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1. Evolutionary analyses and expression patterns of TCP genes in Ranunculales

Author

Catherine Damerval, Carmine Claudot, Martine Le Guilloux, Natalia Conde e Silva, Véronique Brunaud, Ludivine Soubigou-Taconnat, José Caius, Etienne Delannoy, Sophie Nadot, Florian Jabbour, and Yves Deveaux

Subjects
Ranunculales, Nigella damascena, TCP gene family, gene phylogeny, amino acid motifs, gene duplication, Plant culture, SB1-1110
Abstract

TCP transcription factors play a role in a large number of developmental processes and are at the crossroads of numerous hormonal biosynthetic and signaling pathways. The complete repertoire of TCP genes has already been characterized in several plant species, but not in any species of early diverging eudicots. We focused on the order Ranunculales because of its phylogenetic position as sister group to all other eudicots and its important morphological diversity. Results show that all the TCP genes expressed in the floral transcriptome of Nigella damascena (Ranunculaceae) are the orthologs of the TCP genes previously identified from the fully sequenced genome of Aquilegia coerulea. Phylogenetic analyses combined with the identification of conserved amino acid motifs suggest that six paralogous genes of class I TCP transcription factors were present in the common ancestor of angiosperms. We highlight independent duplications in core eudicots and Ranunculales within the class I and class II subfamilies, resulting in different numbers of paralogs within the main subclasses of TCP genes. This has most probably major consequences on the functional diversification of these genes in different plant clades. The expression patterns of TCP genes in Nigella damascena were consistent with the general suggestion that CIN and class I TCP genes may have redundant roles or take part in same pathways, while CYC/TB1 genes have more specific actions. Our findings open the way for future studies at the tissue level, and for investigating redundancy and subfunctionalisation in TCP genes and their role in the evolution of morphological novelties.

Published
2022
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2. BdERECTA controls vasculature patterning and phloem-xylem organization in Brachypodium distachyon

Author

Kaori Sakai, Sylvie Citerne, Sébastien Antelme, Philippe Le Bris, Sylviane Daniel, Axelle Bouder, Angelina D’Orlando, Amy Cartwright, Frédérique Tellier, Stéphanie Pateyron, Etienne Delannoy, Debbie Laudencia-Chingcuanco, Gregory Mouille, Jean Christophe Palauqui, John Vogel, and Richard Sibout

Subjects
Brachypodium, ERECTA, Hormones, Phloem, Xylem, Botany, QK1-989
Abstract

Abstract Background The vascular system of plants consists of two main tissue types, xylem and phloem. These tissues are organized into vascular bundles that are arranged into a complex network running through the plant that is essential for the viability of land plants. Despite their obvious importance, the genes involved in the organization of vascular tissues remain poorly understood in grasses. Results We studied in detail the vascular network in stems from the model grass Brachypodium distachyon (Brachypodium) and identified a large set of genes differentially expressed in vascular bundles versus parenchyma tissues. To decipher the underlying molecular mechanisms of vascularization in grasses, we conducted a forward genetic screen for abnormal vasculature. We identified a mutation that severely affected the organization of vascular tissues. This mutant displayed defects in anastomosis of the vascular network and uncommon amphivasal vascular bundles. The causal mutation is a premature stop codon in ERECTA, a LRR receptor-like serine/threonine-protein kinase. Mutations in this gene are pleiotropic indicating that it serves multiple roles during plant development. This mutant also displayed changes in cell wall composition, gene expression and hormone homeostasis. Conclusion In summary, ERECTA has a pleiotropic role in Brachypodium. We propose a major role of ERECTA in vasculature anastomosis and vascular tissue organization in Brachypodium.

Published
2021
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3. Transcriptome Analysis Reveals Putative Target Genes of APETALA3-3 During Early Floral Development in Nigella damascena L.

Author

Yves Deveaux, Natalia Conde e Silva, Domenica Manicacci, Martine Le Guilloux, Véronique Brunaud, Harry Belcram, Johann Joets, Ludivine Soubigou-Taconnat, Etienne Delannoy, Hélène Corti, Sandrine Balzergue, Jose Caius, Sophie Nadot, and Catherine Damerval

Subjects
APETALA3, RNA-seq, AP3 target genes, petal, Nigella damascena, floral mutant, Plant culture, SB1-1110
Abstract

Even though petals are homoplastic structures, their identity consistently involves genes of the APETALA3 (AP3) lineage. However, the extent to which the networks downstream of AP3 are conserved in species with petals of different evolutionary origins is unknown. In Ranunculaceae, the specificity of the AP3-III lineage offers a great opportunity to identify the petal gene regulatory network in a comparative framework. Using a transcriptomic approach, we investigated putative target genes of the AP3-III ortholog NdAP3-3 in Nigella damascena at early developmental stages when petal identity is determined, and we compared our data with that from selected eudicot species. We generated a de novo reference transcriptome to carry out a differential gene expression analysis between the wild-type and mutant NdAP3-3 genotypes differing by the presence vs. absence of petals at early stages of floral development. Among the 1,620 genes that were significantly differentially expressed between the two genotypes, functional annotation suggested a large involvement of nuclear activities, including regulation of transcription, and enrichment in processes linked to cell proliferation. Comparing with Arabidopsis data, we found that highly conserved genes between the two species are enriched in homologs of direct targets of the AtAP3 protein. Integrating AP3-3 binding site data from another Ranunculaceae species, Aquilegia coerulea, allowed us to identify a set of 18 putative target genes that were conserved between the three species. Our results suggest that, despite the independent evolutionary origin of petals in core eudicots and Ranunculaceae, a small conserved set of genes determines petal identity and early development in these taxa.

Published
2021
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4. The Genomic Impact of Mycoheterotrophy in Orchids

Author

Marcin Jąkalski, Julita Minasiewicz, José Caius, Michał May, Marc-André Selosse, and Etienne Delannoy

Subjects
mycorrhiza, photosynthesis, metabolic evolution, mycoheterotrophy, orchids, transcriptome, Plant culture, SB1-1110
Abstract

Mycoheterotrophic plants have lost the ability to photosynthesize and obtain essential mineral and organic nutrients from associated soil fungi. Despite involving radical changes in life history traits and ecological requirements, the transition from autotrophy to mycoheterotrophy has occurred independently in many major lineages of land plants, most frequently in Orchidaceae. Yet the molecular mechanisms underlying this shift are still poorly understood. A comparison of the transcriptomes of Epipogium aphyllum and Neottia nidus-avis, two completely mycoheterotrophic orchids, to other autotrophic and mycoheterotrophic orchids showed the unexpected retention of several genes associated with photosynthetic activities. In addition to these selected retentions, the analysis of their expression profiles showed that many orthologs had inverted underground/aboveground expression ratios compared to autotrophic species. Fatty acid and amino acid biosynthesis as well as primary cell wall metabolism were among the pathways most impacted by this expression reprogramming. Our study suggests that the shift in nutritional mode from autotrophy to mycoheterotrophy remodeled the architecture of the plant metabolism but was associated primarily with function losses rather than metabolic innovations.

Published
2021
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5. Genome-Wide Transcriptomic Analysis of the Effects of Infection with the Hemibiotrophic Fungus Colletotrichum lindemuthianum on Common Bean

Author

Juan C. Alvarez-Diaz, Richard Laugé, Etienne Delannoy, Stéphanie Huguet, Christine Paysant-Le Roux, Ariane Gratias, and Valérie Geffroy

Subjects
Phaseolus vulgaris, Colletotrichum lindemuthianum, RNA-seq, transcriptome, Co-resistance genes, resistance response, Botany, QK1-989
Abstract

Bean anthracnose caused by the hemibiotrophic fungus Colletotrichum lindemuthianum is one of the most important diseases of common bean (Phaseolus vulgaris) in the world. In the present study, the whole transcriptome of common bean infected with C. lindemuthianum during compatible and incompatible interactions was characterized at 48 and 72 hpi, corresponding to the biotrophy phase of the infection cycle. Our results highlight the prominent role of pathogenesis-related (PR) genes from the PR10/Bet vI family as well as a complex interplay of different plant hormone pathways including Ethylene, Salicylic acid (SA) and Jasmonic acid pathways. Gene Ontology enrichment analysis reveals that infected common bean seedlings responded by down-regulation of photosynthesis, ubiquitination-mediated proteolysis and cell wall modifications. In infected common bean, SA biosynthesis seems to be based on the PAL pathway instead of the ICS pathway, contrarily to what is described in Arabidopsis. Interestingly, ~30 NLR were up-regulated in both contexts. Overall, our results suggest that the difference between the compatible and incompatible reaction is more a question of timing and strength, than a massive difference in differentially expressed genes between these two contexts. Finally, we used RT-qPCR to validate the expression patterns of several genes, and the results showed an excellent agreement with deep sequencing.

Published
2022
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6. Combining laser-assisted microdissection (LAM) and RNA-seq allows to perform a comprehensive transcriptomic analysis of epidermal cells of Arabidopsis embryo

Author

Kaori Sakai, Ludivine Taconnat, Nero Borrega, Jennifer Yansouni, Véronique Brunaud, Christine Paysant-Le Roux, Etienne Delannoy, Marie-Laure Martin Magniette, Loïc Lepiniec, Jean Denis Faure, Sandrine Balzergue, and Bertrand Dubreucq

Subjects
Laser-assisted microdissection, Ultra-low-RNA-seq, Epidermis, Embryo cells, Arabidopsis, Plant culture, SB1-1110, Biology (General), QH301-705.5
Abstract

Abstract Background Genome-wide characterization of tissue- or cell-specific gene expression is a recurrent bottleneck in biology. We have developed a sensitive approach based on ultra-low RNA sequencing coupled to laser assisted microdissection for analyzing different tissues of the small Arabidopsis embryo. Methods and results We first characterized the number of genes detected according to the quantity of tissue yield and total RNA extracted. Our results revealed that as low as 0.02 mm2 of tissue and 50 pg of total RNA can be used without compromising the number of genes detected. The optimised protocol was used to compare the epidermal versus mesophyll cell transcriptomes of cotyledons at the torpedo-shaped stage of embryo development. The approach was validated by the recovery of well-known epidermal genes such AtML1 or AtPDF2 and genes involved in flavonoid and cuticular waxes pathways. Moreover, the interest and sensitivity of this approach were highlighted by the characterization of several transcription factors preferentially expressed in epidermal cells. Conclusion This technical advance unlocks some current limitations of transcriptomic analyses and allows to investigate further and efficiently new biological questions for which only a very small amounts of cells need to be isolated. For instance, it paves the way to increasing the spatial accuracy of regulatory networks in developing small embryo of Arabidopsis or other plant tissues.

Published
2018
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7. Full Length Transcriptome Highlights the Coordination of Plastid Transcript Processing

Author

Marine Guilcher, Arnaud Liehrmann, Chloé Seyman, Thomas Blein, Guillem Rigaill, Benoit Castandet, and Etienne Delannoy

Subjects
Arabidopsis thaliana, plastid, co-maturation, post-transcriptional, nanopore, Biology (General), QH301-705.5, Chemistry, QD1-999
Abstract

Plastid gene expression involves many post-transcriptional maturation steps resulting in a complex transcriptome composed of multiple isoforms. Although short-read RNA-Seq has considerably improved our understanding of the molecular mechanisms controlling these processes, it is unable to sequence full-length transcripts. This information is crucial, however, when it comes to understanding the interplay between the various steps of plastid gene expression. Here, we describe a protocol to study the plastid transcriptome using nanopore sequencing. In the leaf of Arabidopsis thaliana, with about 1.5 million strand-specific reads mapped to the chloroplast genome, we could recapitulate most of the complexity of the plastid transcriptome (polygenic transcripts, multiple isoforms associated with post-transcriptional processing) using virtual Northern blots. Even if the transcripts longer than about 2500 nucleotides were missing, the study of the co-occurrence of editing and splicing events identified 42 pairs of events that were not occurring independently. This study also highlighted a preferential chronology of maturation events with splicing happening after most sites were edited.

Published
2021
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8. Low phosphate activates STOP1-ALMT1 to rapidly inhibit root cell elongation

Author

Coline Balzergue, Thibault Dartevelle, Christian Godon, Edith Laugier, Claudia Meisrimler, Jean-Marie Teulon, Audrey Creff, Marie Bissler, Corinne Brouchoud, Agnès Hagège, Jens Müller, Serge Chiarenza, Hélène Javot, Noëlle Becuwe-Linka, Pascale David, Benjamin Péret, Etienne Delannoy, Marie-Christine Thibaud, Jean Armengaud, Steffen Abel, Jean-Luc Pellequer, Laurent Nussaume, and Thierry Desnos

Subjects
Science
Abstract

Low Pi availability inhibits primary root growth, but the sensory mechanisms are not known. Here the authors uncover a signalling pathway regulating Pi-mediated root growth inhibition inArabidopsis, involving the transcription factor STOP1, its direct target ALMT1, a malate channel, and ferroxidase LPR1.

Published
2017
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9. A systems biology approach uncovers a gene co-expression network associated with cell wall degradability in maize.

Author

Clément Cuello, Aurélie Baldy, Véronique Brunaud, Johann Joets, Etienne Delannoy, Marie-Pierre Jacquemot, Lucy Botran, Yves Griveau, Cécile Guichard, Ludivine Soubigou-Taconnat, Marie-Laure Martin-Magniette, Philippe Leroy, Valérie Méchin, Matthieu Reymond, and Sylvie Coursol

Subjects
Medicine, Science
Abstract

Understanding the mechanisms triggering variation of cell wall degradability is a prerequisite to improving the energy value of lignocellulosic biomass for animal feed or biorefinery. Here, we implemented a multiscale systems approach to shed light on the genetic basis of cell wall degradability in maize. We demonstrated that allele replacement in two pairs of near-isogenic lines at a region encompassing a major quantitative trait locus (QTL) for cell wall degradability led to phenotypic variation of a similar magnitude and sign to that expected from a QTL analysis of cell wall degradability in the F271 × F288 recombinant inbred line progeny. Using DNA sequences within the QTL interval of both F271 and F288 inbred lines and Illumina RNA sequencing datasets from internodes of the selected near-isogenic lines, we annotated the genes present in the QTL interval and provided evidence that allelic variation at the introgressed QTL region gives rise to coordinated changes in gene expression. The identification of a gene co-expression network associated with cell wall-related trait variation revealed that the favorable F288 alleles exploit biological processes related to oxidation-reduction, regulation of hydrogen peroxide metabolism, protein folding and hormone responses. Nested in modules of co-expressed genes, potential new cell-wall regulators were identified, including two transcription factors of the group VII ethylene response factor family, that could be exploited to fine-tune cell wall degradability. Overall, these findings provide new insights into the regulatory mechanisms by which a major locus influences cell wall degradability, paving the way for its map-based cloning in maize.

Published
2019
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10. Unraveling the Developmental and Genetic Mechanisms Underpinning Floral Architecture in Proteaceae

Author

Catherine Damerval, Hélène Citerne, Natalia Conde e Silva, Yves Deveaux, Etienne Delannoy, Johann Joets, Franck Simonnet, Yannick Staedler, Jürg Schönenberger, Jennifer Yansouni, Martine Le Guilloux, Hervé Sauquet, and Sophie Nadot

Subjects
Proteaceae, flower, development, floral symmetry, High Resolution X-Ray Computed Tomography, transcriptome, Plant culture, SB1-1110
Abstract

Proteaceae are a basal eudicot family with a highly conserved floral groundplan but which displays considerable variation in other aspects of floral and inflorescence morphology. Their morphological diversity and phylogenetic position make them good candidates for understanding the evolution of floral architecture, in particular the question of the homology of the undifferentiated perianth with the differentiated perianth of core eudicots, and the mechanisms underlying the repeated evolution of zygomorphy. In this paper, we combine a morphological approach to explore floral ontogenesis and a transcriptomic approach to access the genes involved in floral organ identity and development, focusing on Grevillea juniperina, a species from subfamily Grevilleoideae. We present developmental data for Grevillea juniperina and three additional species that differ in their floral symmetry using stereomicroscopy, SEM and High Resolution X-Ray Computed Tomography. We find that the adnation of stamens to tepals takes place at early developmental stages, and that the establishment of bilateral symmetry coincides with the asymmetrical growth of the single carpel. To set a framework for understanding the genetic basis of floral development in Proteaceae, we generated and annotated de novo a reference leaf/flower transcriptome from Grevillea juniperina. We found Grevillea homologs of all lineages of MADS-box genes involved in floral organ identity. Using Arabidopsis thaliana gene expression data as a reference, we found homologs of other genes involved in floral development in the transcriptome of G. juniperina. We also found at least 21 class I and class II TCP genes, a gene family involved in the regulation of growth processes, including floral symmetry. The expression patterns of a set of floral genes obtained from the transcriptome were characterized during floral development to assess their organ specificity and asymmetry of expression.

Published
2019
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11. The Consequences of a Disruption in Cyto-Nuclear Coadaptation on the Molecular Response to a Nitrate Starvation in Arabidopsis

Author

Fabien Chardon, Gwendal Cueff, Etienne Delannoy, Fabien Aubé, Aurélia Lornac, Magali Bedu, Françoise Gilard, Stéphanie Pateyron, Hélène Rogniaux, Audrey Gargaros, Hakim Mireau, Loïc Rajjou, Marie-Laure Martin-Magniette, and Françoise Budar

Subjects
nutrient stress, natural variation, cytonuclear co adaptation, transcriptome, proteome, metabolome, Botany, QK1-989
Abstract

Mitochondria and chloroplasts are important actors in the plant nutritional efficiency. So, it could be expected that a disruption of the coadaptation between nuclear and organellar genomes impact plant response to nutrient stresses. We addressed this issue using two Arabidopsis accessions, namely Ct-1 and Jea, and their reciprocal cytolines possessing the nuclear genome from one parent and the organellar genomes of the other one. We measured gene expression, and quantified proteins and metabolites under N starvation and non-limiting conditions. We observed a typical response to N starvation at the phenotype and molecular levels. The phenotypical response to N starvation was similar in the cytolines compared to the parents. However, we observed an effect of the disruption of genomic coadaptation at the molecular levels, distinct from the previously described responses to organellar stresses. Strikingly, genes differentially expressed in cytolines compared to parents were mainly repressed in the cytolines. These genes encoded more mitochondrial and nuclear proteins than randomly expected, while N starvation responsive ones were enriched in genes for chloroplast and nuclear proteins. In cytolines, the non-coadapted cytonuclear genomic combination tends to modulate the response to N starvation observed in the parental lines on various biological processes.

Published
2020
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12. The Analysis of the Editing Defects in the dyw2 Mutant Provides New Clues for the Prediction of RNA Targets of Arabidopsis E+-Class PPR Proteins

Author

Bastien Malbert, Matthias Burger, Mauricio Lopez-Obando, Kevin Baudry, Alexandra Launay-Avon, Barbara Härtel, Daniil Verbitskiy, Anja Jörg, Richard Berthomé, Claire Lurin, Mizuki Takenaka, and Etienne Delannoy

Subjects
arabidopsis, genome containing organelles, mutants, pentatricopeptide repeat (ppr) proteins, rna editing, Botany, QK1-989
Abstract

C to U editing is one of the post-transcriptional steps which are required for the proper expression of chloroplast and mitochondrial genes in plants. It depends on several proteins acting together which include the PLS-class pentatricopeptide repeat proteins (PPR). DYW2 was recently shown to be required for the editing of many sites in both organelles. In particular almost all the sites associated with the E+ subfamily of PPR proteins are depending on DYW2, suggesting that DYW2 is required for the function of E+-type PPR proteins. Here we strengthened this link by identifying 16 major editing sites controlled by 3 PPR proteins: OTP90, a DYW-type PPR and PGN and MEF37, 2 E+-type PPR proteins. A re-analysis of the DYW2 editotype showed that the 49 sites known to be associated with the 18 characterized E+-type PPR proteins all depend on DYW2. Considering only the 288 DYW2-dependent editing sites as potential E+-type PPR sites, instead of the 795 known editing sites, improves the performances of binding predictions systems based on the PPR code for E+-type PPR proteins. However, it does not compensate for poor binding predictions.

Published
2020
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13. Mitochondrial Transcriptome Control and Intercompartment Cross-Talk During Plant Development

Author

Adnan Khan Niazi, Etienne Delannoy, Rana Khalid Iqbal, Daria Mileshina, Romain Val, Marta Gabryelska, Eliza Wyszko, Ludivine Soubigou-Taconnat, Maciej Szymanski, Jan Barciszewski, Frédérique Weber-Lotfi, José Manuel Gualberto, and André Dietrich

Subjects
anterograde regulation, cytoplasmic male sterility (CMS), plant mitochondria, retrograde regulation, ribozyme, RNA trafficking, signaling, Cytology, QH573-671
Abstract

We address here organellar genetic regulation and intercompartment genome coordination. We developed earlier a strategy relying on a tRNA-like shuttle to mediate import of nuclear transgene-encoded custom RNAs into mitochondria in plants. In the present work, we used this strategy to drive trans-cleaving hammerhead ribozymes into the organelles, to knock down specific mitochondrial RNAs and analyze the regulatory impact. In a similar approach, the tRNA mimic was used to import into mitochondria in Arabidopsis thaliana the orf77, an RNA associated with cytoplasmic male sterility in maize and possessing sequence identities with the atp9 mitochondrial RNA. In both cases, inducible expression of the transgenes allowed to characterise early regulation and signaling responses triggered by these respective manipulations of the organellar transcriptome. The results imply that the mitochondrial transcriptome is tightly controlled by a “buffering” mechanism at the early and intermediate stages of plant development, a control that is released at later stages. On the other hand, high throughput analyses showed that knocking down a specific mitochondrial mRNA triggered a retrograde signaling and an anterograde nuclear transcriptome response involving a series of transcription factor genes and small RNAs. Our results strongly support transcriptome coordination mechanisms within the organelles and between the organelles and the nucleus.

Published
2019
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14. A novel role for the root cap in phosphate uptake and homeostasis

Author

Satomi Kanno, Jean-François Arrighi, Serge Chiarenza, Vincent Bayle, Richard Berthomé, Benjamin Péret, Hélène Javot, Etienne Delannoy, Elena Marin, Tomoko M Nakanishi, Marie-Christine Thibaud, and Laurent Nussaume

Subjects
root cap, mineral nutrition, phosphate homeostasis, arabidopsis, 33P imaging, Medicine, Science, Biology (General), QH301-705.5
Abstract

The root cap has a fundamental role in sensing environmental cues as well as regulating root growth via altered meristem activity. Despite this well-established role in the control of developmental processes in roots, the root cap’s function in nutrition remains obscure. Here, we uncover its role in phosphate nutrition by targeted cellular inactivation or phosphate transport complementation in Arabidopsis, using a transactivation strategy with an innovative high-resolution real-time 33P imaging technique. Remarkably, the diminutive size of the root cap cells at the root-to-soil exchange surface accounts for a significant amount of the total seedling phosphate uptake (approximately 20%). This level of Pi absorption is sufficient for shoot biomass production (up to a 180% gain in soil), as well as repression of Pi starvation-induced genes. These results extend our understanding of this important tissue from its previously described roles in environmental perception to novel functions in mineral nutrition and homeostasis control.

Published
2016
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15. Mitochondrial RNA Transcript Analysis Assay of Arabidopsis Leaf Tissues

Author

Etienne Delannoy, Andéol Falcon de Longevialle, and Catherine Francs-Small

Subjects
Biology (General), QH301-705.5
Abstract

This qPCR-based assay provides an overview of the expression levels of all mitochondrial transcripts (mRNAs and rRNAs) as well as splicing efficiency in Arabidopsis. It was developed before RNAseq techniques were widely used (de Longevialle et al., 2007), but is nevertheless still useful as it is cheaper to run and the analysis is much easier and faster to perform if the aim is only to look at mitochondrial transcripts. For intron-containing mRNAs, the use of primer sets specifically amplifying spliced or unspliced forms allows the evaluation of the splicing efficiency.

Published
2015
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17. Cell specialization and coordination inArabidopsisleaves upon pathogenic attack revealed by scRNA-seq

Author

Etienne Delannoy, Bastien Batardiere, Stéphanie Pateyron, Ludivine Soubigou-Taconnat, Julien Chiquet, Jean Colcombet, and Julien Lang

Abstract

SummaryPlant defense responses involve several biological processes that allow plants to fight against pathogenic attacks. How these different processes are orchestrated within organs and depend on specific cell types is poorly known. Here, using scRNA-seq technology on three independent biological replicates, we identified 10 distinct cell populations in wild-typeArabidopsisleaves inoculated with the bacterial pathogenPseudomonas syringaeDC3000. Among those, we retrieved major cell types of the leaves (mesophyll, guard, epidermal, companion and vascular S cells) to which we could associate characteristic transcriptional reprogramming and regulators, thereby specifying different cell-type responses to the pathogen. Further analyses of transcriptional dynamics, based on inference of cell trajectories, indicated that the different cell types, in addition to their characteristic defense responses, can also share similar modules of gene reprogramming, allowing for instance vascular S cells, epidermal cells and mesophyll cells to converge towards an identical cell fate, mostly characterized by lignification and detoxification functions. Moreover, it appeared that the defense responses of these three cell types can evolve along a second separate path. As this divergence does not correspond to the differentiation between immune and susceptible cells, we speculate that this might reflect the discrimination between cell-autonomous and non-cell-autonomous responses. Altogether our data provide an upgraded framework to describe, explore and explain the specialization and the coordination of plant cell responses upon pathogenic challenge.

Published
2023

18. Limiting etioplast gene‐expression induces apical hook twisting during skoto‐morphogenesis of Arabidopsis seedlings

Author

Salek Ahmed Sajib, Björn Grübler, Cylia Oukacine, Etienne Delannoy, Florence Courtois, Caroline Mauve, Claire Lurin, Bertrand Gakière, Thomas Pfannschmidt, Livia Merendino, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Université Paris Cité (UPCité), Light Photosynthesis & Metabolism (Photosynthesis), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Université Grenoble Alpes (UGA), Leibniz Universität Hannover=Leibniz University Hannover, PEPS CNRS, PF323-5-2 Deutsche Forschungsgemeinschaft, ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), and ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010)

Subjects
Arabidopsis thaliana, spectinomycin, ROS, skoto-morphogenesis, Cell Biology, Plant Science, rifampicin, gene-expression, mitochondria, AOX1A, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, plastids, apical hook bending
Abstract

International audience; When covered by a layer of soil, seedling development follows a dark-specific program (skoto-morphogenesis) consisting of small, non-green cotyledons, a long hypocotyl and an apical hook to protect meristematic cells. We recently highlighted the role played by mitochondria in the high energy-consuming reprogramming of Arabidopsis skoto-morphogenesis. Here, the role played by plastids, another energy supplying organelle, in skoto-morphogenesis is investigated. This study was conducted in dark conditions to exclude light signals so as to better focus on those produced by plastids. It was found that limitation of plastid gene-expression (PGE) induced an exaggerated apical hook bending. Inhibition of PGE was obtained at the level of transcription and translation using the antibiotics rifampicin and spectinomycin, respectively, as well as plastid RPOTp RNA polymerase mutants. Rifampicin-treated seedlings also showed expression induction of marker nuclear genes for mitochondrial stress, perturbation of the mitochondrial metabolism, increase of ROS levels and an augmented capacity of oxygen consumption by mitochondrial alternative oxidases (AOX). AOX enzymes act to prevent over-reduction of the mitochondrial electron transport chain. Previously, we reported that AOX1A, the main AOX isoform, was a key component in the developmental response to mitochondrial respiration deficiency. In this work, we suggest the involvement of AOX1A in the response to PGE dysfunction and propose the importance of signalling between plastids and mitochondria. Finally, it was found that seedling architecture reprogramming in response to rifampicin was independent of canonical organelle retrograde pathways and the ethylene signaling pathway.

Published
2023

19. Limiting etioplast gene-expression induces apical hook twisting during skoto-morphogenesis ofArabidopsisseedlings

Author

Salek Ahmed Sajib, Björn Grübler, Cylia Oukacine, Etienne Delannoy, Florence Courtois, Caroline Mauve, Claire Lurin, Bertrand Gakière, Thomas Pfannschmidt, and Livia Merendino

Abstract

When covered by a layer of soil, seedling development follows a dark-specific program (skoto-morphogenesis) consisting of small, non-green cotyledons, a long hypocotyl and an apical hook to protect meristematic cells. We recently highlighted the role played by mitochondria in the high energy-consuming reprogramming ofArabidopsisskoto-morphogenesis. Here, the role played by plastids, another energy supplying organelle, in skoto-morphogenesis is investigated. This study was conducted in dark conditions to exclude light signals so as to better focus on those produced by plastids. It was found that limitation of plastid gene-expression (PGE) induced an exaggerated apical hook bending. Inhibition of PGE was obtained at the level of transcription and translation using the antibiotics rifampicin and spectinomycin, respectively, as well as plastid RPOTP RNA polymerase mutants. Rifampicin-treated seedlings also showed expression induction of marker nuclear genes for mitochondrial stress, perturbation of the mitochondrial metabolism, increase of ROS levels and an augmented capacity of oxygen consumption by mitochondrial alternative oxidases (AOX). AOX enzymes act to prevent over-reduction of the mitochondrial electron transport chain. Previously, we reported that AOX1A, the main AOX isoform, was a key component in the developmental response to mitochondrial respiration deficiency. In this work, we suggest the involvement of AOX1A in the response to PGE dysfunction and propose the importance of signalling between plastids and mitochondria. Finally, it was found that seedling architecture reprogramming in response to rifampicin was independent of canonical organelle retrograde pathways and the ethylene signaling pathway.Significance statementIn underground germination conditions, seedling development follows a dark-specific program (skoto-morphogenesis) consisting of small and non-green cotyledons, a long hypocotyl and an apical hook to protect meristematic cells. We show that skoto-morphogenesis is reprogrammed when plastid gene expression is perturbed leading to an exaggeration of apical hook bending. We propose the involvement of the cooperation between plastids and mitochondria, the energy-supplying organelles of the cell.

Published
2022

21. TFIIFα interacts with the Topoisomerase VI complex and selectively controls the expression of genes encoding PPR proteins involved in organellar RNA editing in Arabidopsis

Author

Laura Dimnet, Cécile Vriet, Dorine Achard, Cécile Lecampion, Christian Breuer, Ludivine Soubigou-Taconnat, Keiko Sugimoto, Etienne Delannoy, Christophe Laloi, Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Luminy Génétique et Biophysique des Plantes (LGBP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Ecologie et biologie des interactions (EBI), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), RIKEN Center for Sustainable Resource Science [Yokohama] (RIKEN CSRS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), and Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV]Life Sciences [q-bio]
Abstract

Communication between organelles and the nucleus is referred to as anterograde (nucleus to organelle) and retrograde (organelle to nucleus) signalling. In plants, the pentatricopeptide repeat (PPR) proteins represent a large family of nuclear-encoded proteins that are required for post-transcriptional control of chloroplast and mitochondria gene expression, and hence play a central role in the nuclear anterograde control of organelle genome expression. How PPR gene expression is controlled and regulated by retrograde signals is, however, still unknown. Here, we report a significant role for the general transcription factor TFIIF α-subunit (TFIIFα) in controlling PPR gene expression in Arabidopsis. First, we found that TFIIFα interacts with the BIN4 subunit of the Topoisomerase VI (Topo VI). Transcriptome analysis of TFIIF and Topo VI mutant lines then revealed that many PLS-type PPR genes involved in RNA editing are reciprocally controlled by TFIIF and Topo VI. The misexpression of CLB19 and DYW1 genes in two allelic tfIIfα mutants was associated with editing impairments in their plastid target RNAs rpoA and ndhD, respectively. Interestingly, we also detected a change in NDH activity in tfIIfα plants. We also show that TFIIFα and Topo VI coordinate the expression of NDH subunits encoded by the nuclear and plastid genomes. These results reveal the crucial role of the nuclear TFIIFα and Topo VI complexes in controlling plastid genome expression at multiple levels of regulation, including the particular regulation of PPR gene expression.

Published
2022

22. Untargeted metabolomic analyses reveal the diversity and plasticity of the specialized metabolome in seeds of different Camelina sativa genotypes

Author

A. Monti, François Perreau, Etienne Delannoy, F. Zanetti, Massimiliano Corso, Loïc Lepiniec, Marie-Laure Martin-Magniette, S. Boutet, Grégory Mouille, L. Barreda, Institut Jean-Pierre Bourgin (IJPB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Mathématiques et Informatique Appliquées (MIA Paris-Saclay), Department of Agricultural and Food Sciences, University of Bologna/Università di Bologna, 'Departement de Biologie et Amelioration des Plantes' (BAP) of INRAE (grant 'Appel a projets scientifiques BAP 2020'), IJPB's Plant Observatory technological platforms, IPS2's metabolomic platform, ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), Boutet, Stéphanie, Barreda, Léa, Perreau, Françoi, Totozafy, Jean‐Chrisologue, Mauve, Caroline, Gakière, Bertrand, Delannoy, Etienne, Martin‐Magniette, Marie‐Laure, Monti, Andrea, Lepiniec, Loïc, Zanetti, Federica, and Corso, Massimiliano

Subjects
Genotype, metabolic signature, Camelina sativa, Growing season, Plant Science, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Crop, Flavonols, Metabolomics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], rassicaceae,Camelina sativa, metabolic signature, metabolite decorations, environmentalchanges, molecular networks, untargeted metabolomic, lipidomics, metabolite decorations, Genetics, Metabolome, molecular networks, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Cultivar, chemistry.chemical_classification, biology, food and beverages, [SDV.BBM.MN]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular Networks [q-bio.MN], Cell Biology, biology.organism_classification, Camelina, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, chemistry, Agronomy, environmental changes, Seeds, Brassicaceae, untargeted metabolomics and lipidomics
Abstract

SummaryDespite the essential role of Specialized Metabolites (SMs) in the interaction of plants with the environment, studying the ability of crop seeds to produce these protective compounds has been neglected. Furthermore, seeds produce a myriad of SMs providing an interesting model to investigate their diversity and plasticity. Camelina sativa gained a lot of interest in the past few years as rustic oil seed crop. A characterization of seed SM landscapes in six camelina genotypes grown in the field and harvested during five growing seasons has been undertaken in this work. This allowed a comprehensive annotation of seed SMs combining analyses that cluster SMs based on their chemical structures and co-accumulation patterns. These data showed broad effects of the environment on the stimulation of the seed-specialized metabolome. Among well annotated compounds, flavonols were identified as the metabolic class characterised by high plasticity, revealing significant variable accumulation according to the year and/or the genotype. Lastly, a deeper characterisation of primary metabolites and lipids in two selected genotypes has been performed. We showed that, in addition to flavonols, alkaloids and glucosinolates displayed a higher phenotypic plasticity with respect to most of the primary metabolites, including some sugars and major storage compounds such as fatty acids, proteins and most lipid classes (e.g. DAG, TAG), but similar plasticity compared to free aminoacids and carboxylic acids. This work highlighted major and unexplored effects of the environment on the seed specialized metabolome demonstrating that seeds exhibit a dynamic and plastic metabolism, with an impact on seed quality.Significance statementSeeds produce a myriad of Specialized Metabolites (SMs) with an essential role in the interaction of plants with the environment. We characterized SM landscapes, primary metabolites and lipid composition in the seeds of camelina genotypes grown in the open field in five consecutive growing seasons. Our results showed the predominant effect of the environment on the regulation of the seed - specialized metabolome, with a potential impact on seed quality of camelina that may also occur in other oilseed crops.

Published
2022

23. Full Length Transcriptome Highlights the Coordination of Plastid Transcript Processing

Author

Benoit Castandet, Chloé Seyman, Marine Guilcher, Etienne Delannoy, Arnaud Liehrmann, Thomas Blein, Guillem Rigaill, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Mathématiques et Modélisation d'Evry (LaMME), Université d'Évry-Val-d'Essonne (UEVE)-ENSIIE-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), The IPS2 benefits from the support of Saclay Plant Sciences-SPS (ANR-17-EUR-0007). Thiswork was supported by a grant from the Université Evry-Val d’Essonne to E.D., by the ANR-20-CE20-0004 JOAQUIN to B.C. and by the Evry Genopole to G.R., ANR-17-EURE-0007,SPS-GSR,Ecole Universitaire de Recherche de Sciences des Plantes de Paris-Saclay(2017), and ANR-20-CE20-0004,JOAQUIN,Rôle de la RNase J dans le contrôle qualité des ARN chloroplastiques(2020)

Subjects
Gene isoform, Arabidopsis thaliana, QH301-705.5, Arabidopsis, Computational biology, Biology, Genome, Article, Transcriptome, Gene Expression Regulation, Plant, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gene expression, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plastids, RNA-Seq, Biology (General), Plastid, nanopore, plastid, QD1-999, co-maturation, post-transcriptional, Arabidopsis Proteins, fungi, food and beverages, biology.organism_classification, plant_sciences, Chemistry, Alternative Splicing, RNA, Plant, RNA splicing, Nanopore sequencing
Abstract

Plastid gene expression involves many post-transcriptional maturation steps resulting in a complex transcriptome composed of multiple isoforms. Although short-read RNA-Seq has considerably improved our understanding of the molecular mechanisms controlling these processes, it is unable to sequence full-length transcripts. This information is crucial, however, when it comes to understanding the interplay between the various steps of plastid gene expression. Here, we describe a protocol to study the plastid transcriptome using nanopore sequencing. In the leaf of Arabidopsis thaliana, with about 1.5 million strand-specific reads mapped to the chloroplast genome, we could recapitulate most of the complexity of the plastid transcriptome (polygenic transcripts, multiple isoforms associated with post-transcriptional processing) using virtual Northern blots. Even if the transcripts longer than about 2500 nucleotides were missing, the study of the co-occurrence of editing and splicing events identified 42 pairs of events that were not occurring independently. This study also highlighted a preferential chronology of maturation events with splicing happening after most sites were edited.

Published
2021

24. Analysis of the Plant Mitochondrial Transcriptome

Author

Kevin, Baudry, Etienne, Delannoy, and Catherine, Colas des Francs-Small

Subjects
Sequence Analysis, RNA, Gene Expression Profiling, RNA Splicing, RNA-Seq, Plants, Transcriptome
Abstract

Transcriptome analyses are widely performed, but the analysis of organelle genome expression is often overlooked. In this chapter, we describe three methods to analyse the accumulation, splicing, editing and processing of plant mitochondrial transcript expression: a classical RT-qPCR assay, an RNA-Seq approach with its bioinformatical and statistical analysis pipeline, as well as a useful complementary technique, the Northern-blot analysis, using short biotinylated oligonucleotides as probes.

Published
2021

25. Analysis of the Plant Mitochondrial Transcriptome

Author

Kevin Baudry, Catherine Colas des Francs-Small, Etienne Delannoy, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ARC Center of Excellence for Plant Energy Biology, Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Delannoy, Etienne

Subjects
Transcriptome, [SDV.BV.AP]Life Sciences [q-bio]/Vegetal Biology/Plant breeding, RNA editing, Oligonucleotide, Biotinylation, Organelle, RNA splicing, [SDV.BV.AP] Life Sciences [q-bio]/Vegetal Biology/Plant breeding, Computational biology, Northern blot, Biology, Genome, ComputingMilieux_MISCELLANEOUS
Abstract

Transcriptome analyses are widely performed, but the analysis of organelle genome expression is often overlooked. In this chapter, we describe three methods to analyse the accumulation, splicing, editing and processing of plant mitochondrial transcript expression: a classical RT-qPCR assay, an RNA-Seq approach with its bioinformatical and statistical analysis pipeline, as well as a useful complementary technique, the Northern-blot analysis, using short biotinylated oligonucleotides as probes.

Published
2021

26. In situtranscriptomic and metabolomic study of the loss of photosynthesis in the leaves of mixotrophic plants exploiting fungi

Author

Félix Lallemand, Alexandra Launay‐Avon, Bertrand Gakière, Marie-Laure Martin-Magniette, Françoise Gilard, Etienne Delannoy, Marc-André Selosse, Muséum national d'Histoire naturelle (MNHN), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Université Sorbonne Paris Cité (COMUE) (USPC), University of Gdańsk (UG), Fondation de France (Fondation Ars Cuttoli), LabEx Saclay Plant Sciences-SPS [ANR-10-LABX-0040-SPS], and Institut National de la Recherche Agronomique (INRA)-AgroParisTech

Subjects
0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], albinos, mycorrhiza, Plant Science, Photosynthesis, Plant Roots, 01 natural sciences, Neottieae, 03 medical and health sciences, mycoheterotrophy, Metabolomics, mixotrophy, carbon starvation response, Mycorrhizae, orchids, Botany, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [INFO]Computer Science [cs], Amino Acids, [MATH]Mathematics [math], Mycorrhiza, Orchidaceae, Symbiosis, Gene, 2. Zero hunger, chemistry.chemical_classification, biology, Gene Expression Profiling, Fatty Acids, transcriptomic, Cell Biology, 15. Life on land, Biotic stress, biology.organism_classification, Biological Evolution, Carbon, Amino acid, Plant Leaves, 030104 developmental biology, chemistry, Mixotroph, metabolomic, 010606 plant biology & botany
Abstract

International audience; Mycoheterotrophic plants have lost photosynthesis and obtain carbon through mycorrhizal fungi colonizing their roots. They are likely to have evolved from mixotrophic ancestors, which rely on both photosynthesis and fungal carbon for their development. Whereas our understanding of the ecological and genomic changes associated with the evolutionary shift to mycoheterotrophy is deepening, little information is known about the specific metabolic and physiological features driving this evolution. We investigated this issue in naturally occurring achlorophyllous variants of temperate mixotrophic orchids. We carried out an integrated transcriptomic and metabolomic analysis of the response to achlorophylly in the leaves of three mixotrophic species sampled in natura. Achlorophyllous leaves showed major impairment of their photosynthetic and mineral nutrition functions, strong accumulation of free amino acids, overexpression of enzymes and transporters related to sugars, amino acids and fatty acid catabolism, as well as induction of some autophagy-related and biotic stress genes. Such changes were reminiscent of these reported for variegated leaves and appeared to be symptomatic of a carbon starvation response. Rather than decisive metabolic innovations, we suggest that the evolution towards mycoheterotrophy in orchids is more likely to be reliant on the versatility of plant metabolism and an ability to exploit fungal organic resources, especially amino acids, to replace missing photosynthates.

Published
2019

27. Landscape of the Noncoding Transcriptome Response of Two Arabidopsis Ecotypes to Phosphate Starvation

Author

Aurélie Christ, Martin Crespi, Thomas Roulé, Caroline Hartmann, Christian Godon, Marc Gabriel, Laetitia Scalisi, Coline Balzergue, Marie-Laure Martin-Magniette, Daniel Gautheret, Tracy François, Thomas Blein, Céline Sorin, Thierry Desnos, Laurent Nussaume, Etienne Delannoy, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Plant Environmental Physiology and Stress Signaling (PEPSS), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Séquence, Structure et Fonction des ARN (SSFA), Département Biologie des Génomes (DBG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Mathématiques et Informatique Appliquées (MIA Paris-Saclay), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR–17–EUR–0007 [Saclay Plant SciencesGraduate School of Research] managed under an Investments for theFuture program [grant no. ANR–11–IDEX–0003–02]) and The KingAbdulla University of Science and Technology (KAUST) Interna-tional Program (grant no. OCRF–2014–CRG4), ANR-12-ADAP-0019,RNAdapt,Les ARN non-codants dans l'adaptation de la croissance racinaire à la carence phosphate(2012), ANR-16-CE12-0032,SPLISIL,Dialogue épissage et extinction de l'ARN durant l'expression génétique(2016), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Signalisation de l'Adaptation des Végétaux à l'Environnement (SAVE), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Mathématiques et Informatique Appliquées (MIA-Paris), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-AgroParisTech-Université Paris-Saclay, and Biologie végétale et microbiologie environnementale - UMR7265 (BVME)

Subjects
0106 biological sciences, Physiology, [SDV]Life Sciences [q-bio], Arabidopsis, Plant Science, Plant Roots, 01 natural sciences, Genome, Phosphates, Transcriptome, Gene Expression Regulation, Plant, Stress, Physiological, Gene expression, Genetics, Arabidopsis thaliana, Gene, ComputingMilieux_MISCELLANEOUS, Research Articles, Ecotype, 2. Zero hunger, biology, Genetic Variation, 15. Life on land, biology.organism_classification, Adaptation, Physiological, RNA, Long Noncoding, Adaptation, 010606 plant biology & botany
Abstract

International audience; Thousands of lncRNAs with ecotype-specific expression, including two that likely regulate primary root growth, are potentially linked to the evolution of regulatory mechanisms among ecotypes.Root architecture varies widely between species; it even varies between ecotypes of the same species, despite strong conservation of the coding portion of their genomes. By contrast, noncoding RNAs evolve rapidly between ecotypes and may control their differential responses to the environment, since several long noncoding RNAs (lncRNAs) are known to quantitatively regulate gene expression. Roots from ecotypes Columbia and Landsbergerectaof Arabidopsis (Arabidopsis thaliana) respond differently to phosphate starvation. Here, we compared transcriptomes (mRNAs, lncRNAs, and small RNAs) of root tips from these two ecotypes during early phosphate starvation. We identified thousands of lncRNAs that were largely conserved at the DNA level in these ecotypes. In contrast to coding genes, many lncRNAs were specifically transcribed in one ecotype and/or differentially expressed between ecotypes independent of phosphate availability. We further characterized these ecotype-related lncRNAs and studied their link with small interfering RNAs. Our analysis identified 675 lncRNAs differentially expressed between the two ecotypes, including antisense RNAs targeting key regulators of root-growth responses. Misregulation of several lincRNAs showed that at least two ecotype-related lncRNAs regulate primary root growth in ecotype Columbia. RNA-sequencing analysis following deregulation of lncRNA NPC48 revealed a potential link with root growth and transport functions. This exploration of the noncoding transcriptome identified ecotype-specific lncRNA-mediated regulation in root apexes. The noncoding genome may harbor further mechanisms involved in ecotype adaptation of roots to different soil environments.

Published
2020

28. The genomic impact of mycoheterotrophy: targeted gene losses but extensive expression reprogramming

Author

Jose Caius, Julita Minasiewicz, Marc-André Selosse, Marcin Jakalski, Etienne Delannoy, and Michał May

Subjects
Neottia, Orchidaceae, biology, Epipogium aphyllum, Botany, Fungus, Autotroph, biology.organism_classification, Photosynthesis, Gene, Function (biology)
Abstract

Mycoheterotrophic plants have lost the ability to photosynthesize and they parasitize their associated fungus to get the mineral and organic nutrients they need. Despite involving radical changes in life history traits and ecological requirements, the transition from autotrophy to mycoheterotrophy occurred independently in almost all major lineages of land plants, but most often in Orchidaceae. Yet the molecular mechanisms underlying this shift are still poorly understood. The comparison of the transcriptomes of Epipogium aphyllum and Neottia nidus-avis, two mycoheterotrophic orchids, to other autotrophic and mycoheterotrophic orchids showed massive molecular function losses restricted to photosynthetic activities. In addition to these targeted losses, the analysis of their expression profiles showed that many orthologs had inverted root/shoot ratios compared to autotrophic species. Fatty acid and amino acid biosynthesis as well as primary cell wall metabolism were among the pathways most impacted by this expression reprogramming. Our study suggests that, while associated with function losses rather than metabolic innovations, the shift in nutritional mode from autotrophy to mycoheterotrophy remodeled the architecture of the plant metabolism.

Published
2020

29. The Analysis of the Editing Defects in the dyw2 Mutant Provides New Clues for the Prediction of RNA Targets of Arabidopsis E+-Class PPR Proteins

Author

Daniil Verbitskiy, Richard Berthomé, Mauricio Lopez-Obando, Claire Lurin, Etienne Delannoy, Mizuki Takenaka, Alexandra Launay-Avon, Barbara Härtel, Bastien Malbert, Anja Jörg, Matthias Burger, Kevin Baudry, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Molekulare Botanik, Universität Ulm - Ulm University [Ulm, Allemagne], Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Kyoto University, French Ph.D. fellowships from 'Ministere de la Recherche et de l'Enseignement Superieur', Labex Saclay Plant Sciences-SPS doctoral fellowship, German Research Foundation (DFG) : TA621/10-1, Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT), Japan Society for the Promotion of Science : 18H02462, ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Kyoto University [Kyoto]

Subjects
0106 biological sciences, 0301 basic medicine, Mitochondrial DNA, RNA editing, Subfamily, Mutant, Plant Science, Computational biology, genome containing organelles, 01 natural sciences, 03 medical and health sciences, pentatricopeptide repeat (PPR) proteins, lcsh:Botany, Arabidopsis, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Ecology, Evolution, Behavior and Systematics, arabidopsis, mutants, Vegetal Biology, Ecology, biology, RNA, biology.organism_classification, lcsh:QK1-989, 030104 developmental biology, Pentatricopeptide repeat, Function (biology), Biologie végétale, 010606 plant biology & botany
Abstract

International audience; C to U editing is one of the post-transcriptional steps which are required for the proper expression of chloroplast and mitochondrial genes in plants. It depends on several proteins acting together which include the PLS-class pentatricopeptide repeat proteins (PPR). DYW2 was recently shown to be required for the editing of many sites in both organelles. In particular almost all the sites associated with the E+ subfamily of PPR proteins are depending on DYW2, suggesting that DYW2 is required for the function of E+-type PPR proteins. Here we strengthened this link by identifying 16 major editing sites controlled by 3 PPR proteins: OTP90, a DYW-type PPR and PGN and MEF37, 2 E+-type PPR proteins. A re-analysis of the DYW2 editotype showed that the 49 sites known to be associated with the 18 characterized E+-type PPR proteins all depend on DYW2. Considering only the 288 DYW2-dependent editing sites as potential E+-type PPR sites, instead of the 795 known editing sites, improves the performances of binding predictions systems based on the PPR code for E+-type PPR proteins. However, it does not compensate for poor binding predictions.

Published
2020

31. Thirteen New Plastid Genomes from Mixotrophic and Autotrophic Species Provide Insights into Heterotrophy Evolution in Neottieae Orchids

Author

Maria D. Logacheva, Ekaterina Zheleznaia, Michał May, Marie-Christine Le Paslier, Marc-André Selosse, Etienne Delannoy, Isabelle Le Clainche, Marcin Jakalski, Félix Lallemand, Aurélie Bérard, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Institute for Information Transmission Problems, Russian Academy of Sciences [Moscow] (RAS), Skolkovo Institute of Science and Technology [Moscow] (Skoltech), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), People's Friendship University of Russia [Moscow], University of Gdańsk (UG), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), University of Gdańsk, Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), and Lallemand, Félix

Subjects
0106 biological sciences, Letter, DNA, Plant, [SDV]Life Sciences [q-bio], Genome, Plastid, phylogeny, 010603 evolutionary biology, 01 natural sciences, Genome, Neottieae, 03 medical and health sciences, mycoheterotrophy, Symbiosis, mixotrophy, Phylogenetics, phylogénie, Genetics, Autotroph, Plastid, mycorrhizae, Orchidaceae, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, 0303 health sciences, Autotrophic Processes, Phylogenetic tree, biology, food and beverages, Mycorrhiza, plastome, Heterotrophic Processes, 15. Life on land, biology.organism_classification, Biological Evolution, mixotrophie, Chloroplast DNA, Evolutionary biology
Abstract

Mixotrophic species use both organic and mineral carbon sources. Some mixotrophic plants combine photosynthesis and a nutrition called mycoheterotrophy, where carbon is obtained from fungi forming mycorrhizal symbiosis with their roots. These species can lose photosynthetic abilities and evolve full mycoheterotrophy. Besides morphological changes, the latter transition is associated with a deep alteration of the plastid genome. Photosynthesis-related genes are lost first, followed by housekeeping genes, eventually resulting in a highly reduced genome. Whether relaxation of selective constraints already occurs for the plastid genome of mixotrophic species, which remain photosynthetic, is unclear. This is partly due to the difficulty of comparing plastid genomes of autotrophic, mixotrophic, and mycoheterotrophic species in a narrow phylogenetic framework. We address this question in the orchid tribe Neottieae, where this large assortment of nutrition types occurs. We sequenced 13 new plastid genomes, including 9 mixotrophic species and covering all 6 Neottieae genera. We investigated selective pressure on plastid genes in each nutrition type and conducted a phylogenetic inference of the group. Surprisingly, photosynthesis-related genes did not experience selection relaxation in mixotrophic species compared with autotrophic relatives. Conversely, we observed evidence for selection intensification for some plastid genes. Photosynthesis is thus still under purifying selection, maybe because of its role in fruit formation and thus reproductive success. Phylogenetic analysis resolved most relationships, but short branches at the base of the tree suggest an evolutionary radiation at the beginning of Neottieae history, which, we hypothesize, may be linked to mixotrophy emergence.

Published
2019

32. Mitochondrial Transcriptome Control and Intercompartment Cross-Talk During Plant Development

Author

Etienne Delannoy, Daria Mileshina, Rana Khalid Iqbal, Romain Val, José M. Gualberto, André Dietrich, Jan Barciszewski, Frédérique Weber-Lotfi, Maciej Szymanski, Adnan Khan Niazi, Eliza Wyszko, Ludivine Soubigou-Taconnat, Marta M. Gabryelska, Institut de biologie moléculaire des plantes (IBMP), Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institute of Bioorganic Chemistry [Poznań], Polska Akademia Nauk = Polish Academy of Sciences (PAN), Adam Mickiewicz University in Poznań (UAM), Université de Strasbourg (UNISTRA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), Polska Akademia Nauk (PAN), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Niazi, Adnan Khan, Delannoy, Etienne, Iqbal, Rana Khalid, and Dietrich, André

Subjects
0106 biological sciences, 0301 basic medicine, RNA, Mitochondrial, Arabidopsis, Down-Regulation, Plant Development, Mitochondrion, Biology, cytoplasmic male sterility (CMS), 01 natural sciences, Genome, Article, Transcriptome, retrograde regulation, 03 medical and health sciences, ribozyme, plant mitochondria, Gene Expression Regulation, Plant, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Tobacco, Arabidopsis thaliana, RNA, Catalytic, RNA, Messenger, lcsh:QH301-705.5, RNA trafficking, Cell Nucleus, Base Sequence, Cytoplasmic male sterility, anterograde regulation, signaling, RNA, General Medicine, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, biology.organism_classification, RNA tracking, Cell biology, Mitochondria, Up-Regulation, 030104 developmental biology, lcsh:Biology (General), RNA, Plant, Transfer RNA, Retrograde signaling, 010606 plant biology & botany
Abstract

We address here organellar genetic regulation and intercompartment genome coordination. We developed earlier a strategy relying on a tRNA-like shuttle to mediate import of nuclear transgene-encoded custom RNAs into mitochondria in plants. In the present work, we used this strategy to drive trans-cleaving hammerhead ribozymes into the organelles, to knock down specific mitochondrial RNAs and analyze the regulatory impact. In a similar approach, the tRNA mimic was used to import into mitochondria in Arabidopsis thaliana the orf77, an RNA associated with cytoplasmic male sterility in maize and possessing sequence identities with the atp9 mitochondrial RNA. In both cases, inducible expression of the transgenes allowed to characterise early regulation and signaling responses triggered by these respective manipulations of the organellar transcriptome. The results imply that the mitochondrial transcriptome is tightly controlled by a &ldquo, buffering&rdquo, mechanism at the early and intermediate stages of plant development, a control that is released at later stages. On the other hand, high throughput analyses showed that knocking down a specific mitochondrial mRNA triggered a retrograde signaling and an anterograde nuclear transcriptome response involving a series of transcription factor genes and small RNAs. Our results strongly support transcriptome coordination mechanisms within the organelles and between the organelles and the nucleus.

Published
2019

33. Two ecotype-related long non-coding RNAs in the environmental control of root growth

Author

Laetitia Scalisi, Aurélie Christ, Thomas Roulé, Caroline Hartmann, Marc Gabriel, Thomas Blein, Coline Balzergue, Martin Crespi, Laurent Nussaume, Daniel Gautheret, Thierry Desnos, Céline Sorin, Etienne Delannoy, Marie-Laure Martin-Magniette, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Signalisation de l'Adaptation des Végétaux à l'Environnement (SAVE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Plant Environmental Physiology and Stress Signaling (PEPSS), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
2. Zero hunger, 0106 biological sciences, Genetics, 0303 health sciences, Ecotype, 15. Life on land, Biology, 01 natural sciences, Genome, Transcriptome, 03 medical and health sciences, chemistry.chemical_compound, Intergenic region, chemistry, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Gene expression, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Adaptation, Gene, DNA, 030304 developmental biology, 010606 plant biology & botany
Abstract

BackgroundRoot architecture varies widely between species and even between ecotypes of the same species despite the strong conservation of the protein-coding portion of their genomes. In contrast, non-coding RNAs evolved rapidly between ecotypes and may control their differential responses to the environment as several long non-coding RNAs (lncRNAs) can quantitatively regulate gene expression.ResultsRoots from Columbia (Col) and Landsbergerecta(Ler) ecotypes respond differently to phosphate starvation. We compared complete transcriptomes (mRNAs, lncRNAs and small RNAs) of root tips from these two ecotypes during early phosphate starvation. We identified thousands of new lncRNAs categorized as intergenic or antisense RNAs that were largely conserved at DNA level in these ecotypes. In contrast to coding genes, many lncRNAs were specifically transcribed in one ecotype and/or differentially expressed between ecotypes independently of the phosphate condition. These ecotype-related lncRNAs were characterized by analyzing their sequence variability among plants and their link with siRNAs. Our analysis identified 675 lncRNAs differentially expressed between the two ecotypes including specific antisense RNAs targeting key regulators of root growth responses. Mis-regulation of several intergenic lncRNAs showed that at least two ecotype-related lncRNAs regulate primary root growth in Col.ConclusionsThe in depth exploration of the non-coding transcriptome of two ecotypes identified thousands of new lncRNAs showing specific expression in root apexes. De-regulation of two ecotype-related lncRNAs revealed a new pathway involved in the regulation of primary root growth. The non-coding genome may reveal novel mechanisms involved in ecotype adaptation of roots to different soil environments.

Published
2019

34. Bioinformatic analysis of chloroplast gene expression and RNA posttranscriptional maturations using RNA Sequencing

Author

Etienne Delannoy, Véronique Brunaud, Guillem Rigaill, Claire Lurin, Bastien Malbert, Institut National de la Recherche Agronomique (INRA), Université d'Évry-Val-d'Essonne (UEVE), Université Sorbonne Paris Cité (COMUE) (USPC), Université Paris Saclay (COmUE), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), and Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, 0301 basic medicine, Nuclear gene, Organellar RNAseq, [SDV]Life Sciences [q-bio], RNA, food and beverages, Computational biology, Mitochondrion, Biology, Processing, Splicing, 01 natural sciences, Genome, Editing, Chloroplast, Transcriptome, 03 medical and health sciences, 030104 developmental biology, Gene expression, RNA splicing, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Differentially expressed, Chloroplast transcriptome, 010606 plant biology & botany
Abstract

International audience; Sequencing of total RNA enables the study of the whole plant transcriptome resulting from the simultaneous expression of the three genomes of plant cells (located in the nucleus, mitochondrion and chloroplast). While commonly used for the quantification of the nuclear gene expression, this method remains complex and challenging when applied to organellar genomes and/ or when used to quantify posttranscriptional RNA maturations. Here we propose a complete bioinformatical and statistical pipeline to fully characterize the differences in the chloroplast transcriptome between two conditions. Experimental design as well as bioinformatics and statistical analyses are described in order to quantify both gene expression and RNA posttranscriptional maturations, i.e., RNA splicing, editing, and processing, and identify statistically significant differences.

Published
2018

35. Homoeologous exchanges cause extensive dosage-dependent gene expression changes in an allopolyploid crop

Author

Guillem Rigaill, Eric Jenczewski, Catherine Charpentier, Sandrine Balzergue, Delphine Charif, Andrew H. Lloyd, Aurélien Blary, Etienne Delannoy, Joseph Tran, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université Sorbonne Paris Cité (COMUE) (USPC), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut National de la Recherche Agronomique (INRA), ANR project ANR-2010- BLANC-628 SVSE7- DUPLIC and a grant from the Biology and Plant Breeding division of INRA (AAP-GAP-2012- VARCO), LabEx Saclay Plant Sciences-SPS (ANR-10-LABX-0040-SPS), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0301 basic medicine, Genome evolution, Physiology, Gene Dosage, Plant Science, Biology, Gene dosage, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, Structural variation, Polyploidy, 03 medical and health sciences, homoeologous exchanges, Gene duplication, Gene expression, Genetic variation, Copy-number variation, Gene, Genetics, Recombination, Genetic, meiotic recombination, Brassica napus (Rapeseed), Sequence Analysis, RNA, Brassica napus, polyploid, copy number variation, Genetic Variation, 030104 developmental biology, Organ Specificity, gene expression, Genome, Plant
Abstract

International audience; Structural variation is a major source of genetic diversity and an important substrate for selection. In allopolyploids, homoeologous exchanges (i.e. between the constituent subgenomes) are a very frequent type of structural variant. However, their direct impact on gene content and gene expression had not been determined. Here, we used a tissue-specific mRNA-Seq dataset to measure the consequences of homoeologous exchanges (HE) on gene expression in Brassica napus, a representative allotetraploid crop. We demonstrate that expression changes are proportional to the change in gene copy number triggered by the HEs. Thus, when homoeologous gene pairs have unbalanced transcriptional contributions before the HE, duplication of one copy does not accurately compensate for loss of the other and combined homoeologue expression also changes. These effects are, however, mitigated over time. This study sheds light on the origins, timing and functional consequences of homeologous exchanges in allopolyploids. It demonstrates that the interplay between new structural variation and the resulting impacts on gene expression, influences allopolyploid genome evolution.

Published
2018

36. Low phosphate activates STOP1-ALMT1 to rapidly inhibit root cell elongation

Author

Jean-Marie Teulon, Edith Laugier, Jean Armengaud, Serge Chiarenza, Audrey Creff, Marie-Christine Thibaud, Benjamin Péret, Steffen Abel, Jens Daniel Müller, Agnès Hagège, Coline Balzergue, Pascale David, Thierry Desnos, Marie Bissler, Christian Godon, Noëlle Becuwe-Linka, Corinne Brouchoud, Etienne Delannoy, Thibault Dartevelle, Claudia-Nicole Meisrimler, Laurent Nussaume, Hélène Javot, Jean-Luc Pellequer, Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Biologie végétale et microbiologie environnementale - UMR7265 (BVME), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Signalisation de l'Adaptation des Végétaux à l'Environnement (SAVE), Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale (IBS - UMR 5075), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Leibniz-Institut für Pflanzenbiochemie, Equipe Développement et Plasticité du Système Racinaire (PLASTICITE), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Innovations technologiques pour la Détection et le Diagnostic (LI2D), Service de Pharmacologie et Immunoanalyse (SPI), Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Médicaments et Technologies pour la Santé (MTS), CEA (APTTOX021401, APTTOX021403), ANR11-RSNR-0005,DEMETERRES, ANR-09-BLAN-0118,CHEMIGENA,Génétique d'une voie limitant la croissance racinaire d'Arabidopsis en réponse à la carence phosphatée(2009), ANR-12-ADAP-0019,RNAdapt,Les ARN non-codants dans l'adaptation de la croissance racinaire à la carence phosphate(2012), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de biologie structurale (IBS - UMR 5075 ), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Médicaments et Technologies pour la Santé (MTS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANR-11-RSNR-0005,DEMETERRES,Développement de Méthodes bio-et Eco-Technologiques pour la Remédiation Raisonnée des Effluents et des Sols en appui à une stratégie de réhabilitation agricole post-accidentelle(2011), Plant Environmental Physiology and Stress Signaling (PEPSS), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) ( BIAM ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ), Biologie végétale et microbiologie environnementale - UMR7265 ( BVME ), Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Aix Marseille Université ( AMU ), Biochimie et Physiologie Moléculaire des Plantes ( BPMP ), Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Institut de biologie structurale ( IBS - UMR 5075 ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ), Laboratoire de Biologie du Développement des Plantes ( LBDP ), Université de la Méditerranée - Aix-Marseille 2-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ), Equipe Développement et Plasticité du Système Racinaire ( PLASTICITE ), Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Laboratoire Innovations technologiques pour la Détection et le Diagnostic ( LI2D ), Service de Pharmacologie et Immunoanalyse ( SPI ), Département Médicaments et Technologies pour la Santé ( DMTS ), Direction de Recherche Fondamentale (CEA) ( DRF (CEA) ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) ( DRF (CEA) ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Département Médicaments et Technologies pour la Santé ( DMTS ), Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay-Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Saclay, Biologie cellulaire et moléculaire des plantes et des bactéries ( BCMPB ), and Investissements d'avenir RSNR Demeterres

Subjects
0106 biological sciences, 0301 basic medicine, immunité cellulaire, Arabidopsis, Malates, Organic Anion Transporters, General Physics and Astronomy, Plant Roots, 01 natural sciences, chemistry.chemical_compound, Cell Wall, Gene Expression Regulation, Plant, Arabidopsis thaliana, Multidisciplinary, food and beverages, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Plants, Genetically Modified, Apoplast, Hedgehog signaling pathway, Cell biology, Biochemistry, Oxidoreductases, paroi cellulaire, Signal Transduction, [ SDV.BV.BOT ] Life Sciences [q-bio]/Vegetal Biology/Botanics, Science, Iron, Meristem, Cell Enlargement, Biology, capacité de croissance, Article, General Biochemistry, Genetics and Molecular Biology, Phosphates, Cell wall, 03 medical and health sciences, développement de la plante, Transcription factor, Peroxidase, phosphate, prolifération cellulaire, Arabidopsis Proteins, Cell growth, Callose, arabidopsis thaliana, élongation cellulaire, General Chemistry, biology.organism_classification, racine, 030104 developmental biology, chemistry, Transcription Factors, 010606 plant biology & botany
Abstract

Environmental cues profoundly modulate cell proliferation and cell elongation to inform and direct plant growth and development. External phosphate (Pi) limitation inhibits primary root growth in many plant species. However, the underlying Pi sensory mechanisms are unknown. Here we genetically uncouple two Pi sensing pathways in the root apex of Arabidopsis thaliana. First, the rapid inhibition of cell elongation in the transition zone is controlled by transcription factor STOP1, by its direct target, ALMT1, encoding a malate channel, and by ferroxidase LPR1, which together mediate Fe and peroxidase-dependent cell wall stiffening. Second, during the subsequent slow inhibition of cell proliferation in the apical meristem, which is mediated by LPR1-dependent, but largely STOP1–ALMT1-independent, Fe and callose accumulate in the stem cell niche, leading to meristem reduction. Our work uncovers STOP1 and ALMT1 as a signalling pathway of low Pi availability and exuded malate as an unexpected apoplastic inhibitor of root cell wall expansion., Low Pi availability inhibits primary root growth, but the sensory mechanisms are not known. Here the authors uncover a signalling pathway regulating Pi-mediated root growth inhibition in Arabidopsis, involving the transcription factor STOP1, its direct target ALMT1, a malate channel, and ferroxidase LPR1.

Published
2017

37. Two interacting PPR proteins are major Arabidopsis editing factors in plastid and mitochondria

Author

Benjamin Broche, Etienne Delannoy, Alexandra Avon, Mizuki Takenaka, Damien Guillaumot, Richard Berthomé, Geert De Jaeger, Kevin Baudry, Guillem Rigaill, Andéol Falcon de Longevialle, Mauricio Lopez-Obando, Claire Lurin, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA), Université Paris Sud (Paris 11), Université d'Evry Val d'Essonne, Université Paris-Saclay, Université Paris Diderot - Paris 7 (UPD7), Université Sorbonne Paris Cité (USPC), Laboratoire Plant Process Innovation, Génopole, Molekulare Botanik, Universität Ulm - Ulm University [Ulm, Allemagne], Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Department of Plant Biotechnology and Bioinformatics, Ghent University [Belgium] (UGENT), VIB Center for Plant Systems Biology, Ministere de la Recherche et de l'Enseignement Superieur, Labex Saclay Plant Sciences-SPS postdoctoral fellowship, DFG, Labex Saclay Plant Sciences-SPS : ANR-10-LABX-0040-SPS, Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University [Belgium] (UGENT), Center for Plant Systems Biology (PSB Center), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), Lurin, Claire, and Universiteit Gent = Ghent University (UGENT)

Subjects
0301 basic medicine, RNA editing, Chloroplasts, RNA-binding protein, Biology, plastide, arn mitochondrial, organelles, pentatricopeptide repeat, 03 medical and health sciences, Gene expression, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plastid, plastids, Tandem affinity purification, Genetics, Multidisciplinary, Vegetal Biology, Arabidopsis Proteins, RNA, RNA-Binding Proteins, Biological Sciences, Mitochondria, arabidopsis, 030104 developmental biology, Pentatricopeptide repeat, Biogenesis, Biologie végétale
Abstract

RNA editing is converting hundreds of cytosines into uridines during organelle gene expression of land plants. The pentatricopeptide repeat (PPR) proteins are at the core of this posttranscriptional RNA modification. Even if a PPR protein defines the editing site, a DYW domain of the same or another PPR protein is believed to catalyze the deamination. To give insight into the organelle RNA editosome, we performed tandem affinity purification of the plastidial CHLOROPLAST BIOGENESIS 19 (CLB19) PPR editing factor. Two PPR proteins, dually targeted to mitochondria and chloroplasts, were identified as potential partners of CLB19. These two proteins, a P-type PPR and a member of a small PPR-DYW subfamily, were shown to interact in yeast. Insertional mutations resulted in embryo lethality that could be rescued by embryo-specific complementation. A transcriptome analysis of these complemented plants showed major editing defects in both organelles with a very high PPR type specificity, indicating that the two proteins are core members of E+-type PPR editosomes.

Published
2017

38. Function of the plant DNA polymerase epsilon in replicative stress sensing, a genetic analysis

Author

Etienne Delannoy, Mickael Bourge, Iván del Olmo, Jose A. Jarillo, José Antonio Pedroza-Garcia, Séverine Domenichini, Moussa Benhamed, Manuel Piñeiro, Christelle Mazubert, Rémi Bounon, Catherine Bergounioux, Cécile Raynaud, Zakia Tariq, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), Université Paris-Saclay, Université Sorbonne Paris Cité (USPC), Universidad Politécnica de Madrid (UPM), Institut de Biologie Intégrative de la Cellule (I2BC), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université Paris Sud (Paris 11), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Agence Nationale de la Recherche (ANR) [ANR-2010-JCJC1207-01], Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), UMR 1403 Institut des Sciences des Plantes de Paris Saclay, Institut National de la Recherche Agronomique ( INRA ) -Université Paris Diderot - Paris 7 ( UPD7 ), Université Sorbonne Paris Cité ( USPC ), Universidad Politécnica de Madrid ( UPM ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), and Commissariat à l'Energie Atomique et aux Energies Alternatives

Subjects
DNA Replication, 0301 basic medicine, DNA, Plant, Physiology, DNA repair, DNA damage, DNA polymerase, [SDV]Life Sciences [q-bio], Arabidopsis, DNA polymerase epsilon, Plant Science, DNA polymerase delta, 03 medical and health sciences, chemistry.chemical_compound, Gene Expression Regulation, Plant, Genetics, Hydroxyurea, Polymerase, Nucleic Acid Synthesis Inhibitors, 2. Zero hunger, [ SDV ] Life Sciences [q-bio], Models, Genetic, biology, Arabidopsis Proteins, Reverse Transcriptase Polymerase Chain Reaction, Gene Expression Profiling, DNA replication, Cell Cycle Checkpoints, DNA Polymerase II, Articles, Plants, Genetically Modified, Gene Ontology, 030104 developmental biology, Microscopy, Fluorescence, chemistry, Mutation, biology.protein, RNA Interference, DNA
Abstract

Faithful transmission of the genetic information is essential in all living organisms. DNA replication is therefore a critical step of cell proliferation, because of the potential occurrence of replication errors or DNA damage when progression of a replication fork is hampered causing replicative stress. Like other types of DNA damage, replicative stress activates the DNA damage response, a signaling cascade allowing cell cycle arrest and repair of lesions. The replicative DNA polymerase « (Pol «) was shown to activate the S-phase checkpoint in yeast in response to replicative stress, but whether this mechanism functions in multicellular eukaryotes remains unclear. Here, we explored the genetic interaction between Pol « and the main elements of the DNA damage response in Arabidopsis (Arabidopsis thaliana). We found that mutations affecting the polymerase domain of Pol « trigger ATRdependent signaling leading to SOG1 activation, WEE1-dependent cell cycle inhibition, and tolerance to replicative stress induced by hydroxyurea, but result in enhanced sensitivity to a wide range of DNA damaging agents. Using knock-down lines, we also provide evidence for the direct role of Pol « in replicative stress sensing. Together, our results demonstrate that the role of Pol « in replicative stress sensing is conserved in plants, and provide, to our knowledge, the first genetic dissection of the downstream signaling events in a multicellular eukaryote. © 2017 American Society of Plant Biologists. All rights reserved.

Published
2017

39. Characterization of CYCLOIDEA-like genes in Proteaceae, a basal eudicot family with multiple shifts in floral symmetry

Author

Hervé Sauquet, Etienne Delannoy, Elisabeth Reyes, Martine Le Guilloux, Hélène L. Citerne, Franck Simonnet, Catherine Damerval, Sophie Nadot, Peter H. Weston, Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Université Paris Sud (Paris 11), Centre National de la Recherche Scientifique (CNRS), AgroParisTech, Université Paris-Saclay, Ecologie Systématique et Evolution (ESE), Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), The Royal Botanic Garden Sydney, New South Wales Department of Primary Industries (NSW DPI), PRES UNIVERSUD, Agence Nationale de la Recherche [ANR-07-BLAN-0112], ANR, PRES, Australian Biological Resources Study, Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) ( GQE-Le Moulon ), Institut National de la Recherche Agronomique ( INRA ) -Université Paris-Sud - Paris 11 ( UP11 ) -AgroParisTech-Centre National de la Recherche Scientifique ( CNRS ), Centre National de la Recherche Scientifique ( CNRS ), UMR 8079 Laboratoire Ecologie, Systématique et Evolution, UMR 1403 Institut des Sciences des Plantes de Paris Saclay, Institut National de la Recherche Agronomique ( INRA ) -Université Paris Diderot - Paris 7 ( UPD7 ), and New South Wales Department of Primary Industries ( NSW DPI )

Subjects
0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Plant Science, Flowers, Genes, Plant, CYCLOIDEA, 01 natural sciences, Proteaceae, 03 medical and health sciences, Phylogenetics, Molecular evolution, Gene Expression Regulation, Plant, Botany, Floral symmetry, Eudicots, molecular evolution, Phylogeny, basal eudicots, biology, [ SDV ] Life Sciences [q-bio], fungi, food and beverages, Sequence Analysis, DNA, Original Articles, floral evolution, biology.organism_classification, floral symmetry, 030104 developmental biology, Evolutionary biology, Evolutionary developmental biology, Perianth, Grevillea, 010606 plant biology & botany, Transcription Factors
Abstract

center dot Background and Aims The basal eudicot family Proteaceae (approx. 1700 species) shows considerable variation in floral symmetry but has received little attention in studies of evolutionary development at the genetic level. A framework for understanding the shifts in floral symmetry in Proteaceae is provided by reconstructing ancestral states on an upated phylogeny of the family, and homologues of CYCLOIDEA (CYC), a key gene for the control of floral symmetry in both monocots and eudicots, are characterized. center dot Methods Perianth symmetry transitions were reconstructed on a new species-level tree using parsimony and maximum likelihood. CYC-like genes in 35 species (31 genera) of Proteaceae were sequenced and their phylogeny was reconstructed. Shifts in selection pressure following gene duplication were investigated using nested branch-site models of sequence evolution. Expression patterns of CYC homologues were characterized in three species of Grevillea with different types of floral symmetry. center dot Key Results Zygomorphy has evolved 10-18 times independently in Proteaceae from actinomorphic ancestors, with at least four reversals to actinomorphy. A single duplication of CYC-like genes occurred prior to the diversification of Proteaceae, with putative loss or divergence of the ProtCYC1 paralogue in more than half of the species sampled. No shifts in selection pressure were detected in the branches subtending the two ProtCYC paralogues. However, the amino acid sequence preceding the TCP domain is strongly divergent in Grevillea ProtCYC1 compared with other species. ProtCYC genes were expressed in developing flowers of both actinomorphic and zygomorphic Grevillea species, with late asymmetric expression in the perianth of the latter. center dot Conclusion Proteaceae is a remarkable family in terms of the number of transitions in floral symmetry. Furthermore, although CYC-like genes in Grevillea have unusual sequence characteristics, they display patterns of expression that make them good candidates for playing a role in the establishment of floral symmetry.

Published
2017

40. Synthetic data sets for the identification of key ingredients for RNA-seq differential analysis

Author

Eddy Blondet, Guillem Rigaill, Jose Caius, Cathy Maugis-Rabusseau, Claire Lurin, Véronique Brunaud, Marie-Laure Martin-Magniette, Andrea Rau, Ludivine Soubigou-Taconnat, Odile Rogier, Etienne Delannoy, Sébastien Aubourg, Sandrine Balzergue, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Université Sorbonne Paris Cité (USPC), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut de Mathématiques de Toulouse UMR5219 (IMT), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Université Fédérale Toulouse Midi-Pyrénées, Mathématiques et Informatique Appliquées (MIA-Paris), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Unité de recherche Amélioration, Génétique et Physiologie Forestières (AGPF), Institut National de la Recherche Agronomique (INRA), Université Toulouse Capitole (UT Capitole), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université Toulouse - Jean Jaurès (UT2J), Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse 1 Capitole (UT1)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, 0301 basic medicine, Generalized linear model, Normalization (statistics), Computer science, differential analysis, [SDV]Life Sciences [q-bio], genetic processes, Arabidopsis, Datasets as Topic, RNA-Seq, computer.software_genre, 01 natural sciences, benchmark data set, Differential analysis, 03 medical and health sciences, arn, Histogram, Humans, Computer Simulation, natural sciences, rna, Molecular Biology, Models, Statistical, acide ribonucléique, Arabidopsis Proteins, Sequence Analysis, RNA, Gene Expression Profiling, probabilities, High-Throughput Nucleotide Sequencing, nucleotide sequence, statistique, séquence nucléotidique, Synthetic data sets, Visualization, 030104 developmental biology, probabilité, Parametric model, Data mining, RNA-seq, Transcriptome, computer, Software, 010606 plant biology & botany, Information Systems, expression des gènes
Abstract

Numerous statistical pipelines are now available for the differential analysis of gene expression measured with RNA-sequencing technology. Most of them are based on similar statistical frameworks after normalization, differing primarily in the choice of data distribution, mean and variance estimation strategy and data filtering. We propose an evaluation of the impact of these choices when few biological replicates are available through the use of synthetic data sets. This framework is based on real data sets and allows the exploration of various scenarios differing in the proportion of non-differentially expressed genes. Hence, it provides an evaluation of the key ingredients of the differential analysis, free of the biases associated with the simulation of data using parametric models. Our results show the relevance of a proper modeling of the mean by using linear or generalized linear modeling. Once the mean is properly modeled, the impact of the other parameters on the performance of the test is much less important. Finally, we propose to use the simple visualization of the raw P-value histogram as a practical evaluation criterion of the performance of differential analysis methods on real data sets.

Published
2016

41. A novel role for the root cap in phosphate uptake and homeostasis

Author

Tomoko M. Nakanishi, Laurent Nussaume, Serge Chiarenza, Etienne Delannoy, Hélène Javot, Benjamin Péret, Jean-François Arrighi, Satomi Kanno, Elena Marin, Richard Berthomé, Marie-Christine Thibaud, Vincent Bayle, Biologie végétale et microbiologie environnementale - UMR7265 (BVME), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Plant Environmental Physiology and Stress Signaling (PEPSS), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Tokyo University of Science [Tokyo], CEA-TRANSRAD Transrad 2012 JSPS 22880009 Marie Curie Reintegration grant PIRG05GA2009 249173 PIGR05GA2009 249173, ANR-11-RSNR-0005,DEMETERRES,Développement de Méthodes bio-et Eco-Technologiques pour la Remédiation Raisonnée des Effluents et des Sols en appui à une stratégie de réhabilitation agricole post-accidentelle(2011), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Signalisation de l'Adaptation des Végétaux à l'Environnement (SAVE), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), and ANR11-RSNR-0005,DEMETERRES

Subjects
0106 biological sciences, 0301 basic medicine, QH301-705.5, Science, [SDV]Life Sciences [q-bio], 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Phosphates, 03 medical and health sciences, Transactivation, chemistry.chemical_compound, phosphate homeostasis, Arabidopsis, Botany, Homeostasis, 33P imaging, Biology (General), Psychological repression, Root cap, a. thaliana, arabidopsis, mineral nutrition, plant biology, root cap, 2. Zero hunger, General Immunology and Microbiology, biology, General Neuroscience, Optical Imaging, Phosphorus Isotopes, General Medicine, 15. Life on land, Meristem, biology.organism_classification, Phosphate, Cell biology, Complementation, 030104 developmental biology, Plant Root Cap, chemistry, Medicine, Research Article, 010606 plant biology & botany
Abstract

The root cap has a fundamental role in sensing environmental cues as well as regulating root growth via altered meristem activity. Despite this well-established role in the control of developmental processes in roots, the root cap’s function in nutrition remains obscure. Here, we uncover its role in phosphate nutrition by targeted cellular inactivation or phosphate transport complementation in Arabidopsis, using a transactivation strategy with an innovative high-resolution real-time 33P imaging technique. Remarkably, the diminutive size of the root cap cells at the root-to-soil exchange surface accounts for a significant amount of the total seedling phosphate uptake (approximately 20%). This level of Pi absorption is sufficient for shoot biomass production (up to a 180% gain in soil), as well as repression of Pi starvation-induced genes. These results extend our understanding of this important tissue from its previously described roles in environmental perception to novel functions in mineral nutrition and homeostasis control. DOI: http://dx.doi.org/10.7554/eLife.14577.001, eLife digest All plants need phosphate to grow because it is a major component of DNA and many other biological molecules. Most of the Earth’s soil is poor in phosphate, and so farmland is routinely supplemented with fertilizers to provide crops with this essential nutrient. However, phosphate fertilizers are becoming scarce and their quality is expected to decline in the near future. Plant biologists must therefore determine how to adapt plants to a restricted supply of this resource, in order to sustain high crop yields for the growing world population. Plants are known to absorb phosphate through specific protein-based transporters located in the cells that make up the outer layer of roots. These proteins are highly concentrated at the root tip, and while this specialized tissue is well-known for perceiving gravity and light, it had not been shown to play a role in phosphate absorption. Kanno, Arrighi et al. have now used genetically modified Arabidopsis plants to demonstrate that phosphate can be taken up via the small cells that surround the root tip. The experiments showed that the absorbed phosphate rapidly reaches the leaves within minutes, helps the plant grow and modifies its metabolism. As the root tip can accumulate high amounts of phosphate in order to sustain its own activity, it was important to distinguish uptake of phosphate from the environment from redistribution of phosphate already within the plant. Kanno, Arrighi et al. tackled this issue through the development of a new radioactive micro-imaging technique. Phosphate transporters are also present within the cell layers within the root, but their purpose and activity are not well described. Further studies are needed to analyze the role of other root cell layers in phosphate uptake and transport, and the newly developed techniques will help decipher the mechanisms involved. DOI: http://dx.doi.org/10.7554/eLife.14577.002

Published
2016

44. Role of the Polymerase ϵ sub-unit DPB2 in DNA replication, cell cycle regulation and DNA damage response in Arabidopsis

Author

Zakia Tariq, Jose A. Jarillo, Séverine Domenichini, José Antonio Pedroza-Garcia, Catherine Bergounioux, Elodie Hudik, Cécile Raynaud, Iván del Olmo, Christelle Mazubert, Manuel Piñeiro, Charles I. White, Etienne Delannoy, Mickael Bourge, Moussa Benhamed, Rémi Bounon, White, Charles, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Génétique, Reproduction et Développement (GReD), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Agence Nationale de la Recherche [ANR 2010 JCJC120701], J.A.P.G. benefited from a doctoral contract of the ParisSudUniversity. Funding for open access charge: Agence Nationalede la Recherche [ANR 2010 JCJC1207 01]., Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Génétique, Reproduction et Développement - Clermont Auvergne (GReD), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne (UCA)-Centre National de la Recherche Scientifique (CNRS), Instituto Nacional de Investigación yTecnología Agraria y Alimentaria (INIA ), and Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
0106 biological sciences, 0301 basic medicine, DNA Repair, DNA polymerase, DNA polymerase II, [SDV]Life Sciences [q-bio], Arabidopsis, Eukaryotic DNA replication, [SDV.GEN] Life Sciences [q-bio]/Genetics, Genome Integrity, Repair and Replication, DNA replication, DNA damage response, 01 natural sciences, DNA polymerase delta, 03 medical and health sciences, Control of chromosome duplication, Genetics, S phase, [SDV.GEN]Life Sciences [q-bio]/Genetics, biology, Arabidopsis Proteins, Cell Cycle, DNA Polymerase II, Molecular biology, DNA-Binding Proteins, [SDV] Life Sciences [q-bio], 030104 developmental biology, biology.protein, Origin recognition complex, polymerase ϵ sub-unit DPB2, cell cycle regulation, DNA Damage, 010606 plant biology & botany
Abstract

Faithful DNA replication maintains genome stability in dividing cells and from one generation to the next. This is particularly important in plants because the whole plant body and reproductive cells originate from meristematic cells that retain their proliferative capacity throughout the life cycle of the organism. DNA replication involves large sets of proteins whose activity is strictly regulated, and is tightly linked to the DNA damage response to detect and respond to replication errors or defects. Central to this interconnection is the replicative polymerase DNA Polymerase ϵ (Pol ϵ) which participates in DNA replication per se, as well as replication stress response in animals and in yeast. Surprisingly, its function has to date been little explored in plants, and notably its relationship with DNA Damage Response (DDR) has not been investigated. Here, we have studied the role of the largest regulatory sub-unit of Arabidopsis DNA Pol ϵ DPB2, using an over-expression strategy. We demonstrate that excess accumulation of the protein impairs DNA replication and causes endogenous DNA stress. Furthermore, we show that Pol ϵ dysfunction has contrasting outcomes in vegetative and reproductive cells and leads to the activation of distinct DDR pathways in the two cell types. © 2016 The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Published
2016

45. Arabidopsis CSP41 proteins form multimeric complexes that bind and stabilize distinct plastid transcripts

Author

Ute Armbruster, Andéol Falcon de Longevialle, Dario Leister, Etienne Delannoy, Yafei Qi, Peter Jahns, Ian Small, Christian Schmitz-Linneweber, and Thilo Rühle

Subjects
Chloroplasts, Physiology, RNA-binding protein, Mutant, Arabidopsis, translation, Plant Science, chloroplast, Gene Expression Regulation, Plant, Ribosomal protein, Transcription (biology), Plastids, Plastid, Regulation of gene expression, RNA, Chloroplast, biology, Arabidopsis Proteins, Arabidopsis, chloroplast, gene expression, RNA, RNA-binding protein, transcription, translation, food and beverages, RNA, biology.organism_classification, Research Papers, Molecular biology, Cell biology, Chloroplast, RNA, Plant, gene expression, Protein Multimerization, transcription
Abstract

The spinach CSP41 protein has been shown to bind and cleave chloroplast RNA in vitro. Arabidopsis thaliana, like other photosynthetic eukaryotes, encodes two copies of this protein. Several functions have been described for CSP41 proteins in Arabidopsis, including roles in chloroplast rRNA metabolism and transcription. CSP41a and CSP41b interact physically, but it is not clear whether they have distinct functions. It is shown here that CSP41b, but not CSP41a, is an essential and major component of a specific subset of RNA-binding complexes that form in the dark and disassemble in the light. RNA immunoprecipitation and hybridization to gene chips (RIP-chip) experiments indicated that CSP41 complexes can contain chloroplast mRNAs coding for photosynthetic proteins and rRNAs (16S and 23S), but no tRNAs or mRNAs for ribosomal proteins. Leaves of plants lacking CSP41b showed decreased steady-state levels of CSP41 target RNAs, as well as decreased plastid transcription and translation rates. Representative target RNAs were less stable when incubated with broken chloroplasts devoid of CSP41 complexes, indicating that CSP41 proteins can stabilize target RNAs. Therefore, it is proposed that (i) CSP41 complexes may serve to stabilize non-translated target mRNAs and precursor rRNAs during the night when the translational machinery is less active in a manner responsive to the redox state of the chloroplast, and (ii) that the defects in translation and transcription in CSP41 protein-less mutants are secondary effects of the decreased transcript stability.

Published
2011

46. Rampant Gene Loss in the Underground Orchid Rhizanthella gardneri Highlights Evolutionary Constraints on Plastid Genomes

Author

Catherine Colas des Francs-Small, Sota Fujii, Mark Brundrett, Ian Small, and Etienne Delannoy

Subjects
Rhizanthella gardneri, Chloroplasts, Genomics, Genes, Plant, ENCODE, Genome, Evolution, Molecular, chloroplast, RNA, Transfer, Phylogenetics, Genetics, Cluster Analysis, Photosynthesis, Plastid, Orchidaceae, Molecular Biology, Gene, Research Articles, Phylogeny, Ecology, Evolution, Behavior and Systematics, biology, fungi, tRNA import, food and beverages, Bayes Theorem, gene loss, Plants, biology.organism_classification, Chloroplast, Protein Biosynthesis, mycoheterotroph, Gene Deletion, Genome, Plant
Abstract

Since the endosymbiotic origin of chloroplasts from cyanobacteria 2 billion years ago, the evolution of plastids has been characterized by massive loss of genes. Most plants and algae depend on photosynthesis for energy and have retained ∼110 genes in their chloroplast genome that encode components of the gene expression machinery and subunits of the photosystems. However, nonphotosynthetic parasitic plants have retained a reduced plastid genome, showing that plastids have other essential functions besides photosynthesis. We sequenced the complete plastid genome of the underground orchid, Rhizanthella gardneri. This remarkable parasitic subterranean orchid possesses the smallest organelle genome yet described in land plants. With only 20 proteins, 4 rRNAs, and 9 tRNAs encoded in 59,190 bp, it is the least gene-rich plastid genome known to date apart from the fragmented plastid genome of some dinoflagellates. Despite numerous differences, striking similarities with plastid genomes from unrelated parasitic plants identify a minimal set of protein-encoding and tRNA genes required to reside in plant plastids. This prime example of convergent evolution implies shared selective constraints on gene loss or transfer.

Published
2011

47. Sublethal Cadmium Intoxication In Arabidopsis thaliana Impacts Translation at Multiple Levels

Author

Jean-Pierre Renou, Rodnay Sormani, Sébastien Lageix, Christophe Robaglia, F. Bitton, Jean-Marc Deragon, Elodie Lanet, Etienne Delannoy, Julio Sáez-Vásquez, Institut de Biologie du Développement de Marseille (IBDM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Commissariat a l'Energie Atomique (CEA), Laboratoire Génome et développement des plantes (LGDP), and Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Translation, Transcription, Genetic, Physiology, [SDV]Life Sciences [q-bio], Eukaryotic Initiation Factor-2, Arabidopsis, PROTEIN, Plant Science, 01 natural sciences, Metal poisoning, Gene Expression Regulation, Plant, Eukaryotic initiation factor, Translational regulation, Protein biosynthesis, Arabidopsis eIF2 alpha, GENOME-WIDE ANALYSIS, PHOSPHORYLATION, Cells, Cultured, ComputingMilieux_MISCELLANEOUS, Oligonucleotide Array Sequence Analysis, GENE-EXPRESSION, Regulation of gene expression, 0303 health sciences, Cadmium, OXYGEN DEPRIVATION, General Medicine, Cell biology, POLYRIBOSOME ASSOCIATION, RNA, Plant, MESSENGER-RNA, inorganic chemicals, chemistry.chemical_element, 03 medical and health sciences, Stress, Physiological, Polysome, Botany, TOXIC METAL ACCUMULATION, RNA, Messenger, 030304 developmental biology, Arabidopsis Proteins, RNA, Cell Biology, Abiotic stress, chemistry, Polyribosomes, Protein Biosynthesis, Protein Kinases, STRESS CONDITIONS, MAIZE, 010606 plant biology & botany
Abstract

International audience; To study the impact of translational regulation during heavy metal poisoning, Arabidopsis thaliana cell cultures were submitted to sublethal cadmium stress. At the concentration used, cadmium had a minimal impact on the growth of the culture but induced an accumulation of high molecular weight polysomes without de novo production of new ribosomes together with a reduction of protein synthesis. In addition, cadmium stress induces phosphorylation of eukaryotic initiation factor 2α by GCN2 and, in planta, gcn2 mutants are more sensitive to cadmium stress, suggesting a role for this translational regulation mechanism in the response to cadmium stress. Microarray analysis of total and polysomal RNAs in control and cadmium-treated cells reveals a large class of genes for which a variation in total RNA abundance is not linked to a variation in polysomal loading, suggesting that transcription and translation are uncoupled and that these genes are not recruited at the initiation step of translation.

Published
2011

48. OTP70 is a pentatricopeptide repeat protein of the E subgroup involved in splicing of the plastid transcript rpoC1

Author

Sandra K. Tanz, Sota Fujii, Anne-Laure Chateigner-Boutin, Catherine Colas des Francs-Small, Sabine Kahlau, Etienne Delannoy, Ian Small, and Andéol Falcon de Longevialle

Subjects
0106 biological sciences, Genetics, 0303 health sciences, Exonic splicing enhancer, Intron, food and beverages, Cell Biology, Plant Science, Biology, 01 natural sciences, Post-transcriptional modification, 03 medical and health sciences, SR protein, RNA editing, RNA splicing, Pentatricopeptide repeat, Small nuclear RNA, 030304 developmental biology, 010606 plant biology & botany
Abstract

Summary Over 20 proteins of the pentatricopeptide repeat (PPR) family have been demonstrated to be involved in RNA editing in plant mitochondria and chloroplasts. All of these editing factors contain a so-called ‘E’ domain that has been shown to be essential for editing to occur. The presumption has been that this domain recruits the (unknown) editing enzyme to the RNA. In this report, we show that not all putative E-class PPR proteins are directly involved in RNA editing. Disruption of the OTP70 gene leads to a strong defect in splicing of the plastid transcript rpoC1, leading to a virescent phenotype. The mutant has a chloroplast transcript pattern characteristic of a reduction in plastid-encoded RNA polymerase activity. The E domain of OTP70 is not required for splicing, and can be deleted or replaced by the E domain from the known editing factor CRR4 without loss of rpoC1 splicing. Furthermore, the E domain of OTP70 is incapable of inducing RNA editing when fused to the RNA binding domain of CRR4. We conclude that the truncated E domain of OTP70 is no longer functional in RNA editing, and that the protein has acquired a new function in promoting RNA splicing.

Published
2011

49. The Cytoskeleton and the Peroxisomal-Targeted SNOWY COTYLEDON3 Protein Are Required for Chloroplast Development in Arabidopsis

Author

Etienne Delannoy, Klaus Apel, Ian Small, Murray R. Badger, Verónica Albrecht, Chris Carrie, Klára Šimková, James Whelan, Estelle Giraud, and Barry J. Pogson

Subjects
Chloroplasts, biology, Arabidopsis Proteins, Arabidopsis, food and beverages, Cell Biology, Plant Science, Peroxisome, biology.organism_classification, Plant Leaves, Chloroplast, Mutagenesis, Insertional, Biochemistry, Stroma, Etioplast, Gene Expression Regulation, Plant, Seedlings, Microtubule, Thylakoid, Peroxisomes, Research Articles, Cytoskeleton, Phylogeny, Biogenesis
Abstract

Here, we describe the snowy cotyledon3 (sco3-1) mutation, which impairs chloroplast and etioplast development in Arabidopsis thaliana seedlings. SCO3 is a member of a largely uncharacterized protein family unique to the plant kingdom. The sco3-1 mutation alters chloroplast morphology and development, reduces chlorophyll accumulation, impairs thylakoid formation and photosynthesis in seedlings, and results in photoinhibition under extreme CO2 concentrations in mature leaves. There are no readily apparent changes to chloroplast biology, such as transcription or assembly that explain the disruption to chloroplast biogenesis. Indeed, SCO3 is actually targeted to another organelle, specifically to the periphery of peroxisomes. However, impaired chloroplast development cannot be attributed to perturbed peroxisomal metabolic processes involving germination, fatty acid β-oxidation or photorespiration, though there are so far undescribed changes in low and high CO2 sensitivity in seedlings and young true leaves. Many of the chloroplasts are bilobed, and some have persistent membranous extensions that encircle other cellular components. Significantly, there are changes to the cytoskeleton in sco3-1, and microtubule inhibitors have similar effects on chloroplast biogenesis as sco3-1 does. The localization of SCO3 to the periphery of the peroxisomes was shown to be dependent on a functional microtubule cytoskeleton. Therefore, the microtubule and peroxisome-associated SCO3 protein is required for chloroplast development, and sco3-1, along with microtubule inhibitors, demonstrates an unexpected role for the cytoskeleton and peroxisomes in chloroplast biogenesis.

Published
2010

50. Remodeled Respiration in ndufs4 with Low Phosphorylation Efficiency Suppresses Arabidopsis Germination and Growth and Alters Control of Metabolism at Night

Author

A. Harvey Millar, Etienne H. Meyer, Barry J. Pogson, Gonzalo M. Estavillo, Adam J. Carroll, Ian Small, Tiago Tomaz, Etienne Delannoy, and Sandra K. Tanz

Subjects
Physiology, Cellular respiration, Respiratory chain, NDUFS4, Adenylate kinase, Plant Science, Oxidative phosphorylation, Biology, Mitochondrion, biology.organism_classification, Cell biology, Biochemistry, Arabidopsis, Genetics, Phosphorylation
Abstract

Respiratory oxidative phosphorylation is a cornerstone of cellular metabolism in aerobic multicellular organisms. The efficiency of this process is generally assumed to be maximized, but the presence of dynamically regulated nonphosphorylating bypasses implies that plants can alter phosphorylation efficiency and can benefit from lowered energy generation during respiration under certain conditions. We characterized an Arabidopsis (Arabidopsis thaliana) mutant, ndufs4 (for NADH dehydrogenase [ubiquinone] fragment S subunit 4), lacking complex I of the respiratory chain, which has constitutively lowered phosphorylation efficiency. Through analysis of the changes to mitochondrial function as well as whole cell transcripts and metabolites, we provide insights into how cellular metabolism flexibly adapts to reduced phosphorylation efficiency and why this state may benefit the plant by providing moderate stress tolerance. We show that removal of the single protein subunit NDUFS4 prevents assembly of complex I and removes its function from mitochondria without pleiotropic effects on other respiratory components. However, the lack of complex I promotes broad changes in the nuclear transcriptome governing growth and photosynthetic function. We observed increases in organic acid and amino acid pools in the mutant, especially at night, concomitant with alteration of the adenylate content. While germination is delayed, this can be rescued by application of gibberellic acid, and root growth assays of seedlings show enhanced tolerance to cold, mild salt, and osmotic stress. We discuss these observations in the light of recent data on the knockout of nonphosphorylating respiratory bypass enzymes that show opposite changes in metabolites and stress sensitivity. Our data suggest that the absence of complex I alters the adenylate control of cellular metabolism.

Published
2009

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