Plant-Microbe Symbiosis
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Compact graphical representation of phylogenetic data and metadata with GraPhlAn

Compact graphical representation of phylogenetic data and metadata with GraPhlAn | Plant-Microbe Symbiosis | Scoop.it
The increased availability of genomic and metagenomic data poses challenges at multiple analysis levels, including visualization of very large-scale microbial and microbial community data paired with rich metadata. We developed GraPhlAn (Graphical Phylogenetic Analysis), a computational tool that produces high-quality, compact visualizations of microbial genomes and metagenomes. This includes phylogenies spanning up to thousands of taxa, annotated with metadata ranging from microbial community abundances to microbial physiology or host and environmental phenotypes. GraPhlAn has been developed as an open-source command-driven tool in order to be easily integrated into complex, publication-quality bioinformatics pipelines. It can be executed either locally or through an online Galaxy web application. We present several examples including taxonomic and phylogenetic visualization of microbial communities, metabolic functions, and biomarker discovery that illustrate GraPhlAn’s potential for modern microbial and community genomics.
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Plant-Microbe Symbiosis
Beneficial associations between plants and microbes
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Transcriptional regulation of nitrogen-associated metabolism and growth

Transcriptional regulation of nitrogen-associated metabolism and growth | Plant-Microbe Symbiosis | Scoop.it
Nitrogen is an essential macronutrient for plant growth and basic metabolic processes. The application of nitrogen-containing fertilizer increases yield, which has been a substantial factor in the green revolution1. Ecologically, however, excessive application of fertilizer has disastrous effects such as eutrophication2. A better understanding of how plants regulate nitrogen metabolism is critical to increase plant yield and reduce fertilizer overuse. Here we present a transcriptional regulatory network and twenty-one transcription factors that regulate the architecture of root and shoot systems in response to changes in nitrogen availability. Genetic perturbation of a subset of these transcription factors revealed coordinate transcriptional regulation of enzymes involved in nitrogen metabolism. Transcriptional regulators in the network are transcriptionally modified by feedback via genetic perturbation of nitrogen metabolism. The network, genes and gene-regulatory modules identified here will prove critical to increasing agricultural productivity.

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Impressive study

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Whole-genome landscape of Medicago truncatula symbiotic genes

Whole-genome landscape of Medicago truncatula symbiotic genes | Plant-Microbe Symbiosis | Scoop.it
Advances in deciphering the functional architecture of eukaryotic genomes have been facilitated by recent breakthroughs in sequencing technologies, enabling a more comprehensive representation of genes and repeat elements in genome sequence assemblies, as well as more sensitive and tissue-specific analyses of gene expression. Here we show that PacBio sequencing has led to a substantially improved genome assembly of Medicago truncatula A17, a legume model species notable for endosymbiosis studies1, and has enabled the identification of genome rearrangements between genotypes at a near-base-pair resolution. Annotation of the new M. truncatula genome sequence has allowed for a thorough analysis of transposable elements and their dynamics, as well as the identification of new players involved in symbiotic nodule development, in particular 1,037 upregulated long non-coding RNAs (lncRNAs). We have also discovered that a substantial proportion (~35% and 38%, respectively) of the genes upregulated in nodules or expressed in the nodule differentiation zone colocalize in genomic clusters (270 and 211, respectively), here termed symbiotic islands. These islands contain numerous expressed lncRNA genes and display differentially both DNA methylation and histone marks. Epigenetic regulations and lncRNAs are therefore attractive candidate elements for the orchestration of symbiotic gene expression in the M. truncatula genome.

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Outstanding paper

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First evidences that the ectomycorrhizal fungus Paxillus involutus mobilizes nitrogen and carbon from saprotrophic fungus necromass

Fungal succession in rotting wood shows a surprising abundance of ectomycorrhizal (EM) fungi during the late decomposition stages. To better understand the links between EM fungi and saprotrophic fungi, we investigated the potential capacities of the EM fungus Paxillus involutus to mobilize nutrients from necromass of Postia placenta, a wood rot fungus, and to transfer these elements to its host tree. In this aim, we used pure cultures of P. involutus in the presence of labelled Postia necromass (15N/13C) as nutrient source, and a monoxenic mycorrhized pine experiment also, composed of labelled Postia necromass and P. involutus culture in interaction with pine seedlings. The isotopic labelling was measured in both experiments. In pure culture, P. involutus was able to mobilize N, but C as well, from the Postia necromass. In the symbiotic interaction experiment, we measured high 15N enrichments in all plant and fungal compartments. Interestingly, 13C remains mainly in the mycelium and mycorrhizas, demonstrating that the EM fungus transferred essentially N from the necromass to the tree. These observations reveal that fungal organic matter could represent a significant N source for EM fungi and trees, but also a C source for mycorrhizal fungi, including in symbiotic lifestyle.

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Very nice work

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Sphagnum Species Modulate their Phenolic Profiles and Mycorrhizal Colonization of Surrounding Andromeda polifolia along Peatland Microhabitats

Sphagnum mosses mediate long-term carbon accumulation in peatlands. Given their functional role as keystone species, it is important to consider their responses to ecological gradients and environmental changes through the production of phenolics. We compared the extent to which Sphagnum phenolic production was dependent on species, microhabitats and season, and how surrounding dwarf shrubs responded to Sphagnum phenolics. We evaluated the phenolic profiles of aqueous extracts of Sphagnum fallax and Sphagnum magellanicum over a 6-month period in two microhabitats (wet lawns versus dry hummocks) in a French peatland. Phenolic profiles of water-soluble extracts were measured by UHPLC-QTOF-MS. Andromeda polifolia mycorrhizal colonization was quantified by assessing the intensity of global root cortex colonization. Phenolic profiles of both Sphagnum mosses were species-, season- and microhabitat- dependant. Sphagnum-derived acids were the phenolics mostly recovered; relative quantities were 2.5-fold higher in S. fallax than in S. magellanicum. Microtopography and vascular plant cover strongly influenced phenolic profiles, especially for minor metabolites present in low abundance. Higher mycorrhizal colonization of A. polifolia was found in lawns as compared to hummocks. Mycorrhizal abundance, in contrast to environmental parameters, was correlated with production of minor phenolics in S. fallax. Our results highlight the close interaction between mycorrhizae such as those colonizing A. polifolia and the release of Sphagnum phenolic metabolites and suggest that Sphagnum-derived acids and minor phenolics play different roles in this interaction. This work provides new insight into the ecological role of Sphagnum phenolics by proposing a strong association with mycorrhizal colonization of shrubs.

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The LaCEP1 peptide modulates cluster root morphology in Lupinus albus

White lupin cluster roots are specialized brush‐like root structures that are formed in some species under phosphorus (P)‐deficient conditions. They intensely secrete protons and organic acid anions for solubilization and acquisition of sparingly soluble phosphates. Phytohormones and sucrose modulate cluster root number, but the molecular mechanisms of cluster root formation have been elusive. Here, a novel peptide phytohormone was identified that affects cluster root development. It belongs to the C‐TERMINALLY-ENCODED PEPTIDE (CEP) family. Members of that family arrest root growth and modulate branching in model species. LaCEP1 was highly expressed in the pre‐emergence zone of clusters. Over‐expression of the gene encoding the LaCEP1 propeptide resulted in moderate inhibition of cluster root formation. The primary and lateral root lengths of lupin were little affected by the overexpression, but LaCEP1 reduced cluster rootlet and root hair elongation. Addition of a 15‐mer core peptide derived from LaCEP1 similarly altered root morphology and modified cluster activity, suggesting that a core sequence of the propeptide is functionally sufficient. Stable overexpression in Arabidopsis confirmed the LaCEP1 function in root growth inhibition across species. Taken together, the root inhibitory effects of the LaCEP1 phytohormone suggest a role as of a regulatory module involved in cluster root development in white lupin.

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That's interesting

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Creation and Characterization of a Genomically Hybrid Strain in the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti

Creation and Characterization of a Genomically Hybrid Strain in the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti | Plant-Microbe Symbiosis | Scoop.it
Many bacteria, often associated with eukaryotic hosts and of relevance for biotechnological applications, harbor a multipartite genome composed of more than one replicon. Biotechnologically relevant phenotypes are often encoded by genes residing on the secondary replicons. A synthetic biology approach to developing enhanced strains for biotechnological purposes could therefore involve merging pieces or entire replicons from multiple strains into a single genome. Here we report the creation of a genomic hybrid strain in a model multipartite genome species, the plant-symbiotic bacterium Sinorhizobium meliloti. We term this strain as cis-hybrid, since it is produced by genomic material coming from the same species’ pangenome. In particular, we moved the secondary replicon pSymA (accounting for nearly 20% of total genome content) from a donor S. meliloti strain to an acceptor strain. The cis-hybrid strain was screened for a panel of complex phenotypes (carbon/nitrogen utilization phenotypes, intra- and extracellular metabolomes, symbiosis, and various microbiological tests). Additionally, metabolic network reconstruction and constraint-based modeling were employed for in silico prediction of metabolic flux reorganization. Phenotypes of the cis-hybrid strain were in good agreement with those of both parental strains. Interestingly, the symbiotic phenotype showed a marked cultivar-specific improvement with the cis-hybrid strains compared to both parental strains. These results provide a proof-of-principle for the feasibility of genome-wide replicon-based remodelling of bacterial strains for improved biotechnological applications in precision agriculture.

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Diversity of Bradyrhizobia in Subsahara Africa: A Rich Resource

Diversity of Bradyrhizobia in Subsahara Africa: A Rich Resource | Plant-Microbe Symbiosis | Scoop.it
Making use of biological nitrogen fixation (BNF) with pulses and green manure legumes can help to alleviate nitrogen deficiencies and increase soil fertility, problems faced particularly in smallholder agriculture in Subsahara Africa (SSA). The isolation of indigenous rhizobia provides a basis for the formulation of rhizobial inoculants. Moreover, their identification and characterization contribute to the general understanding of species distribution and ecology. Here we discuss global species discovery of Bradyrhizobium spp. Although recently the number of validly published Bradyrhizobium species is rapidly increasing, their diversity in SSA is not well-represented. We summarize the recent knowledge on species diversity in the Bradyrhizobium yuanmingense lineage to which most SSA isolates belong, and their biogeographic distribution and adaptations. Most indigenous rhizobia appear to differ from species found on other continents. We stress that an as yet hidden diversity may be a rich resource for inoculant development in future. As some species are exceptionally temperature tolerant, they may be potential biofertilizer candidates for global warming scenarios.

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Transcriptomic analysis reveals the possible roles of sugar metabolism and export for positive mycorrhizal growth responses in soybean

To elucidate molecular mechanisms controlling differential growth responses to root colonization by arbuscular mycorrhizal (AM) fungi varying in colonization and cooperative behavior, a pot experiment was carried out using two soybean genotypes and three AM inocula. The results showed that inoculation by cooperative Rhizophagus irregularis (Ri) or less‐cooperative Glomus aggregatum with high AM colonization (Ga‐H) significantly promoted plant growth compared with inoculation by Glomus aggregatum with low AM colonization (Ga‐L). A comparative RNA sequencing analysis of the root transcriptomes showed that fatty acid synthesis pathway was significantly enriched in all three AM inoculation roots. However, sugar metabolism and transport were significantly enriched only in Ri and Ga‐H inoculation, which was consistent with positive growth responses in these two inoculation treatments. Accordingly, the expression levels of the key genes related to sugar metabolism and transport were also up‐regulated in Ri and Ga‐H roots compared with Ga‐L roots. Of them, two SWEET transporter genes, GmSWEET6 (Glyma.04G198600) and GmSWEET15 (Glyma.06G166800), and one invertase (Glyma.17G227900) gene were exclusively induced only in Ri and Ga‐H roots. Promoter analyses in transgenic soybean roots further demonstrated that GUS driven by the GmSWEET6 promoter was highly expressed in arbuscule‐containing cortical cells. Additionally, Ri and Ga‐H inoculation increased the contents of sucrose, glucose and fructose in both shoots and roots compared to those of Ga‐L and NM. These results imply that positive mycorrhizal growth responses in plants might mostly be due to the stimulation of photosynthate metabolism and transport by AM fungal inoculum with high colonization capabilities.

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An efficient CRISPR vector toolbox for engineering large deletions in Arabidopsis thaliana

An efficient CRISPR vector toolbox for engineering large deletions in Arabidopsis thaliana | Plant-Microbe Symbiosis | Scoop.it
Background
Our knowledge of natural genetic variation is increasing at an extremely rapid pace, affording an opportunity to come to a much richer understanding of how effects of specific genes are dependent on the genetic background. To achieve a systematic understanding of such GxG interactions, it is desirable to develop genome editing tools that can be rapidly deployed across many different genetic varieties.

Results
We present an efficient CRISPR/Cas9 toolbox of super module (SM) vectors. These vectors are based on a previously described fluorescence protein marker expressed in seeds allowing identification of transgene-free mutants. We have used this vector series to delete genomic regions ranging from 1.7 to 13 kb in different natural accessions of the wild plant Arabidopsis thaliana. Based on results from 53 pairs of sgRNAs targeting individual nucleotide binding site leucine-rich repeat (NLR) genes, we provide a comprehensive overview of obtaining heritable deletions.

Conclusions
The SM series of CRISPR/Cas9 vectors enables the rapid generation of transgene-free, genome edited plants for a diversity of functional studies.
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Little evidence that farmers should consider abundance or diversity of arbuscular mycorrhizal fungi when managing crops

Arbuscular mycorrhizal fungi (AMF) are ubiquitous in agroecosystems and often stated to be critical for crop yield and agroecosystem sustainability. However, should farmers modify management to enhance the abundance and diversity of AMF? We address this question with a focus on field experiments that manipulated colonisation by indigenous AMF and report crop yield, or investigated community structure and diversity of AMF. We find that the literature presents an overly optimistic view of the importance of AMF in crop yield due, in part, to flawed methodology in field experiments. A small body of rigorous research only sometimes reports a positive impact of high colonisation on crop yield, even under phosphorus limitation. We suggest that studies vary due to the interaction of environment and genotype (crop and mycorrhizal fungal). We also find that the literature can be overly pessimistic about the impact of some common agricultural practices on mycorrhizal fungal communities and that interactions between AMF and soil microbes are complex and poorly understood. We provide a template for future field experiments and a list of research priorities, including phosphorus‐efficient agroecosystems. However, we conclude that management of AMF by farmers will not be warranted until benefits are demonstrated at the field scale under prescribed agronomic management.

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HcPT1.2 participates in Pi acquisition in Hebeloma cylindrosporum external hyphae of ectomycorrhizas under high and low phosphate conditions

Ectomycorrhizal fungi improve tree phosphorus nutrition through transporters specifically localized at soil-hyphae and symbiotic interfaces. In the model symbiosis between the fungus Hebeloma cylindrosporum and the maritime pine (Pinus pinaster), several transporters possibly involved in phosphate fluxes were identified, including three H+:Pi transporters. Among these three, we recently unraveled the function of one of them, named HcPT2, in both pure culture and symbiotic interaction with P. pinaster. Here we investigated the transporter named HcPT1.2, by analyzing inorganic phosphate transport ability in a yeast complementation assay, assessing its expression in the fungus associated or not with the plant, and immunolocalizing the proteins in ectomycorrhizas. We also evaluated the effect of external Pi concentration on expression and localization of HcPT1.2. Our results revealed that HcPT1.2 is involved in Pi acquisition by H. cylindrosporum mycelium, irrespective of the external Pi concentrations.

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An Array-based Comparative Genomic Hybridization Platform for Efficient Detection of Copy Number Variations in Fast Neutron-induced Medicago truncatula Mutants

This protocol provides experimental steps and information about reagents, equipment, and analysis tools for researchers who are interested in carrying out whole genome array-based comparative genomic hybridization (CGH) analysis of copy number variations in plants.

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A plant chitinase controls cortical infection thread progression and nitrogen-fixing symbiosis

Morphogens provide positional information and their concentration is key to the organized development of multicellular organisms. Nitrogen-fixing root nodules are unique organs induced by Nod factor-producing bacteria. Localized production of Nod factors establishes a developmental field within the root where plant cells are reprogrammed to form infection threads and primordia. We found that regulation of Nod factor levels by Lotus japonicus is required for the formation of nitrogen-fixing organs, determining the fate of this induced developmental program. Our analysis of plant and bacterial mutants shows that a host chitinase modulates Nod factor levels possibly in a structure-dependent manner. In Lotus, this is required for maintaining Nod factor signalling in parallel with the elongation of infection threads within the nodule cortex, while root hair infection and primordia formation are not influenced. Our study shows that infected nodules require balanced levels of Nod factors for completing their transition to functional, nitrogen-fixing organs.

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Visualizing Glutamine Accumulation in Root Systems Involved in the Legume–Rhizobia Symbiosis by Placement on Agar Embedded with Companion Biosensor Cells

Visualizing Glutamine Accumulation in Root Systems Involved in the Legume–Rhizobia Symbiosis by Placement on Agar Embedded with Companion Biosensor Cells | Plant-Microbe Symbiosis | Scoop.it
Microbial symbiotic nitrogen fixation (SNF) occurs inside root nodules, where fixed-N (NH4+) from rhizobia is first assimilated into the amino acid glutamine (Gln). Visualization of Gln dynamics in nodulated root systems of different plant species would require re-engineering transgenic Gln reporters specific for each rhizobia/host genotype. Here we demonstrate the use of companion biosensor cells called GlnLux (Escherichia coli auxotrophic for Gln and constitutively expressing lux) to image Gln accumulation in nodulated root systems across a diversity of legume/rhizobia species. Companion GlnLux cells are embedded into agar (GlnLux agar) upon which legume root systems are placed following freeze-thawing to cause Gln leakage. Photons released from nearby activated biosensor cells are captured using a photon capture camera. Using split root systems, we demonstrate that in diverse amide-exporting legumes (alfalfa, lentil, and green pea) and a ureide-exporting legume (soybean) that GlnLux agar imaging is sufficiently sensitive to detect Gln release from individual nodules and can differentiate root systems with active nif+ from inactive nif− nodules. The assay permits visualization of both source and sink dynamics of nodule Gln, specifically, Gln import into nodules from roots (for nodule growth and/or amino acid cycling), Gln assimilated from fixed nitrogen that accumulates inside nodules, and Gln export from nodules into roots from this assimilatory-N. GlnLux agar-based imaging is thus a new research tool to localize the accumulation and transfer of a critical amino acid required for rhizobia symbionts within legume phytobiomes. We discuss the ability of this technology to open new frontiers in basic research and its limitations.

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Genomic Manipulations of the Diazotroph Azotobacter vinelandii

The biological reduction of nitrogen gas to ammonia is limited to a select group of nitrogen-fixing prokaryotes. While nitrogenase is the catalyst of nitrogen fixation in these biological systems, a consortium of additional gene products is required for the synthesis, activation, and catalytic competency of this oxygen-sensitive metalloenzyme. Thus, the biochemical complexity of this process often requires functional studies and isolation of gene products from the native nitrogen-fixing organisms. The strict aerobe Azotobacter vinelandii is the best-studied model bacterium among diazotrophs. This chapter provides a description of procedures for targeted genomic manipulation and isolation of A. vinelandii strains. These methods have enabled identification and characterization of gene products with roles in nitrogen fixation and other related aspects of metabolism. The ability to modify and control expression levels of targeted sequences provides a biotechnological tool to uncover molecular details associated with nitrogen fixation, as well as to exploit this model system as a host for expression of oxygen-sensitive proteins.

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A Dihydroflavonol-4-reductase-like Protein Interacts with NFR5 and Regulates Rhizobial Infection in Lotus japonicus

In almost all symbiotic interactions between rhizobia and leguminous plants, host flavonoid-induced synthesis of Nod factors in rhizobia is required to initiate symbiotic response in plants. In this study, we found that Lotus japonicus Nod Factor Receptor 5 (LjNFR5) might directly regulate flavonoid biosynthesis during symbiotic interaction with rhizobia. A yeast two-hybrid analysis revealed that a dihydroflavonol-4-reductase-like protein (LjDFL1) interacts with LjNFR5. The interaction between MtDFL1 and MtNFP, two Medicago truncatula proteins with homology to LjDFL1 and LjNFR5, respectively, was also shown, suggesting that interaction between these two proteins might be conserved in different legumes. LjDFL1 was highly expressed in root hairs and the epidermal cells of root tips. Lotus ljdfl1 mutants and Medicago mtdfl1 mutants produced significantly fewer infection threads (ITs) than the wild-type control plants following rhizobial treatment. Furthermore, the roots of stable transgenic L. japonicus plants overexpressing LjDFL1 formed more ITs than control roots after exposure to rhizobia. These data indicated that LjDFL1 is a positive regulator of symbiotic signaling. However, the expression of LjDFL1 was suppressed by rhizobial treatment, suggesting that a negative feedback loop might be involved in regulation of the symbiotic response in L. japonicus.

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The Role of Plant Transporters in Mycorrhizal Symbioses

The Role of Plant Transporters in Mycorrhizal Symbioses | Plant-Microbe Symbiosis | Scoop.it
Membrane transport systems are crucial elements for plant nutrition and development as they play a key role in the absorption of mineral nutrients and water at the root level but also in the translocation within the plant. Moreover, membrane transport is involved in signalling and communication e.g. to adapt and interact with the environment. Most plants live in tight contact with beneficial soil microbes, such as bacteria and mycorrhizal fungi, which contribute to plant nutrition in part through modulation of the expression and functioning of plant transporter systems, as ion channels and transporters. In addition, mycorrhizal fungi largely increase the absorption surface of roots thereby promoting plant's access to soil resources as minerals and water. In turn, plants “reward” mycorrhizal fungi with sugars and/or lipids. This “fair trade” requires specific communication and a series of exchanges between the two symbiotic partners enabled by the adaptability and plasticity of their transporters. Here, we summarize recent advances allowing molecular insight in the impact of mycorrhizal symbiosis on the plant “transportome”. We highlight results obtained in ecto- and endomycorrhizal associations for plant transporters involved in the absorption of mineral nutrients and water released by the fungus at the symbiotic interface, and molecular players responsible for carbon and lipid nutrition of the fungal partner. We focus also on plant membrane transport systems implicated in early communication between plant and fungal partners.

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Great job Kevin and Sabine!

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Plant Promoter Analysis: Identification and Characterization of Root Nodule Specific Promoter in the Common Bean

Plant Promoter Analysis: Identification and Characterization of Root Nodule Specific Promoter in the Common Bean | Plant-Microbe Symbiosis | Scoop.it
The upstream sequences of gene coding sequences are termed as promoter sequences. Studying the expression patterns of promoters are very significant in understanding the gene regulation and spatiotemporal expression patterns of target genes. On the other hand, it is also critical to establish promoter evaluation tools and genetic transformation techniques that are fast, efficient, and reproducible. In this study, we investigated the spatiotemporal expression pattern of the rhizobial symbiosis-specific nodule inception (NIN) promoter of Phaseolus vulgaris in the transgenic hairy roots. Using plant genome databases and analysis tools we identified, isolated, and cloned the P. vulgaris NIN promoter in a transcriptional fusion to the chimeric reporter β-glucuronidase (GUS) GUS-enhanced::GFP. Further, this protocol describes a rapid and versatile system of genetic transformation in the P. vulgaris using Agrobacterium rhizogenes induced hairy roots. This system generates ≥2 cm hairy roots at 10 to 12 days after transformation. Next, we assessed the spatiotemporal expression of NIN promoter in Rhizobium inoculated hairy roots at periodic intervals of post-inoculation. Our results depicted by GUS activity show that the NIN promoter was active during the process of nodulation. Together, the present protocol demonstrates how to identify, isolate, clone, and characterize a plant promoter in the common bean hairy roots. Moreover, this protocol is easy to use in non-specialized laboratories.

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Contrasted evolutionary constraints on carbohydrate active enzymes (CAZymes) in selected Frankia strains

Carbohydrate active enzymes (CAZymes) are capable of breaking complex polysaccharides into simpler form. In plant-host-associated microorganisms CAZymes are known to be involved in plant cell wall degradation. However, the biology and evolution of Frankia CAZymes are largely unknown. In the present study, we took a genomic approach to evaluate the presence and putative roles of CAZymes in Frankia. The CAZymes were found to be potentially highly expressed (PHX) proteins and contained more aromatic amino acids, which increased their biosynthetic energy cost. These energy rich amino acids were present in the active sites of CAZymes aiding in their carbohydrate binding capacity. Phylogenetic and evolutionary analyses showed that, in Frankia strains with the capacity to nodulate host plants, CAZymes were evolving slower than the other PHX genes, whereas similar genes from non-nodulating (or ineffectively nodulating) Frankia strains showed little variation in their evolutionary constraints compared to other PHX genes. Thus, the present study revealed the persistence of a strong purifying selection on CAZymes of Frankia indicating their crucial role.

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Does mycorrhizal colonisation vary between maize and sunflower under limitations to radiation source or carbohydrate sink?

The aim of this work was to analyse and compare indigenous arbuscular mycorrhizal colonisation (AMC) in relation to growth and total soluble carbohydrates (TSC) in two major, physiologically contrasting crop species: maize (Zea mays L.) and sunflower (Helianthus annuus L.). In order to promote contrasting TSC concentrations, we modified the radiation source by shading and the carbohydrate sink by manipulating reproductive sinks at different phenological stages during the grain-filling period in two field experiments. We assessed plant dry matter, TSC in stems, and root AMC from flowering until final harvest. AMC during the grain-filling period decreased in maize and increased in sunflower. A sink limitation increased AMC in maize, and reduced it in sunflower. A source limitation decreased AMC in both species, especially in sunflower. AMC was positively related to TSC in maize, but negatively in sunflower. The relationship was affected by shading in sunflower, but not in maize. In both species, a different linear model described the relationship between AMC and TSC in plants submitted to the removal of the reproductive organs. The results highlight the role of carbohydrates in mediating mycorrhizal formation, and show for the first time the opposite AMC–TSC relationships in maize and sunflower.

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A Lotus japonicus E3 ligase interacts with the Nod Factor Receptor 5 and positively regulates nodulation

A Lotus japonicus E3 ligase interacts with the Nod Factor Receptor 5 and positively regulates nodulation | Plant-Microbe Symbiosis | Scoop.it
Background
Post-translational modification of receptor proteins is involved in activation and de-activation of signalling systems in plants. Both ubiquitination and deubiquitination have been implicated in plant interactions with pathogens and symbionts.

Results
Here we present LjPUB13, a PUB-ARMADILLO repeat E3 ligase that specifically ubiquitinates the kinase domain of the Nod Factor receptor NFR5 and has a direct role in nodule organogenesis events in Lotus japonicus. Phenotypic analyses of three LORE1 retroelement insertion plant lines revealed that pub13 plants display delayed and reduced nodulation capacity and retarded growth. LjPUB13 expression is spatially regulated during symbiosis with Mesorhizobium loti, with increased levels in young developing nodules.

Conclusion
LjPUB13 is an E3 ligase with a positive regulatory role during the initial stages of nodulation in L. japonicus.
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NIN interacts with NLPs to mediate nitrate inhibition of nodulation in Medicago truncatula

NIN interacts with NLPs to mediate nitrate inhibition of nodulation in Medicago truncatula | Plant-Microbe Symbiosis | Scoop.it
Legume plants can assimilate inorganic nitrogen and have access to fixed nitrogen through symbiotic interaction with diazotrophic bacteria called rhizobia. Symbiotic nitrogen fixation is an energy-consuming process and is strongly inhibited when sufficient levels of fixed nitrogen are available, but the molecular mechanisms governing this regulation are largely unknown. The transcription factor nodule inception (NIN) is strictly required for nodulation and belongs to a family of NIN-like proteins (NLPs), which have been implicated in the regulation of nitrogen homeostasis in Arabidopsis. Here, we show that mutation or downregulation of NLP genes prevents nitrate inhibition of infection, nodule formation and nitrogen fixation. We find that NIN and NLPs physically interact through their carboxy-terminal PB1 domains. Furthermore, we find that NLP1 is required for the expression of nitrate-responsive genes and that nitrate triggers NLP1 re-localization from the cytosol to the nucleus. Finally, we show that NLP1 can suppress NIN activation of CRE1 expression in Nicotiana benthamiana and Medicago truncatula. Our findings highlight a central role for NLPs in the suppression of nodulation by nitrate.

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Great paper... I love it.

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Mixotrophic orchids do not use photosynthates for perennial underground organs

Mixotrophic orchids do not use photosynthates for perennial underground organs | Plant-Microbe Symbiosis | Scoop.it
Most plants are autotrophic and interact with soil fungi, forming mycorrhizal symbioses (van der Heijden et al., 2015) where plants gain mineral nutrients and provide photosynthates to fungi. Yet, plants repeatedly evolve heterotrophy (Tĕšitel et al., 2018), and several lineages, especially in orchids, import carbon from their mycorrhizal fungi, a strategy called mycoheterotrophy (Merckx, 2013). Green plants that are photosynthetic but also import carbon from their mycorrhizal fungi have raised considerable interest over the past two decades (Julou et al., 2005; Selosse & Roy, 2009). These plants with two carbon sources are termed mixotrophic, and pave the evolutionary way to full mycoheterotrophy (Selosse & Roy, 2009). Mixotrophy enables them to adapt to shaded conditions (Julou et al., 2005; Preiss et al., 2010; with some exceptions: Girlanda et al., 2011; Schiebold et al., 2017) and sometimes drives a reduction of their photosynthetic abilities (Girlanda et al., 2006). Their study is therefore of crucial interest to an understanding of the evolution to full mycoheterotrophy.

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Digging deeper: why we need more proterozoic algal fossils and how to get them

Known Proterozoic algal fossils raise compelling questions about the origin and diversification of cyanobacteria and eukaryotic algae, and their ecological influence in deep time. This perspectives article describes particular examples of persistent evolutionary and biogeochemical issues whose resolution would be aided by additional algal fossil evidence from Proterozoic deposits, which have been the subjects of recent intensive study. New Proterozoic geosciences literature relevant to the early diversification of algae is surveyed. Previously underappreciated algal traits that might improve taxonomic attributions of fossil remains are highlighted. Processes that phycologists could use to improve detection of algal fossils are recommended. Potential geological sources of new Proterozoic fossils are suggested.

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Scooped by Jean-Michel Ané
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Nitrate inhibition of nodule formation in Medicago truncatula is mediated by ACC SYNTHASE 10

Legumes form a mutualistic endosymbiosis with nitrogen-fixing rhizobia. These rhizobia are housed intracellularly in specialised lateral root organs, called nodules. Initiation of these nodules is triggered by bacterial derived signalling molecules, lipochitooligosaccharides (LCO). The process of nitrogen fixation is highly energy-demanding and therefore nodule initiation is tightly regulated. Nitrate is a potent inhibitor of nodulation. However, the precise mechanisms by which nitrate inhibits nodulation is poorly understood. Here, we demonstrate that in Medicago truncatula nitrate interferes with the transcriptional regulation of the ethylene biosynthesis gene ACC SYNTHASE 10. ACSs commit the rate limiting step in ethylene biosynthesis and in M. truncatula ACS10 is highly expressed in the zone of the root where nodulation occurs. Our results show that a reduction in ACS10 expression in response to LCO exposure correlates with the ability to form nodules. In addition, RNAi-mediated knockdown of ACS10 confers nodulation ability under otherwise inhibitory nitrate conditions. This discovery sheds new light on how ethylene is involved in the inhibition of nodulation by nitrate, bringing us one step closer to understanding how plants regulate their susceptibility towards rhizobia.
Jean-Michel Ané's insight:

Nice work @KohlenW

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