Upf1 phosphorylation triggers translational repression during nonsense-mediated mRNA decay

Abstract

In mammalian cells, nonsense-mediated mRNA decay (NMD) generally requires that translation terminates sufficiently upstream of a post-splicing exon junction complex (EJC) during a pioneer round of translation. The subsequent binding of Upf1 to the EJC triggers Upf1 phosphorylation. We provide evidence that phospho-Upf1 functions after nonsense codon recognition during steps that involve the translation initiation factor eIF3 and mRNA decay factors. Phospho-Upf1 interacts directly with eIF3 and inhibits the eIF3-dependent conversion of 40S/Met-tRNA(i)(Met)/mRNA to translationally competent 80S/Met-tRNA(i)(Met)/mRNA initiation complexes to repress continued translation initiation. Consistent with phospho-Upf1 impairing eIF3 function, NMD fails to detectably target nonsense-containing transcripts that initiate translation independently of eIF3 from the CrPV IRES. There is growing evidence that translational repression is a key transition that precedes mRNA delivery to the degradation machinery. Our results uncover a critical step during NMD that converts a pioneer translation initiation complex to a translationally compromised mRNP.

Figure 1. WT Upf1 Preferentially Interacts with SMG-1 and eRF3, whereas Phospho-Upf1 Preferentially Interacts with mRNA Decay Factors

(A) HeLa cells (3–4 × 10⁷) were transiently transfected with pCMV-myc-UPF1^R(WT) or pCMV-myc-UPF1^R(G495R/G497E) (10 µg). Two days later, total-cell lysate was immunoprecipitated using anti(α)-myc or mouse (m)IgG. Western blotting (WB) was performed using the specified antibodies. The four leftmost lanes analyzed decreasing amounts of protein before (−) IP. (B) Essentially as in (A), except cells were transiently transfected with pCMV-myc-UPF1^R(WT) and treated with the specified amount of OA for 3 hr prior to harvesting. All results are representative of three independently performed experiments.

Figure 2. Downregulating the Cellular Abundance of Upf1 Increases Cap-Dependent and HCV IRES-Dependent Translation but Not CrPV IRES-Dependent Translation

(A) Schematic representations of the bicistronic constructs that encode Renilla (R) and Firefly (F) Luciferase (Luc). HeLa cells (2 × 10⁶) were transiently transfected with Upf1 or control siRNA. Two days later, cells were retransfected with a pmCMV-Gl test plasmid, either Norm or 39Ter, the reference phCMV-MUP plasmid, and a reporter plasmid that was either pR/HCV/F or pR/CrPV/F. (B) Western blotting (WB) was used to quantitate the level of Upf1 relative to Vimentin. (C) RT-PCR was used to quantitate the levels of Gl and MUP mRNAs in transfections with either pR/HCV/F or pR/CrPV/F. Numbers below the figure represent the level of Gl mRNA after normalization to the level of MUP mRNA, where the normalized level of Gl Norm mRNA in the presence of each siRNA or no (−) siRNA was defined as 100%. (D) Luminometry was used to quantitate FLucand RLuc activities, which were normalized to levels of R/HCV/F or R/CrPV/F mRNA to control for variations in transfection efficiencies. The normalized levels of Luc activity in transfections with control siRNA were defined as 1. Results are the average of two independently performed experiments.

Figure 3. Translation Initiation from the CrPV IRES, Unlike Translation Initiation from the EMCV IRES, Fails to Support NMD

Cos cells (3 × 10⁶) were transiently transfected with control or Upf1 siRNA and, 2 days later, with php/EMCV(WT)/R-Gl, php/EMCV(GTTA)/R-Gl or php/CrPV/R-Gl, either Norm or 39Ter (10 μg), pFLuc (0.5 μg), and phCMV-MUP (0.3 μg). (A) Diagrams of each R-Gl construct. In the case of 39Ter, 39 specifies the position of the nonsense codon. (B) Western blotting (WB) was used to quantitate the level of Upf1 relative to p62. (C) Luminometry was used to quantitate RLuc and FLuc activities. RLuc activities were normalized to FLuc activities, to control for variations among protein preparations, and R-Gl mRNA levels, to control for variations in cell transfection efficiencies. The normalized level of RLuc activity from php/EMCV(WT)/R-Gl in the presence of control siRNA was defined as 100%. Error bars represent the mean ± standard deviation (SD) of three independently performed experiments. (D) RT-PCR of R-Gl and MUP mRNAs. Numbers below the figure represent the levels of R-Gl mRNA after normalization to the level of MUP mRNA, where the normalized level of R-Gl Norm mRNA in the presence of each php plasmid was defined as 100%. Results are the average of three independently performed experiments.

Figure 4. Phosphorylated Upf1 Represses Cap-Dependent but Not CrPV IRES-Dependent Translation Initiation

(A–C) HeLa cells (1 × 10⁶) were transiently transfected with control or Upf1 siRNA. Two days later, cells were transfected with pCMV-myc-UPF1^R(WT) or pCMV-myc-UPF1^R(G495R/G497E). (A) Western blotting (WB) was used to quantitate the level of myc-Upf1 relative to endogenous Upf1 and SMG-1. (B) RT-PCR analysis of Gl and MUP mRNAs. As in Figure 2C, except the normalized levels of Gl Norm mRNA in transfections that included each pCMV-myc expression vector were defined as 100%. (C) Relative levels of Luc activity. (D and E) HeLa cells(3 × 10⁶) were treated with the specified amount of OA for 3hr prior to harvesting. (D) RT-PCR of Gl and MUP mRNAs. (E) Relative RLuc activity normalized to the level of RLuc mRNA, where the normalized level in the absence of OA is defined as 1. Results are the average of three independently performed experiments. Error bars in (C) and (E) represent the mean ± SD of three independent experiments.

Figure 5. Upf1 Phosphorylation Promotes Upf1 Binding to eIF3 Subunits

(A) HeLa cells were transiently transfected with pCMV-myc-UPF1^R(WT) or pmCMV-UPF1^R(G495R/G497E). Western blotting (WB) was performed using the designated antibody (α) before (−) and after immunoprecipitation (IP) using anti-myc or mouse (m) IgG. The dot specifies a nonspecific band that does not interfere with the analysis. (B) HeLa cells were transiently transfected with pCMV-myc-UPF1^R(WT) and treated with 0 or 75 nM OA for 3 hr prior to harvesting. Cell lysates were subjected to western blot analysis before and after IP. (C) HeLa cells were transiently transfected with control or Upf1 siRNA and 2 days later with pmCMV-UPF1^R(G495R/G497E). Cell lysates were immunoprecipitated using anti-eIF3a or mIgG, and western blotting was performed as noted. (D) As in (B) except IP was performed using anti-eIF3a or mIgG. (E) Coomassie blue staining of baculovirus-produced FLAG-Upf1(WT) and FLAG-Upf1(G495R/G497E). (F) Far-western analysis (FW) of the specified purified proteins using baculovirus-produced FLAG-Upf1(WT) (left) or FLAG-Upf1(G495R/G497E) (right) followed by western blotting using anti-FLAG. eIF3 subunits and BSA were also stained using Coomassie blue (middle). (G) Coomassie blue staining of baculovirus-produced FLAG-Upf1(WT) from insect cells that were (+) or were not (−) treated with 75 nM OA for 3 hr prior to harvesting. (H) As in (F), except proteins shown in (G) were used as probes in the far-western analysis.

Figure 6. Phospho-Upf1 Inhibits the Conversion of 40S/[³⁵S]Met-tRNA_i^Met/mRNA to Translationally Competent 80S/[³⁵S]Met-tRNA_i^Met/mRNA in RRLs

BSA, baculovirus-produced FLAG-Upf1(WT), or baculovirus-produced FLAG-Upf1(G495R/G497E) were added to RRLs prior to the addition of charged [³⁵S]Met-tRNA_i^Met and RLuc mRNA. (A) [³⁵S]Met was quantitated (colored plot) and superimposed on absorbance profiles of subpolysomes and polysomes that were separated by sucrose gradient centrifugation. The positions of 40S, 60S, and 80S complexes are specified. (B) Superimposition of the [³⁵S]Met distribution in sucrose gradients of FLAG-Upf1(WT) or FLAG-Upf1(G495R/G497E) as shown in (A). (C) RT-PCR of RLuc mRNA in sucrose gradients.

Figure 7. Model for Phospho-Upf1-Mediated Repression of Translation Initiation

Upf1, which is primarily hypophosphorylated, forms the SURF complex together with SMG-1, eRF1, and eRF3 when translation terminates during a pioneer round, which involves CBP80/20-bound mRNA. If termination occurs sufficiently upstream of a post-splicing EJC, e.g., at the specified premature termination codon (PTC), then Upf1 and SMG-1 associate with the EJC. Upon association, SMG-1 phosphorylates Upf1. Phospho-Upf1 then represses translation by binding to eIF3 subunits and inhibiting the eIF3-mediated joining of 60S ribosomal subunits to 40S/Met-tRNA_i^Met/mRNA. Phospho-Upf1 also recruits mRNA decay factors, including Dcp1a, Xrn1, and Rrp4.