PXD055907

PXD055907 is an original dataset announced via ProteomeXchange.

Title	The mitochondrial methylation potential gates early and late ribosome assembly
Description	S-adenosylmethionine (SAM) is the principal methyl group donor of the cell, required to modify various molecules, including DNA, RNA and proteins. Inside mitochondria, SAM is associated with several steps of mitochondrial gene expression. However, the exact role and significance of these modifications remains debated. Here, we depleted mitochondria of SAM, constitutively in mouse embryonic fibroblasts or progressively in mouse skeletal muscle. Our data reveal that mitochondrial SAM is crucial for both early and late stages of mitochondrial gene expression. Direct long-read RNA sequencing demonstrated that the mitochondrial ribosomal gene cluster is particularly sensitive to perturbed mitochondrial methylation potential, leading to the accumulation of unprocessed RNA precursors. Stable isotope labelling of amino acids in culture (SILAC) followed by mass spectrometry on ribosome fractions shows that these precursors are associated with processing and ribosome assembly factors. Finally, structural analysis by cryogenic electron microscopy (Cryo-EM) revealed that mitochondrial ribosome assembly is adversely affected by the absence of mitochondrial SAM and that methylation is integral for correct peptidyl transferase centre assembly of the large ribosome subunit. Our data thus identifies two critical steps for methylation during mitochondrial gene expression.
HostingRepository	PRIDE
AnnounceDate	2025-05-19
AnnouncementXML	Submission_2025-05-18_23:35:02.433.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ilian Atanassov
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-09-16 08:42:38	ID requested
⏵ 1	2025-05-18 23:35:02	announced

Dataset with its publication pending

submitter keyword: SAM, RNA processing, ELAC2, methylation, RNaseP, mitochondrial ribosome, mitochondrial translation, S-adenosylmethionine, SAMC, RNaseZ,AdoMet, SLC25A26

Anna Wredenberg
contact affiliation	Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Sweden Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Sweden
contact email	anna.wredenberg@ki.se
lab head
Ilian Atanassov
contact affiliation	Max Planck Institute for Biology of Aging
contact email	Ilian.Atanassov@age.mpg.de
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/PXD055907

PRIDE project URI

• PRIDE
  1. PXD055907
     1. Label: PRIDE project
     2. Name: The mitochondrial methylation potential gates early and late ribosome assembly