PXD062614

PXD062614 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_2025-05-19_02:39:32.376.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Akos Vegvari
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-04 08:45:29	ID requested
⏵ 1	2025-05-19 02:39:32	announced

Dataset with its publication pending

submitter keyword: methylation, ELAC2, Oxford nanopore sequencing, S-adenosylmethionine, RNase P, SAMC,AdoMet, SLC25A26, direct long-range RNA sequencing, SAM, RNA processing, mitochondrial ribosome, RNase Z, mitochondrial translation

Akos Vegvari
contact affiliation	Karolinska Institutet
contact email	akos.vegvari@ki.se
lab head
Akos Vegvari
contact affiliation	Karolinska Institutet
contact email	akos.vegvari@ki.se
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD062614
     1. Label: PRIDE project
     2. Name: The mitochondrial methylation potential gates early and late ribosome assembly