1
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Dong X, Sheng K, Gebert LFR, Aiyer S, MacRae IJ, Lyumkis D, Williamson JR. Assembly of the bacterial ribosome with circularly permuted rRNA. Nucleic Acids Res 2024:gkae636. [PMID: 39036963 DOI: 10.1093/nar/gkae636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 07/02/2024] [Accepted: 07/11/2024] [Indexed: 07/23/2024] Open
Abstract
Co-transcriptional assembly is an integral feature of the formation of RNA-protein complexes that mediate translation. For ribosome synthesis, prior studies have indicated that the strict order of transcription of rRNA domains may not be obligatory during bacterial ribosome biogenesis, since a series of circularly permuted rRNAs are viable. In this work, we report the structural insights into assembly of the bacterial ribosome large subunit (LSU) based on cryo-EM density maps of intermediates that accumulate during in vitro ribosome synthesis using a set of circularly permuted (CiPer) rRNAs. The observed ensemble of 23 resolved ribosome large subunit intermediates reveals conserved assembly routes with an underlying hierarchy among cooperative assembly blocks. There are intricate interdependencies for the formation of key structural rRNA helices revealed from the circular permutation of rRNA. While the order of domain synthesis is not obligatory, the order of domain association does appear to proceed with a particular order, likely due to the strong evolutionary pressure on efficient ribosome synthesis. This work reinforces the robustness of the known assembly hierarchy of the bacterial large ribosomal subunit and offers a coherent view of how efficient assembly of CiPer rRNAs can be understood in that context.
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Affiliation(s)
- Xiyu Dong
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kai Sheng
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Luca F R Gebert
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sriram Aiyer
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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2
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Liao H, Wen J, Nie H, Ling C, Zhang L, Xu F, Dong X. Study on the inhibitory activity and mechanism of Mentha haplocalyx essential oil nanoemulsion against Fusarium oxysporum growth. Sci Rep 2024; 14:16064. [PMID: 38992117 PMCID: PMC11239933 DOI: 10.1038/s41598-024-67054-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 07/08/2024] [Indexed: 07/13/2024] Open
Abstract
Mentha haplocalyx essential oil (MEO) has demonstrated inhibitory effects on Fusarium oxysporum. Despite its environmentally friendly properties as a natural product, the limited water solubility of MEO restricts its practical application in the field. The use of nanoemulsion can improve bioavailability and provide an eco-friendly approach to prevent and control Panax notoginseng root rot. In this study, Tween 80 and anhydrous ethanol (at a mass ratio of 3) were selected as carriers, and the ultrasonic method was utilized to produce a nanoemulsion of MEO (MNEO) with an average particle size of 26.07 nm. Compared to MTEO (MEO dissolved in an aqueous solution of 2% DMSO and 0.1% Tween 80), MNEO exhibited superior inhibition against F. oxysporum in terms of spore germination and hyphal growth. Transcriptomics and metabolomics results revealed that after MNEO treatment, the expression levels of certain genes related to glycolysis/gluconeogenesis, starch and sucrose metabolism were significantly suppressed along with the accumulation of metabolites, leading to energy metabolism disorder and growth stagnation in F. oxysporum. In contrast, the inhibitory effect from MTEO treatment was less pronounced. Furthermore, MNEO also demonstrated inhibition on meiosis, ribosome function, and ribosome biogenesis in F. oxysporum growth process. These findings suggest that MNEO possesses enhanced stability and antifungal activity, which effectively hinders F. oxysporum through inducing energy metabolism disorder, meiotic stagnation, as well as ribosome dysfunction, thus indicating its potential for development as a green pesticide for prevention and control P. notoginseng root rot caused by F.oxyosporum.
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Affiliation(s)
- Hongxin Liao
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650000, China
| | - Jinrui Wen
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650000, China
| | - Hongyan Nie
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650000, China
| | - Cuiqiong Ling
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650000, China
| | - Liyan Zhang
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650000, China
| | - Furong Xu
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650000, China
| | - Xian Dong
- School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, 650000, China.
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3
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Zhuang Y, Guo X, Razorenova OV, Miles CE, Zhao W, Shi X. Coaching ribosome biogenesis from the nuclear periphery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.597078. [PMID: 38948754 PMCID: PMC11212990 DOI: 10.1101/2024.06.21.597078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Severe invagination of the nuclear envelope is a hallmark of cancers, aging, neurodegeneration, and infections. However, the outcomes of nuclear invagination remain unclear. This work identified a new function of nuclear invagination: regulating ribosome biogenesis. With expansion microscopy, we observed frequent physical contact between nuclear invaginations and nucleoli. Surprisingly, the higher the invagination curvature, the more ribosomal RNA and pre-ribosomes are made in the contacted nucleolus. By growing cells on nanopillars that generate nuclear invaginations with desired curvatures, we can increase and decrease ribosome biogenesis. Based on this causation, we repressed the ribosome levels in breast cancer and progeria cells by growing cells on low-curvature nanopillars, indicating that overactivated ribosome biogenesis can be rescued by reshaping nuclei. Mechanistically, high-curvature nuclear invaginations reduce heterochromatin and enrich nuclear pore complexes, which promote ribosome biogenesis. We anticipate that our findings will serve as a foundation for further studies on nuclear deformation.
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Affiliation(s)
- Yinyin Zhuang
- Department of Developmental and Cell Biology, University of California, Irvine; Irvine, CA 92697, United States
| | - Xiangfu Guo
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University; Singapore 637459, Singapore
| | - Olga V. Razorenova
- Department of Molecular Biology and Biochemistry, University of California, Irvine; Irvine, CA 92697, United States
| | - Christopher E. Miles
- Department of Mathematics, University of California, Irvine; Irvine, CA 92697, United States
| | - Wenting Zhao
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University; Singapore 637459, Singapore
| | - Xiaoyu Shi
- Department of Developmental and Cell Biology, University of California, Irvine; Irvine, CA 92697, United States
- Department of Chemistry, University of California, Irvine; Irvine, CA 92697, United States
- Department of Biomedical Engineering, University of California, Irvine; Irvine, CA 92697, United States
- Lead contact
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4
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Dong X, Sheng K, Gebert LFR, Aiyer S, MacRae IJ, Lyumkis D, Williamson JR. Assembly of the Bacterial Ribosome with Circularly Permuted rRNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.10.588894. [PMID: 38644992 PMCID: PMC11030442 DOI: 10.1101/2024.04.10.588894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Co-transcriptional assembly is an integral feature of the formation of RNA-protein complexes that mediate translation. For ribosome synthesis, prior studies have indicated that the strict order of transcription of rRNA domains may not be obligatory during bacterial ribosome biogenesis, since a series of circularly permuted rRNAs are viable. In this work, we report the insights into assembly of the bacterial ribosome large subunit (LSU) based on cryo-EM density maps of intermediates that accumulate during in vitro ribosome synthesis using a set of circularly permuted (CiPer) rRNAs. The observed ensemble of twenty-three resolved ribosome large subunit intermediates reveals conserved assembly routes with an underlying hierarchy among cooperative assembly blocks. There are intricate interdependencies for the formation of key structural rRNA helices revealed from the circular permutation of rRNA. While the order of domain synthesis is not obligatory, the order of domain association does appear to proceed with a particular order, likely due to the strong evolutionary pressure on efficient ribosome synthesis. This work reinforces the robustness of the known assembly hierarchy of the bacterial large ribosomal subunit, and offers a coherent view of how efficient assembly of CiPer rRNAs can be understood in that context.
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Affiliation(s)
- Xiyu Dong
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kai Sheng
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Luca F R Gebert
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sriram Aiyer
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Ian J MacRae
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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5
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Gruffaz C, Smirnov A. GTPase Era at the heart of ribosome assembly. Front Mol Biosci 2023; 10:1263433. [PMID: 37860580 PMCID: PMC10582724 DOI: 10.3389/fmolb.2023.1263433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
Ribosome biogenesis is a key process in all organisms. It relies on coordinated work of multiple proteins and RNAs, including an array of assembly factors. Among them, the GTPase Era stands out as an especially deeply conserved protein, critically required for the assembly of bacterial-type ribosomes from Escherichia coli to humans. In this review, we bring together and critically analyze a wealth of phylogenetic, biochemical, structural, genetic and physiological data about this extensively studied but still insufficiently understood factor. We do so using a comparative and, wherever possible, synthetic approach, by confronting observations from diverse groups of bacteria and eukaryotic organelles (mitochondria and chloroplasts). The emerging consensus posits that Era intervenes relatively early in the small subunit biogenesis and is essential for the proper shaping of the platform which, in its turn, is a prerequisite for efficient translation. The timing of Era action on the ribosome is defined by its interactions with guanosine nucleotides [GTP, GDP, (p)ppGpp], ribosomal RNA, and likely other factors that trigger or delay its GTPase activity. As a critical nexus of the small subunit biogenesis, Era is subject to sophisticated regulatory mechanisms at the transcriptional, post-transcriptional, and post-translational levels. Failure of these mechanisms or a deficiency in Era function entail dramatic generalized consequences for the protein synthesis and far-reaching, pleiotropic effects on the organism physiology, such as the Perrault syndrome in humans.
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Affiliation(s)
- Christelle Gruffaz
- UMR7156- Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, Centre National de la Recherche Scientifique (CNRS), Strasbourg, France
| | - Alexandre Smirnov
- UMR7156- Génétique Moléculaire, Génomique, Microbiologie (GMGM), University of Strasbourg, Centre National de la Recherche Scientifique (CNRS), Strasbourg, France
- University of Strasbourg Institute for Advanced Study (USIAS), Strasbourg, France
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6
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Islam RA, Rallis C. Ribosomal Biogenesis and Heterogeneity in Development, Disease, and Aging. EPIGENOMES 2023; 7:17. [PMID: 37606454 PMCID: PMC10443367 DOI: 10.3390/epigenomes7030017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/23/2023] Open
Abstract
Although reported in the literature, ribosome heterogeneity is a phenomenon whose extent and implications in cell and organismal biology is not fully appreciated. This has been the case due to the lack of the appropriate techniques and approaches. Heterogeneity can arise from alternative use and differential content of protein and RNA constituents, as well as from post-transcriptional and post-translational modifications. In the few examples we have, it is apparent that ribosomal heterogeneity offers an additional level and potential for gene expression regulation and might be a way towards tuning metabolism, stress, and growth programs to external and internal stimuli and needs. Here, we introduce ribosome biogenesis and discuss ribosomal heterogeneity in various reported occasions. We conclude that a systematic approach in multiple organisms will be needed to delineate this biological phenomenon and its contributions to growth, aging, and disease. Finally, we discuss ribosome mutations and their roles in disease.
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Affiliation(s)
- Rowshan Ara Islam
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Charalampos Rallis
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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7
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Qiang L, Zhao N, Liao K, Sun X, Wang Q, Jin H. Metabolomics and transcriptomics reveal the toxic mechanism of Cd and nano TiO 2 coexposure on rice (Oryza sativa L.). JOURNAL OF HAZARDOUS MATERIALS 2023; 453:131411. [PMID: 37062093 DOI: 10.1016/j.jhazmat.2023.131411] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 04/02/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
Engineered nanoparticles (ENPs) can resist heavy metal toxicity in plants, but their coexposure still exhibits toxicity to plants compared to plants without exposure to ENPs and heavy metals. There have been few studies on the toxic mechanism of nano TiO2-heavy metal coexposure and the effect mechanism of nano TiO2 in plants. Thus, transcriptomics and metabolomics were used to study the toxic mechanism of rutile nano TiO2 or TiO2-Cd (rutile nano TiO2 and CdCl2 mixture) on rice (Oryza sativa L.). After 40 days of exposure, the plant height and root dry weight of rice were significantly decreased in the nano TiO2-Cd group compared to the blank group (nano TiO2 and CdCl2 free). After Cd treatment, 423 differentially expressed genes (DEGs) and 16 differential metabolites were identified. Nano TiO2 exposure induced significant regulation of 299 DEGs and 6 metabolites. After nano TiO2-Cd coexposure, 1660 DEGs and 181 differential metabolites were identified. Notably, the EDGs (e.g., chalcone isomerase and hydroxycinnamoyl transferase) and differential metabolites (e.g., chrysin and galangin) demonstrated the disruption of flavonoid biosynthesis in Cd-treated rice. After rice was exposed to nano TiO2, the DEGs were related to ribosome, whereas the differential metabolites were associated with pyruvate metabolism and valine, leucine, and isoleucine biosynthesis. Furthermore, 14 DEGs (e.g., asparaginyl-tRNA synthetase and methionyl-tRNA formyltransferase) involved in aminoacyl-tRNA biosynthetic pathways were significantly upregulated in rice treated with nano TiO2-Cd, in line with the changes in related metabolites (e.g., L-asparagine and 10-formyltetrahydrofolate). Our results show that it is necessary to pay close attention to the toxicity of nano TiO2-Cd coexposure in paddy ecosystems and use ENPs with caution to combat the phytotoxicity of heavy metals.
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Affiliation(s)
- Liwen Qiang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, PR China
| | - Nan Zhao
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Kaizhen Liao
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Xichao Sun
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, PR China
| | - Qiang Wang
- Agro-Environmental Protection Institute, Ministry of Agriculture and Rural Affairs, Tianjin 300191, PR China
| | - Hangbiao Jin
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, PR China.
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8
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Bohnsack KE, Henras AK, Nielsen H, Bohnsack MT. Making ends meet: a universal driver of large ribosomal subunit biogenesis. Trends Biochem Sci 2023; 48:213-215. [PMID: 36207216 DOI: 10.1016/j.tibs.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/10/2022] [Accepted: 09/14/2022] [Indexed: 11/07/2022]
Abstract
A common aspect of ribosome assembly, conserved across all domains of life, is the establishment of connections between the 5' and 3' ends of the large subunit (LSU) ribosomal RNA (rRNA) to initiate rRNA domain compaction and subunit assembly. We discuss the diverse mechanisms employed in different organisms to accomplish this important event.
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Affiliation(s)
- Katherine E Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany.
| | - Anthony K Henras
- Molecular, Cellular and Developmental Biology Unit, University of Toulouse, Toulouse, France
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany; Göttingen Center for Molecular Biosciences, Georg-August University, Göttingen, Germany.
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9
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Forterre P. Carl Woese: Still ahead of our time. MLIFE 2022; 1:359-367. [PMID: 38818481 PMCID: PMC10989812 DOI: 10.1002/mlf2.12049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 06/01/2024]
Affiliation(s)
- Patrick Forterre
- Institut Pasteur, Departement de MicrobiologieParisFrance
- Institute for Integrative Biology of the Cell, équipeBiologie Cellulaire des Archées, Département de MicrobiologieGif sur YvetteFrance
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