PXD067211

PXD067211 is an original dataset announced via ProteomeXchange.

Title	The anti-Shine-Dalgarno element of 16S rRNA is needed for translation of one gene, rpsU, in Flavobacterium johnsoniae
Description	Bacteroidia ribosomes are “blind” to SD sequences, even though they contain the conserved anti-SD (ASD) element of 16S rRNA. A structure of the Flavobacterium johnsoniae ribosome shows that the 3’ tail of 16S rRNA is sequestered in a pocket formed by bS21, bS18, and bS6 on the 30S platform, explaining the basis of ASD inhibition. Interestingly, there is one gene of F. johnsoniae with a strong SD sequence—rpsU, which encodes bS21. F. johnsoniae ribosomes lacking bS21 exhibit a liberated ASD and translate rpsU at a higher rate, which sets up an autoregulatory cycle. Here, we targeted the ASD of each 16S rRNA gene in F. johnsoniae, ablating the core element (CCUCC to GAAGC). Consecutive replacement of each 16S gene with this quadruple-substituted (QS) allele had little effect on cell growth until the last gene was changed. The final strain, containing QS ribosomes only, grows very slowly. This growth defect can be largely rescued by replacing the native translation initiation region (TIR) with the SD-less TIR of tuf. Purified QS ribosomes are unable to translate native rpsU mRNA but are active on other mRNAs. We also selected suppressors of the ASD-ablated strain, many of which carried a single mutation in the SD of rpsU. Interestingly, wild-type ribosomes fail to initiate on these variant rpsU mRNAs, demonstrating that an extended SD-ASD duplex is normally needed for initiation on this message. These findings indicate that the main purpose of the ASD in F. johnsoniae is to facilitate translation of one gene, rpsU.
HostingRepository	PRIDE
AnnounceDate	2026-03-05
AnnouncementXML	Submission_2026-03-05_12:15:29.007.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jenny Moon
SpeciesList	scientific name: Flavobacterium johnsoniae; NCBI TaxID: NEWT:986;
ModificationList	No PTMs are included in the dataset
Instrument	Bruker Daltonics timsTOF series

Revision	Datetime	Status	ChangeLog Entry
0	2025-08-11 13:42:00	ID requested
⏵ 1	2026-03-05 12:15:29	announced

Dataset with its publication pending

submitter keyword: proteomics, 16S rRNA, Flavobacterium johnsoniae, rpsU, LC-MS/MS

Leonard Foster
contact affiliation	Biochemistry and Molecular Biology, Michael Smith Laboratories, University of British Columbia, Canada
contact email	foster@msl.ubc.ca
lab head
Jenny Moon
contact affiliation	University of British Columbia
contact email	kyungmee@mail.ubc.ca
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD067211

PRIDE project URI

• PRIDE
  1. PXD067211
     1. Label: PRIDE project
     2. Name: The anti-Shine-Dalgarno element of 16S rRNA is needed for translation of one gene, rpsU, in Flavobacterium johnsoniae