Publications from The Sainsbury Laboratory
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Science: A Bacterial Tyrosine Phosphatase Inhibits Plant Pattern Recognition Receptor Activation (2014)

Science: A Bacterial Tyrosine Phosphatase Inhibits Plant Pattern Recognition Receptor Activation (2014) | Publications from The Sainsbury Laboratory | Scoop.it

Innate immunity relies on the perception of pathogen-associated molecular patterns (PAMPs) by pattern-recognition receptors (PRRs) located on the host cell’s surface. Many plant PRRs are kinases. Here, we report that the Arabidopsis receptor kinase EF-TU RECEPTOR EFR, which perceives the elf18 peptide derived from bacterial elongation factor Tu, is activated upon ligand binding by phosphorylation on its tyrosine residues. Phosphorylation of a single tyrosine residue, Y836, is required for activation of EFR and downstream immunity to the phytopathogenic bacterium Pseudomonas syringae. A tyrosine phosphatase, HopAO1, secreted by P. syringae, reduces EFR phosphorylation and derails subsequent immune responses. Thus host and pathogen battle to take control of PRR tyrosine phosphorylation used to initiate anti-bacterial immunity.


Via Freddy Monteiro, Jim Alfano, Kamoun Lab @ TSL
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Jim Alfano's curator insight, March 13, 2014 6:21 PM

Very interesting finding - A long sought target of the HopAO1 effector. HopAO1 also suppresses ETI - so additional targets remain undiscovered.

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bioRxiv: TTL proteins scaffold brassinosteroid signaling components at the plasma membrane to optimize signal transduction in plant cells (2018)

bioRxiv: TTL proteins scaffold brassinosteroid signaling components at the plasma membrane to optimize signal transduction in plant cells (2018) | Publications from The Sainsbury Laboratory | Scoop.it
Brassinosteroids (BRs) form a group of steroidal hormones essential for plant growth, development and stress responses. Here, we report that plant-specific TETRATRICOPEPTIDE THIOREDOXIN-LIKE (TTL) proteins are positive regulators of BR signaling functioning as scaffold for BR signaling components in Arabidopsis. TTL3 forms a complex with all core components involved in BR signaling, including the receptor kinase BRASSINOSTEROID INSENSITIVE1 (BRI1), the transcription factor BRASSINAZOLE RESISTANT1 (BZR1) and the phosphatase BRI1-SUPPRESSOR1 (BSU1), but excluding the co-receptor BAK1. TTL3 is mainly localized in the cytoplasm, but BR treatment increases its localization at the plasma membrane, where it strengthens the association with BR signaling components. Consistent with a role in BR signaling, mutations in TTL3 and related TTL1 and TTL4 genes cause reduced BR responsiveness. We propose a mechanistic model for BR signaling, in which cytoplasmic/nuclear BR components bound to TTL proteins are recruited to the plasma membrane upon BR perception, which in turn allows the assembly of a BR signaling complex, leading to the de-phosphorylation and nuclear accumulation of the transcription factors BZR1 and BES1.
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Phytopathology: Transgenic expression of EFR and Bs2 genes for field management of bacterial wilt and bacterial spot of tomato (2018)

Phytopathology: Transgenic expression of EFR and Bs2 genes for field management of bacterial wilt and bacterial spot of tomato (2018) | Publications from The Sainsbury Laboratory | Scoop.it

Field trials were conducted at two locations in Florida to evaluate transgenic tomatoes expressing the EFR gene from Arabidopsis thaliana, the Bs2 gene from pepper, or both Bs2/EFR for managing bacterial wilt caused by Ralstonia solanacearum and bacterial spot caused by Xanthomonas perforans. Expression of EFR or Bs2/EFR, in the susceptible genotype, Fla. 8000, significantly reduced bacterial wilt incidence (50-100%) and increased total yield (57-114%) relative to lines expressing only Bs2 or non-transformed Fla. 8000 control, although the marketable yield was not significantly affected. Following harvest, surviving symptomatic and non-symptomatic plants were assessed for colonization by R. solanacearum. There were no significant differences in the population at the lower stem. Interestingly, in the middle stem, no bacteria could be recovered from EFRor Bs2/EFR lines, but viable bacterial populations were recovered from Bs2 and non-transformed control lines at 102-105 colony forming units (CFU) per gram of stem tissue. In growth chamber experiments, the EFR transgenic tomato lines were found to be effective against seven different R. solanacearum strains isolated from the southeastern U.S, indicating utility across southeast U.S. In all the bacterial spot trials, EFR and Bs2/EFRlines had significantly reduced disease severity (22-98%) compared to Fla. 8000 control. The marketable and total yield of Bs2/EFR were significantly higher (43-170%) than Fla. 8000 control in three out of four field trials. These results demonstrate for the first time the potential of using the EFR gene for field management of bacterial wilt and bacterial spot diseases of tomato.

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Stud Mycol: Two different R gene loci co-evolved with Avr2 of Phytophthora infestans and confer distinct resistance specificities in potato (2018)

Stud Mycol: Two different R gene loci co-evolved with Avr2 of Phytophthora infestans and confer distinct resistance specificities in potato (2018) | Publications from The Sainsbury Laboratory | Scoop.it

Late blight, caused by the oomycete pathogen Phytophthora infestans, is the most devastating disease in potato. For sustainable management of this economically important disease, resistance breeding relies on the availability of resistance (R) genes. Such R genes against P. infestans have evolved in wild tuber-bearing Solanum species from North, Central and South America, upon co-evolution with cognate avirulence (Avr) genes. Here, we report how effectoromics screens with Avr2 of P. infestans revealed defense responses in diverse Solanum species that are native to Mexico and Peru. We found that the response to AVR2 in the Mexican Solanum species is mediated by R genes of the R2 family that resides on a major late blight locus on chromosome IV. In contrast, the response to AVR2 in Peruvian Solanum species is mediated by Rpi-mcq1, which resides on chromosome IX and does not belong to the R2 family. The data indicate that AVR2 recognition has evolved independently on two genetic loci in Mexican and Peruvian Solanum species, respectively. Detached leaf tests on potato cultivar ‘Désirée’ transformed with R genes from either the R2 or the Rpi-mcq1 locus revealed an overlapping, but distinct resistance profile to a panel of 18 diverse P. infestans isolates. The achieved insights in the molecular R – Avr gene interaction can lead to more educated exploitation of R genes and maximize the potential of generating more broad-spectrum, and potentially more durable control of the late blight disease in potato.

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Cell Res: (Research Highlight) Plant G-protein activation: connecting to plant receptor kinases

Cell Res: (Research Highlight) Plant G-protein activation: connecting to plant receptor kinases | Publications from The Sainsbury Laboratory | Scoop.it

Plant heterotrimeric G-proteins function in important signaling pathways mediated by plant receptor kinases (RKs), however, the unique biochemical properties of Gα subunits have complicated our understanding of their regulation in plants. In their new paper in Cell Research, Liang et al. reveal that phosphorylation of the Gα regulator, RGS1, is critical for triggering G-protein signaling downstream of RK activation.

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Plant Biotechnol J: Using CRISPR/Cas9 genome editing in tomato to create a gibberellin‐responsive dominant dwarf DELLA allele (2018)

Plant Biotechnol J: Using CRISPR/Cas9 genome editing in tomato to create a gibberellin‐responsive dominant dwarf DELLA allele (2018) | Publications from The Sainsbury Laboratory | Scoop.it

The tomato PROCERA gene encodes a DELLA protein, and loss‐of‐function mutations derepress growth. We used CRISPR/Cas9 and a single guide RNAs (sgRNA) to target mutations to the PROCERA DELLA domain, and recovered several loss‐of‐function mutations and a dominant dwarf mutation that carries a deletion of one amino acid in the DELLA domain. This is the first report of a dominant dwarf PROCERA allele. This allele retains partial responsiveness to exogenously applied gibberellin (GA). Heterozygotes show an intermediate phenotype at the seedling stage, but adult heterozygotes are as dwarfed as homozygotes.

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Nat Ecol Evol: The ash dieback invasion of Europe was founded by two genetically divergent individuals (2018)

Nat Ecol Evol: The ash dieback invasion of Europe was founded by two genetically divergent individuals (2018) | Publications from The Sainsbury Laboratory | Scoop.it

Accelerating international trade and climate change make pathogen spread an increasing concern. Hymenoscyphus fraxineus, the causal agent of ash dieback, is a fungal pathogen that has been moving across continents and hosts from Asian to European ash. Most European common ash trees (Fraxinus excelsior) are highly susceptible to H.fraxineus, although a minority (~5%) have partial resistance to dieback. Here, we assemble and annotate a H.fraxineus draft genome, which approaches chromosome scale. Pathogen genetic diversity across Europe and in Japan, reveals a strong bottleneck in Europe, though a signal of adaptive diversity remains in key host interaction genes. We find that the European population was founded by two divergent haploid individuals. Divergence between these haplotypes represents the ancestral polymorphism within a large source population. Subsequent introduction from this source would greatly increase adaptive potential of the pathogen. Thus, further introgression of H.fraxineus into Europe represents a potential threat and Europe-wide biological security measures are needed to manage this disease.

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BMC Bioinformatics: nQuire: a statistical framework for ploidy estimation using next generation sequencing (2018)

BMC Bioinformatics: nQuire: a statistical framework for ploidy estimation using next generation sequencing (2018) | Publications from The Sainsbury Laboratory | Scoop.it
Intraspecific variation in ploidy occurs in a wide range of species including pathogenic and nonpathogenic eukaryotes such as yeasts and oomycetes. Ploidy can be inferred indirectly - without measuring DNA content - from experiments using next-generation sequencing (NGS). We present nQuire, a statistical framework that distinguishes between diploids, triploids and tetraploids using NGS. The command-line tool models the distribution of base frequencies at variable sites using a Gaussian Mixture Model, and uses maximum likelihood to select the most plausible ploidy model. nQuire handles large genomes at high coverage efficiently and uses standard input file formats. We demonstrate the utility of nQuire analyzing individual samples of the pathogenic oomycete Phytophthora infestans and the Baker’s yeast Saccharomyces cerevisiae. Using these organisms we show the dependence between reliability of the ploidy assignment and sequencing depth. Additionally, we employ normalized maximized log- likelihoods generated by nQuire to ascertain ploidy level in a population of samples with ploidy heterogeneity. Using these normalized values we cluster samples in three dimensions using multivariate Gaussian mixtures. The cluster assignments retrieved from a S. cerevisiae population recovered the true ploidy level in over 96% of samples. Finally, we show that nQuire can be used regionally to identify chromosomal aneuploidies. nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where intact nuclei are not preserved. It is implemented as a stand-alone Linux command line tool in the C programming language and is available at https://github.com/clwgg/nQuire under the MIT license.
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Mol. Plant: Pm21 from Haynaldia villosa Encodes a CC-NBS-LRR that Confers Powdery Mildew Resistance in Wheat (2018)

Mol. Plant: Pm21 from Haynaldia villosa Encodes a CC-NBS-LRR that Confers Powdery Mildew Resistance in Wheat (2018) | Publications from The Sainsbury Laboratory | Scoop.it
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Nature Plants: An apoplastic peptide activates salicylic acid signalling in maize (2018)

Nature Plants: An apoplastic peptide activates salicylic acid signalling in maize (2018) | Publications from The Sainsbury Laboratory | Scoop.it
Localized control of cell death is crucial for the resistance of plants to pathogens. Papain-like cysteine proteases (PLCPs) regulate plant defence to drive cell death and protection against biotrophic pathogens. In maize (Zea mays), PLCPs are crucial in the orchestration of salicylic acid (SA)-dependent defence signalling. Despite this central role in immunity, it remains unknown how PLCPs are activated, and which downstream signals they induce to trigger plant immunity. Here, we discover an immune signalling peptide, Z. mays immune signalling peptide 1 (Zip1), which is produced after salicylic acid (SA) treatment. In vitro studies demonstrate that PLCPs are required to release bioactive Zip1 from its propeptide precursor. Conversely, Zip1 treatment strongly elicits SA accumulation in leaves. Moreover, transcriptome analyses revealed that Zip1 and SA induce highly overlapping transcriptional changes. Consequently, Zip1 promotes the infection of the necrotrophic fungus Botrytis cinerea, while it reduces virulence of the biotrophic fungus Ustilago maydis. Thus, Zip1 represents the previously missing signal that is released by PLCPs to activate SA defence signalling.
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MPMI: The ELR-SOBIR1 complex functions as a two-component RLK to mount defense against Phytophthora infestans (2018)

MPMI: The ELR-SOBIR1 complex functions as a two-component RLK to mount defense against Phytophthora infestans (2018) | Publications from The Sainsbury Laboratory | Scoop.it
The ELICITIN RESPONSE (ELR) protein from Solanum microdontum can recognize INF1 elicitin of Phytophthora infestans and trigger defense responses. ELR is a receptor-like protein (RLP) that lacks a cytoplasmic signaling domain and is anticipated to require interaction with a signaling-competent receptor-like kinase (RLK). SUPPRESSOR OF BIR1-1 (SOBIR1) has been proposed as a general interactor for RLPs involved in immunity and as such, is a potential interactor for ELR. Here we investigate whether SOBIR1 is required for response to INF1 and resistance to P. infestans and whether it associates with ELR. Our results show that virus-induced gene silencing (VIGS) of SOBIR1 in Nicotiana benthamiana leads to loss of INF1-triggered cell death and increased susceptibility to P. infestans. Using genetic complementation, we found that the kinase activity of SOBIR1 is required for INF1-triggered cell death. Co-immunoprecipitation experiments showed that ELR constitutively associates with potato SOBIR1 in planta, forming a bi-partite receptor complex. Upon INF1 elicitation, this ELR-SOBIR1 complex recruits SOMATIC EMPBRYOGENESIS RECEPTOR KINASE 3 (SERK3) leading to downstream signaling activation. Overall, our study shows that SOBIR1 is required for basal resistance to P. infestans and for INF1-triggered cell death, and functions as an adaptor kinase for ELR.
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bioRxiv: Resistance gene discovery and cloning by sequence capture and association genetics (2018)

bioRxiv: Resistance gene discovery and cloning by sequence capture and association genetics (2018) | Publications from The Sainsbury Laboratory | Scoop.it
Genetic resistance is the most economic and environmentally sustainable approach for crop disease protection. Disease resistance (R) genes from wild relatives are a valuable resource for breeding resistant crops. However, introgression of R genes into crops is a lengthy process often associated with co-integration of deleterious linked genes and pathogens can rapidly evolve to overcome R genes when deployed singly. Introducing multiple cloned R genes into crops as a stack would avoid linkage drag and delay emergence of resistance-breaking pathogen races. However, current R gene cloning methods require segregating or mutant progenies, which are difficult to generate for many wild relatives due to poor agronomic traits. We exploited natural pan-genome variation in a wild diploid wheat by combining association genetics with R gene enrichment sequencing (AgRenSeq) to clone four stem rust resistance genes in <6 months. RenSeq combined with diversity panels is therefore a major advance in isolating R genes for engineering broad-spectrum resistance in crops.
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Nature: An extracellular network of Arabidopsis leucine-rich repeat receptor kinases (2018)

Nature: An extracellular network of Arabidopsis leucine-rich repeat receptor             kinases (2018) | Publications from The Sainsbury Laboratory | Scoop.it
The cells of multicellular organisms receive extracellular signals using surface receptors. The extracellular domains (ECDs) of cell surface receptors function as interaction platforms, and as regulatory modules of receptor activation. Understanding how interactions between ECDs produce signal-competent receptor complexes is challenging because of their low biochemical tractability. In plants, the discovery of ECD interactions is complicated by the massive expansion of receptor families, which creates tremendous potential for changeover in receptor interactions. The largest of these families in Arabidopsis thaliana consists of 225 evolutionarily related leucine-rich repeat receptor kinases (LRR-RKs), which function in the sensing of microorganisms, cell expansion, stomata development and stem-cell maintenance. Although the principles that govern LRR-RK signalling activation are emerging, the systems-level organization of this family of proteins is unknown. Here, to address this, we investigated 40,000 potential ECD interactions using a sensitized high-throughput interaction assay, and produced an LRR-based cell surface interaction network (CSILRR) that consists of 567 interactions. To demonstrate the power of CSILRR for detecting biologically relevant interactions, we predicted and validated the functions of uncharacterized LRR-RKs in plant growth and immunity. In addition, we show that CSILRR operates as a unified regulatory network in which the LRR-RKs most crucial for its overall structure are required to prevent the aberrant signalling of receptors that are several network-steps away. Thus, plants have evolved LRR-RK networks to process extracellular signals into carefully balanced responses.
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bioRxiv: An unconventional NOI/RIN4 domain of a rice NLR protein binds host EXO70 protein to confer fungal immunity (2017)

bioRxiv: An unconventional NOI/RIN4 domain of a rice NLR protein binds host EXO70 protein to confer fungal immunity (2017) | Publications from The Sainsbury Laboratory | Scoop.it
A subset of plant nucleotide-binding domain and leucine-rich repeat-containing (NLR) proteins carry extraneous integrated domains that have been proposed to mediate pathogen effector recognition. The current view is that these unconventional domains function by directly binding or serving as substrates for pathogen effectors, yet only a few domains have been functionally characterized to date. Here we report that the integrated NOI domain of the rice NLR protein Pii-2, together with its partner Pii-1, mediates immunity to the rice blast fungus Magnaporthe oryzae by indirect recognition of the AVR-Pii effector. We discovered that the Pii-2 NOI domain does not physically interact with the effector itself but instead binds the host protein OsExo70-F3, which is a target of AVR-Pii. We further identified mutations within the NOI core motif (PxFGxW) of Pii-2 that abolish both OsExo70-F3 binding and Pii-mediated resistance to M. oryzae expressing AVR-Pii. This led us to propose a novel conceptual model in which an NLR-integrated domain functions to detect host proteins targeted by pathogen effectors, in a framework that extends classical indirect recognition models.
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Science: Receptor networks underpin plant immunity (2018)

Science: Receptor networks underpin plant immunity (2018) | Publications from The Sainsbury Laboratory | Scoop.it
Plants are attacked by a multitude of pathogens and pests, some of which cause epidemics that threaten food security. Yet a fundamental concept in plant pathology is that most plants are actively resistant to most pathogens and pests. Plants fend off their innumerable biotic foes primarily through innate immune receptors that detect the invading pathogens and trigger a robust immune response. The conceptual basis of such interactions was elegantly articulated by Harold H. Flor, who, in 1942, proposed the hypothesis that single genes in plants and pathogens define the outcome of their interactions; that is, a plant harboring a specific gene displays resistance against a pathogen that carries an interacting virulence gene ( 1 ). This gene-for-gene model was hugely insightful and influential—it has helped to guide applied and basic research on disease resistance. However, recent findings are taking the field beyond this simplified binary view of plant-pathogen interactions. Plants carry extremely diverse and dynamic repertoires of immune receptors that are interconnected in complex ways. Conversely, plant pathogens secrete a diversity of virulence proteins and metabolites called effectors, and pathogen genomics has revealed hundreds of effector genes in many species. These effectors have evidently evolved to favor pathogen infection and spread, but a subset of them inadvertently activate plant immune receptors. The emerging paradigm is that dynamic webs of genetic and biochemical networks underpin the early stages of plant-pathogen interactions.
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Phytopathology: Detection of race-specific resistance against Puccinia coronata f. sp. avenae in Brachypodium species (2018)

Phytopathology: Detection of race-specific resistance against Puccinia coronata f. sp. avenae in Brachypodium species (2018) | Publications from The Sainsbury Laboratory | Scoop.it

Oat crown rust caused by Puccinia coronata f. sp. avenae is the most destructive foliar disease of cultivated oat. Characterization of genetic factors controlling resistance responses to Puccinia coronata f. sp. avenae in non-host species could provide new resources for developing disease protection strategies in oat. We examined symptom development and fungal colonization levels of a collection of Brachypodium distachyon and B. hybridum accessions infected with three North American P. coronata f. sp. avenae isolates. Our results demonstrated that colonization phenotypes are dependent on both host and pathogen genotypes, indicating a role for race-specific responses in these interactions. These responses were independent of the accumulation of reactive oxygen species. Expression analysis of several defense-related genes suggested that salicylic acid and ethylene-mediated signaling, but not jasmonic acid are components of resistance reaction to P. coronata f. sp. avenae. Our findings provide the basis to conduct a genetic inheritance study to examine if effector-triggered immunity contributes to non-host resistance to P. coronata f. sp. avenae in Brachypodium species.

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Plant Cell: Receptor-like Cytoplasmic Kinases Directly Link Diverse Pattern Recognition Receptors to the Activation of Mitogen-activated Protein Kinase Cascades in Arabidopsis (2018)

Plant Cell: Receptor-like Cytoplasmic Kinases Directly Link Diverse Pattern Recognition Receptors to the Activation of Mitogen-activated Protein Kinase Cascades in Arabidopsis (2018) | Publications from The Sainsbury Laboratory | Scoop.it
Plants deploy numerous cell surface-localized pattern-recognition receptors (PRRs) to perceive host- and microbe-derived molecular patterns that are specifically released during infection and activate defense responses. The activation of the mitogen-activated protein kinases MPK3, MPK4 and MPK6 (MPK¾/6) is a hallmark of immune system activation by all known PRRs and is crucial for establishing disease resistance. The MAP kinase kinase kinase (MAPKKK) MEKK1 controls MPK4 activation, but the MAPKKKs responsible for MPK3/6 activation downstream of diverse PRRs and how the perception of diverse molecular patterns leads to the activation of MAPKKKs remain elusive. Here we show that two highly related MAPKKKs, MAPKKK3 and MAPKKK5, mediate MPK3/6 activation by at least four PRRs and confer resistance to bacterial and fungal pathogens in Arabidopsis thaliana. The receptor-like cytoplasmic kinases VII (RLCK VII), which act downstream of PRRs, directly phosphorylate MAPKKK5 Ser599, which is required for pattern-triggered MPK3/6 activation, defense gene expression, and disease resistance. Surprisingly, MPK6 further phosphorylates MAPKKK5 Ser682 and Ser692 to enhance MPK3/6 activation and disease resistance, pointing to a positive feedback mechanism. Finally, MEKK1 Ser603 is phosphorylated by both RLCK VII and MPK4, which is required for pattern-triggered MPK4 activation. These findings illustrate central mechanisms by which multiple PRRs activate MAPK cascades and disease resistance.
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Cell Res: (Research Highlight) Deadlier than the malate (2018)

Cell Res: (Research Highlight) Deadlier than the malate (2018) | Publications from The Sainsbury Laboratory | Scoop.it

Plant and animal cells share similar malate-mediated cell death processes, but plants have evolved a unique intracellular communication between organelles in regulating programmed cell death in response to specific photoperiods.

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Phytopathology: A new resistance gene in combination with Rmg8 confers strong resistance against Triticum isolates of Pyricularia oryzae in a common wheat landrace (2018)

Phytopathology: A new resistance gene in combination with Rmg8 confers strong resistance against Triticum isolates of Pyricularia oryzae in a common wheat landrace (2018) | Publications from The Sainsbury Laboratory | Scoop.it

The wheat blast fungus (Triticum pathotype of Pyricularia oryzae) first arose in Brazil in 1985 and has recently spread to Asia. Resistance genes against this new pathogen are very rare in common wheat populations. We screened 520 local landraces of common wheat collected worldwide with Br48, a Triticum isolate collected in Brazil, and found a highly resistant, unique accession, GR119. When F2 seedlings derived from a cross between GR119 and Chinese Spring (CS, susceptible control) were inoculated with Br48, resistant and susceptible seedlings segregated in a 15:1 ratio, suggesting that GR119 carries two resistance genes. When the F2 seedlings were inoculated with Br48△A8 carrying a disrupted allele of AVR-Rmg8 (an avirulence gene corresponding to a previously reported resistance gene, Rmg8), however, the segregation fitted a 3:1 ratio. These results suggest that one of the two genes in GR119 was Rmg8. The other, new gene was tentatively designated as RmgGR119. GR119 was highly resistant to all Triticum isolates tested. Spikes of GR119 were highly resistant to Br48, moderately resistant to Br48△A8 and a hybrid culture carrying avr-Rmg8 (nonfunctional allele), and highly resistant to its transformant carrying AVR-Rmg8. The strong resistance of GR119 was attributed to the combined effects of Rmg8 and RmgGR119.

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mBio: The Blast Fungus Decoded: Genomes in Flux (2018)

mBio: The Blast Fungus Decoded: Genomes in Flux (2018) | Publications from The Sainsbury Laboratory | Scoop.it

Plant disease outbreaks caused by fungi are a chronic threat to global food security. A prime case is blast disease, which is caused by the ascomycete fungus Magnaporthe oryzae (syn. Pyricularia oryzae), which is infamous as the most destructive disease of the staple crop rice. However, despite its Linnaean binomial name, M. oryzae is a multihost pathogen that infects more than 50 species of grasses. A timely study by P. Gladieux and colleagues (mBio 9:e01219-17, 2018, https://doi.org/10.1128/mBio.01219-17) reports the most extensive population genomic analysis of the blast fungus thus far. M. oryzae consists of an assemblage of differentiated lineages that tend to be associated with particular host genera. Nonetheless, there is clear evidence of gene flow between lineages consistent with maintaining M. oryzae as a single species. Here, we discuss these findings with an emphasis on the ecologic and genetic mechanisms underpinning gene flow. This work also bears practical implications for diagnostics, surveillance, and management of blast diseases.

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Curr Opin Plant Biol: The coming of age of EvoMPMI: evolutionary molecular plant–microbe interactions across multiple timescales (2018)

Curr Opin Plant Biol: The coming of age of EvoMPMI: evolutionary molecular plant–microbe interactions across multiple timescales (2018) | Publications from The Sainsbury Laboratory | Scoop.it
Plant–microbe interactions are great model systems to study co-evolutionary dynamics across multiple timescales. However, mechanistic research on plant–microbe interactions has often been conducted with little consideration of evolutionary concepts and methods. Conversely, evolutionary research has rarely integrated the range of mechanisms and models from the molecular plant–microbe interactions field. In recent years, the incipient field of evolutionary molecular plant–microbe interactions (EvoMPMI) has emerged to bridge this gap. Here, we report on some of the recent advances in EvoMPMI. In particular, we highlight new systems to study microbe interactions with early diverging land plants, and new findings from studies of adaptive evolution in pathogens and plants. By linking mechanistic and evolutionary research, EvoMPMI promises to expand our understanding of plant–microbe interactions.
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Theor. Appl. Genet.: Identification and rapid mapping of a gene conferring broad-spectrum late blight resistance in the diploid potato species Solanum verrucosum through DNA capture technologies (2...

Theor. Appl. Genet.: Identification and rapid mapping of a gene conferring broad-spectrum late blight resistance in the diploid potato species Solanum verrucosum through DNA capture technologies (2... | Publications from The Sainsbury Laboratory | Scoop.it
Key message
A broad-spectrum late blight disease-resistance gene from Solanum verrucosum has been mapped to potato chromosome 9. The gene is distinct from previously identified-resistance genes.

Abstract
We have identified and characterised a broad-spectrum resistance to Phytophthora infestans from the wild Mexican species Solanum verrucosum. Diagnostic resistance gene enrichment (dRenSeq) revealed that the resistance is not conferred by previously identified nucleotide-binding, leucine-rich repeat genes. Utilising the sequenced potato genome as a reference, two complementary enrichment strategies that target resistance genes (RenSeq) and single/low-copy number genes (Generic-mapping enrichment Sequencing; GenSeq), respectively, were deployed for the rapid, SNP-based mapping of the resistance through bulked-segregant analysis. Both approaches independently positioned the resistance, referred to as Rpi-ver1, to the distal end of potato chromosome 9. Stringent post-enrichment read filtering identified a total of 64 informative SNPs that corresponded to the expected ratio for significant polymorphisms in the parents as well as the bulks. Of these, 61 SNPs are located on potato chromosome 9 and reside within 27 individual genes, which in the sequenced potato clone DM locate to positions 45.9 to 60.9 Mb. RenSeq- and GenSeq-derived SNPs within the target region were converted into allele-specific PCR-based KASP markers and further defined the position of the resistance to a 4.3 Mb interval at the bottom end of chromosome 9 between positions 52.62–56.98 Mb.
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Genome Biology: Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions (2018)

Genome Biology: Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions (2018) | Publications from The Sainsbury Laboratory | Scoop.it
The plant immune system is innate and encoded in the germline. Using it efficiently, plants are capable of recognizing a diverse range of rapidly evolving pathogens. A recently described phenomenon shows that plant immune receptors are able to recognize pathogen effectors through the acquisition of exogenous protein domains from other plant genes. We show that plant immune receptors with integrated domains are distributed unevenly across their phylogeny in grasses. Using phylogenetic analysis, we uncover a major integration clade, whose members underwent repeated independent integration events producing diverse fusions. This clade is ancestral in grasses with members often found on syntenic chromosomes. Analyses of these fusion events reveals that homologous receptors can be fused to diverse domains. Furthermore, we discover a 43 amino acid long motif associated with this dominant integration clade which is located immediately upstream of the fusion site. Sequence analysis reveals that DNA transposition and/or ectopic recombination are the most likely mechanisms of formation for nucleotide binding leucine rich repeat proteins with integrated domains. The identification of this subclass of plant immune receptors that is naturally adapted to new domain integration will inform biotechnological approaches for generating synthetic receptors with novel pathogen “baits.”
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bioRxiv: The coming of age of EvoMPMI: evolutionary molecular plant-microbe interactions across multiple timescales (2018)

bioRxiv: The coming of age of EvoMPMI: evolutionary molecular plant-microbe interactions across multiple timescales (2018) | Publications from The Sainsbury Laboratory | Scoop.it

Plant-microbe interactions are great model systems to study co-evolutionary dynamics across multiple timescales, ranging from multimillion year macroevolution to extremely rapid evolutionary adaptations. However, mechanistic research on plant-microbe interactions has often been conducted with little consideration of the insights that can be gained from evolutionary concepts and methods. Conversely, evolutionary research has rarely integrated the diverse range of molecular mechanisms and models that continue to emerge from the molecular plant-microbe interactions field. These trends are changing. In recent years, the incipient field of evolutionary molecular plant-microbe interactions (EvoMPMI) has emerged to bridge the gap between mechanistic molecular research and evolutionary approaches. Here, we report on recent advances in EvoMPMI. In particular, we highlight new systems to study microbe interactions with early diverging land plants, and new findings from studies of adaptive evolution in pathogens and plants. By linking mechanistic and evolutionary research, EvoMPMI promises to add a new dimension to our understanding of plant-microbe interactions.


Via Kamoun Lab @ TSL
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Molecular Cell: A Regulatory Module Controlling Homeostasis of a Plant Immune Kinase (2018)

Molecular Cell: A Regulatory Module Controlling Homeostasis of a Plant Immune Kinase (2018) | Publications from The Sainsbury Laboratory | Scoop.it

Plant pattern recognition receptors (PRRs) perceive microbial and endogenous molecular patterns to activate immune signaling. The cytoplasmic kinase BIK1 acts downstream of multiple PRRs as a rate-limiting component, whose phosphorylation and accumulation are central to immune signal propagation. Previous work identified the calcium-dependent protein kinase CPK28 and heterotrimeric G proteins as negative and positive regulators of BIK1 accumulation, respectively. However, mechanisms underlying this regulation remain unknown. Here we show that the plant U-box proteins PUB25 and PUB26 are homologous E3 ligases that mark BIK1 for degradation to negatively regulate immunity. We demonstrate that the heterotrimeric G proteins inhibit PUB25/26 activity to stabilize BIK1, whereas CPK28 specifically phosphorylates conserved residues in PUB25/26 to enhance their activity and promote BIK1 degradation. Interestingly, PUB25/26 specifically target non-activated BIK1, suggesting that activated BIK1 is maintained for immune signaling. Our findings reveal a multi-protein regulatory module that enables robust yet tightly regulated immune responses.

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bioRxiv: An ancient integration in a plant NLR is maintained as a trans-species polymorphism (2017)

bioRxiv: An ancient integration in a plant NLR is maintained as a trans-species polymorphism (2017) | Publications from The Sainsbury Laboratory | Scoop.it
Plant immune receptors are under constant selective pressure to maintain resistance to plant pathogens. Nucleotide-binding leucine-rich repeat (NLR) proteins are one class of cytoplasmic immune receptors whose genes commonly show signatures of adaptive evolution. While it is known that balancing selection contributes to maintaining high intraspecific allelic diversity, the evolutionary mechanism that influences the transmission of alleles during speciation remains unclear. The barley Mla locus has over 30 described alleles conferring isolate-specific resistance to barley powdery mildew and contains three NLR families (RGH1, RGH2, and RGH3). We discovered (using sequence capture and RNAseq) the presence of a novel integrated Exo70 domain in RGH2 in the Mla3 haplotype. Allelic variation across barley accessions includes presence/absence of the integrated domain in RGH2. Expanding our search to several Poaceae species, we found shared interspecific conservation in the RGH2-Exo70 integration. We hypothesise that balancing selection has maintained allelic variation at Mla as a trans-species polymorphism over 24 My, thus contributing to and preserving interspecific allelic diversity during speciation.
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