Sequential rescue and repair of stalled and damaged ribosome by bacterial PrfH and RtcB

Yannan Tian, Fuxing Zeng, Adrika Raybarman, Shirin Fatma, Amy Carruthers, Qingrong Li, Raven H. Huang

Research output: Contribution to journalArticlepeer-review


RtcB is involved in transfer RNA (tRNA) splicing in archaeal and eukaryotic organisms. However, most RtcBs are found in bacteria, whose tRNAs have no introns. Because tRNAs are the substrates of archaeal and eukaryotic RtcB, it is assumed that bacterial RtcBs are for repair of damaged tRNAs. Here, we show that a subset of bacterial RtcB, denoted RtcB2 herein, specifically repair ribosomal damage in the decoding center. To access the damage site for repair, however, the damaged 70S ribosome needs to be dismantled first, and this is accomplished by bacterial PrfH. Peptide-release assays revealed that PrfH is only active with the damaged 70S ribosome but not with the intact one. A 2.55-Å cryo-electron microscopy structure of PrfH in complex with the damaged 70S ribosome provides molecular insight into PrfH discriminating between the damaged and the intact ribosomes via specific recognition of the cleaved 3'-terminal nucleotide. RNA repair assays demonstrated that RtcB2 efficiently repairs the damaged 30S ribosomal subunit but not the damaged tRNAs. Cell-based assays showed that the RtcB2-PrfH pair reverse the damage inflicted by ribosome-specific ribotoxins in vivo. Thus, our combined biochemical, structural, and cell-based studies have uncovered a bacterial defense system specifically evolved to reverse the lethal ribosomal damage in the decoding center for cell survival.

Original languageEnglish (US)
Article numbere2202464119
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number29
StatePublished - Jul 19 2022


  • RNA repair
  • cryo-EM
  • ribosome rescue
  • ribotoxin

ASJC Scopus subject areas

  • General


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