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Rescooped by Nicolas Denancé from TAL effector science
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Mol. Plant: Characterization and DNA-Binding Specificities of Ralstonia TAL-like Effectors (2013)

Mol. Plant: Characterization and DNA-Binding Specificities of Ralstonia TAL-like Effectors (2013) | Effectors and Plant Immunity | Scoop.it

Ralstonia solanacearum TALE-like proteins (RTLs) exhibit similar structural features to TALEs, including a central DNA-binding domain composed of 35 amino acid-long repeats. Here, we characterize the RTLs and show that they localize in the plant cell nucleus, mediate DNA binding, and function as transcriptional activators. RTLs have a unique DNA-binding architecture and are enriched in repeat variable di-residues (RVDs), which determine repeat DNA-binding specificities. We determined the DNA-binding specificities for the RVD sequences ND, HN, NP, and NT. The RVD ND mediates highly specific interactions with C nucleotides, HN interacts specifically with A and G nucleotides, and NP specifically binds to C, A, and G nucleotides. Moreover, we developed a highly efficient repeat assembly approach for engineering RTL effectors. Taken together, our data demonstrate that RTLs are unique DNA-targeting modules that are excellent alternatives to be tailored to bind to user-selected DNA sequences for targeted genomic and epigenomic modifications. These findings will facilitate research concerning RTL molecular biology and RTL roles in the pathogenicity of Ralstonia spp.

 

Lixin Li, Ahmed Atef, Agnieszka Piatek, Zahir Ali, Marek Piatek, Mustapha Aouida, Altan Sharakou, Ali Mahjoub, Guangchao Wang, Suhail Khan, Nina V. Fedoroff, Jian-Kang Zhu and Magdy Mahfouz


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dromius's comment, March 24, 2013 9:01 AM
THIS MANUSCRIPT HAS BEEN RETRACTED BY THE AUTHORS!
Nicolas Denancé's comment, March 24, 2013 10:30 AM
Thanks Dromius for the info. It is always bad news when scientists retract their published work. Is it because they absolutely wanted to be the first to publish data on Ralstonia solanacearum TAL effectors so that they did not check/analyzed their results enough? Sometimes I feel sad because of this publication race. Is it really good for Science?
dromius's comment, March 24, 2013 11:36 AM
There are many reasons/motivation for rushing into publication. It will be interesting to see what follows. The webpage of the journal is not clear about that. It can be an amended version or a retraction note or a new paper...I appreciate that they retracted it rather quickly, as this prevents it from being archived in the heads of people and in reviews.
Effectors and Plant Immunity
Strategies of plant defense and microbe attacks
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Frontiers | Plant Innate Immunity Multicomponent Model | Plant Genetics and Genomics

Frontiers | Plant Innate Immunity Multicomponent Model | Plant Genetics and Genomics | Effectors and Plant Immunity | Scoop.it
Our understanding of plant–pathogen interactions is making rapid advances in order to address issues of global importance such as improving agricultural productivity and sustainable food security. Innate immunity has evolved in plants, resulting in a wide diversity of defence mechanisms adapted to specific threats. The postulated PTI/ETI model describes two perception layers of plant innate immune system, which belong to a first immunity component of defence response activation. To better describe the sophisticated defence system of plants, we propose a new model of plant immunity. This model considers the plant’s ability to distinguish the feeding behaviour of their many foes, such as a second component that modulates innate immunity. This hypothesis provides a new viewpoint highlighting the relevance of hormone crosstalk and primary metabolism in regulating plant defence against the different behaviours of pathogens with the intention to stimulate further interest in this research area.
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Front. Plant Sci.: Editorial: Genomics and Effectomics of the crop killer Xanthomonas (2016)

Phytopathogenic bacteria of the Xanthomonas genus cause severe diseases on hundreds of host plants, including economically important crops, such as bean, cabbage, cassava, citrus, hemp, pepper, rice, sugarcane, tomato or wheat. Diseases occurring in nature comprise bacterial blight, canker, necrosis, rot, scald, spot, streak or wilt. Xanthomonas spp. are distributed worldwide and pathogenic and nonpathogenic strains are essentially found in association to plants. Some phytopathogenic strains are emergent or re-emergent and, consequently, dramatically impact agriculture, economy and food safety. During the last decades, massive efforts were undertaken to decipher Xanthomonas biology. So far, more than one hundred complete or draft genomes from diverse Xanthomonas species have been sequenced (http://www.xanthomonas.org), thus providing powerful tools to study genetic determinants triggering pathogenicity and adaptation to plant habitats. Xanthomonas spp. employ an arsenal of virulence factors to invade its host, including extracellular polysaccharides, plant cell wall-degrading enzymes, adhesins and secreted effectors. In most xanthomonads, type III secretion (T3S) system and secreted effectors (T3Es) are essential to bacterial pathogenicity through the inhibition of plant immunity or the induction of plant susceptibility (S) genes, as reported for Transcription Activation-Like (TAL) effectors. Yet, toxins can also be major virulence determinants in some xanthomonads while nonpathogenic Xanthomonas species do live in sympatry with plant without any T3S systems nor T3Es.
In a context of ever increasing international commercial exchanges and modifications of the climate, monitoring and regulating pathogens spread is of crucial importance for food security. A deep knowledge of the genomic diversity of Xanthomonas spp. is required for scientists to properly identify strains, to help preventing future disease outbreaks and to achieve knowledge informed sustainable disease resistance in crops.
This Research Topic published in the ‘Plant Biotic Interactions’ section of Frontiers in Plant Science and Frontiers in Microbiology aims at illustrating several of the recent achievements of the Xanthomonas community. We collected twelve manuscripts dealing with comparative genomics or T3E repertoires, including five focusing on TAL effectors which we hope will contribute to advance research on plant pathogenic bacteria.

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New Phytol.: Bacterial RNA – a new MAMP on the block? (2015)

New Phytol.: Bacterial RNA – a new MAMP on the block? (2015) | Effectors and Plant Immunity | Scoop.it

To defend themselves against pathogens, plants – like other organisms – need to discriminate ‘self’ from ‘non-self’ and ‘modified/damaged self’. Conserved microbial molecules, so-called pathogen-associated molecular patterns (PAMPs) or microbe-associated molecular patterns (MAMPs) are key indicators of ‘non-self’ (Sanabria et al., 2010), while the occurrence of plant-derived molecules that are normally absent (so-called danger-associated molecular patterns or DAMPs) can be a sign of ‘damaged self’ (Heil & Land, 2014). Both types of molecules are typically released in the context of microbial colonization and thus serve as alarm signals that consequently induce the activation of plant defense responses. In this issue of New Phytologist, Lee et al. (pp. 785–797) provide experimental evidence that ‘non-self’ bacterial RNA can serve as a trigger of innate immunity in Arabidopsis thaliana and thus functions as a PAMP/MAMP (hereafter referred to as MAMP) in plants.

 

R. Panstruga.

 

Commentary on:

 Bacterial RNAs activate innate immunity in Arabidopsis (pages 785–797)
Boyoung Lee, Yong-Soon Park, Soohyun Lee, Geun Cheol Song and Choong-Min Ryu
Article first published online: 26 OCT 2015 | DOI: 10.1111/nph.13717
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Comparison of gene activation by two TAL effectors from Xanthomonas axonopodis pv. manihotis reveals candidate host susceptibility genes in cassava - Cohn - Molecular Plant Pathology - Wiley Online...

Comparison of gene activation by two TAL effectors from Xanthomonas axonopodis pv. manihotis reveals candidate host susceptibility genes in cassava - Cohn - Molecular Plant Pathology - Wiley Online... | Effectors and Plant Immunity | Scoop.it

Cohn et al, 2015

Xanthomonas axonopodis pv. manihotis (Xam) employs transcription activator like (TAL) effectors to promote bacterial growth and symptom formation during infection of cassava. TAL effectors are secreted via the bacterial type III secretion system into plant cells where they are directed to the nucleus, bind DNA in plant promoters, and activate the expression of downstream genes. The DNA binding activity of TAL effectors is carried out by a central domain which contains a series of repeat variable diresidues (RVDs) that dictate the sequence of bound nucleotides. TAL14Xam668 promotes virulence in Xam strain Xam668 and has been shown to activate multiple cassava genes. In this study we used RNA-sequencing to identify the full target repertoire of TAL14Xam668 in cassava which includes over 50 genes. A subset of highly upregulated genes were tested for activation by TAL14CIO151 from Xam strain CIO151. Although TAL14CIO151 and TAL14Xam668 differ by only a single RVD they display differential activation of gene targets. TAL14CIO151 complements the TAL14Xam668 mutant defect, implying that shared target genes are important for TAL14Xam668-mediated disease susceptibility. Complementation with closely related TAL effectors is a novel approach to narrowing down biologically relevant susceptibility genes of TAL effectors with multiple targets. This study provides an example of how TAL effector target activation by two strains within a single species of Xanthomonas can be dramatically affected by a small change in RVD-nucleotide affinity at a single site and reflects the parameters of RVD-nucleotide interaction determined using designer TAL effectors in transient systems. This article is protected by copyright. All rights reserved.


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Rescooped by Nicolas Denancé from Norwich rust group
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Soybean production in eastern and southern Africa and threat of yield loss due to soybean rust caused by Phakopsora pachyrhizi

Soybean production in eastern and southern Africa and threat of yield loss due to soybean rust caused by Phakopsora pachyrhizi | Effectors and Plant Immunity | Scoop.it

The demand for soybean has increased in Africa, driven by the growing feed industry for poultry, aquaculture and home consumption in the form of processed milk, baked beans and for blending with maize and wheat flour.  The demand for soybean in Africa so far outweighs the supply, hence the deficit is mainly covered through imports of soybean products such as soybean meal. The area under soybean production has increased in response to the growing demand, a trend that is expected to continue in the coming years. As the production area increases, diseases and insect pests, declining soil fertility and other abiotic factors pose a major challenge. Soybean rust disease caused by the fungus Phakopsora pachyrhizi presents one of the major threats to soybean production in Africa due to its rapid spread as a result of the ease by which its spores are dispersed by the wind. 


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Norwich Rust Group's curator insight, September 30, 2015 1:15 PM

Great  comprehensive review by Harun Murithi

Rescooped by Nicolas Denancé from Plant & Evolution
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A recently evolved hexose transporter variant confers resistance to multiple pathogens in wheat

As there are numerous pathogen species that cause disease and limit yields of crops, such as wheat (Triticum aestivum), single genes that provide resistance to multiple pathogens are valuable in crop improvement1, 2. The mechanistic basis of multi-pathogen resistance is largely unknown. Here we use comparative genomics, mutagenesis and transformation to isolate the wheat Lr67gene, which confers partial resistance to all three wheat rust pathogen species and powdery mildew. The Lr67 resistance gene encodes a predicted hexose transporter (LR67res) that differs from the susceptible form of the same protein (LR67sus) by two amino acids that are conserved in orthologous hexose transporters. Sugar uptake assays show that LR67sus, and related proteins encoded by homeoalleles, function as high-affinity glucose transporters. LR67res exerts a dominant-negative effect through heterodimerization with these functional transporters to reduce glucose uptake. Alterations in hexose transport in infected leaves may explain its ability to reduce the growth of multiple biotrophic pathogen species.


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BMC Genomics: Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora (2015)

BMC Genomics: Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora (2015) | Effectors and Plant Immunity | Scoop.it

Background. Downy mildews are the most speciose group of oomycetes and affect crops of great economic importance. So far, there is only a single deeply-sequenced downy mildew genome available, from Hyaloperonospora arabidopsidis. Further genomic resources for downy mildews are required to study their evolution, including pathogenicity effector proteins, such as RxLR effectors. Plasmopara halstedii is a devastating pathogen of sunflower and a potential pathosystem model to study downy mildews, as several Avr-genes and R-genes have been predicted and unlike Arabidopsis downy mildew, large quantities of almost contamination-free material can be obtained easily.

 

Results. Here a high-quality draft genome of Plasmopara halstedii is reported and analysed with respect to various aspects, including genome organisation, secondary metabolism, effector proteins and comparative genomics with other sequenced oomycetes. Interestingly, the present analyses revealed further variation of the RxLR motif, suggesting an important role of the conservation of the dEER-motif. Orthology analyses revealed the conservation of 28 RxLR-like core effectors among Phytophthora species. Only six putative RxLR-like effectors were shared by the two sequenced downy mildews, highlighting the fast and largely independent evolution of two of the three major downy mildew lineages. This is seemingly supported by phylogenomic results, in which downy mildews did not appear to be monophyletic.

 

Conclusions. The genome resource will be useful for developing markers for monitoring the pathogen population and might provide the basis for new approaches to fight Phytophthora and downy mildew pathogens by targeting core pathogenicity effectors.


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Rescooped by Nicolas Denancé from The Plant Microbiome
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Allelic variation contributes to bacterial host specificity : Nature Communications

Allelic variation contributes to bacterial host specificity : Nature Communications | Effectors and Plant Immunity | Scoop.it
Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. Together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.

Via Ryohei Thomas Nakano, Stéphane Hacquard
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Microbiomes in light of traits: A phylogenetic perspective

Microbiomes in light of traits: A phylogenetic perspective | Effectors and Plant Immunity | Scoop.it
Microbial communities—microbiomes—are intricately linked to human health and critical ecosystem services. New technologies allow the rapid characterization of hundreds of samples at a time and provide a sweeping perspective on microbiome patterns. However, a systematic understanding of what determines microbiome diversity and composition and its implications for system functioning is still lacking. A focus on the phenotypic characteristics of microorganisms—their traits—offers a path for interpreting the growing amount of microbiome data. Indeed, a variety of trait-based approaches have been proposed for plants and animal communities, and this approach has helped to clarify the mechanisms underlying community assembly, diversity-process relationships, and ecosystem responses to environmental change.

Although there is a growing emphasis on microbial traits, the concept has not been fully appreciated in microbiology. However, a trait focus for microorganisms may present an even larger research opportunity than for macro-organisms. Not only do microorganisms play a central role in nutrient and energy cycling in most systems, but the techniques used to characterize microbiomes usually provide extensive molecular and phylogenetic information.

ADVANCES
One major difference between macro- and microorganisms is the potential for horizontal gene transfer (HGT) in microbes. Higher rates of HGT mean that many microbial traits might be unrelated to the history of the vertically descended parts of the genome. If true, then the taxonomic composition of a microbiome might reveal little about the health or functioning of a system. We first review key aspects of microbial traits and then recent studies that document the distribution of microbial traits onto the tree of life. A synthesis of these studies reveals that, despite the promiscuity of HGT, microbial traits appear to be phylogenetically conserved, or not distributed randomly across the tree of life. Further, microbial traits appear to be conserved in a hierarchical fashion, possibly linked to their biochemical and genetic complexity. For instance, traits such as pH and salinity preference are relatively deeply conserved, such that taxa within deep clades tend to share the trait. In contrast, other traits like the ability to use simple carbon substrates or to take up organic phosphorus are shallowly conserved, and taxa share these traits only within small, shallow clades.

OUTLOOK
The phylogenetic, trait-based framework that emerges offers a path to interpret microbiome variation and its connection to the health and functioning of environmental, engineered, and human systems. In particular, the taxonomic resolution of biogeographic patterns provides information about the traits under selection, even across entirely different systems. Parallels observed among human and free-living communities support this idea. For instance, microbial traits related to growth on different substrates (e.g., proteins, fats, and carbohydrates) in the human gut appear to be conserved at approximately the genus level, a resolution associated with the level of conservation of glycoside hydrolase genes in bacteria generally. A focus on two particular types of traits—response and effect traits—may also aid in microbiome management, whether that means maintaining human health or mitigating climate change impacts. Future work on microbial traits must consider three challenges: the influence of different trait measurements on cross-study comparisons; correlations between traits within and among microorganisms; and interactions among microbial traits, the environment, and other organisms. Our conclusions also have implications for the growing field of community phylogenetics beyond applications to microorganisms.

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Sequence diversity and functional conformity: A comparative molecular characterization of TALE-like proteins - Ph.D. thesis

Sequence diversity and functional conformity: A comparative molecular characterization of TALE-like proteins - Ph.D. thesis | Effectors and Plant Immunity | Scoop.it

Orlando de Lange, 2015

In the introduction of this dissertation, which explores TALE biology, a particular focus will be placed on the DNA binding properties of TALEs and how this can be put to use in TALE technology. After this the RipTALs, Bats and MOrTLs are each introduced, explaining what is known about their provenance and sequence features. The aims of my doctoral work are then listed and expounded in turn. The proximal goal of my doctoral work was to carry out a comparative molecular characterization of each group of non-TALE TALE-likes. In doing so we hoped to gain insights into the principles of TALE-like DNA-binding properties, evolutionary history of the different groups and their potential uses in biotechnology. In the case of the RipTALs this work should begin to unravel the role these proteins play in bacterial wilt disease, as a means to fight this devastating pathogen. The articles I have worked on covering the molecular characterizations of RipTALs, Bats and MOrTLs are then presented in turn. Working together with others I was able to show that repeats from each group of TALE-likes mediate sequence specific DNA binding, revealing a conserved code in each case. This code links position 13 of any TALE-like repeat to a specific DNA base preference in a reliable fashion. I will argue that the TALE-likes represent a fascinating case of conserved structure and function in a diverse sequence space. In addition the TALEs and RipTALs may simply represent one face of the TALE-likes, a protein family mediating as yet unknown biological roles as bacterial DNA binding proteins.


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Rescooped by Nicolas Denancé from Plants and Microbes
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Nature Plants: Immunity: One receptor, many pathogens (2015)

Nature Plants: Immunity: One receptor, many pathogens (2015) | Effectors and Plant Immunity | Scoop.it

Most plant pattern recognition receptors induce immune responses by detecting molecular patterns typical to one group of microbes. A newly identified complex, on the other hand, monitors effector proteins widely distributed among bacteria, fungi and oomycetes, casting a new light on the evolution of pattern recognition in plants.

 

See also Albert et al. An RLP23–SOBIR1–BAK1 complex mediates NLP-triggered immunity. Nature Plants http://www.nature.com/articles/nplants2015140


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TALENs: Methods and Protocols - Springer

TALENs: Methods and Protocols - Springer | Effectors and Plant Immunity | Scoop.it

This volume provides a comprehensive collection of protocols on new technology across various model organisms.  Chapters describe species-specific methods to generate new mutants the content is completed by chapters on natural TAL effectors, TAL element DNA binding principles, TALEN target site prediction, and methods for the efficient construction of TALEN coding regions. While addition chapter focus on the application of TALEN as sequence-specific nucleases and TAL based gene activators or inhibitors and the visualization of chromatin dynamics in live cells.  Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.


Via dromius
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dromius's curator insight, October 9, 2015 5:25 AM

Overview
Specificity
Online Tools
Assembly protocols
Activators and Repressors
Genome Visualisation Tools
Applications for
Ribbed Newt
Bombyx mori
Crickets
Mosquitos
Drosophila
Zebrafish
Xenopus
Mice
Rats

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Front. Microbiol.: Genome sequencing reveals a new lineage associated with lablab bean and genetic exchange between Xanthomonas axonopodis pv. phaseoli and Xanthomonas fuscans subsp. fuscans (2015)

Front. Microbiol.: Genome sequencing reveals a new lineage associated with lablab bean and genetic exchange between Xanthomonas axonopodis pv. phaseoli and Xanthomonas fuscans subsp. fuscans (2015) | Effectors and Plant Immunity | Scoop.it

Common bacterial blight is a devastating seed-borne disease of common beans that also occurs on other legume species including lablab and Lima beans. We sequenced and analyzed the genomes of 26 strains of Xanthomonas axonopodis pv. phaseoli and X. fuscans subsp. fuscans, the causative agents of this disease, collected over four decades and six continents. This revealed considerable genetic variation within both taxa, encompassing both single-nucleotide variants and differences in gene content, that could be exploited for tracking pathogen spread. The bacterial strain from Lima bean fell within the previously described Genetic Lineage 1, along with the pathovar type strain (NCPPB 3035). The strains from lablab represent a new, previously unknown genetic lineage closely related to strains of X. axonopodis pv. glycines. Finally, we identified more than 100 genes that appear to have been recently acquired by Xanthomonas axonopodis pv. phaseoli from X. fuscans subsp. fuscans.

 

Valente Aritua, James Harrison, Melanie Sapp, Robin Buruchara, Julian Smith, David John Studholme

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BMC Genomics: Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species (2016)

BMC Genomics: Genomic and proteomic evidence supporting the division of the plant pathogen Ralstonia solanacearum into three species (2016) | Effectors and Plant Immunity | Scoop.it

Background 

The increased availability of genome sequences has advanced the development of genomic distance methods to describe bacterial diversity. Results of these fast-evolving methods are highly correlated with those of the historically standard DNA-DNA hybridization technique. However, these genomic-based methods can be done more rapidly and less expensively and are less prone to technical and human error. They are thus a technically accessible replacement for species delineation. Here, we use several genomic comparison methods, supported by our own proteomic analyses and metabolic characterization as well as previously published DNA-DNA hybridization analyses, to differentiate members of the Ralstonia solanacearum species complex into three species. This pathogen group consists of diverse and widespread strains that cause bacterial wilt disease on many different plants.

Results 

We used three different methods to compare the complete genomes of 29 strains from the R. solanacearum species complex. In parallel we profiled the proteomes of 73 strains using Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF-MS). Proteomic profiles together with genomic sequence comparisons consistently and comprehensively described the diversity of the R. solanacearum species complex. In addition, genome-driven functional phenotypic assays excitingly supported an old hypothesis (Hayward et al. (J Appl Bacteriol 69:269–80, 1990)), that closely related members of the R. solanacearum could be identified through a simple assay of anaerobic nitrate metabolism. This assay allowed us to clearly and easily differentiate phylotype II and IV strains from phylotype I and III strains. Further, genomic dissection of the pathway distinguished between proposed subspecies within the current phylotype IV. The assay revealed large scale differences in energy production within the R. solanacearum species complex, indicating coarse evolutionary distance and further supporting a repartitioning of this group into separate species.

Conclusions 

Together, the results of these studies support the proposed division of the R. solanacearum species complex into three species, consistent with recent literature, and demonstrate the utility of proteomic and genomic approaches to delineate bacterial species.

 

Philippe Prior, Florent Ailloud, Beth L. Dalsing, Benoit Remenant, Borja Sanchez and Caitilyn Allen

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App. Env. Microbiol.: New Variants of Coffee-infecting Xylella fastidiosa issued from homologous recombination

App. Env. Microbiol.: New Variants of Coffee-infecting Xylella fastidiosa issued from homologous recombination | Effectors and Plant Immunity | Scoop.it

Xylella fastidiosa is a xylem-limited phytopathogenic bacterium endemic to the Americas that has recently emerged in Asia and Europe. Although classified as a quarantine organism in the European Union, importation of plant material from contaminated areas and latent infection in asymptomatic plants have engendered its inevitable introduction. In 2012, four coffee plants (Coffea arabica and C. canephora) with leaf scorch symptoms growing in a confined glasshouse were detected and intercepted in France. After identification of the causal agent, this outbreak was eradicated. Three X. fastidiosa strains were isolated from these plants, confirming a preliminary diagnostic based on immunology. The strains were characterized by multiplex PCR and by multilocus sequence analysis/typing (MLSA-MLST) based on seven housekeeping genes. One strain, CFBP 8073, isolated from C. canephora imported from Mexico, was assigned to X. fastidiosa subsp. fastidiosa/sandyi. This strain harbors a novel sequence type (ST) with novel alleles at two loci. The two other strains, CFBP 8072 and 8074, isolated from C. arabica imported from Ecuador, were allocated to X. fastidiosa subsp. pauca. These two strains shared a novel ST with novel alleles at two loci. These MLST profiles showed evidence of recombination events. We provided genome sequences for CFBP 8072 and CFBP 8073 strains. Comparative genomic analyses of these two genome sequences with publicly available X. fastidiosa genomes, including the Italian strain CoDiRO, confirmed these phylogenetic positions and provided candidate alleles for coffee adaptation. This study demonstrates the global diversity of X. fastidiosa and highlights the diversity of strains isolated from coffee.  

 

Jacques MA, Denancé N, Legendre B, Morel E, Briand M, Mississipi S, Durand K, Olivier V, Portier P, Poliakoff F, and Crouzillat D.

 

App. Env. Microbiol.

AEM Accepted Manuscript Posted Online 28 December 2015
Appl. Environ. Microbiol. doi:10.1128/AEM.03299-15

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Front. Plant. Sci: Comparative genomics of pathogenic and nonpathogenic strains of Xanthomonas arboricola unveil molecular and evolutionary events linked to pathoadaptation (2015)

Front. Plant. Sci: Comparative genomics of pathogenic and nonpathogenic strains of Xanthomonas arboricola unveil molecular and evolutionary events linked to pathoadaptation (2015) | Effectors and Plant Immunity | Scoop.it
The bacterial species Xanthomonas arboricola contains plant pathogenic and nonpathogenic strains. It includes the pathogen X. arboricola pv. juglandis, causing the bacterial blight of Juglans regia. The emergence of a new bacterial disease of Juglans regia in France called vertical oozing canker (VOC) was previously described and the causal agent was identified as a distinct genetic lineage within the pathovar juglandis. Symptoms on walnut leaves and fruits are similar to those of a bacterial blight but VOC includes also cankers on trunk and branches. In this work, we used comparative genomics and physiological tests to detect differences between four X. arboricola strains isolated from walnut tree: strain CFBP 2528 causing walnut blight, strain CFBP 7179 causing VOC and two nonpathogenic strains, CFBP 7634 and CFBP 7651, isolated from healthy walnut buds. Whole genome sequence comparisons revealed that pathogenic strains possess a larger and wider range of mobile genetic elements than nonpathogenic strains. One pathogenic strain, CFBP 7179, possessed a specific integrative and conjugative element of 95 kb encoding genes involved in copper resistance, transport and regulation. The type three effector repertoire was larger in pathogenic strains than in nonpathogenic strains. Moreover, CFBP 7634 strain lacked the type three secretion system encoding genes. The flagellar system appeared incomplete and nonfunctional in the pathogenic strain CFBP 2528. Differential sets of chemoreceptor and different repertoires of genes coding adhesins were identified between pathogenic and nonpathogenic strains. Besides these differences, some strain-specific differences were also observed. Altogether, this study provides valuable insights to highlight the mechanisms involved in ecology, environment perception, plant adhesion and interaction, leading to the emergence of new strains in a dynamic environment.

 

Cesbron S, Briand M, Essakhi S, Gironde S, Boureau T, Manceau C, Fischer-Le Saux M and Jacques M-A

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BMC Genomics: Genomics and transcriptomics of Xanthomonas campestris species challenge the concept of core type III effectome (2015)

BMC Genomics: Genomics and transcriptomics of Xanthomonas campestris species challenge the concept of core type III effectome (2015) | Effectors and Plant Immunity | Scoop.it
Background

The bacterial species Xanthomonas campestris infects a wide range of Brassicaceae. Specific pathovars of this species cause black rot (pv. campestris), bacterial blight of stock (pv. incanae) or bacterial leaf spot (pv. raphani).

Results

In this study, we extended the genomic coverage of the species by sequencing and annotating the genomes of strains from pathovar incanae (CFBP 1606R and CFBP 2527R), pathovar raphani (CFBP 5828R) and a pathovar formerly named barbareae (CFBP 5825R). While comparative analyses identified a large core ORFeome at the species level, the core type III effectome was limited to only three putative type III effectors (XopP, XopF1 and XopAL1). In Xanthomonas, these effector proteins are injected inside the plant cells by the type III secretion system and contribute collectively to virulence. A deep and strand-specific RNA sequencing strategy was adopted in order to experimentally refine genome annotation for strain CFBP 5828R. This approach also allowed the experimental definition of novel ORFs and non-coding RNA transcripts. Using a constitutively active allele of hrpG, a master regulator of the type III secretion system, a HrpG-dependent regulon of 141 genes co-regulated with the type III secretion system was identified. Importantly, all these genes but seven are positively regulated by HrpG and 56 of those encode components of the Hrp type III secretion system and putative effector proteins.

Conclusions

This dataset is an important resource to mine for novel type III effector proteins as well as for bacterial genes which could contribute to pathogenicity of X. campestris.

 

Roux  Brice, Bolot  Stéphanie, Guy  Endrick, Denancé  Nicolas, Lautier  Martine, Jardinaud  Marie-Françoise, Fischer-Le Saux  Marion, Portier  Perrine, Jacques  Marie-Agnès, Gagnevin  Lionel, Pruvost  Olivier, Lauber  Emmanuelle, Arlat  Matthieu, Carrère  Sébastien, Koebnik  Ralf, Noël  Laurent

 

 

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Rescooped by Nicolas Denancé from NOUVELLES DE LA SCIENCE - SCIENCE NEWS
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Le Maroc abrite désormais une partie du patrimoine végétal mondial

Le Maroc abrite désormais une partie du patrimoine végétal mondial | Effectors and Plant Immunity | Scoop.it

TelQuel (Maroc), 22.10.2015

"Environ 38 000 échantillons de semences notamment de blé, d’orge, de lentilles et des pois chiches ont été envoyés au Maroc et au Liban dans des stations de recherche exploitées par le Centre international de recherche agricole dans les zones arides (Icarda).
Suite à la destruction de la banque de gènes de l’Icarda dans la ville syrienne d’Alep, le Centre ..."


Via Katell Rochard, Isabelle Pélissié, Cirad
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Plant Proteases 2016: University of Oxford, April 10-12.

Plant Proteases 2016: University of Oxford, April 10-12. | Effectors and Plant Immunity | Scoop.it

Via Kamoun Lab @ TSL
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A protein-protein interaction network linking the energy-sensor kinase SnRK1 to multiple signaling pathways in Arabidopsis thaliana

A protein-protein interaction network linking the energy-sensor kinase SnRK1 to multiple signaling pathways in Arabidopsis thaliana | Effectors and Plant Immunity | Scoop.it
In plants, the Sucrose non-fermenting (SNF1)–related protein kinase 1 (SnRK1) represents a central integrator of low energy signaling and acclimation towards many environmental stress responses. Although SnRK1 acts as a convergent point for many different environmental and metabolic signals to control growth and development, it is currently unknown how these many different signals could be translated into a cell-type or stimulus specific response since many components of SnRK1-regulated signaling pathways remain unidentified. Recently, we have demonstrated that proteins containing a domain of unknown function (DUF) 581 interact with the catalytic α subunits of SnRK1 (AKIN10/ 11) from Arabidopsis thaliana and could potentially act as mediators conferring tissue- and stimulus-type specific differences in SnRK1 regulation. To further extend the SnRK1 signaling network in plants, we systematically screened for novel DUF581 interaction partners using the yeast two-hybrid system. A deep and exhaustive screening identified 17 interacting partners for 10 of the DUF581 proteins tested. Many of these novel interaction partners are implicated in cellular processes previously associated with SnRK1 signaling. Furthermore, we mined publicly available interaction data to identify additional DUF581 interacting proteins. A protein-protein interaction network resulting from our studies suggests connections between SnRK1 signaling and other central signaling pathways involved in growth regulation and environmental responses. These include TOR and MAP-kinase signaling as well as hormonal pathways. The resulting protein-protein interaction network promises to be effective in generating hypotheses to study the precise mechanisms SnRK1 signaling on a functional level.

Via Suayib Üstün
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Oncotarget: Plant immune receptor decoy: Pathogens in their own trap (2015)

Oncotarget: Plant immune receptor decoy: Pathogens in their own trap (2015) | Effectors and Plant Immunity | Scoop.it

Microbial pathogens have evolved sophisticated strategies to infect their hosts, often resulting in disease. The host, in turn, can produce novel proteins (receptors or antibodies) that recognize pathogen molecules to trigger defense. Unlike animals, plants do not possess any adaptive immunity to defend themselves against pathogens. Therefore, they rely entirely on their genetic resistance capability (innate immunity) conferred by a family of receptors expressed in individual cells. The plant innate immune system can be divided into two layers of defense. The first, known as pattern-triggered immunity (PTI) leading to basal defense, involves the recognition of microbe-associated molecular patterns (MAMPs) by corresponding plasma membrane pattern-recognition receptors (PRRs). PTI can be suppressed by specific pathogen virulence factors (known as effectors). To detect such pathogen molecules or their interference with host proteins, plants have evolved a second layer of defense, known as effector-triggered immunity (ETI) [1]. ETI is mediated by intracellular nucleotide-binding–leucine-rich repeat receptors (NLRs) that resemble mammalian NLRs [2]. The speed with which microbial populations can produce new effectors places enormous pressure on plant hosts to fight back with genetically new or altered receptor recognition modes.

 

Alice Delga, Clémentine Le Roux and Laurent Deslandes

 

 

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DNA-binding proteins from marine bacteria expand the known sequence diversity of TALE-like repeats - Nucl. Acids Res.

DNA-binding proteins from marine bacteria expand the known sequence diversity of TALE-like repeats - Nucl. Acids Res. | Effectors and Plant Immunity | Scoop.it

(via t. Lahaye, thx)

de Lange & Wolf et al, 2015

Transcription Activator-Like Effectors (TALEs) of Xanthomonas bacteria are programmable DNA binding proteins with unprecedented target specificity. Comparative studies into TALE repeat structure and function are hindered by the limited sequence variation among TALE repeats. More sequence-diverse TALE-like proteins are known from Ralstonia solanacearum (RipTALs) and Burkholderia rhizoxinica (Bats), but RipTAL and Bat repeats are conserved with those of TALEs around the DNA-binding residue. We study two novel marine-organism TALE-like proteins (MOrTL1 and MOrTL2), the first to date of non-terrestrial origin. We have assessed their DNA-binding properties and modelled repeat structures. We found that repeats from these proteins mediate sequence specific DNA binding conforming to the TALE code, despite low sequence similarity to TALE repeats, and with novel residues around the BSR. However, MOrTL1 repeats show greater sequence discriminating power than MOrTL2 repeats. Sequence alignments show that there are only three residues conserved between repeats of all TALE-like proteins including the two new additions. This conserved motif could prove useful as an identifier for future TALE-likes. Additionally, comparing MOrTL repeats with those of other TALE-likes suggests a common evolutionary origin for the TALEs, RipTALs and Bats.


Via dromius
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Plant Disease: How Do Plant Diseases Caused by Xylella fastidiosa Emerge? (2015)

Plant Disease: How Do Plant Diseases Caused by Xylella fastidiosa Emerge? (2015) | Effectors and Plant Immunity | Scoop.it

Emerging plant diseases frequently have significant economic, environmental, cultural, and social impacts. The prediction of new disease emergence, associated with new pathogens or not, remains a difficult and controversial topic. The main factors driving epidemics are often only identified several years after outbreaks, generally revealing that a limited number of factors are associated with the emergence of specific groups of pathogens. This pattern is illustrated in the insect-borne xylem-limited bacterium Xylella fastidiosa, an organism associated with several new plant diseases in different regions of the globe. Research during the last decade focusing on several severe disease outbreaks has led to substantial changes in our understanding of X. fastidiosa biology, ecology, and evolution. This new information has not only led to new insights into aspects of the biology of this bacterium and its interactions with plant and insect hosts, but also made available a phylogenetic framework that has allowed for better inferences concerning factors leading to the emergence of diseases. Here we identify and discuss these main pathways leading to epidemics caused by X. fastidiosa. Our ultimate goal was to raise critical questions and issues for academics and regulatory agencies alike, since the information generated during the last decade has both raised new questions but also clarified old ones.

 

Rodrigo P. P. Almeida and Leonard Nunney

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#EffecTours2015 Insects, pathogens, and plant reprogramming: from effector molecules to ecology, Tours, France

Tweets from #EffecTours2015 Insects, pathogens, and plant reprogramming: from effector molecules to ecology, Tours, France, October 5-7, 2015

http://www.lestudium-ias.com/event/insects-pathogens-and-plant-reprogramming-effector-molecules-ecology


Via Kamoun Lab @ TSL
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EJPP: The olive quick decline syndrome in south-east Italy: a threatening phytosanitary emergency (2015)

EJPP: The olive quick decline syndrome in south-east Italy: a threatening phytosanitary emergency (2015) | Effectors and Plant Immunity | Scoop.it

The olive quick decline syndrome (OQDS) is a disease that appeared suddenly a few years ago in the province of Lecce (Salento peninsula, southeastern Italy). Among the factors that may be involved in its aetiology, the most relevant is Xylella fastidiosa, a quarantine pathogen of American origin, whose presence in Italy represents its first confirmed record in the European Union. X. fastidiosa is a Gram-negative bacterium that invades the xylem of a wide range of hosts, from which it is acquired by xylem-feeding insect vectors and transferred to other plants. The bacterium multiplies within the plant vessels and occludes them, thus impairing water uptake. Besides olive, the Salentian strain of X. fastidiosa infects in nature a number of woody (almond, cherry) and shrubby (oleander, broom, Acacia saligna, Polygala myrtifolia, Westringia fruticosa, Rosmarinus officinalis, Rhamnus elaternus, Myrtus communis) hosts, with no evidence for grapevines or citrus being hosts. The bacterium was isolated in culture and identified as a genotype of X. fastidiosa subsp. pauca, molecularly identical to an isolate from Costa Rica. Philaenus spumarius (meadow spittlebug), a froghopper quite common in the Salento area where it thrives on olive, was identified as the main vector. Disease eradication and sanitation of infected olives are unfeasible. However, strategies are being enacted for restraining the spread of pathogen and vector(s) within the boundaries of the currently infected zone.

 

G. P. Martelli, D. Boscia, F. Porcelli, M. Saponari

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