PXD053307-1

PXD053307 is an original dataset announced via ProteomeXchange.

Title	Decapping activators Edc3 and Scd6 act redundantly with Dhh1 in nutrient-replete cells to post-transcriptionally repress starvation-induced pathways
Description	Degradation of many yeast mRNAs involves decapping by Dcp1:Dcp2. Previous studies on decapping activators Edc3 and Scd6 suggested limited roles in promoting mRNA decay in yeast cells. RNA-seq analysis of mutants lacking one or both proteins reveals that Scd6 and Edc3 have largely redundant functions in targeting numerous mRNAs for degradation, whose roles are masked in the single mutants. These mRNAs are also frequently targeted by decapping activators Dhh1 and Pat1 and the decapping enzyme itself, and the data support the proposal that Scd6/Edc3 act interchangeably to recruit Dhh1 to Dcp2 independently of Pat1. Ribosome profiling shows that functional redundancy of Scd6 and Edc3 and cooperation with Dhh1/Pat1 extends to the translational repression of particular transcripts, including a cohort of poorly translated mRNAs displaying interdependent regulation by all four factors. Scd6/Edc3 also partner with Dhh1/Pat1 in nutrient-replete cells for post-transcriptional repression of proteins required for respiration and catabolism of non-optimal carbon sources, which are normally expressed only in cells deprived of glucose. As such, simultaneously eliminating Scd6/Edc3 increases mitochondrial membrane potential and elevates metabolites of the tricarboxylic acid and glyoxylate cycles critical for growth in cells growing without glucose. Thus, Scd6/Edc3 act redundantly and together with decapping activators Dhh1 and Pat1 to post-transcriptionally adjust gene expression to nutrient availability.
HostingRepository	PRIDE
AnnounceDate	2025-10-30
AnnouncementXML	Submission_2025-10-30_08:49:35.106.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD053307
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Rakesh Kumar
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: NEWT:4932;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-22 16:01:06	ID requested
⏵ 1	2025-10-30 08:49:35	announced

10.7554/ELIFE.102287.;

10.6019/PXD053307;

submitter keyword: mRNA decay,Yeast, Translation

Alan G. Hinnebusch
contact affiliation	Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
contact email	alanh@mail.nih.gov
lab head
Rakesh Kumar
contact affiliation	NICHD/NIH
contact email	rakesh.kumar@nih.gov
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD053307
     1. Label: PRIDE project
     2. Name: Decapping activators Edc3 and Scd6 act redundantly with Dhh1 in nutrient-replete cells to post-transcriptionally repress starvation-induced pathways