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ScienceDirect.com - Trends in Biotechnology - Network analysis: tackling complex data to study plant metabolism

ScienceDirect.com - Trends in Biotechnology - Network analysis: tackling complex data to study plant metabolism | Plant-Microbe Interaction | Scoop.it

Incomplete knowledge of biochemical pathways makes the holistic description of plant metabolism a non-trivial undertaking. Sensitive analytical platforms, which are capable of accurately quantifying the levels of the various molecular entities of the cell, can assist in tackling this task. However, the ever-increasing amount of high-throughput data, often from multiple technologies, requires significant computational efforts for integrative analysis. Here we introduce the application of network analysis to study plant metabolism and describe the construction and analysis of correlation-based networks from (time-resolved) metabolomics data. By investigating the interactions between metabolites, network analysis can help to interpret complex datasets through the identification of key network components. The relationship between structural and biological roles of network components can be evaluated and employed to aid metabolic engineering.

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Rescooped by Guogen Yang from Plant Biology Teaching Resources (Higher Education)
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Genetic, evolutionary and plant breeding insights from the domestication of maize

Genetic, evolutionary and plant breeding insights from the domestication of maize | Plant-Microbe Interaction | Scoop.it

by Sarah Hake& Jeffrey Ross-Ibarra

"The natural history of maize began nine thousand years ago when Mexican farmers started to collect the seeds of the wild grass, teosinte. Invaluable as a food source, maize permeated Mexican culture and religion. Its domestication eventually led to its adoption as a model organism, aided in large part by its large chromosomes, ease of pollination and growing agricultural importance. Genome comparisons between varieties of maize, teosinte and other grasses are beginning to identify the genes responsible for the domestication of modern maize and are also providing ideas for the breeding of more hardy varieties."


Via Mary Williams
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Arabidopsis BIRD Zinc Finger Proteins Jointly Stabilize Tissue Boundaries by Confining the Cell Fate Regulator SHORT-ROOT and Contributing to Fate Specification

Arabidopsis BIRD Zinc Finger Proteins Jointly Stabilize Tissue Boundaries by Confining the Cell Fate Regulator SHORT-ROOT and Contributing to Fate Specification | Plant-Microbe Interaction | Scoop.it

BIRD proteins control tissue boundaries through transcriptional control and nuclear retention of targets.
The names of the BIRD Zn-finger proteins originated with the finding that JACKDAW (a kind of crow) is antagonistic to the protein SCARECROW... I seem to remember that SCARECROW is named because the mutant lacks a "heart" (cortex - wizard of oz reference) - plz correct me if I'm wrong.
The genetic interactions for each of several mutant combinations of the BIRD family is outlined in the supplemental materials, which is useful if you want to practice your genetics skills.
http://www.plantcell.org/…/20…/03/31/tpc.114.132407.abstract


Via Mary Williams
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Cytoplastic Glyceraldehyde-3-Phosphate Dehydrogenases Interact with ATG3 to Negatively Regulate Autophagy and Immunity in Nicotiana benthamiana

Cytoplastic Glyceraldehyde-3-Phosphate Dehydrogenases Interact with ATG3 to Negatively Regulate Autophagy and Immunity in Nicotiana benthamiana | Plant-Microbe Interaction | Scoop.it
Autophagy as a conserved catabolic pathway can respond to reactive oxygen species (ROS) and plays an important role in degrading oxidized proteins in plants under various stress conditions. However, how ROS regulates autophagy in response to oxidative stresses is largely unknown. Here, we show that autophagy-related protein 3 (ATG3) interacts with the cytosolic glyceraldehyde-3-phosphate dehydrogenases (GAPCs) to regulate autophagy in Nicotiana benthamiana plants. We found that oxidative stress inhibits the interaction of ATG3 with GAPCs. Silencing of GAPCs significantly activates ATG3-dependent autophagy, while overexpression of GAPCs suppresses autophagy in N. benthamiana plants. Moreover, silencing of GAPCs enhances N gene-mediated cell death and plant resistance against both incompatible pathogens Tobacco mosaic virus and Pseudomonas syringae pv tomato DC3000, as well as compatible pathogen P. syringae pv tabaci. These results indicate that GAPCs have multiple functions in the regulation of autophagy, hypersensitive response, and plant innate immunity.

Via Suayib Üstün
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The Phenylpropanoid Pathway Is Controlled at Different Branches by a Set of R2R3-MYB C2 Repressors in Grapevine

The Phenylpropanoid Pathway Is Controlled at Different Branches by a Set of R2R3-MYB C2 Repressors in Grapevine | Plant-Microbe Interaction | Scoop.it
Because of the vast range of functions that phenylpropanoids possess, their synthesis requires precise spatiotemporal coordination throughout plant development and in response to the environment. The accumulation of these secondary metabolites is transcriptionally controlled by positive and negative regulators from the MYB and basic helix-loop-helix protein families. We characterized four grapevine (Vitis vinifera) R2R3-MYB proteins from the C2 repressor motif clade, all of which harbor the ethylene response factor-associated amphiphilic repression domain but differ in the presence of an additional TLLLFR repression motif found in the strong flavonoid repressor Arabidopsis (Arabidopsis thaliana) AtMYBL2. Constitutive expression of VvMYB4a and VvMYB4b in petunia (Petunia hybrida) repressed general phenylpropanoid biosynthetic genes and selectively reduced the amount of small-weight phenolic compounds. Conversely, transgenic petunia lines expressing VvMYBC2-L1 and VvMYBC2-L3 showed a severe reduction in petal anthocyanins and seed proanthocyanidins together with a higher pH of crude petal extracts. The distinct function of these regulators was further confirmed by transient expression in tobacco (Nicotiana benthamiana) leaves and grapevine plantlets. Finally, VvMYBC2-L3 was ectopically expressed in grapevine hairy roots, showing a reduction in proanthocyanidin content together with the down-regulation of structural and regulatory genes of the flavonoid pathway as revealed by a transcriptomic analysis. The physiological role of these repressors was inferred by combining the results of the functional analyses and their expression patterns in grapevine during development and in response to ultraviolet B radiation. Our results indicate that VvMYB4a and VvMYB4b may play a key role in negatively regulating the synthesis of small-weight phenolic compounds, whereas VvMYBC2-L1 and VvMYBC2-L3 may additionally fine tune flavonoid levels, balancing the inductive effects of transcriptional activators.

Via Christophe Jacquet
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Cell wall composition profiling of parasitic giant dodder (Cuscuta reflexa) and its hosts: a priori differences and induced changes

Cell wall composition profiling of parasitic giant dodder (Cuscuta reflexa) and its hosts: a priori differences and induced changes | Plant-Microbe Interaction | Scoop.it
Host plant penetration is the gateway to survival for holoparasitic Cuscuta and requires host cell wall degradation. Compositional differences of cell walls may explain why some hosts are amenable to such degradation while others can resist infection.Antibody-based techniques for comprehensive profiling of cell wall epitopes and cell wall-modifying enzymes were applied to several susceptible hosts and a resistant host of Cuscuta reflexa and to the parasite itself.Infected tissue of Pelargonium zonale contained high concentrations of de-esterified homogalacturonans in the cell walls, particularly adjacent to the parasite's haustoria. High pectinolytic activity in haustorial extracts and high expression levels of pectate lyase genes suggest that the parasite contributes directly to wall remodeling. Mannan and xylan concentrations were low in P. zonale and in five susceptible tomato introgression lines, but high in the resistant Solanum lycopersicum cv M82, and in C. reflexa itself.Knowledge of the composition of resistant host cell walls and the parasite's own cell walls is useful in developing strategies to prevent infection by parasitic plants.
Via Francis Martin
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Transgenic Expression of the Dicotyledonous Pattern Recognition Receptor EFR in Rice Leads to Ligand-Dependent Activation of Defense Responses

Transgenic Expression of the Dicotyledonous Pattern Recognition Receptor EFR in Rice Leads to Ligand-Dependent Activation of Defense Responses | Plant-Microbe Interaction | Scoop.it

Plant plasma membrane localized pattern recognition receptors (PRRs) detect extracellular pathogen-associated molecules. PRRs such as Arabidopsis EFR and rice XA21 are taxonomically restricted and are absent from most plant genomes. Here we show that rice plants expressing EFR or the chimeric receptor EFR::XA21, containing the EFR ectodomain and the XA21 intracellular domain, sense both Escherichia coli- and Xanthomonas oryzae pv.oryzae (Xoo)-derived elf18 peptides at sub-nanomolar concentrations. Treatment of EFR and EFR::XA21 rice leaf tissue with elf18 leads to MAP kinase activation, reactive oxygen production and defense gene expression. Although expression of EFR does not lead to robust enhanced resistance to fully virulent Xoo isolates, it does lead to quantitatively enhanced resistance to weakly virulent Xoo isolates. EFR interacts with OsSERK2 and the XA21 binding protein 24 (XB24), two key components of the rice XA21-mediated immune response. Rice-EFR plants silenced for OsSERK2, or overexpressing rice XB24 are compromised in elf18-induced reactive oxygen production and defense gene expression indicating that these proteins are also important for EFR-mediated signaling in transgenic rice. Taken together, our results demonstrate the potential feasibility of enhancing disease resistance in rice and possibly other monocotyledonous crop species by expression of dicotyledonous PRRs. Our results also suggest that Arabidopsis EFR utilizes at least a subset of the known endogenous rice XA21 signaling components.


Via Suayib Üstün
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Interplay of Reactive Oxygen Species and Nitric Oxide: Nitric Oxide Coordinates Reactive Oxygen Species Homeostasis

Interplay of Reactive Oxygen Species and Nitric Oxide: Nitric Oxide Coordinates Reactive Oxygen Species Homeostasis | Plant-Microbe Interaction | Scoop.it
Redox reactions are evolutionarily a very old signaling principle, which occur in prokaryotes and eukaryotes. The most important redox molecules are reactive oxygen species (ROS), such as singlet oxygen, hydroxyl radical, superoxide anion, hydrogen peroxide, and nitric oxide (·NO). In plants, they have very important signaling functions and are involved in the regulation of transpiration, gas exchange, plant defense response, cell death, germination, and plant growth and development. The diverse functions may be explained by the fact that ROS and ·NO interact rapidly to form a number of reactive nitrogen species, such as ONOO−, NO2, N2O3, and other NOx species. Besides the direct interactions of these redox molecules, both molecules can act as oxidizing agents on proteins, and in this way they can modify the activity or function of proteins involved in ·NO and ROS signaling as well as metabolism and homeostasis.

Via Christophe Jacquet
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Roles and Programming of Arabidopsis ARGONAUTE Proteins during Turnip Mosaic Virus Infection

Roles and Programming of Arabidopsis ARGONAUTE Proteins during Turnip Mosaic Virus Infection | Plant-Microbe Interaction | Scoop.it

In eukaryotes, ARGONAUTE proteins (AGOs) associate with microRNAs (miRNAs), short interfering RNAs (siRNAs), and other classes of small RNAs to regulate target RNA or target loci. Viral infection in plants induces a potent and highly specific antiviral RNA silencing response characterized by the formation of virus-derived siRNAs. Arabidopsis thaliana has ten AGO genes of which AGO1, AGO2, and AGO7 have been shown to play roles in antiviral defense. A genetic analysis was used to identify and characterize the roles of AGO proteins in antiviral defense against Turnip mosaic virus (TuMV) in Arabidopsis. AGO1, AGO2 and AGO10 promoted anti-TuMV defense in a modular way in various organs, with AGO2 providing a prominent antiviral role in leaves. AGO5, AGO7 and AGO10 had minor effects in leaves. AGO1 and AGO10 had overlapping antiviral functions in inflorescence tissues after systemic movement of the virus, although the roles of AGO1 and AGO10 accounted for only a minor amount of the overall antiviral activity. By combining AGO protein immunoprecipitation with high-throughput sequencing of associated small RNAs, AGO2, AGO10, and to a lesser extent AGO1 were shown to associate with siRNAs derived from silencing suppressor (HC-Pro)-deficient TuMV-AS9, but not with siRNAs derived from wild-type TuMV. Co-immunoprecipitation and small RNA sequencing revealed that viral siRNAs broadly associated with wild-type HC-Pro during TuMV infection. These results support the hypothesis that suppression of antiviral silencing during TuMV infection, at least in part, occurs through sequestration of virus-derived siRNAs away from antiviral AGO proteins by HC-Pro. These findings indicate that distinct AGO proteins function as antiviral modules, and provide a molecular explanation for the silencing suppressor activity of HC-Pro.

 

 


Via Christophe Jacquet
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Rescooped by Guogen Yang from MycorWeb Plant-Microbe Interactions
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Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen

Horizontal gene transfer and gene dosage drives adaptation to wood colonization in a tree pathogen | Plant-Microbe Interaction | Scoop.it
Some of the most damaging tree pathogens can attack woody stems, causing lesions (cankers) that may be lethal. To identify the genomic determinants of wood colonization leading to canker formation, we sequenced the genomes of the poplar canker pathogen, Mycosphaerella populorum, and the closely related poplar leaf pathogen, M. populicola. A secondary metabolite cluster unique to M. populorum is fully activated following induction by poplar wood and leaves. In addition, genes encoding hemicellulose-degrading enzymes, peptidases, and metabolite transporters were more abundant and were up-regulated in M. populorum growing on poplar wood-chip medium compared with M. populicola. The secondary gene cluster and several of the carbohydrate degradation genes have the signature of horizontal transfer from ascomycete fungi associated with wood decay and from prokaryotes. Acquisition and maintenance of the gene battery necessary for growth in woody tissues and gene dosage resulting in gene expression reconfiguration appear to be responsible for the adaptation of M. populorum to infect, colonize, and cause mortality on poplar woody stems.

Via Francis Martin
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Transcriptional control of flavonoid biosynthesis by MYB–bHLH–WDR complexes

Transcriptional control of flavonoid biosynthesis by MYB–bHLH–WDR complexes | Plant-Microbe Interaction | Scoop.it
Highlights



Flavonoid gene expression is tightly regulated by environmental and developmental signals.


Specific R2R3-MYB and bHLH transcription factors interact with WDR proteins to form MBW complexes.


MBW complexes contribute to the tight regulation of late biosynthetic gene expression.


MBW networks provide a powerful model system for the regulation of gene expression.

Flavonoids are widely known for the colors they confer to plant tissues, their contribution to plant fitness and health benefits, and impact on food quality. As convenient biological markers, flavonoids have been instrumental in major genetic and epigenetic discoveries. We review recent advances in the characterization of the underlying regulatory mechanisms of flavonoid biosynthesis, with a special focus on the MBW (MYB–bHLH–WDR) protein complexes. These proteins are well conserved in higher plants. They participate in different types of controls ranging from fine-tuned transcriptional regulation by environmental factors to the initiation of the flavonoid biosynthesis pathway by positive regulatory feedback. The MBW protein complexes provide interesting models for investigating developmentally or environmentally controlled transcriptional regulatory networks.

Via Christophe Jacquet
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Rescooped by Guogen Yang from Plant immunity and legume symbiosis
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Retromer Contributes to Immunity-Associated Cell Death in Arabidopsis

Retromer Contributes to Immunity-Associated Cell Death in Arabidopsis | Plant-Microbe Interaction | Scoop.it
Membrane trafficking is required during plant immune responses, but its contribution to the hypersensitive response (HR), a form of programmed cell death (PCD) associated with effector-triggered immunity, is not well understood. HR is induced by nucleotide binding-leucine-rich repeat (NB-LRR) immune receptors and can involve vacuole-mediated processes, including autophagy. We previously isolated lazarus (laz) suppressors of autoimmunity-triggered PCD in the Arabidopsis thaliana mutant accelerated cell death11 (acd11) and demonstrated that the cell death phenotype is due to ectopic activation of the LAZ5 NB-LRR. We report here that laz4 is mutated in one of three VACUOLAR PROTEIN SORTING35 (VPS35) genes. We verify that LAZ4/VPS35B is part of the retromer complex, which functions in endosomal protein sorting and vacuolar trafficking. We show that VPS35B acts in an endosomal trafficking pathway and plays a role in LAZ5-dependent acd11 cell death. Furthermore, we find that VPS35 homologs contribute to certain forms of NB-LRR protein-mediated autoimmunity as well as pathogen-triggered HR. Finally, we demonstrate that retromer deficiency causes defects in late endocytic/lytic compartments and impairs autophagy-associated vacuolar processes. Our findings indicate important roles of retromer-mediated trafficking during the HR; these may include endosomal sorting of immune components and targeting of vacuolar cargo.

Via Christophe Jacquet
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Rescooped by Guogen Yang from Plant-Microbe Symbioses
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Fungal endophytes associated with roots of nurse cushion species have positive effects on native and invasive beneficiary plants in an alpine ecosystem

Fungal endophytes associated with roots of nurse cushion species have positive effects on native and invasive beneficiary plants in an alpine ecosystem | Plant-Microbe Interaction | Scoop.it
Facilitation has been proposed to be a fundamental mechanism for plant coexistence, being particularly important in highly stressful environments such as alpine environments. In this type of environment, species called “cushion plants” can ameliorate the stressful conditions, acting as nurses for other plants. Of the several mechanisms proposed in the positive-interactions framework, plant–microorganism interaction may be one of the most common, but least documented. Here we show that the presence of endophytes isolated from the roots of cushion plants Laretia acaulis can play a fundamental role in the establishment, performance and survival of both native and exotic plant seedlings that are known to be facilitated by the cushion species.

To test this, we measured survival and growth of two native and one invasive species at 3200 m in the Andes of Central Chile. Plants were grown inside artificial cushions filled with native soil, with or without sterilization, and with or without fungal endophytic inoculation to evaluate the role of fungal endophytes on survival and growth. In addition, we conducted a second experiment in a greenhouse with the invasive species to evaluate the effect of fungal endophytic infection/association on plant ecophysiological performance, dry biomass and seed output.

Overall, our results showed a strong positive effect of fungal endophytes on the survival and growth of both native and invasive species. Moreover, maximum quantum efficiency (Fv/Fm), biomass accumulation and seed production were enhanced in the invasive species when soils were inoculated with endophytes. Thus, facilitation by root endophytic fungi on native and invasive alpine plants could determine survival and establishment in this harsh environment.

Several studies have shown that direct facilitation by cushion plants in alpine environments improves the performance and fitness of both native and exotic plants. Our results suggest that there are indirect effects, mediated by microorganism associations that may also help to explain the successful establishment of native and invasive species in these environments. If indirect plant–plant facilitation through root fungal endophytes proves to be a widespread phenomenon in alpine ecosystems, it could be a key component in the structuring of plant communities in those stressful environments.

Via Jean-Michel Ané
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Rescooped by Guogen Yang from Plants and Microbes
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PLOS Genetics: The Evolution of Fungal Metabolic Pathways (2014)

PLOS Genetics: The Evolution of Fungal Metabolic Pathways (2014) | Plant-Microbe Interaction | Scoop.it

Fungi contain a remarkable range of metabolic pathways, sometimes encoded by gene clusters, enabling them to digest most organic matter and synthesize an array of potent small molecules. Although metabolism is fundamental to the fungal lifestyle, we still know little about how major evolutionary processes, such as gene duplication (GD) and horizontal gene transfer (HGT), have interacted with clustered and non-clustered fungal metabolic pathways to give rise to this metabolic versatility. We examined the synteny and evolutionary history of 247,202 fungal genes encoding enzymes that catalyze 875 distinct metabolic reactions from 130 pathways in 208 diverse genomes. We found that gene clustering varied greatly with respect to metabolic category and lineage; for example, clustered genes in Saccharomycotina yeasts were overrepresented in nucleotide metabolism, whereas clustered genes in Pezizomycotina were more common in lipid and amino acid metabolism. The effects of both GD and HGT were more pronounced in clustered genes than in their non-clustered counterparts and were differentially distributed across fungal lineages; specifically, GD, which was an order of magnitude more abundant than HGT, was most frequently observed in Agaricomycetes, whereas HGT was much more prevalent in Pezizomycotina. The effect of HGT in some Pezizomycotina was particularly strong; for example, we identified 111 HGT events associated with the 15 Aspergillus genomes, which sharply contrasts with the 60 HGT events detected for the 48 genomes from the entire Saccharomycotina subphylum. Finally, the impact of GD within a metabolic category was typically consistent across all fungal lineages, whereas the impact of HGT was variable. These results indicate that GD is the dominant process underlying fungal metabolic diversity, whereas HGT is episodic and acts in a category- or lineage-specific manner. Both processes have a greater impact on clustered genes, suggesting that metabolic gene clusters represent hotspots for the generation of fungal metabolic diversity.


Via Kamoun Lab @ TSL
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Rescooped by Guogen Yang from Plant-Microbe Symbioses
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Medicago truncatula symbiosis mutants affected in the interaction with a biotrophic root pathogen

Medicago truncatula symbiosis mutants affected in the interaction with a biotrophic root pathogen | Plant-Microbe Interaction | Scoop.it
Understanding how plants balance between enabling microbial symbionts and fending off pathogens has direct implications both for basic plant biology and optimal use of crop plants in agriculture. The degree to which the processes associated with these two types of interactions overlap is poorly known. Recent studies revealed that symbiotic and pathogenic filamentous microbes require common plant genetic elements to establish colonization (Wang et al., 2012; Rey et al., 2013), supporting the long-held view that plants have evolved the ability to accommodate microbes (Parniske, 2000) and that pathogens have exploited these pathways. However, the extent to which plant genes implicated in fungal or bacterial symbioses are involved in interactions with biotrophic pathogens is unknown and research has been hampered by the lack of suitable common host experimental systems

Via Christophe Jacquet, Jean-Michel Ané
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Imposed glutathione-mediated redox switch modulates the tobacco wound-induced protein kinase and salicylic acid-induced protein kinase activation state and impacts on defence against Pseudomonas sy...

Imposed glutathione-mediated redox switch modulates the tobacco wound-induced protein kinase and salicylic acid-induced protein kinase activation state and impacts on defence against Pseudomonas sy... | Plant-Microbe Interaction | Scoop.it
The role of the redox-active tripeptide glutathione in plant defence against pathogens has been studied extensively; however, the impact of changes in cellular glutathione redox potential on signalling processes during defence reactions has remained elusive. This study explored the impact of elevated glutathione content on the cytosolic redox potential and on early defence signalling at the level of mitogen-activated protein kinases (MAPKs), as well as on subsequent defence reactions, including changes in salicylic acid (SA) content, pathogenesis-related gene expression, callose depositions, and the hypersensitive response. Wild-type (WT) Nicotiana tabacum L. and transgenic high-glutathione lines (HGL) were transformed with the cytosol-targeted sensor GRX1-roGFP2 to monitor the cytosolic redox state. Surprisingly, HGLs displayed an oxidative shift in their cytosolic redox potential and an activation of the tobacco MAPKs wound-induced protein kinase (WIPK) and SA-induced protein kinase (SIPK). This activation occurred in the absence of any change in free SA content, but was accompanied by constitutively increased expression of several defence genes. Similarly, rapid activation of MAPKs could be induced in WT tobacco by exposure to either reduced or oxidized glutathione. When HGL plants were challenged with adapted or non-adapted Pseudomonas syringae pathovars, the cytosolic redox shift was further amplified and the defence response was markedly increased, showing a priming effect for SA and callose; however, the initial and transient hyperactivation of MAPK signalling was attenuated in HGLs. The results suggest that, in tobacco, MAPK and SA signalling may operate independently, both possibly being modulated by the glutathione redox potential. Possible mechanisms for redox-mediated MAPK activation are discussed.

Via Christophe Jacquet
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Symbiotic plant-fungi interactions stripped down to the root : Nature Genetics

Symbiotic plant-fungi interactions stripped down to the root : Nature Genetics | Plant-Microbe Interaction | Scoop.it
Mycorrhizal fungi live in the roots of host plants and are crucial components of all forest ecosystems. A large-scale study of fungal genomics provides new insights into the evolution of mycorrhizae and a deep exploration of mycorrhizal diversity that helps to uncover the molecular and genetic details of fungal symbiotic relationships with plants.

Via Francis Martin
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S-Nitrosylation Positively Regulates Ascorbate Peroxidase Activity during Plant Stress Responses

S-Nitrosylation Positively Regulates Ascorbate Peroxidase Activity during Plant Stress Responses | Plant-Microbe Interaction | Scoop.it

Nitric oxide (NO) and reactive oxygen species (ROS) are two classes of key signaling molecules involved in various developmental processes and stress responses in plants. The burst of NO and ROS triggered by various stimuli activates downstream signaling pathways to cope with abiotic and biotic stresses. Emerging evidence suggests that the interplay of NO and ROS plays a critical role in regulating stress responses. However, the underpinning molecular mechanism remains poorly understood. Here, we show that NO positively regulates the activity of the Arabidopsis (Arabidopsis thaliana) cytosolic ascorbate peroxidase1 (APX1). We found that S-nitrosylation of APX1 at cysteine (Cys)-32 enhances its enzymatic activity of scavenging hydrogen peroxide, leading to the increased resistance to oxidative stress, whereas a substitution mutation at Cys-32 causes the reduction of ascorbate peroxidase activity and abolishes its responsiveness to the NO-enhanced enzymatic activity. Moreover, S-nitrosylation of APX1 at Cys-32 also plays an important role in regulating immune responses. These findings illustrate a unique mechanism by which NO regulates hydrogen peroxide homeostasis in plants, thereby establishing a molecular link between NO and ROS signaling pathways.


Via Christophe Jacquet
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Rescooped by Guogen Yang from WU_Phyto-Publications
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Nature Plants (2015): Elicitin recognition confers enhanced resistance to P. infestans in potato

Nature Plants (2015): Elicitin recognition confers enhanced resistance to P. infestans in potato | Plant-Microbe Interaction | Scoop.it

Potato late blight, caused by the destructive Irish famine pathogen Phytophthora infestans, is a major threat to global food security. All late blight resistance genes identified to date belong to the coiled-coil, nucleotide-binding, leucine-rich repeat class of intracellular immune receptors. However, virulent races of the pathogen quickly evolved to evade recognition by these cytoplasmic immune receptors. Here we demonstrate that the receptor-like protein ELR (elicitin response) from the wild potato Solanum microdontum mediates extracellular recognition of the elicitin domain, a molecular pattern that is conserved in Phytophthora species. ELR associates with the immune co-receptor BAK1/SERK3 and mediates broad-spectrum recognition of elicitin proteins from several Phytophthora species, including four diverse elicitins from P. infestans. Transfer of ELR into cultivated potato resulted in enhanced resistance to P. infestans. Pyramiding cell surface pattern recognition receptors with intracellular immune receptors could maximize the potential of generating a broader and potentially more durable resistance to this devastating plant pathogen.


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Change of a conserved amino acid in the MYC2 and MYC3 transcription factors leads to release of JAZ repression and increased activity

Change of a conserved amino acid in the MYC2 and MYC3 transcription factors leads to release of JAZ repression and increased activity | Plant-Microbe Interaction | Scoop.it
The bHLH transcription factor MYC2, together with its paralogues MYC3 and MYC4, is a master regulator of the response to the jasmonate (JA) hormone in Arabidopsis (Arabidopsis thaliana). In the absence of JA, JASMONATE ZIM (JAZ) proteins interact with the MYC proteins to block their activity. Understanding of the mechanism and specificity of this interaction is key to unravel JA signalling.We generated mutant MYC proteins and assessed their activity and the specificity of their interaction with the 12 Arabidopsis JAZ proteins.We show that the D94N mutation present in the atr2D allele of MYC3 abolishes the interaction between MYC3 and most JAZ proteins. The same effect is observed when the corresponding conserved Asp (D105) was mutated in MYC2. Accordingly, MYC2D105N activated target genes in the presence of JAZ proteins, in contrast to wild-type MYC2. JAZ1 and JAZ10 were the only JAZ proteins still showing interaction with the mutant MYC proteins, due to a second MYC interaction domain, besides the classical Jas domain.Our results visualize the divergence among JAZ proteins in their interaction with MYC proteins. Ultimately, the transferability of the Asp-to-Asn amino acid change might facilitate the design of hyperactive transcription factors for plant engineering.
Via Francis Martin
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Rescooped by Guogen Yang from Plant Biology Teaching Resources (Higher Education)
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Bringing light into the discussion about GMOs? – A rather long reading list

[updated 08 March, 2015]  

 

These days I received an apparently easy request: “Do you have any recommendations for reading about the debate on GMOs? I think there is a lot of heat, but too little light in the discussion; I trust you can send me some…” To which I answered carelessly: “Sure, I will look into it, select a few references and post them…” 

 

I thought I’d have a quick look into my collection of bookmarks and references and post some of the links to satisfy the request. Obviously there would be too many individual studies and crop-specific or country-specific reports, but focusing only (i) on what was published in recent years, (ii) on sources where all this information was already aggregated (literature reviews, meta-analyses, authoritative statements, FAQs, etc.), and (iii) on academic or publicly funded sources should produce a fairly concise list, I thought. 

 

While not unmanageable, the list has become quite long. To get a rough idea of the current state of knowledge, it may be sufficient to peruse the first 1-2 (starred *) references under each heading, and to have a quick look at the abstracts and summaries of some of the others. (Given the controversy surrounding this topic I did not want to suggest just one or two sources, but show a bit the width of the scientific consensus, and to offer some titbits of related information.) ... 

 

http://ajstein.tumblr.com/post/40504136918/
 

 


Via Alexander J. Stein, Mary Williams
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Jennifer Mach's comment, March 30, 2013 9:05 AM
I admit I haven't read this list... but for future reference, I'll definitely have a look.
Rescooped by Guogen Yang from Plant immunity and legume symbiosis
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Brachypodium as an emerging model for cereal–pathogen interactions

Brachypodium as an emerging model for cereal–pathogen interactions | Plant-Microbe Interaction | Scoop.it
Abstract

Background Cereal diseases cause tens of billions of dollars of losses annually and have devastating humanitarian consequences in the developing world. Increased understanding of the molecular basis of cereal host–pathogen interactions should facilitate development of novel resistance strategies. However, achieving this in most cereals can be challenging due to large and complex genomes, long generation times and large plant size, as well as quarantine and intellectual property issues that may constrain the development and use of community resources. Brachypodium distachyon (brachypodium) with its small, diploid and sequenced genome, short generation time, high transformability and rapidly expanding community resources is emerging as a tractable cereal model.

Scope Recent research reviewed here has demonstrated that brachypodium is either susceptible or partially susceptible to many of the major cereal pathogens. Thus, the study of brachypodium–pathogen interactions appears to hold great potential to improve understanding of cereal disease resistance, and to guide approaches to enhance this resistance. This paper reviews brachypodium experimental pathosystems for the study of fungal, bacterial and viral cereal pathogens; the current status of the use of brachypodium for functional analysis of cereal disease resistance; and comparative genomic approaches undertaken using brachypodium to assist characterization of cereal resistance genes. Additionally, it explores future prospects for brachypodium as a model to study cereal–pathogen interactions.

Conclusions The study of brachypodium–pathogen interactions appears to be a productive strategy for understanding mechanisms of disease resistance in cereal species. Knowledge obtained from this model interaction has strong potential to be exploited for crop improvement.

Via Christophe Jacquet
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Rescooped by Guogen Yang from Publications
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Nature Biotechnology: MutMap accelerates breeding of a salt-tolerant rice cultivar (2015)

Nature Biotechnology: MutMap accelerates breeding of a salt-tolerant rice cultivar (2015) | Plant-Microbe Interaction | Scoop.it

Following the 2011 earthquake and tsunami that affected Japan, >20,000 ha of rice paddy field was inundated with seawater, resulting in salt contamination of the land. As local rice landraces are not tolerant of high salt concentrations, we set out to develop a salt-tolerant rice cultivar. We screened 6,000 ethyl methanesulfonate (EMS) mutant lines of a local elite cultivar, 'Hitomebore', and identified a salt-tolerant mutant that we name hitomebore salt tolerant 1 (hst1). In this Correspondence, we report how we used our MutMap method to rapidly identify a loss-of-function mutation responsible for the salt tolerance of hst1 rice. The salt-tolerant hst1 mutant was used to breed a salt-tolerant variety named 'Kaijin', which differs from Hitomebore by only 201 single-nucleotide polymorphisms (SNPs). Field trials showed that it has the same growth and yield performance as the parental line under normal growth conditions. Notably, production of this salt-tolerant mutant line ready for delivery to farmers took only two years using our approach.


Via Kamoun Lab @ TSL
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Rescooped by Guogen Yang from Plant immunity and legume symbiosis
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“Self” and “Non-Self” in the Control of Phytoalexin Biosynthesis: Plant Phospholipases A2 with Alkaloid-Specific Molecular Fingerprints

“Self” and “Non-Self” in the Control of Phytoalexin Biosynthesis: Plant Phospholipases A2 with Alkaloid-Specific Molecular Fingerprints | Plant-Microbe Interaction | Scoop.it
The overproduction of specialized metabolites requires plants to manage the inherent burdens, including the risk of self-intoxication. We present a control mechanism that stops the expression of phytoalexin biosynthetic enzymes by blocking the antecedent signal transduction cascade. Cultured cells of Eschscholzia californica (Papaveraceae) and Catharanthus roseus (Apocynaceae) overproduce benzophenanthridine alkaloids and monoterpenoid indole alkaloids, respectively, in response to microbial elicitors. In both plants, an elicitor-responsive phospholipase A2 (PLA2) at the plasma membrane generates signal molecules that initiate the induction of biosynthetic enzymes. The final alkaloids produced in the respective plant inhibit the respective PLA, a negative feedback that prevents continuous overexpression. The selective inhibition by alkaloids from the class produced in the “self” plant could be transferred to leaves of Nicotiana benthamiana via recombinant expression of PLA2. The 3D homology model of each PLA2 displays a binding pocket that specifically accommodates alkaloids of the class produced by the same plant, but not of the other class; for example, C. roseus PLA2 only accommodates C. roseus alkaloids. The interaction energies of docked alkaloids correlate with their selective inhibition of PLA2 activity. The existence in two evolutionary distant plants of phospholipases A2 that discriminate “self-made” from “foreign” alkaloids reveals molecular fingerprints left in signal enzymes during the evolution of species-specific, cytotoxic phytoalexins.

Via Christophe Jacquet
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Rescooped by Guogen Yang from Virology and Bioinformatics from Virology.ca
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Origins and evolution of viruses of eukaryotes: The ultimate modularity

Origins and evolution of viruses of eukaryotes: The ultimate modularity | Plant-Microbe Interaction | Scoop.it

Viruses and other selfish genetic elements are dominant entities in the biosphere, with respect to both physical abundance and genetic diversity. Various selfish elements parasitize on all cellular life forms. The relative abundances of different classes of viruses are dramatically different between prokaryotes and eukaryotes. In prokaryotes, the great majority of viruses possess double-stranded (ds) DNA genomes, with a substantial minority of single-stranded (ss) DNA viruses and only limited presence of RNA viruses. In contrast, in eukaryotes, RNA viruses account for the majority of the virome diversity although ssDNA and dsDNA viruses are common as well. Phylogenomic analysis yields tangible clues for the origins of major classes of eukaryotic viruses and in particular their likely roots in prokaryotes. Specifically, the ancestral genome of positive-strand RNA viruses of eukaryotes might have been assembled de novo from genes derived from prokaryotic retroelements and bacteria although a primordial origin of this class of viruses cannot be ruled out. Different groups of double-stranded RNA viruses derive either from dsRNA bacteriophages or from positive-strand RNA viruses. The eukaryotic ssDNA viruses apparently evolved via a fusion of genes from prokaryotic rolling circle-replicating plasmids and positive-strand RNA viruses. Different families of eukaryotic dsDNA viruses appear to have originated from specific groups of bacteriophages on at least two independent occasions. Polintons, the largest known eukaryotic transposons, predicted to also form virus particles, most likely, were the evolutionary intermediates between bacterial tectiviruses and several groups of eukaryotic dsDNA viruses including the proposed order “Megavirales” that unites diverse families of large and giant viruses. Strikingly, evolution of all classes of eukaryotic viruses appears to have involved fusion between structural and replicative gene modules derived from different sources along with additional acquisitions of diverse genes.

 

Graphic by Ed Rybicki

  


Via Ed Rybicki, Chris Upton + helpers
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Ed Rybicki's curator insight, March 19, 6:35 AM

Wow...!  A tour de force.  Quite simply, says it all.  REALLY nice piece of work!!  And of course, they back me up in my view of how ss(-)RNA viruses evolved. Again B-)

Rabenstein, Frank's curator insight, March 23, 10:59 AM

Thank you Ed for this.

Rescooped by Guogen Yang from Plant immunity and legume symbiosis
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Plant-derived antifungal agent poacic acid targets β-1,3-glucan

Plant-derived antifungal agent poacic acid targets β-1,3-glucan | Plant-Microbe Interaction | Scoop.it
Significance

The search for new antifungal compounds is struggling to keep pace with emerging fungicide resistance. Through chemoprospecting of an untapped reservoir of inhibitory compounds, lignocellulosic hydrolysates, we have identified a previously undescribed antifungal agent, poacic acid. Using both chemical genomics and morphological analysis together for the first time, to our knowledge, we identified the cellular target of poacic acid as β-1,3-glucan. Through its action on the glucan layer of fungal cell walls, poacic acid is a natural antifungal agent against economically significant fungi and oomycete plant pathogens. This work highlights the chemical diversity within lignocellulosic hydrolysates as a source of potentially valuable chemicals.
Abstract

A rise in resistance to current antifungals necessitates strategies to identify alternative sources of effective fungicides. We report the discovery of poacic acid, a potent antifungal compound found in lignocellulosic hydrolysates of grasses. Chemical genomics using Saccharomyces cerevisiae showed that loss of cell wall synthesis and maintenance genes conferred increased sensitivity to poacic acid. Morphological analysis revealed that cells treated with poacic acid behaved similarly to cells treated with other cell wall-targeting drugs and mutants with deletions in genes involved in processes related to cell wall biogenesis. Poacic acid causes rapid cell lysis and is synergistic with caspofungin and fluconazole. The cellular target was identified; poacic acid localized to the cell wall and inhibited β-1,3-glucan synthesis in vivo and in vitro, apparently by directly binding β-1,3-glucan. Through its activity on the glucan layer, poacic acid inhibits growth of the fungi Sclerotinia sclerotiorum and Alternaria solani as well as the oomycete Phytophthora sojae. A single application of poacic acid to leaves infected with the broad-range fungal pathogen S. sclerotiorum substantially reduced lesion development. The discovery of poacic acid as a natural antifungal agent targeting β-1,3-glucan highlights the potential side use of products generated in the processing of renewable biomass toward biofuels as a source of valuable bioactive compounds and further clarifies the nature and mechanism of fermentation inhibitors found in lignocellulosic hydrolysates.

Via Christophe Jacquet
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