Publications from The Sainsbury Laboratory
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eLIFE: Illuminating traffic control for cell–division planes (2014)

eLIFE: Illuminating traffic control for cell–division planes (2014) | Publications from The Sainsbury Laboratory | Scoop.it
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When a plant cell divides, four related proteins control the trafficking of vesicles and ensure that cargo that is normally recycled to the plasma membrane is instead re-routed to the plane of cell division.

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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: (Perspective) The quest for durable resistance (2017)

Science: (Perspective) The quest for durable resistance (2017) | Publications from The Sainsbury Laboratory | Scoop.it
Agriculture transformed humans from hunter-gatherers into city dwellers. This was made possible through the domestication of crops, such as wheat and barley. Based on archaeological evidence ( 1 ), we know that our ancestors' crops were constantly plagued by disease, including rusts and mildews on cereals. During the 4th century BCE, Romans sacrificed red cattle, foxes, and dogs to the god Robigus in the belief that it would prevent epidemics of cereal rusts. Today, we understand that crop diseases are caused by plant pathogens. Cereal rusts are fungal pathogens that colonize foliar parts of the plant, such as the stem or leaf. The ability of these pathogens to infect a plant requires the suppression of the plant's immune system. The principal weapon used by pathogens to inhibit immunity are effectors, typically small secreted proteins. Plants recognize pathogens through immune receptors, including those that either directly or indirectly “perceive” pathogen effectors secreted into the plant ( 2 ). On pages 1604 and 1607 of this issue, Salcedo et al. ( 3 ) and Chen et al. ( 4 ), respectively, describe the identification of two effectors from the fungal pathogen Puccinia graminis f. sp. tritici , the causal agent of wheat stem rust. The discovery of these effectors represents a critical milestone for developing an approach to track and prevent the worldwide spread of the rusts of wheat ( 5 ) and improve our understanding of the biology of these devastating pathogens.
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Genome Biology: Stranger in a strange land: the experiences of immigrant researchers (2017)

Genome Biology: Stranger in a strange land: the experiences of immigrant researchers (2017) | Publications from The Sainsbury Laboratory | Scoop.it

Continuing with our Q&A series discussing issues of diversity in STEM fields, Genome Biology spoke with three researchers on their experiences as immigrants.

 

International collaborations are key to advancing scientific research globally and often require mobility on the part of researchers. Migration of scientists enables the spread of ideas and skills around the world, giving researchers the opportunity to follow the best resources. Of course, migration adds a new set of challenges to the already monumental task of starting and running a lab. Genome Biology spoke to Sophien Kamoun, Rosa Lozano-Durán, and Luay Nakhleh about their personal experiences.

 

What influenced your choice to move to your current country?

 

SK: There is this old German expression “wo die Musik spielt”—you go where it’s happening, where the “music is played”. I think that sums it up. When I was a student in the 1980s, almost everyone wanted to do a Ph.D. in the USA. I felt that to have the best training and to be among the best, I had no choice but to study in the USA. I think that was a pretty correct assessment of the state of affairs in the 1980s. Indeed, I had a fantastic experience at the University of California, Davis. Also, at that time, Europe wasn’t really open to non-Western scientists, and international mobility wasn’t recognized like it is today [1]. Later, I moved to the Netherlands and then back to the USA before landing in my current position at The Sainsbury Laboratory (TSL) in Norwich, UK. I moved to Norwich exactly 10 years ago, primarily because of the reputation of the laboratory as a center of excellence for plant pathology research and the generous support provided by David Sainsbury through the Gatsby Foundation. I have had a phenomenal time at TSL these past 10 years, where I have had the opportunity to work with outstanding scientists from perhaps about 30–40 countries. An interesting point is that when TSL was founded in 1988, all the group leaders were British [2], but currently our principal investigators are from all over the world [3]. I think TSL truly reflects the emergence of the #ScienceisGlobal movement on social media [4], which is so evident in the UK and other corners of Europe.

 

RL-D: Three years ago, having worked as a postdoctoral researcher for almost four years, I was eager to establish my own laboratory. I had known what I wanted to devote my research to for a long time and could not wait to get started. Unfortunately, the economic climate in Europe, where I am originally from and where I was working at the time, was not particularly propitious for science in academia, with research budgets being slashed and increasing competition—not the most favorable situation for new group leaders, I heard over and over again. My partner was also a scientist at the same career stage, and so we needed to find two positions, not just one, complicating matters even more. One day, just by chance, we came across a job advertisement for group leader positions at the Shanghai Center for Plant Stress Biology in China. We had heard about the place—a new institute with the ambition to become a powerhouse for plant sciences. I was very excited at the prospects of leading my own research group, and that excitement overrode any qualms or self-imposed geographical restrictions. I am also fortunate enough to have an incredibly supportive family and friends who unconditionally encouraged me to pursue my scientific career, even if that involved moving far away; they may not always understand the nitty-gritty details of what I do, but they know how important it is for me.

It was my first job application, and I was offered the position following an interview at the center. They were willing to support me and give me the freedom to develop my own research program—it was an unbeatable opportunity to start my independent career. And the fact that I would be living in Asia, with the immense chance to broaden my experience that entailed, added some extra appeal (despite the slight vertigo I also felt). There was not much to think about, really—it was a deal I simply could not turn down.

 

LN: I was born to a Christian Arab family in Israel and did my undergraduate studies at the Technion (Israel Institute of Technology). Although I was an atheist by the time I started my studies at the Technion, I still considered myself to be “culturally” Christian, in that I celebrated Christmas and New Year with my family (eating and drinking, not going to church!). However, almost every year, my exams were scheduled on December 25th and January 1st (the Fall semester in Israel starts in October and ends in February). Being unable to take exams on different dates affected my performance in my studies and my interest in pursuing graduate studies at the same institution. Also, more generally, I was the only Christian Arab student in my class, and one of a handful of Arab students; I never felt comfortable at the time. So, I decided to pursue graduate studies in computer science outside Israel. The choice to come to the USA was an easy one because the USA had (and still has, in my opinion) the best graduate programs in computer science.

 


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J. Am. Soc. Brew. Chem: Effects of Barley (Hordeum vulgare L.) Variety and Growing Environment on Beer Flavor (2017)

J. Am. Soc. Brew. Chem: Effects of Barley (Hordeum vulgare L.) Variety and Growing Environment on Beer Flavor (2017) | Publications from The Sainsbury Laboratory | Scoop.it
This research tested the hypothesis that barley genotype can affect beer flavor and assessed the relative contributions of genotype and location to beer sensory descriptors. Golden Promise, Full Pint, 34 of their doubled haploid progeny, and CDC Copeland were grown at three locations in Oregon, U.S.A. Grain from these trials was micromalted and the resulting malts used for nano-brewing. Sensory evaluations were conducted on the nano-brews. Barley genotype had significant effects on many sensory descriptors. The most significant sensory descriptors—when comparing barley genotypes—were cereal, color, floral, fruity, grassy, honey, malty, toasted, toffee, and sweet. Golden Promise was significantly higher in fruity, floral, and grassy flavors, whereas Full Pint was significantly higher in malty, toffee, and toasted flavors. CDC Copeland was closest to neutral for most flavor traits. There were notable differences for some descriptors between locations. New combinations of parental flavor attributes were observed in the progeny. Multitrait analysis revealed regions of the barley genome with significant effects on malting quality and flavor traits. These findings are, of course, applicable only to the barley germplasm tested, the environment sampled, and the protocols used for micromalting and brewing. The necessary larger-scale experiments involving optimized malts and larger volumes of beer are in process.
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bioRxiv: Phytophthora methylomes modulated by expanded 6mA methyltransferases are associated with adaptive genome regions (2017)

bioRxiv: Phytophthora methylomes modulated by expanded 6mA methyltransferases are associated with adaptive genome regions (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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Filamentous plant pathogen genomes often display a bipartite architecture with gene sparse, repeat-rich compartments serving as a cradle for adaptive evolution. However, the extent to which this "two-speed" genome architecture is associated with genome-wide epigenetic modifications is unknown. Here, we show that the oomycete plant pathogens Phytophthora infestans and Phytophthora sojae possess functional adenine N6-methylation (6mA) methyltransferases that modulate patterns of 6mA marks across the genome. In contrast, 5-methylcytosine (5mC) could not be detected in the two Phytophthora species. Methylated DNA IP Sequencing (MeDIP-seq) of each species revealed that 6mA is depleted around the transcriptional starting sites (TSS) and is associated with low expressed genes, particularly transposable elements. Remarkably, genes occupying the gene-sparse regions have higher levels of 6mA compared to the remainder of both genomes, possibly implicating the methylome in adaptive evolution of Phytophthora. Among three putative adenine methyltransferases, DAMT1 and DAMT3 displayed robust enzymatic activities. Surprisingly, single knockouts of each of the 6mA methyltransferases in P. sojae significantly reduced in vivo 6mA levels, indicating that the three enzymes are not fully redundant. MeDIP-seq of the damt3 mutant revealed uneven patterns of 6mA methylation across genes, suggesting that PsDAMT3 may have a preference for gene body methylation after the TSS. Our findings provide evidence that 6mA modification is an epigenetic mark of Phytophthora genomes and that complex patterns of 6mA methylation by the expanded 6mA methyltransferases may be associated with adaptive evolution in these important plant pathogens.
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Nature Biotech: News & Views: Genetics of a hardy crop (2017)

Nature Biotech: News & Views: Genetics of a hardy crop (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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New genomic resources for pearl millet are revealing how crops stand up to challenging environments.
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Plant J: A computational approach for inferring the cell wall properties that govern guard cell dynamics (2017)

Plant J: A computational approach for inferring the cell wall properties that govern guard cell dynamics (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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Guard cells dynamically adjust their shape in order to regulate photosynthetic gas exchange, respiration rates and defend against pathogen entry. Cell shape changes are determined by the interplay of cell wall material properties and turgor pressure. To investigate this relationship between turgor pressure, cell wall properties and cell shape, we focused on kidney-shaped stomata and developed a biomechanical model of a guard cell pair. Treating the cell wall as a composite of the pectin-rich cell wall matrix embedded with cellulose microfibrils, we show that strong, circumferentially oriented fibres are critical for opening. We find that the opening dynamics are dictated by the mechanical stress response of the cell wall matrix, and as the turgor rises, the pectinaceous matrix stiffens. We validate these predictions with stomatal opening experiments in selected Arabidopsis cell wall mutants. Thus, using a computational framework that combines a 3D biomechanical model with parameter optimization, we demonstrate how to exploit subtle shape changes to infer cell wall material properties. Our findings reveal that proper stomatal dynamics are built on two key properties of the cell wall, namely anisotropy in the form of hoop reinforcement and strain stiffening.
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Sci Rep: Comparative secretome analysis of Rhizoctonia solani isolates with different host ranges reveals unique secretomes and cell death inducing effectors (2017)

Sci Rep: Comparative secretome analysis of Rhizoctonia solani isolates with different host ranges reveals unique secretomes and cell death inducing effectors (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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Rhizoctonia solani is a fungal pathogen causing substantial damage to many of the worlds’ largest food crops including wheat, rice, maize and soybean. Despite impacting global food security, little is known about the pathogenicity mechanisms employed by R. solani. To enable prediction of effectors possessing either broad efficacy or host specificity, a combined secretome was constructed from a monocot specific isolate, a dicot specific isolate and broad host range isolate infecting both monocot and dicot hosts. Secretome analysis suggested R. solani employs largely different virulence mechanisms to well-studied pathogens, despite in many instances infecting the same host plants. Furthermore, the secretome of the broad host range AG8 isolate may be shaped by maintaining functions for saprophytic life stages while minimising opportunities for host plant recognition. Analysis of possible co-evolution with host plants and in-planta up-regulation in particular, aided identification of effectors including xylanase and inhibitor I9 domain containing proteins able to induce cell death in-planta. The inhibitor I9 domain was more abundant in the secretomes of a wide range of necrotising fungi relative to biotrophs. These findings provide novel targets for further dissection of the virulence mechanisms and potential avenues to control this under-characterised but important pathogen.
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Methods Mol Biol: Protein–Protein Interaction Assays with Effector–GFP Fusions in Nicotiana benthamiana (2017)

Methods Mol Biol: Protein–Protein Interaction Assays with Effector–GFP Fusions in Nicotiana benthamiana (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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Plant parasites secrete proteins known as effectors into host tissues to manipulate host cell structures and functions. One of the major goals in effector biology is to determine the host cell compartments and the protein complexes in which effectors accumulate. Here, we describe a five-step pipeline that we routinely use in our lab to achieve this goal, which consists of (1) Golden Gate assembly of pathogen effector–green fluorescent protein (GFP) fusions into binary vectors, (2) Agrobacterium-mediated heterologous protein expression in Nicotiana benthamiana leaf cells, (3) laser-scanning confocal microscopy assay, (4) anti-GFP coimmunoprecipitation–liquid chromatography–tandem mass spectrometry (coIP/MS) assay, and (5) anti-GFP western blotting. This pipeline is suitable for rapid, cost-effective, and medium-throughput screening of pathogen effectors in planta.
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bioRxiv: Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions (2017)

bioRxiv: Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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The plant immune system is innate, 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 showed that plant immune receptors with integrated domains are distributed unevenly across their phylogeny in grasses. Using phylogenetic analysis, we uncovered 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 revealed that homologous receptors can be fused to diverse domains. Furthermore, we discovered a 43 amino acids long motif that was associated with this dominant integration clade and was located immediately upstream of the fusion site. Sequence analysis revealed that DNA transposition and/or ectopic recombination are the most likely mechanisms of NLR-ID formation. 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.


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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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Mol. Plant: Vacuole Integrity Maintained by DUF300 Proteins Is Required for Brassinosteroid Signaling Regulation (2017)

Mol. Plant: Vacuole Integrity Maintained by DUF300 Proteins Is Required for Brassinosteroid Signaling Regulation (2017) | Publications from The Sainsbury Laboratory | Scoop.it
Brassinosteroid (BR) hormone signaling controls multiple processes during plant growth and development and is initiated at the plasma membrane through the receptor kinase BRASSINOSTEROID INSENSITIVE1 (BRI1) together with co-receptors such as BRI1-ASSOCIATED RECEPTOR KINASE1 (BAK1). BRI1 abundance is regulated by endosomal recycling and vacuolar targeting, but the role of vacuole-related proteins in BR receptor dynamics and BR responses remain elusive. Here, we show that the absence of two DUF300 domain-containing tonoplast proteins, LAZARUS1 (LAZ1) and LAZ1 HOMOLOG1 (LAZ1H1), causes vacuole morphology defects, growth inhibition, and constitutive activation of BR signaling. Intriguingly, tonoplast accumulation of BAK1 was substantially increased and appeared causally linked to enhanced BRI1 trafficking and degradation in laz1 laz1h1 plants. Since unrelated vacuole mutants exhibited normal BR responses, our findings indicate that DUF300 proteins play distinct roles in the regulation of BR signaling by maintaining vacuole integrity required to balance subcellular BAK1 pools and BR receptor distribution.
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Science: (Perspective) Complex regulation of plant sex by peptides (2017)

Science: (Perspective) Complex regulation of plant sex by peptides (2017) | Publications from The Sainsbury Laboratory | Scoop.it
Most of our food—whether fruit or grain—is the direct result of flowering plant fertilization. As this also underlies the transmission of genetic information over generations, it is essential to understand the molecular events controlling plant reproduction. During fertilization, pollen (the male gametophyte, or reproductive cell) forms a pollen tube which is guided toward the ovule (the female gametophyte), where, upon bursting, it will deliver its sperm cells ( 1 ). All steps—from the perception of compatible pollens by the flower pistil (the female reproductive organ) to pollen tube growth, guidance and, ultimately, rupture—are controlled by a complex molecular dialogue involving numerous plant receptor kinases and endogenous signaling molecules, including secreted peptides ( 2 ). On pages 1596 and 1600 of this issue, Ge et al. ( 3 ) and Mecchia et al. ( 4 ), respectively, characterize signaling events between the male and female gametophytes, which offer exciting insights into the molecular mechanisms controlling plant fertilization and seed setting.
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J. Am. Soc. Brew. Chem: Malt Modification and Its Effects on the Contributions of Barley Genotype to Beer Flavor (2017)

J. Am. Soc. Brew. Chem: Malt Modification and Its Effects on the Contributions of Barley Genotype to Beer Flavor (2017) | Publications from The Sainsbury Laboratory | Scoop.it
Based on prior research that showed significant genetic differences between barley genotypes for beer sensory descriptors, the effects of degree of malt modification on these descriptors were assessed in two experiments. The first experiment involved sensory assessment of nano-beers made from micromalts of Golden Promise, Full Pint, 34 doubled haploid progeny, and the check CDC Copeland. Average degree of modification was assessed by sampling grain from each of the 37 genotypes stored for three postharvest intervals prior to malting and brewing. The second experiment involved sensory assessment of pilot beers made from intentionally under-, properly, and overmodified pilot malts of two barley varieties: Full Pint and CDC Copeland. In both experiments, genotypes were the principal sources of significant variation in sensory descriptors. Degree of modification and genotype × modification interactions were also significant for some descriptors. Based on the results of this study, the genetic characterization of and selection for barley contributions to beer flavor are warranted, even with undermodified malts. The contribution of barley variety to beer flavor will likely be modest compared with the flavors developed during the malting process and the flavors contributed by hops and yeast. However, in certain beer styles, the contributions of barley genotype may be worth the attention of maltsters, brewers, and consumers.
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BMC Genomics: Genome analysis of the foxtail millet pathogen Sclerospora graminicola reveals the complex effector repertoire of graminicolous downy mildews (2017)

BMC Genomics: Genome analysis of the foxtail millet pathogen Sclerospora graminicola reveals the complex effector repertoire of graminicolous downy mildews (2017) | Publications from The Sainsbury Laboratory | Scoop.it

Background. Downy mildew, caused by the oomycete pathogen Sclerospora graminicola, is an economically important disease of Gramineae crops including foxtail millet (Setaria italica). Plants infected with S. graminicola are generally stunted and often undergo a transformation of flower organs into leaves (phyllody or witches’ broom), resulting in serious yield loss. To establish the molecular basis of downy mildew disease in foxtail millet, we carried out whole-genome sequencing and an RNA-seq analysis of S. graminicola.

 

Results. Sequence reads were generated from S. graminicola using an Illumina sequencing platform and assembled de novo into a draft genome sequence comprising approximately 360 Mbp. Of this sequence, 73% comprised repetitive elements, and a total of 16,736 genes were predicted from the RNA-seq data. The predicted genes included those encoding effector-like proteins with high sequence similarity to those previously identified in other oomycete pathogens. Genes encoding jacalin-like lectin-domain-containing secreted proteins were enriched in S. graminicola compared to other oomycetes. Of a total of 1220 genes encoding putative secreted proteins, 91 significantly changed their expression levels during the infection of plant tissues compared to the sporangia and zoospore stages of the S. graminicola lifecycle.

 

Conclusions. We established the draft genome sequence of a downy mildew pathogen that infects Gramineae plants. Based on this sequence and our transcriptome analysis, we generated a catalog of in planta-induced candidate effector genes, providing a solid foundation from which to identify the effectors causing phyllody.


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bioRxiv: The plant calcium-dependent protein kinase CPK3 phosphorylates REM1.3 to restrict viral infection (2017)

bioRxiv: The plant calcium-dependent protein kinase CPK3 phosphorylates REM1.3 to restrict viral infection (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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Plants respond to pathogens through dynamic regulation of plasma membrane-bound signaling pathways. To date, how the plant plasma membrane is involved in responses to viruses is mostly unknown. Here, we show that plant cells sense the Potato virus X (PVX) COAT PROTEIN and TRIPLE GENE BLOCK 1 proteins and subsequently trigger the activation of a membrane-bound calcium-dependent kinase. We show that the Arabidopsis thaliana CALCIUM-DEPENDENT PROTEIN KINASE 3-interacts with group 1 REMORINs in vivo, phosphorylates the intrinsically disordered N-terminal domain of the Group 1 REMORIN REM1.3, and restricts PVX cell-to-cell movement. REM1.3's phospho-status defines its plasma membrane nanodomain organization and is crucial for REM1.3-dependent restriction of PVX cell-to-cell movement by regulation of callose deposition at plasmodesmata. This study unveils plasma membrane nanodomain-associated molecular events underlying the plant immune response to viruses.
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Front. Plant Sci: Enhanced Bacterial Wilt Resistance in Potato Through Expression of Arabidopsis EFR and Introgression of Quantitative Resistance from Solanum commersonii (2017)

Front. Plant Sci: Enhanced Bacterial Wilt Resistance in Potato Through Expression of Arabidopsis EFR and Introgression of Quantitative Resistance from Solanum commersonii (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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The Sainsbury Lab's insight:
Bacterial wilt (BW) caused by Ralstonia solanacearum is responsible for substantial losses in cultivated potato (Solanum tuberosum) crops worldwide. Resistance genes have been identified in wild species; however, introduction of these through classical breeding has achieved only partial resistance, which has been linked to poor agronomic performance. The Arabidopsis thaliana (At) pattern recognition receptor elongation factor-Tu (EF-Tu) receptor (EFR) recognizes the bacterial pathogen-associated molecular pattern EF-Tu (and its derived peptide elf18) to confer anti-bacterial immunity. Previous work has shown that transfer of AtEFR into tomato confers increased resistance to R. solanacearum. Here, we evaluated whether the transgenic expression of AtEFR would similarly increase BW resistance in a commercial potato line (INIA Iporá), as well as in a breeding potato line (09509.6) in which quantitative resistance has been introgressed from the wild potato relative Solanum commersonii. Resistance to R. solanacearum was evaluated by damaged root inoculation under controlled conditions. Both INIA Iporá and 09509.6 potato lines expressing AtEFR showed greater resistance to R. solanacearum, with no detectable bacteria in tubers evaluated by multiplex-PCR and plate counting. Notably, AtEFR expression and the introgression of quantitative resistance from S. commersonii had a significant additive effect in 09509.6-AtEFR lines. These results show that the combination of heterologous expression of AtEFR with quantitative resistance introgressed from wild relatives is a promising strategy to develop BW resistance in potato.
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BMC Biol: Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination (2017)

BMC Biol: Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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Root and tuber crops are a major food source in tropical Africa. Among these crops are several species in the monocotyledonous genus Dioscorea collectively known as yam, a staple tuber crop that contributes enormously to the subsistence and socio-cultural lives of millions of people, principally in West and Central Africa. Yam cultivation is constrained by several factors, and yam can be considered a neglected “orphan” crop that would benefit from crop improvement efforts. However, the lack of genetic and genomic tools has impeded the improvement of this staple crop.
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Methods Mol Biol: MutRenSeq: A Method for Rapid Cloning of Plant Disease Resistance Genes (2017)

Methods Mol Biol: MutRenSeq: A Method for Rapid Cloning of Plant Disease Resistance Genes (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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The Sainsbury Lab's insight:
MutRenSeq is a method to clone disease resistance (R) genes in plants. Tips and detailed experimental protocols for the pipeline, including the complexity reduction by R gene targeted enrichment sequencing, and computational analysis based on comparative genomics are provided in this chapter.
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Plant Cell: The Arabidopsis Leucine-rich Repeat Receptor Kinase BIR3 Negatively Regulates BAK1 Receptor Complex Formation and Stabilizes BAK1 (2017)

Plant Cell: The Arabidopsis Leucine-rich Repeat Receptor Kinase BIR3 Negatively Regulates BAK1 Receptor Complex Formation and Stabilizes BAK1 (2017) | Publications from The Sainsbury Laboratory | Scoop.it
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BAK1 is a co-receptor and positive regulator of multiple ligand-binding leucine-rich-repeat receptor kinases (LRR-RKs) and is involved in brassinosteroid (BR)-dependent growth and development, innate immunity and cell death control. The BAK1-interacting LRR-RKs BIR2 and BIR3 were previously identified by proteomics analyses of in vivo BAK1 complexes. Here we show that BAK1-related pathways such as innate immunity and cell death control are affected by BIR3 in Arabidopsis thaliana. BIR3 also has a strong negative impact on BR signaling. BIR3 directly interacts with the BR receptor BRI1 and other ligand-binding receptors and negatively regulates BR signaling by competitive inhibition of BRI1. BIR3 is released from BAK1 and BRI1 after ligand exposure and directly affects the formation of BAK1 complexes with BRI1 or FLAGELLIN SENSING2. Double mutants of bak1 and bir3 show spontaneous cell death and constitutive activation of defense responses. BAK1 and its closest homolog BKK1 interact with and are stabilized by BIR3, suggesting that bak1 bir3 double mutants mimic the spontaneous cell death phenotype observed in bak1 bkk1 mutants via destabilization of BIR3 target proteins. Our results provide evidence for a negative regulatory mechanism for BAK1 receptor complexes in which BIR3 interacts with BAK1 and inhibits ligand-binding receptors to prevent BAK1 receptor complex formation.
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