NMD resulting from encephalomyocarditis virus IRES-directed translation initiation seems to be restricted to CBP80/20-bound mRNA

Abstract

Nonsense-mediated messenger RNA decay (NMD) generally degrades mRNAs that prematurely terminate translation as a means of quality control. NMD in mammalian cells targets newly spliced mRNA that is bound by the cap-binding protein heterodimer CBP80/20 and one or more post-splicing exon junction complexes during a pioneer round of translation. NMD targets mRNA that initiates translation using the encephalomyocarditis virus (EMCV) internal ribosome entry site (IRES), therefore NMD might target not only CBP80/20-bound mRNA but also its remodelled product, eIF4E-bound mRNA. Here, we provide evidence that NMD triggered by translation initiation at the EMCV IRES, similar to NMD triggered by translation initiation at an mRNA cap, targets CBP80/20-bound mRNA but does not detectably target eIF4E-bound mRNA. We show that EMCV IRES-initiated translation undergoes a CBP80/20-associated pioneer round of translation that results in CBP80/20-dependent and Upf factor-dependent NMD when translation terminates prematurely.

Figure 1

Downregulating Upf1, Upf2, Upf3X or CBP80/20 inhibits nonsense-mediated messenger RNA decay that results from encephalomyocarditis virus internal ribosome entry site-initiated translation. (A) Diagrams of plasmid DNAs. Boxes represent exons, intervening lines signify introns and hp refers to the hairpin structure that blocks translation initiation upstream from the EMCV IRES. ATG and TAA denote translation initiation and termination codons, respectively, and 39 indicates the position of the premature termination codon when present. (B) (upper panel) Western blot analysis (WB) using the specified antibody (anti-) after treatment with Upf1 or control siRNA. The level of p62 was used to control for variations in protein loading. The three leftmost lanes show twofold dilutions of protein, indicating that the analysis was semiquantitative. (lower panel) Reverse transcription–PCR after treatment with Upf1 siRNA or control siRNA. The level of each RLuc-Gl test mRNA was normalized to the level of MUP mRNA. Normalized values were then calculated as a percentage of the normalized value of either RLuc-Gl Norm mRNA or hp-EMCV IRES-RLuc Norm mRNA, each of which was defined as 100%. Values are derived from three independently performed experiments. The five leftmost lanes show twofold dilutions of RNA. (C) As in (B), except that Upf2 siRNA was used instead of Upf1 siRNA. (D) As in (B), except that Upf3X siRNA was used and the level of pb2 was used to control for variations in protein loading as p62 migrates with Upf3X. (E) As in (B), except that CBP80 and CBP20 (CBC) siRNAs were used. CBP20 runs as a smeared band. EMCV, encephalomyocarditis virus; Gl, β-globin; IRES, internal ribosome entry site; Luc, luciferase; MUP, major urinary protein; Norm, PTC-free; R, Renilla; siRNA, short interfering RNA; Ter, PTC-containing.

Figure 2

4E-BP1 expression fails to inhibit nonsense-mediated messenger RNA decay that results from encephalomyocarditis virus internal ribosome entry site-initiated translation. (A) Western blot analysis (WB) shows that 4E-BP1 expression inhibited the bulk of cellular translation, as measured by the reduced level of the secreted MUP. The level of p62 was used to control for variations in protein loading. The four leftmost lanes show twofold dilutions of protein. (B) RLuc activity assays also indicated that 4E-BP1 expression inhibited the bulk of cellular translation. RLuc activity was normalized to the level of the corresponding RLuc mRNA. (C) Reverse transcription–PCR as in Fig 1B (lower panel). Values are derived from three independently performed experiments. EMCV, encephalomyocarditis virus; Gl, β-globin; IRES, internal ribosome entry site; Luc, luciferase; MUP, major urinary protein; Norm, PTC-free; R, Renilla; Ter, PTC-containing.

Figure 3

Nonsense-mediated messenger RNA decay that results from encephalomyocarditis virus internal ribosome entry site-initiated translation reduces the abundance of CBP80-bound mRNA and its eIF4E-bound product to a comparable percentage of the corresponding normal messenger ribonucleoprotein. (A,B, upper panels) Western blot analysis (WB) indicated that the immunoprecipitation (IP) efficiency of CBP80 or eIF4E was 18±4% or 14±2%, respectively—1/100 of each sample was analysed before IP and 1/20 of each sample was analysed after IP. (A,B, lower panels) Reverse transcription–PCR of Gl and MUP mRNAs. Values are derived from two independently performed experiments. EMCV, encephalomyocarditis virus; Gl, β-globin; IRES, internal ribosome entry site; Luc, luciferase; MUP, major urinary protein; Norm, PTC-free; NRS, normal rabbit serum; R, Renilla; Ter, PTC-containing.