Biochemical Journal

Research article

Complexes between the nonsense-mediated mRNA decay pathway factor human upf1 (up-frameshift protein 1) and essential nonsense-mediated mRNA decay factors in HeLa cells

Thomas SCHELL, Thomas KÖCHER, Matthias WILM, Bertrand SERAPHIN, Andreas E. KULOZIK, Matthias W. HENTZE

Abstract

mRNAs harbouring premature translation-termination codons are usually degraded by the nonsense-mediated mRNA decay (NMD) pathway. Human up-frameshift protein 1 (Hupf1) is an NMD factor that is conserved between yeast and mammals. To isolate cellular complexes that are formed with Hupf1 and to explore the role of cellular proteins in NMD, we generated a HeLa cell line that stably expresses Hupf1 bearing a double-affinity tag (termed Hupf1-2tag). Hupf1-2tag is localized in the cytoplasm similar to the endogenous Hupf1 protein, and the Hupf1-2tag cell line is fully NMD-competent. Using affinity chromatography, Hupf1-2tag-associated proteins were isolated. MS and immunoblotting identified the NMD factors Hupf2 and Hupf3a/b as interaction partners of Hupf1. Size-exclusion chromatography indicates that the NMD factors Hupf1, Hupf2 and the large isoform of Hupf3a might exist in a stable, high-molecular-mass complex of approx. 1.3 MDa. Interestingly, the poly(A)-binding protein was also identified by MS to be associated specifically with Hupf1-2tag. In contrast with the interaction with Hupf2 and Hupf3a/b, the association of poly(A)-binding protein with Hupf1 is highly sensitive to treatment of the isolated complexes with RNase. Components of the exon–exon junction complex or the translational eukaryotic release factor (eRF) 3 were not identified in complexes associated with Hupf1-2tag. We discuss these findings in the context of current models of NMD.

  • human up-frameshift protein 1 (upf1)/Rent1
  • nonsense-mediated mRNA decay (NMD)
  • poly(A)-binding protein (Pabp)
  • RNA surveillance
  • tandem-affinity purification

Footnotes

  • Abbreviations used: DMEM, Dulbecco's modified Eagle's medium; EJC, exon–exon junction complex; eRF, eukaryotic release factor; Hupf1, human up-frameshift protein 1; NMD, nonsense-mediated mRNA decay; ORF, open reading frame; Pabp, poly(A)-binding protein; PTC, premature translation-termination codon; SMG, suppressor with morphogenetic effect on genitalia; TEV, tobacco etch virus.