PXD036353

PXD036353 is an original dataset announced via ProteomeXchange.

Title	Ribosomes lacking bS21 gain function to regulate protein synthesis in Flavobacterium johnsoniae
Description	Ribosomes of Bacteroidia (formerly Bacteroidetes) fail to recognize Shine-Dalgarno (SD) sequences even though they harbor the anti-SD (ASD) of 16S rRNA. This is due to sequestration of the 3’ tail of 16S rRNA in a pocket formed by bS21, bS18, and bS6 on the 30S platform, which functionally occludes the ASD. Interestingly, in many Flavobacteriales, the gene encoding bS21, rpsU, contains an extended SD sequence. In this work, we present genetic and biochemical evidence that bS21 synthesis in Flavobacterium johnsoniae is autoregulated via a subpopulation of ribosomes that specifically lack bS21. Mutation or depletion of bS21 in the cell specifically increases translation of reporters with strong SD sequences, such as rpsU’-gfp. Purified ribosomes lacking bS21 (or its C-terminal region) exhibit higher rates of initiation on rpsU mRNA and lower rates of initiation on other (SD-less) mRNAs than control ribosomes. The mechanism of autoregulation depends on extensive pairing between mRNA and 16S rRNA, and exceptionally strong SD sequences, with predicted pairing free energies of < –13 kcal/mol, are characteristic of rpsU across the Bacteroidia. To our knowledge, this is the first example of biochemically-verified specialized ribosomes with a clear regulatory purpose.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:43:13.276.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Jenny Moon
SpeciesList	scientific name: Flavobacterium johnsoniae; NCBI TaxID: 986;
ModificationList	No PTMs are included in the dataset
Instrument	Bruker Daltonics instrument model

Revision	Datetime	Status	ChangeLog Entry
0	2022-08-27 11:13:13	ID requested
1	2023-03-11 06:47:00	announced
⏵ 2	2023-11-14 08:43:18	announced	2023-11-14: Updated project metadata.

McNutt ZA, Roy B, Gemler BT, Shatoff EA, Moon KM, Foster LJ, Bundschuh R, Fredrick K, Ribosomes lacking bS21 gain function to regulate protein synthesis in Flavobacterium johnsoniae. Nucleic Acids Res, 51(4):1927-1942(2023) [pubmed]

submitter keyword: Flavobacterium johnsoniae, proteomics, LCMSMS

Kurt Fredrick
contact affiliation	Department of Microbiology, The Ohio State University, USA
contact email	fredrick.5@osu.edu
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/2023/03/PXD036353

PRIDE project URI

• PRIDE
  1. PXD036353
     1. Label: PRIDE project
     2. Name: Ribosomes lacking bS21 gain function to regulate protein synthesis in Flavobacterium johnsoniae