Effectors and Plant Immunity
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Nature Commun.: CRT1 is a nuclear-translocated MORC endonuclease that participates in multiple levels of plant immunity (2012)

Nature Commun.: CRT1 is a nuclear-translocated MORC endonuclease that participates in multiple levels of plant immunity (2012) | Effectors and Plant Immunity | Scoop.it
Arabidopsis thaliana CRT1 (compromised for recognition of Turnip Crinkle Virus) was previously shown to be required for effector-triggered immunity. Sequence analyses previously revealed that CRT1 contains the ATPase and S5 domains characteristic of Microchidia (MORC) proteins; these proteins are associated with DNA modification and repair. Here we show that CRT1 and its closest homologue, CRH1, are also required for pathogen-associated molecular pattern (PAMP)-triggered immunity, basal resistance, non-host resistance and systemic acquired resistance. Consistent with its role in PAMP-triggered immunity, CRT1 interacted with the PAMP recognition receptor FLS2. Subcellular fractionation and transmission electron microscopy detected a subpopulation of CRT1 in the nucleus, whose levels increased following PAMP treatment or infection with an avirulent pathogen. These results, combined with the demonstration that CRT1 binds DNA, exhibits endonuclease activity, and affects tolerance to the DNA-damaging agent mitomycin C, argue that this prototypic eukaryotic member of the MORC superfamily has important nuclear functions during immune response activation.


Hong-Gu Kang, Hyong Woo Choi, Sabrina von Einem, Patricia Manosalva, Katrin Ehlers, Po-Pu Liu, Stefanie V. Buxa, Magali Moreau, Hyong-Gon Mang, Pradeep Kachroo, Karl-Heinz Kogel and Daniel F. Klessig
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Effectors and Plant Immunity
Strategies of plant defense and microbe attacks
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Plant Biotech. J.: Targeted promoter editing for rice resistance to Xanthomonas oryzae pv. oryzae reveals differential activities for SWEET14-inducing TAL effectors (2016)

Plant Biotech. J.: Targeted promoter editing for rice resistance to Xanthomonas oryzae pv. oryzae reveals differential activities for SWEET14-inducing TAL effectors (2016) | Effectors and Plant Immunity | Scoop.it
As a key virulence strategy to cause Bacterial Leaf Blight, Xanthomonas oryzae pv. oryzae (Xoo) injects into the plant cell DNA-binding proteins called Transcription Activator-Like Effectors (TALEs), that bind to Effector-Binding Elements (EBEs) in a sequence-specific manner, resulting in host gene induction. TALEs AvrXa7, PthXo3, TalC and Tal5, found in geographically distant Xoo strains, all target OsSWEET14, thus considered as a pivotal TALE target acting as major susceptibility factor during rice-Xoo interactions. Here, we report the generation of an allele library of OsSWEET14 promoter through stable expression of TALE-Nuclease (TALEN) constructs in rice. The susceptibility level of lines carrying mutations in AvrXa7, Tal5 or TalC EBEs was assessed. Plants edited in AvrXa7 or Tal5 EBEs were resistant to bacterial strains relying on the corresponding TALE. Surprisingly, although indels within TalC EBE prevented OsSWEET14 induction in response to BAI3 wild-type bacteria relying on TalC, loss of TalC-responsiveness failed to confer resistance to this strain. The TalC EBE mutant line was, however, resistant to a strain expressing an artificial SWEET14-inducing TALE whose EBE was also edited in this line. This work offers the first set of alleles edited in TalC EBE and uncovers a distinct, broader range of activities for TalC compared to AvrXa7 or Tal5. We propose the existence of additional targets for TalC beyond SWEET14, suggesting that TALE-mediated plant susceptibility may result from induction of several, genetically redundant, host susceptibility genes by a single effector.

Servane Blanvillain-Baufumé, Maik Reschke, Montserrat Solé, Florence Auguy, Hinda Doucoure, Boris Szurek, Donaldo Meynard, Murielle Portefaix, Sébastien Cunnac, Emmanuel Guiderdoni, Jens Boch and Ralf Koebnik
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Front. Microbiol.: Xanthomonas Whole Genome Sequencing: Phylogenetics, Host Specificity and Beyond  (2016)

A commentary on Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity by Schwartz, A. R., Potnis, N., Timilsina, S., Wilson, M., Patané, J., Martins, J. Jr., et al. (2015). Front. Microbiol. 6:535. doi: 10.3389/fmicb.2015.00535


http://journal.frontiersin.org/researchtopic/3173/genomics-and-effectomics-of-the-crop-killer-xanthomonas



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Differentiation between MAMP Triggered Defenses in Arabidopsis thaliana

Author Summary Specialized receptors encoded by plants detect different components of bacterial machinery, and initiate an immune response. These recognition events are thought to induce largely redundant defense signaling, the magnitude of which varies quantitatively among populations, perhaps in response to environment specific differences in microbial threat. Here, we sought to determine whether plants evolve distinct or shared responses to two canonical MAMPs within natural populations. We comprehensively tested the extent of functional redundancy in the response of 186 genotypes of Arabidopsis thaliana to variants of each of two classes of bacterial signals, flagellin and EF-Tu. Although plants respond similarly to recognition of different variants of the same MAMP, we found the response to one MAMP class to be largely uncorrelated with the response to the other class. We further investigated the genetic bases underlying growth changes to determine whether similar genes contribute to variation in the response to EF-Tu and flagellin bacterial signals. We find limited genetic similarity, revealing novel MAMP-specific signaling components. The differentiation of these responses reveals MAMP-specific fine tuning of the immune response.

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Annu. Rev. Phytopathol.: Using Ecology, Physiology, and Genomics to Understand Host Specificity in Xanthomonas (2016)

Jacques et al, 2016

How pathogens coevolve with and adapt to their hosts are critical to understanding how host jumps and/or acquisition of novel traits can lead to new disease emergences. The Xanthomonas genus includes Gram-negative plant-pathogenic bacteria that collectively infect a broad range of crops and wild plant species. However, individual Xanthomonas strains usually cause disease on only a few plant species and are highly adapted to their hosts, making them pertinent models to study host specificity. This review summarizes our current understanding of the molecular basis of host specificity in the Xanthomonas genus, with a particular focus on the ecology, physiology, and pathogenicity of the bacterium. Despite our limited understanding of the basis of host specificity, type III effectors, microbe-associated molecular patterns, lipopolysaccharides, transcriptional regulators, and chemotactic sensors emerge as key determinants for shaping host specificity.


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Molecular Plant Pathology: Are lichens potential natural reservoirs for plant pathogens? (2016)

Molecular Plant Pathology: Are lichens potential natural reservoirs for plant pathogens? (2016) | Effectors and Plant Immunity | Scoop.it

Most ecological studies on plant-pathogenic bacteria have focused, perhaps understandably, on the agricultural environment. Interest is increasing, however, in the occurrence of plantpathogenic bacteria in habitats outside of agriculture. The seminal work by Morris et al. (2008), for instance, has shown that Pseudomonas syringae occupies a wide range of niches linked with the water cycle, including alpine lakes, streams and snow. Moreover, it is becoming clear that traits that are linked to adaptation to biotic and abiotic stress in the non-agricultural environment can have a secondary function as virulence factors in plants (Morris et al., 2009). Indeed, adaptation to non-host environments has been suggested to have played a non-trivial role in the evolution of P. syringae phytopathogenicity and


Via Kamoun Lab @ TSL
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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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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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An engineered promoter driving expression of a microbial avirulence gene confers recognition of TAL effectors and reduces growth of diverse Xanthomonas strains in citrus - Mol. Plant Pathol.

An engineered promoter driving expression of a microbial avirulence gene confers recognition of TAL effectors and reduces growth of diverse Xanthomonas strains in citrus - Mol. Plant Pathol. | Effectors and Plant Immunity | Scoop.it

(via T. Lahaye, thx)

Shantharaj et al, 2016

Xanthomonas citri subsp. citri (X. citri), causal agent of citrus canker, uses Transcription Activator-Like Effectors (TALEs) as major pathogenicity factors. TALEs, which are delivered into plant cells through the type III secretion system (T3SS), interact with Effector Binding Elements (EBEs) in host genomes to activate expression of downstream susceptibility genes to promote disease. Predictably, TALEs bind EBEs in host promoters via known combinations of TALE amino acids to DNA bases known as the TALE code. We introduced 14 EBEs, matching to distinct X. citri TALEs, into the promoter of the pepper Bs3 gene (ProBs31EBE) and fused this engineered promoter with multiple EBEs (ProBs314EBE) to either the GUS reporter gene or the coding sequence (cds) of the pepper gene, Bs3. TALE induced expression of the Bs3 cds in citrus leaves resulted in no visible HR. Therefore, we utilized a different approach in which ProBs31EBE and ProBs314EBE were fused to the Xanthomonas gene, avrGf1, which encodes a bacterial effector that elicits a hypersensitive response (HR) in grapefruit and sweet orange. We demonstrate in transient assays that activation of ProBs314EBE by X. citri TALEs is T3SS dependent and that expression of AvrGf1 triggers HR and correlates with reduced bacterial growth. We further demonstrated that all tested virulent X. citri strains from diverse geographic locations activated ProBs314EBE. TALEs are essential for virulence of X. citri strains and, because the engineered promoter traps are activated by multiple TALEs, this concept has potential to confer broad-spectrum, durable resistance to citrus canker in stably transformed plants.


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Convergent evolution of filamentous microbes towards evasion of glycan-triggered immunity

Convergent evolution of filamentous microbes towards evasion of glycan-triggered immunity | Effectors and Plant Immunity | Scoop.it
All filamentous microbes produce and release a wide range of glycans, which are essential determinants of microbe–microbe and microbe–host interactions. Major cell wall constituents, such as chitin and β-glucans, are elicitors of host immune responses. The widespread capacity for glycan perception in plants has driven the evolution of various strategies that help filamentous microbes to evade detection. Common strategies include structural and chemical modifications of cell wall components as well as the secretion of effector proteins that suppress chitin- and β-glucan-triggered immune responses. Thus, the necessity to avoid glycan-triggered immunity represents a driving force in the convergent evolution of filamentous microbes towards its suppression.

Via Francis Martin
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Origins of food crops connect countries worldwide

Origins of food crops connect countries worldwide | Effectors and Plant Immunity | Scoop.it
Research into the origins of food plants has led to the recognition that specific geographical regions around the world have been of particular importance to the development of agricultural crops. Yet the relative contributions of these different regions in the context of current food systems have not been quantified. Here we determine the origins (‘primary regions of diversity’) of the crops comprising the food supplies and agricultural production of countries worldwide. We estimate the degree to which countries use crops from regions of diversity other than their own (‘foreign crops’), and quantify changes in this usage over the past 50 years. Countries are highly interconnected with regard to primary regions of diversity of the crops they cultivate and/or consume. Foreign crops are extensively used in food supplies (68.7% of national food supplies as a global mean are derived from foreign crops) and production systems (69.3% of crops grown are foreign). Foreign crop usage has increased significantly over the past 50 years, including in countries with high indigenous crop diversity. The results provide a novel perspective on the ongoing globalization of food systems worldwide, and bolster evidence for the importance of international collaboration on genetic resource conservation and exchange.

Via Andres Zurita, Loïc Lepiniec
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Plant J.: Ectopic activation of the rice NLR heteropair RGA4/RGA5 confers resistance to bacterial blight and bacterial leaf streak diseases (2016)

Plant J.: Ectopic activation of the rice NLR heteropair RGA4/RGA5 confers resistance to bacterial blight and bacterial leaf streak diseases (2016) | Effectors and Plant Immunity | Scoop.it
Bacterial Blight (BB) and Bacterial Leaf Streak (BLS) are important rice diseases caused, respectively, by Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc). In both bacteria, Transcription Activator-Like (TAL) effectors are major virulence determinants that act by transactivating host genes downstream of Effector-Binding Elements (EBEs) bound in a sequence specific manner. Resistance to Xoo is mostly related to TAL effectors action, either by polymorphisms that prevent induction of susceptibility (S) genes or by executor (R) genes with EBEs embedded in their promoter and that induce cell death and resistance. For Xoc, no resistance sources are known in rice. Here, we investigated whether the recognition of effectors by nucleotide-binding and leucine rich repeat domain immune receptors (NLRs), the most widespread resistance mechanism in plants, is also able to stop BB and BLS. In one instance, transgenic rice lines harboring the AVR1-CO39 effector gene from the rice blast fungus Magnaporthe oryzae, under the control of an inducible promoter, were challenged with transgenic Xoo and Xoc strains carrying a TAL effector designed to transactivate the inducible promoter. This induced AVR1-CO39 expression and triggered BB and BLS resistance when the corresponding Pi-CO39 resistance locus was present. In a second example, transactivation of an auto-active NLR by Xoo-delivered designer TAL effectors resulted in BB resistance, demonstrating that NLR-triggered immune responses efficiently control Xoo. This forms the foundation for future BB and BLS disease control strategies whereupon endogenous TAL effectors will target synthetic promoter regions of Avr or NLR executor genes.

Mathilde Hutin, Stella Césari, Véronique Chalvon, Corinne Michel, Tuan Tu Tran, Jens Boch, Ralf Koebnik, Boris Szurek and Thomas Kroj
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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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Rescooped by Nicolas Denancé from TAL effector science
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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.


Via dromius
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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. 


Via Norwich Rust Group
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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.


Via Pierre-Marc Delaux
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Rescooped by Nicolas Denancé from Publications
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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.


Via Kamoun Lab @ TSL
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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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