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Analytical Chemistry - MS-CleanR: A feature-filtering workflow for untargeted LC-MS based metabolomics 

Analytical Chemistry - MS-CleanR: A feature-filtering workflow for untargeted LC-MS based metabolomics  | LRSV Publications | Scoop.it
Untargeted metabolomics using liquid chromatography-mass spectrometry (LC-MS) is currently the gold-standard technique to determine the full chemical diversity in biological samples. However, this approach still has many limitations; notably, the difficulty of accurately estimating the number of unique metabolites profiled among the thousands of MS ion signals arising from chromatograms. Here, we describe a new workflow, MS-CleanR, based on the MS-DIAL/MS-FINDER suite, which tackles feature degeneracy and improves annotation rates. We show that implementation of MS-CleanR reduces the number of signals by nearly 80% while retaining 95% of unique metabolite features. Moreover, the annotation results from MS-FINDER can be ranked according to the database chosen by the user, which enhance identification accuracy. Application of MS-CleanR to the analysis of Arabidopsis thaliana grown in three different conditions fostered class separation resulting from multivariate data analysis and led to annotation of 75% of the final features. The full workflow was applied to metabolomic profiles from three strains of the leguminous plant Medicago truncatula that have different susceptibilities to the oomycete pathogen Aphanomyces euteiches. A group of glycosylated triterpenoids overrepresented in resistant lines were identified as candidate compounds conferring pathogen resistance. MS-CleanR is implemented through a Shiny interface for intuitive use by end-users (available at: https://github.com/eMetaboHUB/MS-CleanR).
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IJMS - Wood Architecture and Composition Are Deeply Remodeled in Frost Sensitive Eucalyptus Overexpressing CBF/DREB1 Transcription Factors

IJMS - Wood Architecture and Composition Are Deeply Remodeled in Frost Sensitive Eucalyptus Overexpressing CBF/DREB1 Transcription Factors | LRSV Publications | Scoop.it
Eucalypts are the most planted trees worldwide, but most of them are frost sensitive. Overexpressing transcription factors for CRT-repeat binding factors (CBFs) in transgenic Eucalyptus confer cold resistance both in leaves and stems. While wood plays crucial roles in trees and is affected by environmental cues, its potential role in adaptation to cold stress has been neglected. Here, we addressed this question by investigating the changes occurring in wood in response to the overexpression of two CBFs, taking advantage of available transgenic Eucalyptus lines. We performed histological, biochemical, and transcriptomic analyses on xylem samples. CBF ectopic expression led to a reduction of both primary and secondary growth, and triggered changes in xylem architecture with smaller and more frequent vessels and fibers exhibiting reduced lumens. In addition, lignin content and syringyl/guaiacyl (S/G) ratio increased. Consistently, many genes of the phenylpropanoid and lignin branch pathway were upregulated. Most of the features of xylem remodeling induced by CBF overexpression are reminiscent of those observed after long exposure of Eucalyptus trees to chilling temperatures. Altogether, these results suggest that CBF plays a central role in the cross-talk between response to cold and wood formation and that the remodeling of wood is part of the adaptive strategies to face cold stress.
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Plant Cell Environment - Seed mucilage evolution: diverse molecular mechanisms generate versatile ecological functions for particular environments

Plant Cell Environment - Seed mucilage evolution: diverse molecular mechanisms generate versatile ecological functions for particular environments | LRSV Publications | Scoop.it

Plant myxodiasporous species have the ability to release a polysaccharidic mucilage upon imbibition of the seed (myxospermy) or the fruit (myxocarpy). This is a widespread capacity in angiosperms providing multiple ecological functions including higher germination efficiency under environmental stresses. It is unclear whether myxodiaspory has one or multiple evolutionary origins and why it was supposedly lost in several species. Here, we summarize recent advances on three main aspects of myxodiaspory. (i) It represents a combination of highly diverse traits at different levels of observation, ranging from the dual tissular origin of mucilage secretory cells to diverse mucilage polysaccharidic composition and ultrastructural organization. (ii) An asymmetrical selection pressure is exerted on myxospermy‐related genes that was first identified in Arabidopsis thaliana . The A. thaliana and the flax intra‐species mucilage variants show that myxospermy is a fast‐evolving trait due to high polymorphism in a few genes directly acting on mucilage establishment. In A. thaliana , these actors are downstream of a master regulatory complex and an original phylogenetic overview provided here illustrates that this complex has sequentially evolved after the common ancestor of seed plants and was fully established in the common ancestor of the rosid clade. (iii) Newly identified myxodiaspory ecological functions indicate new perspectives such as soil micro‐organism control and plant establishment support.

The ability to secrete mucilage around seeds is widespread among angiosperms. This feature is highly diverse and provides numerous ecological roles. In natural variability, the involved genes show a conservation for master regulators but also a great variability for few direct actors.

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Mycorrhiza - Initiation of arbuscular mycorrhizal symbiosis involves a novel pathway independent from hyphal branching

Mycorrhiza - Initiation of arbuscular mycorrhizal symbiosis involves a novel pathway independent from hyphal branching | LRSV Publications | Scoop.it

The arbuscular mycorrhizal symbiosis is a very common association between plant roots and soil fungi, which greatly contributes to plant nutrition. Root-exuded compounds known as strigolactones act as symbiotic signals stimulating the fungus prior to root colonization. Strigolactones also play an endogenous role in planta as phytohormones and contribute to the regulation of various developmental traits. Structure-activity relationship studies have revealed both similarities and differences between the structural features required for bioactivity in plants and arbuscular mycorrhizal fungi. In the latter case, bioassays usually measured a stimulation of hyphal branching on isolated fungi of the Gigaspora genus, grown in vitro. Here, we extended these investigations with a bioassay that evaluates the bioactivity of strigolactone analogs in a symbiotic situation and the use of the model mycorrhizal fungus Rhizophagus irregularis. Some general structural requirements for bioactivity reported previously for Gigaspora were confirmed. We also tested additional strigolactone analogs bearing modifications on the conserved methylbutenolide ring, a key element of strigolactone perception by plants. A strigolactone analog with an unmethylated butenolide ring could enhance the ability of R. irregularis to colonize host roots. Surprisingly, when applied to the isolated fungus in vitro, this compound stimulated germ tube elongation but inhibited hyphal branching. Therefore, this compound was able to act on the fungal and/or plant partner to facilitate initiation of the arbuscular mycorrhizal symbiosis, independently from hyphal branching and possibly from the strigolactone pathway.

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Development - VAPYRIN-like is required for development of the moss Physcomitrella patens

Development - VAPYRIN-like is required for development of the moss Physcomitrella patens | LRSV Publications | Scoop.it

The VAPYRIN (VPY) gene in Medicago truncatula and Petunia hybrida is required for arbuscular mycorrhizal (AM) symbiosis. The moss Physcomitrella patens has a close homologue (VPY-likeVPYL), although it does not form AM. Here, we explore the phylogeny of VPY and VPYL in land plants, and we study the expression and developmental function of VPYL in P. patens. We show that PpVPYL is expressed primarily in the protonema, the early filamentous stage of moss development, and later in rhizoids arising from the leafy gametophores and in adult phyllids. Knockout mutants have specific phenotypes in branching of the protonema and in cell division of the leaves (phyllids) in gametophores. The mutants are responsive to auxin and strigolactone, which are involved in the regulation of protonemal branching, indicating that the mutants are not affected in hormonal signaling. Taken together, these results suggest that PpVPYL exerts negative regulation of protonemal branching and of cell division in phyllids. We discuss VPY and VPYL phylogeny and function in land plants in the context of AM symbiosis in angiosperms, and of development in the moss.

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Plant Basel - Cellular and Subcellular Compartmentation of the 2C-Methyl-D-Erythritol 4-Phosphate Pathway in the Madagascar Periwinkle

Plant Basel - Cellular and Subcellular Compartmentation of the 2C-Methyl-D-Erythritol 4-Phosphate Pathway in the Madagascar Periwinkle | LRSV Publications | Scoop.it
The Madagascar periwinkle (Catharanthus roseus) synthesizes the highly valuable monoterpene indole alkaloids (MIAs) through a long metabolic route initiated by the 2C-methyl-D-erythritol 4-phosphate (MEP) pathway. In leaves, a complex compartmentation of the MIA biosynthetic pathway occurs at both the cellular and subcellular levels, notably for some gene products of the MEP pathway. To get a complete overview of the pathway organization, we cloned four genes encoding missing enzymes involved in the MEP pathway before conducting a systematic analysis of transcript distribution and protein subcellular localization. RNA in situ hybridization revealed that all MEP pathway genes were coordinately and mainly expressed in internal phloem-associated parenchyma of young leaves, reinforcing the role of this tissue in MIA biosynthesis. At the subcellular level, transient cell transformation and expression of fluorescent protein fusions showed that all MEP pathway enzymes were targeted to plastids. Surprisingly, two isoforms of 1-deoxy-D-xylulose 5-phosphate synthase and 1-deoxy-D-xylulose 5-phosphate reductoisomerase initially exhibited an artifactual aggregated pattern of localization due to high protein accumulation. Immunogold combined with transmission electron microscopy, transient transformations performed with a low amount of transforming DNA and fusion/deletion experiments established that both enzymes were rather diffuse in stroma and stromules of plastids as also observed for the last six enzymes of the pathway. Taken together, these results provide new insights into a potential role of stromules in enhancing MIA precursor exchange with other cell compartments to favor metabolic fluxes towards the MIA biosynthesis.
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IJMS - Internalization of miPEP165a into Arabidopsis Roots Depends on both Passive Diffusion and Endocytosis-Associated Processes

IJMS - Internalization of miPEP165a into Arabidopsis Roots Depends on both Passive Diffusion and Endocytosis-Associated Processes | LRSV Publications | Scoop.it
MiPEPs are short natural peptides encoded by microRNAs in plants. Exogenous application of miPEPs increases the expression of their corresponding miRNA and, consequently, induces consistent phenotypical changes. Therefore, miPEPs carry huge potential in agronomy as gene regulators that do not require genome manipulation. However, to this end, it is necessary to know their mode of action, including where they act and how they enter the plants. Here, after analyzing the effect of Arabidopsis thaliana miPEP165a on root and aerial part development, we followed the internalization of fluorescent-labelled miPEP165a into roots and compared its uptake into endocytosis-altered mutants to that observed in wild-type plants treated or not with endocytosis inhibitors. The results show that entry of miPEP165a involves both a passive diffusion at the root apex and endocytosis-associated internalization in the differentiation and mature zones. Moreover, miPEP165a is unable to enter the central cylinder and does not migrate from the roots to the aerial part of the plant, suggesting that miPEPs have no systemic effect.
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J Exp Bot - Global analysis of non-animal peroxidases provides insights into the evolution of this gene family in the green lineage

The non-animal peroxidases belong to a superfamily of oxidoreductases that reduce the hydrogen peroxide and oxidize numerous substrates. Since their initial characterization in 1992, several advances have provided an understanding into the origin and evolution of this protein family. Here, we report the most comprehensive evolutionary analysis of non-animal peroxidases using integrated in silico and biochemical approaches. Thanks to the availability of numerous genomic sequences from more than 2500 species belonging to 14 kingdoms together with expert and comprehensive annotation of peroxidase sequences centralized in a dedicated database, we have deepened our understanding of the evolutionary process underlying non-animal peroxidases diversification through phylogenetic reconstructions. We analysed the distribution of all non-animal peroxidases in more than 200 eukaryotic organisms in silico. First, we show that the presence or absence of non-animal peroxidases correlate with the presence or absence of certain organelles or with specific biological processes. Scrutinizing in near 2000 organisms, we confirmed that ascorbate peroxidases (APx) and cytochromes c peroxidases (CcP) were detected respectively in chloroplast and mitochondria containing organisms. Plants, which contain both organelles, are an exception and contain only APxs without CcP. Class II peroxidases (CII Prx) only found in fungi with wood decay abilities and plant degradation and Class III peroxidases (CIII Prx) only detected in both streptophyte algae and land plants, have been subjected to large family expansion in the latter group. Moreover, we demonstrate that biochemical activities (APx, CcP and CIII Prx) assayed with protein extracts from 30 different eukaryotic organisms support the distribution of the sequences resulting from our in silico analysis. The biochemical results confirmed both the presence and classification of non-animal peroxidase encoding sequences.

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Journal of Plant Growth Regulation - Ethylene Signaling Causing Tolerance of Arabidopsis thaliana Roots to Low pH Stress is Linked to Class III Peroxidase Activity

Journal of Plant Growth Regulation - Ethylene Signaling Causing Tolerance of Arabidopsis thaliana Roots to Low pH Stress is Linked to Class III Peroxidase Activity | LRSV Publications | Scoop.it

One irreversible consequence of acidic pH for roots is cell death. Growing evidence suggests the role of hormones and cell wall-related enzymes in response to acidic pH that could possibly avoid cell mortality. Here, we have investigated the role of ethylene and class III peroxidases (CIII Prxs) activity on sensitivity to further low pH treatment. Seedlings of Arabidopsis thaliana were pretreated with ethylene, at various concentrations for various times, and then exposed to low pH. In contrast to non-treated roots, roots pretreated with ethylene for 3 h became tolerant to subsequent low pH, with negligible cell mortality in meristematic (MZ), transition (TZ), and early elongation (EZ) zones. This effect of ethylene was time dependent since it was achieved only when seedlings were pre-incubated with ethylene for at least 3 h. This tolerance induced by ethylene was not observed in the gain-of-function mutation etr1-1 (insensitive to ethylene 1–1). Besides, it was prevented by salicylhydroxamic acid (SHAM) which is an inhibitor of CIII Prxs activity. In late EZ, the decrease in cell expansion due to low pH was dependent on both ethylene signaling and a SHAM-sensitive process. The responses mediated by ethylene signaling might involve CIII Prxs-dependent cell wall modifications, leading to tolerance to low pH and arrest in cell expansion during stress.

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Nature Plants - An ancestral signalling pathway is conserved in intracellular symbioses-forming plant lineages

Nature Plants - An ancestral signalling pathway is conserved in intracellular symbioses-forming plant lineages | LRSV Publications | Scoop.it
Plants are the foundation of terrestrial ecosystems, and their colonization of land was probably facilitated by mutualistic associations with arbuscular mycorrhizal fungi. Following this founding event, plant diversification has led to the emergence of a tremendous diversity of mutualistic symbioses with microorganisms, ranging from extracellular associations to the most intimate intracellular associations, where fungal or bacterial symbionts are hosted inside plant cells. Here, through analysis of 271 transcriptomes and 116 plant genomes spanning the entire land-plant diversity, we demonstrate that a common symbiosis signalling pathway co-evolved with intracellular endosymbioses, from the ancestral arbuscular mycorrhiza to the more recent ericoid and orchid mycorrhizae in angiosperms and ericoid-like associations of bryophytes. By contrast, species forming exclusively extracellular symbioses, such as ectomycorrhizae, and those forming associations with cyanobacteria, have lost this signalling pathway. This work unifies intracellular symbioses, revealing conservation in their evolution across 450 million yr of plant diversification. An extensive phylogenomics study based on hundreds of genomes and transcriptomes provides a new interpretation of the evolution of different types of symbiotic associations in land plants, and reveals a conserved ancestral symbiosis pathway.
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MPMI - Arabidopsis Response Regulator 6 (ARR6) modulates plant cell wall composition and disease resistance

The cytokinin signaling pathway, which is mediated by Arabidopsis Response Regulators (ARRs) proteins, has been involved in the modulation of some disease resistance responses. Here, we describe novel functions of ARR6 in the control of plant disease resistance and cell wall composition. Plants impaired in ARR6 function (arr6) were more resistant and susceptible, respectively, to the necrotrophic fungus Plectosphaerella cucumerina and to the vascular bacterium Ralstonia solanacearum, whereas Arabidopsis plants that overexpress ARR6 showed the opposite phenotypes, which further support a role of ARR6 in the modulation of disease resistance responses against these pathogens. Transcriptomics and metabolomics analyses revealed that, in arr6 plants, canonical disease resistance pathways, like those activated by defensive phytohormones, were not altered, whereas immune responses triggered by Microbe-Associated Molecular Patterns were slightly enhanced. Cell wall composition of arr6 plants was found to be severely altered compared to that of wild-type plants. Remarkably, pectin-enriched cell wall fractions extracted from arr6 walls triggered more intense immune responses than those activated by similar wall fractions from wild-type plants, suggesting that arr6 pectin fraction is enriched in wall-related Damage-Associated Molecular Patterns, which trigger immune responses. This work supports a novel function of ARR6 in the control of cell-wall composition and disease resistance and reinforces the role of the plant cell wall in the modulation of specific immune responses.

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New Phytologist - Host‐specific competitiveness to form nodules in Rhizobium leguminosarum symbiovar viciae

New Phytologist - Host‐specific competitiveness to form nodules in Rhizobium leguminosarum symbiovar viciae | LRSV Publications | Scoop.it

Fabeae legumes such as pea and fababean form symbiotic nodules with a large diversity of soil Rhizobium leguminosarum symbiovar viciae (Rlv) bacteria. However, bacteria Competitive to Form root Nodules (CFN) are generally not the most efficient to fix dinitrogen, resulting in a decrease of legume crop yields. Here, we investigate differential selection by host plants on the diversity of Rlv.

A large collection of Rlv was collected by nodule trapping with pea and fababean from soils at five European sites. Representative genomes were sequenced. In parallel, diversity and abundance of Rlv were estimated directly in these soils using metabarcoding. The CFN of isolates was measured with both legume hosts. Pea/fababean CFN were associated to Rlv genomic regions.

Variations of bacterial pea and/or fababean CFN explained the differential abundance of Rlv genotypes in pea and fababean nodules. No evidence was found for genetic association between CFN and variations in the core genome, but variations in specific regions of the nod locus, as well as in other plasmid loci, were associated with differences in CFN.

These findings shed light on the genetic control of CFN in Rlv and emphasize the importance of host plants in controlling rhizobium diversity.

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G3: Genes Genomes Genetics - Long-Read Genome Sequence of the Sugar Beet Rhizosphere Mycoparasite Pythium oligandrum 

G3: Genes Genomes Genetics - Long-Read Genome Sequence of the Sugar Beet Rhizosphere Mycoparasite Pythium oligandrum  | LRSV Publications | Scoop.it

Pythium oligandrum is a soil born free living oomycete able to parasitize fungi and oomycetes prey, including important plant and animals pathogens. Pythium oligandrum can colonize endophytically the root tissues of diverse plants where it induces plant defencesHere we report the first long-read genome sequencing of a P. oligandrum strain sequenced by PacBio technology. Sequencing of genomic DNA loaded onto six SMRT cells permitted the acquisition of 913,728 total reads resulting in 112X genome coverage. The assembly and polishing of the genome sequence yielded180 contigs (N50 = 1.3 Mb; L50 = 12). The size of the genome assembly is 41.9 Mb with a longest contig of 2.7 Mb and 15,007 predicted protein-coding genes among which 95.25 % were supported by RNAseq data, thus constituting a new Pythium genome reference. This data will facilitate genomic comparisons of Pythium species that are commensal, beneficial or pathogenic on plant, or parasitic on fungi and oomycete to identify key genetic determinants underpinning their diverse lifestyles. In addition comparison with plant pathogenic or zoopathogenic species will illuminate genomic adaptations for pathogenesis toward widely diverse hosts.

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IJMS - Implementing the CRISPR/Cas9 Technology in Eucalyptus Hairy Roots Using Wood-Related Genes

IJMS - Implementing the CRISPR/Cas9 Technology in Eucalyptus Hairy Roots Using Wood-Related Genes | LRSV Publications | Scoop.it
Eucalypts are the most planted hardwoods worldwide. The availability of the Eucalyptus grandis genome highlighted many genes awaiting functional characterization, lagging behind because of the lack of efficient genetic transformation protocols. In order to efficiently generate knock-out mutants to study the function of eucalypts genes, we implemented the powerful CRISPR/Cas9 gene editing technology with the hairy roots transformation system. As proofs-of-concept, we targeted two wood-related genes: Cinnamoyl-CoA Reductase1 (CCR1), a key lignin biosynthetic gene and IAA9A an auxin dependent transcription factor of Aux/IAA family. Almost all transgenic hairy roots were edited but the allele-editing rates and spectra varied greatly depending on the gene targeted. Most edition events generated truncated proteins, the prevalent edition types were small deletions but large deletions were also quite frequent. By using a combination of FT-IR spectroscopy and multivariate analysis (partial least square analysis (PLS-DA)), we showed that the CCR1-edited lines, which were clearly separated from the controls. The most discriminant wave-numbers were attributed to lignin. Histochemical analyses further confirmed the decreased lignification and the presence of collapsed vessels in CCR1-edited lines, which are characteristics of CCR1 deficiency. Although the efficiency of editing could be improved, the method described here is already a powerful tool to functionally characterize eucalypts genes for both basic research and industry purposes.
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Plant Science - Coordination of five class III peroxidase-encoding genes for early germination events of Arabidopsis thaliana

Plant Science - Coordination of five class III peroxidase-encoding genes for early germination events of Arabidopsis thaliana | LRSV Publications | Scoop.it

The Class III peroxidases (CIII Prxs) belong to a plant-specific multigene family. Thanks to their double catalytic cycle they can oxidize compounds or release reactive oxygen species (ROS). They are either involved in different cell wall stiffening processes such as lignification and suberization, in cell wall loosening or defense mechanisms. Germination is an important developmental stage requiring specific peroxidase activity. However, little is known about which isoforms are involved. Five CIII Prx encoding genes: AtPrx04AtPrx16AtPrx62AtPrx69, and AtPrx71 were identified from published microarray data mining. Delayed or induced testa and endosperm rupture were observed for the corresponding CIII Prx mutant lines indicating either a gene-specific inducing or repressing role during germination, respectively. Via in situ hybridization AtPrx16AtPrx62AtPrx69 and AtPrx71 transcripts were exclusively localized to the micropylar endosperm facing the radicle, and transcriptomic data analysis enabled positioning the five CIII Prxs in a co-expression network enriched in germination, cell wall, cell wall proteins and xyloglucan hits. Evidence were produced showing that the five CIII Prxs were cell wall-targeted proteins and that the micropylar endosperm displayed a complex cell wall domain topochemistry. Finally, we drew a spatio-temporal model highlighting the fine sequential gene expression and the possible involvement of micropylar endosperm cell wall domains to explain the non-redundant cell wall stiffening and loosening functions of the CIII Prxs in a single cell type. We also highlighted the necessity of a peroxidase homeostasis to accurately control the micropylar endosperm cell wall dynamics during Arabidopsis germination events.

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Current Biology - Plant Evolution: When Arabidopsis Is More Ancestral Than Marchantia

Current Biology - Plant Evolution: When Arabidopsis Is More Ancestral Than Marchantia | LRSV Publications | Scoop.it

The quest for determining how the plants that first lived on land 450 million years ago looked is among the most exciting challenges in evolutionary biology. Recent work indicates that they displayed angiosperm-like stomata.

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Current Biology - Evolution of Plant Metabolism: A (Bio)synthesis

Current Biology - Evolution of Plant Metabolism: A (Bio)synthesis | LRSV Publications | Scoop.it

Studying the evolution of metabolism is technically challenging. A new study combining in silico metabolic maps and phylogenomics allows reconstructing the diversification of plant metabolism across one billion years of evolution.

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Current Biology - Plant Cell Signaling: SUMO Is under the Influence of Steroids and Salt

Current Biology - Plant Cell Signaling: SUMO Is under the Influence of Steroids and Salt | LRSV Publications | Scoop.it
How do plants reduce growth when they experience high salinity? A new study provides
insight into how salt stress impinges on a plant steroid hormone signaling pathway
to dampen plant growth.
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IJMS - The Cell Wall PAC (Proline-Rich, Arabinogalactan Proteins, Conserved Cysteines) Domain-Proteins Are Conserved in the Green Lineage

IJMS - The Cell Wall PAC (Proline-Rich, Arabinogalactan Proteins, Conserved Cysteines) Domain-Proteins Are Conserved in the Green Lineage | LRSV Publications | Scoop.it

Plant cell wall proteins play major roles during plant development and in response to environmental cues. A bioinformatic search for functional domains has allowed identifying the PAC domain (Proline-rich, Arabinogalactan proteins, conserved Cysteines) in several proteins (PDPs) identified in cell wall proteomes. This domain is assumed to interact with pectic polysaccharides and O-glycans and to contribute to non-covalent molecular scaffolds facilitating the remodeling of polysaccharidic networks during rapid cell expansion. In this work, the characteristics of the PAC domain are described in detail, including six conserved Cys residues, their spacing, and the predicted secondary structures. Modeling has been performed based on the crystal structure of a Plantago lanceolata PAC domain. The presence of β-sheets is assumed to ensure the correct folding of the PAC domain as a β-barrel with loop regions. We show that PDPs are present in early divergent organisms from the green lineage and in all land plants. PAC domains are associated with other types of domains: Histidine-rich, extensin, Proline-rich, or yet uncharacterized. The earliest divergent organisms having PDPs are Bryophytes. Like the complexity of the cell walls, the number and complexity of PDPs steadily increase during the evolution of the green lineage. The association of PAC domains with other domains suggests a neo-functionalization and different types of interactions with cell wall polymers

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Antioxidants - Global Evolutionary Analysis of 11 Gene Families Part of Reactive Oxygen Species (ROS) Gene Network in Four Eucalyptus Species

Antioxidants - Global Evolutionary Analysis of 11 Gene Families Part of Reactive Oxygen Species (ROS) Gene Network in Four Eucalyptus Species | LRSV Publications | Scoop.it

Eucalyptus is a worldwide hard-wood species which increasingly focused on. To adapt to various biotic and abiotic stresses, Eucalyptus have evolved complex mechanisms, increasing the cellular concentration of reactive oxygen species (ROS) by numerous ROS controlling enzymes. To better analyse the ROS gene network and discuss the differences between four Eucalyptus species, ROS gene network including 11 proteins families (1CysPrx, 2CysPrx, APx, APx-R, CIII Prx, Diox, GPx, Kat, PrxII, PrxQ and Rboh) were annotated and compared in an expert and exhaustive manner from the genomic data available from E. camaldulensisE. globulusE. grandis, and E. gunnii. In addition, a specific sequencing strategy was performed in order to determine if the missed sequences in at least one organism are the results of gain/loss events or only sequencing gaps. We observed that the automatic annotation applied to multigenic families is the source of miss-annotation. Base on the family size, the 11 families can be categorized into duplicated gene families (CIII Prx, Kat, 1CysPrx, and GPx), which contain a lot of gene duplication events and non-duplicated families (APx, APx-R, Rboh, DiOx, 2CysPrx, PrxII, and PrxQ). The gene family sizes are much larger in Eucalyptus than most of other angiosperms due to recent gene duplications, which could give higher adaptability to environmental changes and stresses. The cross-species comparative analysis shows gene gain and loss events during the evolutionary process. The 11 families possess different expression patterns, while in the Eucalyptus genus, the ROS families present similar expression patterns. Overall, the comparative analysis might be a good criterion to evaluate the adaptation of different species with different characters, but only if data mining is as exhaustive as possible. It is also a good indicator to explore the evolutionary process

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Nature Plants - Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts

Nature Plants - Anthoceros genomes illuminate the origin of land plants and the unique biology of hornworts | LRSV Publications | Scoop.it

Hornworts comprise a bryophyte lineage that diverged from other extant land plants >400 million years ago and bears unique biological features, including a distinct sporophyte architecture, cyanobacterial symbiosis and a pyrenoid-based carbon-concentrating mechanism (CCM). Here, we provide three high-quality genomes of Anthoceros hornworts. Phylogenomic analyses place hornworts as a sister clade to liverworts plus mosses with high support. The Anthoceros genomes lack repeat-dense centromeres as well as whole-genome duplication, and contain a limited transcription factor repertoire. Several genes involved in angiosperm meristem and stomatal function are conserved in Anthoceros and upregulated during sporophyte development, suggesting possible homologies at the genetic level. We identified candidate genes involved in cyanobacterial symbiosis and found that LCIB, a Chlamydomonas CCM gene, is present in hornworts but absent in other plant lineages, implying a possible conserved role in CCM function. We anticipate that these hornwort genomes will serve as essential references for future hornwort research and comparative studies across land plants.

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Plant Physiol - Identification of the Arabidopsis Calmodulin-Dependent NAD+ Kinase That Sustains the Elicitor-Induced Oxidative Burst

Plant Physiol - Identification of the Arabidopsis Calmodulin-Dependent NAD+ Kinase That Sustains the Elicitor-Induced Oxidative Burst | LRSV Publications | Scoop.it

NADP(H) is an essential cofactor of multiple metabolic processes in all living organisms, and in plants, NADP(H) is required as the substrate of Ca2+-dependent NADPH oxidases, which catalyze a reactive oxygen species burst in response to various stimuli. While NADP+ production in plants has long been known to involve a calmodulin (CaM)/Ca2+-dependent NAD+ kinase, the nature of the enzyme catalyzing this activity has remained enigmatic, as has its role in plant physiology. Here, we used proteomic, biochemical, molecular, and in vivo analyses to identify an Arabidopsis (Arabidopsis thaliana) protein that catalyzes NADP+ production exclusively in the presence of CaM/Ca2+. This enzyme, which we named NAD kinase-CaM dependent (NADKc), has a CaM-binding peptide located in its N-terminal region and displays peculiar biochemical properties as well as different domain organization compared with known plant NAD+ kinases. In response to a pathogen elicitor, the activity of NADKc, which is associated with the mitochondrial periphery, contributes to an increase in the cellular NADP+ concentration and to the amplification of the elicitor-induced oxidative burst. Based on a phylogenetic analysis and enzymatic assays, we propose that the CaM/Ca2+-dependent NAD+ kinase activity found in photosynthetic organisms is carried out by NADKc-related proteins. Thus, NADKc represents the missing link between Ca2+ signaling, metabolism, and the oxidative burst.

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Plant Cell - The Medicago truncatula DREPP Protein Triggers Microtubule Fragmentation in Membrane Nanodomains during Symbiotic Infections 

The initiation of intracellular host cell colonization by symbiotic rhizobia in Medicago truncatula requires repolarization of root hairs, which includes the re-arrangement of cytoskeletal filaments. The molecular players governing microtubule (MT) re-organization during rhizobial infections remain to be discovered. Here, we identified M. truncatula DREPP, a member of the microtubule binding DREPP/PCaP protein family and investigated its functions during rhizobial infections. We show that rhizobial colonization of drepp mutant roots as well as transgenic roots over-expressing DREPP is impaired. DREPP re-localizes into symbiosis-specific membrane nanodomains in a stimulus-dependent manner. This subcellular segregation coincides with DREPP-dependent MT fragmentation and a partial loss of the ability to re-organize the MT cytoskeleton in response to rhizobia, which might rely on an interaction between DREPP and the MT organizing protein SPIRAL2 (SPR2). Taken together, our results reveal that establishment of symbiotic associations in M. truncatula require DREPP in order to regulate MT reorganization during initial root hair responses to rhizobia.

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Scientific Report - In silico definition of new ligninolytic peroxidase sub-classes in fungi and putative relation to fungal life style

Scientific Report - In silico definition of new ligninolytic peroxidase sub-classes in fungi and putative relation to fungal life style | LRSV Publications | Scoop.it

Ligninolytic peroxidases are microbial enzymes involved in depolymerisation of lignin, a plant cell wall polymer found in land plants. Among fungi, only Dikarya were found to degrade lignin. The increase of available fungal genomes allows performing an expert annotation of lignin-degrading peroxidase encoding sequences with a particular focus on Class II peroxidases (CII Prx). In addition to the previously described LiP, MnP and VP classes, based on sequence similarity, six new sub-classes have been defined: three found in plant pathogen ascomycetes and three in basidiomycetes. The presence of CII Prxs could be related to fungal life style. Typically, necrotrophic or hemibiotrophic fungi, either ascomycetes or basidiomycetes, possess CII Prxs while symbiotic, endophytic or biotrophic fungi do not. CII Prxs from ascomycetes are rarely subjected to duplications unlike those from basidiomycetes, which can form large recent duplicated families. Even if these CII Prxs classes form two well distinct clusters with divergent gene structures (intron numbers and positions), they share the same key catalytic residues suggesting that they evolved independently from similar ancestral sequences with few or no introns. The lack of CII Prxs encoding sequences in early diverging fungi, together with the absence of duplicated class I peroxidase (CcP) in fungi containing CII Prxs, suggests the potential emergence of an ancestral CII Prx sequence from the duplicated CcP after the separation between ascomycetes and basidiomycetes. As some ascomycetes and basidiomycetes did not possess CII Prx, late gene loss could have occurred.

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IJMS - Cell Wall Proteome of Wheat Grain Endosperm and Outer Layers at Two Key Stages of Early Development

IJMS - Cell Wall Proteome of Wheat Grain Endosperm and Outer Layers at Two Key Stages of Early Development | LRSV Publications | Scoop.it

The cell wall is an important compartment in grain cells that fulfills both structural and functional roles. It has a dynamic structure that is constantly modified during development and in response to biotic and abiotic stresses. Non-structural cell wall proteins (CWPs) are key players in the remodeling of the cell wall during events that punctuate the plant life. Here, a subcellular and quantitative proteomic approach was carried out to identify CWPs possibly involved in changes in cell wall metabolism at two key stages of wheat grain development: the end of the cellularization step and the beginning of storage accumulation. Endosperm and outer layers of wheat grain were analyzed separately as they have different origins (maternal and seed) and functions in grains. Altogether, 734 proteins with predicted signal peptides were identified (CWPs). Functional annotation of CWPs pointed out a large number of proteins potentially involved in cell wall polysaccharide remodeling. In the grain outer layers, numerous proteins involved in cutin formation or lignin polymerization were found, while an unexpected abundance of proteins annotated as plant invertase/pectin methyl esterase inhibitors were identified in the endosperm. In addition, numerous CWPs were accumulating in the endosperm at the grain filling stage, thus revealing strong metabolic activities in the cell wall during endosperm cell differentiation, while protein accumulation was more intense at the earlier stage of development in outer layers. Altogether, our work gives important information on cell wall metabolism during early grain development in both parts of the grain, namely the endosperm and outer layers. The wheat cell wall proteome is the largest cell wall proteome of a monocot species found so far.

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