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Funk HM, Brooks JH, Detmer AE, Creech NN, Guy MP. Identification of Amino Acids in Trm734 Required for 2'- O-Methylation of the tRNA Phe Wobble Residue. ACS OMEGA 2024; 9:25063-25072. [PMID: 38882062 PMCID: PMC11170731 DOI: 10.1021/acsomega.4c02313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/29/2024] [Accepted: 05/27/2024] [Indexed: 06/18/2024]
Abstract
All organisms methylate their nucleic acids, and this methylation is critical for proper gene expression at both the transcriptional and translational levels. For proper translation in eukaryotes, 2'-O-methylation of C32 (Cm32) and G34 (Gm34) in the anticodon loop of tRNAPhe is critical, with defects in these modifications associated with human disease. In yeast, Cm32 is formed by an enzyme that consists of the methyltransferase Trm7 in complex with the auxiliary protein Trm732, and Gm34 is formed by an enzyme that consists of Trm7 in complex with Trm734. The role of Trm732 and Trm734 in tRNA modification is not fully understood, although previous studies have suggested that Trm734 is important for tRNA binding. In this report, we generated Trm734 variants and tested their ability to work with Trm7 to modify tRNAPhe. Using this approach, we identified several regions of amino acids that are important for Trm734 activity and/or stability. Based on the previously determined Trm7-Trm734 crystal structure, these crucial amino acids are near the active site of Trm7 and are not directly involved in Trm7-Trm734 protein-protein interactions. Immunoprecipitation experiments with these Trm734 variants and Trm7 confirm that these residues are not involved in Trm7-Trm734 binding. Further experiments should help determine if these residues are important for tRNA binding or have another role in the modification of the tRNA. Furthermore, our discovery of a nonfunctional, stable Trm734 variant will be useful in determining if the reported roles of Trm734 in other biological processes such as retromer processing and resistance to Ty1 transposition are due to tRNA modification defects or to other bona fide cellular roles of Trm734.
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Affiliation(s)
- Holly M Funk
- Department of Chemistry & Biochemistry, Dorothy Westerman Herrmann Science Center (SC), Room 204F, Northern Kentucky University, Highland Heights, Kentucky 41076, United States of America
| | - Jennifer H Brooks
- Department of Chemistry & Biochemistry, Dorothy Westerman Herrmann Science Center (SC), Room 204F, Northern Kentucky University, Highland Heights, Kentucky 41076, United States of America
| | - Alisha E Detmer
- Department of Chemistry & Biochemistry, Dorothy Westerman Herrmann Science Center (SC), Room 204F, Northern Kentucky University, Highland Heights, Kentucky 41076, United States of America
| | - Natalie N Creech
- Department of Chemistry & Biochemistry, Dorothy Westerman Herrmann Science Center (SC), Room 204F, Northern Kentucky University, Highland Heights, Kentucky 41076, United States of America
| | - Michael P Guy
- Department of Chemistry & Biochemistry, Dorothy Westerman Herrmann Science Center (SC), Room 204F, Northern Kentucky University, Highland Heights, Kentucky 41076, United States of America
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2
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van den Akker GGH, Chabronova A, Housmans BAC, van der Vloet L, Surtel DAM, Cremers A, Marchand V, Motorin Y, Caron MMJ, Peffers MJ, Welting TJM. TGF-β2 Induces Ribosome Activity, Alters Ribosome Composition and Inhibits IRES-Mediated Translation in Chondrocytes. Int J Mol Sci 2024; 25:5031. [PMID: 38732249 PMCID: PMC11084827 DOI: 10.3390/ijms25095031] [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: 03/12/2024] [Revised: 04/29/2024] [Accepted: 05/01/2024] [Indexed: 05/13/2024] Open
Abstract
Alterations in cell fate are often attributed to (epigenetic) regulation of gene expression. An emerging paradigm focuses on specialized ribosomes within a cell. However, little evidence exists for the dynamic regulation of ribosome composition and function. Here, we stimulated a chondrocytic cell line with transforming growth factor beta (TGF-β2) and mapped changes in ribosome function, composition and ribosomal RNA (rRNA) epitranscriptomics. 35S Met/Cys incorporation was used to evaluate ribosome activity. Dual luciferase reporter assays were used to assess ribosomal modus. Ribosomal RNA expression and processing were determined by RT-qPCR, while RiboMethSeq and HydraPsiSeq were used to determine rRNA modification profiles. Label-free protein quantification of total cell lysates, isolated ribosomes and secreted proteins was done by LC-MS/MS. A three-day TGF-β2 stimulation induced total protein synthesis in SW1353 chondrocytic cells and human articular chondrocytes. Specifically, TGF-β2 induced cap-mediated protein synthesis, while IRES-mediated translation was not (P53 IRES) or little affected (CrPv IGR and HCV IRES). Three rRNA post-transcriptional modifications (PTMs) were affected by TGF-β2 stimulation (18S-Gm1447 downregulated, 18S-ψ1177 and 28S-ψ4598 upregulated). Proteomic analysis of isolated ribosomes revealed increased interaction with eIF2 and tRNA ligases and decreased association of eIF4A3 and heterogeneous nuclear ribonucleoprotein (HNRNP)s. In addition, thirteen core ribosomal proteins were more present in ribosomes from TGF-β2 stimulated cells, albeit with a modest fold change. A prolonged stimulation of chondrocytic cells with TGF-β2 induced ribosome activity and changed the mode of translation. These functional changes could be coupled to alterations in accessory proteins in the ribosomal proteome.
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Affiliation(s)
- Guus G. H. van den Akker
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Alzbeta Chabronova
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
- Department of Musculoskeletal Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Bas A. C. Housmans
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Laura van der Vloet
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Don A. M. Surtel
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Andy Cremers
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Virginie Marchand
- UAR2008 IBSLor CNRS-INSERM, Université de Lorraine, BioPole, F54000 Nancy, France; (V.M.); (Y.M.)
| | - Yuri Motorin
- UAR2008 IBSLor CNRS-INSERM, Université de Lorraine, BioPole, F54000 Nancy, France; (V.M.); (Y.M.)
- UMR7365 IMoPA, CNRS, Université de Lorraine, BioPole, F54000 Nancy, France
| | - Marjolein M. J. Caron
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
| | - Mandy J. Peffers
- Department of Musculoskeletal Ageing Science, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - Tim J. M. Welting
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Research School CAPHRI, Faculty of Healthy Medicine and Life Sciences, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.C.); (M.M.J.C.); (T.J.M.W.)
- Laboratory of Experimental Orthopedics, Department of Orthopedic Surgery, Maastricht University Medical Center +, 6229 HX Maastricht, The Netherlands
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3
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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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4
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Parker MD, Brunk ES, Getzler AJ, Karbstein K. The kinase Rio1 and a ribosome collision-dependent decay pathway survey the integrity of 18S rRNA cleavage. PLoS Biol 2024; 22:e3001767. [PMID: 39038273 PMCID: PMC11045238 DOI: 10.1371/journal.pbio.3001767] [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: 07/20/2022] [Accepted: 03/05/2024] [Indexed: 07/24/2024] Open
Abstract
The 18S rRNA sequence is highly conserved, particularly at its 3'-end, which is formed by the endonuclease Nob1. How Nob1 identifies its target sequence is not known, and in vitro experiments have shown Nob1 to be error-prone. Moreover, the sequence around the 3'-end is degenerate with similar sites nearby. Here, we used yeast genetics, biochemistry, and next-generation sequencing to investigate a role for the ATPase Rio1 in monitoring the accuracy of the 18S rRNA 3'-end. We demonstrate that Nob1 can miscleave its rRNA substrate and that miscleaved rRNA accumulates upon bypassing the Rio1-mediated quality control (QC) step, but not in healthy cells with intact QC mechanisms. Mechanistically, we show that Rio1 binding to miscleaved rRNA is weaker than its binding to accurately processed 18S rRNA. Accordingly, excess Rio1 results in accumulation of miscleaved rRNA. Ribosomes containing miscleaved rRNA can translate, albeit more slowly, thereby inviting collisions with trailing ribosomes. These collisions result in degradation of the defective ribosomes utilizing parts of the machinery for mRNA QC. Altogether, the data support a model in which Rio1 inspects the 3'-end of the nascent 18S rRNA to prevent miscleaved 18S rRNA-containing ribosomes from erroneously engaging in translation, where they induce ribosome collisions. The data also demonstrate how ribosome collisions purify cells of altered ribosomes with different functionalities, with important implications for the concept of ribosome heterogeneity.
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Affiliation(s)
- Melissa D. Parker
- The Skaggs Graduate School of Chemical and Biological Sciences, The
Scripps Research Institute, La Jolla, California, United States of
America
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and
Technology, Jupiter, Florida, United States of America
| | - Elise S. Brunk
- The Skaggs Graduate School of Chemical and Biological Sciences, The
Scripps Research Institute, La Jolla, California, United States of
America
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and
Technology, Jupiter, Florida, United States of America
| | - Adam J. Getzler
- The Skaggs Graduate School of Chemical and Biological Sciences, The
Scripps Research Institute, La Jolla, California, United States of
America
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and
Technology, Jupiter, Florida, United States of America
| | - Katrin Karbstein
- The Skaggs Graduate School of Chemical and Biological Sciences, The
Scripps Research Institute, La Jolla, California, United States of
America
- The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and
Technology, Jupiter, Florida, United States of America
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5
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Rajan KS, Madmoni H, Bashan A, Taoka M, Aryal S, Nobe Y, Doniger T, Galili Kostin B, Blumberg A, Cohen-Chalamish S, Schwartz S, Rivalta A, Zimmerman E, Unger R, Isobe T, Yonath A, Michaeli S. A single pseudouridine on rRNA regulates ribosome structure and function in the mammalian parasite Trypanosoma brucei. Nat Commun 2023; 14:7462. [PMID: 37985661 PMCID: PMC10662448 DOI: 10.1038/s41467-023-43263-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 11/05/2023] [Indexed: 11/22/2023] Open
Abstract
Trypanosomes are protozoan parasites that cycle between insect and mammalian hosts and are the causative agent of sleeping sickness. Here, we describe the changes of pseudouridine (Ψ) modification on rRNA in the two life stages of the parasite using four different genome-wide approaches. CRISPR-Cas9 knock-outs of all four snoRNAs guiding Ψ on helix 69 (H69) of the large rRNA subunit were lethal. A single knock-out of a snoRNA guiding Ψ530 on H69 altered the composition of the 80S monosome. These changes specifically affected the translation of only a subset of proteins. This study correlates a single site Ψ modification with changes in ribosomal protein stoichiometry, supported by a high-resolution cryo-EM structure. We propose that alteration in rRNA modifications could generate ribosomes preferentially translating state-beneficial proteins.
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Affiliation(s)
- K Shanmugha Rajan
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Hava Madmoni
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Anat Bashan
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Masato Taoka
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
| | - Saurav Aryal
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Yuko Nobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
| | - Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Beathrice Galili Kostin
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Amit Blumberg
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
| | - Smadar Cohen-Chalamish
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Andre Rivalta
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ella Zimmerman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ron Unger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Toshiaki Isobe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minami-osawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
| | - Ada Yonath
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan, 5290002, Israel.
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Vanden Broeck A, Klinge S. Principles of human pre-60 S biogenesis. Science 2023; 381:eadh3892. [PMID: 37410842 DOI: 10.1126/science.adh3892] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/20/2023] [Indexed: 07/08/2023]
Abstract
During the early stages of human large ribosomal subunit (60S) biogenesis, an ensemble of assembly factors establishes and fine-tunes the essential RNA functional centers of pre-60S particles by an unknown mechanism. Here, we report a series of cryo-electron microscopy structures of human nucleolar and nuclear pre-60S assembly intermediates at resolutions of 2.5 to 3.2 angstroms. These structures show how protein interaction hubs tether assembly factor complexes to nucleolar particles and how guanosine triphosphatases and adenosine triphosphatase couple irreversible nucleotide hydrolysis steps to the installation of functional centers. Nuclear stages highlight how a conserved RNA-processing complex, the rixosome, couples large-scale RNA conformational changes with pre-ribosomal RNA processing by the RNA degradation machinery. Our ensemble of human pre-60S particles provides a rich foundation with which to elucidate the molecular principles of ribosome formation.
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Affiliation(s)
- Arnaud Vanden Broeck
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Sebastian Klinge
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY 10065, USA
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Broeck AV, Klinge S. Principles of human pre-60 S biogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532478. [PMID: 36993238 PMCID: PMC10054963 DOI: 10.1101/2023.03.14.532478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
During early stages of human large ribosomal subunit (60 S ) biogenesis, an ensemble of assembly factors establishes and fine-tunes the essential RNA functional centers of pre-60 S particles by an unknown mechanism. Here, we report a series of cryo-electron microscopy structures of human nucleolar and nuclear pre-60 S assembly intermediates at resolutions of 2.5-3.2 Ã…. These structures show how protein interaction hubs tether assembly factor complexes to nucleolar particles and how GTPases and ATPases couple irreversible nucleotide hydrolysis steps to the installation of functional centers. Nuclear stages highlight how a conserved RNA processing complex, the rixosome, couples large-scale RNA conformational changes to pre-rRNA processing by the RNA degradation machinery. Our ensemble of human pre-60 S particles provides a rich foundation to elucidate the molecular principles of ribosome formation. One-Sentence Summary High-resolution cryo-EM structures of human pre-60S particles reveal new principles of eukaryotic ribosome assembly.
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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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