Nonsense-Mediated Decay (NMD) (Homo sapiens)

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2, 12, 16, 26, 33...3-5, 18, 28...12, 19, 23, 25, 34...1, 3, 10-15, 17...7, 9, 35, 38, 39, 514-6, 8, 20...28, 30, 44Exon JunctionUPF2UPF3 Complex GDP bound eRF3 60S ribosomal complex Cap Binding Complex 60S ribosomal complex Cap Binding Complex 80S ribosome 80S ribosome Translated mRNA Complex with Premature Termination Codon Preceding Exon Junction SMG1UPF1EJCTranslated mRNP mRNA Complex with a Premature Termination Codon Not Preceding an Exon Junction 80S ribosome Translated mRNA Complex with Premature Termination Codon Not Preceding Exon Junction UPF3 UPF3 GDP bound eRF3 cytosolSMG1Phosphorylated UPF1EJCTranslated mRNP 80S ribosome GDP bound eRF3 mRNA Complex with a Premature Termination Codon Preceding an Exon Junction SMG1SMG8SMG9 Complex mRNA Complex with a Premature Termination Codon Not Preceding an Exon Junction 40S ribosomal complex Magoh-Y14 complex 40S ribosomal complex Cap Binding Complex mRNA Cleaved by SMG6 Exon JunctionUPF2UPF3 Complex 40S ribosomal complex 80S ribosome Magoh-Y14 complex Core Exon Junction Complex mRNA Complex with a Premature Termination Codon Preceding an Exon Junction UPF3 PP2A PP2A 40S ribosomal complex Core Exon Junction Complex Exon JunctionUPF2UPF3 Complex 60S ribosomal complex PP2A Translated mRNA Complex with Premature Termination Codon Preceding Exon Junction GDP bound eRF3 SMG1SMG8SMG9 Complex GDP bound eRF3 Cap Binding Complex UPF3 SMG1SMG8SMG9 Complex Cap Binding Complex GDP bound eRF3 Core Exon Junction Complex Core Exon Junction Complex Magoh-Y14 complex 40S ribosomal complex 40S ribosomal complex mRNA Complex with a Premature Termination Codon Preceding an Exon Junction mRNA Complex with a Premature Termination Codon Preceding an Exon Junction 60S ribosomal complex Translated mRNA Complex with Premature Termination Codon Not Preceding Exon Junction Nonsense-mediated Decay Independent of the Exon Junction ComplexCap Binding Complex Exon JunctionUPF2UPF3 Complex Cap Binding Complex Nonsense-mediated Decay Enhanced by the Exon Junction Complex60S ribosomal complex UPF1eRF3 Complex on Translated mRNA 60S ribosomal complex Magoh-Y14 complex Cap Binding Complex Phosphorylated UPF1SMG5SMG7SMG6PP2ATranslated mRNP Translated mRNA Complex with Premature Termination Codon Preceding Exon Junction 80S ribosome Translated mRNA Complex with Premature Termination Codon Preceding Exon Junction RPL23 ADPRPS20 RPS6 RPL4 RPS26 RPL10A RPL3LRPS4Y1RPS23 RPL7A RPL23 RPL35 RPL39 RPS19 UPF1 RPS4X 5S rRNA RPS17 RPL28 RPL8 RPL35 RPS13RPL39 RPL36A RPS14 RPS20 RPS10 RPS3 SMG1RPS2RPL35 RPS12 RPL37A RPL3 RPS2RPL37 RPL19 RPL35A RPS3A 18S rRNA RBM8A RPS15 RPLP2 RPS19 RPS23 5.8S rRNA RPL31 RPS14 PPP2R2ARPS12 RPL13A RNPS1 28S rRNA RPS13RPS10 GSPT2 RPS21 18S rRNA MAGOH RPL5 CASC3 RPS8RPS6 RPS15A FAU RPL23 RPL13RPLP1RPL5 MAGOH EIF4G1 RPS17 UBA52RPS27 NCBP1 18S rRNA RPS27 NCBP2 RPL12 RPS26 RPS15 RPL19 RPL3LFAU RPL22 RPS20 28S rRNA RPL15RPL19 RPL12 RPS23 RPS24 RPS24 RPL13RPL3 RPS5ETF1 RPS14 RPS18 RPL4 RPS5RPS23 RPL9 RPS818S rRNA RPS28 RPS25 RPS13RPL28 RPL31 RPL4 RPL11 RPL13A RPL24 tRNA UPF3B RPS8RPS11 RPLP0 NCBP2 RPS21 RPL23A RPS29 RPS5SMG5 EIF4G1 RPL27RPL30GDP RPL21 UPF1RPS11 RPLP2 RPL41 RPL3LRPL8 RPL9 EIF4G1 RPL15SMG8 tRNA RPL18 RPL31 RPL9 RPL17 RPL21 NCBP1 RPS29 RPS15 PABPC1 RPL3 RPS3A PABPC1RPS29 RPL34 RPL24 RPS15 RPS13RPL24 RPL27A RPS17 RPL19 RPL14 SMG8 RPL36A RPL9 RPS13RPS7 RPLP0 UPF2 28S rRNA RPL14 RPL36 RPS25 RPL26 FAU 28S rRNA RPL27RPL15UBA52RPL18 UPF1 RPS2RPS15 RPL15RPL22 RPL11 RPS6 RNPS1 RPL18A RPS4Y1GDP RPL28 EIF4A3 RPL7 RPS25 RPL3LRBM8A ETF1 RPL13RPL27A 5S rRNA SMG8 EIF4A3 RPL35 RPL15ETF1 RPL21 RPS24 RPS17 RPS19 RPL29 RPS16 RPL13RPS26 UPF3B RPL35 RPS11 RPL10A RPL10 RPS21 RPL12 RPS7 RPS15A RPS3A RPS21 RPL27A RPL36 5S rRNA 5.8S rRNA RPL27PPP2R1ARPS27ARPL23A RPL3 RPL5 RPLP0 RPL4 RPS4X RPL32 RPL32 ETF1 RPS5RPL17 RPS7 RPL3LRPS14 RPL27A MAGOH RPL14 5S rRNA RPL29 RPL35A UBA52RPL29 RPL36 RPL13RPSA GDP RPL26 RPL36A RPS13RPL23 RPS3 RPL13A UPF1eRF3 Complex on Translated mRNARPL27RPL22 RPL27RPL23A RPL41 UPF2 RPS8RPL30RPLP0 RPL34 RPS4X RPSA RPL29 RPL23 RPS27 mRNA Cleaved by SMG6EIF4G1 ETF1 RPS16 RPL36 RPS8RPS4X RPS2RPL26L1RPS19 RPL22 RPL29 RPL36 RPL26L1NCBP1 RPS5RPS20 RPL28 RPL34 RPL6 RPL37A RPL6 RPS28 MAGOH PABPC1 SMG6 UPF3A RPLP2 RPL39 RPLP0 SMG1SMG8SMG9 ComplexRPS12 RPS15A RPL9 5.8S rRNA RPS4Y1RPL4 RPL26 GSPT2 RPS18 RPS3 RPL24 RPS3A RPL9 RPL18 18S rRNA RPL35A PPP2R2APABPC1 RPL38 UPF3B NCBP2 RPL19 RPL28 RPL38 RPS29 RPLP2 RPS23 RPLP2 RPL7A RPL37A tRNA RPL35A EIF4G1 RPS10 RPS24 UBA52NCBP1 RPS2RPS21 RPS16 SMG5RPL37 RPL7 NCBP1 RPL37 RBM8A RPS18 tRNA RPL23 RPL37 RPL35 PPP2R2ARPS27ASMG7RPLP1RPL36A RPLP1RPS17 RPL8 RPLP1RPS29 RPL12 RPL14 RPL30RPL13A GDP RPS8NCBP2 5.8S rRNA PPP2CA RPL7A RPL26L1RPL34 GSPT2 RPL37A RPS9 RPL18 RPS16 RPL37A RPS15A RPL6 RPS4Y1SMG7 RPL32 Translated mRNA Complex with Premature Termination Codon Not Preceding Exon JunctionRPS9 PPP2R1ARPS28 RPS3 RPL17 PPP2CA EIF4A3 RPS14 GSPT2 UPF2 RPS6 RPL10 UPF2 RPL8 5.8S rRNA RPS4X FAU RPS7 RPL6 RPS28 RPL37 RPL30PABPC1 SMG1UPF1EJCTranslated mRNPRPS27ARPL8 RPL5 SMG6 RNPS1 RPL37 28S rRNA SMG7 RPL26L1NCBP1 5S rRNA RPS27 RPL38 RPL15RPL13A RPL3LETF1 UBA52RPL23A 5S rRNA RPL27A RPL23A 5.8S rRNA PPP2CA SMG9RPS12 NCBP2 NCBP2 RPL10 28S rRNA RPLP2 RPS26 RPS10 RPL11 RPL11 RPS3A 18S rRNA RPS20 NCBP1 RPL34 RPS14 SMG1RPL31 RPL8 RPL23A UPF3A RPL6 p-3S1089,S1107-UPF1 RPSA RPS10 RPL27A NCBP1 RPL32 RPL26 PPP2R1ARPL24 RPL18 RPS11 PABPC1 RPL18A RPL31 GSPT2 RPL34 Phosphorylated UPF1SMG5SMG7SMG6PP2ATranslated mRNPRBM8A RPS15A RPS18 RPL14 RPLP0 RPL22 RPL7 UBA52RPS5RPL10A RPS9 RPS27AtRNA SMG9RPL22 NCBP2 UPF3B RPS29 RPS26 RPS18 RPL36A RPL41 RPL4 RPL26L1EIF4G1 RPS15 RPS11 GDP RPL28 RPL10A RPL41 GSPT2 RPL3 RPS6 RPL7 RPS11 RPS28 RPS27 RPL37A FAU RPL41 CASC3 RPSA CASC3 RPL24 RPL13A RPL12 RPL35A PABPC1 RPL5 NCBP2 CASC3 RPS23 RPS17 RPS2RPL29 PABPC1 RPL12 RPS10 RPS25 RPL11 RPL21 RPL21 RPL41 RPS28 RPS15A RPL18 RPL5 RPL17 Cap Binding Complex RPS12 RPS24 p-3S1089,S1107-UPF1 RPL39 UPF3AS-2 RPL39 RPS4Y1Translated mRNA Complex with Premature Termination Codon Preceding Exon JunctionPP2A RPL18A RPL26 SMG5 RPS7 RPS6 RPL3 RPL18A RPS9 RPL31 FAU RPL36 RPL30RPS9 RPS4Y1EIF4G1RPL19 SMG1SMG1Phosphorylated UPF1EJCTranslated mRNPRPS24 RPL38 RPS27 RPL32 EIF4A3 RPL7 RPL18A UPF3A RPSA RPS27AUPF3A RPL7A RPS12 RPS3A RPS27ARPL6 RPS21 RPL10 RPL38 RPL26L1RPS3 RPL11 RPL17 GDP RPLP1SMG6RPL10 RPL38 RPS25 p-3S1089,S1107-UPF1RPL10A RPL27SMG9RPL14 RPL39 RPL36A RPS4X RPL30ATPtRNA RPS16 RPL17 RPS3 RPL10A RPL18A RPS20 RPS26 RPLP1p-3S1089,S1107-UPF1 RPS19 RPL26 EIF4G1 RPL13RNPS1 RPS25 RPS18 RPS16 RPL7A RPL21 RPS9 RPSA RPL7A RPL35A RPL10 RPS7 RPL32 RPL7 RPS19 19434, 457


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_75891 (Reactome)
PP2A mim-catalysisREACT_75794 (Reactome)
Phosphorylated UPF1

SMG5 SMG7 SMG6 PP2A

Translated mRNP		mim-catalysisREACT_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)
SMG1

UPF1 EJC

Translated mRNP		mim-catalysisREACT_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-UPF1mim-catalysisREACT_75794 (Reactome)
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