Characterization of phosphorylation- and RNA-dependent UPF1 interactors by quantitative proteomics.
Human up-frameshift 1 (UPF1) is an ATP-dependent RNA helicase and phosphoprotein implicated in several biological processes but is best known for its key function in nonsense-mediated mRNA decay (NMD). Here we employed a combination of stable isotope labeling of amino acids in cell culture experiments to determine by quantitative proteomics UPF1 interactors. We used this approach to distinguish between RNA-mediated and protein-mediated UPF1 interactors and to determine proteins that preferentially bind the hypo- or the hyper-phosphorylated form of UPF1. Confirming and expanding previous studies, we identified the eukaryotic initiation factor 3 (eIF3) as a prominent protein-mediated interactor of UPF1. However, unlike previously reported, eIF3 binds to UPF1 independently of UPF1's phosphorylation state. Furthermore, our data revealed many nucleus-associated RNA-binding proteins that preferentially associate with hyper-phosphorylated UPF1 in an RNase-sensitive manner, suggesting that UPF1 gets recruited to mRNA and becomes phosphorylated before being exported to the cytoplasm as part of the mRNP.
Department of Chemistry and Biochemistry, University of Bern , Freiestr. 3, Bern 3012, Switzerland.
Valentin
V
Flury
Umberto
U
Restuccia
Angela
A
Bachi
Oliver
O
Mühlemann
D006367:HeLa Cells; D006801:Humans; D047468:Immunoprecipitation; D010766:Phosphorylation; D025941:Protein Interaction Mapping; D060066:Protein Interaction Maps; D011499:Protein Processing, Post-Translational; D040901:Proteomics; D020365:RNA Helicases; D012333:RNA, Messenger / Q000378:metabolism*; D015534:Trans-Activators / Q000378:metabolism*
D012333:RNA, Messenger; D015534:Trans-Activators; D020365:RNA Helicases; C101828:UPF1 protein, human