The nonsense-mediated decay (NMD) pathway subjects mRNAs with premature termination codons (PTCs) to rapid decay. The conserved Upf1–3 complex interacts with the eukaryotic translation release factors, eRF3 and eRF1, and triggers NMD when translation termination takes place at a PTC. Contrasting models postulate central roles in PTC-recognition for the exon junction complex in mammals versus the cytoplasmic poly(A)-binding protein (PABP) in other eukaryotes. Here we present evidence for a unified model for NMD, in which PTC recognition in human cells is mediated by a competition between 3′ UTR–associated factors that stimulate or antagonize recruitment of the Upf complex to the terminating ribosome. We identify cytoplasmic PABP as a human NMD antagonizing factor, which inhibits the interaction between eRF3 and Upf1 in vitro and prevents NMD in cells when positioned in proximity to the termination codon. Surprisingly, only when an extended 3′ UTR places cytoplasmic PABP distally to the termination codon does a downstream exon junction complex enhance NMD, likely through increasing the affinity of Upf proteins for the 3′ UTR. Interestingly, while an artificial 3′ UTR of >420 nucleotides triggers NMD, a large subset of human mRNAs contain longer 3′ UTRs but evade NMD. We speculate that these have evolved to concentrate NMD-inhibiting factors, such as PABP, in spatial proximity of the termination codon.
The nonsense-mediated mRNA decay pathway is responsible for rapidly degrading mRNAs with premature termination codons. This is important because it prevents the production of potentially deleterious truncated proteins from aberrant mRNAs, such as those that have undergone erroneous processing. How does the cell discriminate aberrant mRNAs from those that are normal? Here we present evidence that in human cells, the targeting of an mRNA to nonsense-mediated mRNA decay depends on a competition between proteins associated with the mRNA 3′ UTR that stimulate or antagonize mRNA decay. We show that cytoplasmic poly(A)-binding protein, a protein associated with the mRNA 3′ end poly(A) tail, antagonizes mRNA decay. By contrast, a protein complex deposited onto mRNAs upon pre-mRNA splicing, called the exon junction complex, stimulates mRNA decay. Our observations suggest that the competition between these proteins, and probably other unknown proteins with similar activities, determines whether a key protein complex in the pathway, the Upf complex, is recruited to the mRNA upon translation termination, which leads to mRNA decay.
Human mRNAs with premature termination codons are detected and degraded by nonsense-mediated decay when 3' untranslated region-associated proteins, such as poly(A)-binding protein, are absent from the proximity of the terminating ribosome.
The process of nonsense-mediated decay (NMD) subjects mRNAs with premature termination codons (PTCs) to rapid decay. This helps rid the cell of aberrant mRNAs that have acquired PTCs through mutation or faulty processing [
A fundamental question is how mRNAs with PTCs are distinguished from those with normal termination codons. Despite the conservation of core NMD factors, contrasting models have been proposed in mammalian cells as opposed to other eukaryotes. Evidence in
3′ UTRs of human mRNAs are on average longer (∼750–800 nucleotides [
A fundamental difference between the faux 3′ UTR and the EJC/DSE models for NMD is that the EJC/DSE models propose that NMD-stimulating factors (the EJC and Hrp1p, respectively) trigger NMD when positioned downstream of a termination codon, whereas the faux 3′ UTR model postulates that NMD is caused instead by the absence of NMD-antagonizing factors, such as cytoplasmic PABP, which normally positively influence translation termination and mRNA stability. Here, we present evidence for a merged model for NMD in human cells, which likely can be extended to other eukaryotes. According to this model, PTC recognition is determined by a competition between 3′ UTR–associated factors, which stimulate (including the EJC) or antagonize (including cytoplasmic PABP) the recruitment of the Upf complex to the terminating ribosome. Our observations suggest that the fundamental principles of the NMD pathway are much more conserved between mammals and other eukaryotes than previously anticipated.
The EJC model for human NMD postulates that any translation termination event taking place >50–55 nucleotides upstream of an exon-exon junction should result in NMD. However, during our studies of the human NMD pathway, we observed that a β-globin mRNA, in which the adenovirus major late (AdML) intron was inserted into the 3′ UTR 175 nucleotides downstream of the normal β-globin mRNA translation termination codon, did not show enhanced mRNA decay as compared to the wild-type β-globin mRNA in human HeLa Tet-off cells (compare
(A–E) Decay assays in human HeLa Tet-off cells for β-globin (A,D) or TPI mRNAs (E) with inserted 3′ UTR introns or β-globin wild-type (B) or PTC-39 mutant (C) mRNAs in the presence of Luciferase (Luc) or hUpf1 siRNAs as indicated (knockdown efficiencies are shown in
The observation in
Our observation that 3′ UTR introns are not sufficient for triggering human NMD spurred us to test whether cytoplasmic PABP may antagonize NMD in human cells, as it does in
(A and B) mRNA decay assays showing decay rates of β-globin-derived βGAP, βUAC-GAP, βGFP, and βUAC-GFP mRNAs (see schematics below) in human HeLa Tet-off cells expressing siRNAs against hUpf1, hUpf2, or as a negative control, Luciferase (Luc), as indicated on the left of each panel (knockdown efficiencies are shown in
(C) mRNA decay assays for intron-containing GPx1 mRNA with a PTC (GPx1-UAA) or a GPx1 mRNA with a PTC expressed from an intron-less construct (GPx1Δi-UAA) (see schematics below) in the presence of Luc or hUpf1 siRNAs as indicated on the left. mRNA decay rates for the shown experiments are given on the right and numbers in parentheses indicate the fold stabilization with standard deviation (
Having observed that 3′ UTR introns are not required for NMD, we asked whether a completely intron-less mRNA can undergo NMD. It was observed previously that introduction of PTCs in the naturally intron-less Hsp70 and histone H2A mRNAs does not result in their decreased steady-state levels, which led to speculations that intron-less mRNAs are immune to NMD [
To more directly test whether cytoplasmic PABP antagonizes NMD in human cells, we examined the effect of positioning cytoplasmic PABP in proximity of a PTC using two different approaches. First, as seen in
(A and B) mRNA decay assays for β39–2xMS2-Ex2 and βGAP-4xMS2 mRNAs (see schematics below; MS2 binding sites indicated as black bars and GAPDH sequence in dark gray) in HeLa Tet-off cells expressing the MS2 coat protein fused to PABPC1 (MS2-PABPC1) or PABPN1 (MS2-PABPN1) or individual unfused proteins as indicated on the left of the panels. Constitutively expressed βUAC-GAP or βwt mRNAs were used as internal controls (upper panels).
(C and D) Northern blots showing decay rates of β39 and βGAP mRNAs, with or without A30 or N30 sequences inserted downstream of the PTCs (schematic below). For all panels (A–D), numbers on the right indicate mRNA half-lives (t1/2; in minutes) calculated from the shown experiments, and numbers in parentheses indicate the fold stabilization with standard deviation (
As a second independent approach to ask whether PABP can antagonize human NMD, we tested the effect of inserting a binding site for PABP downstream of the PTCs. As seen in
Our observations raise the question of whether naturally occurring mammalian mRNAs with long 3′ UTRs, which can be several kilobases in length, are normal targets of NMD or whether they have evolved mechanisms to evade the NMD pathway. We noted that mRNAs identified by microarray assays to be upregulated upon hUpf1 knockdown in HeLa cells [
mRNA decay assays for βSmg5, βTram1, and βCript1 mRNAs (schematics with the respective 3′ UTR lengths are shown below) in the presence of Luc or hUpf1 siRNAs. mRNA half-lives are given on the right. The number in parentheses for the βSmg5 mRNAs indicates the fold stabilization with standard deviation (
Our observations that 3′ UTR introns are neither necessary (
Decay assays for βGAP mRNA in the absence or presence of the AdML intron inserted into the GAPDH sequence or exon 3 as indicated. For each panel, schematics are shown for each tested mRNA below the panels; AdML exons are shown in black. mRNA half-lives are given on the right with the fold enhancement of mRNA decay rates and standard deviation (
How does cytoplasmic PABP antagonize NMD when positioned in proximity of the termination codon? Both cytoplasmic PABP and Upf1 have been previously observed to stimulate translation termination in yeast cells [
(A) Co-IP assays showing the co-IP of endogenous hUpf1 and PABPC1 and HuR proteins with an antibody against eRF3 (α-eRF3; 1%, 3%, 10%, 30%, and 100% of pellet loaded in lanes 4–8, respectively), or pre-immune serum (Pre-I, lane 1) as a control. 3% and 0.6% of the total lysate are shown in lanes 2 and 3, respectively.
(B) In vitro pull-down assays showing anti-FLAG Western blots of pull-down pellets (upper panels) resulting after myc-tagged eRF3 (lanes 4–7) or no myc-tagged protein (lanes 1–3), immobilized on an anti-myc antibody resin, was incubated with various amounts of FLAG-tagged hUpf1, PABPC1, or hnRNP A1 as indicated. Estimated amounts of FLAG-tagged proteins in each reaction are given in μM. Bottom panels show 5% of input protein for each reaction. The asterisk (*) and dagger (†) on the right indicates likely degradation products of PABPC1 and cross-reacting Myc-eRF3, respectively.
(C) Lanes 1–6: Western blot for exogenously expressed Myc-tagged eRF3 (wt, lanes 1–3) or eRF3 KAKA mutant protein (KAKA, lanes 4–6) that co-IP with FLAG-tagged PABPC1, hUpf1, or as a negative control, MS2, as indicated above the lanes. Lanes 7–9: Western blot for exogenously expressed Myc-tagged eRF1 that co-IP with FLAG-tagged eRF3, eRF3 KAKA mutant protein, or as a negative control, MS2, as indicated above the lanes. For all lanes, 5% of total input extracts are shown in the bottom panels.
To test whether PABPC1 can antagonize the interaction between eRF3 and hUpf1 in vitro, we immunopurified transiently expressed epitope-tagged eRF3, PABPC1, and hUpf1 proteins from HEK 293T cells and tested the ability of hUpf1 to associate with eRF3 in the presence of increasing amounts of PABPC1. As seen in
To test whether amino acid residues of eRF3, which are important for cytoplasmic PABP interaction, are also important for the interaction with hUpf1, we constructed a eRF3 protein (eRF3 KAKA) mutated in four N-terminal residues that are conserved between cytoplasmic PABP-binding proteins [
Previous contrasting models for PTC-recognition in NMD invoke either 3′ UTR–associated factors that stimulate NMD, the EJC in human cells [
(A) A unified model where NMD is determined by the balance between 3′ UTR–associated factors that stimulate (such as the EJC) or antagonize (such as cytoplasmic PABP) recruitment of the hUpf complex (shown as spheres labeled 1–3) to the terminating ribosome.
(B) Mechanisms by which mammalian mRNAs with long 3′ UTRs may evade NMD (see
How does cytoplasmic PABP antagonize NMD? While PABPC1 can out-compete the association of hUpf1 with eRF3 in vitro (
It is likely that 3′ UTR–associated factors (indicated by a question mark in
Our observations suggest that while artificial long 3′ UTRs trigger NMD (
After the submission of this paper, we have become aware of two other studies reporting that cytoplasmic PABP antagonizes human NMD when placed in proximity to a PTC [
All plasmid sequences are available upon request. Plasmids expressing different β-globin reporter mRNAs were derived from the pcTET2-βwt plasmid that was constructed by inserting the human β-globin gene between HindIII and ApaI sites of a pcDNA3-based plasmid containing six copies of the Tet-operator sequences upstream of the TATA box. For extended 3′ UTR constructs, parts of the GAPDH mRNA coding sequence and the entire GAPDH 3′ UTR (pcTET2-βGAP) or the GFP ORF (pcTET2-βGFP) were inserted between NotI and XbaI sites of the pcTET2-βwt plasmid, thus replacing the β-globin 3′ UTR. The β-globin stop codon was mutated to UAC by site-directed mutagenesis to generate pcTET2-βGAP-UAC and pcTET2-βGFP-UAC. Plasmids expressing βGAP-UAC-696, βGAP-UAC-485, and βGAP-UAC-422 mRNAs were generated by site-directed mutagenesis of pcTET2-βGAP-UAC to introduce a stop codon (UAA) in the GAPDH sequence, respectively, 696, 485, or 422 nucleotides upstream of the polyadenylation site. The plasmid expressing βwt mRNA was described earlier [
Plasmids expressing TPI reporter mRNAs were constructed by inserting the entire human TPI gene between HindIII and XbaI sites of the pcTET2 plasmid. A NotI site was inserted into exon 6 (in a manner that preserved the encoded protein) by site-directed mutagenesis. Codon 189 was mutated to TGA using site-directed mutagenesis to generate pcTET2-TPI-189. To remove intron 6, a NotI-XbaI fragment containing exon6-intron6-exon7 was replaced by the same region amplified from TPI cDNA, to generate pcTET2-TPIΔi6–189. To extend the TPI 3′ UTR, a fragment containing part of the GAPDH coding region and 3′ UTR was inserted into the NotI site of pcTET2-TPIΔi6–189 to generate pcTET2-TPIΔi6–189-GAP, or into the NotI site of pcTET2-TPIΔi6 to give rise to pcTET2-TPIΔi6-GAP. TPI-AdML mRNA–expressing plasmid was constructed by inserting the AdML intron and flanking exonic sequences into the XbaI site of pcTET2-TPI.
The plasmid expressing intron-containing GPx1 mRNA with a PTC (pPC-GPx1-UAA) was described earlier [
The constructs for knockdowns were based on the pSHAG plasmid (a gift from Dr. G. Hannon) and contained inserts expressing precursors to hUpf1, hUpf2, or eIF4AIII siRNAs described earlier [
Plasmids expressing FLAG-hUpf1, FLAG-PABPC1, FLAG-hnRNP A1, and Myc-hnRNP A1 were described earlier [
NMD factor knockdowns were performed by co-transfecting cells with reporter mRNA plasmids and plasmids encoding small hairpin (sh)RNAs targeting hUpf1, hUp2, or eIF4AIII, 60 h before pulse-chase mRNA decay assays were carried out.
mRNA decay assays were performed in HeLa Tet-off cells in DMEM/10% FBS/tetracycline (50 ng/ml) transfected with β-globin mRNA expression plasmids. For each 2-cm well of HeLa Tet-off cells, 10 ng of pcβG or pcβwt (as an internal control) and 0.2 μg of tetracycline-regulated reporter mRNA expression plasmids were co-transfected using TransIT HeLa Monster reagent (Mirus). For knockdowns, 0.5 μg of pSHAG plasmids were co-transfected. In each transfection, empty pcDNA3 vector was added to 1 μg of total plasmid. 36–40 h after transfection, or approximately 60 h in the case of knockdowns, transcription of reporter mRNAs was induced by removal of tetracycline through washing cells with 1 ml of phosphate-buffered saline (PBS) and adding DMEM/10% FBS. 6 h later, transcription was shut off by adding tetracycline to a final concentration of 1 μg/ml. Cells were washed with 1 ml PBS and taken up in 500 μl of TRIzol (Invitrogen) starting 30 min after tetracycline addition (0 min time point), and subsequently at time points indicated in each figure. For analysis of knockdown of endogenous hUpf1, hUpf2, and eIF4AIII, 0.2 μg of the plasmid pSUPERpuro was co-transfected instead of the plasmids expressing β-globin mRNA, and cells were treated and harvested as described earlier [
Rabbit polyclonal anti-sera raised against eIF4AIII (amino acids 1–41), hUpf1 (amino acids 1–416), hUpf2 (C-terminal 206 amino acids), and hUpf3b (full-length) were described earlier [
In immunoprecipitations shown in
Co-IPs between wild-type or KAKA-mutant eRF3 and eRF1 were performed as described above from the cells co-transfected with 0.5 μg of plasmids expressing FLAG-tagged proteins (eRF3, eRF3-KAKA, or MS2 as control), 0.5 μg of plasmids expressing Myc-eRF1, and 0.1 μg of Myc-hnRNP A1 expressing plasmid. Endogenous eRF3 IPs (
Approximately 107 HEK293T cells from a 10-cm plate expressing Myc-eRF3, or Myc-peptide as a negative control, were lysed in 1 ml hypotonic gentle lysis buffer as described above. The RNase A–treated, cleared extracts were subsequently incubated with 40 μl anti-Myc resin (Sigma) at 4 °C for 2–3 h, following which the beads were washed eight times with 1 ml of NET-2 buffer. The beads were divided into eight equal parts, and indicated amounts of FLAG-hUpf1, FLAG-PABP1, or FLAG-hnRNP A1 proteins, which had each been affinity-purified from RNase A–treated HEK293T cell extracts (protein concentrations estimated by comparison in anti-FLAG Western blot to a GST-FLAG fusion protein of known concentration), were incubated in 50 μl of NET-2 supplemented with 0.1 mg/ml BSA and 0.2 mg/ml FLAG peptide. The reactions were gently shaken at 4 °C for 2–3 h following which the beads were washed eight times with 1 ml of NET-2 buffer. The beads were resuspended in 25 μl of SDS-loading buffer (10 mM Tris-HCl [pH 6.8], 2% SDS, 10% glycerol, 0.5% bromophenol blue, and 50 mM DTT), and 10 μl of the protein sample was resolved on SDS-PAGE followed by Western blot analysis using anti-FLAG M2 antibody (Sigma, 1:1,000 dilution).
Western blots showing the efficiency of knockdown of hUpf1 (lanes 5 and 11), hUpf2 (lane 6), and eIF4AIII (lane 12). Protein levels are compared to 100%, 50%, 25%, and 10% of cell extract from cells expressing an siRNA against F-Luciferase (lanes 1–4 and 7–10). hUpf3b levels served as a loading control.
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mRNA decay assays showing decay rates of TPI mRNAs with different length 3′ UTRs, due to insertion of a fragment of GAPDH mRNA (see schematics below), in human HeLa Tet-off cells co-expressing siRNAs targeting hUpf1 or Luciferase (Luc; as a control) as indicated. Constitutively expressed βwt mRNA was used as an internal control for quantification. Numbers indicated above the panels indicate time after transcriptional repression. Schematics on the bottom show the used construct with TPI exons indicated as light-gray bars (not to scale), introns as lines, and GAPDH sequences as dark-gray bars. PTC(189) refers to a PTC at codon 189. Numbers on the right indicate mRNA half-lives (t1/2; in minutes) calculated from the shown experiment with the average fold increase and standard deviation over the half-life of TPI-189Δi6-GAP mRNA in the presence of Luc siRNA calculated from three or more experiments given in parentheses below.
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mRNA decay assays showing decay rates of the β-globin-derived βGAP mRNA with an extended 3′ UTR in human HeLa Tet-off cells knocked down (using RNAi) for eIF4AIII, or as a negative control, Luciferase (Luc), as indicated on the left of each panel (the knockdown efficiency for eIF4AIII is shown in
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Northern blots showing the decay rates of βGAP or βGAP-UAC mRNAs with successively shorter 3′ UTRs. The siRNAs co-expressed are indicated on the left. The mRNA half-lives are given on the right in minutes. The schematics of the pre-mRNAs from which the reporter mRNAs are derived are given below each panel with the distance between the termination codon and the poly(A) tail indicated.
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Western blots showing expression levels of different FLAG-tagged proteins expressed in
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Northern blots showing the decay rates of β39 mRNAs with 2XMS2 binding sites at different positions downstream of the PTC (shown in the schematic below). The exogenously expressed proteins are indicated on the left. The decay rates and fold change as compared to the control (expression of MS2 alone) are given with standard deviation (
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Cumulative histograms showing the distribution of the estimated lengths of 83 human intron-less (black solid line) 3′ UTRs from mRNAs upregulated upon hUpf1 knockdown, as compared to the 3′ UTR lengths of 83 randomly selected mRNAs not regulated by hUpf1 (dashed line). The table shows the median 3′ UTR length and percent of mRNAs with 3′ UTRs > 420 nt for upregulated and control mRNAs.
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We thank Oliver Mühlemann for communication of results prior to publication. Oliver Mühlemann and Tom Blumenthal are thanked for critical comments on the manuscript. Nicole Kennerly is thanked for constructing the βCript1 and βTram1 plasmids. Nicholas Farina is thanked for help with analysis of hUpf1-GEO profiles.
¤ Current address: Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
adenovirus major late intron
co-immunoprecipitation
downstream sequence element
exon junction complex
glyceraldehyde 3-phosphate dehydrogenase
green fluorescent protein
glutathione peroxidase 1
nonsense-mediated mRNA decay
poly(A)-binding protein
premature termination codon
RNA interference
small interfering RNA
triosephosphate isomerase