PXD051518

PXD051518 is an original dataset announced via ProteomeXchange.

Title	Annotation of the genes responsible for helix 69 rRNA modifications in 23S of Bacillus subtilis.
Description	A total of 25 modifications were mapped to 16S and 23S RNA in B. subtilis ribosome, however most of the genes responsible for these modification sites remain unknown. In this work, bottom-up oligonucleotide LC-MS/MS was used to detect rRNA modifications in five single gene knock-out strains: yydA, yhcT, yjbO, ylyB, yqxC. By comparing oligonucleotide modification states between the background 168 strain (annotated as WT) and the mutants: ylyB was confirmed to be a pseudouridine synthase at positions 1940, 1944, 1946 of 23S; yydA is a N3-pseudouridine methyltransferase at 1944 of 23S; and yqxC is a dual 2’O-cytidine methyltransferase at 1417 of 16S and 1949 of 23S. Deletion of yhcT or yjbO does not change rRNA modification pattern.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:52:32.070.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Anna Popova
SpeciesList	scientific name: Bacillus subtilis subsp. subtilis str. 168; NCBI TaxID: 224308;
ModificationList	monomethylated residue
Instrument	impact II

Revision	Datetime	Status	ChangeLog Entry
0	2024-04-16 23:35:48	ID requested
1	2024-08-06 01:08:06	announced
⏵ 2	2024-10-22 06:52:32	announced	2024-10-22: Updated project metadata.

10.1093/NAR/GKAE626;

submitter keyword: pseudouridine, base and ribose methylations,23S, RNA modifications, Bacillus subtilis., ribosomal RNA

James Williamson
contact affiliation	Professor, Department of Integrative Structural & Computational Biology, Department of Chemistry at the Scripps Research Institute
contact email	jrwill@scripps.edu
lab head
Anna Popova
contact affiliation	Scripps Research
contact email	popova@scripps.edu
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/2024/08/PXD051518

PRIDE project URI

• PRIDE
  1. PXD051518
     1. Label: PRIDE project
     2. Name: Annotation of the genes responsible for helix 69 rRNA modifications in 23S of Bacillus subtilis.