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Genome Biology - Drosophila primary microRNA-8 encodes a microRNA-encoded peptide acting in parallel of miR-8 

Genome Biology - Drosophila primary microRNA-8 encodes a microRNA-encoded peptide acting in parallel of miR-8  | LRSV Publications | Scoop.it

Background Recent genome-wide studies of many species reveal the existence of a myriad of RNAs differing in size, coding potential and function. Among these are the long non-coding RNAs, some of them producing functional small peptides via the translation of short ORFs. It now appears that any kind of RNA presumably has a potential to encode small peptides. Accordingly, our team recently discovered that plant primary transcripts of microRNAs (pri-miRs) produce small regulatory peptides (miPEPs) involved in auto-regulatory feedback loops enhancing their cognate microRNA expression which in turn controls plant development. Here we investigate whether this regulatory feedback loop is present in Drosophila melanogaster. Results We perform a survey of ribosome profiling data and reveal that many pri-miRNAs exhibit ribosome translation marks. Focusing on miR-8, we show that pri-miR-8 can produce a miPEP-8. Functional assays performed in Drosophila reveal that miPEP-8 affects development when overexpressed or knocked down. Combining genetic and molecular approaches as well as genome-wide transcriptomic analyses, we show that miR-8 expression is independent of miPEP-8 activity and that miPEP-8 acts in parallel to miR-8 to regulate the expression of hundreds of genes. Conclusion Taken together, these results reveal that several Drosophila pri-miRs exhibit translation potential. Contrasting with the mechanism described in plants, these data shed light on the function of yet undescribed primary-microRNA-encoded peptides in Drosophila and their regulatory potential on genome expression.

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Plant J - Ethylene signaling modulates tomato pollen tube growth, through modifications of cell wall remodeling and calcium gradient

Plant J - Ethylene signaling modulates tomato pollen tube growth, through modifications of cell wall remodeling and calcium gradient | LRSV Publications | Scoop.it

Ethylene modulates plant developmental processes including flower development. Previous studies have suggested ethylene participation in pollen tube (PT) elongation, and both ethylene production and perception seem critical at fertilization time. The full gene set regulated by ethylene during PT growth is unknown. To study this, we used various EThylene Receptors (ETRs) tomato mutants: etr3-ko, a loss-of-function (LOF) mutant; and NR (Never Ripe), a gain of function (GOF) mutant. The etr3-ko PTs grew faster than its wild type, WT. Oppositely, NR PT elongation was slower than its wild type, and PTs displayed larger diameters. ETR mutations created feedbacks on ethylene production. Furthermore, the ethylene treatment of germinating pollen grains increased PT length in etr-ko mutants and WT, but not in NR. Treatments with the ethylene perception inhibitor, 1-MCP, decreased PT length in etr-ko mutants and wild types, but had no effect on NR. This confirmed that ethylene regulates PT growth. The comparison of PT transcriptomes in LOF and GOF mutants, etr3-ko and NR, both mutated on the ETR3 gene, revealed that ethylene perception has major impacts on cell wall- and calcium-related genes as confirmed by microscopic observations showing a modified distribution of the methylesterified homogalacturonan pectic motif and of calcium load. Our results establish links between PT growth, ethylene, calcium and cell wall metabolisms, and also constitute a transcriptomic resource.

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Proteomics - A Tandem Mass Tags (TMTs) labeling approach highlights differences between the shoot proteome of two Arabidopsis thaliana ecotypes, Col‐0 and Ws

Proteomics - A Tandem Mass Tags (TMTs) labeling approach highlights differences between the shoot proteome of two Arabidopsis thaliana ecotypes, Col‐0 and Ws | LRSV Publications | Scoop.it

Arabidopsis has become a powerful model to study morphogenesis, plant growth, development but also plant response to environmental conditions. Over 1000 Arabidopsis genomes are available and show natural genetic variations. Among them, the main reference accessions Wassilewskija (Ws) and Columbia (Col‐0), originally growing at contrasted altitudes and temperatures, are widely studied, but data contributing to their molecular phenotyping are still scarce. A global quantitative proteomics approach using isobaric stable isotope labeling (Tandem Mass Tags, TMT) was performed on Ws and Col‐0. Plants have been hydroponically grown at 16 h/8 h (light/dark cycle) at 23°C day/19°C night for three weeks. A TMT labeling of the proteins extracted from their shoots has been performed and showed a differential pattern of protein abundance between them. These results have allowed identifying several proteins families possibly involved in the differential responses observed for Ws and Col‐0 during plant development and upon environmental changes. In particular, Ws and Col‐0 mainly differ in photosynthesis, cell wall‐related proteins, plant defense/stress, ROS scavenging enzymes/redox homeostasis and DNA/RNA binding/transcription/translation/protein folding.

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Int. J. Mol Sci. - Evidence That Regulation of Pri-miRNA/miRNA Expression Is Not a General Rule of miPEPs Function in Humans

Int. J. Mol Sci. - Evidence That Regulation of Pri-miRNA/miRNA Expression Is Not a General Rule of miPEPs Function in Humans | LRSV Publications | Scoop.it
Some miRNAs are located in RNA precursors (pri-miRNAs) annotated as long non-coding (lncRNAs) due to absence of long open reading frames (ORFs). However, recent studies have shown that some lnc pri-miRNAs encode peptides called miPEPs (miRNA-encoded peptides). Initially discovered in plants, three miPEPs have also been identified in humans. Herein, we found that a dozen human pri-miRNAs potentially encode miPEPs, as revealed by ribosome profiling and proteomic databases survey. So far, the only known function of plant miPEPs is to enhance the transcription of their own pri-miRNAs, thereby increasing the level and activity of their associated miRNAs and downregulating the expression of their target genes. To date, in humans, only miPEP133 was shown to promote a positive autoregulatory loop. We investigated whether other human miPEPs are also involved in regulating the expression of their miRNAs by studying miPEP155, encoded by the lnc MIR155HG, miPEP497, a sORF-encoded peptide within lnc MIR497HG, and miPEP200a, encoded by the pri-miRNA of miR-200a/miR-200b. We show that overexpression of these miPEPs is unable to impact the expression/activity of their own pri-miRNA/miRNAs in humans, indicating that the positive feedback regulation observed with plant miPEPs and human miPEP133 is not a general rule of human miPEP function.
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Current Biology - Formin-mediated bridging of cell wall, plasma membrane, and cytoskeleton in symbiotic infections of Medicago truncatula

Current Biology - Formin-mediated bridging of cell wall, plasma membrane, and cytoskeleton in symbiotic infections of Medicago truncatula | LRSV Publications | Scoop.it

Legumes have maintained the ability to associate with rhizobia to sustain the nitrogen-fixing root nodule symbiosis (RNS). In Medicago truncatula, the Nod factor (NF)-dependent intracellular root colonization by Sinorhizobium meliloti initiates from young, growing root hairs. They form rhizobial traps by physically curling around the symbiont. Although alterations in root hair morphology like branching and swelling have been observed in other plants in response to drug treatments or genetic perturbations, full root hair curling represents a rather specific invention in legumes. The entrapment of the symbiont completes with its full enclosure in a structure called the “infection chamber” (IC), from which a tube-like membrane channel, the “infection thread” (IT), initiates. All steps of rhizobium-induced root hair alterations are aided by a tip-localized cytosolic calcium gradient, global actin re-arrangements, and dense subapical fine actin bundles that are required for the delivery of Golgi-derived vesicles to the root hair tip. Altered actin dynamics during early responses to NFs or rhizobia have mostly been shown in mutants that are affected in the actin-related SCAR/WAVE complex. Here, we identified a polarly localized SYMBIOTIC FORMIN 1 (SYFO1) to be required for NF-dependent alterations in membrane organization and symbiotic root hair responses. We demonstrate that SYFO1 mediates a continuum between the plasma membrane and the cell wall that is required for the onset of rhizobial infections.

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Journal of Experimental Botany - Distinct genetic basis for root responses to lipo-chitooligosaccharide signal molecules from distinct microbial origins

Journal of Experimental Botany - Distinct genetic basis for root responses to lipo-chitooligosaccharide signal molecules from distinct microbial origins | LRSV Publications | Scoop.it

Lipo-chitooligosaccharides (LCOs) were originally found as symbiotic signals called Nod Factors (Nod-LCOs) controlling nodulation of legumes by rhizobia. More recently LCOs were also found in symbiotic fungi and, more surprisingly, very widely in the kingdom fungi including in saprophytic and pathogenic fungi. The LCO-V(C18:1, Fuc/MeFuc), hereafter called Fung-LCOs, are the LCO structures most commonly found in fungi. This raises the question of how legume plants, such as Medicago truncatula, can discriminate between Nod-LCOs and these Fung-LCOs. To address this question, we performed a Genome Wide Association Study on 173 natural accessions of Medicago truncatula, using a root branching phenotype and a newly developed local score approach. Both Nod- and Fung-LCOs stimulated root branching in most accessions but the root responses to these two types of LCO molecules were not correlated. Also, heritability of root response was higher for Nod-LCOs than for Fung-LCOs. We identified 123 loci for Nod-LCO and 71 for Fung-LCO responses, but only one was common. This suggests that Nod- and Fung-LCOs both control root branching but use different molecular mechanisms. The tighter genetic constraint of the root response to Fung-LCOs possibly reflects the ancestral origin of the biological activity of these molecules.

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Science - Plant evolution driven by interactions with symbiotic and pathogenic microbes

Science - Plant evolution driven by interactions with symbiotic and pathogenic microbes | LRSV Publications | Scoop.it

During 450 million years of diversification on land, plants and microbes have evolved together. This is reflected in today’s continuum of associations ranging from parasitism to mutualism. Through phylogenetics, cell biology and reverse genetics extending beyond flowering plants into Bryophytes, scientists have started to unravel the genetic basis and evolutionary trajectories of plant-microbe associations. Protection against pathogens and support of beneficial, symbiotic, microorganisms are sustained by a blend of conserved and clade-specific plant mechanisms evolving at different speeds. We propose that symbiosis consistently emerges from the co-option of protection mechanisms and general cell biology principles. Exploring and harnessing the diversity of molecular mechanisms employed in non-flowering plant-microbe interactions may extend the possibilities for engineering symbiosis-competent and pathogen resilient crops.

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Data in Brief - Cell wall proteomic datasets of stems and leaves of Brachypodium distachyon

Data in Brief - Cell wall proteomic datasets of stems and leaves of Brachypodium distachyon | LRSV Publications | Scoop.it

This article provides experimental data describing the cell wall protein profiles of stems and leaves of Brachypodium distachyon at two different stages of development. The cell wall proteomics data have been obtained from (i) stem internodes at young and mature stages of development, and (ii) leaves at young and mature stages of development. The proteins have been extracted from purified cell walls using buffers containing calcium chloride (0.2 M) or lithium chloride (2 M). They have been identified by LC-MS/MS and bioinformatics. These data allow deepening our knowledge of these cell wall proteomes. They are a valuable resource for people interested in plant cell wall biology to understand the roles of cell wall proteins during the growth of vegetative organs.

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Plant Cell Physiol - Phosphate Starvation Response System: its role in the regulation of plant-microbe interactions

Plant Cell Physiol - Phosphate Starvation Response System: its role in the regulation of plant-microbe interactions | LRSV Publications | Scoop.it

Phosphate (Pi) deficiency is a major factor limiting plant productivity worldwide. Land plants have evolved different strategies to cope with Pi deficiency. For instance, plants activate the so-called Pi Starvation Response (PSR) system, which is regulated by the transcription factor Phosphate Starvation Response1 (PHR1), to adjust plant growth and metabolic activity accordingly. Additionally, land plants can also establish mutualistic associations with soil microbes able to solubilize Pi from plant-inaccessible soil complexes and to transfer it to the host plant. A growing body of evidence indicates that PHR1 and the PSR system not only regulate the plant responses to Pi deficiency in an abiotic context, but they are also crucial for plants to properly interact with beneficial soil microbes able to provide them with soluble Pi. Recent evidence indicates that PHR1 and the PSR system contribute to shaping the plant-associated microbiota through the modulation of the plant immune system. The PSR and immune system outputs are tightly integrated by PHR1. Here, we review how plant-host Pi status influences the establishment of the mutualistic association with soil microbes. We also highlight the role of PHR1 and the PSR system in shaping both the root microbiome and plant responses to Pi deficiency.

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iScience - Highlighting Reactive Oxygen Species (ROS) as multitaskers in root development

iScience - Highlighting Reactive Oxygen Species (ROS) as multitaskers in root development | LRSV Publications | Scoop.it

Reactive oxygen species (ROS) are naturally produced by several redox reactions during plant regular metabolism such as photosynthesis and respiration. Due to their chemical properties and high reactivity, ROS were initially described as detrimental for cells during oxidative stress. However, they have been further recognized as key players in numerous developmental and physiological processes throughout the plant life cycle. Recent studies report the important role of ROS as growth regulators during plant root developmental processes such as in meristem maintenance, in root elongation, and in lateral root, root hair, endodermis and vascular tissue differentiation. All involves multifaceted interplays between steady-state levels of ROS with transcriptional regulators, phytohormones, and nutrients. In this review, we attempt to summarize recent findings about how ROS are involved in multiple stages of plant root development during cell proliferation, elongation and differentiation.

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PLoS One - Phytohormone production by the arbuscular mycorrhizal fungus Rhizophagus irregularis

PLoS One - Phytohormone production by the arbuscular mycorrhizal fungus Rhizophagus irregularis | LRSV Publications | Scoop.it

Arbuscular mycorrhizal symbiosis is a mutualistic interaction between most land plants and fungi of the glomeromycotina subphylum. The initiation, development and regulation of this symbiosis involve numerous signalling events between and within the symbiotic partners. Among other signals, phytohormones are known to play important roles at various stages of the interaction. During presymbiotic steps, plant roots exude strigolactones which stimulate fungal spore germination and hyphal branching, and promote the initiation of symbiosis. At later stages, different plant hormone classes can act as positive or negative regulators of the interaction. Although the fungus is known to reciprocally emit regulatory signals, its potential contribution to the phytohormonal pool has received little attention, and has so far only been addressed by indirect assays. In this study, using mass spectrometry, we analyzed phytohormones released into the medium by germinated spores of the arbuscular mycorrhizal fungus Rhizophagus irregularis. We detected the presence of a cytokinin (isopentenyl adenosine) and an auxin (indole-acetic acid). In addition, we identified a gibberellin (gibberellin A4) in spore extracts. We also used gas chromatography to show that R. irregularis produces ethylene from methionine and the α-keto γ-methylthio butyric acid pathway. These results highlight the possibility for AM fungi to use phytohormones to interact with their host plants, or to regulate their own development.

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Trends in Plant Sciences - Rhizospheric Plant–Microbe Interactions: miRNAs as a Key Mediator

Trends in Plant Sciences - Rhizospheric Plant–Microbe Interactions: miRNAs as a Key Mediator | LRSV Publications | Scoop.it

The importance of microorganisms in plant development, nutrition, and stress resistance is unquestioned and has led to a more holistic approach of plant–microbe interactions, under the holobiont concept. The structure of the plant microbiota is often described as host driven, especially in the rhizosphere, where microbial communities are shaped by diverse rhizodeposits. Gradually, this anthropogenic vision is fading and being replaced by the idea that plants and microorganisms co-shape the plant microbiota.

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J Exp Bot - The many facets of protein ubiquitination and degradation in plant root iron deficiency responses

Organisms need to deal with the absolute requirement for metals, and their possible toxicity. This is achieved through an intricate network of signaling pathways integrated to ultimately fine tune iron uptake and metabolism. The mechanisms by which plants cope with iron limitation and the associated genomic responses are well characterized. On top of this transcriptional cascade is layered another level of regulation involving the post-translational modification and degradation. The ubiquitination and/or degradation of several transcription factors in the iron deficiency signaling pathways and metal transporters recently came to light. In this review we discuss about the mechanisms and on the possible roles of protein modification and turn over in the regulation of root iron deficiency responses. We also highlight the tight coupling between metal sensing by E3 ubiquitin ligases or bifunctional transporters and protein degradation.

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The Plant Cell - Endocytosis of BRASSINOSTEROID INSENSITIVE1 is Partly Driven by a Canonical Tyrosine-based Motif

The Plant Cell - Endocytosis of BRASSINOSTEROID INSENSITIVE1 is Partly Driven by a Canonical Tyrosine-based Motif | LRSV Publications | Scoop.it

Clathrin-mediated endocytosis (CME) and its core endocytic machinery are evolutionarily conserved across all eukaryotes. In mammals, the heterotetrameric adaptor protein complex-2 (AP-2) sorts plasma membrane (PM) cargoes into vesicles through the recognition of motifs based on tyrosine or di-leucine in their cytoplasmic tails. However, in plants, very little is known on how PM proteins are sorted for CME and whether similar motifs are required. In Arabidopsis thaliana, the brassinosteroid (BR) receptor, BR INSENSITIVE1 (BRI1), undergoes endocytosis that depends on clathrin and AP-2. Here we demonstrate that BRI1 binds directly to the medium AP-2 subunit, AP2M. The cytoplasmic domain of BRI1 contains five putative canonical surface-exposed tyrosine-based endocytic motifs. The tyrosine-to-phenylalanine substitution in Y898KAI reduced BRI1 internalization without affecting its kinase activity. Consistently, plants carrying the BRI1Y898F mutation were hypersensitive to BRs. Our study demonstrates that AP-2-dependent internalization of PM proteins via the recognition of functional tyrosine motifs also operates in plants.

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Science - Lipid exchanges drove the evolution of mutualism during plant terrestrialization

Science - Lipid exchanges drove the evolution of mutualism during plant terrestrialization | LRSV Publications | Scoop.it

Symbiosis with arbuscular mycorrhizal fungi (AMF) improves plant nutrition in most land plants, and its contribution to the colonization of land by plants has been hypothesized. Here, we identify a conserved transcriptomic response to AMF among land plants, including the activation of lipid metabolism. Using gain of function, we show the transfer of lipids from the liverwort Marchantia paleacea to AMF and its direct regulation by the transcription factor WRINKLED (WRI). Arbuscules, the nutrient-exchange structures, were not formed in loss-of-function wri mutants in M. paleacea, leading to aborted mutualism. Our results show the orthology of the symbiotic transfer of lipids across land plants and demonstrate that mutualism with arbuscular mycorrhizal fungi was present in the most recent ancestor of land plants 450 million years ago.

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Genome Biology - Drosophila primary microRNA-8 encodes a microRNA-encoded peptide acting in parallel of miR-8 

Genome Biology - Drosophila primary microRNA-8 encodes a microRNA-encoded peptide acting in parallel of miR-8  | LRSV Publications | Scoop.it

Background Recent genome-wide studies of many species reveal the existence of a myriad of RNAs differing in size, coding potential and function. Among these are the long non-coding RNAs, some of them producing functional small peptides via the translation of short ORFs. It now appears that any kind of RNA presumably has a potential to encode small peptides. Accordingly, our team recently discovered that plant primary transcripts of microRNAs (pri-miRs) produce small regulatory peptides (miPEPs) involved in auto-regulatory feedback loops enhancing their cognate microRNA expression which in turn controls plant development. Here we investigate whether this regulatory feedback loop is present in Drosophila melanogaster. Results We perform a survey of ribosome profiling data and reveal that many pri-miRNAs exhibit ribosome translation marks. Focusing on miR-8, we show that pri-miR-8 can produce a miPEP-8. Functional assays performed in Drosophila reveal that miPEP-8 affects development when overexpressed or knocked down. Combining genetic and molecular approaches as well as genome-wide transcriptomic analyses, we show that miR-8 expression is independent of miPEP-8 activity and that miPEP-8 acts in parallel to miR-8 to regulate the expression of hundreds of genes. Conclusion Taken together, these results reveal that several Drosophila pri-miRs exhibit translation potential. Contrasting with the mechanism described in plants, these data shed light on the function of yet undescribed primary-microRNA-encoded peptides in Drosophila and their regulatory potential on genome expression.

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Plant Cell Physiol - Regulation of Root Nutrient Transporters by CIPK23: ‘One Kinase to Rule Them All’ 

Protein kinases constitute essential regulatory components in the majority of cellular processes in eukaryotic cells. The CBL-INTERACTING PROTEIN KINASE (CIPK) family of plant protein kinases functions in calcium (Ca2+)-related signaling pathways and is therefore involved in the response to a wide variety of signals in plants. By covalently linking phosphate groups to their target proteins, CIPKs regulate the activity of downstream targets, their localization, their stability and their ability to interact with other proteins. In Arabidopsis, the CIPK23 kinase has emerged as a major hub driving root responses to diverse environmental stresses, including drought, salinity and nutrient imbalances, such as potassium, nitrate and iron deficiencies, as well as ammonium, magnesium and non-iron metal toxicities. This review will chiefly report on the prominent roles of CIPK23 in the regulation of plant nutrient transporters and on the underlying molecular mechanisms. We will also discuss the different scenarios explaining how a single promiscuous kinase, such as CIPK23, may convey specific responses to a myriad of signals.

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ISME J - Regulation of mating genes during arbuscular mycorrhizal isolate co-existence—where is the evidence?

A recent study published by Mateus et al. [1] claimed that 18 “mating-related” genes are differentially expressed in the model arbuscular mycorrhizal fungus (AMF) Rhizophagus irregularis when genetically distinct fungal strains co-colonize a host plant. To clarify the level of evidence for this interesting conclusion, we first aimed to validate the functional annotation of these 18 Rirregularis genes using orthology predictions. These analyses revealed that, although sequence relationship exists, only 2 of the claimed 18 R. irregularis mating genes are potential orthologues to validated fungal mating genes. We also investigated the RNA-seq data from Mateus et al. [1] using classical RNA-seq methods and statistics. This analysis found that the over-expression during strain co-existence was not significant at the typical cut-off of the R. irregularis strains DAOM197198 and B1 in plants. Overall, we do not find convincing evidence that the genes involved have functions in mating, or that they are reproducibly up or down regulated during co-existence in plants.

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New Phytologist - Taxonomic, phylogenetic, and functional diversity of root‐associated fungi in bromeliads: effects of host identity, life forms, and nutritional modes

New Phytologist - Taxonomic, phylogenetic, and functional diversity of root‐associated fungi in bromeliads: effects of host identity, life forms, and nutritional modes | LRSV Publications | Scoop.it

Bromeliads represent a major component of neotropical forests and encompass a considerable diversity of life forms and nutritional modes. Bromeliads explore highly stressful habitats and root‐associated fungi may play a crucial role but their driving factors and variations in root‐associated fungi remain largely unknown.

We explored root‐associated fungal communities in 17 bromeliad species and their variations linked to host identity, life forms, and nutritional modes by using ITS1 gene‐based high‐throughput sequencing and by characterising fungal functional guilds.

We found a dual association of mycorrhizal and non‐mycorrhizal fungi. The different species, life forms, and nutritional modes among bromeliad hosts had fungal communities that differ in their taxonomical and functional composition. Specifically, roots of epiphytic bromeliads had more endophytic fungi and dark septate endophytes and fewer mycorrhizal fungi than terrestrials and lithophytes.

Our results contribute to a fundamental knowledge base on different fungal groups in previously undescribed Bromeliaceae. The diverse root‐associated fungal communities in bromeliads may enhance plant fitness in both stressful and nutrient‐poor environments and may give more flexibility to the plants to adapt to changing environmental conditions.

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Current Biology - The genome of Geosiphon pyriformis reveals ancestral traits linked to the emergence of the arbuscular mycorrhizal symbiosis

Arbuscular mycorrhizal fungi (AMF) (subphylum Glomeromycotina) are among the most prominent symbionts and form the Arbuscular Mycorrhizal symbiosis (AMS) with over 70% of known land plants. AMS allows plants to efficiently acquire poorly soluble soil nutrients and AMF to receive photosynthetically fixed carbohydrates. This plant-fungus symbiosis dates back more than 400 million years and is thought to be one of the key innovations that allowed the colonization of lands by plants. Genomic and genetic analyses of diverse plant species started to reveal the molecular mechanisms that allowed the evolution of this symbiosis on the host side, but how and when AMS abilities emerged in AMF remain elusive. Comparative phylogenomics could be used to understand the evolution of AMS. However, the availability of genome data covering basal AMF phylogenetic nodes (Archaeosporales, Paraglomerales) is presently based on fragmentary protein coding datasets.  Geosiphon pyriformis (Archaeosporales) is the only fungus known to produce endosymbiosis with nitrogen-fixing cyanobacteria (Nostoc punctiforme) presumably representing the ancestral AMF state. Unlike other AMF, it forms long fungal cells (“bladders”) that enclose cyanobacteria. Once in the bladder, the cyanobacteria are photosynthetically active and fix nitrogen, receiving inorganic nutrients and water from the fungus. Arguably, G. pyriformis represents an ideal candidate to investigate the origin of AMS and the emergence of a unique endosymbiosis. Here, we aimed to advance knowledge in these questions by sequencing the genome of G. pyriformis, using a re-discovered isolate.

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Nature Communications - Genetics of nodulation in Aeschynomene evenia uncovers mechanisms of the rhizobium–legume symbiosis

Nature Communications - Genetics of nodulation in Aeschynomene evenia uncovers mechanisms of the rhizobium–legume symbiosis | LRSV Publications | Scoop.it
Among legumes (Fabaceae) capable of nitrogen-fixing nodulation, several Aeschynomene spp. use a unique symbiotic process that is independent of Nod factors and infection threads. They are also distinctive in developing root and stem nodules with photosynthetic bradyrhizobia. Despite the significance of these symbiotic features, their understanding remains limited. To overcome such limitations, we conduct genetic studies of nodulation in Aeschynomene evenia, supported by the development of a genome sequence for A. evenia and transcriptomic resources for 10 additional Aeschynomene spp. Comparative analysis of symbiotic genes substantiates singular mechanisms in the early and late nodulation steps. A forward genetic screen also shows that AeCRK, coding a receptor-like kinase, and the symbiotic signaling genes AePOLLUX, AeCCamK, AeCYCLOPS, AeNSP2, and AeNIN are required to trigger both root and stem nodulation. This work demonstrates the utility of the A. evenia model and provides a cornerstone to unravel mechanisms underlying the rhizobium–legume symbiosis. The establishment of symbiotic interaction between Aeschynomene evenia and photosynthetic bradyrhizobia doesn’t involve the canonical Nod factors and infection threads. Here, the authors assemble the draft genome of A. evenia and identify a receptor-like kinase in mediating the symbiotic interaction.
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Curr Opin Chem Biol - Recent advances in mass spectrometry–based peptidomics workflows to identify short-open-reading-frame-encoded peptides and explore their functions

Curr Opin Chem Biol - Recent advances in mass spectrometry–based peptidomics workflows to identify short-open-reading-frame-encoded peptides and explore their functions | LRSV Publications | Scoop.it

Short open reading frame (sORF)–encoded polypeptides (SEPs) have recently emerged as key regulators of major cellular processes. Computational methods for the annotation of sORFs combined with transcriptomics and ribosome profiling approaches predicted the existence of tens of thousands of SEPs across the kingdom of life. Although, we still lack unambiguous evidence for most of them. The method of choice to validate the expression of SEPs is mass spectrometry (MS)-based peptidomics. Peptides are less abundant than proteins, which tends to hinder their detection. Therefore, optimization and enrichment methods are necessary to validate the existence of SEPs. In this article, we discuss the challenges for the detection of SEPs by MS and recent developments of biochemical approaches applied to the study of these peptides. We detail the advances made in the different key steps of a typical peptidomics workflow and highlight possible alternatives that have not been explored yet.

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Plant Physiology and Biochemistry: Recombinant N-glycosylation isoforms of Legume lectins: Production and purification from Nicotiana benthamiana leaves following RuBisCO depletion

Plant Physiology and Biochemistry: Recombinant N-glycosylation isoforms of Legume lectins: Production and purification from Nicotiana benthamiana leaves following RuBisCO depletion | LRSV Publications | Scoop.it

An efficient purification of recombinant proteins often requires a high ratio of recombinant to host proteins. In plants, Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the most abundant leaf protein, thus strongly impacting purification yield. Here, we describe a simple and robust purification procedure for recombinant proteins based on a differential precipitation of RuBisCO. In this context, four Legume lectin domains of Arabidopsis thaliana which belong to receptor-like kinases and cell wall proteins were produced from Nicotiana benthamiana leaves. The recombinant proteins exhibit a unique lectin domain consisting of around 250 amino acid residues with several predicted N-glycosylation sites and a six His-tag at the N-terminus. After ammonium sulphate precipitation of total soluble proteins, depletion of RuBisCO was obtained using citrate and succinate buffers during the salting-in step: this depletion was pH-dependent and the presence of di- or tri-carboxylic acids was required. The depleted protein extracts were then subjected to two chromatographic steps which were used in the negative mode to submit a protein fraction enriched as much as possible in recombinant lectin domains to a third chromatographic step (immobilized metal-ion chromatography). Three of the Legume lectin domains were purified near to homogeneity and revealed multiple N-glycosylation isoforms, particularly those from receptor-like kinases, which were characterised using specific lectins and deglycosylation enzymes. The production and purification of recombinant lectin domains will facilitate their biochemical characterisation in the context of cell-to-cell signalling and cell wall organisation.

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Nature Communications - Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

Nature Communications - Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits | LRSV Publications | Scoop.it

Mycorrhizal fungi are mutualists that play crucial roles in nutrient acquisition in terrestrial ecosystems. Mycorrhizal symbioses arose repeatedly across multiple lineages of Mucoromycotina, Ascomycota, and Basidiomycota. Considerable variation exists in the capacity of mycorrhizal fungi to acquire carbon from soil organic matter. Here, we present a combined analysis of 135 fungal genomes from 73 saprotrophic, endophytic and pathogenic species, and 62 mycorrhizal species, including 29 new mycorrhizal genomes. This study samples ecologically dominant fungal guilds for which there were previously no symbiotic genomes available, including ectomycorrhizal Russulales, Thelephorales and Cantharellales. Our analyses show that transitions from saprotrophy to symbiosis involve (1) widespread losses of degrading enzymes acting on lignin and cellulose, (2) co-option of genes present in saprotrophic ancestors to fulfill new symbiotic functions, (3) diversification of novel, lineage-specific symbiosis-induced genes, (4) proliferation of transposable elements and (5) divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild. Mycorrhizal symbioses have evolved repeatedly in diverse fungal lineages. A large phylogenomic analysis sheds light on genomic changes associated with transitions from saprotrophy to symbiosis, including divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.

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Cells - An integrative Study Showing the Adaptation to Sub-Optimal Growth Conditions of Natural Populations of Arabidopsis thaliana: A Focus on Cell Wall Changes

Cells - An integrative Study Showing the Adaptation to Sub-Optimal Growth Conditions of Natural Populations of Arabidopsis thaliana: A Focus on Cell Wall Changes | LRSV Publications | Scoop.it

In the global warming context, plant adaptation occurs, but the underlying molecular mechanisms are poorly described. Studying natural variation of the model plant Arabidopsisthaliana adapted to various environments along an altitudinal gradient should contribute to the identification of new traits related to adaptation to contrasted growth conditions. The study was focused on the cell wall (CW) which plays major roles in the response to environmental changes. Rosettes and floral stems of four newly-described populations collected at different altitudinal levels in the Pyrenees Mountains were studied in laboratory conditions at two growth temperatures (22 vs. 15 °C) and compared to the well-described Col ecotype. Multi-omic analyses combining phenomics, metabolomics, CW proteomics, and transcriptomics were carried out to perform an integrative study to understand the mechanisms of plant adaptation to contrasted growth temperature. Different developmental responses of rosettes and floral stems were observed, especially at the CW level. In addition, specific population responses are shown in relation with their environment and their genetics. Candidate genes or proteins playing roles in the CW dynamics were identified and will deserve functional validation. Using a powerful framework of data integration has led to conclusions that could not have been reached using standard statistical approaches.

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IJMS - The Class III Peroxidase Encoding Gene AtPrx62 Positively and Spatiotemporally Regulates the Low pH-Induced Cell Death in Arabidopsis thaliana Roots

IJMS - The Class III Peroxidase Encoding Gene AtPrx62 Positively and Spatiotemporally Regulates the Low pH-Induced Cell Death in Arabidopsis thaliana Roots | LRSV Publications | Scoop.it

Exogenous low pH stress causes cell death in root cells, limiting root development, and agricultural production. Different lines of evidence suggested a relationship with cell wall (CW) remodeling players. We investigated whether class III peroxidase (CIII Prx) total activity, CIII Prx candidate gene expression, and reactive oxygen species (ROS) could modify CW structure during low pH-induced cell death in Arabidopsis thaliana roots. Wild-type roots displayed a good spatio-temporal correlation between the low pH-induced cell death and total CIII Prx activity in the early elongation (EZs), transition (TZs), and meristematic (MZs) zones. In situ mRNA hybridization showed that AtPrx62 transcripts accumulated only in roots treated at pH 4.6 in the same zones where cell death was induced. Furthermore, roots of the atprx62-1 knockout mutant showed decreased cell mortality under low pH compared to wild-type roots. Among the ROS, there was a drastic decrease in O2·- levels in the MZs of wild-type and atprx62-1 roots upon low pH stress. Together, our data demonstrate that AtPrx62 expression is induced by low pH and that the produced protein could positively regulate cell death. Whether the decrease in O2·- level is related to cell death induced upon low pH treatment remains to be elucidated.

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