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TitleHypoxia-induced ribosomal RNA modifications in the peptidyl-transferase center contribute to anaerobic growth of bacteria.
Journal, issue, pagesMol Cell, Vol. 86, Issue 1, Page 78-96.e10, Year 2026
Publish dateJan 8, 2026
AuthorsKensuke Ishiguro / Karin Midorikawa / Naoki Shigi / Satoshi Kimura / Aivar Liiv / Takeshi Yokoyama / Takuhiro Ito / Mikako Shirouzu / Jaanus Remme / Kenjyo Miyauchi / Tsutomu Suzuki /
PubMed AbstractRibosomal RNAs (rRNAs) contain various modifications that play critical roles in ribosome assembly and function. Here, we discovered two stereoselective methylations of the rRNA backbone in the ...Ribosomal RNAs (rRNAs) contain various modifications that play critical roles in ribosome assembly and function. Here, we discovered two stereoselective methylations of the rRNA backbone in the peptidyl-transferase center (PTC) of the 50S subunit of Escherichia coli cultured under anaerobic conditions. Methylation occurs at carbon 5'(S) of ribose moieties of dihydrouridine at position 2449 (Dm2449) and 2'-O-metylcytidine at position 2498 (Cmm2498). We identified the rlmX gene, encoding a cobalamin-dependent radical S-adenosylmethionine (SAM) methyltransferase responsible for these methylations. Intriguingly, Dm2449, Cmm2498, and 5-hydroxycytidine (hoC2501) in the PTC were elevated under anaerobic growth conditions. A double knockout strain lacking rlmX and rlhA (responsible for hoC2501) impaired anaerobic growth. Biochemical studies showed that these rRNA modifications stimulate protein synthesis. The cryoelectron microscopy (cryo-EM) structure of the ribosome indicated that these hypoxia-induced modifications stabilize the P-site and the PTC. These findings demonstrate that ribosomes are activated by hypoxia-induced modifications to enhance translational capability and thereby survival, under anaerobic conditions.
External linksMol Cell / PubMed:41380683
MethodsEM (single particle)
Resolution2.59 - 2.68 Å
Structure data

60059

8zff

EMDB-60059, PDB-8zff:
Structure of the Bacterial Ribosome without hypoxia-induced rRNA modifications
Method: EM (single particle) / Resolution: 2.59 Å

60060

8zfg

EMDB-60060, PDB-8zfg:
Structure of the Bacterial Ribosome with hypoxia-induced rRNA modifications
Method: EM (single particle) / Resolution: 2.68 Å

Chemicals

ChemComp-MG:
Unknown entry

Source
  • escherichia coli bw25113 (bacteria)
  • escherichia phage t4 (virus)
KeywordsRIBOSOME / rRNA modifications / translation

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