Plant-Microbe Interaction
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Rescooped by Guogen Yang from Genome Engineering & Reprogramming
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Distinct genetic control of homologous recombination repair of Cas9-induced double-strand breaks, nicks and paired nicks

Distinct genetic control of homologous recombination repair of Cas9-induced double-strand breaks, nicks and paired nicks | Plant-Microbe Interaction | Scoop.it
"DNA double-strand breaks (DSBs) are known to be powerful inducers of homologous recombination (HR), but single-strand breaks (nicks) have also been shown to trigger HR. Both DSB- and nick-induced HR (nickHR) are exploited in advanced genome-engineering approaches based on the bacterial RNA-guided nuclease Cas9. However, the mechanisms of nickHR are largely unexplored. Here, we applied Cas9 nickases to study nickHR in mammalian cells. We find that nickHR is unaffected by inhibition of major damage signaling kinases and that it is not suppressed by nonhomologous end-joining (NHEJ) components, arguing that nick processing does not require a DSB intermediate to trigger HR. Relative to a single nick, nicking both strands enhances HR, consistent with a DSB intermediate, even when nicks are induced up to ∼1kb apart. Accordingly, HR and NHEJ compete for repair of these paired nicks, but, surprisingly, only when 5' overhangs or blunt ends can be generated. Our study advances the understanding of molecular mechanisms driving nick and paired-nick repair in mammalian cells and clarify phenomena associated with Cas9-mediated genome editing. " . PMID: 27001513

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Rescooped by Guogen Yang from Plant Pathogenomics
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Web resource: 1000 Fungal Genomes Project (2016)

Web resource: 1000 Fungal Genomes Project (2016) | Plant-Microbe Interaction | Scoop.it

Sequencing unsampled fungal diversity


Via Kamoun Lab @ TSL
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Rescooped by Guogen Yang from Plant-Microbe Symbiosis
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The Symbiosis-Related ERN Transcription Factors Act in Concert to Coordinate Rhizobial Host Root Infection

The Symbiosis-Related ERN Transcription Factors Act in Concert to Coordinate Rhizobial Host Root Infection | Plant-Microbe Interaction | Scoop.it
Legumes improve their mineral nutrition through nitrogen-fixing root nodule symbioses with soil rhizobia. Rhizobial infection of legumes is regulated by a number of transcription factors, including ERF Required for Nodulation 1 (ERN1). Medicago truncatula plants defective in ERN1 are unable to nodulate, but still exhibit early symbiotic responses including rhizobial infection. ERN1 has a close homolog, ERN2, which shows partially overlapping expression patterns. Here we show ern2 mutants exhibit a later nodulation phenotype than ern1, being able to form nodules but with signs of premature senescence. Molecular characterization of the ern2-1 mutation reveals a key role for a conserved threonine for both DNA binding and transcriptional activity. In contrast to either single mutant the double ern1-1 ern2-1 line is completely unable to initiate infection or nodule development. The strong ern1-1 ern2-1 phenotype demonstrates functional redundancy between these two transcriptional regulators and reveals the essential role of ERN1/ERN2 to coordinately induce rhizobial infection and nodule organogenesis. While ERN1/ERN2 act in concert in the root epidermis, only ERN1 can efficiently allow the development of mature nodules in the cortex, probably through an independent pathway. Together, these findings reveal the key roles that ERN1/ERN2 play at the very earliest stages of root nodule development.

Via Christophe Jacquet, Jean-Michel Ané
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Rescooped by Guogen Yang from Plant-Microbe Symbiosis
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A database for the taxonomic and phylogenetic identification of the genus Bradyrhizobium using multilocus sequence analysis

A database for the taxonomic and phylogenetic identification of the genus Bradyrhizobium using multilocus sequence analysis | Plant-Microbe Interaction | Scoop.it
Background
Biological nitrogen fixation, with an emphasis on the legume-rhizobia symbiosis, is a key process for agriculture and the environment, allowing the replacement of nitrogen fertilizers, reducing water pollution by nitrate as well as emission of greenhouse gases. Soils contain numerous strains belonging to the bacterial genus Bradyrhizobium, which establish symbioses with a variety of legumes. However, due to the high conservation of Bradyrhizobium 16S rRNA genes - considered as the backbone of the taxonomy of prokaryotes - few species have been delineated. The multilocus sequence analysis (MLSA) methodology, which includes analysis of housekeeping genes, has been shown to be promising and powerful for defining bacterial species, and, in this study, it was applied to Bradyrhizobium, species, increasing our understanding of the diversity of nitrogen-fixing bacteria.

Description
Classification of bacteria of agronomic importance is relevant to biodiversity, as well as to biotechnological manipulation to improve agricultural productivity. We propose the construction of an online database that will provide information and tools using MLSA to improve phylogenetic and taxonomic characterization of Bradyrhizobium, allowing the comparison of genomic sequences with those of type and representative strains of each species.

Conclusion
A database for the taxonomic and phylogenetic identification of the Bradyrhizobium, genus, using MLSA, will facilitate the use of biological data available through an intuitive web interface. Sequences stored in the on-line database can be compared with multiple sequences of other strains with simplicity and agility through multiple alignment algorithms and computational routines integrated into the database. The proposed database and software tools are available at http://​mlsa.​cnpso.​embrapa.​br, and can be used, free of charge, by researchers worldwide to classify Bradyrhizobium, strains; the database and software can be applied to replicate the experiments presented in this study as well as to generate new experiments. The next step will be expansion of the database to include other rhizobial species.

Via Jean-Michel Ané
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Rescooped by Guogen Yang from Plant-microbe interaction
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The novel tobacco RING E3 ligase NtRFP1 mediates ubiquitination and proteasomal degradation of a geminivirus-encoded βC1: Molecular Plant

The βC1 protein encoded by the Tomato yellow leaf curl China virus associated betasatellite functions as a pathogenicity determinant. To better understand the molecular basis whereby βC1 functions in pathogenicity, a yeast two-hybrid screen of a tobacco cDNA library was carried out using βC1 as bait. The screen revealed that βC1 interacts with a tobacco RING-finger protein designated NtRFP1, and the interaction was confirmed using a bimolecular fluorescence complementation (BiFC) and Co-immunoprecipitation (CoIP) assays in Nicotiana benthamiana cells. NtRFP1 expression was induced by βC1, and in vitro ubiquitination assays showed that NtRFP1 is a functional E3 ubiquitin ligase that mediates βC1 ubiquitination. In addition, βC1 was shown to be ubiquitinated in vivo and degraded by the plant 26S proteasome. After viral infection, plants overexpressing NtRFP1 developed attenuated symptoms, and plants silenced for NtRFP1 expression had severe symptoms. Other lines of evidence showed that NtRFP1 attenuates βC1 symptoms by promoting βC1 degradation by the 26S proteasome. These results suggest that the tobacco RING E3 ligase NtRFP1 attenuates disease symptoms by interacting with βC1 to mediate its ubiquitination and degradation via the ubiquitin/26S proteasome system.

Via Suayib Üstün
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Rescooped by Guogen Yang from Plant immunity and legume symbiosis
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A CCaMK-CYCLOPS-DELLA Complex Activates Transcription of RAM1 to Regulate Arbuscule Branching

A CCaMK-CYCLOPS-DELLA Complex Activates Transcription of RAM1 to Regulate Arbuscule Branching | Plant-Microbe Interaction | Scoop.it
Intracellular arbuscular mycorrhiza symbiosis between plants and glomeromycotan fungi leads to formation of highly branched fungal arbuscules that release mineral nutrients to the plant host. Their development is regulated in plants by a mechanistically unresolved interplay between symbiosis, nutrient, and hormone (gibberellin) signaling. Using a positional cloning strategy and a retrotransposon insertion line, we identify two novel alleles of Lotus japonicus REDUCED ARBUSCULAR MYCORRHIZA1 (RAM1) encoding a GRAS protein. We confirm that RAM1 is a central regulator of arbuscule development: arbuscule branching is arrested in L. japonicus ram1 mutants, and ectopic expression of RAM1 activates genes critical for arbuscule development in the absence of fungal symbionts. Epistasis analysis places RAM1 downstream of CCaMK, CYCLOPS, and DELLA because ectopic expression of RAM1 restores arbuscule formation in cyclops mutants and in the presence of suppressive gibberellin. The corresponding proteins form a complex that activates RAM1 expression via binding of CYCLOPS to a cis element in the RAM1 promoter. We thus reveal a transcriptional cascade in arbuscule development that employs the promoter of RAM1 as integrator of symbiotic (transmitted via CCaMK and CYCLOPS) and hormonal (gibberellin) signals.

Via Pierre-Marc Delaux, Christophe Jacquet
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Rescooped by Guogen Yang from Plants and Microbes
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Science: Plant probiotics to the rescue (2016)

Science: Plant probiotics to the rescue (2016) | Plant-Microbe Interaction | Scoop.it

Via Kamoun Lab @ TSL
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Rescooped by Guogen Yang from MycorWeb Plant-Microbe Interactions
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New Phytologist: Inspirational decoys: a new hunt for effector targets (2016)

New Phytologist: Inspirational decoys: a new hunt for effector targets (2016) | Plant-Microbe Interaction | Scoop.it

Understanding recognition mechanisms of pathogenic microbes by plants is not only pivotal to crop protection programs, but has also revealed fascinating examples of co-evolutionary biology. A new phase has been initiated with a series of exciting discoveries on ‘integrated decoys’. In this issue of New Phytologist, Kroj et al. (pp. 618–626) show that the integrated decoys are diverse, but common in plants and illustrate that this model predicts novel components in plant immunity.

 


Via Kamoun Lab @ TSL, Francis Martin
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Rescooped by Guogen Yang from Plant immunity and legume symbiosis
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PLOS Pathogens: Activation of Plant Innate Immunity by Extracellular High Mobility Group Box 3 and Its Inhibition by Salicylic Acid (2016)

PLOS Pathogens: Activation of Plant Innate Immunity by Extracellular High Mobility Group Box 3 and Its Inhibition by Salicylic Acid (2016) | Plant-Microbe Interaction | Scoop.it

Damage-associated molecular pattern molecules (DAMPs) signal the presence of tissue damage to induce immune responses in plants and animals. Here, we report that High Mobility Group Box 3 (HMGB3) is a novel plant DAMP. Extracellular HMGB3, through receptor-like kinases BAK1 and BKK1, induced hallmark innate immune responses, including i) MAPK activation, ii) defense-related gene expression, iii) callose deposition, and iv) enhanced resistance to Botrytis cinerea. Infection by necrotrophic B. cinerea released HMGB3 into the extracellular space (apoplast). Silencing HMGBs enhanced susceptibility to B. cinerea, while HMGB3 injection into apoplast restored resistance. Like its human counterpart, HMGB3 binds salicylic acid (SA), which results in inhibition of its DAMP activity. An SA-binding site mutant of HMGB3 retained its DAMP activity, which was no longer inhibited by SA, consistent with its reduced SA-binding activity. These results provide cross-kingdom evidence that HMGB proteins function as DAMPs and that SA is their conserved inhibitor.


Via Kamoun Lab @ TSL, Christophe Jacquet
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Rescooped by Guogen Yang from Plants and Microbes
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Molecular Plant: Natural variation in tomato reveals differences in the recognition of AvrPto and AvrPtoB effectors from Pseudomonas syringae (2016)

Molecular Plant: Natural variation in tomato reveals differences in the recognition of AvrPto and AvrPtoB effectors from Pseudomonas syringae (2016) | Plant-Microbe Interaction | Scoop.it

The Pto protein kinase from Solanum pimpinellifolium interacts with Pseudomonas syringae effectors AvrPto or AvrPtoB to activate effector-triggered immunity. The previously solved crystal structures of the AvrPto-Pto and AvrPtoB-Pto complexes revealed that Pto binds each effector through both a shared and a unique interface. Here we use natural variation in wild species of tomato to further investigate Pto recognition of these two effectors. One species, Solanum chmielewskii, was found to have many accessions that recognize only AvrPtoB. The Pto ortholog from one of these accessions was responsible for recognition of AvrPtoB and it differed from Solanum pimpinellifolium Pto by just 14 amino acids, including two in the AvrPto-specific interface, glutamate-49/glycine-51. Converting these two residues to those in Pto (histidine-49/valine-51) did not restore recognition of AvrPto. Subsequent experiments revealed that a single substitution of a histidine-to-aspartate at position 193 in Pto, which is not near the AvrPto-specific interface, was sufficient for conferring recognition of AvrPto in plant cells. The reciprocal substitution of aspartate-to-histidine-193 in Pto abolished AvrPto recognition, confirming the importance of this residue. Our results reveal new aspects about effector recognition by Pto and demonstrate the value of using natural variation to understand the interaction between resistance proteins and pathogen effectors.


Via Kamoun Lab @ TSL
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Rescooped by Guogen Yang from Plant immunity and legume symbiosis
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The Wheat Mediator Subunit TaMED25 Interacts with the Transcription Factor TaEIL1 to Negatively Regulate Disease Resistance against Powdery Mildew

The Wheat Mediator Subunit TaMED25 Interacts with the Transcription Factor TaEIL1 to Negatively Regulate Disease Resistance against Powdery Mildew | Plant-Microbe Interaction | Scoop.it
Powdery mildew, caused by the biotrophic fungal pathogen Blumeria graminis f. sp. tritici, is a major limitation for the production of bread wheat (Triticum aestivum). However, to date, the transcriptional regulation of bread wheat defense against powdery mildew remains largely unknown. Here, we report the function and molecular mechanism of the bread wheat Mediator subunit 25 (TaMED25) in regulating the bread wheat immune response signaling pathway. Three homoalleles of TaMED25 from bread wheat were identified and mapped to chromosomes 5A, 5B, and 5D, respectively. We show that knockdown of TaMED25 by barley stripe mosaic virus-induced gene silencing reduced bread wheat susceptibility to the powdery mildew fungus during the compatible plant-pathogen interaction. Moreover, our results indicate that MED25 may play a conserved role in regulating bread wheat and barley (Hordeum vulgare) susceptibility to powdery mildew. Similarly, bread wheat ETHYLENE INSENSITIVE3-LIKE1 (TaEIL1), an ortholog of Arabidopsis (Arabidopsis thaliana) ETHYLENE INSENSITIVE3, negatively regulates bread wheat resistance against powdery mildew. Using various approaches, we demonstrate that the conserved activator-interacting domain of TaMED25 interacts physically with the separate amino- and carboxyl-terminal regions of TaEIL1, contributing to the transcriptional activation activity of TaEIL1. Furthermore, we show that TaMED25 and TaEIL1 synergistically activate ETHYLENE RESPONSE FACTOR1 (TaERF1) transcription to modulate bread wheat basal disease resistance to B. graminis f. sp. tritici by repressing the expression of pathogenesis-related genes and deterring the accumulation of reactive oxygen species. Collectively, we identify the TaMED25-TaEIL1-TaERF1 signaling module as a negative regulator of bread wheat resistance to powdery mildew.

Via Christophe Jacquet
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Rescooped by Guogen Yang from MycorWeb Plant-Microbe Interactions
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Comparative genome analysis and genome evolution of members of the magnaporthaceae family of fungi

Comparative genome analysis and genome evolution of members of the magnaporthaceae family of fungi | Plant-Microbe Interaction | Scoop.it

Background

Magnaporthaceae, a family of ascomycetes, includes three fungi of great economic importance that cause disease in cereal and turf grasses: Magnaporthe oryzae (rice blast), Gaeumannomyces graminis var. tritici (take-all disease), and Magnaporthe poae (summer patch disease). Recently, the sequenced and assembled genomes for these three fungi were reported. Here, the genomes were compared for orthologous genes in order to identified genes that are unique to the Magnaporthaceae family of fungi. In addition, ortholog clustering was used to identify a core proteome for the Magnaporthaceae, which was examined for diversifying and purifying selection and evidence of two-speed genome evolution.


Results

A genome-scale comparative study was conducted across 74 fungal genomes to identify clusters of orthologous genes unique to the three Magnaporthaceae species as well as species specific genes. We found 1149 clusters that were unique to the Magnaporthaceae family of fungi with 295 of those containing genes from all three species. Gene clusters involved in metabolic and enzymatic activities were highly represented in the Magnaporthaceae specific clusters. Also highly represented in the Magnaporthaceae specific clusters as well as in the species specific genes were transcriptional regulators. In addition, we examined the relationship between gene evolution and distance to repetitive elements found in the genome. No correlations between diversifying or purifying selection and distance to repetitive elements or an increased rate of evolution in secreted and small secreted proteins were observed.


Conclusions
Taken together, these data show that at the genome level, there is no evidence to suggest multi-speed genome evolution or that proximity to repetitive elements play a role in diversification of genes.


Via Francis Martin
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Rescooped by Guogen Yang from Virology and Bioinformatics from Virology.ca
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Computational Clustering for Viral Reference Proteomes

Motivation: The enormous number of redundant sequenced genomes has hindered efforts to analyze and functionally annotate proteins. As the taxonomy of viruses is not uniformly defined, viral proteomes pose special challenges in this regard. Grouping viruses based on the similarity of their proteins at proteome scale can normalize against potential taxonomic nomenclature anomalies.

Results: We present Viral Reference Proteomes (Viral RPs), which are computed from complete virus proteomes within UniProtKB. Viral RPs based on 95%, 75%, 55%, 35% and 15% co-membership in proteome similarity based clusters are provided. Comparison of our computational Viral RPs with UniProt’s curator-selected Reference Proteomes indicates that the two sets are consistent and complementary. Furthermore, each Viral RP represents a cluster of virus proteomes that was consistent with virus or host taxonomy. We provide BLASTP search and FTP download of Viral RP protein sequences, and a browser to facilitate the visualization of Viral RPs.

Availability: http://proteininformationresource.org/rps/viruses/

Via Cindy
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Rescooped by Guogen Yang from MycorWeb Plant-Microbe Interactions
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De novo genome assembly and annotation of rice sheath rot fungus Sarocladium oryzae reveals genes involved in Helvolic acid and Cerulenin biosynthesis pathways

Background
Sheath rot disease caused by Sarocladium oryzae is an emerging threat for rice cultivation at global level. However, limited information with respect to genomic resources and pathogenesis is a major setback to develop disease management strategies. Considering this fact, we sequenced the whole genome of highly virulent Sarocladium oryzae field isolate, Saro-13 with 82x sequence depth.

Results
The genome size of S. oryzae was 32.78 Mb with contig N50 18.07 Kb and 10526 protein coding genes. The functional annotation of protein coding genes revealed that S. oryzae genome has evolved with many expanded gene families of major super family, proteinases, zinc finger proteins, sugar transporters, dehydrogenases/reductases, cytochrome P450, WD domain G-beta repeat and FAD-binding proteins. Gene orthology analysis showed that around 79.80 % of S. oryzae genes were orthologous to other Ascomycetes fungi. The polyketide synthase dehydratase, ATP-binding cassette (ABC) transporters, amine oxidases, and aldehyde dehydrogenase family proteins were duplicated in larger proportion specifying the adaptive gene duplications to varying environmental conditions. Thirty-nine secondary metabolite gene clusters encoded for polyketide synthases, nonribosomal peptide synthase, and terpene cyclases. Protein homology based analysis indicated that nine putative candidate genes were found to be involved in helvolic acid biosynthesis pathway. The genes were arranged in cluster and structural organization of gene cluster was similar to helvolic acid biosynthesis cluster in Metarhizium anisophilae. Around 9.37 % of S. oryzae genes were identified as pathogenicity genes, which are experimentally proven in other phytopathogenic fungi and enlisted in pathogen-host interaction database. In addition, we also report 13212 simple sequences repeats (SSRs) which can be deployed in pathogen identification and population dynamic studies in near future.

Conclusions
Large set of pathogenicity determinants and putative genes involved in helvolic acid and cerulenin biosynthesis will have broader implications with respect to Sarocladium disease biology. This is the first genome sequencing report globally and the genomic resources developed from this study will have wider impact worldwide to understand Rice-Sarocladium interaction.

Via Francis Martin
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Rescooped by Guogen Yang from Plant immunity and legume symbiosis
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The Mechanistic Underpinnings of an ago1-Mediated, Environmentally Dependent, and Stochastic Phenotype

The Mechanistic Underpinnings of an ago1-Mediated, Environmentally Dependent, and Stochastic Phenotype | Plant-Microbe Interaction | Scoop.it
The crucial role of microRNAs in plant development is exceedingly well supported; their importance in environmental robustness is studied in less detail. Here, we describe a novel, environmentally dependent phenotype in hypomorphic argonaute1 (ago1) mutants and uncover its mechanistic underpinnings in Arabidopsis (Arabidopsis thaliana). AGO1 is a key player in microRNA-mediated gene regulation. We observed transparent lesions on embryonic leaves of ago1 mutant seedlings. These lesions increased in frequency in full-spectrum light. Notably, the lesion phenotype was most environmentally responsive in ago1-27 mutants. This allele is thought to primarily affect translational repression, which has been linked with the response to environmental perturbation. Using several lines of evidence, we found that these lesions represent dead and dying tissues due to an aberrant hypersensitive response. Although all three canonical defense hormone pathways (salicylic acid, jasmonate, and jasmonate/ethylene pathways) were up-regulated in ago1 mutants, we demonstrate that jasmonate perception drives the lesion phenotype. Double mutants of ago1 and coronatine insensitive1, the jasmonate receptor, showed greatly decreased frequency of affected seedlings. The chaperone HEAT SHOCK PROTEIN 90 (HSP90), which maintains phenotypic robustness in the face of environmental perturbations, is known to facilitate AGO1 function. HSP90 perturbation has been shown previously to up-regulate jasmonate signaling and to increase plant resistance to herbivory. Although single HSP90 mutants showed subtly elevated levels of lesions, double mutant analysis disagreed with a simple epistatic model for HSP90 and AGO1 interaction; rather, both appeared to act nonadditively in producing lesions. In summary, our study identifies AGO1 as a major, largely HSP90-independent, factor in providing environmental robustness to plants.

Via Christophe Jacquet
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Rescooped by Guogen Yang from Plant-Microbe Symbiosis
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Arabidopsis heterotrimeric G proteins regulate immunity by directly coupling to the FLS2 receptor

Arabidopsis heterotrimeric G proteins regulate immunity by directly coupling to the FLS2 receptor | Plant-Microbe Interaction | Scoop.it
The Arabidopsis immune receptor FLS2 perceives bacterial flagellin epitope flg22 to activate defenses through the central cytoplasmic kinase BIK1. The heterotrimeric G proteins composed of the non-canonical Gα protein XLG2, the Gβ protein AGB1, and the Gγ proteins AGG1 and AGG2 are required for FLS2-mediated immune responses through an unknown mechanism. Here we show that in the pre-activation state, XLG2 directly interacts with FLS2 and BIK1, and it functions together with AGB1 and AGG1/2 to attenuate proteasome-mediated degradation of BIK1, allowing optimum immune activation. Following the activation by flg22, XLG2 dissociates from AGB1 and is phosphorylated by BIK1 in the N terminus. The phosphorylated XLG2 enhances the production of reactive oxygen species (ROS) likely by modulating the NADPH oxidase RbohD. The study demonstrates that the G proteins are directly coupled to the FLS2 receptor complex and regulate immune signaling through both pre-activation and post-activation mechanisms.

Via Christophe Jacquet, Jean-Michel Ané
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Rescooped by Guogen Yang from Plant immunity and legume symbiosis
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SERK co-receptor kinases

SERK co-receptor kinases | Plant-Microbe Interaction | Scoop.it
What are they? Somatic embryogenesis receptor-like kinases (SERKs) are small membrane-embedded signaling proteins. They are part of a plant-specific family of leucine-rich repeat (LRR) receptor kinases (RKs). LRR-RKs are membrane receptors that sense a diverse set of extracellular ligands, and that relay these signals into the cytosol to trigger specific cellular responses (Figure 1). The genome of Arabidopsis thaliana encodes at least 220 LRR-RKs, five of which are SERKs. SERK proteins consist of a small extracellular LRR-domain with 5 repeats, a single membrane-spanning helix and a cytoplasmic kinase domain, which can auto- and trans-phosphorylate on Ser/Thr and Tyr residues (dual-specificity kinase).

Via Christophe Jacquet
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Rescooped by Guogen Yang from Plants and Microbes
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Nature Microbiology: Evidence for the sexual origin of heterokaryosis in arbuscular
mycorrhizal fungi (2016)

Nature Microbiology: Evidence for the sexual origin of heterokaryosis in arbuscular<br/>                    mycorrhizal fungi (2016) | Plant-Microbe Interaction | Scoop.it
Sexual reproduction is ubiquitous among eukaryotes, and fully asexual lineages are extremely rare. Prominent among ancient asexual lineages are the arbuscular mycorrhizal fungi (AMF), a group of plant symbionts with a multinucleate cytoplasm. Genomic divergence among co-existing nuclei was proposed to drive the evolutionary success of AMF in the absence of sex1, but this hypothesis has been contradicted by recent genome analyses that failed to find significant genetic diversity within an AMF isolate2,3. Here, we set out to resolve issues surrounding the genome organization and sexual potential of AMF by exploring the genomes of five isolates of Rhizophagus irregularis, a model AMF. We find that genetic diversity in this species varies among isolates and is structured in a homo-dikaryon-like manner usually linked with the existence of a sexual life cycle. We also identify a putative AMF mating-type locus, containing two genes with structural and evolutionary similarities with the mating-type locus of some Dikarya. Our analyses suggest that this locus may be multi-allelic and that AMF could be heterothallic and bipolar. These findings reconcile opposing views on the genome organization of these ubiquitous plant symbionts and open avenues for strain improvement and environmental application of these organisms.

Via Francis Martin, Kamoun Lab @ TSL
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Rescooped by Guogen Yang from MycorWeb Plant-Microbe Interactions
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Live-cell fluorescence imaging to investigate the dynamics of plant cell death during infection by the rice blast fungus Magnaporthe oryzae

Live-cell fluorescence imaging to investigate the dynamics of plant cell death during infection by the rice blast fungus Magnaporthe oryzae | Plant-Microbe Interaction | Scoop.it

Background. Plant cell death plays important roles during plant-pathogen interactions. To study pathogen-induced cell death, there is a need for cytological tools that allow determining not only host cell viability, but also cellular events leading to cell death with visualization of pathogen development. Here we describe a live cell imaging method to provide insights into the dynamics of cell death in rice (Oryza sativa). This method uses live-cell confocal microscopy of rice sheath cells mechanically damaged or invaded by fluorescently-tagged Magnaporthe oryzae together with fluorescent dyes fluorescein diacetate (FDA) and propidium iodide (PI). FDA stains the cytoplasm of live cells exclusively, thus also visualizing the vacuole, whereas PI stains nuclei of dead cells.


Results. We first demonstrated that confocal microscopy of rice leaf sheaths stained with FDA and PI discriminated between live cells and mechanically-killed cells. FDA-derived fluorescein was confined to the cytoplasm of live cells, indicating the intact vacuolar and plasma membranes. We also observed previously unreported fluorescein patterns in mechanically damaged cells. These patterns include: (1) homogeneous distribution of fluorescein in the increased area of the cytoplasm due to the shrunken vacuole; (2) the increase of the fluorescein intensity; and (3) containment of the brighter fluorescein signal only in affected cells likely due to closure of plasmodesmata. We refer to these as novel fluorescein patterns in this study. Simultaneous imaging of fluorescently-tagged M. oryzae (red) and FDA staining (green) in rice cells revealed characteristic features of the hemibiotrophic interaction. That is, newly invaded cells are alive but subsequently become dead when the fungus spreads into neighbor cells, and biotrophic interfacial complexes are associated with the host cytoplasm. This also revealed novel fluorescein patterns in invaded cells. Time-lapse imaging suggested that the FDA staining pattern in the infected host cell progressed from typical cytoplasmic localization (live cell with the intact vacuole), to novel patterns (dying cell with closed plasmodesmata with the shrunken or ruptured vacuole), to lack of fluorescence (dead cell).


Conclusion. We have developed a method to visualize cellular events leading to host cell death during rice blast disease. This method can be used to compare and contrast host cell death associated with disease resistance and susceptibility in rice-M. oryzae and other host-pathogen interactions.


Via Francis Martin
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Rescooped by Guogen Yang from Plants and Microbes
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PLOS Pathogens: Cellular Tracking and Gene Profiling of Fusarium graminearum during Maize Stalk Rot Disease Development Elucidates Its Strategies in Confronting Phosphorus Limitation in the Host ...

PLOS Pathogens: Cellular Tracking and Gene Profiling of  Fusarium graminearum  during Maize Stalk Rot Disease Development Elucidates Its Strategies in Confronting Phosphorus Limitation in the Host ... | Plant-Microbe Interaction | Scoop.it

The ascomycete fungus Fusarium graminearum causes stalk rot in maize. We tracked this pathogen’s growth in wound-inoculated maize stalks using a fluorescence-labeled fungal isolate and observed that invasive hyphae grew intercellularly up to 24 h post inoculation, grew intra- and inter-cellularly between 36–48 h, and fully occupied invaded cells after 72 h. Using laser microdissection and microarray analysis, we profiled changes in global gene expression during pathogen growth inside pith tissues of maize stalk from 12 h to six days after inoculation and documented transcriptomic patterns that provide further insights into the infection process. Expression changes in transcripts encoding various plant cell wall degrading enzymes appeared to correlate with inter- and intracellular hyphal growth. Genes associated with 36 secondary metabolite biosynthesis clusters were expressed. Expression of several F. graminearum genes potentially involved in mobilization of the storage lipid triacylglycerol and phosphorus-free lipid biosynthesis were induced during early infection time points, and deletion of these genes caused reduction of virulence in maize stalk. Furthermore, we demonstrated that the F. graminearum betaine lipid synthase 1 (BTA1) gene was necessary and sufficient for production of phosphorus-free membrane lipids, and that deletion of BTA1 interfered with F. graminearum’s ability to advance intercellularly. We conclude that F. graminearum produces phosphorus-free membrane lipids to adapt to a phosphate-limited extracellular microenvironment during early stages of its invasion of maize stalk.


Via Kamoun Lab @ TSL
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Rescooped by Guogen Yang from MycorWeb Plant-Microbe Interactions
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Design and synthesis of a minimal bacterial genome

Design and synthesis of a minimal bacterial genome | Plant-Microbe Interaction | Scoop.it
A goal in biology is to understand the molecular and biological function of every gene in a cell. One way to approach this is to build a minimal genome that includes only the genes essential for life. In 2010, a 1079-kb genome based on the genome of Mycoplasma mycoides (JCV-syn1.0) was chemically synthesized and supported cell growth when transplanted into cytoplasm. Hutchison III et al. used a design, build, and test cycle to reduce this genome to 531 kb (473 genes). The resulting JCV-syn3.0 retains genes involved in key processes such as transcription and translation, but also contains 149 genes of unknown function.

Via Jean-Michel Ané, Francis Martin
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Banana fruit NAC transcription factor MaNAC5 cooperates with MaWRKYs to enhance the expression of pathogenesis-related genes against Colletotrichum musae - Molecular Plant Pathology -

Banana fruit NAC transcription factor MaNAC5 cooperates with MaWRKYs to enhance the expression of pathogenesis-related genes against Colletotrichum musae - Molecular Plant Pathology - | Plant-Microbe Interaction | Scoop.it
Plants respond to pathogen attack by the modulation of a large set of genes, which are regulated by different types of transcription factor (TF). NAC (NAM/ATAF/CUC) and WRKY are plant-specific families of TFs, and have received much attention as transcriptional regulators in plant pathogen defence. However, the cooperation between NAC and WRKY TFs in the disease response remains largely unknown. Our previous study has revealed that two banana fruit WRKY TFs, MaWRKY1 and MaWRKY2, are involved in salicylic acid (SA)- and methyl jasmonate (MeJA)-induced resistance against Colletotrichum musae via binding to promoters of pathogenesis-related (PR) genes. Here, we found that MaNAC1, MaNAC2 and MaNAC5 were up-regulated after C. musae infection, and were also significantly enhanced by SA and MeJA treatment. Protein–protein interaction analysis showed that MaNAC5 physically interacted with MaWRKY1 and MaWRKY2. More importantly, dual-luciferase reporter (DLR) assay revealed that MaNAC5, MaWRKY1 and MaWRKY2 were transcriptional activators, and individually or cooperatively activated the transcriptional activities of MaPR1-1, MaPR2, MaPR10c and MaCHIL1 genes. Collectively, our results indicate that MaNAC5 cooperates with MaWRKY1 and MaWRKY2 to regulate the expression of a specific set of PR genes in the disease response, and to contribute at least partially to SA- and MeJA-induced pathogen resistance.

Via Christophe Jacquet
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Rescooped by Guogen Yang from Plant Immunity And Microbial Effectors
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Defense responses of plant cell wall non-catalytic proteins against pathogens

Publication date: Available online 30 March 2016 Source:Physiological and Molecular Plant Pathology Author(s): Abdur Rashid Plant cell wall (CW) associated non-enzymatic proteins (CWPs) are composed mainly of glycoproteins containing a...
Via IPM Lab
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Rescooped by Guogen Yang from Plant immunity and legume symbiosis
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The DELLA Protein SLR1 Integrates and Amplifies Salicylic Acid- and Jasmonic Acid-Dependent Innate Immunity in Rice

The DELLA Protein SLR1 Integrates and Amplifies Salicylic Acid- and Jasmonic Acid-Dependent Innate Immunity in Rice | Plant-Microbe Interaction | Scoop.it
Gibberellins are a class of tetracyclic plant hormones that are well known to promote plant growth by inducing the degradation of a class of nuclear growth-repressing proteins, called DELLAs. In recent years, GA and DELLAs are also increasingly implicated in plant responses to pathogen attack, although our understanding of the underlying mechanisms is still limited, especially in monocotyledonous crop plants. Aiming to further decipher the molecular underpinnings of GA- and DELLA-modulated plant immunity, we studied the dynamics and impact of GA and DELLA during infection of the model crop rice (Oryza sativa) with four different pathogens exhibiting distinct lifestyles and infection strategies. Opposite to previous findings in Arabidopsis (Arabidopsis thaliana), our findings reveal a prominent role of the DELLA protein Slender Rice1 (SLR1) in the resistance toward (hemi)biotrophic but not necrotrophic rice pathogens. Moreover, contrary to the differential effect of DELLA on the archetypal defense hormones salicylic acid (SA) and jasmonic acid (JA) in Arabidopsis, we demonstrate that the resistance-promoting effect of SLR1 is due at least in part to its ability to boost both SA- and JA-mediated rice defenses. In a reciprocal manner, we found JA and SA treatment to interfere with GA metabolism and stabilize SLR1. Together, these findings favor a model whereby SLR1 acts as a positive regulator of hemibiotroph resistance in rice by integrating and amplifying SA- and JA-dependent defense signaling. Our results highlight the differences in hormone defense networking between rice and Arabidopsis and underscore the importance of GA and DELLA in molding disease outcomes.

Via Christophe Jacquet
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Rescooped by Guogen Yang from Plants and Microbes
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Plant Physiology and Biochemistry: Reactive Oxygen Species, essential molecules, during plant-pathogen interactions (2016)

Plant Physiology and Biochemistry: Reactive Oxygen Species, essential molecules, during plant-pathogen interactions (2016) | Plant-Microbe Interaction | Scoop.it

• Description on the best characterized enzymatic systems as NAD(P)H oxidase and apoplastic peroxidases and oxidases involving in the Reactive Oxygen Species (ROS) generation.

 

• ROS as essential molecule during plant-pathogen interactions.

 

• We described how the plant perceive the pathogen invasion and trigger resistance response using ROS as signal molecule.

 

Reactive oxygen species (ROS) are continually generated as a consequence of the normal metabolism in aerobic organisms. Accumulation and release of ROS into cell take place in response to a wide variety of adverse environmental conditions including salt, temperature, cold stresses and pathogen attack, among others. In plants, peroxidases class III, NADPH oxidase (NOX) locates in cell wall and plasma membrane, respectively, may be mainly enzymatic systems involving ROS generation. It is well documented that ROS play a dual role into cells, acting as important signal transduction molecules and as toxic molecules with strong oxidant power, however some aspects related to its function during plant-pathogen interactions remain unclear. This review focuses on the principal enzymatic systems involving ROS generation addressing the role of ROS as signal molecules during plant-pathogen interactions. We described how the chloroplasts, mitochondria and peroxisomes perceive the external stimuli as pathogen invasion, and trigger resistance response using ROS as signal molecule.


Via Kamoun Lab @ TSL
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Rakesh Yashroy's curator insight, February 29, 9:13 PM

Host-pathogen interface is a very important realm of health and disease @ https://en.wikipedia.org/wiki/Host-pathogen_interface