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TitleCryo-EM study and in vivo chemical mapping of the Methanosarcina acetivorans ribosome and its dimerization via a repurposed enzyme and translation factor.
Journal, issue, pagesJ Biol Chem, Vol. 301, Issue 11, Page 110686, Year 2025
Publish dateSep 4, 2025
AuthorsGeorge N R Fordjour / Anwesha Ghosh / James G Ferry / Jean-Paul Armache / Philip C Bevilacqua / Katsuhiko S Murakami /
PubMed AbstractDespite the overall conservation of ribosomes across all domains of life, differences in their 3D architecture, rRNA sequences, ribosomal protein composition, and translation factor requirements ...Despite the overall conservation of ribosomes across all domains of life, differences in their 3D architecture, rRNA sequences, ribosomal protein composition, and translation factor requirements reflect lineage-specific adaptations to environmental niches. In the domain Archaea, structural studies have primarily focused on nonmethanogenic thermophiles and halophiles, leaving it unclear whether these represent the broader Archaea domain. Here, we report the cryo-electron microscopy (cryo-EM) structure of the ribosome from Methanosarcina acetivorans, a previously unreported high-resolution structure from a model mesophilic methanogenic archaeon. Compared to ribosomes from extremophiles, the M. acetivorans ribosome has a simplified architecture, lacking paralogous duplications and containing a reduced complement of ribosomal proteins. Structures of the large subunit (50S) from cells grown with either methanol or acetate show conserved rRNA folding and protein composition. High-resolution structures of the 50S subunit from the two growth substrates enabled us to investigate structural properties that may influence in vivo dimethyl sulfate reactivity, an orthogonal chemical approach used to probe RNA structure. We observed good agreement between in vivo dimethyl sulfate reactivity and ribosome structure. Finally, we identify a previously uncharacterized ribosome dimerization mode involving only 50S subunits and mediated by a heterotetrameric complex of PurH and aEF2-proteins with alternative metabolic and translational roles. This macromolecular assembly, which we term the methanogen ribosome dimerization factor, likely mediates ribosome hibernation, revealing an alternative regulatory mechanism in translation.
External linksJ Biol Chem / PubMed:40914243 / PubMed Central
MethodsEM (single particle)
Resolution2.38 - 3.51 Å
Structure data

49734

9nri

EMDB-49734, PDB-9nri:
Methanosarcina acetivorans 50S subunit obtained from acetate-grown cells
Method: EM (single particle) / Resolution: 2.85 Å

49757

9nta

EMDB-49757, PDB-9nta:
Methanosarcina acetivorans 50S subunit obtained from methanol-grown cells
Method: EM (single particle) / Resolution: 2.38 Å

49998

9o17

EMDB-49998, PDB-9o17:
Cryo-EM structure of Methanosarcina acetivorans 70S ribosome
Method: EM (single particle) / Resolution: 2.92 Å

70864

9ou7

EMDB-70864, PDB-9ou7:
Methanosarcina acetivorans large (50S) subunit dimer
Method: EM (single particle) / Resolution: 3.51 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-K:
Unknown entry

Source
  • methanosarcina acetivorans (archaea)
KeywordsRIBOSOME / Archaea / Methanosarcina acetivorans / Large subunit / 50S subunit / growth conditions / acetate / methanol / 70S ribosome / translation / large subunit dimer / 50S dimer / dimerization / hibernation

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