Cargando…

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

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, w...

Descripción completa

Detalles Bibliográficos
Autores principales: Tian, Yannan, Zeng, Fuxing, Raybarman, Adrika, Fatma, Shirin, Carruthers, Amy, Li, Qingrong, Huang, Raven H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: National Academy of Sciences 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9304027/
https://www.ncbi.nlm.nih.gov/pubmed/35858322
http://dx.doi.org/10.1073/pnas.2202464119
_version_ 1784752009613672448
author Tian, Yannan
Zeng, Fuxing
Raybarman, Adrika
Fatma, Shirin
Carruthers, Amy
Li, Qingrong
Huang, Raven H.
author_facet Tian, Yannan
Zeng, Fuxing
Raybarman, Adrika
Fatma, Shirin
Carruthers, Amy
Li, Qingrong
Huang, Raven H.
author_sort Tian, Yannan
collection PubMed
description 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.
format Online
Article
Text
id pubmed-9304027
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher National Academy of Sciences
record_format MEDLINE/PubMed
spelling pubmed-93040272023-01-12 Sequential rescue and repair of stalled and damaged ribosome by bacterial PrfH and RtcB Tian, Yannan Zeng, Fuxing Raybarman, Adrika Fatma, Shirin Carruthers, Amy Li, Qingrong Huang, Raven H. Proc Natl Acad Sci U S A Biological Sciences 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. National Academy of Sciences 2022-07-12 2022-07-19 /pmc/articles/PMC9304027/ /pubmed/35858322 http://dx.doi.org/10.1073/pnas.2202464119 Text en Copyright © 2022 the Author(s). Published by PNAS https://creativecommons.org/licenses/by-nc-nd/4.0/This article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND) (https://creativecommons.org/licenses/by-nc-nd/4.0/) .
spellingShingle Biological Sciences
Tian, Yannan
Zeng, Fuxing
Raybarman, Adrika
Fatma, Shirin
Carruthers, Amy
Li, Qingrong
Huang, Raven H.
Sequential rescue and repair of stalled and damaged ribosome by bacterial PrfH and RtcB
title Sequential rescue and repair of stalled and damaged ribosome by bacterial PrfH and RtcB
title_full Sequential rescue and repair of stalled and damaged ribosome by bacterial PrfH and RtcB
title_fullStr Sequential rescue and repair of stalled and damaged ribosome by bacterial PrfH and RtcB
title_full_unstemmed Sequential rescue and repair of stalled and damaged ribosome by bacterial PrfH and RtcB
title_short Sequential rescue and repair of stalled and damaged ribosome by bacterial PrfH and RtcB
title_sort sequential rescue and repair of stalled and damaged ribosome by bacterial prfh and rtcb
topic Biological Sciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9304027/
https://www.ncbi.nlm.nih.gov/pubmed/35858322
http://dx.doi.org/10.1073/pnas.2202464119
work_keys_str_mv AT tianyannan sequentialrescueandrepairofstalledanddamagedribosomebybacterialprfhandrtcb
AT zengfuxing sequentialrescueandrepairofstalledanddamagedribosomebybacterialprfhandrtcb
AT raybarmanadrika sequentialrescueandrepairofstalledanddamagedribosomebybacterialprfhandrtcb
AT fatmashirin sequentialrescueandrepairofstalledanddamagedribosomebybacterialprfhandrtcb
AT carruthersamy sequentialrescueandrepairofstalledanddamagedribosomebybacterialprfhandrtcb
AT liqingrong sequentialrescueandrepairofstalledanddamagedribosomebybacterialprfhandrtcb
AT huangravenh sequentialrescueandrepairofstalledanddamagedribosomebybacterialprfhandrtcb