PXD044420-1

PXD044420 is an original dataset announced via ProteomeXchange.

Title	Ccr4-Not ubiquitin ligase signaling regulates ribosomal protein homeostasis and inhibits 40S ribosomal autophagy
Description	The Ccr4-Not complex containing the Not4 ubiquitin ligase regulates gene transcription and mRNA decay, yet it also has poorly defined roles in translation, proteostasis, and endolysosomal-dependent nutrient signaling. To define how Ccr4-Not mediated ubiquitin signaling regulates these additional processes, we performed quantitative proteomics in the yeast Saccharomyces cerevisiae lacking the Not4 ubiquitin ligase and in cells overexpressing either wild-type or functionally inactive ligase. Herein, we provide evidence that both increased and decreased Ccr4-Not ubiquitin signaling disrupts ribosomal protein (RP) homeostasis independently of reduced RP mRNA changes or reductions in known Not4 ribosomal substrates. Surprisingly, we also find that Ccr4-Not inhibits 40S ribosomal autophagy through Not4-dependent ubiquitin signaling and the additional Ccr4 subunit. This 40S autophagy is independent of canonical Atg7-dependent macroautophagy, thus indicating microautophagy activation is responsible. Furthermore, the Not4 ligase genetically interacts with endolysosomal pathway effectors to control both RP expression and 40S autophagy efficiency. Overall, we demonstrate that balanced Ccr4-Not ligase activity maintains RP homeostasis, and that Ccr4-Not ubiquitin signaling interacts with the endolysosomal pathway to regulate RP expression and inhibit 40S ribosomal autophagy.
HostingRepository	PRIDE
AnnounceDate	2024-10-17
AnnouncementXML	Submission_2024-10-17_03:57:34.857.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD044420
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Daniel Johnson
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-07 11:14:09	ID requested
⏵ 1	2024-10-17 03:57:35	announced

Johnson DL, Kumar R, Kakhniashvili D, Pfeffer LM, Laribee RN, Ccr4-not ubiquitin ligase signaling regulates ribosomal protein homeostasis and inhibits 40S ribosomal autophagy. J Biol Chem, 300(8):107582(2024) [pubmed]

10.1016/j.jbc.2024.107582;

10.6019/PXD044420;

submitter keyword: autophagy, endolysomal, ribosome,CCR4-Not, Not4

Ronald Laribee
contact affiliation	Department of Pathology, University of Tennesee Health Science Center
contact email	rlaribee@uthsc.edu
lab head
Daniel Johnson
contact affiliation	University of Tennesssee Health Science Center
contact email	djohn166@uthsc.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD044420
     1. Label: PRIDE project
     2. Name: Ccr4-Not ubiquitin ligase signaling regulates ribosomal protein homeostasis and inhibits 40S ribosomal autophagy