Identification of new interactors of eIF3f by endogenous proximity-dependent biotin labelling in human muscle cells

TL;DR

This study identifies new proteins that interact with eIF3f in human muscle cells, revealing its role in muscle mass regulation and uncovering a new nuclear localization.

Contribution

The study introduces a novel endogenous tagging system for eIF3f and identifies new nuclear and cytoplasmic interactors.

Findings

eIF3f interacts with components of the eIF3 complex and other translation initiation factors in both proliferating and differentiated muscle cells.

eIF3f exhibits a previously unknown nuclear localization in myoblasts and myotubes.

Novel cytoplasmic partners of eIF3f include proteins involved in muscle ultrastructure and lysosomal compartments.

Abstract

Regulation of protein synthesis is central to maintaining skeletal muscle integrity and its understanding is important for the treatment of muscular and neuromuscular pathologies. The eIF3f subunit of the translation initiation factor eIF3 has a key role, as it stands at the crossroad between protein-synthesis-associated hypertrophy and MAFbx/atrogin-1-dependent atrophy. To decipher the molecular mechanisms underpinning the role of eIF3f in regulating muscle mass, we established a cellular model that enables interrogation of eIF3f functionality via identification of proximal interactors. Using CRISPR-Cas9 molecular scissors, we generated single cell clones of immortalised human muscle cells expressing eIF3f fused to the BirA biotin ligase (eIF3f-BioID1 chimera) from the endogenous EIF3F locus. Biotinylated proteins, representing interactors of eIF3f in nanometer range distance, were identified by streptavidin pull-downs and mass spectrometry. In both proliferating and differentiated muscle cells, the eIF3f-BioID1 chimera co-sedimented with ribosomal complexes in polysome profiles and interacted mainly with components of the eIF3 complex, and with the eIF4E, eIF4G, and eIF5 initiation factors. Surprisingly, we identified several nucleus-localised interactors of eIF3f, and the immunofluorescence analyses revealed a previously unknown nuclear localization of eIF3f in both myoblasts and myotubes. We also identified novel cytoplasmic partners of eIF3f, responsible for the maintenance of skeletal muscle ultrastructure (sarcomeric/Z-disc (SYNPO2) bound proteins) and proteins of the lysosomal compartment (LAMP1). The established tagging system should be useful to further advance studies of eIF3f function in hypertrophic and atrophic conditions in skeletal muscle.

The online version contains supplementary material available at 10.1038/s41598-025-32702-7.

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