1
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Takada H, Paternoga H, Fujiwara K, Nakamoto J, Park E, Dimitrova-Paternoga L, Beckert B, Saarma M, Tenson T, Buskirk A, Atkinson G, Chiba S, Wilson D, Hauryliuk V. A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis. Nucleic Acids Res 2024; 52:8483-8499. [PMID: 38811035 PMCID: PMC11317155 DOI: 10.1093/nar/gkae399] [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: 03/16/2024] [Revised: 04/26/2024] [Accepted: 05/06/2024] [Indexed: 05/31/2024] Open
Abstract
Ribosomes trapped on mRNAs during protein synthesis need to be rescued for the cell to survive. The most ubiquitous bacterial ribosome rescue pathway is trans-translation mediated by tmRNA and SmpB. Genetic inactivation of trans-translation can be lethal, unless ribosomes are rescued by ArfA or ArfB alternative rescue factors or the ribosome-associated quality control (RQC) system, which in Bacillus subtilis involves MutS2, RqcH, RqcP and Pth. Using transposon sequencing in a trans-translation-incompetent B. subtilis strain we identify a poorly characterized S4-domain-containing protein YlmH as a novel potential RQC factor. Cryo-EM structures reveal that YlmH binds peptidyl-tRNA-50S complexes in a position analogous to that of S4-domain-containing protein RqcP, and that, similarly to RqcP, YlmH can co-habit with RqcH. Consistently, we show that YlmH can assume the role of RqcP in RQC by facilitating the addition of poly-alanine tails to truncated nascent polypeptides. While in B. subtilis the function of YlmH is redundant with RqcP, our taxonomic analysis reveals that in multiple bacterial phyla RqcP is absent, while YlmH and RqcH are present, suggesting that in these species YlmH plays a central role in the RQC.
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Affiliation(s)
- Hiraku Takada
- Faculty of Life Sciences, Kyoto Sangyo University and Institute for Protein Dynamics, Kamigamo, Motoyama, Kita-ku, Kyoto 603-8555, Japan
- Department of Biotechnology, Toyama Prefectural University,5180 Kurokawa, Imizu, Toyama 939-0398, Japan
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Keigo Fujiwara
- Faculty of Life Sciences, Kyoto Sangyo University and Institute for Protein Dynamics, Kamigamo, Motoyama, Kita-ku, Kyoto 603-8555, Japan
| | - Jose A Nakamoto
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
| | - Esther N Park
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lyudmila Dimitrova-Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Bertrand Beckert
- Dubochet Center for Imaging (DCI) at EPFL, EPFL SB IPHYS DCI, Lausanne, Switzerland
| | - Merilin Saarma
- University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Tanel Tenson
- University of Tartu, Institute of Technology, 50411 Tartu, Estonia
| | - Allen R Buskirk
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Gemma C Atkinson
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
- Virus Centre, Lund University, Lund, Sweden
| | - Shinobu Chiba
- Faculty of Life Sciences, Kyoto Sangyo University and Institute for Protein Dynamics, Kamigamo, Motoyama, Kita-ku, Kyoto 603-8555, Japan
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Vasili Hauryliuk
- Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
- Virus Centre, Lund University, Lund, Sweden
- Science for Life Laboratory, Lund, Sweden
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2
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Holvec S, Barchet C, Lechner A, Fréchin L, De Silva SNT, Hazemann I, Wolff P, von Loeffelholz O, Klaholz BP. The structure of the human 80S ribosome at 1.9 Å resolution reveals the molecular role of chemical modifications and ions in RNA. Nat Struct Mol Biol 2024; 31:1251-1264. [PMID: 38844527 DOI: 10.1038/s41594-024-01274-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 03/14/2024] [Indexed: 08/17/2024]
Abstract
The ribosomal RNA of the human protein synthesis machinery comprises numerous chemical modifications that are introduced during ribosome biogenesis. Here we present the 1.9 Å resolution cryo electron microscopy structure of the 80S human ribosome resolving numerous new ribosomal RNA modifications and functionally important ions such as Zn2+, K+ and Mg2+, including their associated individual water molecules. The 2'-O-methylation, pseudo-uridine and base modifications were confirmed by mass spectrometry, resulting in a complete investigation of the >230 sites, many of which could not be addressed previously. They choreograph key interactions within the RNA and at the interface with proteins, including at the ribosomal subunit interfaces of the fully assembled 80S ribosome. Uridine isomerization turns out to be a key mechanism for U-A base pair stabilization in RNA in general. The structural environment of chemical modifications and ions is primordial for the RNA architecture of the mature human ribosome, hence providing a structural framework to address their role in healthy states and in human diseases.
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Affiliation(s)
- Samuel Holvec
- Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Illkirch, France
- Centre National de la Recherche Scientifique UMR, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Charles Barchet
- Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Illkirch, France
- Centre National de la Recherche Scientifique UMR, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Antony Lechner
- Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Illkirch, France
- Centre National de la Recherche Scientifique UMR, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Strasbourg, France
- Architecture et Réactivité de l'ARN, CNRS UPR9002, Institute of Molecular and Cellular Biology, Université de Strasbourg, Strasbourg, France
| | - Léo Fréchin
- Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Illkirch, France
- Centre National de la Recherche Scientifique UMR, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - S Nimali T De Silva
- Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Illkirch, France
- Centre National de la Recherche Scientifique UMR, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Isabelle Hazemann
- Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Illkirch, France
- Centre National de la Recherche Scientifique UMR, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Philippe Wolff
- Architecture et Réactivité de l'ARN, CNRS UPR9002, Institute of Molecular and Cellular Biology, Université de Strasbourg, Strasbourg, France
| | - Ottilie von Loeffelholz
- Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Illkirch, France
- Centre National de la Recherche Scientifique UMR, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Bruno P Klaholz
- Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Illkirch, France.
- Centre National de la Recherche Scientifique UMR, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France.
- Université de Strasbourg, Strasbourg, France.
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3
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Popova AM, Jain N, Dong X, Abdollah-Nia F, Britton RA, Williamson JR. Complete list of canonical post-transcriptional modifications in the Bacillus subtilis ribosome and their link to RbgA driven large subunit assembly. Nucleic Acids Res 2024:gkae626. [PMID: 39036956 DOI: 10.1093/nar/gkae626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 07/01/2024] [Accepted: 07/11/2024] [Indexed: 07/23/2024] Open
Abstract
Ribosomal RNA modifications in prokaryotes have been sporadically studied, but there is a lack of a comprehensive picture of modification sites across bacterial phylogeny. Bacillus subtilis is a preeminent model organism for gram-positive bacteria, with a well-annotated and editable genome, convenient for fundamental studies and industrial use. Yet remarkably, there has been no complete characterization of its rRNA modification inventory. By expanding modern MS tools for the discovery of RNA modifications, we found a total of 25 modification sites in 16S and 23S rRNA of B. subtilis, including the chemical identity of the modified nucleosides and their precise sequence location. Furthermore, by perturbing large subunit biogenesis using depletion of an essential factor RbgA and measuring the completion of 23S modifications in the accumulated intermediate, we provide a first look at the order of modification steps during the late stages of assembly in B. subtilis. While our work expands the knowledge of bacterial rRNA modification patterns, adding B. subtilis to the list of fully annotated species after Escherichia coli and Thermus thermophilus, in a broader context, it provides the experimental framework for discovery and functional profiling of rRNA modifications to ultimately elucidate their role in ribosome biogenesis and translation.
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Affiliation(s)
- Anna M Popova
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nikhil Jain
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA
- INSITRO, 279 E Grand Ave., South San Francisco, CA 94080, USA
| | - Xiyu Dong
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Farshad Abdollah-Nia
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robert A Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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4
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Bahena-Ceron R, Teixeira C, Ponce JRJ, Wolff P, Couzon F, François P, Klaholz BP, Vandenesch F, Romby P, Moreau K, Marzi S. RlmQ: a newly discovered rRNA modification enzyme bridging RNA modification and virulence traits in Staphylococcus aureus. RNA (NEW YORK, N.Y.) 2024; 30:200-212. [PMID: 38164596 PMCID: PMC10870370 DOI: 10.1261/rna.079850.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024]
Abstract
rRNA modifications play crucial roles in fine-tuning the delicate balance between translation speed and accuracy, yet the underlying mechanisms remain elusive. Comparative analyses of the rRNA modifications in taxonomically distant bacteria could help define their general, as well as species-specific, roles. In this study, we identified a new methyltransferase, RlmQ, in Staphylococcus aureus responsible for the Gram-positive specific m7G2601, which is not modified in Escherichia coli (G2574). We also demonstrate the absence of methylation on C1989, equivalent to E. coli C1962, which is methylated at position 5 by the Gram-negative specific RlmI methyltransferase, a paralog of RlmQ. Both modifications (S. aureus m7G2601 and E. coli m5C1962) are situated within the same tRNA accommodation corridor, hinting at a potential shared function in translation. Inactivation of S. aureus rlmQ causes the loss of methylation at G2601 and significantly impacts growth, cytotoxicity, and biofilm formation. These findings unravel the intricate connections between rRNA modifications, translation, and virulence in pathogenic Gram-positive bacteria.
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Affiliation(s)
- Roberto Bahena-Ceron
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, 67000 Strasbourg, France
| | - Chloé Teixeira
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Jose R Jaramillo Ponce
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, 67000 Strasbourg, France
| | - Philippe Wolff
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, 67000 Strasbourg, France
| | - Florence Couzon
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Pauline François
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Bruno P Klaholz
- Centre for Integrative Biology, Department of Integrated Structural Biology, IGBMC, 67400 Illkirch, France
- CNRS UMR 7104, 67400 Illkirch, France
- Inserm U964, 67400 Illkirch, France
- Université de Strasbourg, 67000 Strasbourg, France
| | - François Vandenesch
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, 69007 Lyon, France
- Institut des agents infectieux, Hospices Civils de Lyon, 69004 Lyon, France
- Centre National de Référence des Staphylocoques, Hospices Civils de Lyon, 69317 Lyon, France
| | - Pascale Romby
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, 67000 Strasbourg, France
| | - Karen Moreau
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Stefano Marzi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, 67000 Strasbourg, France
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5
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Wolff P, Labar G, Lechner A, Van Elder D, Soin R, Gueydan C, Kruys V, Droogmans L, Roovers M. The Bacillus subtilis ywbD gene encodes RlmQ, the 23S rRNA methyltransferase forming m 7G2574 in the A-site of the peptidyl transferase center. RNA (NEW YORK, N.Y.) 2024; 30:105-112. [PMID: 38071475 PMCID: PMC10798245 DOI: 10.1261/rna.079853.123] [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: 10/02/2023] [Accepted: 12/03/2023] [Indexed: 01/18/2024]
Abstract
Ribosomal RNA contains many posttranscriptionally modified nucleosides, particularly in the functional parts of the ribosome. The distribution of these modifications varies from one organism to another. In Bacillus subtilis, the model organism for Gram-positive bacteria, mass spectrometry experiments revealed the presence of 7-methylguanosine (m7G) at position 2574 of the 23S rRNA, which lies in the A-site of the peptidyl transferase center of the large ribosomal subunit. Testing several m7G methyltransferase candidates allowed us to identify the RlmQ enzyme, encoded by the ywbD open reading frame, as the MTase responsible for this modification. The enzyme methylates free RNA and not ribosomal 50S or 70S particles, suggesting that modification occurs in the early steps of ribosome biogenesis.
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Affiliation(s)
- Philippe Wolff
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, F-67084 Strasbourg, France
| | | | - Antony Lechner
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, F-67084 Strasbourg, France
| | - Dany Van Elder
- Laboratoire de Chimie Biologique, Université Libre de Bruxelles (ULB), Labiris, B-1070 Bruxelles, Belgium
| | - Romuald Soin
- Laboratoire de Biologie Moléculaire du Gène, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles (ULB), B-6041 Gosselies, Belgium
| | - Cyril Gueydan
- Laboratoire de Biologie Moléculaire du Gène, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles (ULB), B-6041 Gosselies, Belgium
| | - Véronique Kruys
- Laboratoire de Biologie Moléculaire du Gène, Institut de Biologie et de Médecine Moléculaires, Université Libre de Bruxelles (ULB), B-6041 Gosselies, Belgium
| | - Louis Droogmans
- Laboratoire de Chimie Biologique, Université Libre de Bruxelles (ULB), Labiris, B-1070 Bruxelles, Belgium
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6
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Yelland JN, Bravo JPK, Black JJ, Taylor DW, Johnson AW. A single 2'-O-methylation of ribosomal RNA gates assembly of a functional ribosome. Nat Struct Mol Biol 2023; 30:91-98. [PMID: 36536102 PMCID: PMC9851907 DOI: 10.1038/s41594-022-00891-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 11/04/2022] [Indexed: 12/24/2022]
Abstract
RNA modifications are widespread in biology and abundant in ribosomal RNA. However, the importance of these modifications is not well understood. We show that methylation of a single nucleotide, in the catalytic center of the large subunit, gates ribosome assembly. Massively parallel mutational scanning of the essential nuclear GTPase Nog2 identified important interactions with rRNA, particularly with the 2'-O-methylated A-site base Gm2922. We found that methylation of G2922 is needed for assembly and efficient nuclear export of the large subunit. Critically, we identified single amino acid changes in Nog2 that completely bypass dependence on G2922 methylation and used cryoelectron microscopy to directly visualize how methylation flips Gm2922 into the active site channel of Nog2. This work demonstrates that a single RNA modification is a critical checkpoint in ribosome biogenesis, suggesting that such modifications can play an important role in regulation and assembly of macromolecular machines.
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Affiliation(s)
- James N Yelland
- Interdisciplinary Life Sciences Graduate Program, University of Texas at Austin, Austin, TX, USA
| | - Jack P K Bravo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Joshua J Black
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David W Taylor
- Interdisciplinary Life Sciences Graduate Program, University of Texas at Austin, Austin, TX, USA.
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA.
- Livestrong Cancer Institutes, Dell Medical School, Austin, TX, USA.
| | - Arlen W Johnson
- Interdisciplinary Life Sciences Graduate Program, University of Texas at Austin, Austin, TX, USA.
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
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