PXD060334

PXD060334 is an original dataset announced via ProteomeXchange.

Title	RNF10 and RIOK3 Facilitate 40S Ribosomal Subunit Degradation upon 60S Biogenesis Disruption or Amino Acid Starvation [Fig. 4D, S4D]
Description	Ribosome-associated quality control (RQC) pathways target ribosomes whose progression becomes impaired during various phases of the translation cycle. Ribosome ubiquitylation is a key RQC licensing step. Previous studies identified an initiation specific RQC branch (iRQC) that is activated when translation initiation complexes fail to transition to elongation competent 80S ribosomes. Upon iRQC activation, RNF10 ubiquitylates the 40S proteins uS3 and uS5 which leads to 40S decay. How iRQC is activated in the absence of pharmacological translation inhibitors and what mechanisms govern iRQC capacity and activity remain unanswered questions. Here, we demonstrate that altering ribosome subunit stoichiometry by broadly disrupting 60S biogenesis triggers RNF10-dependent uS3 and uS5 ubiquitylation and 40S decay. Reducing the levels of the critical scanning helicase, eIF4A1, impairs ribosomal protein ubiquitylation and subsequent degradation, indicating that actively scanning translation initiation complexes are required for 40S decay. We show that RNF10 protein abundance increases upon iRQC pathway stimulation through a translational activation mechanism using conserved upstream open reading frames. Amino acid starvation conditions also stimulate 40S decay leading to ribosomal subunit imbalance. We identify RIOK3 as a new and critical iRQC factor that interacts with ubiquitylated 40S subunits to mediate 40S decay. We demonstrate that RIOK3 loss of function blocks 40S degradation triggered by either 60S biogenesis disruption or amino acid starvation despite elevated uS3 and uS5 ubiquitylation. These findings suggest that RIOK3 abundance, and not ribosome ubiquitylation, limits 40S decay capacity. Collectively, these results establish a feed-forward mechanism that regulates iRQC capacity and subsequent 40S decay.
HostingRepository	PRIDE
AnnounceDate	2025-02-07
AnnouncementXML	Submission_2025-02-06_16:59:01.713.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Pierce Ford
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	timsTOF Pro 2

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-29 11:37:54	ID requested
⏵ 1	2025-02-06 16:59:02	announced

Dataset with its publication pending

submitter keyword: RIOK3, ribosome ubiquitylation, initiation ribosome-associated quality control (iRQC), amino acid starvation, RNF10,ribosome biogenesis

Eric Bennett
contact affiliation	UCSD
contact email	e1bennett@ucsd.edu
lab head
Pierce Ford
contact affiliation	UCSD
contact email	pford@ucsd.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD060334
     1. Label: PRIDE project
     2. Name: RNF10 and RIOK3 Facilitate 40S Ribosomal Subunit Degradation upon 60S Biogenesis Disruption or Amino Acid Starvation [Fig. 4D, S4D]