PXD059972

PXD059972 is an original dataset announced via ProteomeXchange.

Title	Identification of new interactors of eIF3f by endogenous proximity-dependent biotin labelling in human muscle cells
Description	Regulation of protein synthesis plays a central role in maintaining skeletal muscle integrity and its understanding is important for treatment of muscular and neuromuscular pathologies. eIF3f is one of the subunits of the translation initiation factor eIF3, having an important regulatory potential. Activity of eIF3f stands at the crossroads between protein synthesis associated hypertrophy and MAFbx/atrogin-1 dependent atrophy in skeletal muscle cells. To date our mechanistic knowledge of eIF3f stems from contradictory studies highlighting its functional divergence in different cell types. To decipher the molecular mechanisms underpinning the role of eIF3f in regulating muscle mass, we established a cellular model to interrogate eIF3f functionality based on proximal interaction network identification. We generated a muscle cell line stably expressing eIF3f fused to the mutated BirA biotin ligase, allowing the irreversible labelling of the interactors of eIF3f in a nanometer range distance. Biotinylated proteins interacting with eIF3f were identified by streptavidin pulldowns and mass spectrometry. We successfully designed a functional eIF3f-BirA(BioID1) chimeric protein and validated its ability to interact with the core eIF3 complex upon transient expression in HEK293 cells. We used CRISPR-Cas9 molecular scissors to generate single cell clones of immortalized human muscle cells expressing the eIF3f-BioID1 chimera in place of the endogenous EIF3F locus. Irrespective of the proliferating or differentiated muscle cell states, we found that endogenously expressed eIF3f-BioID1 chimera mainly interacts with components of the eIF3 complex such as eIF3a/b/cl (c-like)/e, and eIF4E, eIF4G, and eIF5 initiation factors, and co-sediments with ribosomal complexes in polysome profiles. Surprisingly, we identified several nuclear localized interactors of eIF3f, which, together with immunofluorescence analyses, indicates a previously unknown nuclear localization of eIF3f in both myoblasts and myotubes. Further, we identified several novel cytoplasmic binding partners of eIF3f, responsible for the maintenance of cytoplasmic skeletal muscle ultrastructure such as sarcomeric/Z-disc (SYNPO2) bound proteins and proteins of the lysosomal compartment such as LAMP1. We describe here the establishment of an endogenous molecular tagging system for the translation initiation factor eIF3f, unravel its core proximal interactors in skeletal muscle cells, and validate LAMP1 as a new binding partner. We believe this cell line will be used to decipher eIF3f function in hypertrophic and atrophic conditions in skeletal muscle.
HostingRepository	MassIVE
AnnounceDate	2025-03-05
AnnouncementXML	Submission_2025-03-05_07:31:26.010.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Thomas Bock
SpeciesList	scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2025-01-20 04:51:32	ID requested
⏵ 1	2025-03-05 07:31:26	announced

no publication

submitter keyword: eIF3f, DatasetType:Proteomics

Alexander Schmidt
contact affiliation	Biozentrum, Universtiy of Basel, 4056 Basel, Switzerland
contact email	alex.schmidt@unibas.ch
lab head
Thomas Bock
contact affiliation	Uni Basel
contact email	thomas.bock@unibas.ch
dataset submitter

MassIVE dataset URI

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://massive.ucsd.edu/v09/MSV000096896/