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Science: The Tale of the TALEs (2012)

Science: The Tale of the TALEs (2012) | Plant-Microbe Interaction | Scoop.it
Biologists have turned plant pest proteins into tools for studying and reshaping genomes of many species.

Some of biology's best technologies come from unexpected places. The green fluorescent protein that lit up biology with its ability to track proteins and gene expression in cells was borrowed from a jellyfish. A heat-stable enzyme from a bacterium often found in hot springs made the polymerase chain reaction method practical, facilitating the easy copying of DNA fragments needed for a myriad of applications, including the DNA fingerprinting used so widely to identify people. Now, thanks in part to inspiration that struck during a lunchtime discussion, proteins from a feared plant pest are poised to make genome engineering, the large-scale, directed manipulation of genes, routine for researchers studying a variety of organisms, including yeast and humans.
Via Kamoun Lab @ TSL, dromius
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Biswapriya Biswavas Misra's curator insight, December 16, 2012 3:49 AM

Biologists have turned plant pest proteins into tools for studying and reshaping genomes of many species.

Some of biology's best technologies come from unexpected places. The green fluorescent protein that lit up biology with its ability to track proteins and gene expression in cells was borrowed from a jellyfish. A heat-stable enzyme from a bacterium often found in hot springs made the polymerase chain reaction method practical, facilitating the easy copying of DNA fragments needed for a myriad of applications, including the DNA fingerprinting used so widely to identify people. Now, thanks in part to inspiration that struck during a lunchtime discussion, proteins from a feared plant pest are poised to make genome engineering, the large-scale, directed manipulation of genes, routine for researchers studying a variety of organisms, including yeast and humans.

Plant-Microbe Interaction
plant-microbe interaction
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The SWEET family of sugar transporters in grapevine: VvSWEET4 is involved in the interaction with Botrytis cinerea

The SWEET family of sugar transporters in grapevine: VvSWEET4 is involved in the interaction with Botrytis cinerea | Plant-Microbe Interaction | Scoop.it

During plant development, sugar export is determinant in multiple processes such as nectar production, pollen development and long-distance sucrose transport. The plant SWEET family of sugar transporters is a recently identified protein family of sugar uniporters. In rice, SWEET transporters are the target of extracellular bacteria, which have evolved sophisticated mechanisms to modify their expression and acquire sugars to sustain their growth. Here we report the characterization of the SWEET family of sugar transporters in Vitis vinifera. We identified 17 SWEET genes in the V. vinifera 40024 genome and show that they are differentially expressed in vegetative and reproductive organs. Inoculation with the biotrophic pathogens Erysiphe necator and Plasmopara viticola did not result in significant induction of VvSWEET gene expression. However, infection with the necrotroph Botrytis cinerea triggered a strong up-regulation of VvSWEET4 expression. Further characterization of VvSWEET4revealed that it is a glucose transporter localized in the plasma membrane that is up-regulated by inducers of reactive oxygen species and virulence factors from necrotizing pathogens. Finally, Arabidopsis knockout mutants in the orthologous AtSWEET4 were found to be less susceptible to B. cinerea. We propose that stimulation of expression of a developmentally regulated glucose uniporter by reactive oxygen species production and extensive cell death after necrotrophic fungal infection could facilitate sugar acquisition from plant cells by the pathogen.

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From Receptor-Like Kinases to Calcium Spikes: What Are the Missing Links?

From Receptor-Like Kinases to Calcium Spikes: What Are the Missing Links? | Plant-Microbe Interaction | Scoop.it

Via Jean-Michel Ané, Christophe Jacquet
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Suppression of NGB and NAB/ERabp1 in tomato modifies root responses to potato cyst nematode infestation

Suppression of NGB and NAB/ERabp1 in tomato modifies root responses to potato cyst nematode infestation | Plant-Microbe Interaction | Scoop.it

Plant-parasitic nematodes cause significant damage to major crops throughout the world. The small number of genes conferring natural plant resistance and the limitations of chemical control require the development of new protective strategies. RNA interference or the inducible over-expression of nematicidal genes provides an environment-friendly approach to this problem. Candidate genes include NGB, which encodes a small GTP-binding protein, and NAB/ERabp1, which encodes an auxin-binding protein, which were identified as being up-regulated in tomato roots in a transcriptome screen of potato cyst nematode (Globodera rostochiensis) feeding sites. Real-time reverse transcription-polymerase chain reaction (RT-PCR) and in situ hybridization confirmed the localized up-regulation of these genes in syncytia and surrounding cells following nematode infection. Gene-silencing constructs were introduced into tomato, resulting in a 20%–98% decrease in transcription levels. Nematode infection tests conducted on transgenic plants showed 57%–82% reduction in the number of G. rostochiensis females in vitro and 30%–46% reduction in pot trials. Transmission electron microscopy revealed a deterioration of cytoplasm, and degraded mitochondria and plastids, in syncytia induced in plants with reduced NAB/ERabp1 expression. Cytoplasm in syncytia induced in plants with low NGB expression was strongly electron translucent and contained very few ribosomes; however, mitochondria and plastids remained intact. Functional impairments in syncytial cytoplasm of silenced plants may result from NGB's role in ribosome biogenesis; this was confirmed by localization of yellow fluorescent protein (YFP)-labelled NGB protein in nucleoli and co-repression of NGB in plants with reduced NAB/ERabp1 expression. These results demonstrate that NGB and NAB/ERabp1 play important roles in the development of nematode-induced syncytia.


Via Christophe Jacquet
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Putative Orthologous Groups Database v2.0 | A Comparative Genomics Resource

Putative Orthologous Groups Database v2.0 | A Comparative Genomics Resource | Plant-Microbe Interaction | Scoop.it

The Putative orthologous Groups 2 Database (POGs2) integrates information about the inferred proteomes of four plant species (Arabidopsis thaliana, Zea mays, Orza sativa, and Populus trichocarpa) in a display that facilitates comparisons among orthologs and extrapolation of annotations among species. 


Via Elsa Ballini
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Adjustment of Host Cells for Accommodation of Symbiotic Bacteria: Vacuole Defunctionalization, HOPS Suppression, and TIP1g Retargeting in Medicago

Adjustment of Host Cells for Accommodation of Symbiotic Bacteria: Vacuole Defunctionalization, HOPS Suppression, and TIP1g Retargeting in Medicago | Plant-Microbe Interaction | Scoop.it

In legume–rhizobia symbioses, the bacteria in infected cells are enclosed in a plant membrane, forming organelle-like compartments called symbiosomes. Symbiosomes remain as individual units and avoid fusion with lytic vacuoles of host cells. We observed changes in the vacuole volume of infected cells and thus hypothesized that microsymbionts may cause modifications in vacuole formation or function. To examine this, we quantified the volumes and surface areas of plant cells, vacuoles, and symbiosomes in root nodules of Medicago truncatula and analyzed the expression and localization of VPS11 and VPS39, members of the HOPS vacuole-tethering complex. During the maturation of symbiosomes to become N2-fixing organelles, a developmental switch occurs and changes in vacuole features are induced. For example, we found that expression of VPS11 and VPS39 in infected cells is suppressed and host cell vacuoles contract, permitting the expansion of symbiosomes. Trafficking of tonoplast-targeted proteins in infected symbiotic cells is also altered, as shown by retargeting of the aquaporin TIP1g from the tonoplast membrane to the symbiosome membrane. This retargeting appears to be essential for the maturation of symbiosomes. We propose that these alterations in the function of the vacuole are key events in the adaptation of the plant cell to host intracellular symbiotic bacteria.


Via Christophe Jacquet
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Rescooped by Guogen Yang from Plant Immunity And Microbial Effectors
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Secretory Function of Autophagy in Innate Immune Cells

Secretory Function of Autophagy in Innate Immune Cells | Plant-Microbe Interaction | Scoop.it
Summary
Eukaryotic cells utilize two main secretory pathways to transport proteins to the extracellular space.

Via IPM Lab
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Frontiers | Diversifying selection in the wheat stem rust fungus acts predominantly on pathogen-associated gene families and reveals candidate effectors | Plant-Microbe Interaction

Plant pathogens cause severe losses to crop plants and threaten global food production. One striking example is the wheat stem rust fungus, Puccinia graminis f. sp. tritici, which can rapidly evolve new virulent pathotypes in response to resistant host lines. Like several other filamentous fungal and oomycete plant pathogens, its genome features expanded gene families that have been implicated in host-pathogen interactions, possibly encoding effector proteins that interact directly with target host defence proteins. Previous efforts to understand virulence largely relied on the prediction of secreted, small and cysteine-rich proteins as candidate effectors and thus delivered an overwhelming number of candidates. Here, we implement an alternative analysis strategy that uses the signal of adaptive evolution as a line of evidence for effector function, combined with comparative information and expression data. We demonstrate that in planta up-regulated genes that are rapidly evolving are found almost exclusively in pathogen-associated gene families, affirming the impact of host-pathogen co-evolution on genome structure and the adaptive diversification of specialised gene families. In particular, we predict 42 effector candidates that are conserved only across pathogens, induced during infection and rapidly evolving. One of our top candidates has recently been shown to induce genotype-specific hypersensitive cell death in wheat. This shows that comparative genomics incorporating the evolutionary signal of adaptation is powerful for predicting effector candidates for laboratory verification. Our system can be applied to a wide range of pathogens and will give insight into host-pathogen dynamics, ultimately leading to progress in strategies for disease control.

Via IPM Lab
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Ancient human genomes suggest three ancestral populations for present-day Europeans : Nature

Ancient human genomes suggest three ancestral populations for present-day Europeans : Nature | Plant-Microbe Interaction | Scoop.it
We sequenced the genomes of a [sim]7,000-year-old farmer from Germany and eight [sim]8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations/' deep relationships and show that early European farmers had [sim]44% ancestry from a /`basal Eurasian/' population that split before the diversification of other non-African lineages.

Via Francis Martin
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A procedure for the transient expression of genes by agroinfiltration above the permissive threshold to study temperature-sensitive processes in plant–pathogen interactions

A procedure for the transient expression of genes by agroinfiltration above the permissive threshold to study temperature-sensitive processes in plant–pathogen interactions | Plant-Microbe Interaction | Scoop.it

Localized expression of genes in plants from T-DNAs delivered into plant cells by Agrobacterium tumefaciens is an important tool in plant research. The technique, known as agroinfiltration, provides fast, efficient ways to transiently express or silence a desired gene without resorting to the time-consuming, challenging stable transformation of the host, the use of less efficient means of delivery, such as bombardment, or the use of viral vectors, which multiply and spread within the host causing physiological alterations themselves. A drawback of the agroinfiltration technique is its temperature dependence: early studies have shown that temperatures above 29 °C are nonpermissive to tumour induction by the bacterium as a result of failure in pilus formation. However, research in plant sciences is interested in studying processes at these temperatures, above the 25 °C experimental standard, common to many host–environment and host–pathogen interactions in nature, and agroinfiltration is an excellent tool for this purpose. Here, we measured the efficiency of agroinfiltration for the expression of reporter genes in plants from T-DNAs at the nonpermissive temperature of 30 °C, either transiently or as part of viral amplicons, and envisaged procedures that allow and optimize its use for gene expression at this temperature. We applied this technical advance to assess the performance at 30 °C of two viral suppressors of silencing in agropatch assays [Potato virus Y helper component proteinase (HCPro) and Cucumber mosaic virus 2b protein] and, within the context of infection by a Potato virus X (PVX) vector, also assessed indirectly their effect on the overall response of the host Nicotiana benthamiana to the virus.


Via Christophe Jacquet
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Cell Research - A DELLA protein complex controls the arbuscular mycorrhizal symbiosis in plants

Plants establish beneficial symbiotic associations with arbuscular mycorrhizal fungi, which colonize the root cortex, building specialized structures called arbuscules that facilitate nutrient exchange. The association occurs following plant recognition of lipochitooligosaccharides (LCOs) from mycorrhizal fungi, which activates the symbiosis signaling pathway prior to mycorrhizal colonization. Here we show that SLR1/DELLA, a repressor of gibberellic acid (GA) signaling, and its interacting partner protein are required for the mycorrhizal symbiosis. GA treatment inhibits mycorrhizal colonization and leads to the degradation of DELLAs. Consistently, rice lines mutated in DELLA are unable to be colonized by mycorrhizal fungi. DELLAs are members of the GRAS family of transcription factors. We further show that rice DELLA interacts with a second GRAS protein, DIP1 (DELLA Interacting Protein 1). DIP1 is also required for mycorrhizal colonization and in turn interacts with a previously characterized mycorrhizal GRAS protein, RAM1, that has been shown to directly regulate mycorrhizal-associated gene expression. We conclude that a complex of GRAS proteins, including DELLAs, is necessary for regulation of mycorrhizal-associated gene expression and thus colonization.


Via Francis Martin
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The role of forest trees and their mycorrhizal fungi in carbonate rock weathering and its significance for global carbon cycling

The role of forest trees and their mycorrhizal fungi in carbonate rock weathering and its significance for global carbon cycling | Plant-Microbe Interaction | Scoop.it

On million-year timescales, carbonate rock weathering exerts no net effect on atmospheric CO2 concentration. However, on timescales of decades-to-centuries it can contribute to sequestration of anthropogenic CO2 and increase land-ocean alkalinity flux, counteracting ocean acidification. Historical evidence indicates this flux is sensitive to land-use change, and recent experimental evidence suggests that trees and their associated soil microbial communities are major drivers of continental mineral weathering. Here, we review key physical and chemical mechanisms by which the symbiotic mycorrhizal fungi of forest tree roots potentially enhance carbonate rock weathering. Evidence from our ongoing field study at the UK's national pinetum confirms increased weathering of carbonate rocks by a wide range of gymnosperm and angiosperm tree species that form arbuscular (AM) or ectomycorrhizal (EM) fungal partnerships. We demonstrate that calcite-containing rock grains under EM tree species weather significantly faster than those under AM trees, an effect linked to greater soil acidification by EM trees. Weathering and corresponding alkalinity export is likely to increase with rising atmospheric CO2 and associated climate change. Our analyses suggest that strategic planting of fast growing EM angiosperm taxa on calcite-and dolomite rich terrain might accelerate the transient sink for atmospheric CO2 and slow rates of ocean acidification.


Via Christophe Jacquet, Francis Martin
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Large scale germplasm screening for identification of novel rice blast resistance sources

Large scale germplasm screening for identification of novel rice blast resistance sources | Plant-Microbe Interaction | Scoop.it

We conducted a large-scale screen for new rice blast resistance sources in 4246 geographically diverse rice accessions originating from 13 major rice-growing countries. The accessions were selected from a total collection of over 120’000 accessions based on their annotated rice blast resistance information in the International Rice Genebank. A two-step resistance screening protocol was used involving natural infection in a rice uniform blast nursery and subsequent artificial infections with five single rice blast isolates. 289 accessions showed broad-spectrum resistance against all five single rice blast isolates.


Via Elsa Ballini
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Roles of Plant Hormones in Regulating Host-Virus Interactions

Roles of Plant Hormones in Regulating Host-Virus Interactions | Plant-Microbe Interaction | Scoop.it

Abstract

Hormones are tuners of plant responses to biotic and abiotic stresses. They are involved in various complicated networks, through which they modulate responses to different stimuli. Four hormones primarily regulate plant defense to pathogens: salicylic acid (SA), jasmonic acid (JA), ethylene (Et), and abscisic acid (ABA). In susceptible plants, viral infections result in hormonal disruption, which manifests as simultaneous induction of few antagonistic hormones. However, these antagonistic hormones may exhibit some sequential accumulation in resistant lines. Virus propagation is usually restricted by activation of the small interfering RNA (siRNA) antiviral machinery and/or SA signaling pathway. Several studies have investigated these two systems, using different model viruses. However, the roles of hormones other than SA, especially those with antagonistic properties, such as ABA, have been neglected. Increasing evidence indicates that hormones control components of the small RNA system, which regulates many processes (including the siRNA antiviral machinery and the microRNA system) at the transcriptional or post-transcriptional level. Consequently, cross-talk between the antagonistic SA and ABA pathways modulates plant responses at multiple levels. In this review, we summarize recent findings on the different roles of hormones in regulating plant-virus interactions, which are helping us elucidate the fine-tuning of viral and plant systems by hormones.

 

 


Via Christophe Jacquet
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Characterization of novel wheat NBS domain-containing sequences and their utilization, in silico, for genome-scale R-gene mining

Characterization of novel wheat NBS domain-containing sequences and their utilization, in silico, for genome-scale R-gene mining | Plant-Microbe Interaction | Scoop.it

In crop improvement, the isolation, cloning and transfer of disease resistance genes (R-genes) is an ultimate goal usually starting from tentative R-gene analogs (RGAs) that are identified on the basis of their structure. For bread wheat, recent advances in genome sequencing are supporting the efforts of wheat geneticists worldwide. Among wheat R-genes, nucleotide-binding site (NBS)-encoding ones represent a major class. In this study, we have used a polymerase chain reaction-based approach to amplify and clone NBS-type RGAs from a bread wheat cultivar, ‘Salambo 80.’ Four novel complete ORF sequences showing similarities to previously reported R-genes/RGAs were used for in silico analyses. In a first step, where analyses were focused on the NBS domain, these sequences were phylogenetically assigned to two distinct groups: a first group close to leaf rust Lr21 resistance proteins; and a second one similar to cyst nematode resistance proteins. In a second step, sequences were used as initial seeds to walk up and downstream the NBS domain. This procedure enabled identifying 8 loci ranging in size between 2,115 and 7,653 bp. Ab initio gene prediction identified 8 gene models, among which two had complete ORFs. While GenBank survey confirmed the belonging of sequences to two groups, subsequent characterization using IWGSC genomic and proteomic data showed that the 8 gene models, reported in this study, were unique and their loci matched scaffolds on chromosome arms 1AS, 1BS, 4BS and 1DS. The gene model located on 1DS is a pseudo-Lr21 that was shown to have an NBS-LRR domain structure, while the potential association of the RGAs, here reported, is discussed. This study has produced novel R-gene-like loci and models in the wheat genome and provides the first steps toward further elucidation of their role in wheat disease resistance.


Via Christophe Jacquet
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MinION USB stick gene sequencer finally comes to market

MinION USB stick gene sequencer finally comes to market | Plant-Microbe Interaction | Scoop.it
Oxford Nanopore Technologies has finally delivered on its promise to bring personalized genome sequencing to the desktop. It is now time to see what their MinIon USB device can do.

Via Jean-Michel Ané, Francis Martin
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Jean-Michel Ané's curator insight, September 26, 1:03 AM

Watch the video... Now you know what I want for Christmas!

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Identification and Characterisation of a Hyper-Variable Apoplastic Effector Gene Family of the Potato Cyst Nematodes

Identification and Characterisation of a Hyper-Variable Apoplastic Effector Gene Family of the Potato Cyst Nematodes | Plant-Microbe Interaction | Scoop.it

Sedentary endoparasitic nematodes are obligate biotrophs that modify host root tissues, using a suite of effector proteins to create and maintain a feeding site that is their sole source of nutrition. Using assumptions about the characteristics of genes involved in plant-nematode biotrophic interactions to inform the identification strategy, we provide a description and characterisation of a novel group of hyper-variable extracellular effectors termed HYP, from the potato cyst nematode Globodera pallida. HYP effectors comprise a large gene family, with a modular structure, and have unparalleled diversity between individuals of the same population: no two nematodes tested had the same genetic complement of HYP effectors. Individuals vary in the number, size, and type of effector subfamilies. HYP effectors are expressed throughout the biotrophic stages in large secretory cells associated with the amphids of parasitic stage nematodes as confirmed by in situ hybridisation. The encoded proteins are secreted into the host roots where they are detectable by immunochemistry in the apoplasm, between the anterior end of the nematode and the feeding site. We have identified HYP effectors in three genera of plant parasitic nematodes capable of infecting a broad range of mono- and dicotyledon crop species. In planta RNAi targeted to all members of the effector family causes a reduction in successful parasitism.


Via Christophe Jacquet, Francis Martin
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N-acyl-homoserine lactones-producing bacteria protect plants against plant and human pathogens -

N-acyl-homoserine lactones-producing bacteria protect plants against plant and human pathogens - | Plant-Microbe Interaction | Scoop.it

The implementation of beneficial microorganisms for plant protection has a long history. Many rhizobia bacteria are able to influence the immune system of host plants by inducing resistance towards pathogenic microorganisms. In this report, we present a translational approach in which we demonstrate the resistance-inducing effect of Ensifer meliloti (Sinorhizobium meliloti) on crop plants that have a significant impact on the worldwide economy and on human nutrition. Ensifer meliloti is usually associated with root nodulation in legumes and nitrogen fixation. Here, we suggest that the ability of S. meliloti to induce resistance depends on the production of the quorum-sensing molecule, oxo-C14-HSL. The capacity to enhanced resistance provides a possibility to the use these beneficial bacteria in agriculture. Using the Arabidopsis-Salmonella model, we also demonstrate that the application of N-acyl-homoserine lactones-producing bacteria could be a successful strategy to prevent plant-originated infections with human pathogens.


Via Christophe Jacquet
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Comparative Proteomic Analyses Reveal that the Regulators of G-protein Signaling Proteins Regulate Amino Acid Metabolism of the Rice Blast Fungus Magnaporthe oryzae

Comparative Proteomic Analyses Reveal that the Regulators of G-protein Signaling Proteins Regulate Amino Acid Metabolism of the Rice Blast Fungus Magnaporthe oryzae | Plant-Microbe Interaction | Scoop.it

The rice blast fungus Magnaporthe oryzae encodes eight regulators of G-protein signaling (RGS) proteins MoRgs1-MoRgs8 that orchestrate the growth, asexual/sexual production, appressorium differentiation, and pathogenicity. To address the mechanisms by which MoRgs proteins function, we conducted a two-dimensional electrophoresis (2-DE) proteome study and identified 82 differentially expressed proteins by comparing five ∆Morgs mutants with wild type Guy11 strain. We found that the abundances of eight amino acid biosynthesis or degradation-associated proteins were markedly altered in five ∆Morgs mutants, indicating one of the main collective roles for the MoRgs proteins is to influence amino acid metabolism. We showed that MoRgs proteins have distinct roles in amino acid metabolism and nutrient responses from growth assays. In addition, we characterized MoLys20, a homocitrate synthase, whose abundance was significantly decreased in the ∆Morgsmutants. The ∆Molys20 mutant is auxotrophic for lysine and exogenous lysine could partially rescue its auxotrophic defects. Deletion ofMoLYS20 resulted in defects in conidiation and infection, as well as pathogenicity on rice. Overall, our results indicate that one of the critical roles for MoRgs proteins is to regulate amino acid metabolism, and that MoLys20 may be directly or indirectly regulated by MoRgs and participated in lysine biosynthesis, thereby affecting fungal pathogenicity.


Via Elsa Ballini
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Frontiers | Extracellular ATP acts as a damage-associated molecular pattern (DAMP) signal in plants | Plant-Microbe Interaction

Frontiers | Extracellular ATP acts as a damage-associated molecular pattern (DAMP) signal in plants | Plant-Microbe Interaction | Plant-Microbe Interaction | Scoop.it
As sessile organisms, plants have evolved effective mechanisms to protect themselves from environmental stresses. Damaged (i.e., wounded) plants recognize a variety of endogenous molecules as danger signals, referred to as damage-associated molecular patterns (DAMPs). ATP is among the molecules that are released by cell damage, and recent evidence suggests that ATP can serve as a DAMP. Although little studied in plants, extracellular ATP is well known for its signaling role in animals, including acting as a DAMP during the inflammatory response and wound healing. If ATP acts outside the cell, then it is reasonable to expect that it is recognized by a plasma membrane-localized receptor. Recently, DORN1, a lectin receptor kinase, was shown to recognize extracellular ATP in Arabidopsis. DORN1 is the founding member of a new purinoceptor subfamily, P2K (P2 receptor Kinase), which is plant-specific. P2K1 (DORN1) is required for ATP-induced cellular responses (e.g., cytosolic Ca2+ elevation, MAPK phosphorylation, and gene expression). Genetic analysis of loss-of-function mutants and overexpression lines showed that P2K1 participates in the plant wound response, consistent with the role of ATP as a DAMP. In this review, we summarize past research on the roles and mechanisms of extracellular ATP signaling in plants, and discuss the direction of the future research of extracellular ATP as a DAMP signal.

Via Christophe Jacquet
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Cytochrome P450 Monooxygenase CYP53 Family in Fungi: Comparative Structural and Evolutionary Analysis and Its Role as a Common Alternative Anti-Fungal Drug Target

Cytochrome P450 Monooxygenase CYP53 Family in Fungi: Comparative Structural and Evolutionary Analysis and Its Role as a Common Alternative Anti-Fungal Drug Target | Plant-Microbe Interaction | Scoop.it

Cytochrome P450 monooxygenases (CYPs/P450s) are heme-thiolate proteins whose role as a drug target against pathogenic microbes has been explored because of their stereo- and regio-specific oxidation activity. We aimed to assess the CYP53 family's role as a common alternative drug target against animal (including human) and plant pathogenic fungi and its role in fungal-mediated wood degradation. Genome-wide analysis of fungal species revealed the presence of CYP53 members in ascomycetes and basidiomycetes. Basidiomycetes had a higher number of CYP53 members in their genomes than ascomycetes. Only two CYP53 subfamilies were found in ascomycetes and six subfamilies in basidiomycetes, suggesting that during the divergence of phyla ascomycetes lost CYP53 P450s. According to phylogenetic and gene-structure analysis, enrichment of CYP53 P450s in basidiomycetes occurred due to the extensive duplication of CYP53 P450s in their genomes. Numerous amino acids (103) were found to be conserved in the ascomycetes CYP53 P450s, against only seven in basidiomycetes CYP53 P450s. 3D-modelling and active-site cavity mapping data revealed that the ascomycetes CYP53 P450s have a highly conserved protein structure whereby 78% amino acids in the active-site cavity were found to be conserved. Because of this rigid nature of ascomycetes CYP53 P450s' active site cavity, any inhibitor directed against this P450 family can serve as a common anti-fungal drug target, particularly toward pathogenic ascomycetes. The dynamic nature of basidiomycetes CYP53 P450s at a gene and protein level indicates that these P450s are destined to acquire novel functions. Functional analysis of CYP53 P450s strongly supported our hypothesis that the ascomycetes CYP53 P450s ability is limited for detoxification of toxic molecules, whereas basidiomycetes CYP53 P450s play an additional role, i.e. involvement in degradation of wood and its derived components. This study is the first report on genome-wide comparative structural (gene and protein structure-level) and evolutionary analysis of a fungal P450 family.


Via Christophe Jacquet, Steve Marek, Carla Garzon, Elsa Ballini
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First evidence of mutualism between ancient plant lineages (Haplomitriopsida liverworts) and Mucoromycotina fungi and its response to simulated Palaeozoic changes in atmospheric CO2

First evidence of mutualism between ancient plant lineages (Haplomitriopsida liverworts) and Mucoromycotina fungi and its response to simulated Palaeozoic changes in atmospheric CO2 | Plant-Microbe Interaction | Scoop.it

SummaryThe discovery that Mucoromycotina, an ancient and partially saprotrophic fungal lineage, associates with the basal liverwort lineage Haplomitriopsida casts doubt on the widely held view that Glomeromycota formed the sole ancestral plant–fungus symbiosis. Whether this association is mutualistic, and how its functioning was affected by the fall in atmospheric CO2 concentration that followed plant terrestrialization in the Palaeozoic, remains unknown.We measured carbon-for-nutrient exchanges between Haplomitriopsida liverworts and Mucoromycotina fungi under simulated mid-Palaeozoic (1500 ppm) and near-contemporary (440 ppm) CO2 concentrations using isotope tracers, and analysed cytological differences in plant–fungal interactions. Concomitantly, we cultured both partners axenically, resynthesized the associations in vitro, and characterized their cytology.We demonstrate that liverwort–Mucoromycotina symbiosis is mutualistic and mycorrhiza-like, but differs from liverwort–Glomeromycota symbiosis in maintaining functional efficiency of carbon-for-nutrient exchange between partners across CO2 concentrations. Inoculation of axenic plants with Mucoromycotina caused major cytological changes affecting the anatomy of plant tissues, similar to that observed in wild-collected plants colonized by Mucoromycotina fungi.By demonstrating reciprocal exchange of carbon for nutrients between partners, our results provide support for Mucoromycotina establishing the earliest mutualistic symbiosis with land plants. As symbiotic functional efficiency was not compromised by reduced CO2, we suggest that other factors led to the modern predominance of the Glomeromycota symbiosis.


Via Pierre-Marc Delaux, Francis Martin
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Antifungal drug resistance evoked via RNAi-dependent epimutations

Antifungal drug resistance evoked via RNAi-dependent epimutations | Plant-Microbe Interaction | Scoop.it

Microorganisms evolve via a range of mechanisms that may include or involve sexual/parasexual reproduction, mutators, aneuploidy, Hsp90 and even prions. Mechanisms that may seem detrimental can be repurposed to generate diversity. Here we show that the human fungal pathogen Mucor circinelloides develops spontaneous resistance to the antifungal drug FK506 (tacrolimus) via two distinct mechanisms. One involves Mendelian mutations that confer stable drug resistance; the other occurs via an epigenetic RNA interference (RNAi)-mediated pathway resulting in unstable drug resistance. The peptidylprolyl isomerase FKBP12 interacts with FK506 forming a complex that inhibits the protein phosphatase calcineurin1. Calcineurin inhibition by FK506 blocksM. circinelloides transition to hyphae and enforces yeast growth2. Mutations in the fkbAgene encoding FKBP12 or the calcineurin cnbR or cnaA genes confer FK506 resistance and restore hyphal growth. In parallel, RNAi is spontaneously triggered to silence thefkbA gene, giving rise to drug-resistant epimutants. FK506-resistant epimutants readily reverted to the drug-sensitive wild-type phenotype when grown without exposure to the drug. The establishment of these epimutants is accompanied by generation of abundantfkbA small RNAs and requires the RNAi pathway as well as other factors that constrain or reverse the epimutant state. Silencing involves the generation of a double-stranded RNA trigger intermediate using the fkbA mature mRNA as a template to produce antisensefkbA RNA. This study uncovers a novel epigenetic RNAi-based epimutation mechanism controlling phenotypic plasticity, with possible implications for antimicrobial drug resistance and RNAi-regulatory mechanisms in fungi and other eukaryotes.

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Rescooped by Guogen Yang from MycorWeb Plant-Microbe Interactions
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Microbes ride the current

Microbes ride the current | Plant-Microbe Interaction | Scoop.it

How do differences in marine bacterial populations arise in the ocean? On page 1346 of this Science issue, Hellweger et al. (1) investigate this question with a model based on ocean currents, parameterized with data from the most ubiquitous and abundant ocean bacterium, Pelagibacter. The model assumes that mutations are neutral—that is, they cause no change in the fitness of organisms, so that selection cannot act on them. The results show that neutral processes are enough to generate biogeographical patterns in marine bacteria without any adaptive evolution taking place.


Via Francis Martin
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Rescooped by Guogen Yang from Plants&Bacteria
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The Clavibacter michiganensis subsp. michiganensis–Tomato Interactome Reveals the Perception of Pathogen by the Host and Suggests Mechanisms of Infection

The Clavibacter michiganensis subsp. michiganensis–Tomato Interactome Reveals the Perception of Pathogen by the Host and Suggests Mechanisms of Infection | Plant-Microbe Interaction | Scoop.it

The Gram-positive bacterium Clavibacter michiganensis subsp. michiganensis (Cmm) causes wilt and canker disease of tomato (Solanum lycopersicum). Mechanisms of Cmm pathogenicity and tomato response to Cmm infection are not well understood. To explore the interaction between Cmm and tomato, multidimensional protein identification technology (MudPIT) and tandem mass spectrometry were used to analyze in vitro and in planta generated samples. The results show that during infection Cmm senses the plant environment, transmits signals, induces, and then secretes multiple hydrolytic enzymes, including serine proteases of the Pat-1, Ppa, and Sbt familes, the CelA, XysA, and NagA glycosyl hydrolases, and other cell wall-degrading enzymes. Tomato induction of pathogenesis-related (PR) proteins, LOX1, and other defense-related proteins during infection indicates that the plant senses the invading bacterium and mounts a basal defense response, although partial with some suppressed components including class III peroxidases and a secreted serine peptidase. The tomato ethylene-synthesizing enzyme ACC-oxidase was induced during infection with the wild-typeCmm but not during infection with an endophytic Cmm strain, identifying Cmm-triggered host synthesis of ethylene as an important factor in disease symptom development. The proteomic data were also used to improve Cmm genome annotation, and thousands of Cmm gene models were confirmed or expanded.


Via Freddy Monteiro
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Rescooped by Guogen Yang from MycorWeb Plant-Microbe Interactions
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The cryptic role of biodiversity in the emergence of host–microbial mutualisms

The cryptic role of biodiversity in the emergence of host–microbial mutualisms | Plant-Microbe Interaction | Scoop.it

The persistence of mutualisms in host-microbial – or holobiont – systems is difficult to explain because microbial mutualists, who bear the costs of providing benefits to their host, are always prone to being competitively displaced by non-mutualist ‘cheater’ species. This disruptive effect of competition is expected to be particularly strong when the benefits provided by the mutualists entail costs such as reduced competitive ability. Using a metacommunity model, we show that competition between multiple cheaters within the host's microbiome, when combined with the spatial structure of host–microbial interactions, can have a constructive rather than a disruptive effect by allowing the emergence and maintenance of mutualistic microorganisms within the host. These results indicate that many of the microorganisms inhabiting a host's microbiome, including those that would otherwise be considered opportunistic or even potential pathogens, play a cryptic yet critical role in promoting the health and persistence of the holobiont across spatial scales.


Via Jean-Michel Ané, Francis Martin
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