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PLOS Pathogens: Mining Herbaria for Plant Pathogen Genomes: Back to the Future (2014)

PLOS Pathogens: Mining Herbaria for Plant Pathogen Genomes: Back to the Future (2014) | Publications from The Sainsbury Laboratory | Scoop.it

Since the dawn of agriculture, plant pathogens and pests have been a scourge of humanity. Yet we have come a long way since the Romans attempted to mitigate the effects of plant disease by worshipping and honoring the god Robigus. Books in the Middle Ages by Islamic and European scholars described various plant diseases and even proposed particular disease management strategies. Surprisingly, the causes of plant diseases remained a matter of debate over a long period. It took Henri-Louis Duhamel du Monceau's elegant demonstration in his 1728 “Explication Physique” paper that a “contagious” fungus was responsible for a saffron crocus disease to usher in an era of documented scientific inquiry. Confusion and debate about the exact nature of the causal agents of plant diseases continued until the 19th century, which not only saw the first detailed analyses of plant pathogens but also provided much-needed insight into the mechanisms of plant disease. An example of this is Anton de Bary's demonstration that a “fungus” is a cause, not a consequence, of plant disease. This coming of age of plant pathology was timely. In the 19th century, severe plant disease epidemics hit Europe and caused economic and social upheaval. These epidemics were not only widely covered in the press but also recognized as serious political issues by governments. Many of the diseases, including late blight of potato, powdery and downy mildew of grapevine, as well as phylloxera, were due to exotic introductions from the Americas and elsewhere. These and subsequent epidemics motivated scientific investigations into crop breeding and plant disease management that developed into modern plant pathology science over the 20th century.

 

Nowadays, our understanding of plant pathogens and the diseases they cause greatly benefits from molecular genetics and genomics. All aspects of plant pathology, from population biology and epidemiology to mechanistic research, are impacted. The polymerase chain reaction (PCR) first enabled access to plant pathogen DNA sequences from historical specimens deposited in herbaria. Historical records in combination with herbarium specimens have turned out to provide powerful tools for understanding the course of past plant epidemics. Recently, thanks to new developments in DNA sequencing technology, it has become possible to reconstruct the genomes of plant pathogens in herbaria. In this article, we first summarize how whole genome analysis of ancient DNA has been recently used to reconstruct the 19th-century potato-blight epidemic that rapidly spread throughout Europe and triggered the Irish potato famine. We then discuss the exciting prospects offered by the emergence of the discipline of ancient plant pathogen genomics.


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Mary Williams's curator insight, April 25, 2014 3:02 AM

Good overview for students - very accessible and interesting!

Freddy Monteiro's comment, April 25, 2014 4:21 AM
This is a great source of teaching materials for potato late blight. Congrats on the work behind it.

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Mol Plant Path: SOBIR1 requires the GxxxG dimerization motif in its transmembrane domain to form constitutive complexes with receptor-like proteins (2015)

Mol Plant Path: SOBIR1 requires the GxxxG dimerization motif in its transmembrane domain to form constitutive complexes with receptor-like proteins (2015) | Publications from The Sainsbury Laboratory | Scoop.it
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Receptor-like proteins (RLPs), forming an important group of transmembrane receptors in plants, play roles in development and immunity. RLPs contain extracellular leucine-rich repeats (LRRs) and, in contrast to receptor-like kinases (RLKs), lack a cytoplasmic kinase required for initiating downstream signalling. Recent studies revealed that the RLK SOBIR1/EVR (SUPPRESSOR OF BIR1-1/EVERSHED) specifically interacts with RLPs. SOBIR1 stabilizes RLPs and is required for their function. However, the mechanism by which SOBIR1 associates with RLPs and regulates RLP function remains unknown. The Cf immune receptors of tomato (Solanum lycopersicum), mediating resistance to the fungus Cladosporium fulvum, are RLPs that also interact with SOBIR1. Here, we show that both the LRR and kinase domain of SOBIR1 are dispensable for association with the RLP Cf-4, whereas the highly conserved GxxxGxxxG motif present in the transmembrane domain of SOBIR1 is essential for its interaction with Cf-4 and additional RLPs. Complementation assays in Nicotiana benthamiana, in which endogenous SOBIR1 levels were knocked-down by virus-induced gene silencing, showed that the LRR domain as well as kinase activity of SOBIR1 are required for the Cf-4/Avr4-triggered hypersensitive response (HR). In contrast, the LRRs and kinase activity of SOBIR1 are not required for facilitating Cf-4 accumulation. Together, these results suggest that in addition to being a stabilizing scaffold for RLPs, SOBIR1 is also required for initiating downstream signalling through its kinase domain.

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Mol Plant Microbe Interact: A recent expansion of the RXLR effector gene Avrblb2 is maintained in global populations of Phytophthora infestans indicating different contributions to virulence (2015)

Mol Plant Microbe Interact: A recent expansion of the RXLR effector gene Avrblb2 is maintained in global populations of Phytophthora infestans indicating different contributions to virulence (2015) | Publications from The Sainsbury Laboratory | Scoop.it
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The introgression of disease resistance (R) genes encoding immunoreceptors with broad-spectrum recognition into cultivated potato appears to be the most promising approach to achieve sustainable management of late blight caused by the oomycete pathogen Phytophthora infestans. Rpi-blb2 from Solanum bulbocastanum, shows great potential for use in agriculture based on preliminary potato disease trials. Rpi-blb2 confers immunity by recognizing the P. infestans avirulence effector protein AVRblb2 after it is translocated inside the plant cell. This effector belongs to the RXLR class of effectors and is under strong positive selection. Structure-function analyses revealed a key polymorphic amino acid (position 69) in AVRblb2 effector that is critical for activation of Rpi-blb2. In this study, we reconstructed the evolutionary history of the Avrblb2 gene family and further characterized its genetic structure in worldwide populations. Our data indicates that Avrblb2 evolved as a single copy gene in a putative ancestral species of P. infestans and has recently expanded in the Phytophthora species that infect solanaceous hosts. As a consequence, at least four variants of AVRblb2 arose in P. infestans. One of these variants, with a Phe residue at position 69, evades recognition by the cognate resistance gene. Surprisingly, all Avrblb2 variants are maintained in pathogen populations. This suggests a potential benefit for the pathogen in preserving duplicated versions of AVRblb2 possibly because the variants may have different contributions to pathogen fitness in a diversified solanaceous host environment.

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Frontiers: Focus issue on plant immunity: from model systems to crop species (2015)

Focus issue on plant immunity: from model systems to crop species
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One of the largest challenges of our time is to enhance agricultural production to feed a growing population in the midst of a changing climate. According to estimates, the global population will increase from 7 to 9 billion people by 2050 requiring a 60% increase in food in order to meet demand (Alexandratos and Bruinsma, 2012). Only the combination of reduction of food waste together with an increase in food productivity will enable us to meet this daunting challenge (Godfray et al., 2010). Advancements in agricultural practices, technology, food transport, and crop yields on marginal lands will be required to address this looming food production challenge. Crop losses due to plant disease significantly impact agriculture, with ~15% of global crop production lost due to preharvest plant disease (Pinstrup-Andersen, 2001; Oerke, 2006). Studies of model plants, such as Arabidopsis, have significantly enhanced our understanding of plant innate immune perception and signaling. For example, the identification of classical plant resistant genes in Arabidopsis and other model dicots facilitated the successful cloning of multiple wheat rust resistant genes (Ellis et al., 2014; Wulff and Moscou, 2014). With advancements in genome sequencing and analyses, we are now at a stage to exploit the basic knowledge gained in plant model species at a full genome scale in crops (Piquerez et al., 2014).

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PLOS Pathogens: Transgenic Expression of the Dicotyledonous Pattern Recognition Receptor EFR in Rice Leads to Ligand-Dependent Activation of Defense Responses (2015)

PLOS Pathogens: Transgenic Expression of the Dicotyledonous Pattern Recognition Receptor EFR in Rice Leads to Ligand-Dependent Activation of Defense Responses (2015) | Publications from The Sainsbury Laboratory | Scoop.it
Author Summary Plants possess multi-layered immune recognition systems. Early in the infection process, plants use receptor proteins to recognize pathogen molecules. Some of these receptors are present in only in a subset of plant species. Transfer of these taxonomically restricted immune receptors between plant species by genetic engineering is a promising approach for boosting the plant immune system. Here we show the successful transfer of an immune receptor from a species in the mustard family, called EFR, to rice. Rice plants expressing EFR are able to sense the bacterial ligand of EFR and elicit an immune response. We show that the EFR receptor is able to use components of the rice immune signaling pathway for its function. Under laboratory conditions, this leads to an enhanced resistance response to two weakly virulent isolates of an economically important bacterial disease of rice.
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New Phytologist: Plants, fungi and oomycetes: a 400-million year affair that shapes the biosphere (2015)

New Phytologist: Plants, fungi and oomycetes: a 400-million year affair that shapes the biosphere (2015) | Publications from The Sainsbury Laboratory | Scoop.it
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In a rare gathering, genomics met palaeontology at the 10th New Phytologist Workshop on the ‘Origin and evolution of plants and their interactions with fungi’. An eclectic group of 17 experts met at The Natural History Museum (London, UK) on 9–10 September 2014 to discuss the latest findings on plant interactions with fungi (Eumycota) and oomycetes (Oomycota = Peronosporomycota), with topics ranging from the fossil record and comparative genomics to symbiosis and phytopathology. The discussions were largely disseminated via social media (Box 1). Highly diverse plant–fungal interactions have formed the backbone of land ecosystems and biogeochemical cycles since the Palaeozoic (see Fig. 1 for geological timeframe). As summarized by Christine Strullu-Derrien and Paul Kenrick (The Natural History Museum, London, UK) the first land plants arose c. 470 million years (Myr) ago (Kenrick et al., 2012; Edwards et al., 2014), at which time fungi and oomycetes had already colonized terrestrial ecosystems. Following their terrestrialization, these microbes began to abound within plant fossils (Taylor et al., 2014, and references therein). Ultimately, biological interactions sculpted the genomes of plants, fungi and oomycetes (e.g. Schmidt & Panstruga, 2011; Kohler et al., 2015). Here we illustrate the picture that has emerged from the discussions at the 10th New Phytologist Workshop, and point to some pending questions.

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Nature Immunology - News and Views: A new receptor for LPS (2015)

Nature Immunology - News and Views: A new receptor for LPS (2015) | Publications from The Sainsbury Laboratory | Scoop.it
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The innate immune system’s ability to recognize infectious non-self molecules relies on the sensitive perception of conserved pathogen- associated molecular patterns (PAMPs) by host pattern-recognition receptors (PRRs). A stereotypical bacterial PAMP recognized by mammalian cells is lipopolysaccharide (LPS), the major constituent of the outer cell envelope of Gram-negative bacteria. Although plants are also able to perceive LPS and mount innate immune responses, no plant receptor for LPS was known until now. In this issue of Nature Immunology, Ranf et al. report the identification of a plasma-membrane receptor kinase that is required for respon- siveness to LPS in plants and define a type of domain potentially involved in the perception of LPS.

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TAG: Mapping the ‘breaker’ element of the gametocidal locus proximal to a block of sub-telomeric heterochromatin on the long arm of chromosome 4Ssh of Aegilops sharonensis (2015)

TAG: Mapping the ‘breaker’ element of the gametocidal locus proximal to a block of sub-telomeric heterochromatin on the long arm of chromosome 4Ssh of Aegilops sharonensis (2015) | Publications from The Sainsbury Laboratory | Scoop.it
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Key message

The ‘breaker’ element ( GcB ) of the gametocidal locus derived from Aegilops sharonensishas been mapped to a region proximal to a block of sub-telomeric heterochromatin on chromosome 4S sh L.

Abstract

The production of alien chromosome addition lines allows the transfer of useful genetic variation into elite wheat varieties from related wild species. However, some wild relatives of wheat, particularly those within the Sitopsis section of the genus Aegilops, possess chromosomes that are transmitted preferentially to the offspring when addition lines are generated. Species within the Sitopsis group possess the S genome, and among these species, Aegilops sharonensis (2n = 14, SshSsh) carries the Ssh genome which is closely related to the D genome of hexaploid wheat. Some S genome chromosomes carry gametocidal loci, which induce severe chromosome breakage in gametes lacking the gametocidal chromosome, and hence, result in gamete abortion. The preferential transmission of gametocidal loci could be exploited in wheat breeding, because linking gametocidal loci with important agronomic traits in elite wheat varieties would ensure retention of these traits through successive generations. In this study, we have mapped the breaker element of the gametocidal locus derived from Ae. sharonensis to the region immediately proximal to a block of sub-telomeric heterochromatin on the long arm of chromosome 4Ssh.

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Nature Biotech - News & Views: Engineering insect-free cereals (2015)

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Insect pests reduce yields of crops worldwide through direct damage and because they spread devastating viral diseases. In Asia, the brown planthopper (BPH) decimates rice (Oryza sativa) crops, causing the loss of billions of dollars annually1. In this issue, Liu et al.2 report the cloning of a rice genetic locus that confers broad-spectrum resistance to BPH and at least one other planthopper species (white back planthopper). Introducing this locus into plant genomes is likely to provide an effective means of combating insect pests of rice and of other cereals such as maize.

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Scientific Reports: Autoimmunity conferred by chs3-2D relies on CSA1, its adjacent TNL-encoding neighbour (2015)

Scientific Reports: Autoimmunity conferred by chs3-2D relies on CSA1, its adjacent TNL-encoding neighbour (2015) | Publications from The Sainsbury Laboratory | Scoop.it
Plant innate immunity depends on the function of a large number of intracellular immune receptor proteins, the majority of which are structurally similar to mammalian nucleotide-binding oligomerization domain (NOD)-like receptor (NLR) proteins. CHILLING SENSITIVE 3 (CHS3) encodes an atypical Toll/Interleukin 1 Receptor (TIR)-type NLR protein with an additional Lin-11, Isl-1 and Mec-3 (LIM) domain at its C-terminus. The gain-of-function mutant allele chs3-2D exhibits severe dwarfism and constitutively activated defense responses, including enhanced resistance to virulent pathogens, high defence marker gene expression, and salicylic acid accumulation. To search for novel regulators involved in CHS3-mediated immune signaling, we conducted suppressor screens in the chs3-2D and chs3-2D pad4-1 genetic backgrounds. Alleles of sag101 and eds1-90 were isolated as complete suppressors of chs3-2D, and alleles of sgt1b were isolated as partial suppressors of chs3-2D pad4-1. These mutants suggest that SAG101, EDS1-90, and SGT1b are all positive regulators of CHS3-mediated defense signaling. Additionally, the TIR-type NLR-encoding CSA1 locus located genomically adjacent to CHS3 was found to be fully required for chs3-2D-mediated autoimmunity. CSA1 is located 3.9[emsp14]kb upstream of CHS3 and is transcribed in the opposite direction. Altogether, these data illustrate the distinct genetic requirements for CHS3-mediated defense signaling.
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Frontiers in Plant Science: The “sensor domains” of plant NLR proteins: more than decoys? (2015)

Frontiers in Plant Science: The “sensor domains” of plant NLR proteins: more than decoys? (2015) | Publications from The Sainsbury Laboratory | Scoop.it

Our conceptual and mechanistic understanding of how plant nucleotide-binding leucine-rich repeat (NLR or NB-LRR) proteins perceive pathogens continues to advance. NLRs are intracellular multidomain proteins that recognize pathogen-derived effectors either directly or indirectly (Jones and Dangl, 2006; van der Hoorn and Kamoun, 2008; Dodds and Rathjen, 2010; Cesari et al., 2014). In the direct model, the NLR protein binds a pathogen effector or serves as a substrate for the effector’s enzymatic activity. In the indirect model, the NLR recognizes modifications of additional host protein(s) targeted by the effector. Such intermediate host protein(s) are often called effector targets (ETs). However, given that effectors can act on multiple host targets, the specific protein that mediates recognition by the NLR may not be the effector’s operative target and may have evolved to function as a decoy dedicated to pathogen detection. This “decoy” model contrasts with the “guard” model in which the NLR perceives the effector via its action on its operative target (van der Hoorn and Kamoun, 2008). 

In a recent article, Cesari et al. (2014) elegantly synthesized the literature to propose a novel model of how NLRs recognise effectors termed the “integrated decoy” hypothesis. Based on new data from several pathosystems, it appears that some NLRs recognize pathogen effectors through extraneous domains that have evolved by duplication of an ET followed by fusion into the NLR. This NLR-integrated domain mimics the effector binding/substrate property of the original ET to enable pathogen detection. In addition, these “receptor” or “sensor” NLRs typically partner with NLR proteins with a classic architecture that function as signalling partners required for the resistance response (Eitas and Dangl, 2010; Cesari et al., 2013; Cesari et al., 2014; Williams et al., 2014).

Here, we expand on the Cesari et al. (2014) model and introduce the possibility that NLR-integrated domains do not have to be decoys (as in defective mimics) of the effector’s operative target. Indeed, in addition to binding effectors or serving as their substrates, operative targets carry a biochemical activity that is modulated by the effector. The perturbation of this activity by the effector leads to effector-triggered susceptibility, an activity often related to immunity (Boller and He, 2009; Dodds and Rathjen, 2010; Win et al., 2012). Clearly NLR-integrated domains must retain the “sensor” activity of the ancestral ET, but they could also retain their biochemical activity, continuing to function in the effector-targeted pathway even as an extraneous domain within a classic NLR architecture. At present, this possibility cannot be discounted given that the biochemical activities of the ancestral ETs and their NLR-integrated counterparts are generally unknown. Additionally, when NLR-fusions occurred recently, there may not have been enough time for the integrated ET to lose its original function and evolve into a decoy. We therefore propose to refer to the extraneous domains of classic NLR proteins described by Cesari et al. (2014) as sensor domains (SD), a term that is agnostic to any potential biochemical activities of the integrated module.

How to test whether or not SDs are decoys? We propose a straightforward genetic test that can reject the decoy hypothesis. Isogenic plants either carrying or lacking the NLR-SD can be challenged with a pathogen strain that lacks the matching avirulence effector (Figure 1). There are several possible outcomes. If the NLR-SD isogenic lines do not differ in their response to the pathogen without the matching effector, the result is inconclusive and the null decoy hypothesis cannot be rejected. If the presence of NLR-SD without the known matching effector shows higher levels of resistance, and there are no signs of typical effector-triggered immunity, then the SD is likely to have retained the ET biochemical activity and contributes to basal immunity in a manner analogous to the ancestral ET. An even more interesting result would be if in the absence of the matching effector, the NLR-SD line is more susceptible as has been shown for several ETs (van Schie and Takken, 2014). In this scenario, another (unrecognized) effector might still be targeting the original biochemical activity of the SD domain. It would be conceptually fascinating if an NLR that functions as a resistance (R) gene against certain strains of a pathogen becomes a susceptibility (S) gene when exposed to other strains. Once again, this concept emphasizes how the outcome of plant-pathogen interactions is so critically dependent on the genotypes of the interacting organisms – a gene that has a certain impact in a particular genetic combination can have the exact opposite effect in another (Jones and Dangl, 2006; van der Hoorn and Kamoun, 2008; Dodds and Rathjen, 2010; Win et al., 2012).

Our goal is not to engage in an exercise in semantics. However, we wish to avoid conceptually restrictive terminology and urge the plant-microbe interactions community to test a rich spectrum of models and hypotheses. The proposed sensor domain terminology would accommodate this breadth of ideas. Ultimately, it may very well turn out that the majority, if not all, of the NLR integrated domains have lost their biochemical activities and have evolved into decoys. Also, it is possible that the sensor domain has already evolved into a decoy prior to recombination into a NLR. Nonetheless, further genetic and biochemical experiments are required to determine whether sensor domains of NLR-SDs are decoys or biochemically functional duplicates of their ancestral ETs.


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eLIFE: Evidence for suppression of immunity as a driver for genomic introgressions and host range expansion in races of Albugo candida, a generalist parasite (2015)

eLIFE: Evidence for suppression of immunity as a driver for genomic introgressions and host range expansion in races of Albugo candida, a generalist parasite (2015) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

How generalist parasites with wide host ranges can evolve is a central question in parasite evolution. Albugo candida is an obligate biotrophic parasite that consists of many physiological races that each specialize on distinct Brassicaceae host species. By analyzing genome sequence assemblies of five isolates, we show they represent three races that are genetically diverged by ~1%. Despite this divergence, their genomes are mosaic-like, with ~25% being introgressed from other races. Sequential infection experiments show that infection by adapted races enables subsequent infection of hosts by normally non-infecting races. This facilitates introgression and the exchange of effector repertoires, and may enable the evolution of novel races that can undergo clonal population expansion on new hosts. We discuss recent studies on hybridization in other eukaryotes such as yeast, Heliconius butterflies, Darwin's finches, sunflowers and cichlid fishes, and the implications of introgression for pathogen evolution in an agro-ecological environment. - See more at: http://elifesciences.org/content/early/2015/02/27/eLife.04550/article-data#.dpuf

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PLoS Pathogens: The Phylogenetically-Related Pattern Recognition Receptors EFR and XA21 Recruit Similar Immune Signaling Components in Monocots and Dicots (2015)

PLoS Pathogens: The Phylogenetically-Related Pattern Recognition Receptors EFR and XA21 Recruit Similar Immune Signaling Components in Monocots and Dicots (2015) | Publications from The Sainsbury Laboratory | Scoop.it

Pests and diseases cause significant agricultural losses. Plants recognize pathogen-derived molecules via plasma membrane-localized immune receptors (called pattern recognition receptors or PRRs), resulting in pathogen resistance. In recent years, the transfer of PRRs across plant species has emerged as a promising biotechnological approach to improve crop disease resistance. Successful transfers of PRRs suggest that immune signaling components are conserved across plant species. In this study, we demonstrate that the PRR XA21 from the monocot plant rice is functional in the dicot plant Arabidopsis thaliana (Arabidopsis) and that it confers quantitatively enhanced resistance to bacteria. Furthermore, we show that the rice XA21 and the Arabidopsis EFR, which are evolutionary-distant but phylogenetically closely related, recruit similar signaling components for their function, revealing an overall conservation of immune pathways across monocots and dicots. These findings demonstrate evolutionary conservation of downstream signaling from PRRs and indicate that transfer of PRRs is possible between different plant families, but also between monocots and dicots.

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Molecular Plant-Microbe Interactions: Journal - 0(ja): 14-3-3 proteins in plant-pathogen interactions (2015)

Molecular Plant-Microbe Interactions:  Journal - 0(ja): 14-3-3 proteins in plant-pathogen interactions (2015) | Publications from The Sainsbury Laboratory | Scoop.it
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14-3-3 proteins define a eukaryotic-specific protein family with a general role in signal transduction. Primarily, 14-3-3 proteins act as phospho-sensors, binding phosphorylated client proteins and modulating their functions. Since phosphorylation regulates a plethora of different physiological responses in plants, 14-3-3 proteins play roles in multiple signalling pathways, including those controlling metabolism, hormone signalling, cell division, and responses to abiotic and biotic stimuli. Increasing evidence supports a prominent role of 14-3-3 proteins in regulating plant immunity against pathogens at various levels. In this review, potential links between 14-3-3 function and the regulation of plant-pathogen interactions are discussed, with a special focus on the regulation of 14-3-3s in response to pathogen perception, interactions between 14-3-3s and defence-related proteins, and 14-3-3s as targets of pathogen effectors.

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Mol Cell Prot: Identification of regulatory and cargo proteins of endosomal and secretory pathways in Arabidopsis thaliana by proteomic dissection (2015)

Mol Cell Prot: Identification of regulatory and cargo proteins of endosomal and secretory pathways in Arabidopsis thaliana by proteomic dissection (2015) | Publications from The Sainsbury Laboratory | Scoop.it
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The cell's endomembranes comprise an intricate, highly dynamic and well-organised system. In plants the proteins that regulate function of the various endomembrane compartments and their cargo remain largely unknown. Our aim was to dissect subcellular trafficking routes by enriching for partially overlapping subpopulations of endosomal proteomes associated with endomembrane markers. We selected RABD2a/ARA5, RABF2b/ARA7, RABF1/ARA6, and RABG3f as markers for combinations of the Golgi, trans-Golgi Network (TGN), Early Endosomes (EE), secretory vesicles, Late Endosomes (LE), Multivesicular Bodies (MVB) and the tonoplast. As comparisons we used Golgi transport 1 (GOT1), which localises to the Golgi, Clathrin Light Chain 2 (CLC2) labelling Clathrin-coated vesicles and pits and the Vesicle Associated Membrane Protein 711 (VAMP711) present at the tonoplast. We developed an easy-to-use method by refining published protocols based on affinity purification of fluorescent fusion constructs to these seven subcellular marker proteins in Arabidopsis thaliana seedlings. We present a total of 433 proteins, only five of which were shared among all enrichments, while many proteins were common between endomembrane compartments of the same trafficking route. Approximately half, 251 proteins, were assigned to one enrichment only. Our dataset contains known regulators of endosome functions including small GTPases, SNARES and tethering complexes. We identify known cargo proteins such as PIN3, PEN3, CESA and recently defined complexes such as TPLATE. The sub-cellular localisation of two GTPase regulators predicted from our enrichments was validated using live-cell imaging. This is the first proteomic data set to discriminate between such highly overlapping endomembrane compartments in plants and can be used as a general proteomic resource to predict the localisation of proteins, identify the components of regulatory complexes and provides a useful tool for the identification of new protein markers of the endomembrane system.

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BMC Research Notes: Broad application of a simple and affordable protocol for isolating plant RNA (2015)

BMC Research Notes: Broad application of a simple and affordable protocol for isolating plant RNA (2015) | Publications from The Sainsbury Laboratory | Scoop.it
Standard molecular biological methods involve the analysis of gene expression in living organisms under diverse environmental and developmental conditions. One of the most direct approaches to quantify gene expression is the isolation of RNA. Most techniques used to quantify gene expression require the isolation of RNA, usually from a large number of samples. While most published protocols, including those for commercial reagents, are either labour intensive, use hazardous chemicals and/or are costly, a previously published protocol for RNA isolation in Arabidopsis thaliana yields high amounts of good quality RNA in a simple, safe and inexpensive manner.
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Bioinformatics: bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby (2015)

Bioinformatics: bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby (2015) | Publications from The Sainsbury Laboratory | Scoop.it
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Nature Plants: Elicitin recognition confers enhanced resistance to Phytophthora infestans in potato (2015)

Nature Plants: Elicitin recognition confers enhanced resistance to Phytophthora infestans in potato (2015) | Publications from The Sainsbury Laboratory | Scoop.it

Potato late blight, caused by the destructive Irish famine pathogen Phytophthora infestans, is a major threat to global food security1,2. All late blight resistance genes identified to date belong to the coiled-coil, nucleotide-binding, leucine-rich repeat class of intracellular immune receptors3. However, virulent races of the pathogen quickly evolved to evade recognition by these cytoplasmic immune receptors4. Here we demonstrate that the receptor-like protein ELR (elicitin response) from the wild potato Solanum microdontum mediates extracellular recognition of the elicitin domain, a molecular pattern that is conserved in Phytophthora species. ELR associates with the immune co-receptor BAK1/SERK3 and mediates broad-spectrum recognition of elicitin proteins from several Phytophthora species, including four diverse elicitins from P. infestans. Transfer of ELR into cultivated potato resulted in enhanced resistance to P. infestans. Pyramiding cell surface pattern recognition receptors with intracellular immune receptors could maximize the potential of generating a broader and potentially more durable resistance to this devastating plant pathogen.


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Nature Biotechnology: MutMap accelerates breeding of a salt-tolerant rice cultivar (2015)

Nature Biotechnology: MutMap accelerates breeding of a salt-tolerant rice cultivar (2015) | Publications from The Sainsbury Laboratory | Scoop.it
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Following the 2011 earthquake and tsunami that affected Japan, >20,000 ha of rice paddy field was inundated with seawater, resulting in salt contamination of the land. As local rice landraces are not tolerant of high salt concentrations, we set out to develop a salt-tolerant rice cultivar. We screened 6,000 ethyl methanesulfonate (EMS) mutant lines of a local elite cultivar, 'Hitomebore', and identified a salt-tolerant mutant that we name hitomebore salt tolerant 1 (hst1). In this Correspondence, we report how we used our MutMap method to rapidly identify a loss-of-function mutation responsible for the salt tolerance of hst1 rice. The salt-tolerant hst1 mutant was used to breed a salt-tolerant variety named 'Kaijin', which differs from Hitomebore by only 201 single-nucleotide polymorphisms (SNPs). Field trials showed that it has the same growth and yield performance as the parental line under normal growth conditions. Notably, production of this salt-tolerant mutant line ready for delivery to farmers took only two years using our approach.

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TiPS: Importance of tyrosine phosphorylation in receptor kinase complexes (2015)

TiPS: Importance of tyrosine phosphorylation in receptor kinase complexes (2015) | Publications from The Sainsbury Laboratory | Scoop.it
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Highlights

• Components of brassinosteroid and PAMP receptor complexes are phosphorylated on tyrosine residues.

• Tyrosine phosphorylation is an important mechanism for the activation of receptor kinase complexes.
• Phosphorylation of specific tyrosine residues could contribute to specific signaling outcomes.

 

Tyrosine phosphorylation is an important post-translational modification that is known to regulate receptor kinase (RK)-mediated signaling in animals. Plant RKs are annotated as serine/threonine kinases, but recent work has revealed that tyrosine phosphorylation is also crucial for the activation of RK-mediated signaling in plants. These initial observations have paved the way for subsequent detailed studies on the mechanism of activation of plant RKs and the biological relevance of tyrosine phosphorylation for plant growth and immunity. In this Opinion article we review recent reports on the contribution of RK tyrosine phosphorylation in plant growth and immunity; we propose that tyrosine phosphorylation plays a major regulatory role in the initiation and transduction of RK-mediated signaling in plants.

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New Phytologist: Arabidopsis EF-Tu receptor enhances bacterial disease resistance in transgenic wheat (2015)

New Phytologist: Arabidopsis EF-Tu receptor enhances bacterial disease resistance in transgenic wheat (2015) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:
Perception of pathogen (or microbe)-associated molecular patterns (PAMPs/MAMPs) by pattern recognition receptors (PRRs) is a key component of plant innate immunity. The Arabidopsis PRR EF-Tu receptor (EFR) recognizes the bacterial PAMP elongation factor Tu (EF-Tu) and its derived peptide elf18. Previous work revealed that transgenic expression of AtEFR in Solanaceae confers elf18 responsiveness and broad-spectrum bacterial disease resistance.In this study, we developed a set of bioassays to study the activation of PAMP-triggered immunity (PTI) in wheat. We generated transgenic wheat (Triticum aestivum) plants expressing AtEFR driven by the constitutive rice actin promoter and tested their response to elf18.We show that transgenic expression of AtEFR in wheat confers recognition of elf18, as measured by the induction of immune marker genes and callose deposition. When challenged with the cereal bacterial pathogen Pseudomonas syringae pv. oryzae, transgenic EFR wheat lines had reduced lesion size and bacterial multiplication.These results demonstrate that AtEFR can be transferred successfully from dicot to monocot species, further revealing that immune signalling pathways are conserved across these distant phyla. As novel PRRs are identified, their transfer between plant families represents a useful strategy for enhancing resistance to pathogens in crops.
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Nature Comms: Two linked pairs of Arabidopsis TNL resistance genes independently confer recognition of bacterial effector ​AvrRps4 (2015)

Nature Comms: Two linked pairs of Arabidopsis TNL resistance genes independently confer recognition of bacterial effector ​AvrRps4 (2015) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

Plant immunity requires recognition of pathogen effectors by intracellular NB-LRR immune receptors encoded by Resistance (R) genes. Most R proteins recognize a specific effector, but some function in pairs that recognize multiple effectors. Arabidopsis thaliana TIR-NB-LRR proteins RRS1-R and RPS4together recognize two bacterial effectors, AvrRps4 from Pseudomonas syringae and PopP2 from Ralstonia solanacearum. However, AvrRps4, but not PopP2, is recognized in rrs1/rps4 mutants. We reveal an R gene pair that resembles and is linked to RRS1/RPS4, designated as RRS1B/RPS4B, which confers recognition of AvrRps4 but not PopP2. Like RRS1/RPS4, RRS1B/RPS4B proteins associate and activate defence genes upon AvrRps4 recognition. Inappropriate combinations (RRS1/RPS4B or RRS1B/RPS4) are non-functional and this specificity is not TIR domain dependent. Distinct putative orthologues of both pairs are maintained in the genomes of Arabidopsis thalianarelatives and are likely derived from a common ancestor pair. Our results provide novel insights into paired R gene function and evolution.

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bioRxiv: The NLR helper protein NRC3 but not NRC1 is required for Pto-mediated cell death in Nicotiana benthamiana (2015)

bioRxiv: The NLR helper protein NRC3 but not NRC1 is required for Pto-mediated cell death in Nicotiana benthamiana (2015) | Publications from The Sainsbury Laboratory | Scoop.it

Intracellular immune receptors of the nucleotide-binding leucine-rich repeat (NB-LRR or NLR) proteins often function in pairs, with "helper" proteins required for the activity of "sensors" that mediate pathogen recognition. The NLR helper NRC1 (NB-LRR protein required for HR-associated cell death 1) has been described as a signalling hub required for the cell death mediated by both cell surface and intracellular immune receptors in the model plant Nicotiana benthamiana. However, this work predates the availability of the N. benthamiana genome and whether NRC1 is indeed required for the reported phenotypes has not been confirmed. Here, we investigated the NRC family of solanaceous plants using a combination of genome annotation, phylogenetics, gene silencing and genetic complementation experiments. We discovered that a paralog of NRC1, we termed NRC3, is required for the hypersensitive cell death triggered by the disease resistance protein Pto but not Rx and Mi-1.2. NRC3 may also contribute to the hypersensitive cell death triggered by the receptor-like protein Cf-4. Our results highlight the importance of applying genetic complementation to validate gene function in RNA silencing experiments.


Via Kamoun Lab @ TSL
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Genome Biology: Field pathogenomics reveals the emergence of a diverse wheat yellow rust population (2015)

Genome Biology: Field pathogenomics reveals the emergence of a diverse wheat yellow rust population (2015) | Publications from The Sainsbury Laboratory | Scoop.it

Background Emerging and re-emerging pathogens imperil public health and global food security. Responding to these threats requires improved surveillance and diagnostic systems. Despite their potential, genomic tools have not been readily applied to emerging or re-emerging plant pathogens such as the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici (PST). This is due largely to the obligate parasitic nature of PST, as culturing PST isolates for DNA extraction remains slow and tedious. Results To counteract the limitations associated with culturing PST, we developed and applied a field pathogenomics approach by transcriptome sequencing infected wheat leaves collected from the field in 2013. This enabled us to rapidly gain insights into this emerging pathogen population. We found that the PST population across the United Kingdom, UK, underwent a major shift in recent years. Population genetic structure analyses revealed four distinct lineages that correlated to the phenotypic groups determined through traditional pathology-based virulence assays. Furthermore, the genetic diversity between members of a single population cluster for all 2013 PST field samples was much higher than that displayed by historical UK isolates, revealing a more-diverse population of PST. Conclusions Our field pathogenomics approach uncovered a dramatic shift in the PST population in the UK, likely due to a recent introduction of a diverse set of exotic PST lineages. The methodology described herein accelerates genetic analysis of pathogen populations and circumvents the difficulties associated with obligate plant pathogens. In principle, this strategy can be widely applied to a variety of plant pathogens.


Via Kamoun Lab @ TSL
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Molecular Plant-Microbe Interactions: Candidate Effector Proteins of the Rust Pathogen Melampsora Larici-Populina Target Diverse Plant Cell Compartments (2015)

Molecular Plant-Microbe Interactions: Candidate Effector Proteins of the Rust Pathogen Melampsora Larici-Populina Target Diverse Plant Cell Compartments (2015) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

Rust fungi are devastating crop pathogens that deliver effector proteins into infected tissues to modulate plant functions and promote parasitic growth. The genome of the poplar leaf rust fungus Melampsora larici-populina revealed a large catalogue of secreted proteins, some of which have been considered candidate effectors. Unravelling how these proteins function in host cells is key to understanding pathogenicity mechanisms and developing resistant plants. In this study, we used an effectoromics pipeline to select, clone, and express 20 candidate effectors in Nicotiana benthamiana leaf cells to determine their subcellular localisation and identify the plant proteins they interact with. Confocal microscopy revealed that six candidate effectors target the nucleus, nucleoli, chloroplasts, mitochondria and discrete cellular bodies. We also used coimmunoprecipitation and mass spectrometry to identify 606 N. benthamiana proteins that associate with the candidate effectors. Five candidate effectors specifically associated with a small set of plant proteins that may represent biologically relevant interactors. We confirmed the interaction between the candidate effector MLP124017 and the TOPLESS-Related Protein 4 from poplar by in planta coimmunoprecipitation. Altogether, our data enable us to validate effector proteins from M. larici-populina and reveal that these proteins may target multiple compartments and processes in plant cells. It also shows that N. benthamiana can be a powerful heterologous system to study effectors of obligate biotrophic pathogens.

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Bioinformatics: NLR-parser: Rapid annotation of plant NLR complements (2015)

Bioinformatics: NLR-parser: Rapid annotation of plant NLR complements (2015) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

Motivation: The repetitive nature of plant disease resistance genes encoding for nucleotide-binding leucine-rich repeat (NLR) proteins hampers their prediction with standard gene annotation software. Mast has previously been reported as a tool to support annotation of NLR-encoding genes. However the decision if a motif combination represents an NLR protein was entirely manual.
Results: The NLR-parser pipeline is designed to use the MAST output from six-frame translated amino acid sequences and filters for predefined biologically curated motif compositions. Input reads can be derived from, for example, raw long read sequencing data or contigs and scaffolds coming from plant genome projects. The out- put is a tab-separated file with information on start and frame of the first NLR specific motif, whether the identified sequence is a TNL or CNL, potentially full or fragmented. In addition, the output of the NB- ARC domain sequence can directly be used for phylogenetic anal- yses. In comparison to other prediction software, the highly complex NB-ARC domain is described in detail using several individual mo- tifs.

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