Publications from The Sainsbury Laboratory
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bioRxiv: Crowdsourced analysis of ash and ash dieback through the Open Ash Dieback project: A year 1 report on datasets and analyses contributed by a self-organising community (2014)

bioRxiv: Crowdsourced analysis of ash and ash dieback through the Open Ash Dieback project: A year 1 report on datasets and analyses contributed by a self-organising community (2014) | Publications from The Sainsbury Laboratory | Scoop.it

Ash dieback is a fungal disease of ash trees caused by Hymenoscyphus pseudoalbidus that has swept across Europe in the last two decades and is a significant threat to the ash population. This emergent pathogen has been relatively poorly studied and little is known about its genetic make-up. In response to the arrival of this dangerous pathogen in the UK we took the unusual step of providing an open access database and initial sequence datasets to the scientific community for analysis prior to performing an analysis of our own. Our goal was to crowdsource genomic and other analyses and create a community analysing this pathogen. In this report on the evolution of the community and data and analysis obtained in the first year of this activity, we describe the nature and the volume of the contributions and reveal some preliminary insights into the genome and biology of H. pseudoalbidus that emerged. In particular our nascent community generated a first-pass genome assembly containing abundant collapsed AT-rich repeats indicating a typically complex genome structure. Our open science and crowdsourcing effort has brought a wealth of new knowledge about this emergent pathogen within a short time-frame. Our community endeavour highlights the positive impact that open, collaborative approaches can have on fast, responsive modern science.


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Niklaus Grunwald's curator insight, April 26, 2014 5:46 PM

An example of crowdsourcing genomics ...

Publications from The Sainsbury Laboratory
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Nature Biotech: A pigeonpea gene confers resistance to Asian soybean rust in soybean (2016)

Nature Biotech: A pigeonpea gene confers resistance to Asian soybean rust in soybean (2016) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:
Asian soybean rust (ASR), caused by the fungus Phakopsora pachyrhizi, is one of the most economically important crop diseases, but is only treatable with fungicides, which are becoming less effective owing to the emergence of fungicide resistance. There are no commercial soybean cultivars with durable resistance to P. pachyrhizi, and although soybean resistance loci have been mapped, no resistance genes have been cloned. We report the cloning of a P. pachyrhizi resistance gene CcRpp1 (Cajanus cajan Resistance against Phakopsora pachyrhizi 1) from pigeonpea (Cajanus cajan) and show that CcRpp1 confers full resistance to P. pachyrhizi in soybean. Our findings show that legume species related to soybean such as pigeonpea, cowpea, common bean and others could provide a valuable and diverse pool of resistance traits for crop improvement.
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Nature Biotech: Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture (2016)

Nature Biotech: Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture (2016) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:
Wild relatives of domesticated crop species harbor multiple, diverse, disease resistance (R) genes that could be used to engineer sustainable disease control. However, breeding R genes into crop lines often requires long breeding timelines of 5–15 years to break linkage between R genes and deleterious alleles (linkage drag). Further, when R genes are bred one at a time into crop lines, the protection that they confer is often overcome within a few seasons by pathogen evolution1. If several cloned R genes were available, it would be possible to pyramid R genes2 in a crop, which might provide more durable resistance1. We describe a three-step method (MutRenSeq)-that combines chemical mutagenesis with exome capture and sequencing for rapid R gene cloning. We applied MutRenSeq to clone stem rust resistance genes Sr22 and Sr45 from hexaploid bread wheat. MutRenSeq can be applied to other commercially relevant crops and their relatives, including, for example, pea, bean, barley, oat, rye, rice and maize.
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Nature Biotech: News & Views - Plant immunity switched from bacteria to virus (2016)

Nature Biotech: News & Views - Plant immunity switched from bacteria to virus (2016) | Publications from The Sainsbury Laboratory | Scoop.it
Each year, staple crops around the world suffer massive losses in yield owing to the destructive effects of pathogens. Improving the disease resistance of crops by boosting their immunity has been a key objective of agricultural biotech ever since the discovery of plant immune receptors in the 1990s. Nucleotide-binding leucine-rich repeat (NLR) proteins, a family of intracellular immune receptors that recognize pathogen molecules, are promising targets for enhancing pathogen resistance. In a recent paper in Science, Kim et al.1 describe a clever twist on this approach in which the host target protein for the pathogen effector is engineered rather than the NLR protein itself.
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Nature: Class uncorrected errors as misconduct (2016)

Nature: Class uncorrected errors as misconduct (2016) | Publications from The Sainsbury Laboratory | Scoop.it
Post-publication peer review is becoming increasingly popular, but authors need more incentive to self-correct and amend the scientific record (see D. B. Allison et al. Nature 530, 27–29; 2016). We propose that failure by authors to correct their mistakes should be classified as scientific misconduct. This policy has already been implemented by our institute, and we encourage research institutions and funding bodies to follow suit (see go.nature.com/dgifft). The responsibility to correct errors lies mainly with the criticized authors. Snubbing criticism by not addressing it promptly runs counter to our fundamental ethos as scientists, and threatens to erode society's trust in the scientific community.
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MPMI: Colonization of barley by the broad-host hemibiotrophic pathogen Phytophthora palmivora uncovers a leaf development dependent involvement of MLO (2016)

MPMI: Colonization of barley by the broad-host hemibiotrophic pathogen Phytophthora palmivora uncovers a leaf development dependent involvement of MLO (2016) | Publications from The Sainsbury Laboratory | Scoop.it

The discovery of barley MLO demonstrated that filamentous pathogens rely on plant genes to achieve entry and lifecycle completion in barley leaves. Whilst having a dramatic effect on foliar pathogens, it is unclear whether overlapping or distinct mechanisms affect filamentous pathogen infection of roots. To remove the bias connected with using different pathogens to understand colonisation mechanisms in different tissues we have utilized the aggressive hemibiotrophic oomycete pathogen Phytophthora palmivora. P. palmivora colonises root as well as leaf tissues of barley (Hordeum vulgare). The infection is characterized by a transient biotrophy phase with formation of haustoria. Barley accessions varied in degree of susceptibility, with some accessions fully resistant to leaf infection. Notably, there was no overall correlation between degree of susceptibility in roots compared to leaves suggesting that variation in different genes influences host susceptibility above- and belowground. In addition, a developmental gradient influenced infection, with more extensive colonisation observed in mature leaf sectors. Only in young leaf tissues, the mlo5 mutation attenuates P. palmivora infection. The barley - P. palmivora interaction represents a simple system to identify and compare genetic components governing quantitative colonisation in diverse types of barley tissues.


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J Exp Bot: Characterization of a JAZ7 activation-tagged Arabidopsis mutant with increased susceptibility to the fungal pathogen Fusarium oxysporum

J Exp Bot: Characterization of a JAZ7 activation-tagged Arabidopsis mutant with increased susceptibility to the fungal pathogen Fusarium oxysporum | Publications from The Sainsbury Laboratory | Scoop.it
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In Arabidopsis, jasmonate (JA)-signaling plays a key role in mediating Fusarium oxysporum disease outcome. However, the roles of JASMONATE ZIM-domain (JAZ) proteins that repress JA-signaling have not been characterized in host resistance or susceptibility to this pathogen. Here, we found most JAZ genes are induced following F. oxysporum challenge, and screening T-DNA insertion lines in Arabidopsis JAZ family members identified a highly disease-susceptible JAZ7 mutant (jaz7-1D). This mutant exhibited constitutive JAZ7 expression and conferred increased JA-sensitivity, suggesting activation of JA-signaling. Unlike jaz7 loss-of-function alleles, jaz7-1D also had enhanced JA-responsive gene expression, altered development and increased susceptibility to the bacterial pathogen Pst DC3000 that also disrupts host JA-responses. We also demonstrate that JAZ7 interacts with transcription factors functioning as activators (MYC3, MYC4) or repressors (JAM1) of JA-signaling and contains a functional EAR repressor motif mediating transcriptional repression via the co-repressor TOPLESS (TPL). We propose through direct TPL recruitment, in wild-type plants JAZ7 functions as a repressor within the JA-response network and that in jaz7-1D plants, misregulated ectopic JAZ7 expression hyper-activates JA-signaling in part by disturbing finely-tuned COI1-JAZ-TPL-TF complexes.

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J Exp Bot: NB-LRR signaling induces translational repression of viral transcripts and the formation of RNA processing bodies through mechanisms differing from those activated by UV stress and RNAi ...

J Exp Bot: NB-LRR signaling induces translational repression of viral transcripts and the formation of RNA processing bodies through mechanisms differing from those activated by UV stress and RNAi ... | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

Plant NB-LRR proteins confer resistance to multiple pathogens, including viruses. Although the recognition of viruses by NB-LRR proteins is highly specific, previous studies have suggested that NB-LRR activation results in a response that targets all viruses in the infected cell. Using an inducible system to activate NB-LRR defenses, we find that NB-LRR signaling does not result in the degradation of viral transcripts, but rather prevents them from associating with ribosomes and translating their genetic material. This indicates that defense against viruses involves the repression of viral RNA translation. This repression is specific to viral transcripts and does not involve a global shutdown of host cell translation. As a consequence of the repression of viral RNA translation, NB-LRR responses induce a dramatic increase in the biogenesis of RNA processing bodies (PBs). We demonstrate that other pathways that induce translational repression, such as UV irradiation and RNAi, also induce PBs. However, by investigating the phosphorylation status of eIF2α and by using suppressors of RNAi we show that the mechanisms leading to PB induction by NB-LRR signaling are different from these stimuli, thus defining a distinct type of translational control and anti-viral mechanism in plants.

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PLoS Genetics: Adaptive Remodeling of the Bacterial Proteome by Specific Ribosomal Modification Regulates Pseudomonas Infection and Niche Colonisation (2016)

PLoS Genetics: Adaptive Remodeling of the Bacterial Proteome by Specific Ribosomal Modification Regulates  Pseudomonas  Infection and Niche Colonisation (2016) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

Post-transcriptional control of protein abundance is a highly important, underexplored regulatory process by which organisms respond to their environments. Here we describe an important and previously unidentified regulatory pathway involving the ribosomal modification protein RimK, its regulator proteins RimA and RimB, and the widespread bacterial second messenger cyclic-di-GMP (cdG). Disruption of rimK affects motility and surface attachment in pathogenic and commensal Pseudomonas species, with rimK deletion significantly compromising rhizosphere colonisation by the commensal soil bacterium P. fluorescens, and plant infection by the pathogens P. syringae and P. aeruginosa. RimK functions as an ATP-dependent glutamyl ligase, adding glutamate residues to the C-terminus of ribosomal protein RpsF and inducing specific effects on both ribosome protein complement and function. Deletion of rimK in P. fluorescens leads to markedly reduced levels of multiple ribosomal proteins, and also of the key translational regulator Hfq. In turn, reduced Hfq levels induce specific downstream proteomic changes, with significant increases in multiple ABC transporters, stress response proteins and non-ribosomal peptide synthetases seen for both ΔrimK and Δhfqmutants. The activity of RimK is itself controlled by interactions with RimA, RimB and cdG. We propose that control of RimK activity represents a novel regulatory mechanism that dynamically influences interactions between bacteria and their hosts; translating environmental pressures into dynamic ribosomal changes, and consequently to an adaptive remodeling of the bacterial proteome.

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Plant Methods: Meeting report: GARNet/OpenPlant CRISPR-Cas workshop (2016)

Plant Methods: Meeting report: GARNet/OpenPlant CRISPR-Cas workshop (2016) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

Targeted genome engineering has been described as a “game-changing technology” for fields as diverse as human genetics and plant biotechnology. One technique used for precise gene editing utilises the CRISPR-Cas system and is an effective method for genetic engineering in a wide variety of plants. However, many researchers remain unaware of both the technical challenges that emerge when using this technique or of its potential benefits. Therefore in September 2015, GARNet and OpenPlant organized a two-day workshop at the John Innes Centre that provided both background information and hands-on training for this important technology.

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BBA: Biochemical characterization of the tomato phosphatidylinositol-specific phospholipase C (PI-PLC) family and its role in plant immunity (2016)

BBA: Biochemical characterization of the tomato phosphatidylinositol-specific phospholipase C (PI-PLC) family and its role in plant immunity (2016) | Publications from The Sainsbury Laboratory | Scoop.it
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Highlights

Seven genes encoding PLCs form tomato were identified.

 

Recombinant tomato PLC proteins showed typical PLC activity.

Tomato PLC2, PLC4 and PLC5 showed distinct requirements for Ca2 + ions and the pH.

The activity of each tomato PLC enzyme is probably differentially regulated in vivo.

The response to flg22 and FLS2 endocytosis are supressed by inhibition of PLC activity.

Abstract

Plants possess effective mechanisms to quickly respond to biotic and abiotic stresses. The rapid activation of Phosphatidylinositol-specific Phospholipase C (PLC) enzymes occurs early after the stimulation of plant immune-receptors. Genomes of different plant species encode multiple PLC homologs belonging to one class, PLCζ. Here we determined whether all tomato homologs encode active enzymes and whether they can generate signals that are distinct from one another. We searched the recently completed tomato (Solanum lycopersicum) genome sequence and identified a total of seven PLCs. Recombinant proteins were produced for all tomato PLCs, except for SlPLC7. The purified proteins showed typical PLC activity, as different PLC substrates were hydrolysed to produce diacylglycerol. We studied SlPLC2, SlPLC4 and SlPLC5 enzymes in more detail and observed distinct requirements for Ca2 + ions and pH, for both their optimum activity and substrate preference. This indicates that each enzyme could be differentially and specifically regulated in vivo, leading to the generation of PLC homolog-specific signals in response to different stimuli. PLC overexpression and specific inhibition of PLC activity revealed that PLC is required for both specific effector- and more general “pattern”-triggered immunity. For the latter, we found that both the flagellin-triggered response and the internalization of the corresponding receptor, Flagellin Sensing 2 (FLS2) of Arabidopsis thaliana, is supressed by inhibition of PLC activity. Altogether, our data support an important role for PLC enzymes in plant defence signalling downstream of immune receptors.

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J Exp Bot: The Arabidopsis NADPH oxidases RbohD and RbohF display differential expression patterns and contributions during plant immunity (2016)

J Exp Bot: The Arabidopsis NADPH oxidases RbohD and RbohF display differential expression patterns and contributions during plant immunity (2016) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

Plant NADPH oxidases, also known as respiratory burst oxidase homologues (RBOHs), produce reactive oxygen species (ROS) that perform a wide range of functions. RbohD and RbohF, two of the 10 Rboh genes present in Arabidopsis, are pleiotropic and mediate diverse physiological processes including the response to pathogens. We hypothesized that the spatio-temporal control of RbohD and RbohF gene expression might be critical in determining their multiplicity of functions. Transgenic Arabidopsis plants with RbohD and RbohF promoter fusions to β-glucuronidase and Luciferase reporter genes were generated. Analysis of these plants revealed a differential expression pattern for RbohD and RbohF throughout plant development and during immune responses. RbohD and RbohF gene expression was differentially modulated by pathogen-associated molecular patterns. Histochemical stains and in vivoexpression analysis showed a correlation between the level of RbohD and RbohF promoter activity, H2O2 accumulation and the amount of cell death in response to the pathogenic bacterium Pseudomonas syringae pv. tomato DC3000 and the necrotrophic fungus Plectosphaerella cucumerina. A promoter-swap strategy revealed that the promoter region of RbohDwas required to drive production of ROS by this gene in response to pathogens. Moreover, RbohD promoter was activated during Arabidopsis interaction with a non-virulent P. cucumerina isolate, and susceptibility tests with the double mutant rbohD rbohF uncovered a new function for these oxidases in basal resistance. Altogether, our results suggest that differential spatio-temporal expression of the Rboh genes contributes to fine-tune RBOH/NADPH oxidase-dependent ROS production and signaling in Arabidopsis immunity.

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EMBO Reports: Attenuation of pattern recognition receptor signaling is mediated by a MAP kinase kinase kinase (2016)

EMBO Reports: Attenuation of pattern recognition receptor signaling is mediated by a MAP kinase kinase kinase (2016) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

Pattern recognition receptors (PRRs) play a key role in plant and animal innate immunity. PRR binding of their cognate ligand triggers a signaling network and activates an immune response. Activation of PRR signaling must be controlled prior to ligand binding to prevent spurious signaling and immune activation. Flagellin perception in Arabidopsis through FLAGELLIN‐SENSITIVE 2 (FLS2) induces the activation of mitogen‐activated protein kinases (MAPKs) and immunity. However, the precise molecular mechanism that connects activated FLS2 to downstream MAPK cascades remains unknown. Here, we report the identification of a differentially phosphorylated MAP kinase kinase kinase that also interacts with FLS2. Using targeted proteomics and functional analysis, we show that MKKK7 negatively regulates flagellin‐triggered signaling and basal immunity and this requires phosphorylation of MKKK7 on specific serine residues. MKKK7 attenuates MPK6 activity and defense gene expression. Moreover, MKKK7 suppresses the reactive oxygen species burst downstream of FLS2, suggesting that MKKK7‐mediated attenuation of FLS2 signaling occurs through direct modulation of the FLS2 complex.

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New Phyt: Avr4 promotes Cf-4 receptor-like protein association with the BAK1/SERK3 receptor-like kinase to initiate receptor endocytosis and plant immunity (2016)

New Phyt: Avr4 promotes Cf-4 receptor-like protein association with the BAK1/SERK3 receptor-like kinase to initiate receptor endocytosis and plant immunity (2016) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:
The first layer of plant immunity is activated by cell surface receptor-like kinases (RLKs) and proteins (RLPs) that detect infectious pathogens. Constitutive interaction with the SUPPRESSOR OF BIR1 (SOBIR1) RLK contributes to RLP stability and kinase activity. As RLK activation requires transphosphorylation with a second associated RLK, it remains elusive how RLPs initiate downstream signaling.We employed live-cell imaging, gene silencing and coimmunoprecipitation to investigate the requirement of associated kinases for functioning and ligand-induced subcellular trafficking of Cf RLPs that mediate immunity of tomato against Cladosporium fulvum.Our research shows that after elicitation with matching effector ligands Avr4 and Avr9, BRI1-ASSOCIATED KINASE 1/SOMATIC EMBRYOGENESIS RECEPTOR KINASE 3 (BAK1/SERK3) associates with Cf-4 and Cf-9. BAK1/SERK3 is required for the effector-triggered hypersensitive response and resistance of tomato against C. fulvum. Furthermore, Cf-4 interacts with SOBIR1 at the plasma membrane and is recruited to late endosomes upon Avr4 trigger, also depending on BAK1/SERK3.These observations indicate that RLP-mediated resistance and endocytosis require ligand-induced recruitment of BAK1/SERK3, reminiscent of BAK1/SERK3 interaction and subcellular fate of the FLAGELLIN SENSING 2 (FLS2) RLK. This reveals that diverse classes of cell surface immune receptors share common requirements for initiation of resistance and endocytosis.
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Nature Biotech: Accelerated cloning of a potato late blight–resistance gene using RenSeq and SMRT sequencing (2016)

Nature Biotech: Accelerated cloning of a potato late blight–resistance gene using RenSeq and SMRT sequencing (2016) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:
Global yields of potato and tomato crops have fallen owing to potato late blight disease, which is caused by Phytophthora infestans. Although most commercial potato varieties are susceptible to blight, many wild potato relatives show variation for resistance and are therefore a potential source of Resistance to P. infestans (Rpi) genes. Resistance breeding has exploited Rpi genes from closely related tuber-bearing potato relatives, but is laborious and slow1, 2, 3. Here we report that the wild, diploid non-tuber-bearing Solanum americanum harbors multiple Rpi genes. We combine resistance (R) gene sequence capture (RenSeq)4 with single-molecule real-time (SMRT) sequencing (SMRT RenSeq) to clone Rpi-amr3i. This technology should enable de novo assembly of complete nucleotide-binding, leucine-rich repeat receptor (NLR) genes, their regulatory elements and complex multi-NLR loci from uncharacterized germplasm. SMRT RenSeq can be applied to rapidly clone multiple R genes for engineering pathogen-resistant crops.
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Ecol & Evol: Molecular markers for tracking the origin and worldwide distribution of invasive strains of Puccinia striiformis (2016)

Ecol & Evol: Molecular markers for tracking the origin and worldwide distribution of invasive strains of Puccinia striiformis (2016) | Publications from The Sainsbury Laboratory | Scoop.it
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The Sainsbury Lab's insight:
Investigating the origin and dispersal pathways is instrumental to mitigate threats and economic and environmental consequences of invasive crop pathogens. In the case of Puccinia striiformis causing yellow rust on wheat, a number of economically important invasions have been reported, e.g., the spreading of two aggressive and high temperature adapted strains to three continents since 2000. The combination of sequence-characterized amplified region (SCAR) markers, which were developed from two specific AFLP fragments, differentiated the two invasive strains, PstS1 and PstS2 from all other P. striiformis strains investigated at a worldwide level. The application of the SCAR markers on 566 isolates showed that PstS1 was present in East Africa in the early 1980s and then detected in the Americas in 2000 and in Australia in 2002. PstS2 which evolved from PstS1 became widespread in the Middle East and Central Asia. In 2000, PstS2 was detected in Europe, where it never became prevalent. Additional SSR genotyping and virulence phenotyping revealed 10 and six variants, respectively, within PstS1 and PstS2, demonstrating the evolutionary potential of the pathogen. Overall, the results suggested East Africa as the most plausible origin of the two invasive strains. The SCAR markers developed in the present study provide a rapid, inexpensive, and efficient tool to track the distribution of P. striiformis invasive strains, PstS1 and PstS2.
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J. Proteomics: Large-scale identification of membrane proteins based on analysis of trypsin-protected transmembrane segments (2016)

J. Proteomics: Large-scale identification of membrane proteins based on analysis of trypsin-protected transmembrane segments (2016) | Publications from The Sainsbury Laboratory | Scoop.it
Integral membrane proteins are generally under-represented in routine proteomic analyses, mostly because of their relatively low abundance, hydrophobicity and lack of trypsin-cleavage sites. To increase the coverage of membrane proteomes, various strategies have been developed, targeting mostly the extra-membrane segments of membrane proteins. We focused our attention to the rather overlooked hydrophobic transmembrane segments. Such peptides can be isolated after carbonate stripping and protease “shaving” of membranes isolated by simple centrifugation procedure. The treated membranes with embedded hydrophobic peptides can then be solubilized in organic solvents, re-digested with CNBr, delipidated and subjected to LC-MS/MS analysis. We modified the original “hppK” method, and applied it for the analysis of human lymphoma cells. We identified 1224 proteins of which two-thirds were IMPs with 1-16 transmembrane segments. This method allowed us to identify 13 “missing proteins” - proteins with no previous evidence on protein level.
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NbCSPR underlies age-dependent immune responses to bacterial cold shock protein in Nicotiana benthamiana

NbCSPR underlies age-dependent immune responses to bacterial cold shock protein in Nicotiana benthamiana | Publications from The Sainsbury Laboratory | Scoop.it
Plants detect pathogens by surface-localized receptors. Few such receptors are known. The coreceptor BRI1-ASSOCIATED KINASE 1 (BAK1) is a frequent member of activated receptor complexes. The proteomics strategy described here uses BAK1 as molecular bait to identify potential receptors that are specifically activated by pathogen components. We demonstrate this approach by identifying Nicotiana benthamiana RECEPTOR-LIKE PROTEIN REQUIRED FOR CSP22 RESPONSIVENESS (NbCSPR). We show that NbCSPR is required for immune responses initiated by the bacterial cold shock protein, confers age-dependent immunity against bacteria, and restricts the transformation of N. benthamiana cells by Agrobacterium. Manipulation of this gene will provide new options for disease control and genetic transformation of crop species.
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Rakesh Yashroy's curator insight, March 15, 1:05 AM
Host pathogen interface is a vital part of inter-species strife @ https://en.wikipedia.org/wiki/Host-pathogen_interface
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BMC Research Notes: blastjs: a BLAST+ wrapper for Node.js (2016)

BMC Research Notes: blastjs: a BLAST+ wrapper for Node.js (2016) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

To cope with the ever-increasing amount of sequence data generated in the field of genomics, the demand for efficient and fast database searches that drive functional and structural annotation in both large- and small-scale genome projects is on the rise. The tools of the BLAST+ suite are the most widely employed bioinformatic method for these database searches. Recent trends in bioinformatics application development show an increasing number of JavaScript apps that are based on modern frameworks such as Node.js. Until now, there is no way of using database searches with the BLAST+ suite from a Node.js codebase.

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Kihyuck Choi's curator insight, March 18, 3:07 AM

To cope with the ever-increasing amount of sequence data generated in the field of genomics, the demand for efficient and fast database searches that drive functional and structural annotation in both large- and small-scale genome projects is on the rise. The tools of the BLAST+ suite are the most widely employed bioinformatic method for these database searches. Recent trends in bioinformatics application development show an increasing number of JavaScript apps that are based on modern frameworks such as Node.js. Until now, there is no way of using database searches with the BLAST+ suite from a Node.js codebase.

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BMC Biology: Comparative analysis of plant immune receptor architectures uncovers host proteins likely targeted by pathogens (2016)

BMC Biology: Comparative analysis of plant immune receptor architectures uncovers host proteins likely targeted by pathogens (2016) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

Plants deploy immune receptors to detect pathogen-derived molecules and initiate defense responses. Intracellular plant immune receptors called nucleotide-binding leucine-rich repeat (NLR) proteins contain a central nucleotide-binding (NB) domain followed by a series of leucine-rich repeats (LRRs), and are key initiators of plant defense responses. However, recent studies demonstrated that NLRs with non-canonical domain architectures play an important role in plant immunity. These composite immune receptors are thought to arise from fusions between NLRs and additional domains that serve as “baits” for the pathogen-derived effector proteins, thus enabling pathogen recognition. Several names have been proposed to describe these proteins, including “integrated decoys” and “integrated sensors”. We adopt and argue for “integrated domains” or NLR-IDs, which describes the product of the fusion without assigning a universal mode of action.

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PLoS One: Heterologous Expression Screens in Nicotiana benthamiana Identify a Candidate Effector of the Wheat Yellow Rust Pathogen that Associates with Processing Bodies (2016)

PLoS One: Heterologous Expression Screens in  Nicotiana benthamiana  Identify a Candidate Effector of the Wheat Yellow Rust Pathogen that Associates with Processing Bodies (2016) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

Rust fungal pathogens of wheat (Triticum spp.) affect crop yields worldwide. The molecular mechanisms underlying the virulence of these pathogens remain elusive, due to the limited availability of suitable molecular genetic research tools. Notably, the inability to perform high-throughput analyses of candidate virulence proteins (also known as effectors) impairs progress. We previously established a pipeline for the fast-forward screens of rust fungal candidate effectors in the model plant Nicotiana benthamiana. This pipeline involves selecting candidate effectors in silico and performing cell biology and protein-protein interaction assays in planta to gain insight into the putative functions of candidate effectors. In this study, we used this pipeline to identify and characterize sixteen candidate effectors from the wheat yellow rust fungal pathogen Puccinia striiformis f sp tritici. Nine candidate effectors targeted a specific plant subcellular compartment or protein complex, providing valuable information on their putative functions in plant cells. One candidate effector, PST02549, accumulated in processing bodies (P-bodies), protein complexes involved in mRNA decapping, degradation, and storage. PST02549 also associates with the P-body-resident ENHANCER OF mRNA DECAPPING PROTEIN 4 (EDC4) from N. benthamiana and wheat. We propose that P-bodies are a novel plant cell compartment targeted by pathogen effectors.

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bioRxiv: Cell re-entry assays do not support models of pathogen-independent translocation of AvrM and AVR3a effectors into plant cells (2016)

bioRxiv: Cell re-entry assays do not support models of pathogen-independent translocation of AvrM and AVR3a effectors into plant cells (2016) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

The cell re-entry assay is widely used to evaluate pathogen effector protein uptake into plant cells. The assay is based on the premise that effector proteins secreted out of a leaf cell would translocate back into the cytosol of the same cell via a yet unknown host-derived uptake mechanism. Here, we critically assess this assay by expressing domains of the effector proteins AvrM-A of Melampsora lini and AVR3a of Phytophthora infestans fused to a signal peptide and fluorescent proteins in Nicotiana benthamiana. We found that the secreted fusion proteins do not re-enter plant cells from the apoplast and that the assay is prone to false-positives. We therefore emit a cautionary note on the use of the cell re-entry assay for protein trafficking studies.

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The Pub Club's curator insight, February 1, 3:11 PM

From our friends at TSL...

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BMC Plant Biology: Altered glycosylation of exported proteins, including surface immune receptors, compromises calcium and downstream signaling responses to microbe-associated molecular patterns in...

BMC Plant Biology: Altered glycosylation of exported proteins, including surface immune receptors, compromises calcium and downstream signaling responses to microbe-associated molecular patterns in... | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

Calcium, as a second messenger, transduces extracellular signals into cellular reactions. A rise in cytosolic calcium concentration is one of the first plant responses after exposure to microbe-associated molecular patterns (MAMPs). We reported previously the isolation of Arabidopsis thaliana mutants with a “changed calcium elevation” (cce) response to flg22, a 22-amino-acid MAMP derived from bacterial flagellin.

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Frontiers: The poplar Rust-Induced Secreted Protein (RISP) inhibits the growth of the leaf rust pathogen Melampsora larici-populina and triggers cell culture alkalinisation (2016)

Frontiers: The poplar Rust-Induced Secreted Protein (RISP) inhibits the growth of the leaf rust pathogen Melampsora larici-populina and triggers cell culture alkalinisation (2016) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

Plant cells secrete a wide range of proteins in extracellular spaces in response to pathogen attack. The poplar Rust-Induced Secreted Protein (RISP) is a small cationic protein of unknown function that was identified as the most induced gene in poplar leaves during immune responses to the leaf rust pathogen Melampsora larici-populina, an obligate biotrophic parasite. Here, we combined in planta and in vitro molecular biology approaches to tackle the function of RISP. Using a RISP-mCherry fusion transiently expressed in Nicotiana benthamiana leaves, we demonstrated that RISP is secreted into the apoplast. A recombinant RISP specifically binds to M. larici-populina urediniospores and inhibits their germination. It also arrests the growth of the fungus in vitro and on poplar leaves. Interestingly, RISP also triggers poplar cell culture alkalinisation and is cleaved at the C-terminus by a plant-encoded mechanism. Altogether our results indicate that RISP is an antifungal protein that has the ability to trigger cellular responses.

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Jim Alfano's curator insight, January 27, 1:18 PM

Is it secreted when other types of pathogens attack? That is, is it a typical PR protein?

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PNAS: PP2A-3 interacts with ACR4 and regulates formative cell division in the Arabidopsis root (2016)

PNAS: PP2A-3 interacts with ACR4 and regulates formative cell division in the Arabidopsis root (2016) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

Plant growth and development are mediated through a wide range of proteins, including receptor kinases and phosphatases. The receptor kinase ARABIDOPSIS CRINKLY 4 (ACR4) is part of a mechanism controlling formative cell divisions in the Arabidopsis root. However, the regulation of ACR4 signaling and how it affects cell divisions remains completely unknown. We discovered that ACR4 phosphorylates the PROTEIN PHOSPHATASE 2A-3 (PP2A-3) catalytic subunit of the PP2A phosphatase holoenzyme and that PP2A dephosphorylates ACR4. These data exposed a tightly regulated point in the associated biochemical network regulating formative cell divisions in plant roots.

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eLife: An effector of the Irish potato famine pathogen antagonizes a host autophagy cargo receptor (2016)

eLife: An effector of the Irish potato famine pathogen antagonizes a host autophagy cargo receptor (2016) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

Plants use autophagy to safeguard against infectious diseases. However, how plant pathogens interfere with autophagy related processes is unknown. Here we show that PexRD54, an effector from the Irish potato famine pathogen Phytophthora infestans, binds host autophagy protein ATG8CL to stimulate autophagosome formation. PexRD54 depletes the autophagy cargo receptor Joka2 out of ATG8CL complexes and interferes with Joka2's positive effect on pathogen defense. Thus a plant pathogen effector has evolved to antagonize a host autophagy cargo receptor in order to counteract host defenses. - See more at: http://elifesciences.org/content/early/2016/01/14/eLife.10856#sthash.R6yA1fGD.dpuf

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