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Manantsoa FF, Rakotoarisoa MF, Chaintreuil C, Razakatiana ATE, Gressent F, Pervent M, Bourge M, Andrianandrasana MD, Nouwen N, Randriambanona H, Ramanankierana H, Arrighi JF. Occurrence and diversity of stem nodulation in Aeschynomene and Sesbania legumes from wetlands of Madagascar. Sci Rep 2024; 14:5024. [PMID: 38424094 PMCID: PMC10904833 DOI: 10.1038/s41598-024-55247-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/21/2024] [Indexed: 03/02/2024] Open
Abstract
Legumes have the ability to establish a nitrogen-fixing symbiosis with soil rhizobia that they house in specific organs, the nodules. In most rhizobium-legume interactions, nodulation occurs on the root. However, certain tropical legumes growing in wetlands possess a unique trait: the capacity to form rhizobia-harbouring nodules on the stem. Despite the originality of the stem nodulation process, its occurrence and diversity in waterlogging-tolerant legumes remains underexplored, impeding a comprehensive analysis of its genetics and biology. Here, we aimed at filling this gap by surveying stem nodulation in legume species-rich wetlands of Madagascar. Stem nodulation was readily observed in eight hydrophytic species of the legume genera, Aeschynomene and Sesbania, for which significant variations in stem nodule density and morphology was documented. Among these species, A. evenia, which is used as genetic model to study the rhizobial symbiosis, was found to be frequently stem-nodulated. Two other Aeschynomene species, A. cristata and A. uniflora, were evidenced to display a profuse stem-nodulation as occurs in S. rostrata. These findings extend our knowledge on legumes species that are endowed with stem nodulation and further indicate that A. evenia, A. cristata, A. uniflora and S. rostrata are of special interest for the study of stem nodulation. As such, these legume species represent opportunities to investigate different modalities of the nitrogen-fixing symbiosis and this knowledge could provide cues for the engineering of nitrogen-fixation in non-legume crops.
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Affiliation(s)
- Faustin F Manantsoa
- Laboratoire de Microbiologie de l'Environnement-Centre National de Recherches sur l'Environnement, BP 1739, Fiadanana, Antananarivo, Madagascar
| | - Marrino F Rakotoarisoa
- Department of Ethnobotany and Botany, National Center for Applied Pharmaceutical Research, Antananarivo 101, Madagascar
| | - Clémence Chaintreuil
- Plant Health Institute of Montpellier (PHIM), University Montpellier/IRD/INRAE/CIRAD/SupAgro, Campus de Baillarguet, 34398, Montpellier, France
| | - Adamson T E Razakatiana
- Laboratoire de Microbiologie de l'Environnement-Centre National de Recherches sur l'Environnement, BP 1739, Fiadanana, Antananarivo, Madagascar
| | - Frédéric Gressent
- Plant Health Institute of Montpellier (PHIM), University Montpellier/IRD/INRAE/CIRAD/SupAgro, Campus de Baillarguet, 34398, Montpellier, France
| | - Marjorie Pervent
- Plant Health Institute of Montpellier (PHIM), University Montpellier/IRD/INRAE/CIRAD/SupAgro, Campus de Baillarguet, 34398, Montpellier, France
| | - Mickaël Bourge
- Cytometry Facility, Institute for Integrative Biology of the Cell (I2BC), Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, 91198, Gif-Sur-Yvette, France
| | - Martial D Andrianandrasana
- Laboratoire de Microbiologie de l'Environnement-Centre National de Recherches sur l'Environnement, BP 1739, Fiadanana, Antananarivo, Madagascar
| | - Nico Nouwen
- Plant Health Institute of Montpellier (PHIM), University Montpellier/IRD/INRAE/CIRAD/SupAgro, Campus de Baillarguet, 34398, Montpellier, France
| | - Herizo Randriambanona
- Laboratoire de Microbiologie de l'Environnement-Centre National de Recherches sur l'Environnement, BP 1739, Fiadanana, Antananarivo, Madagascar
| | - Heriniaina Ramanankierana
- Laboratoire de Microbiologie de l'Environnement-Centre National de Recherches sur l'Environnement, BP 1739, Fiadanana, Antananarivo, Madagascar
| | - Jean-François Arrighi
- Plant Health Institute of Montpellier (PHIM), University Montpellier/IRD/INRAE/CIRAD/SupAgro, Campus de Baillarguet, 34398, Montpellier, France.
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Hodin J, Lind C, Marmagne A, Espagne C, Bianchi MW, De Angeli A, Abou-Choucha F, Bourge M, Chardon F, Thomine S, Filleur S. Proton exchange by the vacuolar nitrate transporter CLCa is required for plant growth and nitrogen use efficiency. Plant Cell 2023; 35:318-335. [PMID: 36409008 PMCID: PMC9806559 DOI: 10.1093/plcell/koac325] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
Nitrate is a major nutrient and osmoticum for plants. To deal with fluctuating nitrate availability in soils, plants store this nutrient in their vacuoles. Chloride channel a (CLCa), a 2NO3-/1H+ exchanger localized to the vacuole in Arabidopsis (Arabidopsis thaliana), ensures this storage process. CLCa belongs to the CLC family, which includes anion/proton exchangers and anion channels. A mutation in a glutamate residue conserved across CLC exchangers is likely responsible for the conversion of exchangers to channels. Here, we show that CLCa with a mutation in glutamate 203 (E203) behaves as an anion channel in its native membrane. We introduced the CLCaE203A point mutation to investigate its physiological importance into the Arabidopsis clca knockout mutant. These CLCaE203A mutants displayed a growth deficit linked to the disruption of water homeostasis. Additionally, CLCaE203A expression failed to complement the defect in nitrate accumulation of clca and favored higher N-assimilation at the vegetative stage. Further analyses at the post-flowering stages indicated that CLCaE203A expression results in an increase in N uptake allocation to seeds, leading to a higher nitrogen use efficiency compared to the wild-type. Altogether, these results point to the critical function of the CLCa exchanger on the vacuole for plant metabolism and development.
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Affiliation(s)
- Julie Hodin
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
- UFR Sciences du Vivant, Université Paris Cité, F-75205 Paris Cedex 13, France
| | - Christof Lind
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Anne Marmagne
- AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, 78000 Versailles, France
| | - Christelle Espagne
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Michele Wolfe Bianchi
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
- Université Paris-Est-Créteil-Val-de-Marne, 94010 Creteil Cedex, France
| | - Alexis De Angeli
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Fadi Abou-Choucha
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Mickaël Bourge
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Fabien Chardon
- AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Université Paris-Saclay, INRAE, 78000 Versailles, France
| | - Sebastien Thomine
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
| | - Sophie Filleur
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France
- UFR Sciences du Vivant, Université Paris Cité, F-75205 Paris Cedex 13, France
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Zangarelli C, Arnaiz O, Bourge M, Gorrichon K, Jaszczyszyn Y, Mathy N, Escoriza L, Bétermier M, Régnier V. Developmental timing of programmed DNA elimination in Paramecium tetraurelia recapitulates germline transposon evolutionary dynamics. Genome Res 2022; 32:2028-2042. [PMID: 36418061 PMCID: PMC9808624 DOI: 10.1101/gr.277027.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 11/11/2022] [Indexed: 11/24/2022]
Abstract
With its nuclear dualism, the ciliate Paramecium constitutes a unique model to study how host genomes cope with transposable elements (TEs). P. tetraurelia harbors two germline micronuclei (MICs) and a polyploid somatic macronucleus (MAC) that develops from one MIC at each sexual cycle. Throughout evolution, the MIC genome has been continuously colonized by TEs and related sequences that are removed from the somatic genome during MAC development. Whereas TE elimination is generally imprecise, excision of approximately 45,000 TE-derived internal eliminated sequences (IESs) is precise, allowing for functional gene assembly. Programmed DNA elimination is concomitant with genome amplification. It is guided by noncoding RNAs and repressive chromatin marks. A subset of IESs is excised independently of this epigenetic control, raising the question of how IESs are targeted for elimination. To gain insight into the determinants of IES excision, we established the developmental timing of DNA elimination genome-wide by combining fluorescence-assisted nuclear sorting with high-throughput sequencing. Essentially all IESs are excised within only one endoreplication round (32C to 64C), whereas TEs are eliminated at a later stage. We show that DNA elimination proceeds independently of replication. We defined four IES classes according to excision timing. The earliest excised IESs tend to be independent of epigenetic factors, display strong sequence signals at their ends, and originate from the most ancient integration events. We conclude that old IESs have been optimized during evolution for early and accurate excision by acquiring stronger sequence determinants and escaping epigenetic control.
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Affiliation(s)
- Coralie Zangarelli
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Olivier Arnaiz
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Mickaël Bourge
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Kevin Gorrichon
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Yan Jaszczyszyn
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Nathalie Mathy
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Loïc Escoriza
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Mireille Bétermier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France
| | - Vinciane Régnier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette Cedex, France;,Université Paris Cité, UFR Sciences du Vivant, 75205 Paris Cedex 13, France
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Quilbé J, Lamy L, Brottier L, Leleux P, Fardoux J, Rivallan R, Benichou T, Guyonnet R, Becana M, Villar I, Garsmeur O, Hufnagel B, Delteil A, Gully D, Chaintreuil C, Pervent M, Cartieaux F, Bourge M, Valentin N, Martin G, Fontaine L, Droc G, Dereeper A, Farmer A, Libourel C, Nouwen N, Gressent F, Mournet P, D'Hont A, Giraud E, Klopp C, Arrighi JF. Genetics of nodulation in Aeschynomene evenia uncovers mechanisms of the rhizobium-legume symbiosis. Nat Commun 2021; 12:829. [PMID: 33547303 PMCID: PMC7864950 DOI: 10.1038/s41467-021-21094-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 01/07/2021] [Indexed: 01/30/2023] Open
Abstract
Among legumes (Fabaceae) capable of nitrogen-fixing nodulation, several Aeschynomene spp. use a unique symbiotic process that is independent of Nod factors and infection threads. They are also distinctive in developing root and stem nodules with photosynthetic bradyrhizobia. Despite the significance of these symbiotic features, their understanding remains limited. To overcome such limitations, we conduct genetic studies of nodulation in Aeschynomene evenia, supported by the development of a genome sequence for A. evenia and transcriptomic resources for 10 additional Aeschynomene spp. Comparative analysis of symbiotic genes substantiates singular mechanisms in the early and late nodulation steps. A forward genetic screen also shows that AeCRK, coding a receptor-like kinase, and the symbiotic signaling genes AePOLLUX, AeCCamK, AeCYCLOPS, AeNSP2, and AeNIN are required to trigger both root and stem nodulation. This work demonstrates the utility of the A. evenia model and provides a cornerstone to unravel mechanisms underlying the rhizobium-legume symbiosis.
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Affiliation(s)
- Johan Quilbé
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Léo Lamy
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
- Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Laurent Brottier
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Philippe Leleux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
- Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Joël Fardoux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Ronan Rivallan
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Thomas Benichou
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Rémi Guyonnet
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Manuel Becana
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080, Zaragoza, Spain
| | - Irene Villar
- Departamento de Nutrición Vegetal, Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Apartado 13034, 50080, Zaragoza, Spain
| | - Olivier Garsmeur
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Bárbara Hufnagel
- BPMP, Université de Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - Amandine Delteil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Djamel Gully
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Clémence Chaintreuil
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Marjorie Pervent
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Fabienne Cartieaux
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Mickaël Bourge
- Cytometry Facility, Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Nicolas Valentin
- Cytometry Facility, Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Guillaume Martin
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Loïc Fontaine
- BGPI, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, F-34398, Montpellier, France
| | - Gaëtan Droc
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Alexis Dereeper
- Institut de Recherche pour le Développement (IRD), University of Montpellier, DIADE, IPME, Montpellier, France
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, NM, USA
| | - Cyril Libourel
- LRSV, Université de Toulouse, CNRS, UPS, Castanet-Tolosan, France
| | - Nico Nouwen
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Frédéric Gressent
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Pierre Mournet
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Angélique D'Hont
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Eric Giraud
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France
| | - Christophe Klopp
- Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Jean-François Arrighi
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), UMR IRD/ SupAgro/INRAE/ UM2 /CIRAD, TA-A82/J, Campus de Baillarguet 34398, Montpellier, cedex 5, France.
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Malli S, Bories C, Bourge M, Loiseau P, Bouchemal K. Surface-dependent endocytosis of poly(isobutylcyanoacrylate) nanoparticles by Trichomonas vaginalis. Int J Pharm 2018; 548:276-287. [DOI: 10.1016/j.ijpharm.2018.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 06/29/2018] [Accepted: 07/01/2018] [Indexed: 12/14/2022]
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Pirrello J, Deluche C, Frangne N, Gévaudant F, Maza E, Djari A, Bourge M, Renaudin JP, Brown S, Bowler C, Zouine M, Chevalier C, Gonzalez N. Transcriptome profiling of sorted endoreduplicated nuclei from tomato fruits: how the global shift in expression ascribed to DNA ploidy influences RNA-Seq data normalization and interpretation. Plant J 2018; 93:387-398. [PMID: 29172253 DOI: 10.1111/tpj.13783] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/09/2017] [Accepted: 11/14/2017] [Indexed: 06/07/2023]
Abstract
As part of normal development most eukaryotic organisms, ranging from insects and mammals to plants, display variations in nuclear ploidy levels resulting from somatic endopolyploidy. Endoreduplication is the major source of endopolyploidy in higher plants. Endoreduplication is a remarkable characteristic of the fleshy pericarp tissue of developing tomato fruits, where it establishes a highly integrated cellular system that acts as a morphogenetic factor supporting cell growth. However, the functional significance of endoreduplication is not fully understood. Although endoreduplication is thought to increase metabolic activity due to a global increase in transcription, the issue of gene-specific ploidy-regulated transcription remains open. To investigate the influence of endoreduplication on transcription in tomato fruit, we tested the feasibility of a RNA sequencing (RNA-Seq) approach using total nuclear RNA extracted from purified populations of flow cytometry-sorted nuclei based on their DNA content. Here we show that cell-based approaches to the study of RNA-Seq profiles need to take into account the putative global shift in expression between samples for correct analysis and interpretation of the data. From ploidy-specific expression profiles we found that the activity of cells inside the pericarp is related both to the ploidy level and their tissue location.
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Affiliation(s)
- Julien Pirrello
- UMR1332 BFP, INRA, Univ. Bordeaux, 33882, Villenave d'Ornon Cedex, France
- GBF, Université de Toulouse, INRA, 31326, Castanet-Tolosan Cedex, France
| | - Cynthia Deluche
- UMR1332 BFP, INRA, Univ. Bordeaux, 33882, Villenave d'Ornon Cedex, France
| | - Nathalie Frangne
- UMR1332 BFP, INRA, Univ. Bordeaux, 33882, Villenave d'Ornon Cedex, France
| | - Frédéric Gévaudant
- UMR1332 BFP, INRA, Univ. Bordeaux, 33882, Villenave d'Ornon Cedex, France
| | - Elie Maza
- GBF, Université de Toulouse, INRA, 31326, Castanet-Tolosan Cedex, France
| | - Anis Djari
- GBF, Université de Toulouse, INRA, 31326, Castanet-Tolosan Cedex, France
| | - Mickaël Bourge
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | | | - Spencer Brown
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
| | - Chris Bowler
- Département de Biologie, IBENS, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005, Paris, France
| | - Mohamed Zouine
- GBF, Université de Toulouse, INRA, 31326, Castanet-Tolosan Cedex, France
| | | | - Nathalie Gonzalez
- UMR1332 BFP, INRA, Univ. Bordeaux, 33882, Villenave d'Ornon Cedex, France
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Brown SC, Bourge M, Maunoury N, Wong M, Wolfe Bianchi M, Lepers-Andrzejewski S, Besse P, Siljak-Yakovlev S, Dron M, Satiat-Jeunemaître B. DNA Remodeling by Strict Partial Endoreplication in Orchids, an Original Process in the Plant Kingdom. Genome Biol Evol 2017; 9:1051-1071. [PMID: 28419219 PMCID: PMC5546068 DOI: 10.1093/gbe/evx063] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2017] [Indexed: 12/12/2022] Open
Abstract
DNA remodeling during endoreplication appears to be a strong developmental characteristic
in orchids. In this study, we analyzed DNA content and nuclei in 41 species of orchids to
further map the genome evolution in this plant family. We demonstrate that the DNA
remodeling observed in 36 out of 41 orchids studied corresponds to strict partial
endoreplication. Such process is developmentally regulated in each wild
species studied. Cytometry data analyses allowed us to propose a model where nuclear
states 2C, 4E, 8E, etc. form a series comprising a fixed proportion, the euploid genome
2C, plus 2–32 additional copies of a complementary part of the genome. The fixed
proportion ranged from 89% of the genome in Vanilla mexicana down to 19%
in V. pompona, the lowest value for all 148 orchids reported.
Insterspecific hybridization did not suppress this phenomenon. Interestingly, this process
was not observed in mass-produced epiphytes. Nucleolar volumes grow with the number of
endocopies present, coherent with high transcription activity in endoreplicated nuclei.
Our analyses suggest species-specific chromatin rearrangement. Towards understanding
endoreplication, V. planifolia constitutes a tractable system for
isolating the genomic sequences that confer an advantage via endoreplication from those
that apparently suffice at diploid level.
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Affiliation(s)
- Spencer C Brown
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex, France
| | - Mickaël Bourge
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex, France
| | - Nicolas Maunoury
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex, France
| | - Maurice Wong
- Service du Développement Rural, Papeete Tahiti, French Polynesia, France
| | - Michele Wolfe Bianchi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex, France
| | | | - Pascale Besse
- UMR 53, PVBMT Université de la Réunion - Cirad, Pôle de Protection des Plantes, St Pierre, France
| | - Sonja Siljak-Yakovlev
- Ecologie Systématique Evolution, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay Cedex, France
| | - Michel Dron
- Institute of Plant Sciences Paris Saclay IPS2, Université Paris-Sud, CNRS, INRA, Université Evry, Université Paris Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Orsay, France
| | - Béatrice Satiat-Jeunemaître
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex, France
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8
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Dambroise E, Simion M, Bourquard T, Bouffard S, Rizzi B, Jaszczyszyn Y, Bourge M, Affaticati P, Heuzé A, Jouralet J, Edouard J, Brown S, Thermes C, Poupon A, Reiter E, Sohm F, Bourrat F, Joly JS. Postembryonic Fish Brain Proliferation Zones Exhibit Neuroepithelial-Type Gene Expression Profile. Stem Cells 2017; 35:1505-1518. [PMID: 28181357 DOI: 10.1002/stem.2588] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 01/04/2023]
Abstract
In mammals, neuroepithelial cells play an essential role in embryonic neurogenesis, whereas glial stem cells are the principal source of neurons at postembryonic stages. By contrast, neuroepithelial-like stem/progenitor (NE) cells have been shown to be present throughout life in teleosts. We used three-dimensional (3D) reconstructions of cleared transgenic wdr12:GFP medaka brains to demonstrate that this cell type is widespread in juvenile and to identify new regions containing NE cells. We established the gene expression profile of optic tectum (OT) NE cells by cell sorting followed by RNA-seq. Our results demonstrate that most OT NE cells are indeed active stem cells and that some of them exhibit long G2 phases. We identified several novel pathways (e.g., DNA repair pathways) potentially involved in NE cell homeostasis. In situ hybridization studies showed that all NE populations in the postembryonic medaka brain have a similar molecular signature. Our findings highlight the importance of NE progenitors in medaka and improve our understanding of NE-cell biology. These cells are potentially useful not only for neural stem cell studies but also for improving the characterization of neurodevelopmental diseases, such as microcephaly. Stem Cells 2017;35:1505-1518.
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Affiliation(s)
- Emilie Dambroise
- INRA CASBAH Group, Neuro-PSI, UMR 9197, CNRS, Gif-sur-Yvette, France
| | - Matthieu Simion
- INRA CASBAH Group, Neuro-PSI, UMR 9197, CNRS, Gif-sur-Yvette, France
| | | | | | - Barbara Rizzi
- Tefor Core Facility, TEFOR Infrastructure, Neuro-PSI, CNRS, Gif-sur-Yvette, France
| | | | | | - Pierre Affaticati
- Tefor Core Facility, TEFOR Infrastructure, Neuro-PSI, CNRS, Gif-sur-Yvette, France
| | - Aurélie Heuzé
- INRA CASBAH Group, Neuro-PSI, UMR 9197, CNRS, Gif-sur-Yvette, France
| | - Julia Jouralet
- Plateforme BM-Gif, Imagif, UMR 9198, CNRS, Gif-sur-Yvette, France
| | - Joanne Edouard
- UMS AMAGEN CNRS, INRA, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | | | | | | | - Frédéric Sohm
- UMS AMAGEN CNRS, INRA, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Franck Bourrat
- INRA CASBAH Group, Neuro-PSI, UMR 9197, CNRS, Gif-sur-Yvette, France
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9
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Maisonnasse P, Bouguyon E, Bourge M, Piton G, Ezquerra A, Deloizy C, Urien C, Leplat JJ, Simon G, Chevalier C, Vincent-Naulleau S, Crisci E, Montoya M, Schwartz-Cornil I, Bertho N. Pig as a biomedical model: Putting the porcine lung dendritic cells/macrophages network into light. Rev Mal Respir 2017. [DOI: 10.1016/j.rmr.2016.10.867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Chaintreuil C, Gully D, Hervouet C, Tittabutr P, Randriambanona H, Brown SC, Lewis GP, Bourge M, Cartieaux F, Boursot M, Ramanankierana H, D'Hont A, Teaumroong N, Giraud E, Arrighi JF. The evolutionary dynamics of ancient and recent polyploidy in the African semiaquatic species of the legume genus Aeschynomene. New Phytol 2016; 211:1077-1091. [PMID: 27061605 DOI: 10.1111/nph.13956] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/04/2016] [Indexed: 06/05/2023]
Abstract
The legume genus Aeschynomene is notable in the ability of certain semiaquatic species to develop nitrogen-fixing stem nodules. These species are distributed in two clades. In the first clade, all the species are characterized by the use of a unique Nod-independent symbiotic process. In the second clade, the species use a Nod-dependent symbiotic process and some of them display a profuse stem nodulation as exemplified in the African Aeschynomene afraspera. To facilitate the molecular analysis of the symbiotic characteristics of such legumes, we took an integrated molecular and cytogenetic approach to track occurrences of polyploidy events and to analyze their impact on the evolution of the African species of Aeschynomene. Our results revealed two rounds of polyploidy: a paleopolyploid event predating the African group and two neopolyploid speciations, along with significant chromosomal variations. Hence, we found that A. afraspera (8x) has inherited the contrasted genomic properties and the stem-nodulation habit of its parental lineages (4x). This study reveals a comprehensive picture of African Aeschynomene diversification. It notably evidences a history that is distinct from the diploid Nod-independent clade, providing clues for the identification of the specific determinants of the Nod-dependent and Nod-independent symbiotic processes, and for comparative analysis of stem nodulation.
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Affiliation(s)
- Clémence Chaintreuil
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
| | - Djamel Gully
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
| | - Catherine Hervouet
- CIRAD, UMR AGAP, Plateau de Cytogénétique Moléculaire, 34398, Montpellier, France
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Herizo Randriambanona
- Laboratoire de Microbiologie de l'Environnement/Centre National de Recherche sur l'Environnement, Antananarivo, 101, Madagascar
| | - Spencer C Brown
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91 198, Gif-sur-Yvette, France
| | - Gwilym P Lewis
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AB, UK
| | - Mickaël Bourge
- Institute of Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91 198, Gif-sur-Yvette, France
| | - Fabienne Cartieaux
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
| | - Marc Boursot
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
| | - Heriniaina Ramanankierana
- Laboratoire de Microbiologie de l'Environnement/Centre National de Recherche sur l'Environnement, Antananarivo, 101, Madagascar
| | - Angélique D'Hont
- CIRAD, UMR AGAP, Plateau de Cytogénétique Moléculaire, 34398, Montpellier, France
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Eric Giraud
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
| | - Jean-François Arrighi
- Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, UMR LSTM, Campus International de Baillarguet, 34398, Montpellier, France
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11
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Maisonnasse P, Bouguyon E, Piton G, Ezquerra A, Urien C, Deloizy C, Bourge M, Leplat JJ, Simon G, Chevalier C, Vincent-Naulleau S, Crisci E, Montoya M, Schwartz-Cornil I, Bertho N. The respiratory DC/macrophage network at steady-state and upon influenza infection in the swine biomedical model. Mucosal Immunol 2016; 9:835-49. [PMID: 26530136 DOI: 10.1038/mi.2015.105] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 08/12/2015] [Indexed: 02/04/2023]
Abstract
Human and mouse respiratory tracts show anatomical and physiological differences, which will benefit from alternative experimental models for studying many respiratory diseases. Pig has been recognized as a valuable biomedical model, in particular for lung transplantation or pathologies such as cystic fibrosis and influenza infection. However, there is a lack of knowledge about the porcine respiratory immune system. Here we segregated and studied six populations of pig lung dendritic cells (DCs)/macrophages (Mθs) as follows: conventional DCs (cDC) 1 and cDC2, inflammatory monocyte-derived DCs (moDCs), monocyte-derived Mθs, and interstitial and alveolar Mθs. The three DC subsets present migratory and naive T-cell stimulation capacities. As observed in human and mice, porcine cDC1 and cDC2 were able to induce T-helper (Th)1 and Th2 responses, respectively. Interestingly, porcine moDCs increased in the lung upon influenza infection, as observed in the mouse model. Pig cDC2 shared some characteristics observed in human but not in mice, such as the expression of FCɛRIα and Langerin, and an intra-epithelial localization. This work, by unraveling the extended similarities of the porcine and human lung DC/Mθ networks, highlights the relevance of pig, both as an exploratory model of DC/Mθ functions and as a model for human inflammatory lung pathologies.
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Affiliation(s)
- P Maisonnasse
- Virologie et Immunologie Moléculaires UR892, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | - E Bouguyon
- Virologie et Immunologie Moléculaires UR892, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | - G Piton
- INRA, UMR Génétique Animale et Biologie Intégrative (GABI), Equipe Génétique Immunité Santé, Jouy-en-Josas, France.,Laboratoire de Radiobiologie et Etude du genome, CEA, Direction des Sciences du Vivant, Institut de Radiobiologie Cellulaire et Moléculaire, Jouy-en-Josas, France
| | - A Ezquerra
- Dpto. de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - C Urien
- Virologie et Immunologie Moléculaires UR892, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | - C Deloizy
- Virologie et Immunologie Moléculaires UR892, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | - M Bourge
- I2BC, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
| | - J-J Leplat
- INRA, UMR Génétique Animale et Biologie Intégrative (GABI), Equipe Génétique Immunité Santé, Jouy-en-Josas, France.,Laboratoire de Radiobiologie et Etude du genome, CEA, Direction des Sciences du Vivant, Institut de Radiobiologie Cellulaire et Moléculaire, Jouy-en-Josas, France
| | - G Simon
- Anses, Laboratoire de Ploufragan/Plouzané, Unité Virologie Immunologie Porcines, BP53, Ploufragan, France.,Université Européenne de Bretagne, Rennes, France
| | - C Chevalier
- Virologie et Immunologie Moléculaires UR892, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | - S Vincent-Naulleau
- INRA, UMR Génétique Animale et Biologie Intégrative (GABI), Equipe Génétique Immunité Santé, Jouy-en-Josas, France.,Laboratoire de Radiobiologie et Etude du genome, CEA, Direction des Sciences du Vivant, Institut de Radiobiologie Cellulaire et Moléculaire, Jouy-en-Josas, France
| | - E Crisci
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Spain
| | - M Montoya
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallès), Spain.,The Pirbright Institute, Surrey, UK
| | - I Schwartz-Cornil
- Virologie et Immunologie Moléculaires UR892, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
| | - N Bertho
- Virologie et Immunologie Moléculaires UR892, Institut National de la Recherche Agronomique, Jouy-en-Josas, France
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12
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Guefrachi I, Pierre O, Timchenko T, Alunni B, Barrière Q, Czernic P, Villaécija-Aguilar JA, Verly C, Bourge M, Fardoux J, Mars M, Kondorosi E, Giraud E, Mergaert P. Bradyrhizobium BclA Is a Peptide Transporter Required for Bacterial Differentiation in Symbiosis with Aeschynomene Legumes. Mol Plant Microbe Interact 2015; 28:1155-66. [PMID: 26106901 DOI: 10.1094/mpmi-04-15-0094-r] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Nodules of legume plants are highly integrated symbiotic systems shaped by millions of years of evolution. They harbor nitrogen-fixing rhizobium bacteria called bacteroids. Several legume species produce peptides called nodule-specific cysteine-rich (NCR) peptides in the symbiotic nodule cells which house the bacteroids. NCR peptides are related to antimicrobial peptides of innate immunity. They induce the endosymbionts into a differentiated, enlarged, and polyploid state. The bacterial symbionts, on their side, evolved functions for the response to the NCR peptides. Here, we identified the bclA gene of Bradyrhizobium sp. strains ORS278 and ORS285, which is required for the formation of differentiated and functional bacteroids in the nodules of the NCR peptide-producing Aeschynomene legumes. The BclA ABC transporter promotes the import of NCR peptides and provides protection against the antimicrobial activity of these peptides. Moreover, BclA can complement the role of the related BacA transporter of Sinorhizobium meliloti, which has a similar symbiotic function in the interaction with Medicago legumes.
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Affiliation(s)
- Ibtissem Guefrachi
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
- 2 Research Unit Biodiversity & Valorization of Arid Areas Bioressources (BVBAA), Faculty of Sciences, Gabès, Tunisia
| | - Olivier Pierre
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Tatiana Timchenko
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Benoît Alunni
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Quentin Barrière
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Pierre Czernic
- 3 Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | | | - Camille Verly
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Mickaël Bourge
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Joël Fardoux
- 3 Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Mohamed Mars
- 2 Research Unit Biodiversity & Valorization of Arid Areas Bioressources (BVBAA), Faculty of Sciences, Gabès, Tunisia
| | - Eva Kondorosi
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
- 4 Institute of Biochemistry, Hungarian Academy of Sciences, Biological Research Centre, Szeged, Hungary
| | - Eric Giraud
- 3 Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Peter Mergaert
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
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13
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Jégu T, Domenichini S, Blein T, Ariel F, Christ A, Kim SK, Crespi M, Boutet-Mercey S, Mouille G, Bourge M, Hirt H, Bergounioux C, Raynaud C, Benhamed M. A SWI/SNF Chromatin Remodelling Protein Controls Cytokinin Production through the Regulation of Chromatin Architecture. PLoS One 2015; 10:e0138276. [PMID: 26457678 PMCID: PMC4601769 DOI: 10.1371/journal.pone.0138276] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 08/26/2015] [Indexed: 02/07/2023] Open
Abstract
Chromatin architecture determines transcriptional accessibility to DNA and consequently gene expression levels in response to developmental and environmental stimuli. Recently, chromatin remodelers such as SWI/SNF complexes have been recognized as key regulators of chromatin architecture. To gain insight into the function of these complexes during root development, we have analyzed Arabidopsis knock-down lines for one sub-unit of SWI/SNF complexes: BAF60. Here, we show that BAF60 is a positive regulator of root development and cell cycle progression in the root meristem via its ability to down-regulate cytokinin production. By opposing both the deposition of active histone marks and the formation of a chromatin regulatory loop, BAF60 negatively regulates two crucial target genes for cytokinin biosynthesis (IPT3 and IPT7) and one cell cycle inhibitor (KRP7). Our results demonstrate that SWI/SNF complexes containing BAF60 are key factors governing the equilibrium between formation and dissociation of a chromatin loop controlling phytohormone production and cell cycle progression.
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Affiliation(s)
- Teddy Jégu
- Institut de Biologie des Plantes, UMR8618 CNRS-Université Paris-Sud XI, Saclay Plant Sciences, Orsay, France
| | - Séverine Domenichini
- Institut de Biologie des Plantes, UMR8618 CNRS-Université Paris-Sud XI, Saclay Plant Sciences, Orsay, France
| | - Thomas Blein
- Institut des Sciences du Végétal, UPR2355 CNRS, Saclay Plant Sciences, Gif-sur-Yvette, France
| | - Federico Ariel
- Institut des Sciences du Végétal, UPR2355 CNRS, Saclay Plant Sciences, Gif-sur-Yvette, France
| | - Aurélie Christ
- Institut des Sciences du Végétal, UPR2355 CNRS, Saclay Plant Sciences, Gif-sur-Yvette, France
| | - Soon-Kap Kim
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
| | - Martin Crespi
- Institut des Sciences du Végétal, UPR2355 CNRS, Saclay Plant Sciences, Gif-sur-Yvette, France
| | | | - Grégory Mouille
- Institut Jean-Pierre Bourgin, UMR1318 INRA/AgroParisTech, Versailles, France
| | - Mickaël Bourge
- Pôle de Biologie Cellulaire, Imagif, Centre de Recherche de Gif, CNRS, IFR87, Gif-sur-Yvette, France
| | - Heribert Hirt
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
| | - Catherine Bergounioux
- Institut de Biologie des Plantes, UMR8618 CNRS-Université Paris-Sud XI, Saclay Plant Sciences, Orsay, France
| | - Cécile Raynaud
- Institut de Biologie des Plantes, UMR8618 CNRS-Université Paris-Sud XI, Saclay Plant Sciences, Orsay, France
| | - Moussa Benhamed
- Institut de Biologie des Plantes, UMR8618 CNRS-Université Paris-Sud XI, Saclay Plant Sciences, Orsay, France
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology KAUST, Thuwal, Saudi Arabia
- * E-mail:
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14
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Vu Manh TP, Elhmouzi-Younes J, Urien C, Ruscanu S, Jouneau L, Bourge M, Moroldo M, Foucras G, Salmon H, Marty H, Quéré P, Bertho N, Boudinot P, Dalod M, Schwartz-Cornil I. Defining Mononuclear Phagocyte Subset Homology Across Several Distant Warm-Blooded Vertebrates Through Comparative Transcriptomics. Front Immunol 2015; 6:299. [PMID: 26150816 PMCID: PMC4473062 DOI: 10.3389/fimmu.2015.00299] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/25/2015] [Indexed: 12/24/2022] Open
Abstract
Mononuclear phagocytes are organized in a complex system of ontogenetically and functionally distinct subsets, that has been best described in mouse and to some extent in human. Identification of homologous mononuclear phagocyte subsets in other vertebrate species of biomedical, economic, and environmental interest is needed to improve our knowledge in physiologic and physio-pathologic processes, and to design intervention strategies against a variety of diseases, including zoonotic infections. We developed a streamlined approach combining refined cell sorting and integrated comparative transcriptomics analyses which revealed conservation of the mononuclear phagocyte organization across human, mouse, sheep, pigs and, in some respect, chicken. This strategy should help democratizing the use of omics analyses for the identification and study of cell types across tissues and species. Moreover, we identified conserved gene signatures that enable robust identification and universal definition of these cell types. We identified new evolutionarily conserved gene candidates and gene interaction networks for the molecular regulation of the development or functions of these cell types, as well as conserved surface candidates for refined subset phenotyping throughout species. A phylogenetic analysis revealed that orthologous genes of the conserved signatures exist in teleost fishes and apparently not in Lamprey.
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Affiliation(s)
- Thien-Phong Vu Manh
- UM2, Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université , Marseille , France ; U1104, INSERM , Marseille , France ; UMR7280, CNRS , Marseille , France
| | - Jamila Elhmouzi-Younes
- UR892, Virologie et Immunologie Moléculaires, INRA, Domaine de Vilvert , Jouy-en-Josas , France
| | - Céline Urien
- UR892, Virologie et Immunologie Moléculaires, INRA, Domaine de Vilvert , Jouy-en-Josas , France
| | - Suzana Ruscanu
- UR892, Virologie et Immunologie Moléculaires, INRA, Domaine de Vilvert , Jouy-en-Josas , France
| | - Luc Jouneau
- UR892, Virologie et Immunologie Moléculaires, INRA, Domaine de Vilvert , Jouy-en-Josas , France
| | - Mickaël Bourge
- IFR87 La Plante et son Environnement, IMAGIF CNRS , Gif-sur-Yvette , France
| | - Marco Moroldo
- CRB GADIE, Génétique Animale et Biologie Intégrative, INRA, Domaine de Vilvert , Jouy-en-Josas , France
| | - Gilles Foucras
- UMR1225, Université de Toulouse, INPT, ENVT , Toulouse , France ; UMR1225, Interactions Hôtes-Agents Pathogènes, INRA , Toulouse , France
| | - Henri Salmon
- UMR1282, Infectiologie et Santé Publique, INRA , Nouzilly , France ; UMR1282, Université François Rabelais de Tours , Tours , France
| | - Hélène Marty
- UMR1282, Infectiologie et Santé Publique, INRA , Nouzilly , France ; UMR1282, Université François Rabelais de Tours , Tours , France
| | - Pascale Quéré
- UMR1282, Infectiologie et Santé Publique, INRA , Nouzilly , France ; UMR1282, Université François Rabelais de Tours , Tours , France
| | - Nicolas Bertho
- UR892, Virologie et Immunologie Moléculaires, INRA, Domaine de Vilvert , Jouy-en-Josas , France
| | - Pierre Boudinot
- UR892, Virologie et Immunologie Moléculaires, INRA, Domaine de Vilvert , Jouy-en-Josas , France
| | - Marc Dalod
- UM2, Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université , Marseille , France ; U1104, INSERM , Marseille , France ; UMR7280, CNRS , Marseille , France
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Bourge M, Fort C, Soler MN, Satiat-Jeunemaître B, Brown SC. A pulse-chase strategy combining click-EdU and photoconvertible fluorescent reporter: tracking Golgi protein dynamics during the cell cycle. New Phytol 2015; 205:938-50. [PMID: 25266734 DOI: 10.1111/nph.13069] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 08/13/2014] [Indexed: 05/12/2023]
Abstract
Imaging or quantifying protein synthesis in cellulo through a well-resolved analysis of the cell cycle (also defining G1 subcompartments) is a methodological challenge. Click chemistry is the method of choice to reveal the thymidine analogue 5-ethynyl-2'-deoxyuridine (EdU) and track proliferating nuclei undergoing DNA synthesis. However, the click reaction quenches fluorescent proteins. Our challenge was to reconcile these two tools. A robust protocol based on a high-resolution cytometric cell cycle analysis in tobacco (Nicotiana tabacum) BY2 cells expressing fluorescent Golgi markers has been established. This was broadly applicable to tissues, cell clusters, and other eukaryotic material, and compatible with Scale clearing. EdU was then used with the photoconvertible protein sialyl transferase (ST)-Kaede as a Golgi marker in a photoconversion pulse-chase cytometric configuration resolving, in addition, subcompartments of G1. Quantitative restoration of protein fluorescence was achieved by introducing acidic EDTA washes to strip the copper from these proteins which were then imaged at neutral pH. The rate of synthesis of this Golgi membrane marker was low during early G1, but in the second half of G1 (30% of cycle duration) much of the synthesis occurred. Marker synthesis then persisted during S and G2. These insights into Golgi biology are discussed in terms of the cell's ability to adapt exocytosis to cell growth needs.
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Affiliation(s)
- Mickaël Bourge
- Pôle de Biologie Cellulaire, Imagif, Centre de Recherche de Gif (FRC3115), CNRS, Saclay Plant Sciences, 91198, Gif-sur-Yvette Cedex, France
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Hudik E, Yoshioka Y, Domenichini S, Bourge M, Soubigout-Taconnat L, Mazubert C, Yi D, Bujaldon S, Hayashi H, De Veylder L, Bergounioux C, Benhamed M, Raynaud C. Chloroplast dysfunction causes multiple defects in cell cycle progression in the Arabidopsis crumpled leaf mutant. Plant Physiol 2014; 166:152-67. [PMID: 25037213 PMCID: PMC4149703 DOI: 10.1104/pp.114.242628] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The majority of research on cell cycle regulation is focused on the nuclear events that govern the replication and segregation of the genome between the two daughter cells. However, eukaryotic cells contain several compartmentalized organelles with specialized functions, and coordination among these organelles is required for proper cell cycle progression, as evidenced by the isolation of several mutants in which both organelle function and overall plant development were affected. To investigate how chloroplast dysfunction affects the cell cycle, we analyzed the crumpled leaf (crl) mutant of Arabidopsis (Arabidopsis thaliana), which is deficient for a chloroplastic protein and displays particularly severe developmental defects. In the crl mutant, we reveal that cell cycle regulation is altered drastically and that meristematic cells prematurely enter differentiation, leading to reduced plant stature and early endoreduplication in the leaves. This response is due to the repression of several key cell cycle regulators as well as constitutive activation of stress-response genes, among them the cell cycle inhibitor SIAMESE-RELATED5. One unique feature of the crl mutant is that it produces aplastidic cells in several organs, including the root tip. By investigating the consequence of the absence of plastids on cell cycle progression, we showed that nuclear DNA replication occurs in aplastidic cells in the root tip, which opens future research prospects regarding the dialogue between plastids and the nucleus during cell cycle regulation in higher plants.
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Affiliation(s)
- Elodie Hudik
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Yasushi Yoshioka
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Séverine Domenichini
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Mickaël Bourge
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Ludivine Soubigout-Taconnat
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Christelle Mazubert
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Dalong Yi
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Sandrine Bujaldon
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Hiroyuki Hayashi
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Lieven De Veylder
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Catherine Bergounioux
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Moussa Benhamed
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
| | - Cécile Raynaud
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique Université-Paris Sud, Laboratoire d'Excellence Saclay Plant Science, bât 630 91405 Orsay, France (E.H., S.D., C.M., C.B., M.Be., C.R.);Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan (Y.Y.);Fédération de Recherche de Gif FRC3115, Pôle de Biologie Cellulaire, 91198 Gif-sur-Yvette, France (M.Bo.);Unité de Recherche en Génomique Végétale, CP5708 Evry, France (L.S.-T.);Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium (D.Y., L.D.V.);Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium (D.Y., L.D.V.);Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7141, Laboratoire de Physiologie Membranaire et Moléculaire du Chloroplaste, Institut de Biologie Physico-Chimique, 75005 Paris, France (S.B.);Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan (H.H.); andDivision of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia (M.Be.)
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Pirrello J, Bourdon M, Cheniclet C, Bourge M, Brown SC, Renaudin JP, Frangne N, Chevalier C. How fruit developmental biology makes use of flow cytometry approaches. Cytometry A 2013; 85:115-25. [PMID: 24273206 DOI: 10.1002/cyto.a.22417] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 09/20/2013] [Accepted: 10/26/2013] [Indexed: 12/15/2022]
Abstract
Fleshy fruit species such as tomato are important because of their nutritional and economic value. Several stages of fruit development such as ovary formation, fruit set, and fruit maturation have already been the subject of many developmental studies. However, fruit growth per se has been much less addressed. Fruit growth like all plant organs depends upon the developmental processes of cell division and cell expansion. The activity of cell divisions sets the number of cells that will compose the fruit; the cell expansion activity then determines its final size. Among the various mechanisms that may influence the determination of cell size, endopolyploidy by the means of endoreduplication, i.e. genome amplification in the absence of mitosis, appears to be of great importance in fleshy fruits. In tomato fruit, endoreduplication is associated with DNA-dependent cell expansion: cell size can reach spectacular levels such as hundreds of times its initial size (e.g. >0.5 mm in diameter), with as much as a 256-fold increase in nuclear DNA content. Using tomato fruit development as a model, recent investigations combining the use of flow cytometry, cellular imaging and molecular analyses have provided new data in favor of the long-standing karyoplasmic ratio theory, stating that cells tend to adjust their cytoplasmic volume to the nuclear DNA content. By establishing a highly structured cellular system where multiple physiological functions are integrated, endoreduplication acts as a morphogenetic factor supporting cell growth during tomato fruit development. In the context of plant breeding, deciphering the mechanisms controlling fruit growth, in particular those connecting the process of nuclear endoreduplication with modulation of gene expression, the regulation of cell size and final fruit size and composition, is necessary to understand better the establishment of fleshy fruit quality traits.
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Affiliation(s)
- Julien Pirrello
- INRA, Unité Mixte de Recherche 1332 Biologie du Fruit et Pathologie, CS20032, F-33882 Villenave d'Ornon, France
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Pineau B, Bourge M, Marion J, Mauve C, Gilard F, Maneta-Peyret L, Moreau P, Satiat-Jeunemaître B, Brown SC, De Paepe R, Danon A. The importance of cardiolipin synthase for mitochondrial ultrastructure, respiratory function, plant development, and stress responses in Arabidopsis. Plant Cell 2013; 25:4195-208. [PMID: 24151294 PMCID: PMC3877823 DOI: 10.1105/tpc.113.118018] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Cardiolipin (CL) is the signature phospholipid of the mitochondrial inner membrane. In animals and yeast (Saccharomyces cerevisiae), CL depletion affects the stability of respiratory supercomplexes and is thus crucial to the energy metabolism of obligate aerobes. In eukaryotes, the last step of CL synthesis is catalyzed by CARDIOLIPIN SYNTHASE (CLS), encoded by a single-copy gene. Here, we characterize a cls mutant in Arabidopsis thaliana, which is devoid of CL. In contrast to yeast cls, where development is little affected, Arabidopsis cls seedlings are slow developing under short-day conditions in vitro and die if they are transferred to long-day (LD) conditions. However, when transferred to soil under LD conditions under low light, cls plants can reach the flowering stage, but they are not fertile. The cls mitochondria display abnormal ultrastructure and reduced content of respiratory complex I/complex III supercomplexes. The marked accumulation of tricarboxylic acid cycle derivatives and amino acids demonstrates mitochondrial dysfunction. Mitochondrial and chloroplastic antioxidant transcripts are overexpressed in cls leaves, and cls protoplasts are more sensitive to programmed cell death effectors, UV light, and heat shock. Our results show that CLS is crucial for correct mitochondrial function and development in Arabidopsis under both optimal and stress conditions.
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Affiliation(s)
- Bernard Pineau
- Institut de Biologie des Plantes, Saclay Plant Science, Université de Paris-Sud XI, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8618, 91405 Orsay cedex, France
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Jégu T, Latrasse D, Delarue M, Mazubert C, Bourge M, Hudik E, Blanchet S, Soler MN, Charon C, De Veylder L, Raynaud C, Bergounioux C, Benhamed M. Multiple functions of Kip-related protein5 connect endoreduplication and cell elongation. Plant Physiol 2013; 161:1694-705. [PMID: 23426196 PMCID: PMC3613449 DOI: 10.1104/pp.112.212357] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 02/01/2013] [Indexed: 05/18/2023]
Abstract
Despite considerable progress in our knowledge regarding the cell cycle inhibitor of the Kip-related protein (KRP) family in plants, less is known about the coordination of endoreduplication and cell differentiation. In animals, the role of cyclin-dependent kinase (CDK) inhibitors as multifunctional factors coordinating cell cycle regulation and cell differentiation is well documented and involves not only the inhibition of CDK/cyclin complexes but also other mechanisms, among them the regulation of transcription. Interestingly, several plant KRPs have a punctuated distribution in the nucleus, suggesting that they are associated with heterochromatin. Here, one of these chromatin-bound KRPs, KRP5, has been studied in Arabidopsis (Arabidopsis thaliana). KRP5 is expressed in endoreduplicating cells, and loss of KRP5 function decreases endoreduplication, indicating that KRP5 is a positive regulator of endoreduplication. This regulation relies on several mechanisms: in addition to its role in cyclin/CDK kinase inhibition previously described, chromatin immunoprecipitation sequencing data combined with transcript quantification provide evidence that KRP5 regulates the transcription of genes involved in cell wall organization. Furthermore, KRP5 overexpression increases chromocenter decondensation and endoreduplication in the Arabidopsis trithorax-related protein5 (atxr5) atxr6 double mutant, which is deficient for the deposition of heterochromatin marks. Hence, KRP5 could bind chromatin to coordinately control endoreduplication and chromatin structure and allow the expression of genes required for cell elongation.
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Bourdon M, Pirrello J, Cheniclet C, Coriton O, Bourge M, Brown S, Moïse A, Peypelut M, Rouyère V, Renaudin JP, Chevalier C, Frangne N. Evidence for karyoplasmic homeostasis during endoreduplication and a ploidy-dependent increase in gene transcription during tomato fruit growth. Development 2012; 139:3817-26. [PMID: 22991446 DOI: 10.1242/dev.084053] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Endopolyploidy is a widespread process that corresponds to the amplification of the genome in the absence of mitosis. In tomato, very high ploidy levels (up to 256C) are reached during fruit development, concomitant with very large cell sizes. Using cellular approaches (fluorescence and electron microscopy) we provide a structural analysis of endoreduplicated nuclei at the level of chromatin and nucleolar organisation, nuclear shape and relationship with other cellular organelles such as mitochondria. We demonstrate that endopolyploidy in pericarp leads to the formation of polytene chromosomes and markedly affects nuclear structure. Nuclei manifest a complex shape, with numerous deep grooves that are filled with mitochondria, affording a fairly constant ratio between nuclear surface and nuclear volume. We provide the first direct evidence that endopolyploidy plays a role in increased transcription of rRNA and mRNA on a per-nucleus basis. Overall, our results provide quantitative evidence in favour of the karyoplasmic theory and show that endoreduplication is associated with complex cellular organisation during tomato fruit development.
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Affiliation(s)
- Matthieu Bourdon
- University of Bordeaux, UMR1332 Biologie du Fruit et Pathologie, BP 81, F-33140 Villenave d'Ornon, France
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Domenichini S, Benhamed M, De Jaeger G, Van De Slijke E, Blanchet S, Bourge M, De Veylder L, Bergounioux C, Raynaud C. Evidence for a role of Arabidopsis CDT1 proteins in gametophyte development and maintenance of genome integrity. Plant Cell 2012; 24:2779-91. [PMID: 22773747 PMCID: PMC3426114 DOI: 10.1105/tpc.112.100156] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Meristems retain the ability to divide throughout the life cycle of plants, which can last for over 1000 years in some species. Furthermore, the germline is not laid down early during embryogenesis but originates from the meristematic cells relatively late during development. Thus, accurate cell cycle regulation is of utmost importance to avoid the accumulation of mutations during vegetative growth and reproduction. The Arabidopsis thaliana genome encodes two homologs of the replication licensing factor CDC10 Target1 (CDT1), and overexpression of CDT1a stimulates DNA replication. Here, we have investigated the respective functions of Arabidopsis CDT1a and CDT1b. We show that CDT1 proteins have partially redundant functions during gametophyte development and are required for the maintenance of genome integrity. Furthermore, CDT1-RNAi plants show endogenous DNA stress, are more tolerant than the wild type to DNA-damaging agents, and show constitutive induction of genes involved in DNA repair. This DNA stress response may be a direct consequence of reduced CDT1 accumulation on DNA repair or may relate to the ability of CDT1 proteins to form complexes with DNA polymerase ε, which functions in DNA replication and in DNA stress checkpoint activation. Taken together, our results provide evidence for a crucial role of Arabidopsis CDT1 proteins in genome stability.
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Affiliation(s)
- Séverine Domenichini
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Moussa Benhamed
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Geert De Jaeger
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Eveline Van De Slijke
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Sophie Blanchet
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Mickaël Bourge
- Pôle de Biologie Cellulaire, Imagif, Centre de Recherche de Gif, CNRS, IFR87, 91198 Gif-sur-Yvette cedex, France
| | - Lieven De Veylder
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Catherine Bergounioux
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Cécile Raynaud
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
- Address correspondence to
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Perazza D, Laporte F, Balagué C, Chevalier F, Remo S, Bourge M, Larkin J, Herzog M, Vachon G. GeBP/GPL transcription factors regulate a subset of CPR5-dependent processes. Plant Physiol 2011; 157:1232-42. [PMID: 21875893 PMCID: PMC3252139 DOI: 10.1104/pp.111.179804] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 08/28/2011] [Indexed: 05/22/2023]
Abstract
The CONSTITUTIVE EXPRESSOR OF PATHOGENESIS-RELATED GENES5 (CPR5) gene of Arabidopsis (Arabidopsis thaliana) encodes a putative membrane protein of unknown biochemical function and displays highly pleiotropic functions, particularly in pathogen responses, cell proliferation, cell expansion, and cell death. Here, we demonstrate a link between CPR5 and the GLABRA1 ENHANCER BINDING PROTEIN (GeBP) family of transcription factors. We investigated the primary role of the GeBP/GeBP-like (GPL) genes using transcriptomic analysis of the quadruple gebp gpl1,2,3 mutant and one overexpressing line that displays several cpr5-like phenotypes including dwarfism, spontaneous necrotic lesions, and increased pathogen resistance. We found that GeBP/GPLs regulate a set of genes that represents a subset of the CPR5 pathway. This subset includes genes involved in response to stress as well as cell wall metabolism. Analysis of the quintuple gebp gpl1,2,3 cpr5 mutant indicates that GeBP/GPLs are involved in the control of cell expansion in a CPR5-dependent manner but not in the control of cell proliferation. In addition, to our knowledge, we provide the first evidence that the CPR5 protein is localized in the nucleus of plant cells and that a truncated version of the protein with no transmembrane domain can trigger cpr5-like processes when fused to the VP16 constitutive transcriptional activation domain. Our results provide clues on how CPR5 and GeBP/GPLs play opposite roles in the control of cell expansion and suggest that the CPR5 protein is involved in transcription.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Gilles Vachon
- Institut Albert Bonniot, Institut National de la Santé et de la Recherche Médicale/Université Joseph Fourier U823, Equipe Interference ARN et Epigenetique, Rond-point de la Chantourne, 38706 La Tronche cedex, France (D.P.); Laboratoire d’Ecologie Alpine, Université Joseph Fourier and Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5553, 2233, F–38041 Grenoble cedex 9, France (F.L., M.H.); Laboratoire des Interactions Plantes-Microorganismes Unité Mixte de Recherche Centre National de la Recherche Scientifique/Institut National de la Recherche Agronomique 2594/441 BP 52627, 31326 Castanet-Tolosan cedex, France (C.B.); Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 2594, F–31326 Castanet-Tolosan, France (C.B.); Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70808 (S.R., J.L.); Institut des Sciences Végétales Centre National de la Recherche Scientifique, F–91198 Gif-sur-Yvette cedex, France (M.B.); Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherche 5168, Centre National de la Recherche Scientifique/Commissariat à l'Energie Atomique et aux Energies Alternatives/Institut National de la Recherche Agronomique/Université Joseph Fourier, Commissariat à l'Energie Atomique et aux Energies Alternatives, 38054 Grenoble cedex 9, France (G.V.)
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Fontaine G, Bourge M, Vankemmel P. [Bixler's syndrome or the H.M.C. syndrome (apropos of a new case)]. LARC Med 1982; 2:774, 776. [PMID: 7162280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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