1
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Mishra RK, Sharma P, Khaja FT, Uday AB, Hussain T. Cryo-EM structure of wheat ribosome reveals unique features of the plant ribosomes. Structure 2024; 32:562-574.e3. [PMID: 38458197 DOI: 10.1016/j.str.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/16/2023] [Accepted: 02/12/2024] [Indexed: 03/10/2024]
Abstract
Plants being sessile organisms exhibit unique features in ribosomes, which might aid in rapid gene expression and regulation in response to varying environmental conditions. Here, we present high-resolution structures of the 60S and 80S ribosomes from wheat, a monocot staple crop plant (Triticum aestivum). While plant ribosomes have unique plant-specific rRNA modification (Cm1847) in the peptide exit tunnel (PET), the zinc-finger motif in eL34 is absent, and uL4 is extended, making an exclusive interaction network. We note differences in the eL15-helix 11 (25S) interaction, eL6-ES7 assembly, and certain rRNA chemical modifications between monocot and dicot ribosomes. In eukaryotes, we observe highly conserved rRNA modification (Gm75) in 5.8S rRNA and a flipped base (G1506) in PET. These features are likely involved in sensing or stabilizing nascent chain. Finally, we discuss the importance of the universal conservation of three consecutive rRNA modifications in all ribosomes for their interaction with A-site aminoacyl-tRNA.
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Affiliation(s)
- Rishi Kumar Mishra
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru PIN-560012, India
| | - Prafful Sharma
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru PIN-560012, India
| | - Faisal Tarique Khaja
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru PIN-560012, India
| | - Adwaith B Uday
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru PIN-560012, India
| | - Tanweer Hussain
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru PIN-560012, India.
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2
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Sklias A, Cruciani S, Marchand V, Spagnuolo M, Lavergne G, Bourguignon V, Brambilla A, Dreos R, Marygold S, Novoa E, Motorin Y, Roignant JY. Comprehensive map of ribosomal 2'-O-methylation and C/D box snoRNAs in Drosophila melanogaster. Nucleic Acids Res 2024; 52:2848-2864. [PMID: 38416577 PMCID: PMC11014333 DOI: 10.1093/nar/gkae139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 02/09/2024] [Accepted: 02/26/2024] [Indexed: 03/01/2024] Open
Abstract
During their maturation, ribosomal RNAs (rRNAs) are decorated by hundreds of chemical modifications that participate in proper folding of rRNA secondary structures and therefore in ribosomal function. Along with pseudouridine, methylation of the 2'-hydroxyl ribose moiety (Nm) is the most abundant modification of rRNAs. The majority of Nm modifications in eukaryotes are placed by Fibrillarin, a conserved methyltransferase belonging to a ribonucleoprotein complex guided by C/D box small nucleolar RNAs (C/D box snoRNAs). These modifications impact interactions between rRNAs, tRNAs and mRNAs, and some are known to fine tune translation rates and efficiency. In this study, we built the first comprehensive map of Nm sites in Drosophila melanogaster rRNAs using two complementary approaches (RiboMethSeq and Nanopore direct RNA sequencing) and identified their corresponding C/D box snoRNAs by whole-transcriptome sequencing. We de novo identified 61 Nm sites, from which 55 are supported by both sequencing methods, we validated the expression of 106 C/D box snoRNAs and we predicted new or alternative rRNA Nm targets for 31 of them. Comparison of methylation level upon different stresses show only slight but specific variations, indicating that this modification is relatively stable in D. melanogaster. This study paves the way to investigate the impact of snoRNA-mediated 2'-O-methylation on translation and proteostasis in a whole organism.
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Affiliation(s)
- Athena Sklias
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Sonia Cruciani
- Center For Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, Epitranscriptomics and RNA sequencing (EpiRNA-Seq) Core Facility (UAR2008/US40 IBSLor) and UMR7365 IMoPA, Nancy, France
| | - Mariangela Spagnuolo
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, Germany
| | - Guillaume Lavergne
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Valérie Bourguignon
- Université de Lorraine, CNRS, INSERM, Epitranscriptomics and RNA sequencing (EpiRNA-Seq) Core Facility (UAR2008/US40 IBSLor) and UMR7365 IMoPA, Nancy, France
| | - Alessandro Brambilla
- Proteomics and Modomics Experimental Core (PROMEC), Norwegian University of Science and Technology and the Central Norway Regional Health Authority, Trondheim, Norway
| | - René Dreos
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
| | - Steven J Marygold
- FlyBase, Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, United Kingdom
| | - Eva Maria Novoa
- Center For Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
- University Pompeu Fabra (UPF), Dr Aiguader 88, 08003 Barcelona, Spain
| | - Yuri Motorin
- Université de Lorraine, CNRS, INSERM, Epitranscriptomics and RNA sequencing (EpiRNA-Seq) Core Facility (UAR2008/US40 IBSLor) and UMR7365 IMoPA, Nancy, France
| | - Jean-Yves Roignant
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, 1015 Lausanne, Switzerland
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128 Mainz, Germany
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3
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Shanmugam T, Chaturvedi P, Streit D, Ghatak A, Bergelt T, Simm S, Weckwerth W, Schleiff E. Low dose ribosomal DNA P-loop mutation affects development and enforces autophagy in Arabidopsis. RNA Biol 2024; 21:1-15. [PMID: 38156797 PMCID: PMC10761087 DOI: 10.1080/15476286.2023.2298532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2023] [Indexed: 01/03/2024] Open
Abstract
Arabidopsis contains hundreds of ribosomal DNA copies organized within the nucleolar organizing regions (NORs) in chromosomes 2 and 4. There are four major types of variants of rDNA, VAR1-4, based on the polymorphisms of 3' external transcribed sequences. The variants are known to be differentially expressed during plant development. We created a mutant by the CRISPR-Cas9-mediated excision of ~ 25 nt from predominantly NOR4 ribosomal DNA copies, obtaining mosaic mutational events on ~ 5% of all rDNA copies. The excised region consists of P-loop and Helix-82 segments of 25S rRNA. The mutation led to allelic, dosage-dependent defects marked by lateral root inhibition, reduced size, and pointy leaves, all previously observed for defective ribosomal function. The mutation in NOR4 led to dosage compensation from the NOR2 copies by elevated expression of VAR1 in mutants and further associated single-nucleotide variants, thus, resulting in altered rRNA sub-population. Furthermore, the mutants exhibited rRNA maturation defects specifically in the minor pathway typified by 32S pre-rRNA accumulation. Density-gradient fractionation and subsequent RT-PCR of rRNA analyses revealed that mutated copies were not incorporated into the translating ribosomes. The mutants in addition displayed an elevated autophagic flux as shown by the autophagic marker GFP-ATG8e, likely related to ribophagy.
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Affiliation(s)
- Thiruvenkadam Shanmugam
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Palak Chaturvedi
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Deniz Streit
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Thorsten Bergelt
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Stefan Simm
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Enrico Schleiff
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany
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4
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Kravchenko OV, Baymukhametov TN, Afonina ZA, Vassilenko KS. High-Resolution Structure and Internal Mobility of a Plant 40S Ribosomal Subunit. Int J Mol Sci 2023; 24:17453. [PMID: 38139282 PMCID: PMC10743738 DOI: 10.3390/ijms242417453] [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: 11/23/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Ribosome is a major part of the protein synthesis machinery, and analysis of its structure is of paramount importance. However, the structure of ribosomes from only a limited number of organisms has been resolved to date; it especially concerns plant ribosomes and ribosomal subunits. Here, we report a high-resolution cryo-electron microscopy reconstruction of the small subunit of the Triticum aestivum (common wheat) cytoplasmic ribosome. A detailed atomic model was built that includes the majority of the rRNA and some of the protein modifications. The analysis of the obtained data revealed structural peculiarities of the 40S subunit in the monocot plant ribosome. We applied the 3D Flexible Refinement approach to analyze the internal mobility of the 40S subunit and succeeded in decomposing it into four major motions, describing rotations of the head domain and a shift in the massive rRNA expansion segment. It was shown that these motions are almost uncorrelated and that the 40S subunit is flexible enough to spontaneously adopt any conformation it takes as a part of a translating ribosome or ribosomal complex. Here, we introduce the first high-resolution structure of an isolated plant 40S subunit and the first quantitative analysis of the flexibility of small ribosomal subunits, hoping that it will help in studying various aspects of ribosome functioning.
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Affiliation(s)
- Olesya V. Kravchenko
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (O.V.K.)
| | - Timur N. Baymukhametov
- National Research Center, “Kurchatov Institute”, Akademika Kurchatova pl. 1, 123182 Moscow, Russia;
| | - Zhanna A. Afonina
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (O.V.K.)
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5
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Xie Y, Chan LY, Cheung MY, Li MW, Lam HM. Current technical advancements in plant epitranscriptomic studies. THE PLANT GENOME 2023; 16:e20316. [PMID: 36890704 DOI: 10.1002/tpg2.20316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
The growth and development of plants are the result of the interplay between the internal developmental programming and plant-environment interactions. Gene expression regulations in plants are made up of multi-level networks. In the past few years, many studies were carried out on co- and post-transcriptional RNA modifications, which, together with the RNA community, are collectively known as the "epitranscriptome." The epitranscriptomic machineries were identified and their functional impacts characterized in a broad range of physiological processes in diverse plant species. There is mounting evidence to suggest that the epitranscriptome provides an additional layer in the gene regulatory network for plant development and stress responses. In the present review, we summarized the epitranscriptomic modifications found so far in plants, including chemical modifications, RNA editing, and transcript isoforms. The various approaches to RNA modification detection were described, with special emphasis on the recent development and application potential of third-generation sequencing. The roles of epitranscriptomic changes in gene regulation during plant-environment interactions were discussed in case studies. This review aims to highlight the importance of epitranscriptomics in the study of gene regulatory networks in plants and to encourage multi-omics investigations using the recent technical advancements.
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Affiliation(s)
- Yichun Xie
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Long-Yiu Chan
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ming-Yan Cheung
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Man-Wah Li
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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6
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Montacié C, Riondet C, Wei L, Darrière T, Weiss A, Pontvianne F, Escande ML, de Bures A, Jobet E, Barbarossa A, Carpentier MC, Aarts MGM, Attina A, Hirtz C, David A, Marchand V, Motorin Y, Curie C, Mari S, Reichheld JP, Sáez-Vásquez J. NICOTIANAMINE SYNTHASE activity affects nucleolar iron accumulation and impacts rDNA silencing and RNA methylation in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4384-4400. [PMID: 37179467 PMCID: PMC10433931 DOI: 10.1093/jxb/erad180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/11/2023] [Indexed: 05/15/2023]
Abstract
In plant cells, a large pool of iron (Fe) is contained in the nucleolus, as well as in chloroplasts and mitochondria. A central determinant for intracellular distribution of Fe is nicotianamine (NA) generated by NICOTIANAMINE SYNTHASE (NAS). Here, we used Arabidopsis thaliana plants with disrupted NAS genes to study the accumulation of nucleolar iron and understand its role in nucleolar functions and more specifically in rRNA gene expression. We found that nas124 triple mutant plants, which contained lower quantities of the iron ligand NA, also contained less iron in the nucleolus. This was concurrent with the expression of normally silenced rRNA genes from nucleolar organizer regions 2 (NOR2). Notably, in nas234 triple mutant plants, which also contained lower quantities of NA, nucleolar iron and rDNA expression were not affected. In contrast, in both nas124 and nas234, specific RNA modifications were differentially regulated in a genotype dependent manner. Taken together, our results highlight the impact of specific NAS activities in RNA gene expression. We discuss the interplay between NA and nucleolar iron with rDNA functional organization and RNA methylation.
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Affiliation(s)
- Charlotte Montacié
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Christophe Riondet
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Lili Wei
- Institut Agro, BPMP, CNRS, INRAE, Université Montpellier, 34060 Montpellier, France
| | - Tommy Darrière
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Alizée Weiss
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Frédéric Pontvianne
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Marie-Line Escande
- Observatoire Océanologique de Banyuls s/ mer, CNRS, 66650 Banyuls-sur-mer, France
- BioPIC Platform of the OOB, 66650 Banyuls-sur-mer, France
| | - Anne de Bures
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Edouard Jobet
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Adrien Barbarossa
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Mark G M Aarts
- Laboratory of Genetics, Wageningen University & Research, 6700AA Wageningen, Netherlands
| | - Aurore Attina
- INSERM, CHU Montpellier, CNRS, IRMB, Université Montpellier, 34090Montpellier, France
| | - Christophe Hirtz
- INSERM, CHU Montpellier, CNRS, IRMB, Université Montpellier, 34090Montpellier, France
| | - Alexandre David
- IGF, CNRS, INSERM, Université Montpellier, 34090Montpellier, France
| | - Virginie Marchand
- Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, CNRS, INSERM, IBSLor (UMS2008/US40), Université de Lorraine, F-54000 Nancy, France
| | - Yuri Motorin
- Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, CNRS, INSERM, IBSLor (UMS2008/US40), Université de Lorraine, F-54000 Nancy, France
- CNRS, IMoPA (UMR 7365), Université de Lorraine, F-54000 Nancy, France
| | - Catherine Curie
- Institut Agro, BPMP, CNRS, INRAE, Université Montpellier, 34060 Montpellier, France
| | - Stéphane Mari
- Institut Agro, BPMP, CNRS, INRAE, Université Montpellier, 34060 Montpellier, France
| | - Jean-Philippe Reichheld
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
| | - Julio Sáez-Vásquez
- Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, CNRS, 66860 Perpignan, France
- LGDP, UMR 5096, Université Perpignan Via Domitia, 66860 Perpignan, France
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7
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Gao S, Sun Y, Chen X, Zhu C, Liu X, Wang W, Gan L, Lu Y, Schaarschmidt F, Herde M, Witte CP, Chen M. Pyrimidine catabolism is required to prevent the accumulation of 5-methyluridine in RNA. Nucleic Acids Res 2023; 51:7451-7464. [PMID: 37334828 PMCID: PMC10415118 DOI: 10.1093/nar/gkad529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 05/31/2023] [Accepted: 06/08/2023] [Indexed: 06/21/2023] Open
Abstract
5-Methylated cytosine is a frequent modification in eukaryotic RNA and DNA influencing mRNA stability and gene expression. Here we show that free 5-methylcytidine (5mC) and 5-methyl-2'-deoxycytidine are generated from nucleic acid turnover in Arabidopsis thaliana, and elucidate how these cytidines are degraded, which is unclear in eukaryotes. First CYTIDINE DEAMINASE produces 5-methyluridine (5mU) and thymidine which are subsequently hydrolyzed by NUCLEOSIDE HYDROLASE 1 (NSH1) to thymine and ribose or deoxyribose. Interestingly, far more thymine is generated from RNA than from DNA turnover, and most 5mU is directly released from RNA without a 5mC intermediate, since 5-methylated uridine (m5U) is an abundant RNA modification (m5U/U ∼1%) in Arabidopsis. We show that m5U is introduced mainly by tRNA-SPECIFIC METHYLTRANSFERASE 2A and 2B. Genetic disruption of 5mU degradation in the NSH1 mutant causes m5U to occur in mRNA and results in reduced seedling growth, which is aggravated by external 5mU supplementation, also leading to more m5U in all RNA species. Given the similarities between pyrimidine catabolism in plants, mammals and other eukaryotes, we hypothesize that the removal of 5mU is an important function of pyrimidine degradation in many organisms, which in plants serves to protect RNA from stochastic m5U modification.
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Affiliation(s)
- Shangyu Gao
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yu Sun
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoguang Chen
- Department of Molecular Nutrition and Biochemistry of Plants, Institute of Plant Nutrition, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Changhua Zhu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoye Liu
- Department of Criminal Science and Technology, Nanjing Forest Police College, Nanjing 210023, China
| | - Wenlei Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lijun Gan
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yanwu Lu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Frank Schaarschmidt
- Department of Biostatistics, Institute of Cell Biology and Biophysics, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Marco Herde
- Department of Molecular Nutrition and Biochemistry of Plants, Institute of Plant Nutrition, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Institute of Plant Nutrition, Leibniz University Hannover, Herrenhäuser Str. 2, D-30419 Hannover, Germany
| | - Mingjia Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
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8
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Delorme-Hinoux V, Mbodj A, Brando S, De Bures A, Llauro C, Covato F, Garrigue J, Guisset C, Borrut J, Mirouze M, Reichheld JP, Sáez-Vásquez J. 45S rDNA Diversity In Natura as One Step towards Ribosomal Heterogeneity in Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2023; 12:2722. [PMID: 37514338 PMCID: PMC10386311 DOI: 10.3390/plants12142722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023]
Abstract
The keystone of ribosome biogenesis is the transcription of 45S rDNA. The Arabidopsis thaliana genome contains hundreds of 45S rDNA units; however, they are not all transcribed. Notably, 45S rDNA units contain insertions/deletions revealing the existence of heterogeneous rRNA genes and, likely, heterogeneous ribosomes for rRNAs. In order to obtain an overall picture of 45S rDNA diversity sustaining the synthesis of rRNAs and, subsequently, of ribosomes in natura, we took advantage of 320 new occurrences of Arabidopsis thaliana as a metapopulation named At66, sampled from 0 to 1900 m of altitude in the eastern Pyrenees in France. We found that the 45S rDNA copy number is very dynamic in natura and identified new genotypes for both 5' and 3' External Transcribed Spacers (ETS). Interestingly, the highest 5'ETS genotype diversity is found in altitude while the highest 3'ETS genotype diversity is found at sea level. Structural analysis of 45S rDNA also shows conservation in natura of specific 5'ETS and 3'ETS sequences/features required to control rDNA expression and the processing of rRNAs. In conclusion, At66 is a worthwhile natural laboratory, and unraveled 45S rDNA diversity represents an interesting starting material to select subsets for rDNA transcription and alter the rRNA composition of ribosomes both intra- and inter-site.
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Affiliation(s)
- Valérie Delorme-Hinoux
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- EMR LGDP/MANGO, Mechanisms of Adaptation and Genomics, IRD-CNRS-UPVD, 66860 Perpignan, France
- Association Charles Flahault, 66350 Toulouges, France
| | - Assane Mbodj
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- EMR LGDP/MANGO, Mechanisms of Adaptation and Genomics, IRD-CNRS-UPVD, 66860 Perpignan, France
- Institut de Recherche pour le Développement (IRD), ECOBIO, 34000 Montpellier, France
| | - Sophie Brando
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
| | - Anne De Bures
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
| | - Christel Llauro
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- EMR LGDP/MANGO, Mechanisms of Adaptation and Genomics, IRD-CNRS-UPVD, 66860 Perpignan, France
| | - Fabrice Covato
- FRNC, Fédération des Réserves Naturelles Catalanes, 66500 Prades, France
| | - Joseph Garrigue
- FRNC, Fédération des Réserves Naturelles Catalanes, 66500 Prades, France
| | - Claude Guisset
- Association Charles Flahault, 66350 Toulouges, France
- FRNC, Fédération des Réserves Naturelles Catalanes, 66500 Prades, France
| | | | - Marie Mirouze
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- EMR LGDP/MANGO, Mechanisms of Adaptation and Genomics, IRD-CNRS-UPVD, 66860 Perpignan, France
- Institut de Recherche pour le Développement (IRD), ECOBIO, 34000 Montpellier, France
| | - Jean-Philippe Reichheld
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
| | - Julio Sáez-Vásquez
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
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9
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Smirnova J, Loerke J, Kleinau G, Schmidt A, Bürger J, Meyer EH, Mielke T, Scheerer P, Bock R, Spahn CMT, Zoschke R. Structure of the actively translating plant 80S ribosome at 2.2 Å resolution. NATURE PLANTS 2023; 9:987-1000. [PMID: 37156858 PMCID: PMC10281867 DOI: 10.1038/s41477-023-01407-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/29/2023] [Indexed: 05/10/2023]
Abstract
In plant cells, translation occurs in three compartments: the cytosol, the plastids and the mitochondria. While the structures of the (prokaryotic-type) ribosomes in plastids and mitochondria are well characterized, high-resolution structures of the eukaryotic 80S ribosomes in the cytosol have been lacking. Here the structure of translating tobacco (Nicotiana tabacum) 80S ribosomes was solved by cryo-electron microscopy with a global resolution of 2.2 Å. The ribosome structure includes two tRNAs, decoded mRNA and the nascent peptide chain, thus providing insights into the molecular underpinnings of the cytosolic translation process in plants. The map displays conserved and plant-specific rRNA modifications and the positions of numerous ionic cofactors, and it uncovers the role of monovalent ions in the decoding centre. The model of the plant 80S ribosome enables broad phylogenetic comparisons that reveal commonalities and differences in the ribosomes of plants and those of other eukaryotes, thus putting our knowledge about eukaryotic translation on a firmer footing.
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Affiliation(s)
- Julia Smirnova
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Justus Loerke
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gunnar Kleinau
- Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Andrea Schmidt
- Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jörg Bürger
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Microscopy and Cryo-Electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Etienne H Meyer
- Department III, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- Institut für Pflanzenphysiologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Thorsten Mielke
- Microscopy and Cryo-Electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Patrick Scheerer
- Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ralph Bock
- Department III, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
| | - Christian M T Spahn
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Reimo Zoschke
- Department III, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
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10
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Ghouili E, Sassi K, Hidri Y, M’Hamed HC, Somenahally A, Xue Q, Jebara M, Nefissi Ouertani R, Riahi J, de Oliveira AC, Abid G, Muhovski Y. Effects of Date Palm Waste Compost Application on Root Proteome Changes of Barley ( Hordeum vulgare L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:526. [PMID: 36771612 PMCID: PMC9921465 DOI: 10.3390/plants12030526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Proteomic analysis was performed to investigate the differentially abundant proteins (DAPs) in barley roots during the tillering stage. Bioinformatic tools were used to interpret the biological function, the pathway analysis and the visualisation of the network amongst the identified proteins. A total of 72 DAPs (33 upregulated and 39 downregulated) among a total of 2580 proteins were identified in response to compost treatment, suggesting multiple pathways of primary and secondary metabolism, such as carbohydrates and energy metabolism, phenylpropanoid pathway, glycolysis pathway, protein synthesis and degradation, redox homeostasis, RNA processing, stress response, cytoskeleton organisation, and phytohormone metabolic pathways. The expression of DAPs was further validated by qRT-PCR. The effects on barley plant development, such as the promotion of root growth and biomass increase, were associated with a change in energy metabolism and protein synthesis. The activation of enzymes involved in redox homeostasis and the regulation of stress response proteins suggest a protective effect of compost, consequently improving barley growth and stress acclimation through the reduction of the environmental impact of productive agriculture. Overall, these results may facilitate a better understanding of the molecular mechanism of compost-promoted plant growth and provide valuable information for the identification of critical genes/proteins in barley as potential targets of compost.
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Affiliation(s)
- Emna Ghouili
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Khaled Sassi
- Laboratory of Agronomy, National Agronomy Institute of Tunisia (INAT), University of Carthage, Avenue Charles Nicolle, Tunis-Mahrajène, P.O. Box 43, Tunis 1082, Tunisia
| | - Yassine Hidri
- Laboratory of Integrated Olive Production in the Humid, Sub-humid and Semi-arid Region (LR16IO3), Olive Tree Institute, Cité Mahragène, P.O. Box 208, Tunis 1082, Tunisia
| | - Hatem Cheikh M’Hamed
- Agronomy Laboratory, National Institute of Agronomic Research of Tunis (INRAT), Carthage University, Hedi Karray Street, Ariana 2049, Tunisia
| | - Anil Somenahally
- Department of Soil and Crop Sciences, Texas A&M University, 370 Olsen Blvd, College Station, TX 77843-2474, USA
| | - Qingwu Xue
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX 79403-6603, USA
| | - Moez Jebara
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Rim Nefissi Ouertani
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj Cedria, P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Jouhaina Riahi
- Laboratory of Agronomy, National Agronomy Institute of Tunisia (INAT), University of Carthage, Avenue Charles Nicolle, Tunis-Mahrajène, P.O. Box 43, Tunis 1082, Tunisia
| | - Ana Caroline de Oliveira
- Biological Engineering Unit, Department of Life Sciences, Walloon Agricultural Research Centre, Chaussée de Charleroi, P.O. Box 234, 5030 Gembloux, Belgium
| | - Ghassen Abid
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Yordan Muhovski
- Biological Engineering Unit, Department of Life Sciences, Walloon Agricultural Research Centre, Chaussée de Charleroi, P.O. Box 234, 5030 Gembloux, Belgium
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11
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Wang Y, Deng XW, Zhu D. From molecular basics to agronomic benefits: Insights into noncoding RNA-mediated gene regulation in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2290-2308. [PMID: 36453685 DOI: 10.1111/jipb.13420] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The development of plants is largely dependent on their growth environment. To better adapt to a particular habitat, plants have evolved various subtle regulatory mechanisms for altering gene expression. Non coding RNAs (ncRNAs) constitute a major portion of the transcriptomes of eukaryotes. Various ncRNAs have been recognized as important regulators of the expression of genes involved in essential biological processes throughout the whole life cycles of plants. In this review, we summarize the current understanding of the biogenesis and contributions of small nucle olar RNA (snoRNA)- and regulatory long non coding RNA (lncRNA)-mediated gene regulation in plant development and environmental responses. Many regulatory ncRNAs appear to be associated with increased yield, quality and disease resistance of various species and cultivars. These ncRNAs may potentially be used as genetic resources for improving agronomic traits and for molecular breeding. The challenges in understanding plant ncRNA biology and the possibilities to make better use of these valuable gene resources in the future are discussed in this review.
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Affiliation(s)
- Yuqiu Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325, China
| | - Danmeng Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
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12
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Cao Y, Wang J, Wu S, Yin X, Shu J, Dai X, Liu Y, Sun L, Zhu D, Deng XW, Ye K, Qian W. The small nucleolar RNA SnoR28 regulates plant growth and development by directing rRNA maturation. THE PLANT CELL 2022; 34:4173-4190. [PMID: 36005862 PMCID: PMC9614442 DOI: 10.1093/plcell/koac265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are noncoding RNAs (ncRNAs) that guide chemical modifications of structural RNAs, which are essential for ribosome assembly and function in eukaryotes. Although numerous snoRNAs have been identified in plants by high-throughput sequencing, the biological functions of most of these snoRNAs remain unclear. Here, we identified box C/D SnoR28.1s as important regulators of plant growth and development by screening a CRISPR/Cas9-generated ncRNA deletion mutant library in Arabidopsis thaliana. Deletion of the SnoR28.1 locus, which contains a cluster of three genes producing SnoR28.1s, resulted in defects in root and shoot growth. SnoR28.1s guide 2'-O-ribose methylation of 25S rRNA at G2396. SnoR28.1s facilitate proper and efficient pre-rRNA processing, as the SnoR28.1 deletion mutants also showed impaired ribosome assembly and function, which may account for the growth defects. SnoR28 contains a 7-bp antisense box, which is required for 2'-O-ribose methylation of 25S rRNA at G2396, and an 8-bp extra box that is complementary to a nearby rRNA methylation site and is partially responsible for methylation of G2396. Both of these motifs are required for proper and efficient pre-rRNA processing. Finally, we show that SnoR28.1s genetically interact with HIDDEN TREASURE2 and NUCLEOLIN1. Our results advance our understanding of the roles of snoRNAs in Arabidopsis.
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Affiliation(s)
- Yuxin Cao
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Jiayin Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Songlin Wu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaochang Yin
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Jia Shu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Xing Dai
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
| | - Yannan Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Linhua Sun
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Danmeng Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China
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13
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Muñoz-Díaz E, Sáez-Vásquez J. Nuclear dynamics: Formation of bodies and trafficking in plant nuclei. FRONTIERS IN PLANT SCIENCE 2022; 13:984163. [PMID: 36082296 PMCID: PMC9445803 DOI: 10.3389/fpls.2022.984163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/04/2022] [Indexed: 06/01/2023]
Abstract
The existence of the nucleus distinguishes prokaryotes and eukaryotes. Apart from containing most of the genetic material, the nucleus possesses several nuclear bodies composed of protein and RNA molecules. The nucleus is separated from the cytoplasm by a double membrane, regulating the trafficking of molecules in- and outwards. Here, we investigate the composition and function of the different plant nuclear bodies and molecular clues involved in nuclear trafficking. The behavior of the nucleolus, Cajal bodies, dicing bodies, nuclear speckles, cyclophilin-containing bodies, photobodies and DNA damage foci is analyzed in response to different abiotic stresses. Furthermore, we research the literature to collect the different protein localization signals that rule nucleocytoplasmic trafficking. These signals include the different types of nuclear localization signals (NLSs) for nuclear import, and the nuclear export signals (NESs) for nuclear export. In contrast to these unidirectional-movement signals, the existence of nucleocytoplasmic shuttling signals (NSSs) allows bidirectional movement through the nuclear envelope. Likewise, nucleolar signals are also described, which mainly include the nucleolar localization signals (NoLSs) controlling nucleolar import. In contrast, few examples of nucleolar export signals, called nucleoplasmic localization signals (NpLSs) or nucleolar export signals (NoESs), have been reported. The existence of consensus sequences for these localization signals led to the generation of prediction tools, allowing the detection of these signals from an amino acid sequence. Additionally, the effect of high temperatures as well as different post-translational modifications in nuclear and nucleolar import and export is discussed.
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Affiliation(s)
- Eduardo Muñoz-Díaz
- Centre National de la Recherche Scientifique (CNRS), Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
- Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
| | - Julio Sáez-Vásquez
- Centre National de la Recherche Scientifique (CNRS), Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
- Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France
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14
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Ramakrishnan M, Rajan KS, Mullasseri S, Palakkal S, Kalpana K, Sharma A, Zhou M, Vinod KK, Ramasamy S, Wei Q. The plant epitranscriptome: revisiting pseudouridine and 2'-O-methyl RNA modifications. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1241-1256. [PMID: 35445501 PMCID: PMC9241379 DOI: 10.1111/pbi.13829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/11/2022] [Accepted: 04/18/2022] [Indexed: 06/01/2023]
Abstract
There is growing evidence that post-transcriptional RNA modifications are highly dynamic and can be used to improve crop production. Although more than 172 unique types of RNA modifications have been identified throughout the kingdom of life, we are yet to leverage upon the understanding to optimize RNA modifications in crops to improve productivity. The contributions of internal mRNA modifications such as N6-methyladenosine (m6 A) and 5-methylcytosine (m5 C) methylations to embryonic development, root development, leaf morphogenesis, flowering, fruit ripening and stress response are sufficiently known, but the roles of the two most abundant RNA modifications, pseudouridine (Ψ) and 2'-O-methylation (Nm), in the cell remain unclear due to insufficient advances in high-throughput technologies in plant development. Therefore, in this review, we discuss the latest methods and insights gained in mapping internal Ψ and Nm and their unique properties in plants and other organisms. In addition, we discuss the limitations that remain in high-throughput technologies for qualitative and quantitative mapping of these RNA modifications and highlight future challenges in regulating the plant epitranscriptome.
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Affiliation(s)
- Muthusamy Ramakrishnan
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingJiangsuChina
- Bamboo Research InstituteNanjing Forestry UniversityNanjingJiangsuChina
| | - K. Shanmugha Rajan
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology InstituteBar‐Ilan University52900Ramat‐GanIsrael
- Department of Chemical and Structural BiologyWeizmann Institute7610001RehovotIsrael
| | - Sileesh Mullasseri
- School of Ocean Science and TechnologyKerala University of Fisheries and Ocean StudiesCochinIndia
| | - Sarin Palakkal
- The Institute for Drug ResearchSchool of PharmacyThe Hebrew University of JerusalemJerusalemIsrael
| | - Krishnan Kalpana
- Department of Plant PathologyAgricultural College and Research InstituteTamilnadu Agricultural University625 104MaduraiTamil NaduIndia
| | - Anket Sharma
- State Key Laboratory of Subtropical SilvicultureZhejiang A&F UniversityHangzhouZhejiangChina
| | - Mingbing Zhou
- State Key Laboratory of Subtropical SilvicultureZhejiang A&F UniversityHangzhouZhejiangChina
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High‐Efficiency UtilizationZhejiang A&F UniversityHangzhouZhejiangChina
| | | | - Subbiah Ramasamy
- Cardiac Metabolic Disease LaboratoryDepartment of BiochemistrySchool of Biological SciencesMadurai Kamaraj UniversityMaduraiTamil NaduIndia
| | - Qiang Wei
- Co‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingJiangsuChina
- Bamboo Research InstituteNanjing Forestry UniversityNanjingJiangsuChina
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15
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Darriere T, Jobet E, Zavala D, Escande ML, Durut N, de Bures A, Blanco-Herrera F, Vidal EA, Rompais M, Carapito C, Gourbiere S, Sáez-Vásquez J. Upon heat stress processing of ribosomal RNA precursors into mature rRNAs is compromised after cleavage at primary P site in Arabidopsis thaliana. RNA Biol 2022; 19:719-734. [PMID: 35522061 PMCID: PMC9090299 DOI: 10.1080/15476286.2022.2071517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Transcription and processing of 45S rRNAs in the nucleolus are keystones of ribosome biogenesis. While these processes are severely impacted by stress conditions in multiple species, primarily upon heat exposure, we lack information about the molecular mechanisms allowing sessile organisms without a temperature-control system, like plants, to cope with such circumstances. We show that heat stress disturbs nucleolar structure, inhibits pre-rRNA processing and provokes imbalanced ribosome profiles in Arabidopsis thaliana plants. Notably, the accuracy of transcription initiation and cleavage at the primary P site in the 5’ETS (5’ External Transcribed Spacer) are not affected but the levels of primary 45S and 35S transcripts are, respectively, increased and reduced. In contrast, precursors of 18S, 5.8S and 25S RNAs are rapidly undetectable upon heat stress. Remarkably, nucleolar structure, pre-rRNAs from major ITS1 processing pathway and ribosome profiles are restored after returning to optimal conditions, shedding light on the extreme plasticity of nucleolar functions in plant cells. Further genetic and molecular analysis to identify molecular clues implicated in these nucleolar responses indicate that cleavage rate at P site and nucleolin protein expression can act as a checkpoint control towards a productive pre-rRNA processing pathway.
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Affiliation(s)
- T Darriere
- CNRS, Laboratoire Génome et D#x0E9;veloppement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France.,Univ. Perpignan Via Domitia, LGDP, UMR 5096, Perpignan, France
| | - E Jobet
- CNRS, Laboratoire Génome et D#x0E9;veloppement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France.,Univ. Perpignan Via Domitia, LGDP, UMR 5096, Perpignan, France
| | - D Zavala
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - M L Escande
- CNRS, Observatoire Océanologique de Banyuls s/ mer, Banyuls-sur-mer, France.,BioPIC Platform of the OOB, Banyuls-sur-mer, France
| | - N Durut
- CNRS, Laboratoire Génome et D#x0E9;veloppement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France.,Univ. Perpignan Via Domitia, LGDP, UMR 5096, Perpignan, France
| | - A de Bures
- CNRS, Laboratoire Génome et D#x0E9;veloppement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France.,Univ. Perpignan Via Domitia, LGDP, UMR 5096, Perpignan, France
| | - F Blanco-Herrera
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,Millennium Institute for Integrative Biology (IBio), Santiago, Chile
| | - E A Vidal
- Millennium Institute for Integrative Biology (IBio), Santiago, Chile.,Bioinformática, Facultad de Ciencias, Universidad MayorCentro de Genómica y , Santiago, Chile
| | - M Rompais
- Laboratoire de Spectrométrie de Masse BioOrganique, Institut Pluridisciplinaire Hubert Curien, UMR7178 CNRS/Université de Strasbourg, Strasbourg, France
| | - C Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique, Institut Pluridisciplinaire Hubert Curien, UMR7178 CNRS/Université de Strasbourg, Strasbourg, France
| | - S Gourbiere
- CNRS, Laboratoire Génome et D#x0E9;veloppement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France.,Univ. Perpignan Via Domitia, LGDP, UMR 5096, Perpignan, France
| | - J Sáez-Vásquez
- CNRS, Laboratoire Génome et D#x0E9;veloppement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France.,Univ. Perpignan Via Domitia, LGDP, UMR 5096, Perpignan, France
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16
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Tang XM, Ye TT, You XJ, Yin XM, Ding JH, Shao WX, Chen MY, Yuan BF, Feng YQ. Mass spectrometry profiling analysis enables the identification of new modifications in ribosomal RNA. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.05.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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17
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Shoaib Y, Usman B, Kang H, Jung KH. Epitranscriptomics: An Additional Regulatory Layer in Plants' Development and Stress Response. PLANTS (BASEL, SWITZERLAND) 2022; 11:1033. [PMID: 35448761 PMCID: PMC9027318 DOI: 10.3390/plants11081033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
Epitranscriptomics has added a new layer of regulatory machinery to eukaryotes, and the advancement of sequencing technology has revealed more than 170 post-transcriptional modifications in various types of RNAs, including messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), and long non-coding RNA (lncRNA). Among these, N6-methyladenosine (m6A) and N5-methylcytidine (m5C) are the most prevalent internal mRNA modifications. These regulate various aspects of RNA metabolism, mainly mRNA degradation and translation. Recent advances have shown that regulation of RNA fate mediated by these epitranscriptomic marks has pervasive effects on a plant's development and responses to various biotic and abiotic stresses. Recently, it was demonstrated that the removal of human-FTO-mediated m6A from transcripts in transgenic rice and potatoes caused a dramatic increase in their yield, and that the m6A reader protein mediates stress responses in wheat and apple, indicating that regulation of m6A levels could be an efficient strategy for crop improvement. However, changing the overall m6A levels might have unpredictable effects; therefore, the identification of precise m6A levels at a single-base resolution is essential. In this review, we emphasize the roles of epitranscriptomic modifications in modulating molecular, physiological, and stress responses in plants, and provide an outlook on epitranscriptome engineering as a promising tool to ensure food security by editing specific m6A and m5C sites through robust genome-editing technology.
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Affiliation(s)
- Yasira Shoaib
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin-si 17104, Korea; (Y.S.); (B.U.)
| | - Babar Usman
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin-si 17104, Korea; (Y.S.); (B.U.)
| | - Hunseung Kang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Korea;
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin-si 17104, Korea; (Y.S.); (B.U.)
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18
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Machine learning algorithm for precise prediction of 2’-O-methylation (Nm) sites from experimental RiboMethSeq datasets. Methods 2022; 203:311-321. [DOI: 10.1016/j.ymeth.2022.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/09/2022] [Accepted: 03/16/2022] [Indexed: 12/18/2022] Open
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19
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Wang L, Xu D, Scharf K, Frank W, Leister D, Kleine T. The RNA-binding protein RBP45D of Arabidopsis promotes transgene silencing and flowering time. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1397-1415. [PMID: 34919766 DOI: 10.1111/tpj.15637] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
RNA-directed DNA methylation (RdDM) helps to defend plants against invasive nucleic acids. In the canonical form of RdDM, 24-nt small interfering RNAs (siRNAs) are produced by DICER-LIKE 3 (DCL3). The siRNAs are loaded onto ARGONAUTE (AGO) proteins leading ultimately to de novo DNA methylation. Here, we introduce the Arabidopsis thaliana prors1 (LUC) transgenic system, in which 24-nt siRNAs are generated to silence the promoter-LUC construct. A forward genetic screen performed with this system identified, besides known components of RdDM (NRPD2A, RDR2, AGO4 and AGO6), the RNA-binding protein RBP45D. RBP45D is involved in CHH (where H is A, C or T) DNA methylation, and maintains siRNA production originating from the LUC transgene. RBP45D is localized to the nucleus, where it is associated with small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). RNA-Seq analysis showed that in CRISPR/Cas-mediated rbp-ko lines FLOWERING LOCUS C (FLC) mRNA levels are upregulated and several loci differentially spliced, among them FLM. In consequence, loss of RBP45D delays flowering, presumably mediated by the release of FLC levels and/or alternative splicing of FLM. Moreover, because levels and processing of transcripts of known RdDM genes are not altered in rbp-ko lines, RBP45D should have a more direct function in transgene silencing, probably independent of the canonical RdDM pathway. We suggest that RBP45D facilitates siRNA production by stabilizing either the precursor RNA or the slicer protein. Alternatively, RBP45D could be involved in chromatin modifications, participate in retention of Pol IV transcripts and/or in Pol V-dependent lncRNA retention in chromatin to enable their scaffold function.
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Affiliation(s)
- Liangsheng Wang
- Plant Molecular Biology (Botany), Faculty of Biology, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Duorong Xu
- Plant Molecular Biology (Botany), Faculty of Biology, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Kristin Scharf
- Plant Molecular Cell Biology, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Wolfgang Frank
- Plant Molecular Cell Biology, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Dario Leister
- Plant Molecular Biology (Botany), Faculty of Biology, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
| | - Tatjana Kleine
- Plant Molecular Biology (Botany), Faculty of Biology, Ludwig-Maximilians-Universität München, 82152, Planegg-Martinsried, Germany
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20
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Fractional 2'-O-methylation in the ribosomal RNA of Dictyostelium discoideum supports ribosome heterogeneity in Amoebozoa. Sci Rep 2022; 12:1952. [PMID: 35121764 PMCID: PMC8817022 DOI: 10.1038/s41598-022-05447-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/07/2022] [Indexed: 12/02/2022] Open
Abstract
A hallmark of ribosomal RNA (rRNA) are 2′-O-methyl groups that are introduced sequence specifically by box C/D small nucleolar RNAs (snoRNAs) in ribonucleoprotein particles. Most data on this chemical modification and its impact on RNA folding and stability are derived from organisms of the Opisthokonta supergroup. Using bioinformatics and RNA-seq data, we identify 30 novel box C/D snoRNAs in Dictyostelium discoideum, many of which are differentially expressed during the multicellular development of the amoeba. By applying RiboMeth-seq, we find 49 positions in the 17S and 26S rRNA 2′-O-methylated. Several of these nucleotides are substoichiometrically modified, with one displaying dynamic modification levels during development. Using homology-based models for the D. discoideum rRNA secondary structures, we localize many modified nucleotides in the vicinity of the ribosomal A, P and E sites. For most modified positions, a guiding box C/D snoRNA could be identified, allowing to determine idiosyncratic features of the snoRNA/rRNA interactions in the amoeba. Our data from D. discoideum represents the first evidence for ribosome heterogeneity in the Amoebozoa supergroup, allowing to suggest that it is a common feature of all eukaryotes.
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21
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Jaafar M, Paraqindes H, Gabut M, Diaz JJ, Marcel V, Durand S. 2'O-Ribose Methylation of Ribosomal RNAs: Natural Diversity in Living Organisms, Biological Processes, and Diseases. Cells 2021; 10:1948. [PMID: 34440717 PMCID: PMC8393311 DOI: 10.3390/cells10081948] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 01/21/2023] Open
Abstract
Recent findings suggest that ribosomes, the translational machineries, can display a distinct composition depending on physio-pathological contexts. Thanks to outstanding technological breakthroughs, many studies have reported that variations of rRNA modifications, and more particularly the most abundant rRNA chemical modification, the rRNA 2'O-ribose methylation (2'Ome), intrinsically occur in many organisms. In the last 5 years, accumulating reports have illustrated that rRNA 2'Ome varies in human cell lines but also in living organisms (yeast, plant, zebrafish, mouse, human) during development and diseases. These rRNA 2'Ome variations occur either within a single cell line, organ, or patient's sample (i.e., intra-variability) or between at least two biological conditions (i.e., inter-variability). Thus, the ribosomes can tolerate the absence of 2'Ome at some specific positions. These observations question whether variations in rRNA 2'Ome could provide ribosomes with particular translational regulatory activities and functional specializations. Here, we compile recent studies supporting the heterogeneity of ribosome composition at rRNA 2'Ome level and provide an overview of the natural diversity in rRNA 2'Ome that has been reported up to now throughout the kingdom of life. Moreover, we discuss the little evidence that suggests that variations of rRNA 2'Ome can effectively impact the ribosome activity and contribute to the etiology of some human diseases.
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Affiliation(s)
| | | | | | | | - Virginie Marcel
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, CEDEX 08, F-69373 Lyon, France; (M.J.); (H.P.); (M.G.); (J.-J.D.)
| | - Sébastien Durand
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, CEDEX 08, F-69373 Lyon, France; (M.J.); (H.P.); (M.G.); (J.-J.D.)
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22
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Streit D, Schleiff E. The Arabidopsis 2'-O-Ribose-Methylation and Pseudouridylation Landscape of rRNA in Comparison to Human and Yeast. FRONTIERS IN PLANT SCIENCE 2021; 12:684626. [PMID: 34381476 PMCID: PMC8351944 DOI: 10.3389/fpls.2021.684626] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/16/2021] [Indexed: 05/25/2023]
Abstract
Eukaryotic ribosome assembly starts in the nucleolus, where the ribosomal DNA (rDNA) is transcribed into the 35S pre-ribosomal RNA (pre-rRNA). More than two-hundred ribosome biogenesis factors (RBFs) and more than two-hundred small nucleolar RNAs (snoRNA) catalyze the processing, folding and modification of the rRNA in Arabidopsis thaliana. The initial pre-ribosomal 90S complex is formed already during transcription by association of ribosomal proteins (RPs) and RBFs. In addition, small nucleolar ribonucleoprotein particles (snoRNPs) composed of snoRNAs and RBFs catalyze the two major rRNA modification types, 2'-O-ribose-methylation and pseudouridylation. Besides these two modifications, rRNAs can also undergo base methylations and acetylation. However, the latter two modifications have not yet been systematically explored in plants. The snoRNAs of these snoRNPs serve as targeting factors to direct modifications to specific rRNA regions by antisense elements. Today, hundreds of different sites of modifications in the rRNA have been described for eukaryotic ribosomes in general. While our understanding of the general process of ribosome biogenesis has advanced rapidly, the diversities appearing during plant ribosome biogenesis is beginning to emerge. Today, more than two-hundred RBFs were identified by bioinformatics or biochemical approaches, including several plant specific factors. Similarly, more than two hundred snoRNA were predicted based on RNA sequencing experiments. Here, we discuss the predicted and verified rRNA modification sites and the corresponding identified snoRNAs on the example of the model plant Arabidopsis thaliana. Our summary uncovers the plant modification sites in comparison to the human and yeast modification sites.
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Affiliation(s)
- Deniz Streit
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt, Germany
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt, Germany
- Frankfurt Institute for Advanced Studies (FIAS), Frankfurt, Germany
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