PXD054109

PXD054109 is an original dataset announced via ProteomeXchange.

Title	Dysregulation of 18S pre-rRNA processing in plant mitochondria decreases the efficiency of mitochondrial PNPase
Description	In plant mitochondria, polynucleotide phosphorylase (mtPNPase) is a key 3??5? exoribonuclease. Here, we describe the accumulation of mtPNPase substrates in Arabidopsis mutants, such as rps10 (deficient in the mitoribosomal protein uS10m), mtran1 2/2 2 (lacking the mitoribosomal proteins mTRAN1 and mTRAN2), and rpoTmp (deficient in plastid- and mitochondrial-targeted RNA polymerase). This accumulation is not due to a reduced mtPNPase expression; instead, all three mutants exhibit perturbations in mitoribosome biogenesis associated with inefficient mtPNPase dependent 3? end processing of 18S pre rRNA. We propose a spatial sequestration model in which mtPNPase becomes trapped by incompletely matured 18S precursors, limiting its availability for other substrates. In addition, the rps10 mutant displays a partial shift of both mtPNPase and mitoribosomes from membrane associated to soluble fractions, suggesting a mutant specific alteration that may further modulate mtPNPase function. Together, these findings demonstrate that proper mitochondrial small subunit (mtSSU) biogenesis is essential for effective mtPNPase function and balanced mitochondrial RNA metabolism. Thus, mitoribosomes act not only as translation machines but also as regulators of mitochondrial RNA homeostasis, linking ribosome biogenesis to the composition and turnover of the mitochondrial transcriptome. Shotgun proteomic experiments were conducted on a timsTOF Pro mass spectrometer connected to a nanoElute HPLC. Please note that the initial version of the manuscript also included complexome profiling experiments, which were performed using a Q-Exactive mass spectrometer coupled to an Ultimate3000 HPLC. Complexome profiling experiments were removed from the final manuscript during the review process, but are still included in the submitted dataset here as they still represent a valuable resourve for the community.
HostingRepository	MassIVE
AnnounceDate	2026-06-08
AnnouncementXML	Submission_2026-06-08_23:05:11.234.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Noah Ditz
SpeciesList	scientific name: Arabidopsis thaliana; common name: thale cress; NCBI TaxID: 3702;
ModificationList	CarbamidomethylDTT
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2024-07-22 05:24:17	ID requested
⏵ 1	2026-06-08 23:05:11	announced

no publication

submitter keyword: shotgun, mitochondria, PNPase

Holger Eubel
contact affiliation	Leibniz University Hannover
contact email	heubel@genetik.uni-hannover.de
lab head
Noah Ditz
contact affiliation	Leibniz University Hannover
contact email	ditz@genetik.uni-hannover.de
dataset submitter

MassIVE dataset URI

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