signifying that the major role for RNA silencing in oomycetes is to limit the expansion of these elements. We also found that sRNAs may act to regulate the expression of duplicated genes. Other sRNAs mapped to several gene families, and this number was higher in Pythium spp., suggesting a role of RNA silencing in regulating gene expression. Genes for most effector classes were the source of sRNAs of variable size, but some gene families showed a preference for specific classes of sRNAs, such as 25/26 nt sRNAs targeting RxLR effector genes in Phytophthora species. Novel miRNA-like RNAs (milRNAs) were discovered in all species, and two were predicted to target transcripts for RxLR effectors in Ph. plurivora and Ph. cactorum, indicating a putative role in regulating infection. Moreover, milRNAs from the biocontrol Pythium species had matches in the predicted transcriptome of Phytophthora infestans and Botrytis cinerea, and L. giganteum milRNAs matched candidate genes in the mosquito Aedes aegypti. This suggests that trans-boundary RNA silencing may have a role in the biocontrol action of these oomycetes.

The cytosolic iron-sulphur cluster assembly mechanism in grapevine is one target of a virulent Crinkler effector from Plasmopara viticola

Grapevine downy mildew is one of the most devastating diseases in grape production worldwide, but its pathogenesis remains largely unknown. A thorough understanding of the interaction between grapevine and the causal agent, Plasmopara viticola, is helpful to develop alternative disease control measures. Effector proteins that could be secreted to the interaction interface by pathogens are responsible for the susceptibility of host plants. In this study, a Crinkler effector, named PvCRN17, which is from P. viticola and showed virulent effects towards Nicotiana benthamiana previously, was further investigated. Consistently, PvCRN17 showed a virulent effect on grapevine plants. Protein-protein interaction experiments identified grapevine VAE7L1 (Vitis protein ASYMMETRIC LEAVES 1/2 ENHANCER 7-Like 1) as one target of PvCRN17. VAE7L1 was found to interact with VvCIA1 and VvAE7, thus it may function in the cytosolic iron-sulphur cluster assembly (CIA) pathway. Transient expression of VAE7L1 in Vitis riparia and N. benthamiana leaves enhanced the host resistance to oomycete pathogens. Downstream of the CIA pathway in grapevine, three iron-sulphur (Fe-S) proteins showed an enhancing effect on the disease resistance of N. benthamiana. Competitive co-immunoprecipitation assay showed PvCRN17 could compete with VvCIA1 to bind with VAE7L1 and VvAE7. Moreover, PvCRN17 and VAE7L1 were colocalized at the plasma membrane of the plant cell. To conclude, after intruding into the grapevine cell, PvCRN17 would compete with VCIA1 to bind with VAE7L1 and VAE7, demolishing the CIA Fe-S cluster transfer complex, interrupting the maturation of Fe-S proteins, to suppress Fe-S proteins-mediated defence responses.

Systematic identification and functional characterization of the CFEM proteins in poplar fungus Marssonina brunnea

Proteins containing Common in Fungal Extracellular Membrane (CFEM) domains uniquely exist in fungi and play significant roles in their whole life history. In this study, a total of 11 MbCFEM proteins were identified from Marssonina brunnea f. sp. multigermtubi (MULT), a hemibiotrophic pathogenic fungus on poplars that causes severe leaf diseases. Phylogenic analysis showed that the 11 proteins (MbCFEM1-11) were divided into three clades based on the trans-membrane domain and the CFEM domain. Sequence alignment and WebLogo analysis of CFEM domains verified the amino acids conservatism therein. All of them possess eight cysteines except MbCFEM4 and MbCFEM11, which lack two cysteines each. Six MbCFEM proteins with a signal peptide and without trans-membrane domain were considered as candidate effectors for further functional analysis. Three-dimensional (3D) models of their CFEM domains presented a helical-basket structure homologous to the crucial virulence factor Csa2 of Candida albicans. Afterward, four (MbCFEM1, 6, 8, and 9) out of six candidate effectors were successfully cloned and a yeast signal sequence trap (YSST) assay confirmed their secretion activity. Pathogen challenge assays demonstrated that the transient expression of four candidate MbCFEM effectors in Nicotiana benthamiana promoted Fusarium proliferatum infection, respectively. In an N. benthamiana heterogeneous expression system, MbCFEM1, MbCFEM6, and MbCFEM9 appeared to suppress both BAX/INF1-triggered PCD, whereas MbCFEM8 could only defeat BAX-triggered PCD. Additionally, subcellular localization analysis indicated that the four candidate MbCFEM effectors accumulate in the cell membrane, nucleus, chloroplast, and cytosolic bodies. These results demonstrate that MbCFEM1, MbCFEM6, MbCFEM8, and MbCFEM9 are effectors of M. brunnea and provide valuable targets for further dissection of the molecular mechanisms underlying the poplar-M. brunnea interaction.

Chromosome-level assembly of the Phytophthora agathidicida genome reveals adaptation in effector gene families

Phytophthora species are notorious plant pathogens, with some causing devastating tree diseases that threaten the survival of their host species. One such example is Phytophthora agathidicida, the causal agent of kauri dieback - a root and trunk rot disease that kills the ancient, iconic and culturally significant tree species, Agathis australis (New Zealand kauri). A deeper understanding of how Phytophthora pathogens infect their hosts and cause disease is critical for the development of effective treatments. Such an understanding can be gained by interrogating pathogen genomes for effector genes, which are involved in virulence or pathogenicity. Although genome sequencing has become more affordable, the complete assembly of Phytophthora genomes has been problematic, particularly for those with a high abundance of repetitive sequences. Therefore, effector genes located in repetitive regions could be truncated or missed in a fragmented genome assembly. Using a combination of long-read PacBio sequences, chromatin conformation capture (Hi-C) and Illumina short reads, we assembled the P. agathidicida genome into ten complete chromosomes, with a genome size of 57 Mb including 34% repeats. This is the first Phytophthora genome assembled to chromosome level and it reveals a high level of syntenic conservation with the complete genome of Peronospora effusa, the only other completely assembled genome sequence of an oomycete. All P. agathidicida chromosomes have clearly defined centromeres and contain candidate effector genes such as RXLRs and CRNs, but in different proportions, reflecting the presence of gene family clusters. Candidate effector genes are predominantly found in gene-poor, repeat-rich regions of the genome, and in some cases showed a high degree of duplication. Analysis of candidate RXLR effector genes that occur in multicopy gene families indicated half of them were not expressed in planta. Candidate CRN effector gene families showed evidence of transposon-mediated recombination leading to new combinations of protein domains, both within and between chromosomes. Further analysis of this complete genome assembly will help inform new methods of disease control against P. agathidicida and other Phytophthora species, ultimately helping decipher how Phytophthora pathogens have evolved to shape their effector repertoires and how they might adapt in the future.

Ancestral Chromosomes for Family Peronosporaceae Inferred from a Telomere-to-Telomere Genome Assembly of Peronospora effusa

Downy mildew disease of spinach, caused by the oomycete Peronospora effusa, causes major losses to spinach production. In this study, the 17 chromosomes of P. effusa were assembled telomere-to-telomere, using Pacific Biosciences high-fidelity reads. Of these, 16 chromosomes are complete and gapless; chromosome 15 contains one gap bridging the nucleolus organizer region. This is the first telomere-to-telomere genome assembly for an oomycete. Putative centromeric regions were identified on all chromosomes. This new assembly enables a reevaluation of the genomic composition of Peronospora spp.; the assembly was almost double the size and contained more repeat sequences than previously reported for any Peronospora species. Genome fragments consistently underrepresented in six previously reported assemblies of P. effusa typically encoded repeats. Some genes annotated as encoding effectors were organized into multigene clusters on several chromosomes. Putative effectors were annotated on 16 of the 17 chromosomes. The intergenic distances between annotated genes were consistent with compartmentalization of the genome into gene-dense and gene-sparse regions. Genes encoding putative effectors were enriched in gene-sparse regions. The near-gapless assembly revealed apparent horizontal gene transfer from Ascomycete fungi. Gene order was highly conserved between P. effusa and the genetically oriented assembly of the oomycete Bremia lactucae; high levels of synteny were also detected with Phytophthora sojae. Extensive synteny between phylogenetically distant species suggests that many other oomycete species may have similar chromosome organization. Therefore, this assembly provides the foundation for genomic analyses of diverse oomycetes.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Unraveling Plant Cell Death during Phytophthora Infection

Oomycetes form a distinct phylogenetic lineage of fungus-like eukaryotic microorganisms, of which several hundred organisms are considered among the most devastating plant pathogens—especially members of the genus Phytophthora. Phytophthora spp. have a large repertoire of effectors that aid in eliciting a susceptible response in host plants. What is of increasing interest is the involvement of Phytophthora effectors in regulating programed cell death (PCD)—in particular, the hypersensitive response. There have been numerous functional characterization studies, which demonstrate Phytophthora effectors either inducing or suppressing host cell death, which may play a crucial role in Phytophthora’s ability to regulate their hemi-biotrophic lifestyle. Despite several advances in techniques used to identify and characterize Phytophthora effectors, knowledge is still lacking for some important species, including Phytophthora cinnamomi. This review discusses what the term PCD means and the gap in knowledge between pathogenic and developmental forms of PCD in plants. We also discuss the role cell death plays in the virulence of Phytophthora spp. and the effectors that have so far been identified as playing a role in cell death manipulation. Finally, we touch on the different techniques available to study effector functions, such as cell death induction/suppression.

Comparative analysis of Phytophthora genomes data

The data presented here are related to the article entitled “Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in crops” [1]. These data contain the description of genomic structure of the two plant pathogens, P. fragariae and P. rubi and characterize several gene families associated with pathogenicity of them: P450, ACX gene families, CAZymes and effector. This data presents the relevant results of two newly sequenced P. fragariae and P. rubi, so as to provide data for further studies by researchers.

Functional Characterization of the Nep1-Like Protein Effectors of the Necrotrophic Pathogen - Alternaria brassicae

Alternaria brassicae is an important necrotrophic pathogen that infects the Brassicaceae family. A. brassicae, like other necrotrophs, also secretes various proteinaceous effectors and metabolites that cause cell death to establish itself in the host. However, there has been no systematic study of A. brassicae effectors and their roles in pathogenesis. The availability of the genome sequence of A. brassicae in public domain has enabled the search for effectors and their functional characterization. Nep1-like proteins (NLPs) are a superfamily of proteins that induce necrosis and ethylene biosynthesis. They have been reported from a variety of microbes including bacteria, fungi, and oomycetes. In this study, we identified two NLPs from A. brassicae viz. AbrNLP1 and AbrNLP2 and functionally characterized them. Although both AbrNLPs were found to be secretory in nature, they localized differentially inside the plant. AbrNLP2 was found to induce necrosis in both host and non-host species, while AbrNLP1 could not induce necrosis in both species. Additionally, AbrNLP2 was shown to induce pathogen-associated molecular pattern (PAMP)-triggered immunity in both host and non-host species. Overall, our study indicates that AbrNLPs are functionally and spatially (subcellular location) distinct and may play different but important roles during the pathogenesis of A. brassicae.

Remote homology clustering identifies lowly conserved families of effector proteins in plant-pathogenic fungi

Plant diseases caused by fungal pathogens are typically initiated by molecular interactions between 'effector' molecules released by a pathogen and receptor molecules on or within the plant host cell. In many cases these effector-receptor interactions directly determine host resistance or susceptibility. The search for fungal effector proteins is a developing area in fungal-plant pathology, with more than 165 distinct confirmed fungal effector proteins in the public domain. For a small number of these, novel effectors can be rapidly discovered across multiple fungal species through the identification of known effector homologues. However, many have no detectable homology by standard sequence-based search methods. This study employs a novel comparison method (RemEff) that is capable of identifying protein families with greater sensitivity than traditional homology-inference methods, leveraging a growing pool of confirmed fungal effector data to enable the prediction of novel fungal effector candidates by protein family association. Resources relating to the RemEff method and data used in this study are available from https://figshare.com/projects/Effector_protein_remote_homology/87965.

Haustorium formation and a distinct biotrophic transcriptome characterize infection of Nicotiana benthamiana by the tree pathogen Phytophthora kernoviae

Phytophthora species cause some of the most serious diseases of trees and threaten forests in many parts of the world. Despite the generation of genome sequence assemblies for over 10 tree-pathogenic Phytophthora species and improved detection methods, there are many gaps in our knowledge of how these pathogens interact with their hosts. To facilitate cell biology studies of the infection cycle we examined whether the tree pathogen Phytophthora kernoviae could infect the model plant Nicotiana benthamiana. We transformed P. kernoviae to express green fluorescent protein (GFP) and demonstrated that it forms haustoria within infected N. benthamiana cells. Haustoria were also formed in infected cells of natural hosts, Rhododendron ponticum and European beech (Fagus sylvatica). We analysed the transcriptome of P. kernoviae in cultured mycelia, spores, and during infection of N. benthamiana, and detected 12,559 transcripts. Of these, 1,052 were predicted to encode secreted proteins, some of which may function as effectors to facilitate disease development. From these, we identified 87 expressed candidate RXLR (Arg-any amino acid-Leu-Arg) effectors. We transiently expressed 12 of these as GFP fusions in N. benthamiana leaves and demonstrated that nine significantly enhanced P. kernoviae disease progression and diversely localized to the cytoplasm, nucleus, nucleolus, and plasma membrane. Our results show that N. benthamiana can be used as a model host plant for studying this tree pathogen, and that the interaction likely involves suppression of host immune responses by RXLR effectors. These results establish a platform to expand the understanding of Phytophthora tree diseases.

Diverse Trajectories Drive the Expression of a Giant Virus in the Oomycete Plant Pathogen Phytophthora parasitica

Giant viruses of amoebas, recently classified in the class Megaviricetes, are a group of viruses that can infect major eukaryotic lineages. We previously identified a set of giant virus sequences in the genome of Phytophthora parasitica, an oomycete and a devastating major plant pathogen. How viral insertions shape the structure and evolution of the invaded genomes is unclear, but it is known that the unprecedented functional potential of giant viruses is the result of an intense genetic interplay with their hosts. We previously identified a set of giant virus sequences in the genome of P. parasitica, an oomycete and a devastating major plant pathogen. Here, we show that viral pieces are found in a 550-kb locus and are organized in three main clusters. Viral sequences, namely RNA polymerases I and II and a major capsid protein, were identified, along with orphan sequences, as a hallmark of giant viruses insertions. Mining of public databases and phylogenetic reconstructions suggest an ancient association of oomycetes and giant viruses of amoeba, including faustoviruses, African swine fever virus (ASFV) and pandoraviruses, and that a single viral insertion occurred early in the evolutionary history of oomycetes prior to the Phytophthora–Pythium radiation, estimated at ∼80 million years ago. Functional annotation reveals that the viral insertions are located in a gene sparse region of the Phytophthora genome, characterized by a plethora of transposable elements (TEs), effectors and other genes potentially involved in virulence. Transcription of viral genes was investigated through analysis of RNA-Seq data and qPCR experiments. We show that most viral genes are not expressed, and that a variety of mechanisms, including deletions, TEs insertions and RNA interference may contribute to transcriptional repression. However, a gene coding a truncated copy of RNA polymerase II along a set of neighboring sequences have been shown to be expressed in a wide range of physiological conditions, including responses to stress. These results, which describe for the first time the endogenization of a giant virus in an oomycete, contribute to challenge our view of Phytophthora evolution.

Late blight in tomato: insights into the pathogenesis of the aggressive pathogen Phytophthora infestans and future research priorities

This review provides insights into the molecular interactions between Phytophthora infestans and tomato and highlights research gaps that need further attention. Late blight in tomato is caused by the oomycota hemibiotroph Phytophthora infestans, and this disease represents a global threat to tomato farming. The pathogen is cumbersome to control because of its fast-evolving nature, ability to overcome host resistance and inefficient natural resistance obtained from the available tomato germplasm. To achieve successful control over this pathogen, the molecular pathogenicity of P. infestans and key points of vulnerability in the host plant immune system must be understood. This review primarily focuses on efforts to better understand the molecular interaction between host pathogens from both perspectives, as well as the resistance genes, metabolomic changes, quantitative trait loci with potential for improvement in disease resistance and host genome manipulation via transgenic approaches, and it further identifies research gaps and provides suggestions for future research priorities.

Characterization of CRN-Like Genes From Plasmopara viticola: Searching for the Most Virulent Ones

Grapevine downy mildew is an insurmountable disease that endangers grapevine production and the wine industry worldwide. The causal agent of the disease is the obligate biotrophic oomycete Plasmopara viticola, for which the pathogenic mechanism remains largely unknown. Crinkling and necrosis proteins (CRN) are an ancient class of effectors utilized by pathogens, including oomycetes, that interfere with host plant defense reactions. In this study, 27 CRN-like genes were cloned from the P. viticola isolate YL genome, hereafter referred to as PvCRN genes, and characterized in silico and in planta. PvCRN genes in ‘YL’ share high sequence identities with their ortholog genes in the other three previously sequenced P. viticola isolates. Sequence divergence among the genes in the PvCRN family indicates that different PvCRN genes have different roles. Phylogenetic analysis of the PvCRN and the CRN proteins encoded by genes in the P. halstedii genome suggests that various functions might have been acquired by the CRN superfamily through independent evolution of Plasmopara species. When transiently expressed in plant cells, the PvCRN protein family shows multiple subcellular localizations. None of the cloned PvCRN proteins induced hypersensitive response (HR)-like cell death on the downy mildew-resistant grapevine Vitis riparia. This was in accordance with the result that most PvCRN proteins, except PvCRN11, failed to induce necrosis in Nicotiana benthamiana. Pattern-triggered immunity (PTI) induced by INF1 was hampered by several PvCRN proteins. In addition, 15 PvCRN proteins prevented Bax-induced plant programmed cell death. Among the cell death-suppressing members, PvCRN17, PvCRN20, and PvCRN23 were found to promote the susceptibility of N. benthamiana to Phytophthora capsici, which is a semi-biotrophic oomycete. Moreover, the nucleus-targeting member, PvCRN19, promoted the susceptibility of N. benthamiana to P. capsici. Therefore, these PvCRN proteins were estimated to be virulent effectors involved in the pathogenicity of P. viticola YL. Collectively, this study provides comprehensive insight into the CRN effector repertoire of P. viticola YL, which will help further elucidate the molecular mechanisms of the pathogenesis of grapevine downy mildew.

A Phytophthora sojae CRN effector mediates phosphorylation and degradation of plant aquaporin proteins to suppress host immune signaling

Phytophthora genomes encode a myriad of Crinkler (CRN) effectors, some of which contain putative kinase domains. Little is known about the host targets of these kinase-domain-containing CRNs and their infection-promoting mechanisms. Here, we report the host target and functional mechanism of a conserved kinase CRN effector named CRN78 in a notorious oomycete pathogen, Phytophthora sojae. CRN78 promotes Phytophthora capsici infection in Nicotiana benthamiana and enhances P. sojae virulence on the host plant Glycine max by inhibiting plant H₂O₂ accumulation and immunity-related gene expression. Further investigation reveals that CRN78 interacts with PIP2-family aquaporin proteins including NbPIP2;2 from N. benthamiana and GmPIP2-13 from soybean on the plant plasma membrane, and membrane localization is necessary for virulence of CRN78. Next, CRN78 promotes phosphorylation of NbPIP2;2 or GmPIP2-13 using its kinase domain in vivo, leading to their subsequent protein degradation in a 26S-dependent pathway. Our data also demonstrates that NbPIP2;2 acts as a H₂O₂ transporter to positively regulate plant immunity and reactive oxygen species (ROS) accumulation. Phylogenetic analysis suggests that the phosphorylation sites of PIP2 proteins and the kinase domains of CRN78 homologs are highly conserved among higher plants and oomycete pathogens, respectively. Therefore, this study elucidates a conserved and novel pathway used by effector proteins to inhibit host cellular defenses by targeting and hijacking phosphorylation of plant aquaporin proteins.

CRN effectors are conserved in diverse pathogens of plants, animals, and insects, and highly expanded in Phytophthora species. Nevertheless, little is known about their functions, targets, and action mechanisms. Here, we characterized a kinase-domain-containing CRN effector (CRN78) in a notorious oomycete pathogen, P. sojae. CRN78 is a virulence-essential effector of P. sojae infection, and acts via suppression of plant H₂O₂ accumulation and defense gene expressions. We demonstrated that CRN78 might interact with plant PIP2-family aquaporin proteins, including N. benthamiana NbPIP2;2 and soybean GmPIP2-13, and regulate their phosphorylation, resulting in subsequent 26S-dependent protein degradation. Furthermore, we revealed that NbPIP2;2 was an apoplast-to-cytoplast H₂O₂ transporter and positively regulated plant immunity and ROS accumulation. Importantly, this phosphorylation may be highly conserved in many plant aquaporin proteins. Thus, this study identifies a virulence-related effector from P. sojae and a novel plant immunity-related gene, and reveals a detailed mechanism of effector-mediated phosphorylation and degradation of plant aquaporin proteins.

Comparative analysis of Phytophthora genomes reveals oomycete pathogenesis in crops

The oomycete genus Phytophthora includes devastating plant pathogens that are found in almost all ecosystems. We sequenced the genomes of two quarantined Phytophthora species–P. fragariae and P. rubi. Comparing these Phytophthora species and related genera allowed reconstruction of the phylogenetic relationships within the genus Phytophthora and revealed Phytophthora genomic features associated with infection and pathogenicity. We found that several hundred Phytophthora genes are putatively inherited from red algae, but Phytophthora does not have vestigial plastids originating from phototrophs. The horizontally-transferred Phytophthora genes are abundant transposons that “transmit” exogenous gene to Phytophthora species thus bring about the gene recombination possibility. Several expansion events of Phytophthora gene families associated with cell wall biogenesis can be used as mutational targets to elucidate gene function in pathogenic interactions with host plants. This work enhanced the understanding of Phytophthora evolution and will also be helpful for the design of phytopathological control strategies.

A Conserved Oomycete CRN Effector Targets Tomato TCP14-2 to Enhance Virulence

Phytophthora spp. secrete vast arrays of effector molecules during infection to aid in host colonization. The crinkling and necrosis (CRN) protein family forms an extensive repertoire of candidate effectors that accumulate in the host nucleus to perturb processes required for immunity. Here, we show that CRN12_997 from Phytophthora capsici binds a TCP transcription factor, SlTCP14-2, to inhibit its immunity-associated activity against Phytophthora spp. Coimmunoprecipitation and bimolecular fluorescence complementation studies confirm a specific CRN12_997-SlTCP14-2 interaction in vivo. Coexpression of CRN12_997 specifically counteracts the TCP14-enhanced immunity phenotype, suggesting that CRN mediated perturbation of SlTCP14-2 function. We show that SlTCP14-2 associates with nuclear chromatin and that CRN12_997 diminishes SlTCP14-2 DNA binding. Collectively, our data support a model in which SlTCP14-2 associates with chromatin to enhance immunity. The interaction between CRN12_997 and SlTCP14-2 reduces DNA binding of the immune regulator. We propose that the modulation of SlTCP14-2 chromatin affinity, caused by CRN12-997, enhances susceptibility to P. capsici.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

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.

Filamentous Phytophthora Pathogens Deploy Effectors to Interfere With Bacterial Growth and Motility

Phytophthora comprises a group of filamentous plant pathogens that cause serious crop diseases worldwide. It is widely known that a complex effector repertoire was secreted by Phytophthora pathogens to manipulate plant immunity and determine resistance and susceptibility. It is also recognized that Phytophthora pathogens may inhabit natural niches within complex environmental microbes, including bacteria. However, how Phytophthora pathogens interact with their cohabited microbes remains poorly understood. Here, we present such an intriguing case by using Phytophthora–bacteria interaction as a working system. We found that under co-culture laboratory conditions, several Phytophthora pathogens appeared to block the contact of an ecologically relevant bacterium, including Pseudomonas fluorescence and a model bacterium, Escherichia coli. We further observed that Phytophthora sojae utilizes a conserved Crinkler (CRN) effector protein, PsCRN63, to impair bacterial growth. Phytophthora capsici deploys another CRN effector, PcCRN173, to interfere with bacterial flagellum- and/or type IV pilus-mediated motility whereas a P. capsici-derived RxLR effector, PcAvh540, inhibits bacterial swimming motility, but not twitching motility and biofilm formation, suggesting functional diversification of effector-mediated Phytophthora–bacteria interactions. Thus, our studies provide a first case showing that the filamentous Phytophthora pathogens could deploy effectors to interfere with bacterial growth and motility, revealing an unprecedented effector-mediated inter-kingdom interaction between Phytophthora pathogens and bacterial species and thereby uncovering ecological significance of effector proteins in filamentous plant pathogens besides their canonical roles involving pathogen–plant interaction.

Transcriptomic and Ultrastructural Signatures of K+-Induced Aggregation in Phytophthora parasitica Zoospores

Most pathogenic oomycetes of the genus Phytophthora spread in water films as flagellated zoospores. Zoospores perceive and produce signals attracting other zoospores, resulting in autoaggregation in vitro or biofilm formation on plant surface. The mechanisms underlying intercellular communication and consequent attraction, adhesion and aggregation are largely unknown. In Phytophthora parasitica, the perception of a K⁺ gradient induces coordinated motion and aggregation. To define cellular and molecular events associated with oomycete aggregation, we combined transcriptomic and ultrastructural analyses. Results indicate involvement of electroception in K⁺ sensing. They establish that the transcriptome repertoire required for swimming and aggregation is already fully functional at zoospore release. At the time points analyzed, aggregates are mainly constituted of zoospores. They produce vesicular and fibrillary material discharged at cell-to-cell contacts. Consistently, the signature of transcriptome dynamics during transition to aggregates is an upregulation of genes potentially related to vesicular trafficking. Moreover, transcriptomic and functional analyses show a strong enhancement of carbonic anhydrase activity, indicating that pH homeostasis may contribute to aggregation by acting on both zoospore movement and adhesion. This study poses the molecular and cellular bases of aggregative behavior within oomycetes and expands the current knowledge of ion perception-mediated dissemination of propagules in the rhizosphere.

Apoplastic Cell Death-Inducing Proteins of Filamentous Plant Pathogens: Roles in Plant-Pathogen Interactions

Filamentous pathogens, such as phytopathogenic oomycetes and fungi, secrete a remarkable diversity of apoplastic effector proteins to facilitate infection, many of which are able to induce cell death in plants. Over the past decades, over 177 apoplastic cell death-inducing proteins (CDIPs) have been identified in filamentous oomycetes and fungi. An emerging number of studies have demonstrated the role of many apoplastic CDIPs as essential virulence factors. At the same time, apoplastic CDIPs have been documented to be recognized by plant cells as pathogen-associated molecular patterns (PAMPs). The recent findings of extracellular recognition of apoplastic CDIPs by plant leucine-rich repeat-receptor-like proteins (LRR-RLPs) have greatly advanced our understanding of how plants detect them and mount a defense response. This review summarizes the latest advances in identifying apoplastic CDIPs of plant pathogenic oomycetes and fungi, and our current understanding of the dual roles of apoplastic CDIPs in plant-filamentous pathogen interactions.

Organize, Don't Agonize: Strategic Success of Phytophthora Species

Plants are constantly challenged by various environmental stressors ranging from abiotic-sunlight, elevated temperatures, drought, and nutrient deficits, to biotic factors-microbial pathogens and insect pests. These not only affect the quality of harvest but also the yield, leading to substantial annual crop losses, worldwide. Although plants have a multi-layered immune system, phytopathogens such as species of the oomycete genus Phytophthora, can employ elaborate mechanisms to breach this defense. For the last two decades, researchers have focused on the co-evolution between Phytophthora and interacting hosts to decouple the mechanisms governing their molecular associations. This has provided a comprehensive understanding of the pathobiology of plants affected by oomycetes. Ultimately, this is important for the development of strategies to sustainably improve agricultural production. Therefore, this paper discusses the present-day state of knowledge of the strategic mode of operation employed by species of Phytophthora for successful infection. Specifically, we consider motility, attachment, and host cell wall degradation used by these pathogenic species to obtain nutrients from their host. Also discussed is an array of effector types from apoplastic (hydrolytic proteins, protease inhibitors, elicitins) to cytoplastic (RxLRs, named after Arginine-any amino acid-Leucine-Arginine consensus sequence and CRNs, for CRinkling and Necrosis), which upon liberation can subvert the immune response and promote diseases in plants.

Effector Repertoire of Phytophthora betacei: In Search of Possible Virulence Factors Responsible for Its Host Specificity

Phytophthora betacei is an oomycete plant pathogen closely related to Phytophthora infestans. It infects tree tomato (Solanum betaceum) in northern South America, but is, under natural conditions, unable to infect potatoes or tomatoes, the main hosts of its sister species P. infestans. We characterized, and compared the effector repertoires of P. betacei and other Phytophthora species. To this end, we used in silico approaches to predict and describe the repertoire of secreted proteins in Phytophthora species and determine unique and core effectors. P. betacei has the largest proteome and secretome of all Phytophthora species evaluated. We identified between 450 and 1933 candidate effector genes in Phytophthora ramorum, Phytophthora sojae, Phytophthora cactorum, Phytophthora parasitica, Phytophthora palmivora, P. infestans, and P. betacei genomes. The P. betacei predicted secretome contains 5653 proteins, 1126 of which are apoplastic effectors and 807cytoplasmic effectors. Genes encoding cytoplasmic effectors include 791 genes with an RxLR domain (the largest number known so far in a Phytophthora species) and 16 with a Crinkler (CRN) domain. We detected homologs of previously described avirulence gene (Avr) present in Phytophthora spp., such as Avr1, Avr3b, Avr4, and Avrblb1, suggesting a high level of effector gene conservation among Phytophthora species. Nonetheless, fewer CRN effectors were obtained in P. betacei compared to all other Phytophthora species analyzed. The comparison between P. infestans and P. betacei effector profiles shows unique features in P. betacei that might be involved in pathogenesis and host preference. Indeed, 402 unique predicted effector genes were detected in P. betacei, corresponding to 197 apoplastic effector genes, 203 RxLR cytoplasmic effector genes, and 2 effector genes with CRN domain. This is the first characterization of the effector profile of P. betacei and the broadest comparison of predicted effector repertoires in the genus Phytophthora following a standardized prediction pipeline. The resultant P. betacei putative effector repertoire provides a reasonable set of proteins whose experimental validation could lead to understand the specific virulence factors responsible for the host specificity of this species.

Novel Aspects on The Interaction Between Grapevine and Plasmopara viticola: Dual-RNA-Seq Analysis Highlights Gene Expression Dynamics in The Pathogen and The Plant During The Battle For Infection

Mgaloblishvili, a Vitis vinifera cultivar, exhibits unique resistance traits against Plasmopara viticola, the downy mildew agent. This offers the unique opportunity of exploring the molecular responses in compatible and incompatible plant-pathogen interaction. In this study, whole transcriptomes of Mgaloblishvili, Pinot noir (a V. vinifera susceptible cultivar), and Bianca (a resistant hybrid) leaves, inoculated and non-inoculated with the pathogen, were used to identify P. viticola effector-encoding genes and plant susceptibility/resistance genes. Multiple effector-encoding genes were identified in P. viticola transcriptome, with remarkable expression differences in relation to the inoculated grapevine cultivar. Intriguingly, five apoplastic effectors specifically associated with resistance in V. vinifera. Gene coexpression network analysis identified specific modules and metabolic changes occurring during infection in the three grapevine cultivars. Analysis of these data allowed, for the first time, the detection in V. vinifera of a putative P. viticola susceptibility gene, encoding a LOB domain-containing protein. Finally, the de novo assembly of Mgaloblishvili, Pinot noir, and Bianca transcriptomes and their comparison highlighted novel candidate genes that might be at the basis of the resistant phenotype. These results open the way to functional analysis studies and to new perspectives in molecular breeding of grapevine for resistance to P. viticola.

Long-Read Genome Sequence of the Sugar Beet Rhizosphere Mycoparasite Pythium oligandrum

Pythium oligandrum is a soil born free living oomycete able to parasitize fungi and oomycetes prey, including important plant and animals pathogens. Pythium oligandrum can colonize endophytically the root tissues of diverse plants where it induces plant defenses. Here we report the first long-read genome sequencing of a P. oligandrum strain sequenced by PacBio technology. Sequencing of genomic DNA loaded onto six SMRT cells permitted the acquisition of 913,728 total reads resulting in 112X genome coverage. The assembly and polishing of the genome sequence yielded180 contigs (N50 = 1.3 Mb; L50 = 12). The size of the genome assembly is 41.9 Mb with a longest contig of 2.7 Mb and 15,007 predicted protein-coding genes among which 95.25% were supported by RNAseq data, thus constituting a new Pythium genome reference. This data will facilitate genomic comparisons of Pythium species that are commensal, beneficial or pathogenic on plant, or parasitic on fungi and oomycete to identify key genetic determinants underpinning their diverse lifestyles. In addition comparison with plant pathogenic or zoopathogenic species will illuminate genomic adaptations for pathogenesis toward widely diverse hosts.

Scientific Opinion on the update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA (2017-2019)

The qualified presumption of safety (QPS) was developed to provide a safety pre-assessment within EFSA for microorganisms. Strains belonging to QPS taxonomic units (TUs) still require an assessment based on a specific data package, but QPS status facilitates fast track evaluation. QPS TUs are unambiguously defined biological agents assessed for the body of knowledge, their safety and their end use. Safety concerns are, where possible, to be confirmed at strain or product level, and reflected as 'qualifications'. Qualifications need to be evaluated at strain level by the respective EFSA units. The lowest QPS TU is the species level for bacteria, yeasts and protists/algae, and the family for viruses. The QPS concept is also applicable to genetically modified microorganisms used for production purposes if the recipient strain qualifies for the QPS status, and if the genetic modification does not indicate a concern. Based on the actual body of knowledge and/or an ambiguous taxonomic position, the following TUs were excluded from the QPS assessment: filamentous fungi, oomycetes, streptomycetes, Enterococcus faecium, Escherichia coli and bacteriophages. The list of QPS-recommended biological agents was reviewed and updated in the current opinion and therefore now becomes the valid list. For this update, reports on the safety of previously assessed microorganisms, including bacteria, yeasts and viruses (the latter only when used for plant protection purposes) were reviewed, following an Extensive Literature Search strategy. All TUs previously recommended for 2016 QPS list had their status reconfirmed as well as their qualifications. The TUs related to the new notifications received since the 2016 QPS opinion was periodically evaluated for QPS status in the Statements of the BIOHAZ Panel, and the QPS list was also periodically updated. In total, 14 new TUs received a QPS status between 2017 and 2019: three yeasts, eight bacteria and three algae/protists.

PpCRN7 and PpCRN20 of Phythophthora parasitica regulate plant cell death leading to enhancement of host susceptibility

BACKGROUND

Phytophthora species secrete cytoplasmic effectors from a family named Crinkler (CRN), which are characterised by the presence of conserved specific domains in the N- and C-terminal regions. P. parasitica causes disease in a wide range of host plants, however the role of CRN effectors in these interactions remains unclear. Here, we aimed to: (i) identify candidate CRN encoding genes in P. parasitica genomes; (ii) evaluate the transcriptional expression of PpCRN (Phytophthora parasitica Crinkler candidate) during the P. parasitica interaction with Citrus sunki (high susceptible) and Poncirus trifoliata (resistant); and (iii) functionally characterize two PpCRNs in the model plant Nicotiana benthamiana.

RESULTS

Our in silico analyses identified 80 putative PpCRN effectors in the genome of P. parasitica isolate 'IAC 01/95.1'. Transcriptional analysis revealed differential gene expression of 20 PpCRN candidates during the interaction with the susceptible Citrus sunki and the resistant Poncirus trifoliata. We have also found that P. parasitica is able to recognize different citrus hosts and accordingly modulates PpCRNs expression. Additionally, two PpCRN effectors, namely PpCRN7 and PpCRN20, were further characterized via transient gene expression in N. benthamiana leaves. The elicitin INF-1-induced Hypersensitivity Response (HR) was increased by an additive effect driven by PpCRN7 expression, whereas PpCRN20 expression suppressed HR response in N. benthamiana leaves. Despite contrasting functions related to HR, both effectors increased the susceptibility of plants to P. parasitica.

CONCLUSIONS

PpCRN7 and PpCRN20 have the ability to increase P. parasitica pathogenicity and may play important roles at different stages of infection. These PpCRN-associated mechanisms are now targets of biotechnological studies aiming to break pathogen's virulence and to promote plant resistance.

DNA-Damaging Effectors: New Players in the Effector Arena

In animal cells, nuclear DNA is the target of genotoxins produced by bacterial pathogens that cause genomic mutations eventually leading to apoptosis, senescence, and carcinogenic development. In response to the insult, the DNA damage response (DDR) is activated to ensure lesion repair. Accumulation of DNA breaks is also detected in plants during microbial infection. In this opinion article we propose that phytopathogens can produce DNA-damaging effectors. The recent identification of a functional genotoxin in devastating eukaryotic plant pathogens, such as oomycetes, supports the concept that DNA-damaging effectors may contribute to pathogenicity. Additionally, this raises the question of how plants can perceive these damages and whether this perception can be connected to the plant immune system.

The RXLR Effector PcAvh1 Is Required for Full Virulence of Phytophthora capsici

Plant pathogens employ diverse secreted effector proteins to manipulate host physiology and defense in order to foster diseases. The destructive Phytophthora pathogens encode hundreds of cytoplasmic effectors, which are believed to function inside the plant cells. Many of these cytoplasmic effectors contain the conserved N-terminal RXLR motif. Understanding the virulence function of RXLR effectors will provide important knowledge of Phytophthora pathogenesis. Here, we report the characterization of RXLR effector PcAvh1 from the broad-host range pathogen Phytophthora capsici. Only expressed during infection, PcAvh1 is quickly induced at the early infection stages. CRISPR/Cas9-knockout of PcAvh1 in P. capsici severely impairs virulence while overexpression enhances disease development in Nicotiana benthamiana and bell pepper, demonstrating that PcAvh1 is an essential virulence factor. Ectopic expression of PcAvh1 induces cell death in N. benthamiana, tomato, and bell pepper. Using yeast two-hybrid screening, we found that PcAvh1 interacts with the scaffolding subunit of the protein phosphatase 2A (PP2Aa) in plant cells. Virus-induced gene silencing of PP2Aa in N. benthamiana attenuates resistance to P. capsici and results in dwarfism, suggesting that PP2Aa regulates plant immunity and growth. Collectively, these results suggest that PcAvh1 contributes to P. capsici infection, probably through its interaction with host PP2Aa.

Expression of the GAF Sensor, Carbohydrate-Active Enzymes, Elicitins, and RXLRs Differs Markedly Between Two Phytophthora cactorum Isolates

The phytopathogen Phytophthora cactorum infects economically important herbaceous and woody plant species. P. cactorum isolates differ in host specificity; for example, strawberry crown rot is often caused by a specialized pathotype. Here we compared the transcriptomes of two P. cactorum isolates that differ in their virulence to garden strawberry (Pc407: high virulence; Pc440: low virulence). De novo transcriptome assembly and clustering of contigs resulted in 19,372 gene clusters. Two days after inoculation of Fragaria vesca roots, 3,995 genes were differently expressed between the P. cactorum isolates. One of the genes that were highly expressed only in Pc407 encodes a GAF sensor protein potentially involved in membrane trafficking processes. Two days after inoculation, elicitins were highly expressed in Pc407 and lipid catabolism appeared to be more active than in Pc440. Of the carbohydrate-active enzymes, those that degrade pectin were often more highly expressed in Pc440, whereas members of glycosyl hydrolase family 1, potentially involved in the metabolism of glycosylated secondary metabolites, were more highly expressed in Pc407 at the time point studied. Differences were also observed among the RXLR effectors: Pc407 appears to rely on a smaller set of key RXLR effectors, whereas Pc440 expresses a greater number of RXLRs. This study is the first step toward improving understanding of the molecular basis of differences in the virulence of P. cactorum isolates. Identification of the key effectors is important, as it enables effector-assisted breeding strategies toward crown rot-resistant strawberry cultivars.

The emergence of the multi-species NIP1 effector in Rhynchosporium was accompanied by high rates of gene duplications and losses

Plant pathogens secrete effector proteins to manipulate the host and facilitate infection. Cognate hosts trigger strong defence responses upon detection of these effectors. Consequently, pathogens and hosts undergo rapid coevolutionary arms races driven by adaptive evolution of effectors and receptors. Because of their high rate of turnover, most effectors are thought to be species-specific and the evolutionary trajectories are poorly understood. Here, we investigate the necrosis-inducing protein 1 (NIP1) effector in the multihost pathogen genus Rhynchosporium. We retraced the evolutionary history of the NIP1 locus using whole-genome assemblies of 146 strains covering four closely related species. NIP1 orthologues were present in all species but the locus consistently segregated presence-absence polymorphisms suggesting long-term balancing selection. We also identified previously unknown paralogues of NIP1 that were shared among multiple species and showed substantial copy-number variation within R. commune. The NIP1A paralogue was under significant positive selection suggesting that NIP1A is the dominant effector variant coevolving with host immune receptors. Consistent with this prediction, we found that copy number variation at NIP1A had a stronger effect on virulence than NIP1B. Our analyses unravelled the origins and diversification mechanisms of a pathogen effector family shedding light on how pathogens gain adaptive genetic variation.

Necrotrophic Exploitation and Subversion of Plant Defense: A Lifestyle or Just a Phase, and Implications in Breeding Resistance

Breeding disease-resistant plants is a critical, environmentally friendly component of any strategy to sustainably feed and clothe the 9.8 billion people expected to live on Earth by 2050. Here, I review current literature detailing plant defense responses as they relate to diverse biological outcomes; disease resistance, susceptibility, and establishment of mutualistic plant-microbial relationships. Of particular interest is the degree to which these outcomes are a function of plant-associated microorganisms' lifestyles; biotrophic, hemibiotrophic, necrotrophic, or mutualistic. For the sake of brevity, necrotrophic pathogens and the necrotrophic phase of pathogenicity are emphasized in this review, with special attention given to the host-specific pathogens that exploit defense. Defense responses related to generalist necrotrophs and mutualists are discussed in the context of excellent reviews by others. In addition, host evolutionary trade-offs of disease resistance with other desirable traits are considered in the context of breeding for durable disease resistance.

Arms race: diverse effector proteins with conserved motifs

Effector proteins play important roles in the infection by pathogenic oomycetes and fungi or the colonization by endophytic and mycorrhizal fungi. They are either translocated into the host plant cells via specific translocation mechanisms and function in the host's cytoplasm or nucleus, or they reside in the apoplast of the plant cells and act at the extracellular host-microbe interface. Many effector proteins possess conserved motifs (such as the RXLR, CRN, LysM, RGD, DELD, EAR, RYWT, Y/F/WXC or CFEM motifs) localized in their N- or C-terminal regions. Analysis of the functions of effector proteins, especially so-called "core effectors", is crucial for the understanding of pathogenicity/symbiosis mechanisms and plant defense strategies, and helps to develop breeding strategies for pathogen-resistant cultivars, and to increase crop yield and quality as well as abiotic stress resistance. This review summarizes current knowledge about these effector proteins with the conversed motifs and their involvement in pathogenic or mutualistic plant/fungal interactions.

Bioinformatic characterisation of the effector repertoire of the strawberry pathogen Phytophthora cactorum

The oomycete pathogen Phytophthora cactorum causes crown rot, a major disease of cultivated strawberry. We report the draft genome of P. cactorum isolate 10300, isolated from symptomatic Fragaria x ananassa tissue. Our analysis revealed that there are a large number of genes encoding putative secreted effectors in the genome, including nearly 200 RxLR domain containing effectors, 77 Crinklers (CRN) grouped into 38 families, and numerous apoplastic effectors, such as phytotoxins (PcF proteins) and necrosis inducing proteins. As in other Phytophthora species, the genomic environment of many RxLR and CRN genes differed from core eukaryotic genes, a hallmark of the two-speed genome. We found genes homologous to known Phytophthora infestans avirulence genes including Avr1, Avr3b, Avr4, Avrblb1 and AvrSmira2 indicating effector sequence conservation between Phytophthora species of clade 1a and clade 1c. The reported P. cactorum genome sequence and associated annotations represent a comprehensive resource for avirulence gene discovery in other Phytophthora species from clade 1 and, will facilitate effector informed breeding strategies in other crops.

RiCRN1, a Crinkler Effector From the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis, Functions in Arbuscule Development

Arbuscular mycorrhizal (AM) symbiosis is one of the most prominent and beneficial plant–microbe interactions that facilitates mineral nutrition and confers tolerance to biotic and abiotic stresses. AM fungi colonize the root cortex and develop specialized structures called arbuscules where the nutrient exchange takes place. Arbuscule development is a highly controlled and coordinated process requiring the involvement of many plant proteins recruited at that interface. In contrast, much less is known about the fungal proteins involved in this process. Here, we have identified an AM fungal effector that participates in this developmental step of the symbiosis. RiCRN1 is a crinkler (CRN) effector that belongs to a subfamily of secreted CRN proteins from R. irregularis. CRNs have been so far only functionally characterized in pathogenic microbes and shown to participate in processes controlling plant cell death and immunity. RiCRN1 accumulates during symbiosis establishment parallel to MtPT4, the gene coding for an arbuscule-specific phosphate transporter. Expression in Nicotiana benthamiana leaves and in Medicago truncatula roots suggest that RiCRN1 is not involved in cell death processes. RiCRN1 dimerizes and localizes to nuclear bodies, suggesting that, similar to other CRNs, it functions in the plant nucleus. Downregulation of RiCRN1 using host-induced gene silencing led to an impairment of the symbiosis in M. truncatula and to a reduction of MtPT4, while ectopic expression of RiCRN1, surprisingly, led to a drastic reduction in arbuscule size that correlated with a decrease not only in MtPT4 but also in MtBCP1, a marker for initial stages of arbuscule development. Altogether, our results suggest that a tightly regulated expression in time and space of RiCRN1 is critical for symbiosis progression and for the proper initiation of arbuscule development.

Transcriptome alteration in Phytophthora infestans in response to phenazine-1-carboxylic acid production by Pseudomonas fluorescens strain LBUM223

Background

Phytophthora infestans is responsible for late blight, one of the most important potato diseases. Phenazine-1-carboxylic acid (PCA)-producing Pseudomonas fluorescens strain LBUM223 isolated in our laboratory shows biocontrol potential against various plant pathogens. To characterize the effect of LBUM223 on the transcriptome of P. infestans, we conducted an in vitro time-course study. Confrontational assay was performed using P. infestans inoculated alone (control) or with LBUM223, its phzC- isogenic mutant (not producing PCA), or exogenically applied PCA. Destructive sampling was performed at 6, 9 and 12 days and the transcriptome of P. infestans was analysed using RNA-Seq. The expression of a subset of differentially expressed genes was validated by RT-qPCR.

Results

Both LBUM223 and exogenically applied PCA significantly repressed P. infestans’ growth at all times. Compared to the control treatment, transcriptomic analyses showed that the percentages of all P. infestans’ genes significantly altered by LBUM223 and exogenically applied PCA increased as time progressed, from 50 to 61% and from to 32 to 46%, respectively. When applying an absolute cut-off value of 3 fold change or more for all three harvesting times, 207 genes were found significantly differentially expressed by PCA, either produced by LBUM223 or exogenically applied. Gene ontology analysis revealed that both treatments altered the expression of key functional genes involved in major functions like phosphorylation mechanisms, transmembrane transport and oxidoreduction activities. Interestingly, even though no host plant tissue was present in the in vitro system, PCA also led to the overexpression of several genes encoding effectors. The mutant only slightly repressed P. infestans’ growth and barely altered its transcriptome.

Conclusions

Our study suggests that PCA is involved in P. infestans’ growth repression and led to important transcriptomic changes by both up- and down-regulating gene expression in P. infestans over time. Different metabolic functions were altered and many effectors were found to be upregulated, suggesting their implication in biocontrol.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4852-1) contains supplementary material, which is available to authorized users.

Random mutagenesis screen shows that Phytophthora capsici CRN83_152-mediated cell death is not required for its virulence function(s)

With the increasing availability of plant pathogen genomes, secreted proteins that aid infection (effectors) have emerged as key factors that help to govern plant-microbe interactions. The conserved CRN (CRinkling and Necrosis) effector family was first described in oomycetes by their capacity to induce host cell death. Despite recent advances towards the elucidation of CRN virulence functions, the relevance of CRN-induced cell death remains unclear. In planta over-expression of PcCRN83_152, a CRN effector from Phytophthora capsici, causes host cell death and boosts P. capsici virulence. We used these features to ask whether PcCRN83_152-induced cell death is linked to its virulence function. By randomly mutating this effector, we generated PcCRN83_152 variants with no cell death (NCD) phenotypes, which were subsequently tested for activity towards enhanced virulence. We showed that a subset of PcCRN83_152 NCD variants retained their ability to boost P. capsici virulence. Moreover, NCD variants were shown to have a suppressive effect on PcCRN83_152-mediated cell death. Our work shows that PcCRN83_152-induced cell death and virulence function can be separated. Moreover, if these findings hold true for other cell death-inducing CRN effectors, this work, in turn, will provide a framework for studies aimed at unveiling the virulence functions of these effectors.

Genomics analysis of Aphanomyces spp. identifies a new class of oomycete effector associated with host adaptation

Background

Oomycetes are a group of filamentous eukaryotic microorganisms that have colonized all terrestrial and oceanic ecosystems, and they include prominent plant pathogens. The Aphanomyces genus is unique in its ability to infect both plant and animal species, and as such exemplifies oomycete versatility in adapting to different hosts and environments. Dissecting the underpinnings of oomycete diversity provides insights into their specificity and pathogenic mechanisms.

Results

By carrying out genomic analyses of the plant pathogen A. euteiches and the crustacean pathogen A. astaci, we show that host specialization is correlated with specialized secretomes that are adapted to the deconstruction of the plant cell wall in A. euteiches and protein degradation in A. astaci. The A. euteiches genome is characterized by a large repertoire of small secreted protein (SSP)-encoding genes that are highly induced during plant infection, and are not detected in other oomycetes. Functional analysis revealed an SSP from A. euteiches containing a predicted nuclear-localization signal which shuttles to the plant nucleus and increases plant susceptibility to infection.

Conclusion

Collectively, our results show that Aphanomyces host adaptation is associated with evolution of specialized secretomes and identify SSPs as a new class of putative oomycete effectors.

Electronic supplementary material

The online version of this article (10.1186/s12915-018-0508-5) contains supplementary material, which is available to authorized users.

Application of alignment-free bioinformatics methods to identify an oomycete protein with structural and functional similarity to the bacterial AvrE effector protein

Diverse plant pathogens export effector proteins to reprogram host cells. One of the most challenging goals in the molecular plant-microbe field is to functionally characterize the complex repertoires of effectors secreted by these pathogens. For bacterial pathogens, the predominant class of effectors is delivered to host cells by Type III secretion. For oomycetes, the predominant class of effectors is defined by a signal peptide that mediates secretion from the oomycete and a conserved RxLR motif. Downy mildew pathogens and Phytophthora species maintain hundreds of candidate RxLR effector genes in their genomes. Although no primary sequence similarity is evident between bacterial Type III effectors (T3Es) and oomycete RXLR effectors, some bacterial and oomycete effectors have convergently evolved to target the same host proteins. Such effectors might have evolved domains that are functionally similar but sequence-unrelated. We reasoned that alignment-free bioinformatics approaches could be useful to identify structural similarities between bacterial and oomycete effectors. To test this approach, we used partial least squares regression, alignment-free bioinformatics methods to identify effector proteins from the genome of the oomycete Hyaloperonospora arabidopsidis that are similar to the well-studied AvrE1 effector from Pseudomonas syringae. This approach identified five RxLR proteins with putative structural similarity to AvrE1. We focused on one, HaRxL23, because it is an experimentally validated effector and it is conserved between distantly related oomycetes. Several experiments indicate that HaRxL23 is functionally similar to AvrE1, including the ability to partially rescue an AvrE1 loss-of-function mutant. This study provides an example of how an alignment-free bioinformatics approach can identify functionally similar effector proteins in the absence of primary sequence similarity. This approach could be useful to identify effectors that have convergently evolved regardless of whether the shared host target is known.

Melatonin Attenuates Potato Late Blight by Disrupting Cell Growth, Stress Tolerance, Fungicide Susceptibility and Homeostasis of Gene Expression in Phytophthora infestans

Phytophthora infestans (P. infestans) is the causal agent of potato late blight, which caused the devastating Irish Potato Famine during 1845-1852. Until now, potato late blight is still the most serious threat to potato growth and has caused significant economic losses worldwide. Melatonin can induce plant innate immunity against pathogen infection, but the direct effects of melatonin on plant pathogens are poorly understood. In this study, we investigated the direct effects of melatonin on P. infestans. Exogenous melatonin significantly attenuated the potato late blight by inhibiting mycelial growth, changing cell ultrastructure, and reducing stress tolerance of P. infestans. Notably, synergistic anti-fungal effects of melatonin with fungicides on P. infestans suggest that melatonin could reduce the dose levels and enhance the efficacy of fungicide against potato late blight. A transcriptome analysis was carried out to mine downstream genes whose expression levels were affected by melatonin. The analysis of the transcriptome suggests that 66 differentially expressed genes involved in amino acid metabolic processes were significantly affected by melatonin. Moreover, the differentially expressed genes associated with stress tolerance, fungicide resistance, and virulence were also affected. These findings contribute to a new understanding of the direct functions of the melatonin on P. infestans and provide a potential ecofriendly biocontrol approach using a melatonin-based paradigm and application to prevent potato late blight.