Publications from The Sainsbury Laboratory
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Current Opinion in Plant Biology: DNA assembly for plant biology: techniques and tools (2014)

Current Opinion in Plant Biology: DNA assembly for plant biology: techniques and tools (2014) | Publications from The Sainsbury Laboratory | Scoop.it
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As the speed and accuracy of genome sequencing improves, there are ever-increasing resources available for the design and construction of synthetic DNA parts. These can be used to engineer plant genomes to produce new functions or to elucidate the function of endogenous sequences. Until recently the assembly of amplified or cloned sequences into large and complex designs was a limiting step in plant synthetic biology and biotechnology. A number of new methods for assembling DNA molecules have been developed in the last few years, several of which have been applied to the production of molecules used to modify plant genomes.

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Plant & Cell Phys: Latest Advances in Plant Development and Environmental Response, the inaugural Cold Spring Harbor Asia Plant Biology Meeting in Japan (2017)

Plant & Cell Phys: Latest Advances in Plant Development and Environmental Response, the inaugural Cold Spring Harbor Asia Plant Biology Meeting in Japan (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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With stunning ocean views over Osaka Bay, Awaji Island played host to the first Cold Spring Harbor Asia Plant Biology meeting in Japan. The meeting, “Latest Advances in Plant Development and Environmental Response” (#CSHAPB), provided a platform to promote scientific communication and collaboration in the pan-pacific region. The event welcomed almost 200 scientists from around the world to showcase their cutting-edge research. Exemplary speakers from diverse research fields presented their latest discoveries, ranging from developmental mechanisms to host-pathogen interactions, environmental responses and stress memory. Here we seek to review the meeting and highlight some of the salient themes that emerged over the course of the three days.
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The Biochemist: Guarding the granary (2017)

The Biochemist: Guarding the granary (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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The introduction of microbial plant pathogens can cause tremendous damage to crops, food security, the economy and ecosystems in very little time. What do we know about these invaders? And what can be done to defend our crops and respond quickly to new threats?
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Lynne Reuber's curator insight, June 19, 12:02 PM
Emerging plant diseases have threatened food security throughout history and still do today.
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Methods in Mol Biol: Detection and Analyses of Endocytosis of Plant Receptor Kinases (2017)

Methods in Mol Biol: Detection and Analyses of Endocytosis of Plant Receptor Kinases (2017) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:
Genetic dissection has led to a sophisticated understanding of receptor kinases in plant development and responses to abiotic and biotic stresses. Fluorescence confocal microscopy is essential to identify the (sub)cellular locations of resting and signaling receptor kinases that trigger molecular events in plant cells upon ligand perception. In this regard, the internalization of plasma membrane-localized FLAGELLIN SENSING 2 (FLS2) into endosomes induced by its ligand flg22, a peptide derived from bacterial flagellin, is a model system for studying activation status-dependent and endosomal receptor kinase trafficking routes and can be used in screens to identify pathogen effectors that target these trafficking routes for virulence promotion. In this chapter we describe approaches of visualizing fluorescently tagged FLS2, including protocols for flg22-induced endocytosis, instrument parameters, and image analysis. These approaches can be easily adapted for other receptor kinases, using the fast transient expression system in Nicotiana benthamiana for microscopic inspection.
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bioRxiv: nQuire: A Statistical Framework For Ploidy Estimation Using Next Generation Sequencing (2017)

bioRxiv: nQuire: A Statistical Framework For Ploidy Estimation Using Next Generation Sequencing (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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nQuire is a statistical framework that distinguishes between diploids, triploids and tetraploids using next generation sequencing. 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. Availability and Implementation: The model is implemented as a stand-alone Linux command line tool in the C programming language and is available at github under the MIT licence. Please also refer to github.com/clwgg/nQuire for usage instructions.
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PNAS: Arabidopsis glycosylphosphatidylinositol-anchored protein LLG1 associates with and modulates FLS2 to regulate innate immunity (2017)

PNAS: Arabidopsis glycosylphosphatidylinositol-anchored protein LLG1 associates with and modulates FLS2 to regulate innate immunity (2017) | Publications from The Sainsbury Laboratory | Scoop.it
National Academy of Sciences
The Sainsbury Lab's insight:
Plants detect and respond to pathogen invasion with membrane-localized pattern recognition receptors (PRRs), which recognize pathogen-associated molecular patterns (PAMPs) and activate downstream immune responses. Here we report that Arabidopsis thaliana LORELEI-LIKE GPI-ANCHORED PROTEIN 1 (LLG1), a coreceptor of the receptor-like kinase FERONIA, regulates PRR signaling. In a forward genetic screen for suppressors of enhanced disease resistance 1 (edr1), we identified the point mutation llg1-3, which suppresses edr1 disease resistance but does not affect plant growth and development. The llg1 mutants show enhanced susceptibility to various virulent pathogens, indicating that LLG1 has an important role in plant immunity. LLG1 constitutively associates with the PAMP receptor FLAGELLIN SENSING 2 (FLS2) and the elongation factor-Tu receptor, and forms a complex with BRASSINOSTEROID INSENSITIVE 1-ASSOCIATED RECEPTOR KINASE 1 in a ligand-dependent manner, indicating that LLG1 functions as a key component of PAMP-recognition immune complexes. Moreover, LLG1 contributes to accumulation and ligand-induced degradation of FLS2, and is required for downstream innate immunity responses, including ligand-induced phosphorylation of BOTRYTIS-INDUCED KINASE 1 and production of reactive oxygen species. Taken together, our findings reveal that LLG1 associates with PAMP receptors and modulates their function to regulate disease responses. As LLG1 functions as a coreceptor of FERONIA and plays central roles in plant growth and development, our findings indicate that LLG1 participates in separate pathways, and may suggest a potential connection between development and innate immunity in plants.
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BMC Biol: Can a biologist fix a smartphone?—Just hack it! (2017)

BMC Biol: Can a biologist fix a smartphone?—Just hack it! (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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Biological systems integrate multiscale processes and networks and are, therefore, viewed as difficult to dissect. However, because of the clear-cut separation between the software code (the information encoded in the genome sequence) and hardware (organism), genome editors can operate as software engineers to hack biological systems without any particularly deep understanding of the complexity of the systems.

This article was inspired by the influential and entertaining essay by Yuri Lazebnik who argued that there are fundamental flaws in how biologists approach problems [1]. Lazebnik proposed that the complexity of biological systems calls for a systems approach to the study of living systems using a radio as a colourful metaphor to illustrate his points [1]. He postulated that, conceptually, a radio functions similarly to a biological system by converting a signal from one form into another using a signal transduction pathway [1]. Here I argue that Lazebnik’s thesis is limited by two fundamental principles of biology. First, the clear-cut separation between the software code—the operating information for living systems as written in the genome sequence—and hardware, or the organism itself [2, 3]. Second, biological systems are not optimally designed but are shaped by historicity—the historical constraints that are integral to their evolution [4]. This limits the extent to which principles of design and engineering can be useful in understanding and manipulating the structures and functions of living organisms. In contrast, modern day biologists are starting to operate as software engineers to hack biological systems and write apps despite a somewhat superficial understanding of the underlying complexity of these systems.
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PLoS Genetics: The highly buffered Arabidopsis immune signaling network conceals the functions of its components (2017)

PLoS Genetics: The highly buffered Arabidopsis immune signaling network conceals the functions of its components (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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The Sainsbury Lab's insight:
Plant immunity protects plants from numerous potentially pathogenic microbes. The biological network that controls plant inducible immunity must function effectively even when network components are targeted and disabled by pathogen effectors. Network buffering could confer this resilience by allowing different parts of the network to compensate for loss of one another’s functions. Networks rich in buffering rely on interactions within the network, but these mechanisms are difficult to study by simple genetic means. Through a network reconstitution strategy, in which we disassemble and stepwise reassemble the plant immune network that mediates Pattern-Triggered-Immunity, we have resolved systems-level regulatory mechanisms underlying the Arabidopsis transcriptome response to the immune stimulant flagellin-22 (flg22). These mechanisms show widespread evidence of interactions among major sub-networks—we call these sectors—in the flg22-responsive transcriptome. Many of these interactions result in network buffering. Resolved regulatory mechanisms show unexpected patterns for how the jasmonate (JA), ethylene (ET), phytoalexin-deficient 4 (PAD4), and salicylate (SA) signaling sectors control the transcriptional response to flg22. We demonstrate that many of the regulatory mechanisms we resolved are not detectable by the traditional genetic approach of single-gene null-mutant analysis. Similar to potential pathogenic perturbations, null-mutant effects on immune signaling can be buffered by the network.
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PLoS Pathogens: Arabidopsis leucine-rich repeat receptor–like kinase NILR1 is required for induction of innate immunity to parasitic nematodes (2017)

PLoS Pathogens: Arabidopsis leucine-rich repeat receptor–like kinase NILR1 is required for induction of innate immunity to parasitic nematodes (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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The Sainsbury Lab's insight:
Plant-parasitic nematodes are destructive pests causing losses of billions of dollars annually. An effective plant defence against pathogens relies on the recognition of pathogen-associated molecular patterns (PAMPs) by surface-localised receptors leading to the activation of PAMP-triggered immunity (PTI). Extensive studies have been conducted to characterise the role of PTI in various models of plant-pathogen interactions. However, far less is known about the role of PTI in roots in general and in plant-nematode interactions in particular. Here we show that nematode-derived proteinaceous elicitor/s is/are capable of inducing PTI in Arabidopsis in a manner dependent on the common immune co-receptor BAK1. Consistent with the role played by BAK1, we identified a leucine-rich repeat receptor-like kinase, termed NILR1 that is specifically regulated upon infection by nematodes. We show that NILR1 is essential for PTI responses initiated by nematodes and nilr1 loss-of-function mutants are hypersusceptible to a broad category of nematodes. To our knowledge, NILR1 is the first example of an immune receptor that is involved in induction of basal immunity (PTI) in plants or in animals in response to nematodes. Manipulation of NILR1 will provide new options for nematode control in crop plants in future.
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Microbiol Mol Biol Rev: Effectors of Filamentous Plant Pathogens: Commonalities amid Diversity (2017)

Microbiol Mol Biol Rev: Effectors of Filamentous Plant Pathogens: Commonalities amid Diversity (2017) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:
Fungi and oomycetes are filamentous microorganisms that include a diversity of highly developed pathogens of plants. These are sophisticated modulators of plant processes that secrete an arsenal of effector proteins to target multiple host cell compartments and enable parasitic infection. Genome sequencing revealed complex catalogues of effectors of filamentous pathogens, with some species harboring hundreds of effector genes. Although a large fraction of these effector genes encode secreted proteins with weak or no sequence similarity to known proteins, structural studies have revealed unexpected similarities amid the diversity. This article reviews progress in our understanding of effector structure and function in light of these new insights. We conclude that there is emerging evidence for multiple pathways of evolution of effectors of filamentous plant pathogens but that some families have probably expanded from a common ancestor by duplication and diversification. Conserved folds, such as the oomycete WY and the fungal MAX domains, are not predictive of the precise function of the effectors but serve as a chassis to support protein structural integrity while providing enough plasticity for the effectors to bind different host proteins and evolve unrelated activities inside host cells. Further effector evolution and diversification arise via short linear motifs, domain integration and duplications, and oligomerization.
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BMC Biology: Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thalian...

BMC Biology: Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thalian... | Publications from The Sainsbury Laboratory | Scoop.it
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The Sainsbury Lab's insight:
Plants are exposed to diverse pathogens and pests, yet most plants are resistant to most plant pathogens. Non-host resistance describes the ability of all members of a plant species to successfully prevent colonization by any given member of a pathogen species. White blister rust caused by Albugo species can overcome non-host resistance and enable secondary infection and reproduction of usually non-virulent pathogens, including the potato late blight pathogen Phytophthora infestans on Arabidopsis thaliana. However, the molecular basis of host defense suppression in this complex plant–microbe interaction is unclear. Here, we investigate specific defense mechanisms in Arabidopsis that are suppressed by Albugo infection.
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Nature: Genomic innovation for crop improvement (2017)

Nature: Genomic innovation for crop improvement (2017) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:
Crop production needs to increase to secure future food supplies, while reducing its impact on ecosystems. Detailed characterization of plant genomes and genetic diversity is crucial for meeting these challenges. Advances in genome sequencing and assembly are being used to access the large and complex genomes of crops and their wild relatives. These have helped to identify a wide spectrum of genetic variation and permitted the association of genetic diversity with diverse agronomic phenotypes. In combination with improved and automated phenotyping assays and functional genomic studies, genomics is providing new foundations for crop-breeding systems.
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bioRxiv: Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen (2017)

bioRxiv: Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen (2017) | Publications from The Sainsbury Laboratory | Scoop.it

Outbreaks caused by asexual lineages of fungal and oomycete pathogens are an expanding threat to crops, wild animals and natural ecosystems (Fisher et al. 2012, Kupferschmidt 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl and Thomma 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Cooke et al. 2012, Yoshida et al. 2013, Yoshida et al. 2014). Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by compared sibling strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Forbes et al. 1997, Oyarzun et al. 1998, Delgado et al. 2013, Yoshida et al. 2013, Yoshida et al. 2014). We detected numerous examples of structural variation, nucleotide polymorphisms and gene conversion within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. These results highlight the exceptional genetic and phenotypic plasticity that underpins host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen.


Via Kamoun Lab @ TSL
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PNAS Commentary: Two-faced TIRs trip the immune switch (2017)

PNAS Commentary: Two-faced TIRs trip the immune switch (2017) | Publications from The Sainsbury Laboratory | Scoop.it
National Academy of Sciences
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Ann Rev Phytopath: Function, Discovery, and Exploitation of Plant Pattern Recognition Receptors for Broad-Spectrum Disease Resistance (2017)

Ann Rev Phytopath: Function, Discovery, and Exploitation of Plant Pattern Recognition Receptors for Broad-Spectrum Disease Resistance (2017) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:
Plants are constantly exposed to would-be pathogens and pests, and thus have a sophisticated immune system to ward off these threats, which otherwise can have devastating ecological and economic consequences on ecosystems and agriculture. Plants employ receptor kinases (RKs) and receptor-like proteins (RLPs) as pattern recognition receptors (PRRs) to monitor their apoplastic environment and detect non-self and damaged-self patterns as signs of potential danger. Plant PRRs contribute to both basal and non-host resistances, and treatment with pathogen-/microbe-associated molecular patterns (PAMPs/MAMPs) or damage-associated molecular patterns (DAMPs) recognized by plant PRRs induces both local and systemic immunity. Here, we comprehensively review known PAMPs/DAMPs recognized by plants as well as the plant PRRs described to date. In particular, we describe the different methods that can be used to identify PAMPs/DAMPs and PRRs. Finally, we emphasize the emerging biotechnological potential use of PRRs to improve broad-spectrum, and potentially durable, disease resistance in crops.
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PLoS Genet: The Arabidopsis leucine-rich repeat receptor kinase MIK2/LRR-KISS connects cell wall integrity sensing, root growth and response to abiotic and biotic stresses (2017)

PLoS Genet: The Arabidopsis leucine-rich repeat receptor kinase MIK2/LRR-KISS connects cell wall integrity sensing, root growth and response to abiotic and biotic stresses (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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The Sainsbury Lab's insight:
Plants actively perceive and respond to perturbations in their cell walls which arise during growth, biotic and abiotic stresses. However, few components involved in plant cell wall integrity sensing have been described to date. Using a reverse-genetic approach, we identified the Arabidopsis thaliana leucine-rich repeat receptor kinase MIK2 as an important regulator of cell wall damage responses triggered upon cellulose biosynthesis inhibition. Indeed, loss-of-function mik2 alleles are strongly affected in immune marker gene expression, jasmonic acid production and lignin deposition. MIK2 has both overlapping and distinct functions with THE1, a malectin-like receptor kinase previously proposed as cell wall integrity sensor. In addition, mik2 mutant plants exhibit enhanced leftward root skewing when grown on vertical plates. Notably, natural variation in MIK2 (also named LRR-KISS) has been correlated recently to mild salt stress tolerance, which we could confirm using our insertional alleles. Strikingly, both the increased root skewing and salt stress sensitivity phenotypes observed in the mik2 mutant are dependent on THE1. Finally, we found that MIK2 is required for resistance to the fungal root pathogen Fusarium oxysporum. Together, our data identify MIK2 as a novel component in cell wall integrity sensing and suggest that MIK2 is a nexus linking cell wall integrity sensing to growth and environmental cues.
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Frontiers: Insights into Host Cell Modulation and Induction of New Cells by the Corn Smut Ustilago maydis (2017)

Frontiers: Insights into Host Cell Modulation and Induction of New Cells by the Corn Smut Ustilago maydis (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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Many filamentous fungal pathogens induce drastic modulation of host cells causing abnormal infectious structures such as galls, or tumors that arise as a result of re-programming in the original developmental cell fate of a colonized host cell. Developmental consequences occur predominantly with biotrophic phytopathogens. This suggests that these host structures result as an outcome of efficient defense suppression and intimate fungal–host interaction to suit the pathogen’s needs for completion of its infection cycle. This mini-review mainly summarizes host cell re-programming that occurs in the Ustilago maydis – maize interaction, in which the pathogen deploys cell-type specific effector proteins with varying activities. The fungus senses the physiological status and identity of colonized host cells and re-directs the endogenous developmental program of its host. The disturbance of host cell physiology and cell fate leads to novel cell shapes, increased cell size, and/or the number of host cells. We particularly highlight the strategies of U. maydis to induce physiologically varied host organs to form the characteristic tumors in both vegetative and floral parts of maize.
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bioRxiv: An Oomycete Effector Protein Induces Shade Avoidance In Arabidopsis And Attenuates Salicylate Signaling By Binding To Host Proteins Of The RADICAL-INDUCED CELL DEATH1 Family (2017)

bioRxiv: An Oomycete Effector Protein Induces Shade Avoidance In Arabidopsis And Attenuates Salicylate Signaling By Binding To Host Proteins Of The RADICAL-INDUCED CELL DEATH1 Family (2017) | Publications from The Sainsbury Laboratory | Scoop.it
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
The Sainsbury Lab's insight:
The oomycete pathogen Hyaloperonospora arabidopsidis (Hpa) causes downy mildew disease on Arabidopsis. During infection, Hpa like other biotrophic pathogens, suppresses activation of plant innate immunity by translocating effector proteins into host cells. Some of these effectors localize to the host cell nucleus where they may manipulate transcriptional reprogramming of plant defense genes. Here we report that the nuclear-localized Hpa effector HaRxL106, when expressed in Arabidopsis, induces shade avoidance and attenuates the transcriptional response to the defense signaling molecule salicylic acid. HaRxL106 interacts with RADICAL-INDUCED CELL DEATH1 (RCD1) and loss of RCD1 function renders Arabidopsis resilient against HaRxL106-mediated suppression of immunity. To further characterize the molecular functions of RCD1 we solved a crystal structure of the RCD1 Poly-(ADP-ribose)-Polymerase (PARP) domain and, based on non-conservation of amino acids constituting the active site of canonical PARPs, conclude that RCD1 has no PARP activity. We report that RCD1-type proteins are phosphorylated and identified histone-modifying Mut9-like kinases (MLKs) as RCD1-interacting proteins. A mlk1,3,4 triple mutant exhibits stronger SA-induced defense marker gene expression compared to wild-type plants. Our data suggest that HaRxL106 suppresses Arabidopsis innate immunity by manipulating the function(s) of RCD1 in the host cell nucleus and point towards a role of RCD1 as a transcriptional co-regulator that integrates signals from light and pathogen sensors.
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Curr Opin Plant Biol: NLR diversity, helpers and integrated domains: making sense of the NLR IDentity (2017)

Curr Opin Plant Biol: NLR diversity, helpers and integrated domains: making sense of the NLR IDentity (2017) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:
Plant innate immunity relies on genetically predetermined repertoires of immune receptors to detect pathogens and trigger an effective immune response. A large proportion of these receptors are from the Nucletoide Binding Leucine Rich Repeat (NLR) gene family. As plants live longer than most pathogens, maintaining diversity of NLRs and deploying efficient ‘pathogen traps’ is necessary to withstand the evolutionary battle. In this review, we summarize the sources of diversity in NLR plant immune receptors giving an overview of genomic, regulatory as well as functional studies, including the latest concepts of NLR helpers and NLRs with integrated domains.
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PLoS Pathogens: Protein-protein interactions in the RPS4/RRS1 immune receptor complex (2017)

PLoS Pathogens: Protein-protein interactions in the RPS4/RRS1 immune receptor complex (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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Plant NLR (Nucleotide-binding domain and Leucine-rich Repeat) immune receptor proteins are encoded by Resistance (R) genes and confer specific resistance to pathogen races that carry the corresponding recognized effectors. Some NLR proteins function in pairs, forming receptor complexes for the perception of specific effectors. We show here that the Arabidopsis RPS4 and RRS1 NLR proteins are both required to make an authentic immune complex. Over-expression of RPS4 in tobacco or in Arabidopsis results in constitutive defense activation; this phenotype is suppressed in the presence of RRS1. RRS1 protein co-immunoprecipitates (co-IPs) with itself in the presence or absence of RPS4, but in contrast, RPS4 does not associate with itself in the absence of RRS1. In the presence of RRS1, RPS4 associates with defense signaling regulator EDS1 solely in the nucleus, in contrast to the extra-nuclear location found in the absence of RRS1. The AvrRps4 effector does not disrupt RPS4-EDS1 association in the presence of RRS1. In the absence of RRS1, AvrRps4 interacts with EDS1, forming nucleocytoplasmic aggregates, the formation of which is disturbed by the co-expression of PAD4 but not by SAG101. These data indicate that the study of an immune receptor protein complex in the absence of all components can result in misleading inferences, and reveals an NLR complex that dynamically interacts with the immune regulators EDS1/PAD4 or EDS1/SAG101, and with effectors, during the process by which effector recognition is converted to defense activation.
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Genome Res: An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations (2017)

Genome Res: An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations (2017) | Publications from The Sainsbury Laboratory | Scoop.it
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
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Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNA-seq and Pacific Biosciences (PacBio) full-length cDNAs to identify 104,091 high-confidence protein-coding genes and 10,156 noncoding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop.
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MPMI: Foundational and translational research opportunities to improve plant health (2017)

MPMI: Foundational and translational research opportunities to improve plant health (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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This whitepaper reports the deliberations of a workshop focused on biotic challenges to plant health held in Washington, D.C. in September 2016. Ensuring health of food plants is critical to maintaining the quality and productivity of crops and for sustenance of the rapidly growing human population. There is a close linkage between food security and societal stability; however, global food security is threatened by the vulnerability of our agricultural systems to numerous pests, pathogens, weeds, and environmental stresses. These threats are aggravated by climate change, the globalization of agriculture, and an over-reliance on non-sustainable inputs. New analytical and computational technologies are providing unprecedented resolution at a variety of molecular, cellular, organismal, and population scales for crop plants as well as pathogens, pests, beneficial microbes, and weeds. It is now possible to both characterize useful or deleterious variation as well as precisely manipulate it. Data-driven, informed decisions based on knowledge of the variation of biotic challenges and of natural and synthetic variation in crop plants will enable deployment of durable interventions throughout the world. These should be integral, dynamic components of agricultural strategies for sustainable agriculture.

Specific findings:
● Genetic improvement of crops is the most reliable, least expensive management strategy when suitable genetic variation is available. Nonetheless, some interventions have not proved durable due to the evolution and global dispersal of virulent pathogens and pests as well as herbicide-resistant weeds.
● Additional strategies are becoming essential as multiple fungicides, nematicides, and herbicides become ineffective due to the evolution of resistance and/or are phased out due to registration withdrawals.
● Strategies are needed that maximize the evolutionary hurdles for pathogens, pests, and weeds to overcome control measures. Interventions need to evolve as fast as the biotic challenges. Moreover, deployments of interventions must be driven by knowledge of the evolutionary capacity of the biotic challenge.
● Considerable knowledge exists but more research into the mechanisms of plant immunity and other forms of resistance is needed as the foundation for translational applications.
● Several new technologies are increasing foundational knowledge and providing numerous opportunities for generating crops with durable resistance to pests and diseases as well as control of weeds and reduction of the environmental impact of agriculture.
● There are multiple strategies for counteracting biotic challenges involving canonical and non-canonical disease resistance genes, genes encoding susceptibility factors, small RNAs, or immunomodulators. Simultaneous deployment of disease resistance strategies with different modes of action, as well as the judicious use of fungicides, will enhance durability of control measures.
● Pathogen effectors provide tools for discovering resistance genes and susceptibility factors as well as for dissecting/manipulating plant biology and breeding plants for durable disease resistance.
● There are several, as yet little exploited, opportunities for leveraging beneficial interactions among plants, microbes, insects and other organisms in the phytobiome to enhance plant health and productivity as well as breeding plants to promote beneficial phytobiome communities.
● Global monitoring of plant health is feasible and desirable in order to anticipate and counter threats.
● Climate change increases the need for continual global monitoring of pathogens, pests, and weeds and adjusting of control strategies.
● There are numerous current and future opportunities for knowledge exchange and partnerships between developed and developing countries to foster improved local and global food security.
● Both genetically modified (GM) and non-GM strategies are needed to maximize plant health and food security.
● Significant, sustained financial support is required if the beneficial impacts of foundational and translational research on global food security are to be realized.

The needs, opportunities, approaches, and deliverables for addressing biotic challenges to plant health are detailed in Table 1. These can be broadly classified as assessing variation, characterizing it in detail at a variety of scales, and deploying beneficial interventions. Immediate investments in global monitoring of pathogens/pests and in situ and ex-situ determination of what natural variation exists in crop plants for countering challenges and threats should be a high priority. Detailed investigations of the molecular basis of the various types of plant resistance and of the basis of pathogen/pest virulence are critical for providing the foundation for novel intervention strategies; these will be facilitated by development of high resolution structural and functional analytical techniques. Optimization of protocols for delivery of reagents for allele replacement and gene insertions into diverse major and minor crop plants should be a high priority. Monitoring and deployment should be a global endeavor involving multinational partnerships and knowledge exchanges in order to ensure that interventions are locally relevant and globally durable.
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Sci Rep: Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion (2017)

Sci Rep: Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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Genome editing has emerged as a technology with a potential to revolutionize plant breeding. In this study, we report on generating, in less than ten months, Tomelo, a non-transgenic tomato variety resistant to the powdery mildew fungal pathogen using the CRISPR/Cas9 technology. We used whole-genome sequencing to show that Tomelo does not carry any foreign DNA sequences but only carries a deletion that is indistinguishable from naturally occurring mutations. We also present evidence for CRISPR/Cas9 being a highly precise tool, as we did not detect off-target mutations in Tomelo. Using our pipeline, mutations can be readily introduced into elite or locally adapted tomato varieties in less than a year with relatively minimal effort and investment.
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Nature: Plant signalling in symbiosis and immunity (2017)

Nature: Plant signalling in symbiosis and immunity (2017) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:
Plants encounter a myriad of microorganisms, particularly at the root–soil interface, that can invade with detrimental or beneficial outcomes. Prevalent beneficial associations between plants and microorganisms include those that promote plant growth by facilitating the acquisition of limiting nutrients such as nitrogen and phosphorus. But while promoting such symbiotic relationships, plants must restrict the formation of pathogenic associations. Achieving this balance requires the perception of potential invading microorganisms through the signals that they produce, followed by the activation of either symbiotic responses that promote microbial colonization or immune responses that limit it.
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Theor Appl Genet: Discovery and characterization of two new stem rust resistance genes in Aegilops sharonensis (2017)

Theor Appl Genet: Discovery and characterization of two new stem rust resistance genes in Aegilops sharonensis (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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The Sainsbury Lab's insight:
Stem rust is one of the most important diseases of wheat in the world. When single stem rust resistance (Sr) genes are deployed in wheat, they are often rapidly overcome by the pathogen. To this end, we initiated a search for novel sources of resistance in diverse wheat relatives and identified the wild goatgrass species Aegilops sharonesis (Sharon goatgrass) as a rich reservoir of resistance to wheat stem rust. The objectives of this study were to discover and map novel Sr genes in Ae. sharonensis and to explore the possibility of identifying new Sr genes by genome-wide association study (GWAS). We developed two biparental populations between resistant and susceptible accessions of Ae. sharonensis and performed QTL and linkage analysis. In an F6 recombinant inbred line and an F2 population, two genes were identified that mapped to the short arm of chromosome 1Ssh, designated as Sr-1644-1Sh, and the long arm of chromosome 5Ssh, designated as Sr-1644-5Sh. The gene Sr-1644-1Sh confers a high level of resistance to race TTKSK (a member of the Ug99 race group), while the gene Sr-1644-5Sh conditions strong resistance to TRTTF, another widely virulent race found in Yemen. Additionally, GWAS was conducted on 125 diverse Ae. sharonensis accessions for stem rust resistance. The gene Sr-1644-1Sh was detected by GWAS, while Sr-1644-5Sh was not detected, indicating that the effectiveness of GWAS might be affected by marker density, population structure, low allele frequency and other factors.
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eLife: Plant immune and growth receptors share common signalling components but localise to distinct plasma membrane nanodomains (2017)

eLife: Plant immune and growth receptors share common signalling components but localise to distinct plasma membrane nanodomains (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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The Sainsbury Lab's insight:
Cell surface receptors govern a multitude of signalling pathways in multicellular organisms. In plants, prominent examples are the receptor kinases FLS2 and BRI1, which activate immunity and steroid-mediated growth, respectively. Intriguingly, despite inducing distinct signalling outputs, both receptors employ common downstream signalling components, which exist in plasma membrane (PM)-localised protein complexes. An important question is thus how these receptor complexes maintain signalling specificity. Live-cell imaging revealed that FLS2 and BRI1 form PM nanoclusters. Using single-particle tracking we could discriminate both cluster populations and we observed spatiotemporal separation between immune and growth signalling platforms. This finding was confirmed by visualising FLS2 and BRI1 within distinct PM nanodomains marked by specific remorin proteins and differential co-localisation with the cytoskeleton. Our results thus suggest that signalling specificity between these pathways may be explained by the spatial separation of FLS2 and BRI1 with their associated signalling components within dedicated PM nanodomains.
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