PXD067949-1

PXD067949 is an original dataset announced via ProteomeXchange.

Title	Codon-specific ribosome stalling reshapes translational dynamics during branched-chain amino acid starvation
Description	This study investigates the immediate effects of single, double, and triple branched-chain amino acid (BCAA) deprivation on translational dynamics in NIH3T3 cells. Using a multi-omics approach combining RNA-seq, ribosome profiling (Ribo-seq), quantitative proteomics, and tRNA charging assays, we systematically assessed global translational output and codon-specific ribosome dwell times. Our findings reveal that BCAA starvation induces diverse and non-additive translational control patterns, reflecting a complex interplay between mTORC1 and GCN2 pathway activation, tRNA isoacceptor availability, and transcript codon usage. Notably, we identified a positional effect where the enrichment of valine codons at the 5' end of transcripts creates an elongation bottleneck under valine and triple BCAA starvation, impacting downstream ribosome occupancy and overall protein output. This study uncovers a previously underappreciated layer of complexity in BCAA-specific translational regulation.
HostingRepository	PRIDE
AnnounceDate	2025-09-13
AnnouncementXML	Submission_2025-09-13_04:31:31.334.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Cédric Gobet
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2025-09-01 05:35:14	ID requested
⏵ 1	2025-09-13 04:31:31	announced

Dataset with its publication pending

submitter keyword: proteomics, elongation bottleneck, nutrient stress response, mass spectrometry, NIH3T3 cells, ribosome profiling, amino acid starvation,translation regulation, tRNA charging, codon-specific stalling

Felix Naef
contact affiliation	Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
contact email	felix.naef@epfl.ch
lab head
Cédric Gobet
contact affiliation	EPFL - École Polytechnique Fédérale de Lausanne
contact email	cedric.gobet@epfl.ch
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/2025/09/PXD067949

PRIDE project URI

• PRIDE
  1. PXD067949
     1. Label: PRIDE project
     2. Name: Codon-specific ribosome stalling reshapes translational dynamics during branched-chain amino acid starvation