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TitlePseudouridine increases ribosome stability in a thermophilic eukaryote.
Journal, issue, pagesNucleic Acids Res, Vol. 53, Issue 22, Year 2025
Publish dateNov 26, 2025
AuthorsKlemens Wild / Marius Klein / Alicia Burkard / Virginie Marchand / Nikola Kellner / Antonio Paez / Stefan Pastore / Tamer Butto / Yuri Motorin / Mark Helm / Irmgard Sinning /
PubMed AbstractRNA modifications alter stability, folding space, and interaction network of RNA molecules. Ribosomal RNA (rRNA) modifications stabilize the structure of ribosomes and cluster around functionally ...RNA modifications alter stability, folding space, and interaction network of RNA molecules. Ribosomal RNA (rRNA) modifications stabilize the structure of ribosomes and cluster around functionally important sites such as the peptidyl transferase center, ribosomal subunit bridges, and the polypeptide tunnel. Here, we investigate the rRNA modifications of the thermophilic fungus Chaetomium thermophilum (ct), a model organism for eukaryotic thermophily and structural stability. Using LC-MS/MS, orthogonal second and third generation RNA-sequencing and high-resolution cryo-electron microscopy, we describe a cross-correlating method to assign and quantify all ct rRNA modifications. Overall, a doubling of rRNA modifications to 4% explains ribosomal thermostability with an extended distribution towards peripheral functional sites. The 2.4 Å structure of the idle ct60S ribosome, retaining nascent chains and including metal ions, polyamines, and water molecules, allows for a comprehensive structure-function analysis. Comparison with mesophilic ribosomes from Chaetomium globosum, yeast, and human highlights the significant increase of pseudouridines (Ψs). The number of Ψs linearly correlates with growth temperature, suggesting statistical modification. A ct-specific Ψ substitution forming a 'Ψ-turn' at the polypeptide tunnel exit close to the third constriction exemplifies mechanistic adaptations of the ribosome at elevated temperatures.
External linksNucleic Acids Res / PubMed:41432034 / PubMed Central
MethodsEM (single particle)
Resolution2.38 Å
Structure data

52576

9i1w

EMDB-52576, PDB-9i1w:
High resolution structure of the thermophilic 60S ribosomal subunit of Chaetomium thermophilum
Method: EM (single particle) / Resolution: 2.38 Å

Chemicals

ChemComp-SPD:
SPERMIDINE

ChemComp-SPM:
SPERMINE

ChemComp-MG:
Unknown entry

ChemComp-K:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER

Source
  • Thermochaetoides thermophila (fungus)
  • thermochaetoides thermophila dsm 1495 (fungus)
KeywordsRIBOSOME / 60S ribosomal subunit thermophilic eukaryote RNA modification pseudouridine

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