PXD025875

PXD025875 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2021-05-07 04:31:12	ID requested
⏵ 1	2022-02-16 08:45:15	announced

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]

submitter keyword: RNA modifications, ribosome, E. coli, oxidative stress, RlhA, Dps

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

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PRIDE project URI

• PRIDE
  1. PXD025875
     1. Label: PRIDE project
     2. Name: Dynamic 23S rRNA modification ho5C2501 benefits Escherichia coli under oxidative stress