PXD050205

PXD050205 is an original dataset announced via ProteomeXchange.

Title	Protein bL38 facilitates incorporation of uL6 during assembly of the 50S subunit in Flavobacterium johnsoniae
Description	Previous studies of the 70S ribosome from Flavobacterium johnsoniae revealed a novel ribosomal protein, bL38, which interacts with uL6 on the 50S subunit. This 5.6 kDa protein is conserved across the Bacteroidia and encoded downstream of bL28 and bL33 in a three-gene operon. Here, we show that bL38 is critical for the growth of F. johnsoniae, and depletion of bL38 leads to accumulation of immature 50S particles which lack uL6 and retain precursor rRNA sequences. Cryo-EM analysis of these particles reveals several putative assembly intermediates, all which show an absence of electron density for uL6 and the entire uL12 stalk base, and additional density corresponding to unprocessed ends of the pre-23S rRNA. One structural class reveals a Der-bound pre-50S intermediate in which the GTPase is tucked behind and appears to reposition helix H68. Extra copies of the uL6 gene can rescue the phenotypes caused by bL38 depletion, strongly suggesting that bL38 facilitates uL6 incorporation during 50S subunit biogenesis. Cryo-EM analysis of 50S particles from this rescued strain reveals nearly twice as many intermediates, suggesting a broader and more robust assembly landscape. Collectively, these data show the importance of bL38 and its role in assembly of the 50S subunit of the Bacteroidia.
HostingRepository	PRIDE
AnnounceDate	2025-05-06
AnnouncementXML	Submission_2025-05-06_13:27:01.029.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Brenna Hay
SpeciesList	scientific name: Flavobacterium johnsoniae; NCBI TaxID: 986;
ModificationList	No PTMs are included in the dataset
Instrument	Bruker Daltonics timsTOF series

Revision	Datetime	Status	ChangeLog Entry
0	2024-02-27 18:20:16	ID requested
⏵ 1	2025-05-06 13:27:01	announced

10.1093/nar/gkaf120;

Alom MS, Arpin D, Zhu H, Hay BN, Foster LJ, Ortega J, Fredrick K, Protein bL38 facilitates incorporation of uL6 during assembly of the 50S subunit in Flavobacterium johnsoniae. Nucleic Acids Res, 53(4):(2025) [pubmed]

submitter keyword: ribosomes, LC-MS/MS

Leonard J. Foster
contact affiliation	Department of Biochemistry and Biology, UBC
contact email	foster@msl.ubc.ca
lab head
Brenna Hay
contact affiliation	UBC
contact email	b_hay@live.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/2025/05/PXD050205

PRIDE project URI

• PRIDE
  1. PXD050205
     1. Label: PRIDE project
     2. Name: Protein bL38 facilitates incorporation of uL6 during assembly of the 50S subunit in Flavobacterium johnsoniae