PXD052929-1

PXD052929 is an original dataset announced via ProteomeXchange.

Title	Yeast poly(A)-binding protein (Pab1) controls translation initiation in vivo primarily by blocking mRNA decapping and decay
Description	Poly(A)-binding protein (Pab1 in yeast) is involved in mRNA decay and translation initiation, but its molecular functions are incompletely understood. In this study, we employed a comprehensive multiomics strategy encompassing Ribosome profiling, spike-in normalized RNA-seq, SMPAT-seq, and CAGE-seq to gain mechanistic insights into Pab1's role in Saccharomyces cerevisiae. We found that auxin-induced degradation of Pab1 reduced bulk mRNA and polysome abundance in a manner suppressed by deleting the catalytic subunit of decapping enzyme (dcp2∆), demonstrating that enhanced decapping/degradation is the major driver of reduced mRNA abundance and protein synthesis at limiting Pab1 levels. An increased median poly(A) tail length conferred by Pab1 depletion was also nullified by dcp2∆, suggesting that mRNA isoforms with shorter tails are preferentially decapped/degraded at limiting Pab1. In contrast to findings on mammalian cells, the translational efficiencies (TEs) of many mRNAs were altered by Pab1 depletion; however, these changes were broadly diminished by dcp2∆, suggesting that reduced mRNA abundance is a major driver of translational reprogramming at limiting Pab1. Thus, assembly of the closed-loop mRNP via PABP-eIF4G interaction appears to be dispensable for normal translation of most yeast mRNAs in vivo at normal mRNA levels. Interestingly, histone mRNAs and proteins are preferentially diminished on Pab1 depletion dependent on Dcp2, accompanied by activation of internal cryptic promoters in the manner expected for reduced nucleosome occupancies, revealing a new layer of post-transcriptional control of histone gene expression.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-06_18:39:55.830.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD052929
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Poonam Poonia
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-07 08:03:42	ID requested
⏵ 1	2025-05-06 18:39:56	announced

Poonia P, Valabhoju V, Li T, Iben J, Niu X, Lin Z, Hinnebusch AG, Yeast poly(A)-binding protein (Pab1) controls translation initiation in vivo primarily by blocking mRNA decapping and decay. Nucleic Acids Res, 53(5):(2025) [pubmed]

10.6019/PXD052929;

10.1093/nar/gkaf143;

submitter keyword: mRNA decay,Pab1, 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
Poonam Poonia
contact affiliation	Postdoc
contact email	poonam.poonia@nih.gov
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/05/PXD052929

PRIDE project URI

• PRIDE
  1. PXD052929
     1. Label: PRIDE project
     2. Name: Yeast poly(A)-binding protein (Pab1) controls translation initiation in vivo primarily by blocking mRNA decapping and decay