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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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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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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] [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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