MycorWeb Plant-Microbe Interactions
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Network Modeling to Understand Plant Immunity

Network Modeling to Understand Plant Immunity | MycorWeb Plant-Microbe Interactions | Scoop.it

Deciphering the networks that underpin complex biological processes using experimental data remains a significant, but promising, challenge, a task made all the harder by the added complexity of host-pathogen interactions. The aim of this article is to review the progress in understanding plant immunity made so far by applying network modeling algorithms and to show how this computational/mathematical strategy is facilitating a systems view of plant defense. We review the different types of network modeling that have been used, the data required, and the type of insight that such modeling can provide. We discuss the current challenges in modeling the regulatory networks that underlie plant defense and the future developments that may help address these challenges.


Via Christophe Jacquet
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Rescooped by Francis Martin from Plant:microbe Interactions
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Symbiotic interplay of fungi, algae, and bacteria within the lung lichen Lobaria pulmonaria L. Hoffm. as assessed by state-of-the-art metaproteomics

Symbiotic interplay of fungi, algae, and bacteria within the lung lichen Lobaria pulmonaria  L. Hoffm. as assessed by state-of-the-art metaproteomics | MycorWeb Plant-Microbe Interactions | Scoop.it
Lichens are recognized by macroscopic structures formed by a heterotrophic fungus, the mycobiont, which hosts internal autotrophic photosynthetic algal and/or cyanobacterial partners, referred to as the photobiont. We analyzed structure and functionality of the entire lung lichen Lobaria pulmonaria L. Hoffm. collected from two different sites by state-of-the-art metaproteomics. In addition to the green algae and the ascomycetous fungus, a lichenicolous fungus, as well as a complex prokaryotic community (different from the cyanobacteria) was found, the latter dominated by methanotrophic Rhizobiales. Various partner-specific proteins could be assigned to the different lichen symbionts, e.g. fungal proteins involved in vesicle transport, algal proteins functioning in photosynthesis, cyanobacterial nitrogenase and GOGAT involved in nitrogen-fixation, and bacterial enzymes responsible for methanol/C1-compounds metabolism as well as CO-detoxification. Structural and functional information on proteins expressed by the lichen community complemented and extended our recent symbiosis model depicting the functional multi-player network of single holobiont partners. Our new metaproteome analysis strongly supports the hypothesis (i) that interactions within the self-supporting association are multifaceted and (ii) that the strategy of functional diversification within the single lichen partners may support the longevity of L. pulmonaria under certain ecological conditions.

Via Jonathan Plett
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Rescooped by Francis Martin from microbial pathogenesis and plant immunity
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A Phytophthora Effector Manipulates Host Histone Acetylation and Reprograms Defense Gene Expression to Promote Infection 

A Phytophthora Effector Manipulates Host Histone Acetylation and Reprograms Defense Gene Expression to Promote Infection  | MycorWeb Plant-Microbe Interactions | Scoop.it
Immune response during pathogen infection requires extensive transcription reprogramming. A fundamental mechanism of transcriptional regulation is histone acetylation. However, how pathogens interfere with this process to promote disease remains largely unknown. Here we demonstrate that the cytoplasmic effector PsAvh23 produced by the soybean pathogen Phytophthora sojae acts as a modulator of histone acetyltransferase (HAT) in plants. PsAvh23 binds to the ADA2 subunit of the HAT complex SAGA and disrupts its assembly by interfering with the association of ADA2 with the catalytic subunit GCN5. As such, PsAvh23 suppresses H3K9 acetylation mediated by the ADA2/GCN5 module and increases plant susceptibility. Expression of PsAvh23 or silencing of GmADA2/GmGCN5 resulted in misregulation of defense-related genes, most likely due to decreased H3K9 acetylation levels at the corresponding loci. This study highlights an effective counter-defense mechanism by which a pathogen effector suppresses the activation of defense genes by interfering with the function of the HAT complex during infection.

Via Suayib Üstün, Tatsuya Nobori, Jim Alfano
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Rescooped by Francis Martin from Plant Sciences
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Nature Insight: Plants

Nature Insight: Plants | MycorWeb Plant-Microbe Interactions | Scoop.it
Plants are a valuable source of nutrition, fuel and building materials, but their sessile nature makes them vulnerable to the environment and pathogens. This Insight highlights pertinent issues in plant research, including signalling in plant immunity, plant interactions with the environment, progress in agricultural genomics and harnessing the quantum properties of photosynthesis for human-made energy conversion systems.

Via Loïc Lepiniec, Saclay Plant Sciences
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Rescooped by Francis Martin from Plant:microbe Interactions
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Root microbiota drive direct integration of phosphate stress and immunity

Root microbiota drive direct integration of phosphate stress and immunity | MycorWeb Plant-Microbe Interactions | Scoop.it
Plants live in biogeochemically diverse soils with diverse microbiota. Plant organs associate intimately with a subset of these microbes, and the structure of the microbial community can be altered by soil nutrient content. Plant-associated microbes can compete with the plant and with each other for nutrients, but may also carry traits that increase the productivity of the plant. It is unknown how the plant immune system coordinates microbial recognition with nutritional cues during microbiome assembly. Here we establish that a genetic network controlling the phosphate stress response influences the structure of the root microbiome community, even under non-stress phosphate conditions. We define a molecular mechanism regulating coordination between nutrition and defence in the presence of a synthetic bacterial community. We further demonstrate that the master transcriptional regulators of phosphate stress response in Arabidopsis thaliana also directly repress defence, consistent with plant prioritization of nutritional stress over defence. Our work will further efforts to define and deploy useful microbes to enhance plant performance.

Via Jonathan Plett
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Root morphogenic pathways in Eucalyptus grandis are modified by the activity of protein arginine methyltransferases

Root morphogenic pathways in Eucalyptus grandis are modified by the activity of protein arginine methyltransferases | MycorWeb Plant-Microbe Interactions | Scoop.it
Methylation of proteins at arginine residues, catalysed by members of the protein arginine methyltransferase (PRMT) family, is crucial for the regulation of gene transcription and for protein function in eukaryotic organisms. Inhibition of the activity of PRMTs in annual model plants has demonstrated wide-ranging involvement of PRMTs in key plant developmental processes, however, PRMTs have not been characterised or studied in long-lived tree species. Taking advantage of the recently available genome for Eucalyptus grandis, we demonstrate that most of the major plant PRMTs are conserved in E. grandis as compared to annual plants and that they are expressed in all major plant tissues. Proteomic and transcriptomic analysis in roots suggest that the PRMTs of E. grandis control a number of regulatory proteins and genes related to signalling during cellular/root growth and morphogenesis. We demonstrate here, using chemical inhibition of methylation and transgenic approaches, that plant type I PRMTs are necessary for normal root growth and branching in E. grandis. We further show that EgPRMT1 has a key role in root hair initiation and elongation and is involved in the methylation of β-tubulin, a key protein in cytoskeleton formation. Together, our data demonstrate that PRMTs encoded by E. grandis methylate a number of key proteins and alter the transcription of a variety of genes involved in developmental processes. Appropriate levels of expression of type I PRMTs are necessary for the proper growth and development of E. grandis roots.

Via Jonathan Plett
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Pseudomonas fluorescens Transportome is Linked to Strain-Specific Plant Growth Promotion in Aspen Seedlings Under Nutrient Stress

Diverse communities of bacteria colonize plant roots and the rhizosphere. Many of these rhizobacteria are symbionts and provide plant growth promotion (PGP) services, protecting the plant from biotic and abiotic stresses and increasing plant productivity by providing access to nutrients that would otherwise be unavailable to roots. In return, these symbiotic bacteria receive photosynthetically-derived carbon (C), in the form of sugars and organic acids, from plant root exudates. PGP activities have been characterized for a variety of forest tree species and are important in C cycling and sequestration in terrestrial ecosystems. The molecular mechanisms of these PGP activities, however, are less well known. In a previous analysis of Pseudomonas genomes, we found that the bacterial transportome, the aggregate activity of a bacteria’s transmembrane transporters, was most predictive for the ecological niche of Pseudomonads in the rhizosphere. Here, we used Populus tremuloides Michx. (trembling aspen) seedlings inoculated with one of three Pseudomonas fluorescens strains (Pf0-1, SBW25, and WH6) and one Pseudomonas protegens (Pf-5) as a laboratory model to further investigate the relationships between the predicted transportomic capacity of a bacterial strain and its observed PGP effects in laboratory cultures. Conditions of low nitrogen (N) or low phosphorus (P) availability and the corresponding replete media conditions were investigated. We measured phenotypic and biochemical parameters of P. tremuloides seedlings and correlated P. fluorescens strain-specific transportomic capacities with P. tremuloides seedling phenotype to predict the strain and nutrient environment-specific transporter functions that lead to experimentally observed, strain and media-specific PGP activities and the capacity to protect plants against nutrient stress. These predicted transportomic functions fall in three groups: (i) transport of compounds that modulate aspen seedling root architecture, (ii) transport of compounds that help to mobilize nutrients for aspen roots, and (iii) transporters that enable bacterial acquisition of C sources from seedling root exudates. These predictions point to specific molecular mechanisms of PGP activities that can be directly tested through future, hypothesis-driven biological experiments.
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Rescooped by Francis Martin from Plant pathogens and pests
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A small secreted protein in Zymoseptoria tritici is responsible for avirulence on wheat cultivars carrying the Stb6 resistance gene

A small secreted protein in Zymoseptoria tritici is responsible for avirulence on wheat cultivars carrying the Stb6 resistance gene | MycorWeb Plant-Microbe Interactions | Scoop.it
Zymoseptoria tritici is the causal agent of Septoria tritici blotch, a major pathogen of wheat globally and the most damaging pathogen of wheat in Europe. A gene-for-gene (GFG) interaction between Z. tritici and wheat cultivars carrying the Stb6 resistance gene has been postulated for many years, but the genes have not been identified.
We identified AvrStb6 by combining quantitative trait locus mapping in a cross between two Swiss strains with a genome-wide association study using a natural population of c. 100 strains from France. We functionally validated AvrStb6 using ectopic transformations.
AvrStb6 encodes a small, cysteine-rich, secreted protein that produces an avirulence phenotype on wheat cultivars carrying the Stb6 resistance gene. We found 16 nonsynonymous single nucleotide polymorphisms among the tested strains, indicating that AvrStb6 is evolving very rapidly. AvrStb6 is located in a highly polymorphic subtelomeric region and is surrounded by transposable elements, which may facilitate its rapid evolution to overcome Stb6 resistance.
AvrStb6 is the first avirulence gene to be functionally validated in Z. tritici, contributing to our understanding of avirulence in apoplastic pathogens and the mechanisms underlying GFG interactions between Z. tritici and wheat.

Via Christophe Jacquet
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Insect Pathogenic Fungi: Genomics, Molecular Interactions, and Genetic Improvements

Entomopathogenic fungi play a pivotal role in the regulation of insect populations in nature, and representative species have been developed as promising environmentally friendly mycoinsecticides. Recent advances in the genome biology of insect pathogenic fungi have revealed genomic features associated with fungal adaptation to insect hosts and different host ranges, as well as the evolutionary relationships between insect and noninsect pathogens. By using species in the Beauveria and Metarhizium genera as models, molecular biology studies have revealed the genes that function in fungus-insect interactions and thereby contribute to fungal virulence. Taken together with efforts toward genetic improvement of fungal virulence and stress resistance, knowledge of entomopathogenic fungi will potentiate cost-effective applications of mycoinsecticides for pest control in the field. Relative to our advanced insights into the mechanisms of fungal pathogenesis in plants and humans, future studies will be necessary to unravel the gene-for-gene relationships in fungus-insect interactive models.
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Rescooped by Francis Martin from Plants & Evolution
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A phenol-enriched cuticle is ancestral to lignin evolution in land plants

A phenol-enriched cuticle is ancestral to lignin evolution in land plants | MycorWeb Plant-Microbe Interactions | Scoop.it

Lignin, one of the most abundant biopolymers on Earth, derives from the plant phenolic metabolism. It appeared upon terrestrialization and is thought critical for plant colonization of land. Early diverging land plants do not form lignin, but already have elements of its biosynthetic machinery. Here we delete in a moss the P450 oxygenase that defines the entry point in angiosperm lignin metabolism, and find that its pre-lignin pathway is essential for development. This pathway does not involve biochemical regulation via shikimate coupling, but instead is coupled with ascorbate catabolism, and controls the synthesis of the moss cuticle, which prevents desiccation and organ fusion. These cuticles share common features with lignin, cutin and suberin, and may represent the extant representative of a common ancestor. Our results demonstrate a critical role for the ancestral phenolic metabolism in moss erect growth and cuticle permeability, consistent with importance in plant adaptation to terrestrial conditions.


Via Pierre-Marc Delaux
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A Perspective on CRN Proteins in the Genomics Age: Evolution, Classification, Delivery and Function Revisited

A Perspective on CRN Proteins in the Genomics Age: Evolution, Classification, Delivery and Function Revisited | MycorWeb Plant-Microbe Interactions | Scoop.it
Plant associated microbes rely on secreted virulence factors (effectors) to modulate host immunity and ensure progressive infection. Amongst the secreted protein repertoires defined and studied in pathogens to date, the CRNs (for CRinkling and Necrosis) have emerged as one of only a few highly conserved protein families, spread across several kingdoms. CRN proteins were first identified in plant pathogenic oomycetes where they were found to be modular factors that are secreted and translocated inside host cells by means of a conserved N-terminal domain. Subsequent localization and functional studies have led to the view that CRN C-termini execute their presumed effector function in the host nucleus, targeting processes required for immunity. These findings have led to great interest in this large protein family and driven the identification of additional CRN-like proteins in other organisms. The identification of CRN proteins and subsequent functional studies have markedly increased the number of candidate CRN protein sequences, expanded the range of phenotypes tentatively associated with function and revealed some of their molecular functions toward virulence. The increased number of characterized CRNs also has presented a set of challenges that may impede significant progress in the future. Here, we summarize our current understanding of the CRNs and re-assess some basic assumptions regarding this protein family. We will discuss the latest findings on CRN biology and highlight exciting new hypotheses that have emanated from the field. Finally, we will discuss new approaches to study CRN functions that would lead to a better understanding of CRN effector biology as well as the processes that lead to host susceptibility and immunity.
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Sequencing all life captivates biologists

Sequencing all life captivates biologists | MycorWeb Plant-Microbe Interactions | Scoop.it
At a biogenomics meeting in Washington, D.C., last week, researchers publicly unveiled the Earth BioGenome Project (EBP). The audacious goal of the still-unfunded effort is to decipher the genomes of every species, starting with the 1.5 million named eukaryotes—the group of organisms that includes all plants, animals, and single-celled organisms such as amoebas. Researchers drew parallels to the Human Genome Project, which also began as an ambitious, controversial, and technically daunting proposal. The EBP would focus on the natural world, providing a better understanding of biodiversity by first sequencing in great detail the DNA of a member of each eukaryotic family (about 9000 in all) and eventually generating coarser genomes for the other eukaryotes. Although many biologists are excited about these goals, they point out that significant challenges lie ahead, including funding, sample collection, and broadening international participation.
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Epigenetic regulation of antagonistic receptors confers rice blast resistance with yield balance

Epigenetic regulation of antagonistic receptors confers rice blast resistance with yield balance | MycorWeb Plant-Microbe Interactions | Scoop.it
Crop breeding aims to balance disease resistance with yield; however, single resistance (R) genes can lead to resistance breakdown, and R gene pyramiding may affect growth fitness. Here we report that the rice Pigm locus contains a cluster of genes encoding nucleotide-binding leucine-rich repeat (NLR) receptors that confer durable resistance to the fungus Magnaporthe oryzae without yield penalty. Among these NLR receptors, PigmR confers broad-spectrum resistance, whereas PigmS competitively attenuates PigmR homodimerization to suppress resistance. PigmS expression, and thus PigmR-mediated resistance, are subjected to tight epigenetic regulation. PigmS increases seed production to counteract the yield cost induced by PigmR. Therefore, our study reveals a mechanism balancing high disease resistance and yield through epigenetic regulation of paired antagonistic NLR receptors, providing a tool to develop elite crop varieties.
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The Mutualistic Interaction between Plants and Arbuscular Mycorrhizal Fungi

The Mutualistic Interaction between Plants and Arbuscular Mycorrhizal Fungi | MycorWeb Plant-Microbe Interactions | Scoop.it
Mycorrhizal fungi belong to several taxa and develop mutualistic symbiotic associations with over 90% of all plant species, from liverworts to angiosperms. While descriptive approaches have dominated the initial studies of these fascinating symbioses, the advent of molecular biology, live cell imaging, and “omics” techniques have provided new and powerful tools to decipher the cellular and molecular mechanisms that rule mutualistic plant-fungus interactions. In this article we focus on the most common mycorrhizal association, arbuscular mycorrhiza (AM), which is formed by a group of soil fungi belonging to Glomeromycota. AM fungi are believed to have assisted the conquest of dry lands by early plants around 450 million years ago and are found today in most land ecosystems. AM fungi have several peculiar biological traits, including obligate biotrophy, intracellular development inside the plant tissues, coenocytic multinucleate hyphae, and spores, as well as unique genetics, such as the putative absence of a sexual cycle, and multiple ecological functions. All of these features make the study of AM fungi as intriguing as it is challenging, and their symbiotic association with most crop plants is currently raising a broad interest in agronomic contexts for the potential use of AM fungi in sustainable production under conditions of low chemical input.
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Bob Reeves's curator insight, March 8, 8:11 PM
Just think of this for a moment; how many living things in Nature (that haven't changed in 450(+?) million years) are still with us today? No adaptation via sexual re-calibration - they are just the same as they always were. And they are not on the margins of life on the planet today, they are ubiquitous, world-wide, essential partners to vascular plants - plants that didn't even exist when 'they' first evolved. 
Plants in every ecosystem support these non-evolving organisms today, feeding them with 30% or more of their photosynthates. And, did I mention, 'they' are an obligate biotroph of plants - they can't/won't exist unless they perform a valued service for their plant hosts. Maybe they've figured out how to be... Indispensable? I wish I could figure that trick out. 
Nature seems to be holding up a big neon sign saying 'Hey, hey you with the big brain - check this out - we've been waiting a very long time for you to notice us'.
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Distribution and diversity of enzymes for polysaccharide degradation in fungi

Distribution and diversity of enzymes for polysaccharide degradation in fungi | MycorWeb Plant-Microbe Interactions | Scoop.it
Fungi are important polysaccharide degraders in the environment and for biotechnology. Here, the increasing number of sequenced fungal genomes allowed for systematic identification of genes and proteins involved in polysaccharide degradation in 218 fungi. Globally, 9,003 sequences for glycoside hydrolases and lytic polysaccharide mono-oxygenases targeting cellulose, xylan, and chitin, were identified. Although abundant in most lineages, the distribution of these enzymes is variable even between organisms from the same genus. However, most fungi are generalists possessing several enzymes for polysaccharide deconstruction. Most identified enzymes were small proteins with simple domain organization or eventually consisted of one catalytic domain associated with a non-catalytic accessory domain. Thus unlike bacteria, fungi's ability to degrade polysaccharides relies on apparent redundancy in functional traits and the high frequency of lytic polysaccharide mono-oxygenases, as well as other physiological adaptation such as hyphal growth. Globally, this study provides a comprehensive framework to further identify enzymes for polysaccharide deconstruction in fungal genomes and will help identify new strains and enzymes with potential for biotechnological application
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Plant signalling in symbiosis and immunity

Plant signalling in symbiosis and immunity | MycorWeb Plant-Microbe Interactions | Scoop.it
Plants encounter a myriad of microorganisms, particularly at the root–soil interface, that can invade with detrimental or beneficial outcomes. Prevalent beneficial associations between plants and microorganisms include those that promote plant growth by facilitating the acquisition of limiting nutrients such as nitrogen and phosphorus. But while promoting such symbiotic relationships, plants must restrict the formation of pathogenic associations. Achieving this balance requires the perception of potential invading microorganisms through the signals that they produce, followed by the activation of either symbiotic responses that promote microbial colonization or immune responses that limit it.
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The plant perceptron connects environment to development : Nature 

The plant perceptron connects environment to development : Nature  | MycorWeb Plant-Microbe Interactions | Scoop.it
Plants cope with the environment in a variety of ways, and ecological analyses attempt to capture this through life-history strategies or trait-based categorization. These approaches are limited because they treat the trade-off mechanisms that underlie plant responses as a black box. Approaches that involve the molecular or physiological analysis of plant responses to the environment have elucidated intricate connections between developmental and environmental signals, but in only a few well-studied model species. By considering diversity in the plant response to the environment as the adaptation of an information-processing network, new directions can be found for the study of life-history strategies, trade-offs and evolution in plants.

Via Loïc Lepiniec
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Reconstructing the genome of the most recent common ancestor of flowering plants

We describe here the reconstruction of the genome of the most recent common ancestor (MRCA) of modern monocots and eudicots, accounting for 95% of extant angiosperms, with its potential repertoire of 22,899 ancestral genes conserved in present-day crops. The MRCA provides a starting point for deciphering the reticulated evolutionary plasticity between species (rapidly versus slowly evolving lineages), subgenomes (pre- versus post-duplication blocks), genomic compartments (stable versus labile loci), genes (ancestral versus species-specific genes) and functions (gained versus lost ontologies), the key mutational forces driving the success of polyploidy in crops. The estimation of the timing of angiosperm evolution, based on MRCA genes, suggested that this group emerged 214 million years ago during the late Triassic era, before the oldest recorded fossil. Finally, the MRCA constitutes a unique resource for scientists to dissect major agronomic traits in translational genomics studies extending from model species to crops.

Via Pierre-Marc Delaux
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Many shades of gray—The context-dependent performance of organic agriculture

Many shades of gray—The context-dependent performance of organic agriculture | MycorWeb Plant-Microbe Interactions | Scoop.it
Organic agriculture is often proposed as a more sustainable alternative to current conventional agriculture. We assess the current understanding of the costs and benefits of organic agriculture across multiple production, environmental, producer, and consumer dimensions. Organic agriculture shows many potential benefits (including higher biodiversity and improved soil and water quality per unit area, enhanced profitability, and higher nutritional value) as well as many potential costs including lower yields and higher consumer prices. However, numerous important dimensions have high uncertainty, particularly the environmental performance when controlling for lower organic yields, but also yield stability, soil erosion, water use, and labor conditions. We identify conditions that influence the relative performance of organic systems, highlighting areas for increased research and policy support.
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Exploitation of endophytes for sustainable agricultural intensification

Exploitation of endophytes for sustainable agricultural intensification | MycorWeb Plant-Microbe Interactions | Scoop.it
Intensive agriculture, which depends on unsustainable levels of agrochemical inputs, is environmentally harmful, and the expansion of these practices to meet future needs is not economically feasible. Other options should be considered to meet the global food security challenge. The plant microbiome has been linked to improved plant productivity and, in this microreview, we consider the endosphere – a subdivision of the plant microbiome. We suggest a new definition of microbial endophyte status, the need for synergy between fungal and bacterial endophyte research efforts, as well as potential strategies for endophyte application to agricultural systems.

Via Christophe Jacquet
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Bob Reeves's curator insight, March 9, 4:57 PM
Exactly. The train we're on is running out of track. Work with the natural microbiome - starting now.
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Stepwise evolution of a buried inhibitor peptide over 45 million years 

The de novo evolution of genes and the novel proteins they encode has stimulated much interest in the contribution such innovations make to the diversity of life. Most research on this de novo evolution focuses on transcripts, so studies on the biochemical steps that can enable completely new proteins to evolve and the time required to do so have been lacking. Sunflower PawS1 is an unusual albumin precursor because in addition to producing albumin it also yields a potent, bicyclic protease-inhibitor called SFTI-1. Here we show how this inhibitor peptide evolved stepwise over tens of millions of years. To trace the origin of the inhibitor peptide SFTI-1 we assembled seed transcriptomes for 110 sunflower relatives whose evolution could be resolved by a chronogram, which allowed dates to be estimated for the various stages of molecular evolution. A genetic insertion event in an albumin precursor gene ∼45 million years ago introduced two additional cleavage sites for protein maturation and conferred duality upon PawS1-Like genes such that they also encode a small buried macrocycle. Expansion of this region, including two Cys residues, enlarged the peptide ∼34 million years ago and made the buried peptides bicyclic. Functional specialization into a protease inhibitor occurred ∼23 million years ago. These findings document the evolution of a novel peptide inside a benign region of a pre-existing protein. We illustrate how a novel peptide can evolve without de novo gene evolution and, critically, without affecting the function of what becomes the protein host. One sentence summary: A peptide is born within another protein and evolves stepwise into a protease inhibitor

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Expression of eukaryotic-like protein in the microbiome of sponges

Expression of eukaryotic-like protein in the microbiome of sponges | MycorWeb Plant-Microbe Interactions | Scoop.it
Eukaryotic-like proteins (ELPs) are classes of proteins that are found in prokaryotes, but have a likely evolutionary origin in eukaryotes. ELPs have been postulated to mediate host–microbiome interactions. Recent work has discovered that prokaryotic symbionts of sponges contain abundant and diverse genes for ELPs, which could modulate interactions with their filter-feeding and phagocytic host. However, the extent to which these ELP genes are actually used and expressed by the symbionts is poorly understood. Here, we use metatranscriptomics to investigate ELP expression in the microbiomes of three different sponges (Cymbastella concentrica, Scopalina sp. and Tedania anhelens). We developed a workflow with optimized rRNA removal and in silico subtraction of host sequences to obtain a reliable symbiont metatranscriptome. This showed that between 1.3% and 2.3% of all symbiont transcripts contain genes for ELPs. Two classes of ELPs (cadherin and tetratricopeptide repeats) were abundantly expressed in the C. concentrica and Scopalina sp. microbiomes, while ankyrin repeat ELPs were predominant in the T. anhelens metatranscriptome. Comparison with transcripts that do not encode ELPs indicated a constitutive expression of ELPs across a range of bacterial and archaeal symbionts. Expressed ELPs also contained domains involved in protein secretion and/or were co-expressed with proteins involved in extracellular transport. This suggests these ELPs are likely exported, which could allow for direct interaction with the sponge. Our study shows that ELP genes in sponge symbionts represent actively expressed functions that could mediate molecular interaction between symbiosis partners.
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Inner Workings: Fermented foods offer up a versatile microbial model system

Inner Workings: Fermented foods offer up a versatile microbial model system | MycorWeb Plant-Microbe Interactions | Scoop.it
Scientists have a lot to learn from sauerkraut, says Wolfe, and from other fermented foods, like kombucha and cheese. By studying how these microbial communities form and how their member species interact, he says, researchers can gain insight into the dynamics that shape much more complex communities, such as those found on the human body (1). Understanding how individuals in such communities interact and affect each other could point to efficient ways of manipulating the human microbiome, which, a growing body of research suggests, has a big influence on myriad aspects of health and well-being. “Nobody has ever tried to test these kinds of questions, yet they are very important for things, like fecal transplants, where [doctors] are trying to replace entire microbial communities.”

“I just find it fascinating,” says Jeffrey Dangl, a Howard Hughes Medical Institute investigator studying plant pathogen interactions at the University of North Carolina. “You can do repeated experiments perturbing the system, and then glean generalities” about more complex microbial interactions, he explains.

We now know that humans and other organisms, be they plant or animal, live symbiotically with collections of microorganisms that grow in, on, and around them, but the diversity of these communities is so vast and so complex that teasing out how the components of the system interact has so far been an overwhelming challenge. The microbial communities responsible for food fermentation, however, hit a sort of diversity sweet spot: rather than hundreds or thousands of species, they might contain 30. These communities are relatively reproducible as well as experimentally manipulable; after all, they have been optimized by humans over thousands of years to produce specific flavors and textures, which makes them a powerful model system. “It’s what we call tractable complexity,” says Wolfe. “You can actually take all the members and understand how they’re interacting.”
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Persistent effects of pre-Columbian plant domestication on Amazonian forest composition

Persistent effects of pre-Columbian plant domestication on Amazonian forest composition | MycorWeb Plant-Microbe Interactions | Scoop.it
The extent to which pre-Columbian societies altered Amazonian landscapes is hotly debated. We performed a basin-wide analysis of pre-Columbian impacts on Amazonian forests by overlaying known archaeological sites in Amazonia with the distributions and abundances of 85 woody species domesticated by pre-Columbian peoples. Domesticated species are five times more likely than nondomesticated species to be hyperdominant. Across the basin, the relative abundance and richness of domesticated species increase in forests on and around archaeological sites. In southwestern and eastern Amazonia, distance to archaeological sites strongly influences the relative abundance and richness of domesticated species. Our analyses indicate that modern tree communities in Amazonia are structured to an important extent by a long history of plant domestication by Amazonian peoples.
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Identification of the phosphorylation targets of symbiotic receptor‐like kinases using a high‐throughput multiplexed assay for kinase specificity

Identification of the phosphorylation targets of symbiotic receptor‐like kinases using a high‐throughput multiplexed assay for kinase specificity | MycorWeb Plant-Microbe Interactions | Scoop.it

Detecting the phosphorylation substrates of multiple kinases in a single experiment is a challenge, and new techniques are being developed to overcome this challenge. Here, we utilized a multiplexed assay for kinase specificity (MAKS) to identify the substrates directly and to map the phosphorylation site(s) of plant symbiotic receptor-like kinases. The symbiotic receptor-like kinases Nodulation Receptor-like Kinase (NORK) and Lysin motif domain-containing receptor-like kinase 3 (LYK3) are indispensable for the establishment of root nodule symbiosis. Although some interacting proteins have been identified for these symbiotic receptor-like kinases, very little is known about their phosphorylation substrates. Using this high-throughput approach, we identified several other potential phosphorylation targets for both these symbiotic receptor-like kinases. In particular, we also discovered the phosphorylation of LYK3 by NORK itself which was also confirmed by pair-wise kinase assays. Motif analysis of potential targets for these kinases revealed that the acidic motif xxxsDxxx was common to both of them. In summary, this high-throughput technique catalogs the potential phosphorylation substrates of multiple kinases in a single efficient experiment, the biological characterization of which should provide a better understanding of phosphorylation signaling cascade in symbiosis.


Via Pierre-Marc Delaux
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Rhamnose synthase activity is required for pathogenicity of the vascular wilt fungus Verticillium dahliae

Rhamnose synthase activity is required for pathogenicity of the vascular wilt fungus Verticillium dahliae | MycorWeb Plant-Microbe Interactions | Scoop.it
The initial interaction of a pathogenic fungus with its host is complex and involves numerous metabolic pathways and regulatory proteins. Considerable attention has been devoted to proteins that play a crucial role in these interactions, with an emphasis on so-called effector molecules that are secreted by the invading microbe to establish the symbiosis. However, the contribution of other types of molecules, such as glycans, is less well appreciated. Here, we present a random genetic screen that enabled us to identify 58 novel candidate genes that are involved in the pathogenic potential of the fungal pathogen Verticillium dahliae, which causes vascular wilt diseases in over 200 dicotyledonous plant species, including economically important crops. One of the candidate genes that was identified concerns a putative biosynthetic gene involved in nucleotide sugar precursor formation, as it encodes a putative nucleotide-rhamnose synthase/epimerase-reductase (NRS/ER). This enzyme has homology to bacterial enzymes involved in the biosynthesis of the nucleotide sugar deoxy-thymidine diphosphate (dTDP)-rhamnose, a precursor of L-rhamnose, which has been shown to be required for virulence in several human pathogenic bacteria. Rhamnose is known to be a minor cell wall glycan in fungi and has therefore not been suspected as a crucial molecule in fungal–host interactions. Nevertheless, our study shows that deletion of the VdNRS/ER gene from the V. dahliae genome results in complete loss of pathogenicity on tomato and Nicotiana benthamiana plants, whereas vegetative growth and sporulation are not affected. We demonstrate that VdNRS/ER is a functional enzyme in the biosynthesis of uridine diphosphate (UDP)-rhamnose, and further analysis has revealed that VdNRS/ER deletion strains are impaired in the colonization of tomato roots. Collectively, our results demonstrate that rhamnose, although only a minor cell wall component, is essential for the pathogenicity of V. dahliae.
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