Impact of high atmospheric carbon dioxide on the biotic stress response of the model cereal species Brachypodium distachyon

Losses due to disease and climate change are among the most important issues currently facing crop production. It is therefore important to establish the impact of climate change, and particularly of high carbon dioxide (hCO2), on plant immunity in cereals, which provide 60% of human calories. The aim of this study was to determine if hCO2 impacts Brachypodium distachyon immunity, a model plant for temperate cereals. Plants were grown in air (430 ppm CO2) and at two high CO2 conditions, one that is relevant to projections within the coming century (1000 ppm) and a concentration sufficient to saturate photosynthesis (3000 ppm). The following measurements were performed: phenotyping and growth, salicylic acid contents, pathogen resistance tests, and RNAseq analysis of the transcriptome. Improved shoot development was observed at both 1000 and 3000 ppm. A transcriptomic analysis pointed to an increase in primary metabolism capacity under hCO2. Alongside this effect, up-regulation of genes associated with secondary metabolism was also observed. This effect was especially evident for the terpenoid and phenylpropanoid pathways, and was accompanied by enhanced expression of immunity-related genes and accumulation of salicylic acid. Pathogen tests using the fungus Magnaporthe oryzae revealed that hCO2 had a complex effect, with enhanced susceptibility to infection but no increase in fungal development. The study reveals that immunity in B. distachyon is modulated by growth at hCO2 and allows identification of pathways that might play a role in this effect

An mTRAN-mRNA interaction mediates mitochondrial translation initiation in plants

Plant mitochondria represent the largest group of respiring organelles on the planet. Plant mitochondrial messenger RNAs (mRNAs) lack Shine-Dalgarno-like ribosome-binding sites, so it is unknown how plant mitoribosomes recognize mRNA. We show that “mitochondrial translation factors” mTRAN1 and mTRAN2 are land plant–specific proteins, required for normal mitochondrial respiration chain biogenesis. Our studies suggest that mTRANs are noncanonical pentatricopeptide repeat (PPR)–like RNA binding proteins of the mitoribosomal “small” subunit. We identified conserved Adenosine (A)/Uridine (U)-rich motifs in the 5′ regions of plant mitochondrial mRNAs. mTRAN1 binds this motif, suggesting that it is a mitoribosome homing factor to identify mRNAs. We demonstrate that mTRANs are likely required for translation of all plant mitochondrial mRNAs. Plant mitochondrial translation initiation thus appears to use a protein-mRNA interaction that is divergent from bacteria or mammalian mitochondria

Retrograde signalling from the mitochondria to the nucleus translates the positive effect of ethylene on dormancy breaking of Arabidopsis thaliana seeds

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DiffSegR: an RNA-seq data driven method for differential expression analysis using changepoint detection

International audienceAbstract To fully understand gene regulation, it is necessary to have a thorough understanding of both the transcriptome and the enzymatic and RNA-binding activities that shape it. While many RNA-Seq-based tools have been developed to analyze the transcriptome, most only consider the abundance of sequencing reads along annotated patterns (such as genes). These annotations are typically incomplete, leading to errors in the differential expression analysis. To address this issue, we present DiffSegR - an R package that enables the discovery of transcriptome-wide expression differences between two biological conditions using RNA-Seq data. DiffSegR does not require prior annotation and uses a multiple changepoints detection algorithm to identify the boundaries of differentially expressed regions in the per-base log2 fold change. In a few minutes of computation, DiffSegR could rightfully predict the role of chloroplast ribonuclease Mini-III in rRNA maturation and chloroplast ribonuclease PNPase in (3′/5′)-degradation of rRNA, mRNA and tRNA precursors as well as intron accumulation. We believe DiffSegR will benefit biologists working on transcriptomics as it allows access to information from a layer of the transcriptome overlooked by the classical differential expression analysis pipelines widely used today. DiffSegR is available at https://aliehrmann.github.io/DiffSegR/index.html

Custom methods to identify conserved genetic modules applied to novel transcriptomic data from Amborella trichopoda

International audienceAbstract We have devised a procedure for the inter-species comparison of transcriptomic data and used this to reconstruct the expression dynamics of major genetic modules that were present at least 149 million years ago in the most recent common ancestor (MRCA) of living angiosperms. We begin by using Laser-Assisted Microdissection to generate novel transcriptomic data from female flower tissues of Amborella trichopoda, the likely sister to all other living angiosperms. We then employ a gene-expression clustering method, followed by a custom procedure to compare genetic modules on the basis of gene-orthology between Amborella and the molecular-genetic model angiosperm Arabidopsis thaliana (Arabidopsis). Using this protocol, we have succeeded in identifying nine major genetic modules that appear to have conserved their expression dynamics from an early stage in angiosperm evolution. The genes of these modules, representing over 5000 orthogroups, include around a third of those known to control female reproductive development in Arabidopsis. Our study constitutes a proof-of-concept for the comparison of transcriptomic data between widely diverged plant species and represents a first step in the large-scale analysis of gene expression dynamics in a macro-evolutionary context

Antagonistic Effect of Sucrose Availability and Auxin on Rosa Axillary Bud Metabolism and Signaling, Based on the Transcriptomics and Metabolomics Analysis

International audienceShoot branching is crucial for successful plant development and plant response to environmental factors. Extensive investigations have revealed the involvement of an intricate regulatory network including hormones and sugars. Recent studies have demonstrated that two major systemic regulators-auxin and sugar-antagonistically regulate plant branching. However, little is known regarding the molecular mechanisms involved in this crosstalk. We carried out two complementary untargeted approaches-RNA-seq and metabolomics-on explant stem buds fed with different concentrations of auxin and sucrose resulting in dormant and non-dormant buds. Buds responded to the combined effect of auxin and sugar by massive reprogramming of the transcriptome and metabolome. The antagonistic effect of sucrose and auxin targeted several important physiological processes, including sink strength, the amino acid metabolism, the sulfate metabolism, ribosome biogenesis, the nucleic acid metabolism, and phytohormone signaling. Further experiments revealed a role of the TOR-kinase signaling pathway in bud outgrowth through at least downregulation of Rosa hybrida BRANCHED1 (RhBRC1). These new findings represent a cornerstone to further investigate the diverse molecular mechanisms that drive the integration of endogenous factors during shoot branching

Impact of high atmospheric carbon dioxide on the biotic stress response of the model cereal species Brachypodium distachyon

International audienceLosses due to disease and climate change are among the most important issues currently facing crop production. It is therefore important to establish the impact of climate change, and particularly of high carbon dioxide (hCO 2 ), on plant immunity in cereals, which provide 60% of human calories. The aim of this study was to determine if hCO 2 impacts Brachypodium distachyon immunity, a model plant for temperate cereals. Plants were grown in air (430 ppm CO 2 ) and at two high CO 2 conditions, one that is relevant to projections within the coming century (1000 ppm) and a concentration sufficient to saturate photosynthesis (3000 ppm). The following measurements were performed: phenotyping and growth, salicylic acid contents, pathogen resistance tests, and RNAseq analysis of the transcriptome. Improved shoot development was observed at both 1000 and 3000 ppm. A transcriptomic analysis pointed to an increase in primary metabolism capacity under hCO 2 . Alongside this effect, up-regulation of genes associated with secondary metabolism was also observed. This effect was especially evident for the terpenoid and phenylpropanoid pathways, and was accompanied by enhanced expression of immunity-related genes and accumulation of salicylic acid. Pathogen tests using the fungus Magnaporthe oryzae revealed that hCO 2 had a complex effect, with enhanced susceptibility to infection but no increase in fungal development. The study reveals that immunity in B. distachyon is modulated by growth at hCO 2 and allows identification of pathways that might play a role in this effect

Chloroplast biogenesis: towards the role of localized translation in Arabidopsis

International audienceChloroplasts are a major component of plant cells. Until recently, all nuclear-encoded proteins destined to chloroplast were believed to possess an N-terminal and cleavable chloroplast targeting peptide, and to engage the TOC/TIC machinery. However, recent studies have revealed that alternative routes also exists and identified a series of nuclear-encoded proteins imported via such pathways. Recent proteomic studies, conducted by our team (Bouchnak et al., Mol Cell Proteomics 2019), identified a list of cyto-ribosomal subunits associated to chloroplasts, thus suggesting that localized translation might occur at the chloroplast surface. We were recently able to isolate plastid-associated cyto-ribosomes and to decipher their composition when compared to purified whole cell cyto-ribosomes. Interestingly, these plastid-associated cyto-ribosomes contain a few non cyto-ribosomal proteins which might participate to the control of localized translation at the chloroplast surface. These non cyto-ribosomal proteins were first fused to GFP to analyze their subcellular location. Then, we isolated Arabidopsis knock-out mutants affected in the expression of two of these specific proteins and initiated their phenotypical characterization. Finally, with the aim to identify the nature of the nuclear-encoded mRNAs that are translated by these chloroplast-associated cyto-ribosomes, the identification of mRNAs trapped within these plastid-associated cyto-ribosomes was performed

Chloroplast biogenesis: towards the role of localized translation in Arabidopsis

International audienceChloroplasts are a major component of plant cells. Until recently, all nuclear-encoded proteins destined to chloroplast were believed to possess an N-terminal and cleavable chloroplast targeting peptide, and to engage the TOC/TIC machinery. However, recent studies have revealed that alternative routes also exists and identified a series of nuclear-encoded proteins imported via such pathways. Recent proteomic studies, conducted by our team (Bouchnak et al., Mol Cell Proteomics 2019), identified a list of cyto-ribosomal subunits associated to chloroplasts, thus suggesting that localized translation might occur at the chloroplast surface. We were recently able to isolate plastid-associated cyto-ribosomes and to decipher their composition when compared to purified whole cell cyto-ribosomes. Interestingly, these plastid-associated cyto-ribosomes contain a few non cyto-ribosomal proteins which might participate to the control of localized translation at the chloroplast surface. These non cyto-ribosomal proteins were first fused to GFP to analyze their subcellular location. Then, we isolated Arabidopsis knock-out mutants affected in the expression of two of these specific proteins and initiated their phenotypical characterization. Finally, with the aim to identify the nature of the nuclear-encoded mRNAs that are translated by these chloroplast-associated cyto-ribosomes, the identification of mRNAs trapped within these plastid-associated cyto-ribosomes was performed

Chloroplast biogenesis: towards the role of localized translation in Arabidopsis

International audienceChloroplasts are a major component of plant cells. Until recently, all nuclear-encoded proteins destined to chloroplast were believed to possess an N-terminal and cleavable chloroplast targeting peptide, and to engage the TOC/TIC machinery. However, recent studies have revealed that alternative routes also exists and identified a series of nuclear-encoded proteins imported via such pathways. Recent proteomic studies, conducted by our team (Bouchnak et al., Mol Cell Proteomics 2019), identified a list of cyto-ribosomal subunits associated to chloroplasts, thus suggesting that localized translation might occur at the chloroplast surface. We were recently able to isolate plastid-associated cyto-ribosomes and to decipher their composition when compared to purified whole cell cyto-ribosomes. Interestingly, these plastid-associated cyto-ribosomes contain a few non cyto-ribosomal proteins which might participate to the control of localized translation at the chloroplast surface. Finally, with the aim to identify the nature of the nuclear-encoded mRNAs that are translated by these chloroplast-associated cyto-ribosomes, the identification of mRNAs trapped within these plastid-associated cyto-ribosomes was performed