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| Title | Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome. |
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| Journal, issue, pages | Cell, Vol. 188, Issue 24, Page 6825-6844.e28, Year 2025 |
| Publish date | Nov 26, 2025 |
 Authors | Miguel A Garcia-Campos / Joe Georgeson / Ronit Nir / Robert Reichelt / Kristin A Fluke / Donna Matzov / Vinithra Iyer / Brett W Burkhart / Lauren Lui / Anatoly Kustanovich / Felix Grünberger / Supuni Thalalla-Gamage / Shereen A Howpay-Manage / Milan Gerovac / Nicolas Alexandre / Yuko Nobe / Jakub S Nowak / Manoj Perera / Alexander Apostle / Shiyue Fang / Sebastian Glatt / Ghil Jona / Sébastien Ferreira-Cerca / Jörg Vogel / Masato Taoka / Jordan L Meier / Eric Westhof / Thomas J Santangelo / Dina Grohmann / Moran Shalev-Benami / Schraga Schwartz /         |
| PubMed Abstract | Ribosomal RNA (rRNA) constitutes the core of ribosomes and is extensively chemically modified. Technical challenges have precluded systematically dissecting rRNA modifications and their dynamics. We ...Ribosomal RNA (rRNA) constitutes the core of ribosomes and is extensively chemically modified. Technical challenges have precluded systematically dissecting rRNA modifications and their dynamics. We develop Pan-Mod-seq, permitting inference of 16 distinct modifications across dozens of samples in parallel. We applied Pan-Mod-seq to RNA from 14 species spanning all domains of life, cultured under highly diverse conditions. While dynamic modifications are rare in mesophiles, in extreme hyperthermophiles, ∼50% of modifications are dynamic. We dissect the biogenesis and function of a conserved module of tandem mC-acC modifications, co-induced at high temperatures, via enzymes intrinsically regulated by temperature and required for growth at higher temperatures. Cryo-electron microscopy (cryo-EM) structures of ribosomes from wild-type (WT) and enzyme-deficient archaea reveal recurrent molecular interactions through which they confer structural stability, and biophysical studies demonstrate their synergistic thermostabilizing role. Our findings systematically dissect rRNA modification plasticity and pave the way for surveying the rRNA epitranscriptome in health and disease. |
 External links | Cell / PubMed:41130207 / PubMed Central |
| Methods | EM (single particle) |
| Resolution | 2.54 - 2.9 Å |
| Structure data |  EMDB-53068: Cryo-EM map of P. furiosus 70S grown at 95 degrees  EMDB-53069: Cryo-EM map of P. furiosus 70S grown at 95 degC, focused on the lsu  EMDB-53070: Cryo-EM map of P. furiosus 70S grown at 95 degC, focused on the ssu body  EMDB-53071: Cryo-EM map of P. furiosus 70S grown at 95 degC, focused on the ssu head  EMDB-53072: Consensus cryo-EM map of P furiosus 70S grown at 102degC  EMDB-53073: Cryo-EM map of P. furiosus 70S grown at 102 degC, focused on the lsu  EMDB-53074: Cryo-EM map of P. furiosus 70S grown at 102 degC, focused on the ssu body  EMDB-53076: Cryo-EM map of P. furiosus 70S grown at 102 degC, focused on the ssu head  EMDB-53077: Consensus cryo-EM map of P. furiosus 70S in RsmB deleted strain  EMDB-53078: Cryo-EM map of P. furiosus 70S in RsmB deleted strain, focused on the lsu  EMDB-53079: Cryo-EM map of P. furiosus 70S in RsmB deleted strain, focused on the ssu body  EMDB-53080: Cryo-EM map of P. furiosus 70S in RsmB deleted strain, focused on the ssu head EMDB-53098, PDB-9qf4: EMDB-53099, PDB-9qf5: EMDB-53100, PDB-9qf6: |
| Chemicals |  ChemComp-ZN:  ChemComp-HOH: |
| Source |
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 Keywords | RIBOSOME / RNA modification / cryo-EM |
pyrococcus furiosus (archaea)