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The Ubiquitin Ligase PUB22 Targets a Subunit of the Exocyst Complex Required for PAMP-Triggered Responses in Arabidopsis

The Ubiquitin Ligase PUB22 Targets a Subunit of the Exocyst Complex Required for PAMP-Triggered Responses in Arabidopsis | Plant-Microbe Interaction | Scoop.it

Plant pathogens are perceived by pattern recognition receptors, which are activated upon binding to pathogen-associated molecular patterns (PAMPs). Ubiquitination and vesicle trafficking have been linked to the regulation of immune signaling. However, little information exists about components of vesicle trafficking involved in immune signaling and the mechanisms that regulate them. In this study, we identified Arabidopsis thaliana Exo70B2, a subunit of the exocyst complex that mediates vesicle tethering during exocytosis, as a target of the plant U-box–type ubiquitin ligase 22 (PUB22), which acts in concert with PUB23 and PUB24 as a negative regulator of PAMP-triggered responses. We show that Exo70B2 is required for both immediate and later responses triggered by all tested PAMPs, suggestive of a role in signaling. Exo70B2 is also necessary for the immune response against different pathogens. Our data demonstrate that PUB22 mediates the ubiquitination and degradation of Exo70B2 via the 26S Proteasome. Furthermore, degradation is regulated by the autocatalytic turnover of PUB22, which is stabilized upon PAMP perception. We therefore propose a mechanism by which PUB22-mediated degradation of Exo70B2 contributes to the attenuation of PAMP-induced signaling.

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Rescooped by Guogen Yang from Plant Biology Teaching Resources (Higher Education)
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Plant Cell: The Root Hair “Infectome” of Medicago truncatula Uncovers Changes in Cell Cycle Genes and Reveals a Requirement for Auxin Signaling in Rhizobial Infection

Plant Cell: The Root Hair “Infectome” of Medicago truncatula Uncovers Changes in Cell Cycle Genes and Reveals a Requirement for Auxin Signaling in Rhizobial Infection | Plant-Microbe Interaction | Scoop.it
The Root Hair “Infectome” of Medicago truncatula Uncovers Changes in Cell Cycle Genes and Reveals a Requirement for Auxin Signaling in Rhizobial Infection

Via Mary Williams
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Mary Williams's curator insight, December 22, 7:45 AM

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Rescooped by Guogen Yang from Plant-microbe interactions (on the plant's side)
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Silencing of OPR3 in tomato reveals the role of OPDA in callose deposition during the activation of defense responses against Botrytis cinerea

Silencing of OPR3 in tomato reveals the role of OPDA in callose deposition during the activation of defense responses against Botrytis cinerea | Plant-Microbe Interaction | Scoop.it
Cis-(+)-12-oxo-phytodienoic acid (OPDA) is likely to play signaling roles in plant defense that do not depend on its further conversion to the phytohormone jasmonic acid. To elucidate the role of OPDA in Solanum lycopersicum (tomato) plant defense, we have silenced the 12-oxophytodienoate reductase 3 (OPR3) gene. Two independent transgenic tomato lines (SiOPR3-1 and SiOPR3-2) showed significantly reduced OPR3 expression upon infection with the necrotrophic pathogen Botrytis cinerea. Moreover, SiOPR3 plants are more susceptible to this pathogen, and this susceptibility is accompanied by a significant decrease in OPDA levels and by the production of JA-Ile being almost abolished. OPR3 silencing also leads to a major reduction in the expression of other genes of the jasmonic acid (JA) synthesis and signaling pathways after infection. These results confirm that in tomato plants, as in Arabidopsis, OPR3 determines OPDA availability for JA biosynthesis. In addition, we show that an intact JA biosynthetic pathway is required for proper callose deposition, as its pathogen-induced accumulation is reduced in SiOPR3 plants. Interestingly, OPDA, but not JA, treatment restored basal resistance to B. cinerea and induced callose deposition in SiOPR3-1 and SiOPR3-2 transgenic plants. These results provide clear evidence that OPDA by itself plays a major role in the basal defense of tomato plants against this necrotrophic pathogen.

Via Christophe Jacquet
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Rescooped by Guogen Yang from Plant-Microbe Symbioses
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plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants

plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants | Plant-Microbe Interaction | Scoop.it
High-throughput sequencing techniques have made it possible to assay an organism's entire repertoire of small non-coding RNAs (ncRNAs) in an efficient and cost-effective manner. The moderate size of small RNA-seq datasets makes it feasible to provide free web services to the research community that provide many basic features of a small RNA-seq analysis, including quality control, read normalization, ncRNA quantification, and the prediction of putative novel ncRNAs. DARIO is one such system that so far has been focussed on animals. Here we introduce an extension of this system to plant short non-coding RNAs (sncRNAs). It includes major modifications to cope with plant-specific sncRNA processing. The current version of plantDARIO covers analyses of mapping files, small RNA-seq quality control, expression analyses of annotated sncRNAs, including the prediction of novel miRNAs and snoRNAs from unknown expressed loci and expression analyses of user-defined loci. At present Arabidopsis thaliana, Beta vulgaris, and Solanum lycopersicum are covered. The web tool links to a plant specific visualization browser to display the read distribution of the analyzed sample. The easy-to-use platform of plantDARIO quantifies RNA expression of annotated sncRNAs from different sncRNA databases together with new sncRNAs, annotated by our group. The plantDARIO website can be accessed at http://plantdario.bioinf.uni-leipzig.de/.

Via Jean-Michel Ané
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Ten Simple Rules for Finishing Your PhD

Ten Simple Rules for Finishing Your PhD | Plant-Microbe Interaction | Scoop.it

After years of research and with completion in sight, the final year of the PhD often represents the most challenging time of a student's career, in which the ultimate reward is the PhD honor itself. A large investment in time, energy, and motivation is needed, with many tasks to be completed; concluding experiments must be carried out, results interpreted, and a research story mapped out in preparation for writing the final thesis. All the while, administrative obligations need attention (e.g., university credits and mandatory documents), papers may need to be published, students mentored, and due consideration paid to planning for the next career move. Without some form of strategic action plan and the employment of project management skills, students run the risk of becoming overwhelmed and run down or of not meeting their final deadlines. Personal time management and stress resilience are competences that can be developed and honed during this final period of the PhD.

Here, we present ten simple rules on how to deal with time issues and conflict situations when facing the last year of a PhD in science. The rules focus on defining research goals in advance and designing a plan of action. Moreover, we discuss the importance of managing relationships with supervisors and colleagues, as well as early career planning.


Via Francis Martin, Jean-Michel Ané
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Rescooped by Guogen Yang from Plant Immunity And Microbial Effectors
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Oxaloacetate acetylhydrolase gene mutants of Sclerotinia sclerotiorum do not accumulate oxalic acid, but do produce limited lesions on host plants

Oxaloacetate acetylhydrolase gene mutants of Sclerotinia sclerotiorum do not accumulate oxalic acid, but do produce limited lesions on host plants | Plant-Microbe Interaction | Scoop.it
Summary
The oxaloacetate acetylhydrolase (OAH, EC 3.7.1.1)-encoding gene Ss-oah1 was cloned and functionally characterized from Sclerotinia sclerotiorum.

Via IPM Lab
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Rescooped by Guogen Yang from Plant-Microbe Symbioses
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Detection and characterization of broad-spectrum anti-pathogen activity of novel rhizobacterial isolates and suppression of Fusarium crown and root rot disease of tomato

Aims
To detect and characterize broad-spectrum anti-pathogen activity of indigenous bacterial isolates obtained from potato soil and soybean leaves for their potential to be developed as biofungicides to control soilborne diseases such as Fusarium crown and root rot of tomato (FCRR) caused by Fusarium oxysporum f. sp. radicis-lycopersici (Forl).

Methods and Results
Thirteen bacterial isolates [Bacillus amyloliquefaciens (four isolates), Paenibacillus polymyxa (three isolates), Pseudomonas chlororaphis (two isolates), Pseudomonas fluorescens (two isolates), Bacillus subtilis (one isolate), and Pseudomosas sp. (one isolate)] or their volatiles showed antagonistic activity against most of the ten plant pathogens in plate assays. Cell-free culture filtrates (CF) of five isolates or 1-butanol-extracts of CFs also inhibited growth of most pathogen mycelia in plate assays. PCR analysis confirmed the presence of most antibiotic biosynthetic genes such as phlD, phzFA, prnD, pltC in most Pseudomonas isolates and bmyB, bacA, ituD, srfAA, fenD in most Bacillus isolates. These bacterial isolates varied in production of HCN, siderophores, β-1,3-glucanases, chitinases, proteases, indole-3-acetic acid, salicylic acid, and for nitrogen fixation and phosphate solubilisation. GC-MS analysis identified ten volatile compounds from ten isolates and 18 compounds from 1-butanol extracts of CFs of five isolates. Application of irradiated peat formulation of six isolates to tomato roots prior to transplanting in a Forl-infested potting mix and field soil provided protection of tomato plants from FCRR disease and enhanced plant growth under greenhouse conditions.

Conclusions
Five of the 13 indigenous bacterial isolates were antagonistic to eight plant pathogens, both in vitro and in vivo. Antagonistic and plant-growth promotion activities of these isolates might be related to the production of several types of antibiotics, lytic enzymes, phytohormones, secondary metabolites, siderophores, and volatile compounds; however, any specific role of each needs to be determined.

Significance and Impact of the Study
Indigenous antagonistic bacterial isolates have the potential to be developed as biofungicides for minimizing early crop losses due to soilborne diseases caused by Fusarium and other soilborne pathogens.

Via Jean-Michel Ané
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Rescooped by Guogen Yang from Plant-Microbe Symbioses
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Enabling plant synthetic biology through genome engineering

Enabling plant synthetic biology through genome engineering | Plant-Microbe Interaction | Scoop.it
Synthetic biology seeks to create new biological systems, including user-designed plants and plant cells. These systems can be employed for a variety of purposes, ranging from producing compounds of industrial or therapeutic value, to reducing crop losses by altering cellular responses to pathogens or climate change. To realize the full potential of plant synthetic biology, techniques are required that provide control over the genetic code – enabling targeted modifications to DNA sequences within living plant cells. Such control is now within reach owing to recent advances in the use of sequence-specific nucleases to precisely engineer genomes. We discuss here the enormous potential provided by genome engineering for plant synthetic biology.

Via Jean-Michel Ané
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Rescooped by Guogen Yang from Plant-microbe interactions (on the plant's side)
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Silicon-mediated resistance of Arabidopsis against powdery mildew involves mechanisms other than the salicylic acid (SA)-dependent defence pathway

Silicon-mediated resistance of Arabidopsis against powdery mildew involves mechanisms other than the salicylic acid (SA)-dependent defence pathway | Plant-Microbe Interaction | Scoop.it
On absorption by plants, silicon (Si) offers protection against many fungal pathogens, including powdery mildews. The mechanisms by which Si exerts its prophylactic role remain enigmatic, although a prevailing hypothesis suggests that Si positively influences priming. Attempts to decipher Si properties have been limited to plants able to absorb Si, which excludes the model plant Arabidopsis because it lacks Si influx transporters. In this work, we were able to engineer Arabidopsis plants with an Si transporter from wheat (TaLsi1) and to exploit mutants (pad4 and sid2) deficient in salicylic acid (SA)-dependent defence responses to study their phenotypic response and changes in defence expression against Golovinomyces cichoracearum (Gc) following Si treatment. Our results showed that TaLsi1 plants contained significantly more Si and were significantly more resistant to Gc infection than control plants when treated with Si, the first such demonstration in a plant transformed with a heterologous Si transporter. The resistant plants accumulated higher levels of SA and expressed higher levels of transcripts encoding defence genes, thus suggesting a role for Si in the process. However, TaLsi1 pad4 and TaLsi1 sid2 plants were also more resistant to Gc than were pad4 and sid2 plants following Si treatment. Analysis of the resistant phenotypes revealed a significantly reduced production of SA and expression of defence genes comparable with susceptible controls. These results indicate that Si contributes to Arabidopsis defence priming following pathogen infection, but highlight that Si will confer protection even when priming is altered. We conclude that Si-mediated protection involves mechanisms other than SA-dependent defence responses.

Via Christophe Jacquet
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Rescooped by Guogen Yang from Plant-Microbe Symbioses
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The soil microbial community predicts the importance of plant traits in plant–soil feedback

The soil microbial community predicts the importance of plant traits in plant–soil feedback | Plant-Microbe Interaction | Scoop.it
Reciprocal interaction between plant and soil (plant–soil feedback, PSF) can determine plant community structure. Understanding which traits control interspecific variation of PSF strength is crucial for plant ecology. Studies have highlighted either plant-mediated nutrient cycling (litter-mediated PSF) or plant–microbe interaction (microbial-mediated PSF) as important PSF mechanisms, each attributing PSF variation to different traits. However, this separation neglects the complex indirect interactions between the two mechanisms.
We developed a model coupling litter- and microbial-mediated PSFs to identify the relative importance of traits in controlling PSF strength, and its dependency on the composition of root-associated microbes (i.e. pathogens and/or mycorrhizal fungi).
Results showed that although plant carbon: nitrogen (C : N) ratio and microbial nutrient acquisition traits were consistently important, the importance of litter decomposability varied. Litter decomposability was not a major PSF determinant when pathogens are present. However, its importance increased with the relative abundance of mycorrhizal fungi as nutrient released from the mycorrhizal-enhanced litter production to the nutrient-depleted soils result in synergistic increase of soil nutrient and mycorrhizal abundance. Data compiled from empirical studies also supported our predictions.
We propose that the importance of litter decomposability depends on the composition of root-associated microbes. Our results provide new perspectives in plant invasion and trait-based ecology.

Via Jean-Michel Ané
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Rescooped by Guogen Yang from Plant Biology Teaching Resources (Higher Education)
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Why start from scratch when you can recycle and adapt?

Why start from scratch when you can recycle and adapt? | Plant-Microbe Interaction | Scoop.it

Leaf development is such a fascinating topic, because it reveals the molecular processes the are involved in pattern formation. Interestingly, several genes and small molecules (e.g., auxin) are used repeatedly during the initiation and elaboration of leaves. A pair of papers out in Plant Cell highlights this thrifty genetic strategy.
In the first, we see how the development of the ligule in a maize leaf involves the redeployment of several genes that are involved in leaf initiation, a process that occurs much earlier in the developmental pathway.


Transcriptomic Analyses Indicate That Maize Ligule Development Recapitulates Gene Expression Patterns That Occur during Lateral Organ Initiation (www.plantcell.org/…/early/2014/12/16/tpc.114.132688.abstract).
In the second, we see the KNOX1 / GA module that is so important in leaf developmental patterning also contributes to the environtmental responsiveness of leaf shape (heterophylly), as found in aquatic plants such as Rorippa aquatica.
Regulation of the KNOX-GA Gene Module Induces Heterophyllic Alteration in North American Lake Cress (http://www.plantcell.org/…/20…/12/16/tpc.114.130229.abstract).
These studies also reinforce our understanding of process of evolution; why start from scratch when you can just tweak something that aleady works in another context?

 


Via Mary Williams
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Rescooped by Guogen Yang from MycorWeb Plant-Microbe Interactions
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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

The 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 Francis Martin
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Patellins 3 and 6, two members of the Plant Patellin family, interact with the movement protein of Alfalfa mosaic virus and interfere with viral movement

Patellins 3 and 6, two members of the Plant Patellin family, interact with the movement protein of Alfalfa mosaic virus and interfere with viral movement | Plant-Microbe Interaction | Scoop.it
Movement proteins (MPs) encoded by plant viruses interact with host proteins to facilitate or interfere with intra- and/or intercellular viral movement. Using yeast two-hybrid and bimolecular fluorescence complementation assays, we herein present in vivo evidence for the interaction between Alfalfa mosaic virus (AMV) MP and Arabidopsis Patellin 3 (atPATL3) and Patellin 6 (atPATL6), two proteins containing a Sec14 domain. Proteins with Sec14 domains are implicated in membrane trafficking, cytoskeleton dynamics, lipid metabolism and lipid-mediated regulatory functions. Interestingly, the overexpression of atPATL3 and/or atPATL6 interfered with the plasmodesmata targeting of AMV MP and correlated with reduced infection foci size. Consistently, the viral RNA levels increased in the single and double Arabidopsis knockout mutants for atPATL3 and atPATL6. Our results indicate that, in general, MP–PATL interactions interfere with the correct subcellular targeting of MP, thus rendering the intracellular transport of viral MP-containing complexes less efficient and diminishing cell-to-cell movement.

Via Christophe Jacquet
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Rescooped by Guogen Yang from Virology and Bioinformatics from Virology.ca
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#bioinformatics New #MAUVE from the Darling lab | computational (meta)genomics

The Darling lab at the University of Technology Sydney. We develop computational and molecular techniques to characterize the hidden world of microbes.

Via Chris Upton + helpers
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Plasma membrane protein trafficking in plant–microbe interactions: a plant cell point of view

Plasma membrane protein trafficking in plant–microbe interactions: a plant cell point of view | Plant-Microbe Interaction | Scoop.it

In order to ensure their physiological and cellular functions, plasma membrane (PM) proteins must be properly conveyed from their site of synthesis, i.e., the endoplasmic reticulum, to their final destination, the PM, through the secretory pathway. PM protein homeostasis also relies on recycling and/or degradation, two processes that are initiated by endocytosis. Vesicular membrane trafficking events to and from the PM have been shown to be altered when plant cells are exposed to mutualistic or pathogenic microbes. In this review, we will describe the fine-tune regulation of such alterations, and their consequence in PM protein activity. We will consider the formation of intracellular perimicrobial compartments, the PM protein trafficking machinery of the host, and the delivery or retrieval of signaling and transport proteins such as pattern-recognition receptors, producers of reactive oxygen species, and sugar transporters.

 

 


Via Christophe Jacquet
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Fungal associations of basal vascular plants: reopening a closed book?

Fungal associations of basal vascular plants: reopening a closed book? | Plant-Microbe Interaction | Scoop.it
The widely held hypothesis that Glomeromycota fungi alone formed the ancestral land plant–fungus symbiosis (Pirozynski & Dalpé, 1989; Selosse & Le Tacon, 1998; Wang & Qiu, 2006; Parniske, 2008) has recently been challenged by new lines of evidence from molecular, cytological, functional and palaeontological studies. First, liverworts of the earliest divergent clade, the Haplomitriopsida, form a mutualistic mycorrhiza-like relationship, whereby there is reciprocal exchange of plant carbon (C) for fungal nitrogen (N) and phosphorus (P), with members of the Mucoromycotina (Bidartondo et al., 2011; Field et al., 2014), a fungal lineage considered basal or sister to the Glomeromycota (James et al., 2006; Lin et al., 2014). Secondly, other basal plants, including complex and simple thalloid liverworts and hornworts, enter into associations with both Mucoromycotina and Glomeromycota fungi, sometimes simultaneously (Bidartondo et al., 2011; Desirò et al., 2013). Thirdly, dual partnerships involving fungi with affinities to Glomeromycota and Mucoromycotina have been reported in fossils of early vascular plants from the Devonian (Strullu-Derrien et al., 2014).

Turning to the fungal associations of the extant representatives of the early diverging vascular plant lineages, the glomeromycete identity of fungi in ferns (Monilophyta) has never been questioned – a consensus borne out by cytology and limited DNA sequencing data (Wang & Qiu, 2006; Ogura-Tsujita et al., 2013). By contrast, the unusual cytology of fungal colonization in lycopods (Lycopodiophyta), highly reminiscent of the cytology reported in the Haplomitriopsida genus Treubia (Duckett et al., 2006), suggested unique fungal partnerships or ‘lycopodioid mycothallus interactions’ (Duckett & Ligrone, 1992; Schmid & Oberwinkler, 1993) until a molecular study detected Glomeromycota in this group (Winther & Friedman, 2008), thus ‘laying to rest over a century of speculations and uncertainty’ surrounding their identity (Leake et al., 2008). However, Winther & Friedman's study, and a more recent investigation proposing a basidiomycete as the main symbiont in a member of the Lycopodiaceae (Horn et al., 2013; but see rebuttal in Strullu-Derrien et al., 2014 criticizing their limited molecular and microscopical data), used methods that do not detect Mucoromycotina fungi. Therefore, it remains to be determined whether members of the Mucoromycotina related to the fungi known to enter into mutualism with basal liverworts (Field et al., 2014) also form associations with vascular plants. To test this possibility, we carried out molecular and microscopical analyses of the fungal associations of all the major lineages of lycopods and ferns.

Via Jean-Michel Ané
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Rescooped by Guogen Yang from MycorWeb Plant-Microbe Interactions
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Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history

Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history | Plant-Microbe Interaction | Scoop.it
Colobines are a unique group of Old World monkeys that principally eat leaves and seeds rather than fruits and insects. We report the sequencing at 146× coverage, de novo assembly and analyses of the genome of a male golden snub-nosed monkey (Rhinopithecus roxellana) and resequencing at 30× coverage of three related species (Rhinopithecus bieti, Rhinopithecus brelichi and Rhinopithecus strykeri). Comparative analyses showed that Asian colobines have an enhanced ability to derive energy from fatty acids and to degrade xenobiotics. We found evidence for functional evolution in the colobine RNASE1 gene, encoding a key secretory RNase that digests the high concentrations of bacterial RNA derived from symbiotic microflora. Demographic reconstructions indicated that the profile of ancient effective population sizes for R. roxellana more closely resembles that of giant panda rather than its congeners. These findings offer new insights into the dietary adaptations and evolutionary history of colobine primates

Via Francis Martin
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Rescooped by Guogen Yang from Plants and Microbes
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Plant Cell: Virulence Factors of Geminivirus Interact with MYC2 to Subvert Plant Resistance and Promote Vector Performance (2014)

Plant Cell: Virulence Factors of Geminivirus Interact with MYC2 to Subvert Plant Resistance and Promote Vector Performance (2014) | Plant-Microbe Interaction | Scoop.it

A pathogen may cause infected plants to promote the performance of its transmitting vector, which accelerates the spread of the pathogen. This positive effect of a pathogen on its vector via their shared host plant is termed indirect mutualism. For example, terpene biosynthesis is suppressed in begomovirus-infected plants, leading to reduced plant resistance and enhanced performance of the whiteflies (Bemisia tabaci) that transmit these viruses. Although begomovirus-whitefly mutualism has been known, the underlying mechanism is still elusive. Here, we identified βC1 of Tomato yellow leaf curl China virus, a monopartite begomovirus, as the viral genetic factor that suppresses plant terpene biosynthesis. βC1 directly interacts with the basic helix-loop-helix transcription factor MYC2 to compromise the activation of MYC2-regulated terpene synthase genes, thereby reducing whitefly resistance. MYC2 associates with the bipartite begomoviral protein BV1, suggesting that MYC2 is an evolutionarily conserved target of begomoviruses for the suppression of terpene-based resistance and the promotion of vector performance. Our findings describe how this viral pathogen regulates host plant metabolism to establish mutualism with its insect vector.


Via Kamoun Lab @ TSL
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Ed Rybicki's curator insight, December 18, 6:31 AM

Cunning trick, for a small virus!

Rescooped by Guogen Yang from Plant-Microbe Symbioses
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Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution | Plant-Microbe Interaction | Scoop.it
The standard approach to analyzing 16S tag sequence data, which relies on clustering reads by sequence similarity into Operational Taxonomic Units (OTUs), underexploits the accuracy of modern sequencing technology. We present a clustering-free approach to multi-sample Illumina data sets that can identify independent bacterial subpopulations regardless of the similarity of their 16S tag sequences. Using published data from a longitudinal time-series study of human tongue microbiota, we are able to resolve within standard 97% similarity OTUs up to 20 distinct subpopulations, all ecologically distinct but with 16S tags differing by as little as one nucleotide (99.2% similarity). A comparative analysis of oral communities of two cohabiting individuals reveals that most such subpopulations are shared between the two communities at 100% sequence identity, and that dynamical similarity between subpopulations in one host is strongly predictive of dynamical similarity between the same subpopulations in the other host. Our method can also be applied to samples collected in cross-sectional studies and can be used with the 454 sequencing platform. We discuss how the sub-OTU resolution of our approach can provide new insight into factors shaping community assembly.

Via Jean-Michel Ané
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Rescooped by Guogen Yang from Virology and Bioinformatics from Virology.ca
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Virology Journal | Full text | Plant-based vaccines against viruses

Plant-made or “biofarmed” viral vaccines are some of the earliest products of the technology of plant molecular farming, and remain some of the brightest prospects for the success of this field. Proofs of principle and of efficacy exist for many candidate viral veterinary vaccines; the use of plant-made viral antigens and of monoclonal antibodies for therapy of animal and even human viral disease is also well established. This review explores some of the more prominent recent advances in the biofarming of viral vaccines and therapies, including the recent use of ZMapp for Ebolavirus infection, and explores some possible future applications of the technology.

Via Chris Upton + helpers
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Rescooped by Guogen Yang from Plant-microbe interactions (on the plant's side)
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Insights into post-transcriptional regulation during legume-rhizobia symbiosis

Insights into post-transcriptional regulation during legume-rhizobia symbiosis | Plant-Microbe Interaction | Scoop.it
During the past ten years, changes in the transcriptome have been assessed at different stages of the legume-rhizobia association by the use of DNA microarrays and, more recently, by RNA sequencing technologies. These studies allowed the identification of hundred or thousand of genes whose steady-state mRNA levels increase or decrease upon bacterial infection or in nodules as compared with uninfected roots. However, transcriptome based-approaches do not distinguish between mRNAs that are being actively translated, stored as messenger ribonucleoproteins (mRNPs) or targeted for degradation. Despite that the increase in steady-state levels of an mRNA does not necessarily correlate with an increase in abundance or activity of the encoded protein, this information has been commonly used to select genes that are candidates to play a role during nodule organogenesis or bacterial infection. Such criterion does not take into account the post-transcriptional mechanisms that contribute to the regulation of gene expression. One of such mechanisms, which has significant impact on gene expression, is the selective recruitment of mRNAs to the translational machinery.  Here, we review the post-transcriptional mechanisms that contribute to the regulation of gene expression in the context of the ecological and agronomical important symbiotic interaction established between roots of legumes and the nitrogen fixing bacteria collectively known as rhizobia. In addition, we discuss how the development of new technologies that allow the assessment of these regulatory layers would help to understand the genetic network governing legume rhizobia symbiosis.

Via Jean-Michel Ané, Christophe Jacquet
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Rescooped by Guogen Yang from Rice Blast
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Assessment of sensitivity and virulence fitness costs of the AvrPik alleles from Magnaporthe oryzae to isoprothiolane

The in vitro sensitivity of AvrPik allele isolates of Magnaporthe oryzae to isoprothiolane was examined and the virulence fitness costs of AvrPik allele isolates to isoprothiolane were assessed. Isoprothiolane was found to suppress the radial growth of AvrPik allele isolates at all concentrations (1, 5, 10, 15, and 20 μg/mL). Generally, a higher isoprothiolane concentration has a stronger inhibitory effect on mycelial growth in AvrPik allele isolates at 6 and 10 days after inoculation. The inhibitory effect of isoprothiolane also increased with treatment time. To determine whether a correlation existed between the in vitro sensitivity of AvrPik allele isolates and virulence, the half-maximal inhibitor concentration and 75% of the maximum inhibitor concentration were calculated for each mutation isolate and wild-type isolate. Based on these values and virulence, no significant correlation between the susceptibility of AvrPik allele isolates and virulence was detected. In summary, no fitness costs were associated with sensitivity of blast isolates carrying specific AvrPik alleles to different virulence.


Via Elsa Ballini
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Rescooped by Guogen Yang from WU_Phyto-Publications
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PhD Thesis Yan Wang (2014): Understanding the role of L-type lectin receptor kinases in Phytophthora resistance

PhD Thesis Yan Wang (2014): Understanding the role of L-type lectin receptor kinases in Phytophthora resistance | Plant-Microbe Interaction | Scoop.it

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Rescooped by Guogen Yang from TAL effector science
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Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases - Nature Biotech.

Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases - Nature Biotech. | Plant-Microbe Interaction | Scoop.it

Frock et al, 2014

Although great progress has been made in the characterization of the off-target effects of engineered nucleases, sensitive and unbiased genome-wide methods for the detection of off-target cleavage events and potential collateral damage are still lacking. Here we describe a linear amplification–mediated modification of a previously published high-throughput, genome-wide, translocation sequencing (HTGTS) method that robustly detects DNA double-stranded breaks (DSBs) generated by engineered nucleases across the human genome based on their translocation to other endogenous or ectopic DSBs. HTGTS with different Cas9:sgRNA or TALEN nucleases revealed off-target hotspot numbers for given nucleases that ranged from a few or none to dozens or more, and extended the number of known off-targets for certain previously characterized nucleases more than tenfold. We also identified translocations between bona fide nuclease targets on homologous chromosomes, an undesired collateral effect that has not been described previously. Finally, HTGTS confirmed that the Cas9D10A paired nickase approach suppresses off-target cleavage genome-wide.


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Fesquet didier's curator insight, December 19, 5:53 AM

off target ou pas off targets...the debate is still on going...hope the wt has reported does not induce that much OT...can't believe

Rescooped by Guogen Yang from MycorWeb Plant-Microbe Interactions
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Overexpression of Laccaria bicolor aquaporin JQ585595 alters root water transport properties in ectomycorrhizal white spruce (Picea glauca) seedlings

Overexpression of Laccaria bicolor aquaporin JQ585595 alters root water transport properties in ectomycorrhizal white spruce (Picea glauca) seedlings | Plant-Microbe Interaction | Scoop.it
The contribution of hyphae to water transport in ectomycorrhizal (ECM) white spruce (Picea glauca) seedlings was examined by altering expression of a major water-transporting aquaporin in Laccaria bicolor.
Picea glauca was inoculated with wild-type (WT), mock transgenic or L. bicolor aquaporin JQ585595-overexpressing (OE) strains and exposed to root temperatures ranging from 5 to 20°C to examine the root water transport properties, physiological responses and plasma membrane intrinsic protein (PIP) expression in colonized plants.
Mycorrhization increased shoot water potential, transpiration, net photosynthetic rates, root hydraulic conductivity and root cortical cell hydraulic conductivity in seedlings. At 20°C, OE plants had higher root hydraulic conductivity compared with WT plants and the increases were accompanied by higher expression of P. glauca PIP GQ03401_M18.1 in roots. In contrast to WT L. bicolor, the effects of OE fungi on root and root cortical cell hydraulic conductivities were abolished at 10 and 5°C in the absence of major changes in the examined transcript levels of P. glauca root PIPs.
The results provide evidence for the importance of fungal aquaporins in root water transport of mycorrhizal plants. They also demonstrate links between hyphal water transport, root aquaporin expression and root water transport in ECM plants.

Via Francis Martin
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