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New Phytologist: A novel Arabidopsis CHITIN ELICITOR RECEPTOR KINASE 1 (CERK1) mutant with enhanced pathogen-induced cell death and altered receptor processing (2014)

New Phytologist: A novel Arabidopsis CHITIN ELICITOR RECEPTOR KINASE 1 (CERK1) mutant with enhanced pathogen-induced cell death and altered receptor processing (2014) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:
Plants detect pathogens by sensing microbe-associated molecular patterns (MAMPs) through pattern recognition receptors. Pattern recognition receptor complexes also have roles in cell death control, but the underlying mechanisms are poorly understood. Here, we report isolation of cerk1-4, a novel mutant allele of the Arabidopsis chitin receptor CERK1 with enhanced defense responses.We identified cerk1-4 in a forward genetic screen with barley powdery mildew and consequently characterized it by pathogen assays, mutant crosses and analysis of defense pathways. CERK1 and CERK1-4 proteins were analyzed biochemically.The cerk1-4 mutation causes an amino acid exchange in the CERK1 ectodomain. Mutant plants maintain chitin signaling capacity but exhibit hyper-inducible salicylic acid concentrations and deregulated cell death upon pathogen challenge. In contrast to chitin signaling, the cerk1-4 phenotype does not require kinase activity and is conferred by the N-terminal part of the receptor. CERK1 undergoes ectodomain shedding, a well-known process in animal cell surface proteins. Wild-type plants contain the full-length CERK1 receptor protein as well as a soluble form of the CERK1 ectodomain, whereas cerk1-4 plants lack the N-terminal shedding product.Our work suggests that CERK1 may have a chitin-independent role in cell death control and is the first report of ectodomain shedding in plants.
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Plant Physiology: Efficient gene editing in tomato in the first generation using the CRISPR/Cas9 system (2014)

Plant Physiology: Efficient gene editing in tomato in the first generation using the CRISPR/Cas9 system (2014) | Publications from The Sainsbury Laboratory | Scoop.it
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The CRISPR/Cas9 system is highly efficient at generating targeted mutations in stable transgenic tomato plants, and homozygous deletions of a desired size can be created in the first generation.

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J Exp Bot: Expression patterns of FLAGELLIN SENSING 2 map to bacterial entry sites in plant shoots and roots (2014)

J Exp Bot: Expression patterns of FLAGELLIN SENSING 2 map to bacterial entry sites in plant shoots and roots (2014) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

Pathogens can colonize all plant organs and tissues. To prevent this, each cell must be capable of autonomously triggering defence. Therefore, it is generally assumed that primary sensors of the immune system are constitutively present. One major primary sensor against bacterial infection is the FLAGELLIN SENSING 2 (FLS2) pattern recognition receptor (PRR). To gain insights into its expression pattern, the FLS2 promoter activity in β-glucuronidase (GUS) reporter lines was monitored. The data show that pFLS2::GUS activity is highest in cells and tissues vulnerable to bacterial entry and colonization, such as stomata, hydathodes, and lateral roots. GUS activity is also high in the vasculature and, by monitoring Ca2+responses in the vasculature, it was found that this tissue contributes to flg22-induced Ca2+ burst. The FLS2 promoter is also regulated in a tissue- and cell type-specific manner and is responsive to hormones, damage, and biotic stresses. This results in stimulus-dependent expansion of the FLS2 expression domain. In summary, a tissue- and cell type-specific map of FLS2 expression has been created correlating with prominent entry sites and target tissues of plant bacterial pathogens.

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BMC Genomics: Reference-free SNP detection: dealing with the data deluge (2014)

BMC Genomics: Reference-free SNP detection: dealing with the data deluge (2014) | Publications from The Sainsbury Laboratory | Scoop.it
Reference-free SNP detection, that is identifying SNPs between samples directly from comparison of primary sequencing data with other primary sequencing data and not to a pre-assembled reference genome is an emergent and potentially disruptive technology that is beginning to open up new vistas in variant identification that reveals new applications in non-model organisms and metagenomics. The modern, effcient data structures these tools use enables researchers with a reference sequence to sample many more individuals with lower computing storage and processing overhead. In this article we will discuss the technologies and tools implementing reference-free SNP detection and the potential impact on studies of genetic variation in model and non-model organisms, metagenomics and personal genomics and medicine.
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Bioinformatics: The GOBLET Training Portal: A Global Repository of Bioinformatics Training Materials, Courses and Trainers (2014)

Bioinformatics: The GOBLET Training Portal: A Global Repository of Bioinformatics Training Materials, Courses and Trainers (2014) | Publications from The Sainsbury Laboratory | Scoop.it
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Rapid technological advances have led to an explosion of biomedical data in recent years. The pace of change has inspired new, collaborative approaches for sharing materials and resources to help train life scientists both in the use of cutting-edge bioinformatics tools and databases, and in how to analyse and interpret large datasets. A prototype platform for sharing such training resources was recently created by the Bioinformatics Training Network (BTN). Building on this work, we have created a centralised portal for sharing training materials and courses, including a catalogue of trainers and course organisers, and an announcement service for training events. For course organisers, the portal provides opportunities to promote their training events; for trainers, the portal offers an environment for sharing materials, for gaining visibility for their work and promoting their skills; for trainees, it offers a convenient one-stop shop for finding suitable training resources and identifying relevant training events and activities locally and world-wide.

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EMBO Journal: Negative control of BAK1 by protein phosphatase 2A during plant innate immunity (2014)

EMBO Journal: Negative control of BAK1 by protein phosphatase 2A during plant innate immunity (2014) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

Recognition of pathogen‐associated molecular patterns (PAMPs) by surface‐localized pattern‐recognition receptors (PRRs) activates plant innate immunity, mainly through activation of numerous protein kinases. Appropriate induction of immune responses must be tightly regulated, as many of the kinases involved have an intrinsic high activity and are also regulated by other external and endogenous stimuli. Previous evidences suggest that PAMP‐triggered immunity (PTI) is under constant negative regulation by protein phosphatases but the underlying molecular mechanisms remain unknown. Here, we show that protein Ser/Thr phosphatase type 2A (PP2A) controls the activation of PRR complexes by modulating the phosphostatus of the co‐receptor and positive regulator BAK1. A potential PP2A holoenzyme composed of the subunits A1, C4, and B’η/ζ inhibits immune responses triggered by several PAMPs and anti‐bacterial immunity. PP2A constitutively associates with BAK1 in planta. Impairment in this PP2A‐based regulation leads to increased steady‐state BAK1 phosphorylation, which can poise enhanced immune responses. This work identifies PP2A as an important negative regulator of plant innate immunity that controls BAK1 activation in surface‐localized immune receptor complexes.

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Plant Cell: The Arabidopsis Malectin-Like Leucine-Rich Repeat Receptor-Like Kinase IOS1 Associates with the Pattern Recognition Receptors FLS2 and EFR and Is Critical for Priming of Pattern-Trigger...

Plant Cell: The Arabidopsis Malectin-Like Leucine-Rich Repeat Receptor-Like Kinase IOS1 Associates with the Pattern Recognition Receptors FLS2 and EFR and Is Critical for Priming of Pattern-Trigger... | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

Plasma membrane-localized pattern recognition receptors such as FLAGELLIN SENSING2 (FLS2) and EF-TU RECEPTOR (EFR) recognize microbe-associated molecular patterns (MAMPs) to activate the first layer of plant immunity termed pattern-triggered immunity (PTI). A reverse genetics approach with genes responsive to the priming agent β-aminobutyric acid (BABA) revealed IMPAIRED OOMYCETE SUSCEPTIBILITY1 (IOS1) as a critical PTI player. Arabidopsis thaliana ios1 mutants were hypersusceptible to Pseudomonas syringae bacteria. Accordingly, ios1 mutants demonstrated defective PTI responses, notably delayed upregulation of PTI marker genes, lower callose deposition, and mitogen-activated protein kinase activities upon bacterial infection or MAMP treatment. Moreover, Arabidopsis lines overexpressing IOS1 were more resistant to P. syringae and demonstrated a primed PTI response. In vitro pull-down, bimolecular fluorescence complementation, coimmunoprecipitation, and mass spectrometry analyses supported the existence of complexes between the membrane-localized IOS1 and FLS2 and EFR. IOS1 also associated with BRASSINOSTEROID INSENSITIVE1-ASSOCIATED KINASE1 (BAK1) in a ligand-independent manner and positively regulated FLS2/BAK1 complex formation uponMAMP treatment. Finally, ios1 mutants were defective in BABA-induced resistance and priming. This work reveals IOS1 as a regulatory protein of FLS2- and EFR-mediated signaling that primes PTI activation upon bacterial elicitation.

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New Phytologist: Gate control: guard cell regulation by microbial stress (2014)

New Phytologist: Gate control: guard cell regulation by microbial stress (2014) | Publications from The Sainsbury Laboratory | Scoop.it
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Terrestrial plants rely on stomata, small pores in the leaf surface, for photosynthetic gas exchange and transpiration of water. The stomata, formed by a pair of guard cells, dynamically increase and decrease their volume to control the pore size in response to environmental cues. Stresses can trigger similar or opposing movements: for example, drought induces closure of stomata, whereas many pathogens exploit stomata and cause them to open to facilitate entry into plant tissues. The latter is an active process as stomatal closure is part of the plant's immune response. Stomatal research has contributed much to clarify the signalling pathways of abiotic stress, but guard cell signalling in response to microbes is a relatively new area of research. In this article, we discuss present knowledge of stomatal regulation in response to microbes and highlight common points of convergence, and differences, compared to stomatal regulation by abiotic stresses. We also expand on the mechanisms by which pathogens manipulate these processes to promote disease, for example by delivering effectors to inhibit closure or trigger opening of stomata. The study of pathogen effectors in stomatal manipulation will aid our understanding of guard cell signalling.

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Trends in Immunology: Plant pattern-recognition receptors (2014)

Trends in Immunology: Plant pattern-recognition receptors (2014) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:
Plant PRRs are surface-localized receptor kinases or receptor-like proteins.Plant PRRs recognize a wide range of microbe- or plant-derived molecules.Known plant PAMP/PRR pairs illustrate distinct molecular-recognition mechanisms.PRRs can be used to engineer broad-spectrum disease resistance in crop plants.

 

Plants are constantly exposed to would-be pathogens in their immediate environment. Yet, despite relying on innate immunity only, plants are resistant to most microbes. They employ pattern-recognition receptors (PRRs) for sensitive and rapid detection of the potential danger caused by microbes and pests. Plant PRRs are either surface-localized receptor kinases (RKs) or receptor-like proteins (RLPs) containing various ligand-binding ectodomains that perceive pathogen-associated molecular patterns (PAMPs) or damage-associated molecular patterns (DAMPs). In this review, I summarize our current knowledge of plant PRRs and their ligands, illustrating the multiple molecular strategies employed by plant PRRs to activate innate immune signaling to survive.

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Science: Ancient hybridizations among the ancestral genomes of bread wheat (2014)

Science: Ancient hybridizations among the ancestral genomes of bread wheat (2014) | Publications from The Sainsbury Laboratory | Scoop.it
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The allohexaploid bread wheat genome consists of three closely related subgenomes (A, B, and D), but a clear understanding of their phylogenetic history has been lacking. We used genome assemblies of bread wheat and five diploid relatives to analyze genome-wide samples of gene trees, as well as to estimate evolutionary relatedness and divergence times. We show that the A and B genomes diverged from a common ancestor ~7 million years ago and that these genomes gave rise to the D genome through homoploid hybrid speciation 1 to 2 million years later. Our findings imply that the present-day bread wheat genome is a product of multiple rounds of hybrid speciation (homoploid and polyploid) and lay the foundation for a new framework for understanding the wheat genome as a multilevel phylogenetic mosaic.

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Plant Physiology: The plant membrane-associated REM1.3 remorin accumulates in discrete perihaustorial domains and enhances susceptibility to Phytophthora infestans (2014)

Plant Physiology: The plant membrane-associated REM1.3 remorin accumulates in discrete perihaustorial domains and enhances susceptibility to Phytophthora infestans (2014) | Publications from The Sainsbury Laboratory | Scoop.it

Filamentous pathogens such as the oomycete Phytophthora infestans infect plants by developing specialized structures termed haustoria inside the host cells. Haustoria are thought to enable secretion of effector proteins into the plant cells. Haustorium biogenesis is therefore critical for pathogen accommodation in the host tissue. Haustoria are enveloped by a specialized host-derived membrane, the extrahaustorial membrane (EHM), which is distinct from the plant plasma membrane. The mechanisms underlying the biogenesis of the EHM are unknown. Remarkably, several plasma membrane localised proteins are excluded from the EHM but the remorin REM1.3 accumulates around P. infestans haustoria. Here, we used overexpression, co-localization with reporter proteins, and super-resolution microscopy in cells infected by P. infestans to reveal discrete EHM domains labelled by REM1.3 and P. infestans effector AVRblb2. Moreover, SYT1 synaptotagmin, another previously identified perihaustorial protein, localized to subdomains which are mainly not labelled by REM1.3 and AVRblb2. Functional characterization of REM1.3 revealed that it is a susceptibility factor that promotes infection by P. infestans. This activity, and REM1.3 recruitment to the EHM, require REM1.3 membrane binding domain. Our results implicate REM1.3 membrane micro-domains in plant susceptibility to an oomycete pathogen.


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Jean-Michel Ané's curator insight, May 14, 1:17 PM

I know that it is not a symbiont but... some people will guess why I am scooping this :-)

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BMC Genomics: EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics (2014)

BMC Genomics: EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics (2014) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

EXpression Profiling through Randomly Sheared cDNA tag Sequencing (EXPRSS) employs adaptive focused acoustics to randomly shear cDNA and generate sequence tags at a relatively defined position (~150-200 bp) from the 3' end of each mRNA. EXPRSS is a strand specific and restriction enzyme independent tag sequencing method that does not require cDNA length-based data transformations, reveals alternative polyadenylation, polyadenylated antisense transcripts and is highly reproducible. It is high-throughput, cost-effective using barcoded multiplexing, avoids the biases of existing SAGE and derivative methods and can reveal polyadenylation position from paired-end sequencing. Implementation of the EXPRSS method was verified through comparative analysis of expression data generated from EXPRSS, NlaIII-DGE and Affymetrix microarray and through qPCR quantification of selected genes. Unlike array-based methods, it can be applied to genomes for which high-quality reference sequences are unavailable.

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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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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, 12:02 AM

Good overview for students - very accessible and interesting!

Freddy Monteiro's comment, April 25, 1:21 AM
This is a great source of teaching materials for potato late blight. Congrats on the work behind it.
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Cell Host & Microbe: Convergent Targeting of a Common Host Protein-Network by Pathogen Effectors from Three Kingdoms of Life (2014)

Cell Host & Microbe: Convergent Targeting of a Common Host Protein-Network by Pathogen Effectors from Three Kingdoms of Life (2014) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

Highlights

 

 - Powdery mildew fungus G. orontii virulence effectors and their host-interactors identified

 - Integrated network map reveals interspecies effector convergence onto shared host proteins

 - Mutants of convergent effector-targeted host proteins display altered infection phenotypes

 - Host genes under balancing selection encode indirect targets of pathogen effectors

 

Summary

While conceptual principles governing plant immunity are becoming clear, its systems-level organization and the evolutionary dynamic of the host-pathogen interface are still obscure. We generated a systematic protein-protein interaction network of virulence effectors from the ascomycete pathogen Golovinomyces orontii and Arabidopsis thaliana host proteins. We combined this data set with corresponding data for the eubacterial pathogen Pseudomonas syringae and the oomycete pathogen Hyaloperonospora arabidopsidis. The resulting network identifies host proteins onto which intraspecies and interspecies pathogen effectors converge. Phenotyping of 124 Arabidopsis effector-interactor mutants revealed a correlation between intraspecies and interspecies convergence and several altered immune response phenotypes. Several effectors and the most heavily targeted host protein colocalized in subnuclear foci. Products of adaptively selected Arabidopsis genes are enriched for interactions with effector targets. Our data suggest the existence of a molecular host-pathogen interface that is conserved across Arabidopsis accessions, while evolutionary adaptation occurs in the immediate network neighborhood of effector targets.

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PLOS ONE: Variation in Capsidiol Sensitivity between Phytophthora infestans and Phytophthora capsici Is Consistent with Their Host Range (2014)

PLOS ONE: Variation in Capsidiol Sensitivity between Phytophthora infestans and Phytophthora capsici Is Consistent with Their Host Range (2014) | Publications from The Sainsbury Laboratory | Scoop.it
PLOS ONE: an inclusive, peer-reviewed, open-access resource from the PUBLIC LIBRARY OF SCIENCE. Reports of well-performed scientific studies from all disciplines freely available to the whole world.
The Sainsbury Lab's insight:

Plants protect themselves against a variety of invading pathogenic organisms via sophisticated defence mechanisms. These responses include deployment of specialized antimicrobial compounds, such as phytoalexins, that rapidly accumulate at pathogen infection sites. However, the extent to which these compounds contribute to species-level resistance and their spectrum of action remain poorly understood. Capsidiol, a defense related phytoalexin, is produced by several solanaceous plants including pepper and tobacco during microbial attack. Interestingly, capsidiol differentially affects growth and germination of the oomycete pathogensPhytophthora infestans and Phytophthora capsici, although the underlying molecular mechanisms remain unknown. In this study we revisited the differential effect of capsidiol on P. infestans and P. capsici, using highly pure capsidiol preparations obtained from yeast engineered to express the capsidiol biosynthetic pathway. Taking advantage of transgenicPhytophthora strains expressing fluorescent markers, we developed a fluorescence-based method to determine the differential effect of capsidiol on Phytophtora growth. Using these assays, we confirm major differences in capsidiol sensitivity between P. infestans and P. capsici and demonstrate that capsidiol alters the growth behaviour of both Phytophthoraspecies. Finally, we report intraspecific variation within P. infestans isolates towards capsidiol tolerance pointing to an arms race between the plant and the pathogens in deployment of defence related phytoalexins.

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Frontiers: Effector proteins of rust fungi (2014)

Frontiers: Effector proteins of rust fungi (2014) | Publications from The Sainsbury Laboratory | Scoop.it
Rust fungi include many species that are devastating crop pathogens. To develop resistant plants, a better understanding of rust virulence factors, or effector proteins, is needed. Thus far, only six rust effector proteins have been described: AvrP123, AvrP4, AvrL567, AvrM, RTP1 and PGTAUSPE-10-1. Although some are well established model proteins used to investigate mechanisms of immune receptor activation (avirulence activities) or entry into plant cells, how they work inside host tissues to promote fungal growth remains unknown. The genome sequences of four rust fungi (two Melampsoraceae and two Pucciniaceae) have been analyzed so far. Genome-wide analyses of these species, as well as transcriptomics performed on a broader range of rust fungi, revealed hundreds of small secreted proteins considered as rust candidate secreted effector proteins (CSEPs). The rust community now needs high-throughput approaches (effectoromics) to accelerate effector discovery/characterization and to better understand how they function in planta. However, this task is challenging due to the non-amenability of rust pathosystems (obligate biotrophs infecting crop plants) to traditional molecular genetic approaches mainly due to difficulties in culturing these species in vitro. The use of heterologous approaches should be promoted in the future.
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Molecular Plant Pathology: The Top 10 oomycete pathogens in molecular plant pathology (2014)

Molecular Plant Pathology: The Top 10 oomycete pathogens in molecular plant pathology (2014) | Publications from The Sainsbury Laboratory | Scoop.it

Oomycetes form a deep lineage of eukaryotic organisms that includes a large number of plant pathogens that threaten natural and managed ecosystems. We undertook a survey to query the community for their ranking of plant pathogenic oomycete species based on scientific and economic importance. In total, we received 263 votes from 62 scientists in 15 countries for a total of 33 species. The Top 10 species and their ranking are: (1) Phytophthora infestans; (2, tied) Hyaloperonospora arabidopsidis; (2, tied) Phytophthora ramorum; (4) Phytophthora sojae; (5) Phytophthora capsici; (6) Plasmopara viticola; (7) Phytophthora cinnamomi; (8, tied) Phytophthora parasitica; (8, tied) Pythium ultimum; and (10) Albugo candida. The article provides an introduction to these 10 taxa and a snapshot of current research. We hope that the list will serve as a benchmark for future trends in oomycete research.


See also [link below]:

 

Top 10 plant-parasitic nematodes in molecular plant pathology
Top 10 plant viruses in molecular plant pathology
Top 10 plant pathogenic bacteria in molecular plant pathology
The Top 10 fungal pathogens in molecular plant pathology

 

http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1364-3703/homepage/free_poster.htm


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Molecular Breeding: Hypersensitive response to Potato virus Y in potato cultivar Sárpo Mira is conferred by the Ny-Smira gene located on the long arm of chromosome IX (2014)

Molecular Breeding: Hypersensitive response to Potato virus Y in potato cultivar Sárpo Mira is conferred by the Ny-Smira gene located on the long arm of chromosome IX (2014) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

Potato virus Y (PVY, Potyvirus) is the fifth most important plant virus worldwide in terms of economic and scientific impact. It infects members of the family Solanaceae and causes losses in potato, tomato, tobacco, pepper and petunia production. In potato and its wild relatives, two types of resistance genes against PVY have been identified. While Ry genes confer symptomless extreme resistance, Ny genes cause a hypersensitive response visible as local necrosis that may also be able to prevent the virus from spreading under certain environmental conditions. The potato cultivar Sárpo Mira originates from Hungary and is highly resistant to PVY, although the source of this resistance remains unknown. We show that cv. Sárpo Mira reacts with a hypersensitive response leading to necrosis after PVYNTN infection in detached leaf, whole plant and grafting assays. The hypersensitivity to PVYNTN segregated amongst 140 individuals of tetraploid progeny of cvs. Sárpo Mira × Maris Piper in a 1:1 ratio, indicating that it was conferred by a single, dominant gene in simplex. Moreover, we identified five DNA markers linked to this trait and located the underlying locus (Ny-Smira) to the long arm of potato chromosome IX. This position corresponds to the location of the Ry chc and Ny-1 genes for PVY resistance. A simple PCR marker, located 1 cM from the Ny-Smira gene, can be recommended for selection of PVY-resistant progeny of cv. Sárpo Mira.

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New Phytologist: A novel Arabidopsis CHITIN ELICITOR RECEPTOR KINASE 1 (CERK1) mutant with enhanced pathogen-induced cell death and altered receptor processing (2014)

New Phytologist: A novel Arabidopsis CHITIN ELICITOR RECEPTOR KINASE 1 (CERK1) mutant with enhanced pathogen-induced cell death and altered receptor processing (2014) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:
Plants detect pathogens by sensing microbe-associated molecular patterns (MAMPs) through pattern recognition receptors. Pattern recognition receptor complexes also have roles in cell death control, but the underlying mechanisms are poorly understood. Here, we report isolation of cerk1-4, a novel mutant allele of the Arabidopsis chitin receptor CERK1 with enhanced defense responses.We identified cerk1-4 in a forward genetic screen with barley powdery mildew and consequently characterized it by pathogen assays, mutant crosses and analysis of defense pathways. CERK1 and CERK1-4 proteins were analyzed biochemically.The cerk1-4 mutation causes an amino acid exchange in the CERK1 ectodomain. Mutant plants maintain chitin signaling capacity but exhibit hyper-inducible salicylic acid concentrations and deregulated cell death upon pathogen challenge. In contrast to chitin signaling, the cerk1-4 phenotype does not require kinase activity and is conferred by the N-terminal part of the receptor. CERK1 undergoes ectodomain shedding, a well-known process in animal cell surface proteins. Wild-type plants contain the full-length CERK1 receptor protein as well as a soluble form of the CERK1 ectodomain, whereas cerk1-4 plants lack the N-terminal shedding product.Our work suggests that CERK1 may have a chitin-independent role in cell death control and is the first report of ectodomain shedding in plants.
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PLoS One: Comprehensive Transcriptome Analysis Unravels the Existence of Crucial Genes Regulating Primary Metabolism during Adventitious Root Formation in Petunia hybrida (2014)

PLoS One: Comprehensive Transcriptome Analysis Unravels the Existence of Crucial Genes Regulating Primary Metabolism during Adventitious Root Formation in Petunia hybrida (2014) | Publications from The Sainsbury Laboratory | Scoop.it
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To identify specific genes determining the initiation and formation of adventitious roots (AR), a microarray-based transcriptome analysis in the stem base of the cuttings of Petunia hybrida (line W115) was conducted. A microarray carrying 24,816 unique, non-redundant annotated sequences was hybridized to probes derived from different stages of AR formation. After exclusion of wound-responsive and root-regulated genes, 1,354 of them were identified which were significantly and specifically induced during various phases of AR formation. Based on a recent physiological model distinguishing three metabolic phases in AR formation, the present paper focuses on the response of genes related to particular metabolic pathways. Key genes involved in primary carbohydrate metabolism such as those mediating apoplastic sucrose unloading were induced at the early sink establishment phase of AR formation. Transcriptome changes also pointed to a possible role of trehalose metabolism and SnRK1 (sucrose non-fermenting 1- related protein kinase) in sugar sensing during this early step of AR formation. Symplastic sucrose unloading and nucleotide biosynthesis were the major processes induced during the later recovery and maintenance phases. Moreover, transcripts involved in peroxisomal beta-oxidation were up-regulated during different phases of AR formation. In addition to metabolic pathways, the analysis revealed the activation of cell division at the two later phases and in particular the induction of G1-specific genes in the maintenance phase. Furthermore, results point towards a specific demand for certain mineral nutrients starting in the recovery phase.

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Journal of Proteome Research: Identification of related peptides through the analysis of fragment ion mass shifts (2014)

Journal of Proteome Research: Identification of related peptides through the analysis of fragment ion mass shifts (2014) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

Mass spectrometry (MS) has become the method of choice to identify and quantify proteins, typically by fragmenting peptides and inferring protein identification by reference to sequence databases. Well-established programs have largely solved the problem of identifying peptides in complex mixtures. However, to prevent the search space from becoming prohibitively large most search engines need a list of expected modifications. Therefore, unexpected modifications limit both the identification of proteins and peptide-based quantification. We developed Mass Spectrometry-Peak Shift Analysis (MS-PSA) to rapidly identify related spectra in large datasets without reference to databases or specified modifications. Peptide identifications from established tools, such as MASCOT or SEQUEST, may be propagated onto MS-PSA results. Modification of a peptide alters the mass of the precursor ion and some of the fragmentation ions. MS-PSA identifies characteristic fragmentation masses from MS/MS spectra. Related spectra are identified by pattern matching of unchanged and mass-shifted fragment ions. We illustrate the use of MS-PSA with simple and complex mixtures with both high and low mass accuracy datasets. MS-PSA is not limited to the analysis of peptides but can be used for the identification of related groups of spectra in any set of fragmentation patterns.

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Journal of Cell Biology: Identification of unique SUN-interacting nuclear envelope proteins with diverse functions in plants (2014)

Journal of Cell Biology: Identification of unique SUN-interacting nuclear envelope proteins with diverse functions in plants (2014) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

Although a plethora of nuclear envelope (NE) transmembrane proteins (NETs) have been identified in opisthokonts, plant NETs are largely unknown. The only known NET homologues in plants are Sad1/UNC-84 (SUN) proteins, which bind Klarsicht/ANC-1/Syne-1 homology (KASH) proteins. Therefore, de novo identification of plant NETs is necessary. Based on similarities between opisthokont KASH proteins and the only known plant KASH proteins, WPP domain–interacting proteins, we used a computational method to identify the KASH subset of plant NETs. Ten potential plant KASH protein families were identified, and five candidates from four of these families were verified for their NE localization, depending on SUN domain interaction. Of those, Arabidopsis thaliana SINE1 is involved in actin-dependent nuclear positioning in guard cells, whereas its paralogue SINE2 contributes to innate immunity against an oomycete pathogen. This study dramatically expands our knowledge of plant KASH proteins and suggests that plants and opisthokonts have recruited different KASH proteins to perform NE regulatory functions.

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BMC Plant Biology: Defining the full tomato NB-LRR resistance gene repertoire using genomic and cDNA RenSeq (2014)

BMC Plant Biology: Defining the full tomato NB-LRR resistance gene repertoire using genomic and cDNA RenSeq (2014) | Publications from The Sainsbury Laboratory | Scoop.it
The Sainsbury Lab's insight:

The availability of draft crop plant genomes allows the prediction of the full complement of genes that encode NB-LRR resistance gene homologs, enabling a more targeted breeding for disease resistance. Recently, we developed the RenSeq method to reannotate the full NB-LRR gene complement in potato and to identify novel sequences that were not picked up by the automated gene prediction software. Here, we established RenSeq on the reference genome of tomato (Solanum lycopersicum) Heinz 1706, using 260 previously identified NB-LRR genes in an updated Solanaceae RenSeq bait library.

Result: Using 250-bp MiSeq reads after RenSeq on genomic DNA of Heinz 1706, we identified 105 novel NB-LRR sequences. Reannotation included the splitting of gene models, combination of partial genes to a longer sequence and closing of assembly gaps. Within the draft S. pimpinellifolium LA1589 genome, RenSeq enabled the annotation of 355 NB-LRR genes. The majority of these are however fragmented, with 5[prime]- and 3[prime]-end located on the edges of separate contigs. Phylogenetic analyses show a high conservation of all NB-LRR classes between Heinz 1706, LA1589 and the potato clone DM, suggesting that all sub-families were already present in the last common ancestor. A phylogenetic comparison to the Arabidopsis thaliana NB-LRR complement verifies the high conservation of the more ancient CCRPW8-type NB-LRRs. Use of RenSeq on cDNA from uninfected and late blight-infected tomato leaves allows the avoidance of sequence analysis of non-expressed paralogues.

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Mol Cell: Plant PRRs and the Activation of Innate Immune Signaling (2014)

Mol Cell: Plant PRRs and the Activation of Innate Immune Signaling (2014) | Publications from The Sainsbury Laboratory | Scoop.it

Despite being sessile organisms constantly exposed to potential pathogens and pests, plants are surprisingly resilient to infections. Plants can detect invaders via the recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs). Plant PRRs are surface-localized receptor-like kinases, which comprise a ligand-binding ectodomain and an intracellular kinase domain, or receptor-like proteins, which do not exhibit any known intracellular signaling domain. In this review, we summarize recent discoveries that shed light on the molecular mechanisms underlying ligand perception and subsequent activation of plant PRRs. Notably, plant PRRs appear as central components of multiprotein complexes at the plasma membrane that contain additional transmembrane and cytosolic kinases required for the initiation and specificity of immune signaling. PRR complexes are under tight control by protein phosphatases, E3 ligases, and other regulatory proteins, illustrating the exquisite and complex regulation of these molecular machines whose proper activation underlines a crucial layer of plant immunity.


Via Kamoun Lab @ TSL
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Rescooped by The Sainsbury Lab from Plant Pathogenomics
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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.


Via Kamoun Lab @ TSL
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Niklaus Grunwald's curator insight, April 26, 9:46 AM

An example of crowdsourcing genomics ...