Nonsense-Mediated Decay (NMD) (Homo sapiens)

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5, 6, 12, 23, 26...39, 50, 567, 10, 11, 14, 19...3-6, 8, 9, 13...1, 9, 11, 25, 34...2, 11, 19-21, 38...3, 29, 32, 42, 47...Core Exon Junction Complex 80S ribosome mRNA Complex with a Premature Termination Codon Preceding an Exon Junction Exon JunctionUPF2UPF3 Complex mRNA Complex with a Premature Termination Codon Preceding an Exon Junction Exon JunctionUPF2UPF3 Complex 40S ribosomal complex 40S ribosomal complex GDP bound eRF3 Translated mRNA Complex with Premature Termination Codon Preceding Exon Junction Cap Binding Complex 40S ribosomal complex GDP bound eRF3 SMG1SMG8SMG9 Complex SMG1UPF1EJCTranslated mRNP 80S ribosome Translated mRNA Complex with Premature Termination Codon Preceding Exon Junction 40S ribosomal complex 80S ribosome Cap Binding Complex SMG1Phosphorylated UPF1EJCTranslated mRNP Cap Binding Complex 60S ribosomal complex UPF3 60S ribosomal complex UPF1eRF3 Complex on Translated mRNA Cap Binding Complex Core Exon Junction Complex 60S ribosomal complex 40S ribosomal complex UPF3 Magoh-Y14 complex Cap Binding Complex mRNA Cleaved by SMG6 Phosphorylated UPF1SMG5SMG7SMG6PP2ATranslated mRNP Cap Binding Complex 60S ribosomal complex Magoh-Y14 complex Core Exon Junction Complex mRNA Complex with a Premature Termination Codon Not Preceding an Exon Junction Translated mRNA Complex with Premature Termination Codon Preceding Exon Junction GDP bound eRF3 80S ribosome PP2A 80S ribosome Exon JunctionUPF2UPF3 Complex SMG1SMG8SMG9 Complex Translated mRNA Complex with Premature Termination Codon Preceding Exon Junction Exon JunctionUPF2UPF3 Complex 80S ribosome Magoh-Y14 complex Magoh-Y14 complex UPF3 60S ribosomal complex 60S ribosomal complex Cap Binding Complex Cap Binding Complex mRNA Complex with a Premature Termination Codon Preceding an Exon Junction GDP bound eRF3 cytosolTranslated mRNA Complex with Premature Termination Codon Not Preceding Exon Junction Core Exon Junction Complex PP2A Nonsense-mediated Decay Independent of the Exon Junction ComplexmRNA Complex with a Premature Termination Codon Not Preceding an Exon Junction Translated mRNA Complex with Premature Termination Codon Not Preceding Exon Junction mRNA Complex with a Premature Termination Codon Preceding an Exon Junction UPF3 Nonsense-mediated Decay Enhanced by the Exon Junction ComplexPP2A GDP bound eRF3 40S ribosomal complex GDP bound eRF3 SMG1SMG8SMG9 Complex RPL23A RPS21 RPS7 UBA52RPS27 RPL11 RPL30RPS5RPS24 RPL8 RPL23A RPL35A RPL4 RPS15A ETF1 RPS4Y15.8S rRNA RPS18 RPL29 RPL9 RPL35A RPS14 RPL4 RPL5 RPS15 RPS21 RPS11 FAU Translated mRNA Complex with Premature Termination Codon Preceding Exon JunctionRPS20 RPL35A RPS13RPL38 RPL3LRPS20 RPL37A RPL21 RPL36 RPS4X RPLP0 MAGOH RPS16 RPL10 RPS15A RPS24 28S rRNA RPL32 RPS15 PPP2CA RPS13RPL14 UPF3A NCBP2 RPS14 RPS11 GDP RPS23 RPLP0 UPF2 RPL6 RBM8A RPS9 RPS7 RPS2RPS3A RPL23A RPL13A RPLP2 RPL6 UPF2 p-3S1089,S1107-UPF1RPS18 RPL41 RPS27AEIF4G1RPLP0 RPS27ANCBP1 RPL13RPS27 RPS16 RPL21 RPL30RPS3A RPL23 RPS21 NCBP2 RPL17 RPL21 RPL13RPS24 RPS25 RPS25 RPL13A RPL3LRPS6 GSPT2 RPS15 RPS19 UBA52RPS6 RPS24 5S rRNA RPS9 RPLP0 RPS29 RPS26 RPS14 RPL29 RPL32 UBA52RPL12 RPL14 RPL26 RPS10 SMG8 RPS9 RPS12 RPLP1NCBP1 RPS23 RPL24 RPS3 RPS6 SMG7 EIF4A3 RPL27A RPL31 tRNA RPL22 RPS12 RPL10 RPL36A RPL30RPL9 5S rRNA EIF4A3 RPL17 SMG9RPS10 RPL18A RPL32 5S rRNA RPL18 RPL22 PABPC1 RPS3 RPS16 EIF4G1 RPL3LRPS4X Translated mRNA Complex with Premature Termination Codon Not Preceding Exon JunctionRPS3 RPL35 RPL26 RPS16 RPS14 RPL26 RPL28 RPS18 RPL21 RPL15SMG9RPL5 5S rRNA RPS14 RPS8RPLP1RNPS1 NCBP2 RPL15RPL37 RPS26 RPL26L1RPS3A NCBP2 RPL27A RPL17 RPL41 RPL18A SMG1Phosphorylated UPF1EJCTranslated mRNPRPS20 RPS16 RPL17 RPL23 RPL12 RPS7 UPF3A RPL19 RPS5tRNA RPL29 CASC3 RPL7A RPS26 RPL30MAGOH GSPT2 RPL13A RPL28 5.8S rRNA SMG9CASC3 RPL35A RPL17 GSPT2 RPL22 RPS25 RPS18 RPS15A RPL3 RPS17 RPL13A RPS27 UPF1SMG1UPF1EJCTranslated mRNPRPL35A RPS12 RPL11 RPL10A RPS23 RPL13RPS8RPS2RPS4X RPS23 RPL28 RPL37 5.8S rRNA 28S rRNA RPL27A PPP2R2ARPS28 RPL24 RPL3LRPL6 RPLP1UBA52RPS4Y1RPL34 RPL34 GSPT2 RPS6 RPL18 RPS8RPL30RPS15 RPL28 UPF2 RPL155.8S rRNA RPL3 RPL36 RPL41 RPL3 RPL37 RPL13A 18S rRNA tRNA RPL26L1RPL5 RPS14 RPL23A FAU RPL14 UPF1 RPL27A RPL23 RPL27A RPL24 RPL36A RNPS1 RPS9 RPL31 RPLP1RPL35 RPS4Y118S rRNA RPL3 RPL23A RPS27ANCBP2 UPF1eRF3 Complex on Translated mRNAGSPT2 RPS17 RPL37 RPS9 RPS4Y1RPS20 RPL27RPS15A RPL23 RPL3 RPL37 RPL27PABPC1 RPS6 RPS21 RPL29 RPL35 RPL7 RPL38 RPL7 RPS29 UPF2 EIF4G1 p-3S1089,S1107-UPF1 UPF3B RPL10 RPL4 RPLP1SMG8 RPS13RPS25S rRNA 28S rRNA RPS5UBA52RPL26L1GDP RPS19 FAU RPL26 RPS4X 5S rRNA RPL18A RPLP0 RPL36 PPP2CA EIF4G1 RPL39 SMG8 NCBP1 RPL21 RPL29 RPL39 RPS3 RPL10 RPS24 RPL10 RPL8 RPL38 RPS10 RPL36 SMG5 RPS11 RPS25 RPL41 PABPC1 RPS20 RPS23 RPS17 Phosphorylated UPF1SMG5SMG7SMG6PP2ATranslated mRNPRPL37A RPL7A PABPC1 RPL37A MAGOH RPS19 RPS10 RPL23A RPL37A RPL35A PPP2CA RPS28 PP2A RPLP2 RPL5 RPLP2 RPS18 RPL9 RPLP2 RPS3 RPL13RPL15RPL31 RPL14 tRNA RPS9 NCBP1 28S rRNA SMG5RPL8 RPL27RPL35 GDP RPL38 RPSA RPL18A RPS17 RPL38 RPS2RPL7 RPS5p-3S1089,S1107-UPF1 RPL34 ETF1 RPSA PPP2R2ARPS29 FAU RPL18 ETF1 CASC3 RPS15 GDP RNPS1 RPS7 RPL10A RNPS1 RPL9 28S rRNA RPS4Y1RPS3A RPS8RPL7 RPS29 RPL37A RPL31 EIF4G1 ETF1 RPS28 RPL9 RPL6 SMG6UPF3A RPL37A NCBP2 Cap Binding Complex RPL27PABPC1 5.8S rRNA RPS27ARPL39 RPL17 RPL14 RPL30GSPT2 RPL41 RPL24 5.8S rRNA RPL28 RPL24 28S rRNA PABPC1 SMG1RPS13NCBP1 NCBP1 RPL10A NCBP2 RPL10 RPS27 RPS11 RPL12 RPL12 RPS4X RPLP0 RPS21 PABPC1 RPL35 RPS15 UPF1 RPL32 RPL9 RPL24 UPF3B RPL7 SMG718S rRNA RPS11 RPL28 PPP2R1ARPL34 RPL26L1PPP2R2ARPL26 RPL18A RPS12 EIF4G1 RPL19 RPL32 GDP RPL35 SMG5 MAGOH RPS2RPS19 RPL15RPLP1RPL23 RPL7A RPL41 RPS6 RPL11 RPSA RPS28 RPS10 SMG1RPL23 NCBP1 UPF3AS-2 RPS3 RPS27 RPS19 RPL5 RPL36A UBA52RPL27EIF4A3 RPS16 RPS12 tRNA RPL29 RPL11 RPL36A GDP RPL3LRPS7 RPL7A RPS12 RPS29 RPS27ARPL38 RPS3A RPL36A RBM8A 18S rRNA RBM8A RPL26 RPL14 RPL13RPL36 SMG6 RPL6 NCBP1 RBM8A RPS24 RPS18 RPS20 RPL3 EIF4G1 RPL13RPS11 RPS26 RPL12 RPL22 RPL22 RPL36A RPS29 RPS2RPL18A RPL6 RPL18 NCBP2 RPS13RPS25 PPP2R1ARPL4 SMG1SMG8SMG9 ComplexSMG6 RPL4 RPS5ETF1 PPP2R1ARPL19 RPL26L1SMG7 RPS8RPS7 RPL3LRPL19 RPSA RPL32 RPS3A RPL37 RPL31 RPSA RPS5PABPC1RPL21 p-3S1089,S1107-UPF1 ETF1 RPS25 RPL39 RPS27ARPL34 CASC3 RPL7A RPL19 UPF3B 18S rRNA RPS28 UPF3B RPL8 RPS13RPS4X RPS28 RPL7 RPS23 RPL10A RPL39 RPL27FAU RPL12 RPL18 tRNA RPLP2 mRNA Cleaved by SMG6RPL10A RPL39 RPS26 ATPRPL11 RPL27A SMG1RPL15RPL4 RPL5 RPS4Y1RPL31 ADPRPS10 RPS17 RPL18 FAU RPL11 RPL19 RPS21 RPS27 RPLP2 EIF4G1 RPS15A RPL26L1EIF4A3 RPL13A UPF3A RPS26 RPS19 RPS17 RPL8 RPL22 RPSA 18S rRNA RPL8 RPL36 RPL10A RPS8RPL34 RPL7A RPS15A 192992, 11


Description

The Nonsense-Mediated Decay (NMD) pathway activates the destruction of mRNAs containing premature termination codons (PTCs) (reviewed in Isken and Maquat 2007, Chang et al. 2007, Behm-Ansmant et al. 2007, Neu-Yilik and Kulozik 2008, Rebbapragada and Lykke-Andersen 2009, Bhuvanagiri et al. 2010, Nicholson et al. 2010, Durand and Lykke-Andersen 2011). In mammalian cells a termination codon can be recognized as premature if it precedes an exon-exon junction by at least 50-55 nucleotides or if it is followed by an abnormal 3' untranslated region (UTR). While length of the UTR may play a part, the qualifications for being "abnormal" have not been fully elucidated. Also, some termination codons preceding exon junctions are not degraded by NMD so the criteria for triggering NMD are not yet fully known (reviewed in Rebbapragada and Lykke-Andersen 2009). While about 30% of disease-associated mutations in humans activate NMD, about 10% of normal human transcripts are also degraded by NMD (reviewed in Stalder and Muhlemann 2008, Neu-Yilik and Kulozik 2008, Bhuvanagiri et al. 2010, Nicholson et al. 2010). Thus NMD is a normal physiological process controlling mRNA stability in unmutated cells.
Exon junction complexes (EJCs) are deposited on an mRNA during splicing in the nucleus and are displaced by ribosomes during the first round of translation. When a ribosome terminates translation the A site encounters the termination codon and the eRF1 factor enters the empty A site and recruits eRF3. Normally, eRF1 cleaves the translated polypeptide from the tRNA in the P site and eRF3 interacts with Polyadenylate-binding protein (PABP) bound to the polyadenylated tail of the mRNA.
During activation of NMD eRF3 interacts with UPF1 which is contained in a complex with SMG1, SMG8, and SMG9. NMD can arbitrarily be divided into EJC-enhanced and EJC-independent pathways. In EJC-enhanced NMD, an exon junction is located downstream of the PTC and the EJC remains on the mRNA after termination of the pioneer round of translation. The core EJC is associated with UPF2 and UPF3, which interact with UPF1 and stimulate NMD. Once bound near the PTC, UPF1 is phosphorylated by SMG1. The phosphorylation is the rate-limiting step in NMD and causes UPF1 to recruit either SMG6, which is an endoribonuclease, or SMG5 and SMG7, which recruit ribonucleases. SMG6 and SMG5:SMG7 recruit phosphatase PP2A to dephosphorylate UPF1 and allow further rounds of degradation. How EJC-independent NMD is activated remains enigmatic but may involve competition between PABP and UPF1 for eRF3. Original Pathway at Reactome: http://www.reactome.org/PathwayBrowser/#DB=gk_current&FOCUS_SPECIES_ID=48887&FOCUS_PATHWAY_ID=927802

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Bibliography

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History

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CompareRevisionActionTimeUserComment
114999view16:53, 25 January 2021ReactomeTeamReactome version 75
113443view11:52, 2 November 2020ReactomeTeamReactome version 74
112643view16:02, 9 October 2020ReactomeTeamReactome version 73
101558view11:43, 1 November 2018ReactomeTeamreactome version 66
101094view21:25, 31 October 2018ReactomeTeamreactome version 65
100623view20:00, 31 October 2018ReactomeTeamreactome version 64
100174view16:44, 31 October 2018ReactomeTeamreactome version 63
99724view15:12, 31 October 2018ReactomeTeamreactome version 62 (2nd attempt)
99298view12:46, 31 October 2018ReactomeTeamreactome version 62
93761view13:34, 16 August 2017ReactomeTeamreactome version 61
93285view11:19, 9 August 2017ReactomeTeamreactome version 61
88067view14:29, 25 July 2016RyanmillerOntology Term : 'regulatory pathway' added !
86369view09:16, 11 July 2016ReactomeTeamreactome version 56
83339view10:50, 18 November 2015ReactomeTeamVersion54
81759view10:00, 26 August 2015ReactomeTeamVersion53
76924view08:19, 17 July 2014ReactomeTeamFixed remaining interactions
76629view12:00, 16 July 2014ReactomeTeamFixed remaining interactions
75960view10:01, 11 June 2014ReactomeTeamRe-fixing comment source
75662view10:56, 10 June 2014ReactomeTeamReactome 48 Update
75017view13:53, 8 May 2014AnweshaFixing comment source for displaying WikiPathways description
74661view08:43, 30 April 2014ReactomeTeamNew pathway

External references

DataNodes

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NameTypeDatabase referenceComment
18S rRNA ProteinX03205 (EMBL)
28S rRNA ProteinM11167 (EMBL)
5.8S rRNA ProteinJ01866 (EMBL)
5S rRNA ProteinV00589 (EMBL)
ADPMetaboliteCHEBI:16761 (ChEBI)
ATPMetaboliteCHEBI:15422 (ChEBI)
CASC3 ProteinO15234 (Uniprot-TrEMBL)
Cap Binding Complex ComplexREACT_3506 (Reactome)
EIF4A3 ProteinP38919 (Uniprot-TrEMBL)
EIF4G1 ProteinQ04637 (Uniprot-TrEMBL)
EIF4G1ProteinQ04637 (Uniprot-TrEMBL)
ETF1 ProteinP62495 (Uniprot-TrEMBL)
FAU ProteinP62861 (Uniprot-TrEMBL)
GDP MetaboliteCHEBI:17552 (ChEBI)
GSPT2 ProteinQ8IYD1 (Uniprot-TrEMBL)
MAGOH ProteinP61326 (Uniprot-TrEMBL)
NCBP1 ProteinQ09161 (Uniprot-TrEMBL)
NCBP2 ProteinP52298 (Uniprot-TrEMBL)
PABPC1 ProteinP11940 (Uniprot-TrEMBL)
PABPC1ProteinP11940 (Uniprot-TrEMBL)
PP2A ComplexREACT_76435 (Reactome)
PPP2CA ProteinP67775 (Uniprot-TrEMBL)
PPP2R1AProteinP30153 (Uniprot-TrEMBL)
PPP2R2AProteinP63151 (Uniprot-TrEMBL)
Phosphorylated UPF1

SMG5 SMG7 SMG6 PP2A

Translated mRNP		ComplexREACT_76275 (Reactome)
RBM8A ProteinQ9Y5S9 (Uniprot-TrEMBL)
RNPS1 ProteinQ15287 (Uniprot-TrEMBL)
RPL10 ProteinP27635 (Uniprot-TrEMBL)
RPL10A ProteinP62906 (Uniprot-TrEMBL)
RPL11 ProteinP62913 (Uniprot-TrEMBL)
RPL12 ProteinP30050 (Uniprot-TrEMBL)
RPL13A ProteinP40429 (Uniprot-TrEMBL)
RPL13ProteinP26373 (Uniprot-TrEMBL)
RPL14 ProteinP50914 (Uniprot-TrEMBL)
RPL15ProteinP61313 (Uniprot-TrEMBL)
RPL17 ProteinP18621 (Uniprot-TrEMBL)
RPL18 ProteinQ07020 (Uniprot-TrEMBL)
RPL18A ProteinQ02543 (Uniprot-TrEMBL)
RPL19 ProteinP84098 (Uniprot-TrEMBL)
RPL21 ProteinP46778 (Uniprot-TrEMBL)
RPL22 ProteinP35268 (Uniprot-TrEMBL)
RPL23 ProteinP62829 (Uniprot-TrEMBL)
RPL23A ProteinP62750 (Uniprot-TrEMBL)
RPL24 ProteinP83731 (Uniprot-TrEMBL)
RPL26 ProteinP61254 (Uniprot-TrEMBL)
RPL26L1ProteinQ9UNX3 (Uniprot-TrEMBL)
RPL27A ProteinP46776 (Uniprot-TrEMBL)
RPL27ProteinP61353 (Uniprot-TrEMBL)
RPL28 ProteinP46779 (Uniprot-TrEMBL)
RPL29 ProteinP47914 (Uniprot-TrEMBL)
RPL3 ProteinP39023 (Uniprot-TrEMBL)
RPL30ProteinP62888 (Uniprot-TrEMBL)
RPL31 ProteinP62899 (Uniprot-TrEMBL)
RPL32 ProteinP62910 (Uniprot-TrEMBL)
RPL34 ProteinP49207 (Uniprot-TrEMBL)
RPL35 ProteinP42766 (Uniprot-TrEMBL)
RPL35A ProteinP18077 (Uniprot-TrEMBL)
RPL36 ProteinQ9Y3U8 (Uniprot-TrEMBL)
RPL36A ProteinP83881 (Uniprot-TrEMBL)
RPL37 ProteinP61927 (Uniprot-TrEMBL)
RPL37A ProteinP61513 (Uniprot-TrEMBL)
RPL38 ProteinP63173 (Uniprot-TrEMBL)
RPL39 ProteinP62891 (Uniprot-TrEMBL)
RPL3LProteinQ92901 (Uniprot-TrEMBL)
RPL4 ProteinP36578 (Uniprot-TrEMBL)
RPL41 ProteinP62945 (Uniprot-TrEMBL)
RPL5 ProteinP46777 (Uniprot-TrEMBL)
RPL6 ProteinQ02878 (Uniprot-TrEMBL)
RPL7 ProteinP18124 (Uniprot-TrEMBL)
RPL7A ProteinP62424 (Uniprot-TrEMBL)
RPL8 ProteinP62917 (Uniprot-TrEMBL)
RPL9 ProteinP32969 (Uniprot-TrEMBL)
RPLP0 ProteinP05388 (Uniprot-TrEMBL)
RPLP1ProteinP05386 (Uniprot-TrEMBL)
RPLP2 ProteinP05387 (Uniprot-TrEMBL)
RPS10 ProteinP46783 (Uniprot-TrEMBL)
RPS11 ProteinP62280 (Uniprot-TrEMBL)
RPS12 ProteinP25398 (Uniprot-TrEMBL)
RPS13ProteinP62277 (Uniprot-TrEMBL)
RPS14 ProteinP62263 (Uniprot-TrEMBL)
RPS15 ProteinP62841 (Uniprot-TrEMBL)
RPS15A ProteinP62244 (Uniprot-TrEMBL)
RPS16 ProteinP62249 (Uniprot-TrEMBL)
RPS17 ProteinP08708 (Uniprot-TrEMBL)
RPS18 ProteinP62269 (Uniprot-TrEMBL)
RPS19 ProteinP39019 (Uniprot-TrEMBL)
RPS20 ProteinP60866 (Uniprot-TrEMBL)
RPS21 ProteinP63220 (Uniprot-TrEMBL)
RPS23 ProteinP62266 (Uniprot-TrEMBL)
RPS24 ProteinP62847 (Uniprot-TrEMBL)
RPS25 ProteinP62851 (Uniprot-TrEMBL)
RPS26 ProteinP62854 (Uniprot-TrEMBL)
RPS27 ProteinP42677 (Uniprot-TrEMBL)
RPS27AProteinP62979 (Uniprot-TrEMBL)
RPS28 ProteinP62857 (Uniprot-TrEMBL)
RPS29 ProteinP62273 (Uniprot-TrEMBL)
RPS2ProteinP15880 (Uniprot-TrEMBL)
RPS3 ProteinP23396 (Uniprot-TrEMBL)
RPS3A ProteinP61247 (Uniprot-TrEMBL)
RPS4X ProteinP62701 (Uniprot-TrEMBL)
RPS4Y1ProteinP22090 (Uniprot-TrEMBL)
RPS5ProteinP46782 (Uniprot-TrEMBL)
RPS6 ProteinP62753 (Uniprot-TrEMBL)
RPS7 ProteinP62081 (Uniprot-TrEMBL)
RPS8ProteinP62241 (Uniprot-TrEMBL)
RPS9 ProteinP46781 (Uniprot-TrEMBL)
RPSA ProteinP08865 (Uniprot-TrEMBL)
SMG1

Phosphorylated UPF1 EJC

Translated mRNP		ComplexREACT_76156 (Reactome)
SMG1

SMG8

SMG9 Complex		ComplexREACT_76062 (Reactome)
SMG1

UPF1 EJC

Translated mRNP		ComplexREACT_76647 (Reactome)
SMG1ProteinQ96Q15 (Uniprot-TrEMBL)
SMG5 ProteinQ9UPR3 (Uniprot-TrEMBL)
SMG5ProteinQ9UPR3 (Uniprot-TrEMBL)
SMG6 ProteinQ86US8 (Uniprot-TrEMBL)
SMG6ProteinQ86US8 (Uniprot-TrEMBL)
SMG7 ProteinQ92540 (Uniprot-TrEMBL)
SMG7ProteinQ92540 (Uniprot-TrEMBL)
SMG8 ProteinQ8ND04 (Uniprot-TrEMBL)
SMG9ProteinQ9H0W8 (Uniprot-TrEMBL)
Translated mRNA Complex with Premature Termination Codon Not Preceding Exon JunctionComplexREACT_76767 (Reactome)
Translated mRNA Complex with Premature Termination Codon Preceding Exon JunctionComplexREACT_76510 (Reactome)
UBA52ProteinP62987 (Uniprot-TrEMBL)
UPF1 eRF3 Complex on Translated mRNAComplexREACT_76212 (Reactome)
UPF1 ProteinQ92900 (Uniprot-TrEMBL)
UPF1ProteinQ92900 (Uniprot-TrEMBL)
UPF2 ProteinQ9HAU5 (Uniprot-TrEMBL)
UPF3A ProteinQ9H1J1 (Uniprot-TrEMBL)
UPF3AS-2 ProteinQ9H1J1-2 (Uniprot-TrEMBL)
UPF3B ProteinQ9BZI7 (Uniprot-TrEMBL)
mRNA Cleaved by SMG6ComplexREACT_76273 (Reactome)
p-3S1089,S1107-UPF1 ProteinQ92900 (Uniprot-TrEMBL)
p-3S1089,S1107-UPF1ProteinQ92900 (Uniprot-TrEMBL)
tRNA MetaboliteCHEBI:17843 (ChEBI)

Annotated Interactions

View all...
SourceTargetTypeDatabase referenceComment
ADPArrowREACT_75910 (Reactome)
ATPREACT_75910 (Reactome)
Cap Binding Complex ArrowREACT_75794 (Reactome)
EIF4G1ArrowREACT_75794 (Reactome)
PABPC1ArrowREACT_75794 (Reactome)
PP2A ArrowREACT_75794 (Reactome)
PP2A REACT_75794 (Reactome)
PP2A REACT_75891 (Reactome)
Phosphorylated UPF1

SMG5 SMG7 SMG6 PP2A

Translated mRNP		REACT_75787 (Reactome)
REACT_75753 (Reactome) The presence of an exon junction complex (EJC) downstream of a termination codon enhances nonsense-mediated decay (NMD) but is not absolutely required for NMD. The EJC is deposited during splicing and remains bound to the mRNA until a ribosome dislodges it during the pioneer round of translation, distinguished by the presence of the cap-binding complex at the 5' end. If translation terminates at least 50-55 nucleotides 5' to an EJC during the pioneer round then termination factors (eRF1 and eRF3) and the EJC recruit UPF1 and other NMD machinery (Lykke-Andersen et al. 2001, Ishigaki et al. 2001, Le Hir et al. 2001, Gehring et al. 2003, Hosoda et al. 2005, Kashima et al. 2006, Singh et al. 2007, Chamieh et al. 2008, Ivanov et al. 2008, Buchwald et al. 2010).
A current model for NMD enhanced by the EJC posits recruitment of UPF1, SMG1, SMG8, and SMG9 to eRF3 at the ribosome to form the SURF complex (Kashima et al. 2006, Chang et al. 2007, Isken et al. 2008, Muhlemann et al. 2008, Stalder and Muhlemann 2008, Chamieh et al. 2009, Maquat and Gong 2009, Rebbapragada and Lykke-Andersen 2009, Hwang et al. 2010, Nicholson et al. 2010). UPF1 and SMG1 then interact with components of the EJC, activating phosphorylation of UPF1 by SMG1.
The model of the NMD mechanism is inferred from known protein interactions:
eRF1 and eRF3 interact with UPF1, the key regulator of NMD which also binds SMG1, UPF2, and UPF3 (UPF3a or UPF3b) to form the SURF complex (Kashima et al.2006, Ivanov et al. 2008, Clerici et al. 2009, Chakrabarti et al. 2011). UPF1 also interacts with CBP80 at the cap of the mRNA (Hwang et al. 2010).
SMG8 and SMG9 associate with SMG1 and the SURF complex and modulate the phosphorylation activity of SMG1 (Yamashita et al. 2009).
UPF2 and UPF3 are peripheral components of the EJC and thus may link the EJC to the SURF complex (Chamieh et al. 2008). UPF3b binds UPF1 and a composite surface formed by the Y14, MAGOH, and eIF4A3 subunits of the core EJC (Gehring et al. 2003, Kunz et al. 2006, Buchwald et al. 2010). SMG1 also interacts with the EJC (Kashima et al. 2006, Yamashita et al. 2009). UPF3a more weakly activates NMD than does UPF3b (Kunz et al. 2006) and UPF3a levels increase in response to loss of UPF3b (Chan et al. 2009).
The binding of UPF1 to translated RNAs may occur in two steps: Binding of the SURF complex to the terminating ribosome followed by transfer of UPF1 and SMG1 to the EJC (Kashima et al. 2006, Hwang et al. 2010).
The core EJC (Y14, MAGOH, eIF4A3, and BTZ) can activate NMD without UPF2, however RNPS1, another EJC subunit, requires UPF2 to activate NMD (Gehring et al. 2005). RNAs show differential dependence on RNPS1-activated NMD (Gehring et al. 2005). Also, NMD of some transcripts requires EJC component eIF4A3 but not UPF3b (Chan et al. 2007) therefore there may be more than one route to activating NMD via the EJC.
REACT_75787 (Reactome) SMG6 is an endoribonuclease which cleaves the mRNA bound by UPF1 near the premature termination codon (Glavan et al. 2006, Eberle et al. 2009).
REACT_75794 (Reactome) SMG6 endonucleolytically cleaves an mRNA it is believed that the resulting fragments are degraded by exonucleases, possibly XRN1, a 5'-to-3' nuclease, and the exosome complex, a 3'-to-5' nuclease (Huntzinger et al. 2008, Eberle et al. 2009). Inhibition of XRN1 is observed to cause accumulation of SMG6-cleaved intermediates therefore XRN1 is postulated to act downstream of SMG6 (Huntzinger et al. 2008).
In general, during Nonsense-Mediated Decay mRNAs are observed to be deadenlyated (implicating the PAN2 complex, PARN complex, and CCR4 complex), decapped (implicating the DCP1:DCP2 complex), and exoribonucleolytically digested (implicating the XRN1 5'-to-3' exonuclease and exosome 3'-to-5' exonuclease) (Lykke-Andersen 2002, Chen et al. 2003, Lejeune et al. 2003, Couttet and Grange 2004, Unterholzner and Izaurralde 2004, Yamashita et al. 2005). UPF1 is observed to associate with the decapping enzymes DCP1a and DCP2, however the specific decay reactions that occur after SMG6, SMG5 and SMG7 have associated with an mRNA are unknown (Lykke-Andersen et al. 2002). Likewise, SMG6 may be present in complexes separate from SMG5 and SMG7 and these complexes may have different routes of decay (reviewed in Nicholson et al. 2010, Muhlemann and Lykke-Andersen 2010).
ATPase activity of UPF1 is necessary for NMD and may reflect ATP-dependent helicase activity that disassembles the mRNA-protein complex (Franks et al. 2010). UPF1 must be dephosphorylated by PP2A for NMD to continue (Ohnishi et al. 2003, Chiu et al. 2003). Presumably the dephosphoryation recycles UPF1 for interaction with other mRNA complexes.
REACT_75891 (Reactome) SMG6, SMG5 and SMG7 contain 14-3-3 domains which are believed to bind phosphorylated SQ motifs in UPF1 (Chiu et al. 2003, Ohnishi et al. 2003, Unterholzner and Izaurralde 2004, Fukuhara et al. 2005, Durand et al. 2007). SMG7 has been shown to bind UPF1 directly, target UPF1 for dephosphorylation by PP2A, and recruit enzymes that degrade RNA (Ohnishi et al. 2003, Unterholzner and Izaurralde 2004, Fukuhara et al. 2005). UPF3AS (the small isoform of UPF3A) also associates with the complex (Ohnishi et al. 2003). SMG6 is an endoribonuclease that cleaves the mRNA bound by UPF1 and also recruits phosphatase PP2A to dephosphorylate UPF1 (Chiu et al. 2003, Glavan et al. 2006, Eberle et al. 2009) .
Though immunofluorescence in vivo indicates that SMG5 and SMG7 exist in separate complexes from SMG6 (Unterholzner and Izaurralde 2004) immunoprecipitation shows that SMG6 is present in complexes that also contain SMG5, SMG7, UPF1, UPF2, Y14, Magoh, and PABP (Kashima et al. 2010). SMG5, SMG6, and SMG7 are therefore represented here together in the same RNP complex. It is possible that some complexes contain only SMG6 or SMG5:SMG7 (reviewed in Nicholson et al. 2010, Muhlemann and Lykke-Andersen 2010). Note that "Smg5/7a" in Chiu et al. 2003 actually refers to SMG6.
Phosphorylated UPF1 also inhibits translation initiation by inhibiting conversion of 40S:tRNAmet:mRNA to 80S:tRNAmet:mRNA complexes (Isken et al. 2008)
REACT_75910 (Reactome) SMG1 phosphorylates UPF1 in vitro and in vivo (Denning et al. 2001, Yamashita et al. 2001, Kashima et al. 2006). Serines 1073, 1078, 1096, and 1116 in isoform 2 (Serines 1084, 1089, 1107, 1127 in isoform 1) are phosphorylated in vitro and phosphorylation at serines 1078 and 1096 has been confirmed in vivo (Yamashita et al. 2001, Ohnishi et al. 2003, Kashima et al. 2006). UPF1 also contains additional serine and threonine residues that could be phosphorylated. SMG8 and SMG9 associate with SMG1 and regulate the kinase activity of SMG1 (Yamashita et al. 2009). The phosphorylation reaction is rate-limiting in nonsense-mediated decay and is therefore regarded as a licensing step (reviewed in Rebbapragada and Lykke-Andersen 2009). Phosphorylation is enhanced by the exon junction complex, which can interact with UPF1 via UPF2 and/or UPF3 (Kashima et al. 2006, Ivanov et al. 2008) or via Y14:Magoh (Ivanov et al. 2008). SMG8 and SMG9 bind SMG1 and regulate its kinase activity (Yamashita et al. 2009, Fernandez et al. 2011).
REACT_75917 (Reactome) Nonsense-mediated decay of an mRNA can be triggered even if the termination codon does not precede an exon junction (Buhler et al. 2006, Eberle et al. 2008, Silva et al. 2008, Singh et al. 2008, Ivanov et al. 2008). UPF1 and PABP seem to modulate the efficiency of translation termination and PABP in the proximity of a termination codon prevents NMD likely by outcompeting UPF1 for interaction with eRF3 (Singh et al. 2008, Ivanov et al. 2008, Silva et al. 2008). Factors in the competition may be the length and secondary structure of the 3' UTR (Buhler et al. 2006, Eberle et al. 2008). UPF1 preferentially binds some but not all longer UTRs (Hogg and Goff 2010).
Interaction of eRF3 with PABP stimulates ribosome dissociation and initiation of a new round of translation on the mRNA. Interaction of eRF3 with UPF1 appears to promote nonsense-mediated decay. It is possible but not yet demonstrated that all components of the SURF complex (SMG1, UPF1, eRF1, eRF3) are assembled on an mRNA without an exon junction complex and that UPF1 is phosphorylated by SMG1.
SMG1

Phosphorylated UPF1 EJC

Translated mRNP		ArrowREACT_75910 (Reactome)
SMG1

Phosphorylated UPF1 EJC

Translated mRNP		REACT_75891 (Reactome)
SMG1

SMG8

SMG9 Complex		REACT_75753 (Reactome)
SMG1

UPF1 EJC

Translated mRNP		REACT_75910 (Reactome)
SMG5ArrowREACT_75794 (Reactome)
SMG5REACT_75891 (Reactome)
SMG6ArrowREACT_75794 (Reactome)
SMG6REACT_75891 (Reactome)
SMG7ArrowREACT_75794 (Reactome)
SMG7REACT_75891 (Reactome)
Translated mRNA Complex with Premature Termination Codon Not Preceding Exon JunctionREACT_75917 (Reactome)
Translated mRNA Complex with Premature Termination Codon Preceding Exon JunctionREACT_75753 (Reactome)
UPF1ArrowREACT_75794 (Reactome)
UPF1REACT_75753 (Reactome)
UPF1REACT_75917 (Reactome)
p-3S1089,S1107-UPF1REACT_75794 (Reactome)
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