PXD025875 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Dynamic 23S rRNA modification ho5C2501 benefits Escherichia coli under oxidative stress |
Description | Post-transcriptional modifications are added to ribosomal RNAs (rRNAs) to govern ribosome biogenesis and to fine-tune protein biosynthesis. RlhA, a dedicated modification enzyme, adds a unique 5-hydroxycytidine (ho5C) at 23S rRNA position 2501 in E. coli and related bacteria. However, the molecular and biological functions as well as the regulation of ho5C2501 remain unclear. We conducted extensive growth curves with the modification-deficient ∆rlhA strain and quantified the extent of the modification during different conditions by mass spectrometry and reverse transcription. The levels of ho5C2501 in E. coli ribosomes turned out to be highly dynamic and growth phase-dependent, with the most effective hydroxylation yields observed in the stationary phase. We demonstrated a direct effect of ho5C2501 on translation efficiencies in vitro and in vivo. High ho5C2501 levels reduced protein biosynthesis which however turned out to be beneficial for E. coli for adapting to oxidative stress. This functional advantage was small under optimal conditions or during heat or cold shock, but becomes pronounced in the presence of hydrogen peroxide. Taken together, these data provided first functional insights into the role of this unique 23S rRNA modification for ribosome functions and bacterial growth under oxidative stress. |
HostingRepository | PRIDE |
AnnounceDate | 2022-02-16 |
AnnouncementXML | Submission_2022-02-16_08:45:14.909.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Manfred Heller |
SpeciesList | scientific name: Escherichia coli; NCBI TaxID: 562; |
ModificationList | acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | LTQ Orbitrap |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-05-07 04:31:12 | ID requested | |
⏵ 1 | 2022-02-16 08:45:15 | announced | |
Publication List
Fasnacht M, Gallo S, Sharma P, Himmelsto, ß M, Limbach PA, Willi J, Polacek N, Dynamic 23S rRNA modification ho5C2501 benefits Escherichia coli under oxidative stress. Nucleic Acids Res, 50(1):473-489(2022) [pubmed] |
Keyword List
submitter keyword: RNA modifications, ribosome, E. coli, oxidative stress, RlhA, Dps |
Contact List
Norbert Polacek |
contact affiliation | Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland |
contact email | norbert.polacek@dcb.unibe.ch |
lab head | |
Manfred Heller |
contact affiliation | Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland |
contact email | pmscf@dbmr.unibe.ch |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD025875
- Label: PRIDE project
- Name: Dynamic 23S rRNA modification ho5C2501 benefits Escherichia coli under oxidative stress