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The Arabidopsis ROP GTPase AtROP6 functions in developmental and pathogen response pathways

The Arabidopsis ROP GTPase AtROP6 functions in developmental and pathogen response pathways | Plant-Microbe Interaction | Scoop.it

How plants coordinate developmental processes and environmental stress responses is a pressing question. Here, we show that Arabidopsis AtROP6 integrates developmental and pathogen response signaling. AtROP6 expression is induced by auxin and detected in the root meristem, lateral root initials, and leaf hydathodes. Plants expressing a dominant negative AtROP6 (rop6DN) under regulation of its endogenous promoter are small, have multiple inflorescence stems, twisted leaves, deformed leaf epidermis pavement cells, and differentially organized cytoskeleton. Microarrays analyses of rop6DN plants revealed that major changes in gene expression are associated with constitutive salicylic acid (SA)-mediated defense responses. In agreement, the free and total SA levels resembled that of wild-type plants inoculated with a virulent powdery mildew pathogen. The constitutive SA-associated response in rop6DN was suppressed in mutant backgrounds defective in SA signaling (npr1) or biosynthesis (sid2). However, the rop6DN npr1 or rop6DN sid2 double mutants retained the aberrant developmental phenotypes, indicating that the constitutive SA response can be uncoupled from ROP function(s) in development. rop6DN plants exhibited enhanced pre-invasive defense responses to a host-adapted virulent powdery mildew fungus, but were impaired in pre-invasive defenses upon inoculation with a non-adapted powdery mildew. The host-adapted powdery mildew had a reduced reproductive fitness on rop6DN plants, which was retained in mutant backgrounds defective in SA biosynthesis or signaling. Our findings indicate that both the morphological aberrations and altered sensitivity to powdery mildews of rop6DN plants result from perturbations that are independent from the SA-associated response. These perturbations uncouple SA-dependent defense signaling from disease resistance execution.


Via Suayib Üstün
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Rescooped by Guogen Yang from MycorWeb Plant-Microbe Interactions
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The Virtual Cell Animation Collection: Tools for Teaching Molecular and Cellular Biology

The Virtual Cell Animation Collection: Tools for Teaching Molecular and Cellular Biology | Plant-Microbe Interaction | Scoop.it
A cell is a minifactory in which structures and molecules are assembled, rearranged, disassembled, packaged, sorted, and transported. Because cellular structures and molecules are invisible to the human eye, students often have difficulty conceptualizing the dynamic nature of cells that function at multiple scales across time and space. To represent these dynamic cellular processes, the Virtual Cell Productions team at North Dakota State University develops freely available multimedia materials to support molecular and cellular biology learning inside and outside the high school and university classroom.

Via Francis Martin
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Rescooped by Guogen Yang from Plant Biology Teaching Resources (Higher Education)
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Hyperspectral phenotyping on the microscopic scale: towards automated characterization of plant-pathogen interactions

Hyperspectral phenotyping on the microscopic scale: towards automated characterization of plant-pathogen interactions | Plant-Microbe Interaction | Scoop.it

Background The detection and characterization of resistance reactions of crop plants against fungal pathogens are essential to select resistant genotypes. In breeding practice phenotyping of plant genotypes is realized by time consuming and expensive visual rating. In this context hyperspectral imaging (HSI) is a promising non-invasive sensor technique in order to accelerate and to automate classical phenotyping methods.A hyperspectral microscope was established to determine spectral changes on the leaf and cellular level of barley (Hordeum vulgare) during resistance reactions against powdery mildew (Blumeria graminis f.sp. hordei, isolate K1). Experiments were conducted with near isogenic barley lines of cv. Ingrid, including the susceptible wild type (WT), mildew locus a 12 (Mla12 based resistance) and the resistant mildew locus o 3 (mlo3 based resistance), respectively. The reflection of inoculated and non-inoculated leaves was recorded daily with a hyperspectral linescanner in the visual (400 – 700 nm) and near infrared (700 – 1000 nm) range 3 to 14 days after inoculation.Results  Data analysis showed no significant differences in spectral signatures between non-inoculated genotypes. Barley leaves of the near-isogenic genotypes, inoculated with B. graminis f.sp. hordeidiffered in the spectral reflectance over time, respectively. The susceptible genotypes (WT, Mla12) showed an increase in reflectance in the visible range according to symptom development. However, the spectral signature of the resistant mlo-genotype did not show significant changes over the experimental period. In addition, a recent data driven approach for automated discovery of disease specific signatures, which is based on a new representation of the data using Simplex Volume Maximization (SiVM) was applied. The automated approach - evaluated in only a fraction of time revealed results similar to the time and labor intensive manually assessed hyperspectral signatures. The new representation determined by SiVM was also used to generate intuitive and easy to interpretable summaries, e.g. fingerprints or traces of hyperspectral dynamics of the different genotypes.Conclusion  With this HSI based and data driven phenotyping approach an evaluation of host-pathogen interactions over time and a discrimination of barley genotypes differing in susceptibility to powdery mildew is possible.


Via IPM Lab, Steve Marek, Mary Williams
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Beyond Glycolysis: GAPDHs Are Multi-functional Enzymes Involved in Regulation of ROS, Autophagy, and Plant Immune Responses

Beyond Glycolysis: GAPDHs Are Multi-functional Enzymes Involved in Regulation of ROS, Autophagy, and Plant Immune Responses | Plant-Microbe Interaction | Scoop.it
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an important enzyme in energy metabolism with diverse cellular regulatory roles in vertebrates, but few reports have investigated the importance of plant GAPDH isoforms outside of their role in glycolysis. While animals possess one GAPDH isoform, plants possess multiple isoforms. In this study, cell biological and genetic approaches were used to investigate the role of GAPDHs during plant immune responses. Individual Arabidopsis GAPDH knockouts (KO lines) exhibited enhanced disease resistance phenotypes upon inoculation with the bacterial plant pathogen Pseudomonas syringae pv. tomato. KO lines exhibited accelerated programmed cell death and increased electrolyte leakage in response to effector triggered immunity. Furthermore, KO lines displayed increased basal ROS accumulation as visualized using the fluorescent probe H2DCFDA. The gapa1-2 and gapc1 KOs exhibited constitutive autophagy phenotypes in the absence of nutrient starvation. Due to the high sequence conservation between vertebrate and plant cytosolic GAPDH, our experiments focused on cytosolic GAPC1 cellular dynamics using a complemented GAPC1-GFP line. Confocal imaging coupled with an endocytic membrane marker (FM4-64) and endosomal trafficking inhibitors (BFA, Wortmannin) demonstrated cytosolic GAPC1 is localized to the plasma membrane and the endomembrane system, in addition to the cytosol and nucleus. After perception of bacterial flagellin, GAPC1 dynamically responded with a significant increase in size of fluorescent puncta and enhanced nuclear accumulation. Taken together, these results indicate that plant GAPDHs can affect multiple aspects of plant immunity in diverse sub-cellular compartments.

Via Suayib Üstün
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Rescooped by Guogen Yang from MycorWeb Plant-Microbe Interactions
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Fungal Effectors and Plant Susceptibility - Annual Review of Plant Biology

Fungal Effectors and Plant Susceptibility - Annual Review of Plant Biology | Plant-Microbe Interaction | Scoop.it
Plants can be colonized by fungi that have adopted highly diverse lifestyles, ranging from symbiotic to necrotrophic. Colonization is governed in all systems by hundreds of secreted fungal effector molecules. These effectors suppress plant defense responses and modulate plant physiology to accommodate fungal invaders and provide them with nutrients. Fungal effectors either function in the interaction zone between the fungal hyphae and host or are transferred to plant cells. This review describes the effector repertoires of 84 plant-colonizing fungi. We focus on the mechanisms that allow these fungal effectors to promote virulence or compatibility, discuss common plant nodes that are targeted by effectors, and provide recent insights into effector evolution. In addition, we address the issue of effector uptake in plant cells and highlight open questions and future challenges.

Via Christophe Jacquet, Francis Martin
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Jasmonate signalling in Arabidopsis involves SGT1b–HSP70–HSP90 chaperone complexes

Jasmonate signalling in Arabidopsis involves SGT1b–HSP70–HSP90 chaperone complexes | Plant-Microbe Interaction | Scoop.it
Plant hormones play pivotal roles in growth, development and stress responses. Although it is essential to our understanding of hormone signalling, how plants maintain a steady state level of hormone receptors is poorly understood. We show that mutation of the Arabidopsis thaliana co-chaperone SGT1b impairs responses to the plant hormones jasmonate, auxin and gibberellic acid, but not brassinolide and abscisic acid, and that SGT1b and its homologue SGT1a are involved in maintaining the steady state levels of the F-box proteins COI1 and TIR1, receptors for jasmonate and auxin, respectively. The association of SGT1b with COI1 is direct and is independent of the Arabidopsis SKP1 protein, ASK1. We further show that COI1 is a client protein of SGT1b–HSP70–HSP90 chaperone complexes and that the complexes function in hormone signalling by stabilizing the COI1 protein. This study extends the SGT1b–HSP90 client protein list and broadens the functional scope of SGT1b–HSP70–HSP90 chaperone complexes.

Via Suayib Üstün
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Molecular principles of membrane microdomain targeting in plants: Trends in Plant Science

Molecular principles of membrane microdomain targeting in plants: Trends in Plant Science | Plant-Microbe Interaction | Scoop.it
Highlights


•Proteins and lipids segregate into distinct and coexisting membrane microdomains in vivo.
•New microscopy techniques will facilitate the visualization of membrane microdomains and protein dynamics in vivo.
•Protein targeting to specific sites in the PM is dynamic and a consequence of combinatorial events.
•The cell wall–PM–cytoskeleton continuum is a hallmark of membrane microdomain assembly in plants.


Plasma membranes (PMs) are heterogeneous lipid bilayers comprising diverse subdomains. These sites can be labeled by various proteins in vivo and may serve as hotspots for signal transduction. They are found at apical, basal, and lateral membranes of polarized cells, at cell equatorial planes, or almost isotropically distributed throughout the PM. Recent advances in imaging technologies and understanding of mechanisms that allow proteins to target specific sites in PMs have provided insights into the dynamics and complexity of their specific segregation. Here we present a comprehensive overview of the different types of membrane microdomain and describe the molecular modes that determine site-directed targeting of membrane-resident proteins at the PM.


Via Suayib Üstün
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Rescooped by Guogen Yang from Plant-microbe interaction
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The Xanthomonas campestris Type III Effector XopJ Proteolytically Degrades Proteasome Subunit RPT6

The Xanthomonas campestris Type III Effector XopJ Proteolytically Degrades Proteasome Subunit RPT6 | Plant-Microbe Interaction | Scoop.it
Many animal and plant pathogenic bacteria inject type III effector (T3E) proteins into their eukaryotic host cells to suppress immunity. The Yersinia outer protein J (YopJ) family of T3Es is a widely distributed family of effector proteins found in both animal and plant pathogens, and its members are highly diversified in virulence functions. Some members have been shown to possess acetyltransferase activity; however, whether this is a general feature of YopJ family T3Es is currently unknown. The T3E Xanthomonas outer protein J (XopJ), a YopJ family effector from the plant pathogen Xanthomonas campestris pv vesicatoria, interacts with the proteasomal subunit Regulatory Particle AAA-ATPase6 (RPT6) in planta to suppress proteasome activity, resulting in the inhibition of salicylic acid-related immune responses. Here, we show that XopJ has protease activity to specifically degrade RPT6, leading to reduced proteasome activity in the cytoplasm as well as in the nucleus. Proteolytic degradation of RPT6 was dependent on the localization of XopJ to the plasma membrane as well as on its catalytic triad. Mutation of the Walker B motif of RPT6 prevented XopJ-mediated degradation of the protein but not XopJ interaction. This indicates that the interaction of RPT6 with XopJ is dependent on the ATP-binding activity of RPT6, but proteolytic cleavage additionally requires its ATPase activity. Inhibition of the proteasome impairs the proteasomal turnover of Nonexpressor of Pathogenesis-Related1 (NPR1), the master regulator of salicylic acid responses, leading to the accumulation of ubiquitinated NPR1, which likely interferes with the full induction of NPR1 target genes. Our results show that YopJ family T3Es are not only highly diversified in virulence function but also appear to possess different biochemical activities.

Via Suayib Üstün
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Suayib Üstün's curator insight, April 29, 3:58 PM

Our latest paper is finally out in the new issue of plant physiology! 

Rescooped by Guogen Yang from MycorWeb Plant-Microbe Interactions
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Genomics in a changing arctic: critical questions await the molecular ecologist

Genomics in a changing arctic: critical questions await the molecular ecologist | Plant-Microbe Interaction | Scoop.it

Molecular ecology is poised to tackle a host of interesting questions in the coming years. The Arctic provides a unique and rapidly changing environment with a suite of emerging research needs that can be addressed through genetics and genomics. Here we highlight recent research on boreal and tundra ecosystems and put forth a series of questions related to plant and microbial responses to climate change that can benefit from technologies and analytical approaches contained within the molecular ecologist's toolbox. These questions include understanding (i) the mechanisms of plant acquisition and uptake of N in cold soils, (ii) how these processes are mediated by root traits, (iii) the role played by the plant microbiome in cycling C and nutrients within high-latitude ecosystems and (iv) plant adaptation to extreme Arctic climates. We highlight how contributions can be made in these areas through studies that target model and nonmodel organisms and emphasize that the sequencing of the Populus and Salix genomes provides a valuable resource for scientific discoveries related to the plant microbiome and plant adaptation in the Arctic. Moreover, there exists an exciting role to play in model development, including incorporating genetic and evolutionary knowledge into ecosystem and Earth System Models. In this regard, the molecular ecologist provides a valuable perspective on plant genetics as a driver for community biodiversity, and how ecological and evolutionary forces govern community dynamics in a rapidly changing climate.


Via Francis Martin
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Rescooped by Guogen Yang from Plant immunity and legume symbiosis
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The dominant negative ARM domain uncovers multiple functions of PUB13 in Arabidopsis immunity, flowering, and senescence

The dominant negative ARM domain uncovers multiple functions of PUB13 in Arabidopsis immunity, flowering, and senescence | Plant-Microbe Interaction | Scoop.it
Regulating the intensity and duration of immune responses is crucial to combat infections without deleterious side effects. Arabidopsis FLS2, the receptor for bacterial flagellin, activates immune signalling by association with its partner BAK1. Upon flagellin (flg22) perception, the plant U-box E3 ubiquitin ligases PUB12 and PUB13 complex with FLS2 in a BAK1-dependent manner, and ubiquitinate FLS2 for protein degradation, thereby down-regulating flagellin signalling. Domain deletion analysis indicates that the ARM domain of PUB13 interacts with the FLS2–BAK1 complex and is phosphorylated by BAK1. Overexpression of the PUB13 ARM domain alone inhibits flg22-induced FLS2–PUB13 association and PUB12/13-mediated FLS2 ubiquitination and degradation in Arabidopsis, suggesting that ectopic expression of the ARM domain in planta generates a dominant negative effect via blocking the ubiquitination activity. Similar to the pub12pub13 double mutant, transgenic plants expressing the PUB13 ARM domain display enhanced immune responses compared with wild-type plants. Moreover, PUB13ARM transgenic plants and the pub12pub13 mutant are more sensitive to stress-induced leaf senescence accompanied by elevated expression of stress-induced senescence marker genes. The resemblance between PUB13ARM transgenic plants and the pub12pub13 mutant provides genetic evidence that ectopic expression of the PUB ARM domain serves as an alternative approach to dissect the overlapping functions of closely related PUB genes.

Via Christophe Jacquet
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Rescooped by Guogen Yang from Publications
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MPMI: A recent expansion of the RXLR effector gene Avrblb2 is maintained in global populations of Phytophthora infestans indicating different contributions to virulence (2015)

MPMI: A recent expansion of the RXLR effector gene Avrblb2 is maintained in global populations of Phytophthora infestans indicating different contributions to virulence (2015) | Plant-Microbe Interaction | Scoop.it

The introgression of disease resistance (R) genes encoding immunoreceptors with broad-spectrum recognition into cultivated potato appears to be the most promising approach to achieve sustainable management of late blight caused by the oomycete pathogen Phytophthora infestans. Rpi-blb2 from Solanum bulbocastanum, shows great potential for use in agriculture based on preliminary potato disease trials. Rpi-blb2 confers immunity by recognizing the P. infestans avirulence effector protein AVRblb2 after it is translocated inside the plant cell. This effector belongs to the RXLR class of effectors and is under strong positive selection. Structure-function analyses revealed a key polymorphic amino acid (position 69) in AVRblb2 effector that is critical for activation of Rpi-blb2. In this study, we reconstructed the evolutionary history of the Avrblb2 gene family and further characterized its genetic structure in worldwide populations. Our data indicates that Avrblb2 evolved as a single copy gene in a putative ancestral species of P. infestans and has recently expanded in the Phytophthora species that infect solanaceous hosts. As a consequence, at least four variants of AVRblb2 arose in P. infestans. One of these variants, with a Phe residue at position 69, evades recognition by the cognate resistance gene. Surprisingly, all Avrblb2 variants are maintained in pathogen populations. This suggests a potential benefit for the pathogen in preserving duplicated versions of AVRblb2 possibly because the variants may have different contributions to pathogen fitness in a diversified solanaceous host environment.


Via Kamoun Lab @ TSL
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Rescooped by Guogen Yang from Publications
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Cover: Molecular Plant Pathology, April 2015

Cover: Molecular Plant Pathology, April 2015 | Plant-Microbe Interaction | Scoop.it

Cover caption: The sculpture by Rowan Gillespie is one of the many Great Famine memorials around the world. It depicts figures walking towards emigration ships on the Dublin Quayside. Photo courtesy of Michael Seidl.

 

The Top 10 oomycete pathogens in molecular plant pathology, Mol Plant Pathol http://onlinelibrary.wiley.com/doi/10.1111/mpp.12190/abstract


Via Kamoun Lab @ TSL
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Rescooped by Guogen Yang from Plant Immunity And Microbial Effectors
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Using Hierarchical Clustering of Secreted Protein Families to Classify and Rank Candidate Effectors of Rust Fungi

Using Hierarchical Clustering of Secreted Protein Families to Classify and Rank Candidate Effectors of Rust Fungi | Plant-Microbe Interaction | Scoop.it
Rust fungi are obligate biotrophic pathogens that cause considerable damage on crop plants. Puccinia graminis f. sp. tritici , the causal agent of wheat stem rust, and Melampsora larici-populina , the poplar leaf rust pathogen, have strong deleterious impacts on wheat and poplar wood production, respectively. Filamentous pathogens such as rust fungi secrete molecules called disease effectors that act as modulators of host cell physiology and can suppress or trigger host immunity. Current kn

Via IPM Lab
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Rescooped by Guogen Yang from MycorWeb Plant-Microbe Interactions
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Deciphering the uniqueness of Mucoromycotina cell walls by combining biochemical and phylogenomic approaches

Deciphering the uniqueness of Mucoromycotina cell walls by combining biochemical and phylogenomic approaches | Plant-Microbe Interaction | Scoop.it
Most fungi from the Mucoromycotina lineage occur in ecosystems as saprobes, although some species are phytopathogens or may induce human mycosis. Mucoromycotina represent early diverging models that are most valuable for understanding fungal evolution. Here we reveal the uniqueness of the cell wall structure of the Mucoromycotina Rhizopus oryzae and Phycomyces blakesleeanus compared with the better characterized cell wall of the ascomycete Neurospora crassa. We have analysed the corresponding polysaccharide biosynthetic and modifying pathways, and highlight their evolutionary features and higher complexity in terms of gene copy numbers compared with species from other lineages. This work uncovers the presence in Mucoromycotina of abundant fucose-based polysaccharides similar to algal fucoidans. These unexpected polymers are associated with unusually low amounts of glucans and a higher proportion of chitin compared with N. crassa. The specific structural features are supported by the identification of genes potentially involved in the corresponding metabolic pathways. Phylogenomic analyses of genes encoding carbohydrate synthases, polysaccharide modifying enzymes and enzymes involved in nucleotide-sugar formation provide evidence for duplication events during evolution of cell wall metabolism in fungi. Altogether, the data highlight the specificity of Mucoromycotina cell walls and pave the way for a finer understanding of their metabolism.

Via Francis Martin
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Rescooped by Guogen Yang from MycorWeb Plant-Microbe Interactions
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The Cryptococcus neoformans Alkaline Response Pathway: Identification of a Novel Rim Pathway Activator

The  Cryptococcus neoformans  Alkaline Response Pathway: Identification of a Novel Rim Pathway Activator | Plant-Microbe Interaction | Scoop.it
The Rim101/PacC transcription factor acts in a fungal-specific signaling pathway responsible for sensing extracellular pH signals. First characterized in ascomycete fungi such as Aspergillus nidulans and Saccharomyces cerevisiae, the Rim/Pal pathway maintains conserved features among very distantly related fungi, where it coordinates cellular adaptation to alkaline pH signals and micronutrient deprivation. However, it also directs species-specific functions in fungal pathogens such as Cryptococcus neoformans, where it controls surface capsule expression. Moreover, disruption of the Rim pathway central transcription factor, Rim101, results in a strain that causes a hyper-inflammatory response in animal infection models. Using targeted gene deletions, we demonstrate that several genes encoding components of the classical Rim/Pal pathway are present in the C. neoformans genome. Many of these genes are in fact required for Rim101 activation, including members of the ESCRT complex (Vps23 and Snf7), ESCRT-interacting proteins (Rim20 and Rim23), and the predicted Rim13 protease. We demonstrate that in neutral/alkaline pH, Rim23 is recruited to punctate regions on the plasma membrane. This change in Rim23 localization requires upstream ESCRT complex components but does not require other Rim101 proteolysis components, such as Rim20 or Rim13. Using a forward genetics screen, we identified the RRA1 gene encoding a novel membrane protein that is also required for Rim101 protein activation and, like the ESCRT complex, is functionally upstream of Rim23-membrane localization. Homologs of RRA1 are present in other Cryptococcus species as well as other basidiomycetes, but closely related genes are not present in ascomycetes. These findings suggest that major branches of the fungal Kingdom developed different mechanisms to sense and respond to very elemental extracellular signals such as changing pH levels.

Via Francis Martin
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Rescooped by Guogen Yang from Plant immunity and legume symbiosis
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A Stress-Induced Small RNA Modulates Alpha-Rhizobial Cell Cycle Progression

A Stress-Induced Small RNA Modulates Alpha-Rhizobial Cell Cycle Progression | Plant-Microbe Interaction | Scoop.it

Mechanisms adjusting replication initiation and cell cycle progression in response to environmental conditions are crucial for microbial survival. Functional characterization of the trans-encoded small non-coding RNA (trans-sRNA) EcpR1 in the plant-symbiotic alpha-proteobacterium Sinorhizobium meliloti revealed a role of this class of riboregulators in modulation of cell cycle regulation. EcpR1 is broadly conserved in at least five families of the Rhizobiales and is predicted to form a stable structure with two defined stem-loop domains. In S. meliloti, this trans-sRNA is encoded downstream of the divK-pleD operon. ecpR1 belongs to the stringent response regulon, and its expression was induced by various stress factors and in stationary phase. Induced EcpR1 overproduction led to cell elongation and increased DNA content, while deletion of ecpR1 resulted in reduced competitiveness. Computationally predicted EcpR1 targets were enriched with cell cycle-related mRNAs. Post-transcriptional repression of the cell cycle key regulatory genes gcrA and dnaA mediated by mRNA base-pairing with the strongly conserved loop 1 of EcpR1 was experimentally confirmed by two-plasmid differential gene expression assays and compensatory changes in sRNA and mRNA. Evidence is presented for EcpR1 promoting RNase E-dependent degradation of the dnaA mRNA. We propose that EcpR1 contributes to modulation of cell cycle regulation under detrimental conditions.

 

 


Via Christophe Jacquet
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Rescooped by Guogen Yang from Rice Blast
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Genome-Wide Distribution, Organisation and Functional Characterization of Disease Resistance and Defence Response Genes across Rice Species

Genome-Wide Distribution, Organisation and Functional Characterization of Disease Resistance and Defence Response Genes across Rice Species | Plant-Microbe Interaction | Scoop.it

The resistance (R) genes and defense response (DR) genes have become very important resources for the development of disease resistant cultivars. In the present investigation, genome-wide identification, expression, phylogenetic and synteny analysis was done for R and DR-genes across three species of rice viz: Oryza sativa ssp indica cv 93-11, Oryza sativa ssp japonica and wild rice species, Oryza brachyantha. We used the in silico approach to identify and map 786 R -genes and 167 DR-genes, 672 R-genes and 142 DR-genes, 251 R-genes and 86 DR-genes in the japonica, indica and O. brachyanth a genomes, respectively. Our analysis showed that 60.5% and 55.6% of the R-genes are tandemly repeated within clusters and distributed over all the rice chromosomes in indica and japonica genomes, respectively. The phylogenetic analysis along with motif distribution shows high degree of conservation of R- and DR-genes in clusters. In silico expression analysis of R-genes and DR-genes showed more than 85% were expressed genes showing corresponding EST matches in the databases. This study gave special emphasis on mechanisms of gene evolution and duplication for R and DR genes across species. Analysis of paralogs across rice species indicated 17% and 4.38% R-genes, 29% and 11.63% DR-genes duplication in indica and Oryza brachyantha, as compared to 20% and 26% duplication of R-genes and DR-genes in japonica respectively. We found that during the course of duplication only 9.5% of R- and DR-genes changed their function and rest of the genes have maintained their identity. Syntenic relationship across three genomes inferred that more orthology is shared between indica and japonica genomes as compared to brachyantha genome. Genome wide identification of R-genes and DR-genes in the rice genome will help in allele mining and functional validation of these genes, and to understand molecular mechanism of disease resistance and their evolution in rice and related species.


Via Christophe Jacquet, Biswapriya Biswavas Misra, Elsa Ballini
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Rescooped by Guogen Yang from Plant immunity and legume symbiosis
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Hormone activities and the cell cycle machinery in immunity-triggered growth inhibition

Hormone activities and the cell cycle machinery in immunity-triggered growth inhibition | Plant-Microbe Interaction | Scoop.it
Biotic stress and diseases caused by pathogen attack pose threats in crop production and significantly reduce crop yields. Enhancing immunity against pathogens is therefore of outstanding importance in crop breeding. However, this must be balanced, as immune activation inhibits plant growth. This immunity-coupled growth trade-off does not support resistance but is postulated to reflect the reallocation of resources to drive immunity. There is, however, increasing evidence that growth–immunity trade-offs are based on the reconfiguration of hormone pathways, shared by growth and immunity signalling. Studies in roots revealed the role of hormones in orchestrating growth across different cell types, with some hormones showing a defined cell type-specific activity. This is apparently highly relevant for the regulation of the cell cycle machinery and might be part of the growth–immunity cross-talk. Since plants are constantly exposed to Immuno-activating microbes under agricultural conditions, the transition from a growth to an immunity operating mode can significantly reduce crop yield and can conflict our efforts to generate next-generation crops with improved yield under climate change conditions. By focusing on roots, we outline the current knowledge of hormone signalling on the cell cycle machinery to explain growth trade-offs induced by immunity. By referring to abiotic stress studies, we further introduce how root cell type-specific hormone activities might contribute to growth under immunity and discuss the feasibility of uncoupling the growth–immunity cross-talk.

Via Christophe Jacquet
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Rescooped by Guogen Yang from Effectors and Plant Immunity
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J. Exp. Bot.: Identification of a molecular dialogue between developing seeds of Medicago truncatula and seedborne xanthomonads (2015)

J. Exp. Bot.: Identification of a molecular dialogue between developing seeds of Medicago truncatula and seedborne xanthomonads (2015) | Plant-Microbe Interaction | Scoop.it

Plant pathogenic bacteria disseminate and survive mainly in association with seeds. This study addresses whether seeds are passive carriers or engage a molecular dialogue with pathogens during their development. We developed two pathosystems using Medicago truncatula with Xanthomonas alfalfae subsp. alfalfae (Xaa), the natural Medicago sp. pathogen and Xanthomonas campestris pv. campestris (Xcc), a Brassicaceae pathogen. Three days after flower inoculation, the transcriptome of Xcc-infected pods showed activation of an innate immune response that was strongly limited in Xcc mutated in the type three secretion system, demonstrating an incompatible interaction of Xcc with the reproductive structures. In contrast, the presence of Xaa did not result in an activation of defence genes. Transcriptome profiling during development of infected seeds exhibited time-dependent and differential responses to Xcc and Xaa. Gene network analysis revealed that the transcriptome of Xcc-infected seeds was mainly affected during seed filling whereas that of Xaa-infected seeds responded during late maturation. The Xcc-infected seed transcriptome exhibited an activation of defence response and a repression of targeted seed maturation pathways. Fifty-one percent of putative ABSCISIC ACID INSENSITIVE3 targets were deregulated by Xcc, including oleosin, cupin, legumin and chlorophyll degradation genes. At maturity, these seeds displayed decreased weight and increased chlorophyll content. In contrast, these traits were not affected by Xaa infection. These findings demonstrate the existence of a complex molecular dialogue between xanthomonads and developing seeds and provides insights into a previously unexplored trade-off between seed development and pathogen defence.

 

Emmanuel Terrasson, Armelle Darrasse, Karima Righetti, Julia Buitink, David Lalanne, Benoit Ly Vu, Sandra Pelletier, William Bolingue, Marie-Agnès Jacques, and Olivier Leprince


Via Nicolas Denancé
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Rescooped by Guogen Yang from The science toolbox
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Hybrid De Novo Genome Assembly Using MiSeq and SOLiD Short Read Data

Hybrid  De Novo  Genome Assembly Using MiSeq and SOLiD Short Read Data | Plant-Microbe Interaction | Scoop.it

"A hybrid de novo assembly pipeline was constructed to utilize both MiSeq and SOLiD short read data in combination in the assembly. The short read data were converted to a standard format of the pipeline, and were supplied to the pipeline components such as ABySS and SOAPdenovo. The assembly pipeline proceeded through several stages, and either MiSeq paired-end data, SOLiD mate-paired data, or both of them could be specified as input data at each stage separately. The pipeline was examined on the filamentous fungus Aspergillus oryzae RIB40, by aligning the assembly results against the reference sequences. Using both the MiSeq and the SOLiD data in the hybrid assembly, the alignment length was improved by a factor of 3 to 8, compared with the assemblies using either one of the data types. The number of the reproduced gene cluster regions encoding secondary metabolite biosyntheses (SMB) was also improved by the hybrid assemblies. These results imply that the MiSeq data with long read length are essential to construct accurate nucleotide sequences, while the SOLiD mate-paired reads with long insertion length enhance long-range arrangements of the sequences. The pipeline was also tested on the actinomycete Streptomyces avermitilis MA-4680, whose gene is known to have high-GC content. Although the quality of the SOLiD reads was too low to perform any meaningful assemblies by themselves, the alignment length to the reference was improved by a factor of 2, compared with the assembly using only the MiSeq data."

 


Via Niklaus Grunwald
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Rescooped by Guogen Yang from How microbes emerge
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The population biology of fungal invasions - Gladieux - 2015 - Molecular Ecology - Wiley Online Library

The population biology of fungal invasions - Gladieux - 2015 - Molecular Ecology - Wiley Online Library | Plant-Microbe Interaction | Scoop.it

Fungal invasions are increasingly recognized as a significant component of global changes, threatening ecosystem health and damaging food production. Invasive fungi also provide excellent models to evaluate the generality of results based on other eukaryotes. We first consider here the reasons why fungal invasions have long been overlooked: they tend to be inconspicuous, and inappropriate methods have been used for species recognition. We then review the information available on the patterns and mechanisms of fungal invasions. We examine the biological features underlying invasion success of certain fungal species. We review population structure analyses, revealing native source populations and strengths of bottlenecks. We highlight the documented ecological and evolutionary changes in invaded regions, including adaptation to temperature, increased virulence, hybridization, shifts to clonality and association with novel hosts. We discuss how the huge census size of most fungi allows adaptation even in bottlenecked, clonal invaders. We also present new analyses of the invasion of the anther-smut pathogen on white campion in North America, as a case study illustrating how an accurate knowledge of species limits and phylogeography of fungal populations can be used to decipher the origin of invasions. This case study shows that successful invasions can occur even when life history traits are particularly unfavourable to long-distance dispersal and even with a strong bottleneck. We conclude that fungal invasions are valuable models to contribute to our view of biological invasions, in particular by providing insights into the traits as well as ecological and evolutionary processes allowing successful introductions.


Via Steve Marek, Niklaus Grunwald
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PLOS ONE: Novel Mutations Detected in Avirulence Genes Overcoming Tomato Cf Resistance Genes in Isolates of a Japanese Population of Cladosporium fulvum (2015)

PLOS ONE: Novel Mutations Detected in Avirulence Genes Overcoming Tomato  Cf  Resistance Genes in Isolates of a Japanese Population of  Cladosporium fulvum (2015) | Plant-Microbe Interaction | Scoop.it

Leaf mold of tomato is caused by the biotrophic fungus Cladosporium fulvum which complies with the gene-for-gene system. The disease was first reported in Japan in the 1920s and has since been frequently observed. Initially only race 0 isolates were reported, but since the consecutive introduction of resistance genes Cf-2, Cf-4, Cf-5 and Cf-9 new races have evolved. Here we first determined the virulence spectrum of 133 C. fulvum isolates collected from 22 prefectures in Japan, and subsequently sequenced the avirulence (Avr) genes Avr2, Avr4, Avr4E, Avr5 and Avr9 to determine the molecular basis of overcoming Cf genes. Twelve races of C. fulvum with a different virulence spectrum were identified, of which races 9, 2.9, 4.9, 4.5.9 and 4.9.11 occur only in Japan. The Avr genes in many of these races contain unique mutations not observed in races identified elsewhere in the world including (i) frameshift mutations and (ii) transposon insertions in Avr2, (iii) point mutations in Avr4 and Avr4E, and (iv) deletions of Avr4E, Avr5 and Avr9. New races have developed by selection pressure imposed by consecutive introductions of Cf-2, Cf-4, Cf-5 and Cf-9 genes in commercially grown tomato cultivars. Our study shows that molecular variations to adapt to different Cf genes in an isolated C. fulvum population in Japan are novel but overall follow similar patterns as those observed in populations from other parts of the world. Implications for breeding of more durable C. fulvumresistant varieties are discussed.


Via Kamoun Lab @ TSL
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PNAS: Phytophthora effector targets a novel component of small RNA pathway in plants to promote infection (2015)

PNAS: Phytophthora effector targets a novel component of small RNA pathway in plants to promote infection (2015) | Plant-Microbe Interaction | Scoop.it

Phytophthora is a major threat to agriculture. However, the molecular interaction of these severe pathogens with plant hosts is poorly understood. Here, we report that the Phytophthora Suppressor of RNA Silencing 1 (PSR1) effectively promotes infection in Arabidopsis thaliana by directly targeting an essential protein containing a aspartate–glutamate–alanine–histidine-box RNA helicase domain. This PSR1-Interacting Protein 1 (PINP1) is required for the accumulation of distinct classes of endogenous small RNAs and acts as a positive regulator of plant immunity. Silencing of PINP1 impaired the assembly of microRNA-processing complexes in the nucleus, leading to defects in development and immunity. This study revealed a conserved RNA helicase as a regulator of RNA silencing and provides mechanistic insight into Phytophthora pathogenesis.


Via Kamoun Lab @ TSL
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Plant Cell: A Secreted Effector Protein of Ustilago maydis Guides Maize Leaf Cells to Form Tumors (2015)

Plant Cell: A Secreted Effector Protein of Ustilago maydis Guides Maize Leaf Cells to Form Tumors (2015) | Plant-Microbe Interaction | Scoop.it

The biotrophic smut fungus Ustilago maydis infects all aerial organs of maize (Zea mays) and induces tumors in the plant tissues. U. maydis deploys many effector proteins to manipulate its host. Previously, deletion analysis demonstrated that several effectors have important functions in inducing tumor expansion specifically in maize leaves. Here, we present the functional characterization of the effector See1 (Seedling efficient effector1). See1 is required for the reactivation of plant DNA synthesis, which is crucial for tumor progression in leaf cells. By contrast, See1 does not affect tumor formation in immature tassel floral tissues, where maize cell proliferation occurs independent of fungal infection. See1 interacts with a maize homolog of SGT1 (Suppressor of G2 allele of skp1), a factor acting in cell cycle progression in yeast (Saccharomyces cerevisiae) and an important component of plant and human innate immunity. See1 interferes with the MAPK-triggered phosphorylation of maize SGT1 at a monocot-specific phosphorylation site. We propose that See1 interferes with SGT1 activity, resulting in both modulation of immune responses and reactivation of DNA synthesis in leaf cells. This identifies See1 as a fungal effector that directly and specifically contributes to the formation of leaf tumors in maize.


Via Kamoun Lab @ TSL, Francis Martin
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Molecular Plant Pathology: A new look at plant viruses and their potential beneficial roles in crops (2015)

Molecular Plant Pathology: A new look at plant viruses and their potential beneficial roles in crops (2015) | Plant-Microbe Interaction | Scoop.it

Twenty years ago most people (including many scientists) thought of bacteria solely as agents of disease, best treated with disinfectants and antibiotics. Today, most of us are aware that bacteria make up almost 90% of the cells in our bodies, and play a critical role in digestion and the immune response. In plants, bacteria also form important mutualistic relationships, providing nitrogen fixation, growth enhancement and defence against pathogens, and undoubtedly a host of other functions that have yet to be described. The stigma of bacteria has changed dramatically in recent decades, and most people are aware that we need our good microbes.

 

Although there have been recent efforts to characterize the plant microbiome with a focus on finding beneficial microbes, viruses generally have not been included in the beneficial microbe lists (Berg et al., 2014, and references cited therein). Recent work has indicated that they can also play important and beneficial roles in plants, especially in extreme environments in which they are involved in conferring tolerance to drought, cold and hot soil temperatures (Roossinck, 2011). Beneficial viruses are defined for the purposes of this discussion as viruses that provide a trait to crop plants that increases their value or growth potential, or decreases the need for the use of chemical fertilizers or pesticides.

 

See also http://www.noble.org/ag/research/microbes/


Via Kamoun Lab @ TSL
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The population biology of fungal invasions - Gladieux - 2015 - Molecular Ecology - Wiley Online Library

The population biology of fungal invasions - Gladieux - 2015 - Molecular Ecology - Wiley Online Library | Plant-Microbe Interaction | Scoop.it
Fungal invasions are increasingly recognized as a significant component of global changes, threatening ecosystem health and damaging food production. Invasive fungi also provide excellent models to evaluate the generality of results based on other eukaryotes. We first consider here the reasons why fungal invasions have long been overlooked: they tend to be inconspicuous, and inappropriate methods have been used for species recognition. We then review the information available on the patterns and mechanisms of fungal invasions. We examine the biological features underlying invasion success of certain fungal species. We review population structure analyses, revealing native source populations and strengths of bottlenecks. We highlight the documented ecological and evolutionary changes in invaded regions, including adaptation to temperature, increased virulence, hybridization, shifts to clonality and association with novel hosts. We discuss how the huge census size of most fungi allows adaptation even in bottlenecked, clonal invaders. We also present new analyses of the invasion of the anther-smut pathogen on white campion in North America, as a case study illustrating how an accurate knowledge of species limits and phylogeography of fungal populations can be used to decipher the origin of invasions. This case study shows that successful invasions can occur even when life history traits are particularly unfavourable to long-distance dispersal and even with a strong bottleneck. We conclude that fungal invasions are valuable models to contribute to our view of biological invasions, in particular by providing insights into the traits as well as ecological and evolutionary processes allowing successful introductions.

Via Francis Martin
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