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Alpha-Bazin B, Gorlas A, Lagorce A, Joulié D, Boyer JB, Dutertre M, Gaillard JC, Lopes A, Zivanovic Y, Dedieu A, Confalonieri F, Armengaud J. Lysine-specific acetylated proteome from the archaeon Thermococcus gammatolerans reveals the presence of acetylated histones. J Proteomics 2020; 232:104044. [PMID: 33161166 DOI: 10.1016/j.jprot.2020.104044] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 10/26/2020] [Accepted: 11/02/2020] [Indexed: 11/20/2022]
Abstract
Thermococcus gammatolerans EJ3 is an extremophile archaeon which was revealed as one of the most radioresistant organisms known on Earth, withstanding up to 30 kGy gamma-ray radiations. While its theoretical proteome is rather small, T. gammatolerans may enhance its toolbox by post-translational modification of its proteins. Here, we explored its extent of Nε-acetylation of lysines. For this, we immunopurified with two acetylated-lysine antibodies the acetylated peptides resulting from a proteolysis of soluble proteins with trypsin. The comparison of acetylated proteomes of two archaea highlights some common acetylation patterns but only 4 out of 26 orthologous proteins found to be acetylated in both species, are acetylated on the same lysine site. We evidenced that histone B is acetylated in T. gammatolerans at least at two different sites (K27 and K36), and a peptide common at the C-terminus of histones A and B is also acetylated. We verified that acetylation of histones is a common trait among Thermococcales after recording data on Thermococcus kodakaraensis histones and identifying three acetylated sites. This discovery reinforces the strong evolutionary link between Archaea and Eukaryotes and should be an incentive for further investigation on the extent and role of acetylation of histones in Archaea. SIGNIFICANCE: Acetylation is an important post-translational modification of proteins that has been extensively described in Eukaryotes, and more recently in Bacteria. Here, we report for the first time ever that histones in Archaea are also modified by acetylation after a systematic survey of acetylated peptides in Thermococcus gammatolerans. Structural models of histones A and B indicates that acetylation of the identified modified residues may play an important role in histone assembly and/or interaction with DNA. The in-depth protein acetylome landscape in T. gammatolerans includes at least 181 unique protein sequences, some of them being modified on numerous residues. Proteins involved in metabolic processes, information storage and processing mechanisms are over-represented categories in this dataset, highlighting the ancient role of this protein post-translational modification in primitive cells.
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Affiliation(s)
- Béatrice Alpha-Bazin
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Aurore Gorlas
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Arnaud Lagorce
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France; IHPE, Université de Montpellier, CNRS, Ifremer, Université de Perpignan, Via Domitia, Perpignan, France
| | - Damien Joulié
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Jean-Baptiste Boyer
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Murielle Dutertre
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Jean-Charles Gaillard
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Anne Lopes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Yvan Zivanovic
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Alain Dedieu
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France
| | - Fabrice Confalonieri
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols-sur-Cèze, France.
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Barbier E, Lagorce A, Hachemi A, Dutertre M, Gorlas A, Morand L, Saint-Pierre C, Ravanat JL, Douki T, Armengaud J, Gasparutto D, Confalonieri F, Breton J. Oxidative DNA Damage and Repair in the Radioresistant Archaeon Thermococcus gammatolerans. Chem Res Toxicol 2016; 29:1796-1809. [PMID: 27676238 DOI: 10.1021/acs.chemrestox.6b00128] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The hyperthermophilic archaeon Thermococcus gammatolerans can resist huge doses of γ-irradiation, up to 5.0 kGy, without loss of viability. The potential to withstand such harsh conditions is probably due to complementary passive and active mechanisms, including repair of damaged chromosomes. In this work, we documented the formation and repair of oxidative DNA lesions in T. gammatolerans. The basal level of the oxidized nucleoside, 8-oxo-2'-deoxyguanosine (8-oxo-dGuo), was established at 9.2 (± 0.9) 8-oxo-dGuo per 106 nucleosides, a higher level than those usually measured in eukaryotic cells or bacteria. A significant increase in oxidative damage, i.e., up to 24.2 (± 8.0) 8-oxo-dGuo/106 nucleosides, was measured for T. gammatolerans exposed to a 5.0 kGy dose of γ-rays. Surprisingly, the yield of radiation-induced modifications was lower than those previously observed for human cells exposed to doses corresponding to a few grays. One hour after irradiation, 8-oxo-dGuo levels were significantly reduced, indicating an efficient repair. Two putative base excision repair (BER) enzymes, TGAM_1277 and TGAM_1653, were demonstrated both by proteomics and transcriptomics to be present in the cells without exposure to ionizing radiation. Their transcripts were moderately upregulated after gamma irradiation. After heterologous production and purification of these enzymes, biochemical assays based on electrophoresis and MALDI-TOF (matrix-assisted laser desorption ionization-time of flight) mass spectrometry indicated that both have a β-elimination cleavage activity. TGAM_1653 repairs 8-oxo-dGuo, whereas TGAM_1277 is also able to remove lesions affecting pyrimidines (1-[2-deoxy-β-d-erythro-pentofuranosyl]-5-hydroxyhydantoin (5-OH-dHyd) and 1-[2-deoxy-β-d-erythro-pentofuranosyl]-5-hydroxy-5-methylhydantoin (5-OH-5-Me-dHyd)). This work showed that in normal growth conditions or in the presence of a strong oxidative stress, T. gammatolerans has the potential to rapidly reduce the extent of DNA oxidation, with at least these two BER enzymes as bodyguards with distinct substrate ranges.
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Affiliation(s)
- Ewa Barbier
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Arnaud Lagorce
- University of Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France.,University of Perpignan, IHPE - UMR 5244 CNRS/IFREMER/Univ. Montpellier, Montpellier, F-34095, France
| | - Amine Hachemi
- University of Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Murielle Dutertre
- University of Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Aurore Gorlas
- University of Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Lucie Morand
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Christine Saint-Pierre
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Jean-Luc Ravanat
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Thierry Douki
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Jean Armengaud
- CEA, DSV-Li2D, Laboratory "Innovative Technologies for Detection and Diagnostics", BP 17171, Bagnols-sur-Cèze, F-30207, France
| | - Didier Gasparutto
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
| | - Fabrice Confalonieri
- University of Paris-Sud, Institute for Integrative Biology of the Cell (I2BC), Université Paris Saclay, CEA, CNRS, Orsay, France
| | - Jean Breton
- University of Grenoble Alpes, INAC, LCIB , F-38000 Grenoble, France.,CEA, INAC, SyMMES, F-38000 Grenoble, France
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PprA Protein Is Involved in Chromosome Segregation via Its Physical and Functional Interaction with DNA Gyrase in Irradiated Deinococcus radiodurans Bacteria. mSphere 2016; 1:mSphere00036-15. [PMID: 27303692 PMCID: PMC4863600 DOI: 10.1128/msphere.00036-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 12/09/2015] [Indexed: 11/30/2022] Open
Abstract
D. radiodurans is one of the most radiation-resistant organisms known. This bacterium is able to cope with high levels of DNA lesions generated by exposure to extreme doses of ionizing radiation and to reconstruct a functional genome from hundreds of radiation-induced chromosomal fragments. Here, we identified partners of PprA, a radiation-induced Deinococcus-specific protein, previously shown to be required for radioresistance. Our study leads to three main findings: (i) PprA interacts with DNA gyrase after irradiation, (ii) treatment of cells with novobiocin results in defects in chromosome segregation that are aggravated by the absence of PprA, and (iii) PprA stimulates the decatenation activity of DNA gyrase. Our results extend the knowledge of how D. radiodurans cells survive exposure to extreme doses of gamma irradiation and point out the link between DNA repair, chromosome segregation, and DNA gyrase activities in the radioresistant D. radiodurans bacterium. PprA, a radiation-induced Deinococcus-specific protein, was previously shown to be required for cell survival and accurate chromosome segregation after exposure to ionizing radiation. Here, we used an in vivo approach to determine, by shotgun proteomics, putative PprA partners coimmunoprecipitating with PprA when cells were exposed to gamma rays. Among them, we found the two subunits of DNA gyrase and, thus, chose to focus our work on characterizing the activities of the deinococcal DNA gyrase in the presence or absence of PprA. Loss of PprA rendered cells hypersensitive to novobiocin, an inhibitor of the B subunit of DNA gyrase. We showed that treatment of bacteria with novobiocin resulted in induction of the radiation desiccation response (RDR) regulon and in defects in chromosome segregation that were aggravated by the absence of PprA. In vitro, the deinococcal DNA gyrase, like other bacterial DNA gyrases, possesses DNA negative supercoiling and decatenation activities. These two activities are inhibited in vitro by novobiocin and nalidixic acid, whereas PprA specifically stimulates the decatenation activity of DNA gyrase. Together, these results suggest that PprA plays a major role in chromosome decatenation via its interaction with the deinococcal DNA gyrase when D. radiodurans cells are recovering from exposure to ionizing radiation. IMPORTANCED. radiodurans is one of the most radiation-resistant organisms known. This bacterium is able to cope with high levels of DNA lesions generated by exposure to extreme doses of ionizing radiation and to reconstruct a functional genome from hundreds of radiation-induced chromosomal fragments. Here, we identified partners of PprA, a radiation-induced Deinococcus-specific protein, previously shown to be required for radioresistance. Our study leads to three main findings: (i) PprA interacts with DNA gyrase after irradiation, (ii) treatment of cells with novobiocin results in defects in chromosome segregation that are aggravated by the absence of PprA, and (iii) PprA stimulates the decatenation activity of DNA gyrase. Our results extend the knowledge of how D. radiodurans cells survive exposure to extreme doses of gamma irradiation and point out the link between DNA repair, chromosome segregation, and DNA gyrase activities in the radioresistant D. radiodurans bacterium.
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Abby E, Tourpin S, Ribeiro J, Daniel K, Messiaen S, Moison D, Guerquin J, Gaillard JC, Armengaud J, Langa F, Toth A, Martini E, Livera G. Implementation of meiosis prophase I programme requires a conserved retinoid-independent stabilizer of meiotic transcripts. Nat Commun 2016; 7:10324. [PMID: 26742488 PMCID: PMC4729902 DOI: 10.1038/ncomms10324] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 11/27/2015] [Indexed: 12/28/2022] Open
Abstract
Sexual reproduction is crucially dependent on meiosis, a conserved, specialized cell division programme that is essential for the production of haploid gametes. Here we demonstrate that fertility and the implementation of the meiotic programme require a previously uncharacterized meiosis-specific protein, MEIOC. Meioc invalidation in mice induces early and pleiotropic meiotic defects in males and females. MEIOC prevents meiotic transcript degradation and interacts with an RNA helicase that binds numerous meiotic mRNAs. Our results indicate that proper engagement into meiosis necessitates the specific stabilization of meiotic transcripts, a previously little-appreciated feature in mammals. Remarkably, the upregulation of MEIOC at the onset of meiosis does not require retinoic acid and STRA8 signalling. Thus, we propose that the complete induction of the meiotic programme requires both retinoic acid-dependent and -independent mechanisms. The latter process involving post-transcriptional regulation likely represents an ancestral mechanism, given that MEIOC homologues are conserved throughout multicellular animals. Meiosis is a cell division program that produces haploid gametes and is initiated by a retinoic acid-dependent process. Here the authors report that a meiosis-specific protein, MEIOC, is upregulated in a retinoic acid-independent manner and is required to stabilise meiosis-specific transcripts.
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Affiliation(s)
- Emilie Abby
- Université Paris Diderot, Sorbonne Paris Cité, Laboratory of Development of the Gonads, Unit of Stem Cells and Radiation, UMR-967, BP 6, Fontenay-aux-Roses 92265, France.,CEA, DSV, iRCM, SCSR, LDG, Fontenay-aux-Roses 92265, France.,INSERM, Unité 967, Fontenay-aux-Roses F-92265, France.,Université Paris-Sud, UMR-967, Fontenay-aux-Roses F-92265, France
| | - Sophie Tourpin
- Université Paris Diderot, Sorbonne Paris Cité, Laboratory of Development of the Gonads, Unit of Stem Cells and Radiation, UMR-967, BP 6, Fontenay-aux-Roses 92265, France.,CEA, DSV, iRCM, SCSR, LDG, Fontenay-aux-Roses 92265, France.,INSERM, Unité 967, Fontenay-aux-Roses F-92265, France.,Université Paris-Sud, UMR-967, Fontenay-aux-Roses F-92265, France
| | - Jonathan Ribeiro
- Université Paris Diderot, Sorbonne Paris Cité, Laboratory of Development of the Gonads, Unit of Stem Cells and Radiation, UMR-967, BP 6, Fontenay-aux-Roses 92265, France.,CEA, DSV, iRCM, SCSR, LDG, Fontenay-aux-Roses 92265, France.,INSERM, Unité 967, Fontenay-aux-Roses F-92265, France.,Université Paris-Sud, UMR-967, Fontenay-aux-Roses F-92265, France
| | - Katrin Daniel
- Molecular Cell Biology Group/Experimental Center, Institute of Physiological Chemistry, Medical School, MTZ, Dresden University of Technology, Fiedlerstrasse 42, Dresden 01307, Germany
| | - Sébastien Messiaen
- Université Paris Diderot, Sorbonne Paris Cité, Laboratory of Development of the Gonads, Unit of Stem Cells and Radiation, UMR-967, BP 6, Fontenay-aux-Roses 92265, France.,CEA, DSV, iRCM, SCSR, LDG, Fontenay-aux-Roses 92265, France.,INSERM, Unité 967, Fontenay-aux-Roses F-92265, France.,Université Paris-Sud, UMR-967, Fontenay-aux-Roses F-92265, France
| | - Delphine Moison
- Université Paris Diderot, Sorbonne Paris Cité, Laboratory of Development of the Gonads, Unit of Stem Cells and Radiation, UMR-967, BP 6, Fontenay-aux-Roses 92265, France.,CEA, DSV, iRCM, SCSR, LDG, Fontenay-aux-Roses 92265, France.,INSERM, Unité 967, Fontenay-aux-Roses F-92265, France.,Université Paris-Sud, UMR-967, Fontenay-aux-Roses F-92265, France
| | - Justine Guerquin
- Université Paris Diderot, Sorbonne Paris Cité, Laboratory of Development of the Gonads, Unit of Stem Cells and Radiation, UMR-967, BP 6, Fontenay-aux-Roses 92265, France.,CEA, DSV, iRCM, SCSR, LDG, Fontenay-aux-Roses 92265, France.,INSERM, Unité 967, Fontenay-aux-Roses F-92265, France.,Université Paris-Sud, UMR-967, Fontenay-aux-Roses F-92265, France
| | - Jean-Charles Gaillard
- CEA, DSV/IBITEC-S/SPI/Li2D, Laboratory 'Innovative Technologies for Detection and Diagnostic', CEA-Marcoule, BP 17171, Bagnols-sur-Cèze F-30200, France
| | - Jean Armengaud
- CEA, DSV/IBITEC-S/SPI/Li2D, Laboratory 'Innovative Technologies for Detection and Diagnostic', CEA-Marcoule, BP 17171, Bagnols-sur-Cèze F-30200, France
| | - Francina Langa
- Centre d'Ingénierie Génétique Murine, Institut Pasteur, Paris 75015, France
| | - Attila Toth
- Molecular Cell Biology Group/Experimental Center, Institute of Physiological Chemistry, Medical School, MTZ, Dresden University of Technology, Fiedlerstrasse 42, Dresden 01307, Germany
| | - Emmanuelle Martini
- Université Paris Diderot, Sorbonne Paris Cité, Laboratory of Development of the Gonads, Unit of Stem Cells and Radiation, UMR-967, BP 6, Fontenay-aux-Roses 92265, France.,CEA, DSV, iRCM, SCSR, LDG, Fontenay-aux-Roses 92265, France.,INSERM, Unité 967, Fontenay-aux-Roses F-92265, France.,Université Paris-Sud, UMR-967, Fontenay-aux-Roses F-92265, France
| | - Gabriel Livera
- Université Paris Diderot, Sorbonne Paris Cité, Laboratory of Development of the Gonads, Unit of Stem Cells and Radiation, UMR-967, BP 6, Fontenay-aux-Roses 92265, France.,CEA, DSV, iRCM, SCSR, LDG, Fontenay-aux-Roses 92265, France.,INSERM, Unité 967, Fontenay-aux-Roses F-92265, France.,Université Paris-Sud, UMR-967, Fontenay-aux-Roses F-92265, France
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