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Novel Entries in a Fungal Biofilm Matrix Encyclopedia

Novel Entries in a Fungal Biofilm Matrix Encyclopedia | MycorWeb Plant-Microbe Interactions | Scoop.it

Virulence of Candida is linked with its ability to form biofilms. Once established, biofilm infections are nearly impossible to eradicate. Biofilm cells live immersed in a self-produced matrix, a blend of extracellular biopolymers, many of which are uncharacterized. In this study, we provide a comprehensive analysis of the matrix manufactured by Candida albicans both in vitro and in a clinical niche animal model. We further explore the function of matrix components, including the impact on drug resistance. We uncovered components from each of the macromolecular classes (55% protein, 25% carbohydrate, 15% lipid, and 5% nucleic acid) in the C. albicans biofilm matrix. Three individual polysaccharides were identified and were suggested to interact physically. Surprisingly, a previously identified polysaccharide of functional importance, β-1,3-glucan, comprised only a small portion of the total matrix carbohydrate. Newly described, more abundant polysaccharides included α-1,2 branched α-1,6-mannans (87%) associated with unbranched β-1,6-glucans (13%) in an apparent mannan-glucan complex (MGCx). Functional matrix proteomic analysis revealed 458 distinct activities. The matrix lipids consisted of neutral glycerolipids (89.1%), polar glycerolipids (10.4%), and sphingolipids (0.5%). Examination of matrix nucleic acid identified DNA, primarily noncoding sequences. Several of the in vitro matrix components, including proteins and each of the polysaccharides, were also present in the matrix of a clinically relevant in vivo biofilm. Nuclear magnetic resonance (NMR) analysis demonstrated interaction of aggregate matrix with the antifungal fluconazole, consistent with a role in drug impedance and contribution of multiple matrix components.

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The Plasmodiophora brassicae genome reveals insights in its life cycle and ancestry of chitin synthases : Scientific Reports : Nature Publishing Group

The Plasmodiophora brassicae genome reveals insights in its life cycle and ancestry of chitin synthases : Scientific Reports : Nature Publishing Group | MycorWeb Plant-Microbe Interactions | Scoop.it

Plasmodiophora brassicae causes clubroot, a major disease of Brassica oil and vegetable crops worldwide. P. brassicae is a Plasmodiophorid, obligate biotrophic protist in the eukaryotic kingdom of Rhizaria. Here we present the 25.5 Mb genome draft of P. brassicae, developmental stage-specific transcriptomes and a transcriptome of Spongospora subterranea, the Plasmodiophorid causing powdery scab on potato. Like other biotrophic pathogens both Plasmodiophorids are reduced in metabolic pathways. Phytohormones contribute to the gall phenotypes of infected roots. We report a protein (PbGH3) that can modify auxin and jasmonic acid. Plasmodiophorids contain chitin in cell walls of the resilient resting spores. If recognized, chitin can trigger defense responses in plants. Interestingly, chitin-related enzymes of Plasmodiophorids built specific families and the carbohydrate/chitin binding (CBM18) domain is enriched in the Plasmodiophorid secretome. Plasmodiophorids chitin synthases belong to two families, which were present before the split of the eukaryotic Stramenopiles/Alveolates/Rhizaria/Plantae and Metazoa/Fungi/Amoebozoa megagroups, suggesting chitin synthesis to be an ancient feature of eukaryotes. This exemplifies the importance of genomic data from unexplored eukaryotic groups, such as the Plasmodiophorids, to decipher evolutionary relationships and gene diversification of early eukaryotes.

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Alejandro Rojas's curator insight, June 25, 9:44 AM

This is an special case since it is not a fungal or oomycete pathogen.  However, it is interesting case on pathogenesis and the resemblance of other pathogens.  In this case the oomycetes, specially pathogens like the Pythium species.  

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Ancient origin of the biosynthesis of lignin precursors

Ancient origin of the biosynthesis of lignin precursors | MycorWeb Plant-Microbe Interactions | Scoop.it
Lignin plays an important role in plant structural support and water transport, and is considered one of the hallmarks of land plants. The recent discovery of lignin or its precursors in various algae has raised questions on the evolution of its biosynthetic pathway, which could be much more ancient than previously thought. To determine the taxonomic distribution of the lignin biosynthesis genes, we screened all publicly available genomes of algae and their closest non-photosynthetic relatives, as well as representative land plants. We also performed phylogenetic analysis of these genes to decipher the evolution and origin(s) of lignin biosynthesis.

Via Pierre-Marc Delaux
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Is Zymoseptoria tritici a hemibiotroph?

The growth of microorganisms in planta is often categorized based on their methods of nutrient acquisition and the physical appearance of symptoms on the host. For example, biotrophs thrive on living tissue while necrotrophic pathogens often quickly lyse cells to access nutrients. Hemibiotrophs are pathogens that initially feed on living host tissue without causing visible symptoms prior to switching to necrotrophy. During infection of wheat, the pathogen Zymoseptoria tritici undergoes a prolonged and asymptomatic phase during which it grows slowly and protects itself from host defenses prior to eliciting a strong necrotic response. However careful analyses of the asymptomatic phase indicate that the pathogen does not alter host growth, casting doubt on the biotrophic nature of this asymptomatic period. Consequently, we question whether Z. tritici is correctly defined as a hemibiotroph.
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Reconstructing ancient genomes and epigenomes : Nature Reviews Genetics : Nature Publishing Group

Reconstructing ancient genomes and epigenomes : Nature Reviews Genetics : Nature Publishing Group | MycorWeb Plant-Microbe Interactions | Scoop.it

Research involving ancient DNA (aDNA) has experienced a true technological revolution in recent years through advances in the recovery of aDNA and, particularly, through applications of high-throughput sequencing. Formerly restricted to the analysis of only limited amounts of genetic information, aDNA studies have now progressed to whole-genome sequencing for an increasing number of ancient individuals and extinct species, as well as to epigenomic characterization. Such advances have enabled the sequencing of specimens of up to 1 million years old, which, owing to their extensive DNA damage and contamination, were previously not amenable to genetic analyses. In this Review, we discuss these varied technical challenges and solutions for sequencing ancient genomes and epigenomes.


Via Niklaus Grunwald
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Development of the Populus-Laccaria bicolor ectomycorrhiza modifies root auxin metabolism, signalling and response

Root systems of host trees are known to establish ectomycorrhizal (ECM) interactions with rhizospheric fungi. This mutualistic association leads to dramatic developmental modifications in root architecture with the formation of numerous short and swollen lateral roots ensheathed by a fungal mantle. Knowing that auxin plays a crucial role in root development, we investigated how auxin metabolism, signalling and response are affected in Populus-Laccaria bicolor ECM roots. The plant-fungus interaction leads to the arrest of lateral root growth with simultaneous attenuation of the DR5 auxin response. Measurement of auxin-related metabolites in the free-living partners revealed that the mycelium of L. bicolor produces high concentrations of the auxin indole-3-acetic acid (IAA). Metabolic profiling showed an accumulation of IAA and changes in the indol-3-pyruvic acid dependent IAA biosynthesis, and IAA conjugation and degradation pathways during ECM formation. The global analysis of auxin response gene expression and the regulation of PtaAFB5s, PtaAux/IAAs and PtaARFs expression in ECM roots suggested that a symbiosis-dependent auxin signalling is activated during the colonization by L. bicolor. Taking all this evidence into account, we propose a model in which auxin signalling plays a crucial role in the modification of root growth during ECM formation.


Via Pierre-Marc Delaux
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Competitive binding of antagonistic peptides fine-tunes stomatal patterning

Competitive binding of antagonistic peptides fine-tunes stomatal patterning | MycorWeb Plant-Microbe Interactions | Scoop.it

During development, cells interpret complex and often conflicting signals to make optimal decisions. Plant stomata, the cellular interface between a plant and the atmosphere, develop according to positional cues, which include a family of secreted peptides called epidermal patterning factors (EPFs). How these signalling peptides orchestrate pattern formation at a molecular level remains unclear. Here we report in Arabidopsis that Stomagen (also called EPF-LIKE9) peptide, which promotes stomatal development, requires ERECTA (ER)-family receptor kinases and interferes with the inhibition of stomatal development by the EPIDERMAL PATTERNING FACTOR 2 (EPF2)–ER module. Both EPF2 and Stomagen directly bind to ER and its co-receptor TOO MANY MOUTHS. Stomagen peptide competitively replaced EPF2 binding to ER. Furthermore, application of EPF2, but not Stomagen, elicited rapid phosphorylation of downstream signalling components in vivo. Our findings demonstrate how a plant receptor agonist and antagonist define inhibitory and inductive cues to fine-tune tissue patterning on the plant epidermis.

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RNA–protein interactions in plant disease: hackers at the dinner table

RNA–protein interactions in plant disease: hackers at the dinner table | MycorWeb Plant-Microbe Interactions | Scoop.it
Plants are the source of most of our food, whether directly or as feed for the animals we eat. Our dinner table is a trophic level we share with the microbes that also feed on the primary photosynthetic producers. Microbes that enter into close interactions with plants need to evade or suppress detection and host immunity to access nutrients. They do this by deploying molecular tools – effectors – which target host processes. The mode of action of effector proteins in these events is varied and complex. Recent data from diverse systems indicate that RNA-interacting proteins and RNA itself are delivered by eukaryotic microbes, such as fungi and oomycetes, to host plants and contribute to the establishment of successful interactions. This is evidence that pathogenic microbes can interfere with the host software. We are beginning to see that pathogenic microbes are capable of hacking into the plants' immunity programs.
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Diazotrophic Endophytes of Poplar and Willow for Growth Promotion of Rice Plants in Nitrogen-Limited Conditions

Rice (Oryza sativa L.) is one of the most important staple food crops. Its cultivation requires a relatively high input of N fertilizers; however, rice plants do not absorb a significant proportion of added fertilizers, resulting in soil and water pollution. The use of diazotrophic (N-fixing) endophytes can provide benefits for rice cultivation by reducing the demand of N fertilizers. Diazotrophic endophytes from the early successional plant species poplar (Populus trichocarpa Torr. & A. Gray) and willow (Salix sitchensis C. A. Sanson ex Bong.) were added to rice seedlings. Inoculated rice plants were grown in N-limited conditions in the greenhouse, and plant physical characteristics were assessed. Endophyte-inoculated rice plants had greater biomass, higher tiller numbers, and taller plant stature than mock-inoculated controls. Endophyte populations were quantified and visualized in planta within rice plants using fluorescent microscopy. The endophytes colonized rice plants effectively in both roots and foliage. These results demonstrated that diazotrophic endophytes of the eudicots poplar and willow can colonize rice plants and enhance plant growth in N-limited conditions.

Via Jean-Michel Ané
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Xyloglucan, galactomannan, glucuronoxylan, and rhamnogalacturonan I do not have identical structures in soybean root and root hair cell walls

Xyloglucan, galactomannan, glucuronoxylan, and rhamnogalacturonan I do not have identical structures in soybean root and root hair cell walls | MycorWeb Plant-Microbe Interactions | Scoop.it
Abstract
Main conclusion

Chemical analyses and glycome profiling demonstrate differences in the structures of the xyloglucan, galactomannan, glucuronoxylan, and rhamnogalacturonan I isolated from soybean ( Glycine max ) roots and root hair cell walls.

The root hair is a plant cell that extends only at its tip. All other root cells have the ability to grow in different directions (diffuse growth). Although both growth modes require controlled expansion of the cell wall, the types and structures of polysaccharides in the walls of diffuse and tip-growing cells from the same plant have not been determined. Soybean (Glycine max) is one of the few plants whose root hairs can be isolated in amounts sufficient for cell wall chemical characterization. Here, we describe the structural features of rhamnogalacturonan I, rhamnogalacturonan II, xyloglucan, glucomannan, and 4-O-methyl glucuronoxylan present in the cell walls of soybean root hairs and roots stripped of root hairs. Irrespective of cell type, rhamnogalacturonan II exists as a dimer that is cross-linked by a borate ester. Root hair rhamnogalacturonan I contains more neutral oligosaccharide side chains than its root counterpart. At least 90 % of the glucuronic acid is 4-O-methylated in root glucuronoxylan. Only 50 % of this glycose is 4-O-methylated in the root hair counterpart. Mono O-acetylated fucose-containing subunits account for at least 60 % of the neutral xyloglucan from root and root hair walls. By contrast, a galacturonic acid-containing xyloglucan was detected only in root hair cell walls. Soybean homologs of the Arabidopsis xyloglucan-specific galacturonosyltransferase are highly expressed only in root hairs. A mannose-rich polysaccharide was also detected only in root hair cell walls. Our data demonstrate that the walls of tip-growing root hairs cells have structural features that distinguish them from the walls of other roots cells.

Via Christophe Jacquet
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My response to the OSTP's RFI on the microbiome

The Office of Science and Technology Policy (OSTP) recently released a request for information (RFI) to “to solicit feedback from industry, academia, research laboratories, and other stakeholder groups on both the overarching questions that unite all microbiome research and the tools, technologies, and training that are needed to answer these questions.” This is a draft of a letter that I will be submitting regarding the need for bioinformatic tool development, continued software maintenance, and training.

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The Casuarina NIN gene is transcriptionally activated throughout Frankia root infection as well as in response to bacterial diffusible signals

The Casuarina NIN gene is transcriptionally activated throughout Frankia root infection as well as in response to bacterial diffusible signals | MycorWeb Plant-Microbe Interactions | Scoop.it
Root nodule symbioses (RNS) allow plants to acquire atmospheric nitrogen by establishing an intimate relationship with either rhizobia, the symbionts of legumes or Frankia in the case of actinorhizal plants. In legumes, NIN (Nodule INception) genes encode key transcription factors involved in nodulation.
Here we report the characterization of CgNIN, a NIN gene from the actinorhizal tree Casuarina glauca using both phylogenetic analysis and transgenic plants expressing either ProCgNIN::reporter gene fusions or CgNIN RNAi constructs.
We have found that CgNIN belongs to the same phylogenetic group as other symbiotic NIN genes and CgNIN is able to complement a legume nin mutant for the early steps of nodule development. CgNIN expression is correlated with infection by Frankia, including preinfection stages in developing root hairs, and is induced by culture supernatants. Knockdown mutants were impaired for nodulation and early root hair deformation responses were severely affected. However, no mycorrhizal phenotype was observed and no induction of CgNIN expression was detected in mycorrhizas.
Our results indicate that elements specifically required for nodulation include NIN and possibly related gene networks derived from the nitrate signalling pathways.

Via Jean-Michel Ané
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Impact of metal pollution on fungal diversity and community structures

Impact of metal pollution on fungal diversity and community structures | MycorWeb Plant-Microbe Interactions | Scoop.it
The impact of metal pollution on plant communities has been studied extensively in the past, but little is known about the effects of metal pollution on fungal communities that occur in metal-polluted soils. Metal-tolerant ecotypes of the ectomycorrhizal fungus Suillus luteus are frequently found in pioneer pine forests in the Campine region in Belgium on metal-polluted soils. We hypothesized that metal pollution would play an important role in shaping below-ground fungal communities that occur in these soils and that Suillus luteus would be a dominant player. To test these hypotheses, the fungal communities in a young pine plantation in soil polluted with zinc, and cadmium were studied using 454 amplicon pyrosequencing. Results show that zinc, cadmium and soil organic matter content were strongly correlated with the fungal community composition, but no effects on fungal diversity were observed. As hypothesized, S. luteus was found to be a dominant member of the studied fungal communities. However, other dominant fungal species, such as Sistotrema sp., Wilcoxina mikolae and Cadophora finlandica were found as well. Their presence in metal-polluted sites is discussed.
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50-plus years of fungal viruses

50-plus years of fungal viruses | MycorWeb Plant-Microbe Interactions | Scoop.it

Highlights
• Historical perspective of fungal virus research.
• Description, classification and diversity of fungal virus families.
• Structural features of fungal virus particles.
• Hypovirulence and exploitation of mycoviruses in biological control of plant pathogenic fungi.


Via Steve Marek
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An integrated database of wood-formation related genes in plants : Scientific Reports : Nature Publishing Group

An integrated database of wood-formation related genes in plants : Scientific Reports : Nature Publishing Group | MycorWeb Plant-Microbe Interactions | Scoop.it

Wood, which consists mainly of plant cell walls, is an extremely important resource in daily lives. Genes whose products participate in the processes of cell wall and wood formation are therefore major subjects of plant science research. The Wood-Formation Related Genes database (WFRGdb, http://me.lzu.edu.cn/woodformation/) serves as a data resource center for genes involved in wood formation. To create this database, we collected plant genome data published in other online databases and predicted all cell wall and wood formation related genes using BLAST and HMMER. To date, 47 gene families and 33 transcription factors from 57 genomes (28 herbaceous, 22 woody and 7 non-vascular plants) have been covered and more than 122,000 genes have been checked and recorded. To provide easy access to these data, we have developed several search methods, which make it easy to download targeted genes or groups of genes free of charge in FASTA format. Sequence and phylogenetic analyses are also available online. WFRGdb brings together cell wall and wood formation related genes from all available plant genomes, and provides an integrative platform for gene inquiry, downloading and analysis. This database will therefore be extremely useful for those who focuses on cell wall and wood research.

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Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens

Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens | MycorWeb Plant-Microbe Interactions | Scoop.it

Background. Trunk diseases threaten the longevity and productivity of grapevines in all viticulture production systems. They are caused by distantly-related fungi that form chronic wood infections. Variation in wood-decay abilities and production of phytotoxic compounds are thought to contribute to their unique disease symptoms. We recently released the draft sequences of Eutypa lata, Neofusicoccum parvum and Togninia minima, causal agents of Eutypa dieback, Botryosphaeria dieback and Esca, respectively. In this work, we first expanded genomic resources to three important trunk pathogens, Diaporthe ampelina, Diplodia seriata, and Phaeomoniella chlamydospora, causal agents of Phomopsis dieback, Botryosphaeria dieback, and Esca, respectively. Then we integrated all currently-available information into a genome-wide comparative study to identify gene families potentially associated with host colonization and disease development.

 

Results. The integration of RNA-seq, comparative and ab initio approaches improved the protein-coding gene prediction in T. minima, whereas shotgun sequencing yielded nearly complete genome drafts of Dia. ampelina, Dip. seriata, and P. chlamydospora. The predicted proteomes of all sequenced trunk pathogens were annotated with a focus on functions likely associated with pathogenesis and virulence, namely (i) wood degradation, (ii) nutrient uptake, and (iii) toxin production. Specific patterns of gene family expansion were described using Computational Analysis of gene Family Evolution, which revealed lineage-specific evolution of distinct mechanisms of virulence, such as specific cell wall oxidative functions and secondary metabolic pathways in N. parvum, Dia. ampelina, and E. lata. Phylogenetically-informed principal component analysis revealed more similar repertoires of expanded functions among species that cause similar symptoms, which in some cases did not reflect phylogenetic relationships, thereby suggesting patterns of convergent evolution.

 

Conclusions. This study describes the repertoires of putative virulence functions in the genomes of ubiquitous grapevine trunk pathogens. Gene families with significantly faster rates of gene gain can now provide a basis for further studies of in planta gene expression, diversity by genome re-sequencing, and targeted reverse genetic approaches. The functional validation of potential virulence factors will lead to a more comprehensive understanding of the mechanisms of pathogenesis and virulence, which ultimately will enable the development of accurate diagnostic tools and effective disease management.

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Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus

Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus | MycorWeb Plant-Microbe Interactions | Scoop.it

The genus Microbotryum includes plant pathogenic fungi afflicting a wide variety of hosts with anther smut disease. Microbotryum lychnidis-dioicae infects Silene latifolia and replaces host pollen with fungal spores, exhibiting biotrophy and necrosis associated with altering plant development.

We determined the haploid genome sequence for M. lychnidis-dioicae and analyzed whole transcriptome data from plant infections and other stages of the fungal lifecycle, revealing the inventory and expression level of genes that facilitate pathogenic growth. Compared to related fungi, an expanded number of major facilitator superfamily transporters and secretory lipases were detected; lipase gene expression was found to be altered by exposure to lipid compounds, which signaled a switch to dikaryotic, pathogenic growth. In addition, while enzymes to digest cellulose, xylan, xyloglucan, and highly substituted forms of pectin were absent, along with depletion of peroxidases and superoxide dismutases that protect the fungus from oxidative stress, the repertoire of glycosyltransferases and of enzymes that could manipulate host development has expanded. A total of 14 % of the genome was categorized as repetitive sequences. Transposable elements have accumulated in mating-type chromosomal regions and were also associated across the genome with gene clusters of small secreted proteins, which may mediate host interactions.

 

The unique absence of enzyme classes for plant cell wall degradation and maintenance of enzymes that break down components of pollen tubes and flowers provides a striking example of biotrophic host adaptation.

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A host plant genome (Zizania latifolia) after a century-long endophyte infection - Guo - The Plant Journal - Wiley Online Library

A host plant genome (Zizania latifolia) after a century-long endophyte infection - Guo - The Plant Journal - Wiley Online Library | MycorWeb Plant-Microbe Interactions | Scoop.it
Despite the importance of host-microbe interactions in natural ecosystems, agriculture and medicine, the impact of long-term (especially decades or longer) microbial colonization on the dynamics of host genomes is not well understood. The vegetable crop “Jiaobai” with enlarged edible stems was domesticated from wild Zizania latifolia (Oryzeae) approximately 2,000 years ago as a result of persistent infection by a fungal endophyte, Ustilago esculenta. Asexual propagation via infected rhizomes is the only means of Jiaobai production and the Z. latifolia-endophyte complex has been maintained continuously for two centuries. Here, genomic analysis revealed that cultivated Z. latifolia has a significantly smaller repertoire of immune receptors compared with wild Z. latifolia. There are widespread gene losses/mutations and expression changes in the plant-pathogen interaction pathway in Jiaobai. These results show that continuous long-standing endophyte association can have a major effect on the evolution of the structural and transcriptomic components of the host genome.
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Forest forecasts - Genes to Genomes

Forest forecasts - Genes to Genomes | MycorWeb Plant-Microbe Interactions | Scoop.it
In 2009, after five years parching under the arid blue skies of Calcena in northeastern Spain, dozens of neat rows of maritime pine seedlings had grown unevenly. Some of the seedlings had died years ago, some were stunted but hanging … Read More
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Plant science: Precision positioning with peptides : Nature

Plant science: Precision positioning with peptides : Nature | MycorWeb Plant-Microbe Interactions | Scoop.it
Two related peptides compete for binding to the same receptor to regulate the spacing of cells on the lower surfaces of leaves. This discovery highlights the complexity of cell signalling in plants.

Being fixed in position, plants must be able to respond to a multitude of environmental and developmental inputs over appropriate time frames. To do this, they use organic molecules such as auxin or ethylene, as well as signalling molecules analogous to those used in animals, including peptides (short strings of amino acids) and hormones. But plant peptide signalling pathways, particularly interactions between peptides and their receptor proteins, are poorly understood. In a paper published on Nature's website today, Lee et al.1 define a plant signalling pathway in which two peptides compete for binding to one receptor, exerting opposing effects on the development of tiny openings called stomata on the lower surfaces of leaves.
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Structure and function of SemiSWEET and SWEET sugar transporters: Trends in Biochemical Sciences

Structure and function of SemiSWEET and SWEET sugar transporters: Trends in Biochemical Sciences | MycorWeb Plant-Microbe Interactions | Scoop.it

SemiSWEETs and SWEETs have emerged as unique sugar transporters. First discovered in plants with the help of fluorescent biosensors, homologs exist in all kingdoms of life. Bacterial and plant homologs transport hexoses and sucrose, whereas animal SWEETs transport glucose. Prokaryotic SemiSWEETs are small and comprise a parallel homodimer of an approximately 100 amino acid-long triple helix bundle (THB). Duplicated THBs are fused to create eukaryotic SWEETs in a parallel orientation via an inversion linker helix, producing a similar configuration to that of SemiSWEET dimers. Structures of four SemiSWEETs have been resolved in three states: open outside, occluded, and open inside, indicating alternating access. As we discuss here, these atomic structures provide a basis for exploring the evolution of structure–function relations in this new class of transporters.


Via Kevin Garcia
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The evolution of mutualism from reciprocal parasitism: more ecological clothes for the Prisoner’s Dilemma

The evolution of mutualism from reciprocal parasitism: more ecological clothes for the Prisoner’s Dilemma | MycorWeb Plant-Microbe Interactions | Scoop.it
Many mutualisms involve reciprocal exploitation, such that each species in a mutualism is a consumer of a resource provided by the other. Frequently, such mutualisms are reformed each generation, and where they involve close physiological contact, such as between mycorrhizal fungi and plants, they can be considered as examples of reciprocal parasitism. Here we place such interactions in the framework of the Prisoner’s Dilemma, and examine the conditions for the spread of mutualism using a population genetics model analogous to that used for understanding the genetic and numerical dynamics of host-parasite interactions. Genetic variants within each of two species determine whether the interaction is mutualistic or selfish, the latter being represented by resistance to being exploited or parasitized. We assume that there are fitness costs to resistance which are present even in the absence of the interaction. Just as in host-parasite interactions, we examine the effect of assuming that encounter rates between potential mutualists (and therefore entry into the Prisoner’s Dilemma ‘game’) depend on the density and frequency of the different types interacting individuals. These elements of ecological realism greatly facilitate the evolution of mutualism even in the absence of spatial structure or iterative encounters. Moreover, stable genetic polymorphisms for resistant (selfish) and susceptible (mutualistic) alleles can be maintained, something that is not possible with the classical Prisoner’s Dilemma formulation. The sensitivity of the outcomes to levels of density-dependence and mortality rate suggests environmental as well as genetic processes are likely to be important in determining directions in this pathway to mutualism.

Via Jean-Michel Ané
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Complete Genome Sequence of Sporisorium scitamineum and Biotrophic Interaction Transcriptome with Sugarcane

Complete Genome Sequence of  Sporisorium scitamineum  and Biotrophic Interaction Transcriptome with Sugarcane | MycorWeb Plant-Microbe Interactions | Scoop.it
Sporisorium scitamineum is a biotrophic fungus responsible for the sugarcane smut, a worldwide spread disease. This study provides the complete sequence of individual chromosomes of S. scitamineum from telomere to telomere achieved by a combination of PacBio long reads and Illumina short reads sequence data, as well as a draft sequence of a second fungal strain. Comparative analysis to previous available sequences of another strain detected few polymorphisms among the three genomes. The novel complete sequence described herein allowed us to identify and annotate extended subtelomeric regions, repetitive elements and the mitochondrial DNA sequence. The genome comprises 19,979,571 bases, 6,677 genes encoding proteins, 111 tRNAs and 3 assembled copies of rDNA, out of our estimated number of copies as 130. Chromosomal reorganizations were detected when comparing to sequences of S. reilianum, the closest smut relative, potentially influenced by repeats of transposable elements. Repetitive elements may have also directed the linkage of the two mating-type loci. The fungal transcriptome profiling from in vitro and from interaction with sugarcane at two time points (early infection and whip emergence) revealed that 13.5% of the genes were differentially expressed in planta and particular to each developmental stage. Among them are plant cell wall degrading enzymes, proteases, lipases, chitin modification and lignin degradation enzymes, sugar transporters and transcriptional factors. The fungus also modulates transcription of genes related to surviving against reactive oxygen species and other toxic metabolites produced by the plant. Previously described effectors in smut/plant interactions were detected but some new candidates are proposed. Ten genomic islands harboring some of the candidate genes unique to S. scitamineum were expressed only in planta. RNAseq data was also used to reassure gene predictions.

Via Christophe Jacquet
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Multilayered Organization of Jasmonate Signalling in the Regulation of Root Growth

Multilayered Organization of Jasmonate Signalling in the Regulation of Root Growth | MycorWeb Plant-Microbe Interactions | Scoop.it
Physical damage can strongly affect plant growth, reducing the biomass of developing organs situated at a distance from wounds. These effects, previously studied in leaves, require the activation of jasmonate (JA) signalling. Using a novel assay involving repetitive cotyledon wounding in Arabidopsis seedlings, we uncovered a function of JA in suppressing cell division and elongation in roots. Regulatory JA signalling components were then manipulated to delineate their relative impacts on root growth. The new transcription factor mutant myc2-322B was isolated. In vitro transcription assays and whole-plant approaches revealed that myc2-322B is a dosage-dependent gain-of-function mutant that can amplify JA growth responses. Moreover, myc2-322B displayed extreme hypersensitivity to JA that totally suppressed root elongation. The mutation weakly reduced root growth in undamaged plants but, when the upstream negative regulator NINJA was genetically removed, myc2-322B powerfully repressed root growth through its effects on cell division and cell elongation. Furthermore, in a JA-deficient mutant background, ninja1 myc2-322B still repressed root elongation, indicating that it is possible to generate JA-responses in the absence of JA. We show that NINJA forms a broadly expressed regulatory layer that is required to inhibit JA signalling in the apex of roots grown under basal conditions. By contrast, MYC2, MYC3 and MYC4 displayed cell layer-specific localisations and MYC3 and MYC4 were expressed in mutually exclusive regions. In nature, growing roots are likely subjected to constant mechanical stress during soil penetration that could lead to JA production and subsequent detrimental effects on growth. Our data reveal how distinct negative regulatory layers, including both NINJA-dependent and -independent mechanisms, restrain JA responses to allow normal root growth. Mechanistic insights from this work underline the importance of mapping JA signalling components to specific cell types in order to understand and potentially engineer the growth reduction that follows physical damage.
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Scooped by Francis Martin
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Up-regulation of genes involved in N -acetylglucosamine uptake and metabolism suggests a recycling mode of chitin in intraradical mycelium of arbuscular mycorrhizal fungi

Up-regulation of genes involved in N -acetylglucosamine uptake and metabolism suggests a recycling mode of chitin in intraradical mycelium of arbuscular mycorrhizal fungi | MycorWeb Plant-Microbe Interactions | Scoop.it
Arbuscular mycorrhizal (AM) fungi colonize roots and form two kinds of mycelium, intraradical mycelium (IRM) and extraradical mycelium (ERM). Arbuscules are characteristic IRM structures that highly branch within host cells in order to mediate resource exchange between the symbionts. They are ephemeral structures and at the end of their life span, arbuscular branches collapse from the tip, fungal cytoplasm withdraws, and the whole arbuscule shrinks into fungal clumps. The exoskeleton of an arbuscule contains structured chitin, which is a polymer of N-acetylglucosamine (GlcNAc), whereas a collapsed arbuscule does not. The molecular mechanisms underlying the turnover of chitin in AM fungi remain unknown. Here, a GlcNAc transporter, RiNGT, was identified from the AM fungus Rhizophagus irregularis. Yeast mutants defective in endogenous GlcNAc uptake and expressing RiNGT took up 14C-GlcNAc, and the optimum uptake was at acidic pH values (pH 4.0–4.5). The transcript levels of RiNGT in IRM in mycorrhizal Lotus japonicus roots were over 1000 times higher than those in ERM. GlcNAc-6-phosphate deacetylase (DAC1) and glucosamine-6-phosphate isomerase (NAG1) genes, which are related to the GlcNAc catabolism pathway, were also induced in IRM. Altogether, data suggest the existence of an enhanced recycling mode of GlcNAc in IRM of AM fungi.
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Identifying and Naming Plant-Pathogenic Fungi: Past, Present, and Future - Annual Review of Phytopathology

Identifying and Naming Plant-Pathogenic Fungi: Past, Present, and Future - Annual Review of Phytopathology | MycorWeb Plant-Microbe Interactions | Scoop.it

Scientific names are crucial in communicating knowledge about fungi. In plant pathology, they link information regarding the biology, host range, distribution, and potential risk. Our understanding of fungal biodiversity and fungal systematics has undergone an exponential leap, incorporating genomics, web-based systems, and DNA data for rapid identification to link species to metadata. The impact of our ability to recognize hitherto unknown organisms on plant pathology and trade is enormous and continues to grow. Major challenges for phytomycology are intertwined with the Genera of Fungi project, which adds DNA barcodes to known biodiversity and corrects the application of old, established names via epi- or neotypification. Implementing the one fungus–one name system and linking names to validated type specimens, cultures, and reference sequences will provide the foundation on which the future of plant pathology and the communication of names of plant pathogens will rest.


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Steve Marek's curator insight, June 9, 12:45 PM

Essential reading for mycological plant pathologists