Deadenylation-dependent mRNA decay (Homo sapiens)

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15, 22, 35, 40, 46...6, 15, 16, 22, 35...5, 15, 18, 22, 29...8, 10, 14, 15, 20...9, 11, 12, 15, 22...3, 15, 22, 25, 34...4, 15, 22, 31, 32, 35...7, 15, 22, 27, 35...13, 15, 22, 31, 32, 35...eIF4A Lsm1-7 Complex cytosolLsm1-7 Complex PAN2-PAN3 Complex eIF4A Deadenylated mRNALsm1-7 Complex CNOT7 or CNOT8 Partially Deadenylated mRNA Complex Lsm1-7 Complex PARN homodimer CCR4-NOT Complex DCP1-DCP2 Decapping Complex Exosome Complex CNOT6 or CNOT6L Decapped mRNALSM1-7 Complex Exosome Ring Hexamer Translatable mRNA Complex PAN2 DCP2 Deadenylated mRNALsm1-7 ComplexCNOT4 AMPEIF4A2 EXOSC3 TNKS1BP1 PAN2-PAN3 ComplexTranslatable mRNA ComplexPATL1 H2OCNOT10 GMPEXOSC5 mature mRNA CMPLSM1 LSM3H2OEXOSC9 EXOSC8 H2OEIF4A1EXOSC4 DDX6 Exosome ComplexPATL1 EIF4A1H2OCMPEIF4A3 Decapped mRNALSM1-7 ComplexH2OEIF4G1EIF4E PARN DCP1A DCPSeIF4APAN3EDC3 DIS3 H2Ooligoribonucleotide with a 5'-diphosphateRQCD1 EIF4G1 CNOT6L LSM1 EIF4E 7-MeGDPPABPC1 EIF4A2 EXOSC7 Partially Deadenylated mRNA ComplexLSM3CNOT3 XRN1GMPEXOSC2 CCR4-NOT ComplexDCP1BEXOSC1 AMPLSM7 CNOT1 PARN homodimerLSM6 EIF4G1 CNOT6 LSM5UMPLSM7 LSM1 CNOT11 EIF4A3 LSM5CNOT7 PABPC1 UMPPATL1 LSM6 LSM2 LSM5LSM4 EXOSC6 EIF4BLSM4 EIF4EEDC4 EIF4BCNOT8 LSM7 CNOT2 Lsm1-7 ComplexLSM3PAIP1LSM6 LSM2 DCP1-DCP2 Decapping ComplexAMPEIF4B7-MeGMPPAIP1 capped oligoribonucleotidePABPC1PAIP1 LSM4 LSM2 371533, 391, 1923, 27, 30, 4917, 28, 472


Description

After undergoing rounds of translation, mRNA is normally destroyed by the deadenylation-dependent pathway. Though the trigger is unclear, deadenylation likely proceeds in two steps: one catalyzed by the PAN2-PAN3 complex that shortens the poly(A) tail from about 200 adenosine residues to about 80 residues and one catalyzed by the CCR4-NOT complex or by the PARN enzyme that shortens the tail to about 10-15 residues.
After deadenylation the mRNA is then hydrolyzed by either the 5' to 3' pathway or the 3' to 5' pathway. It is unknown what determinants target a mRNA to one pathway or the other.
The 5' to 3' pathway is initiated by binding of the Lsm1-7 complex to the 3' oligoadenylate tail followed by decapping by the DCP1-DCP2 complex. The 5' to 3' exoribonuclease XRN1 then hydrolyzes the remaining RNA.
The 3' to 5' pathway is initiated by the exosome complex at the 3' end of the mRNA. The exosome processively hydrolyzes the mRNA from 3' to 5', leaving only a capped oligoribonucleotide. The cap is then removed by the scavenging decapping enzyme DCPS. Original Pathway at Reactome: http://www.reactome.org/PathwayBrowser/#DB=gk_current&FOCUS_SPECIES_ID=48887&FOCUS_PATHWAY_ID=429914

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Bibliography

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History

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CompareRevisionActionTimeUserComment
115026view16:56, 25 January 2021ReactomeTeamReactome version 75
113471view11:54, 2 November 2020ReactomeTeamReactome version 74
112670view16:06, 9 October 2020ReactomeTeamReactome version 73
101587view11:45, 1 November 2018ReactomeTeamreactome version 66
101123view21:29, 31 October 2018ReactomeTeamreactome version 65
100651view20:03, 31 October 2018ReactomeTeamreactome version 64
100201view16:48, 31 October 2018ReactomeTeamreactome version 63
99752view15:14, 31 October 2018ReactomeTeamreactome version 62 (2nd attempt)
99316view12:46, 31 October 2018ReactomeTeamreactome version 62
93995view13:50, 16 August 2017ReactomeTeamreactome version 61
93604view11:28, 9 August 2017ReactomeTeamreactome version 61
87169view19:22, 18 July 2016MkutmonOntology Term : 'pathway pertinent to DNA replication and repair, cell cycle, maintenance of genomic integrity, RNA and protein biosynthesis' added !
86710view09:24, 11 July 2016ReactomeTeamreactome version 56
83258view10:34, 18 November 2015ReactomeTeamVersion54
81369view12:53, 21 August 2015ReactomeTeamVersion53
76837view08:06, 17 July 2014ReactomeTeamFixed remaining interactions
76541view11:52, 16 July 2014ReactomeTeamFixed remaining interactions
75874view09:52, 11 June 2014ReactomeTeamRe-fixing comment source
75574view10:39, 10 June 2014ReactomeTeamReactome 48 Update
74929view13:45, 8 May 2014AnweshaFixing comment source for displaying WikiPathways description
74573view08:37, 30 April 2014ReactomeTeamNew pathway

External references

DataNodes

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NameTypeDatabase referenceComment
7-MeGDPMetaboliteCHEBI:20794 (ChEBI)
7-MeGMPMetaboliteCHEBI:17825 (ChEBI)
AMPMetaboliteCHEBI:16027 (ChEBI)
CCR4-NOT ComplexComplexREACT_21110 (Reactome) The human CCR4-NOT complex contains 7 core subunits: CNOT1, CNOT2, CNOT3, CNOT9/RCD1, CNOT10, TAB182, and C2ORF29. Complexes contain either CNOT7 or CNOT8 (with CNOT8-containing complexes apparently involved in nuclear RNA splicing and CNOT7-containing complexes involved in cytoplasmic mRNA decay) and CNOT6 or CNOT6L. CNOT6 and CNOT6L are catalytic exoribonucleases. CNOT7 and CNOT8 also have ribonuclease activity. CNOT1 is the largest subunit and, based on yeast two-hybrid assays, interacts with CNOT2, CNOT7, CNOT8, and CNOT9, thus acting as a scaffold.
CMPMetaboliteCHEBI:17361 (ChEBI)
CNOT1 ProteinA5YKK6 (Uniprot-TrEMBL)
CNOT10 ProteinQ9H9A5 (Uniprot-TrEMBL)
CNOT11 ProteinQ9UKZ1 (Uniprot-TrEMBL)
CNOT2 ProteinQ9NZN8 (Uniprot-TrEMBL)
CNOT3 ProteinO75175 (Uniprot-TrEMBL)
CNOT4 ProteinO95628 (Uniprot-TrEMBL)
CNOT6 ProteinQ9ULM6 (Uniprot-TrEMBL)
CNOT6L ProteinQ96LI5 (Uniprot-TrEMBL)
CNOT7 ProteinQ9UIV1 (Uniprot-TrEMBL)
CNOT8 ProteinQ9UFF9 (Uniprot-TrEMBL)
DCP1-DCP2 Decapping ComplexComplexREACT_20836 (Reactome)
DCP1A ProteinQ9NPI6 (Uniprot-TrEMBL)
DCP1BProteinQ8IZD4 (Uniprot-TrEMBL)
DCP2 ProteinQ8IU60 (Uniprot-TrEMBL)
DCPSProteinQ96C86 (Uniprot-TrEMBL)
DDX6 ProteinP26196 (Uniprot-TrEMBL)
DIS3 ProteinQ9Y2L1 (Uniprot-TrEMBL)
Deadenylated mRNA Lsm1-7 ComplexComplexREACT_20909 (Reactome)
Decapped mRNA LSM1-7 ComplexComplexREACT_21085 (Reactome)
EDC3 ProteinQ96F86 (Uniprot-TrEMBL)
EDC4 ProteinQ6P2E9 (Uniprot-TrEMBL)
EIF4A1ProteinP60842 (Uniprot-TrEMBL)
EIF4A2 ProteinQ14240 (Uniprot-TrEMBL)
EIF4A3 ProteinP38919 (Uniprot-TrEMBL)
EIF4BProteinP23588 (Uniprot-TrEMBL)
EIF4E ProteinP06730 (Uniprot-TrEMBL)
EIF4EProteinP06730 (Uniprot-TrEMBL)
EIF4G1 ProteinQ04637 (Uniprot-TrEMBL)
EIF4G1ProteinQ04637 (Uniprot-TrEMBL)
EXOSC1 ProteinQ9Y3B2 (Uniprot-TrEMBL)
EXOSC2 ProteinQ13868 (Uniprot-TrEMBL)
EXOSC3 ProteinQ9NQT5 (Uniprot-TrEMBL)
EXOSC4 ProteinQ9NPD3 (Uniprot-TrEMBL)
EXOSC5 ProteinQ9NQT4 (Uniprot-TrEMBL)
EXOSC6 ProteinQ5RKV6 (Uniprot-TrEMBL)
EXOSC7 ProteinQ15024 (Uniprot-TrEMBL)
EXOSC8 ProteinQ96B26 (Uniprot-TrEMBL)
EXOSC9 ProteinQ06265 (Uniprot-TrEMBL)
Exosome ComplexComplexREACT_20841 (Reactome) The exosome complex comprises a ring and associated subunits. The ring contains EXOSC2, EXOSC7, EXOSC8, EXOSC9, EXOSC5, and EXOSC6. The subunits EXOSC1, EXOSC2, EXOSC3, and RRP44 bind the ring. The catalytic ribonuclease site is located in RRP44, which yields ribonucleotides having 5'-monophosphates.
GMPMetaboliteCHEBI:17345 (ChEBI)
H2OMetaboliteCHEBI:15377 (ChEBI)
LSM1 ProteinO15116 (Uniprot-TrEMBL)
LSM2 ProteinQ9Y333 (Uniprot-TrEMBL)
LSM3ProteinP62310 (Uniprot-TrEMBL)
LSM4 ProteinQ9Y4Z0 (Uniprot-TrEMBL)
LSM5ProteinQ9Y4Y9 (Uniprot-TrEMBL)
LSM6 ProteinP62312 (Uniprot-TrEMBL)
LSM7 ProteinQ9UK45 (Uniprot-TrEMBL)
Lsm1-7 ComplexComplexREACT_21014 (Reactome)
PABPC1 ProteinP11940 (Uniprot-TrEMBL)
PABPC1ProteinP11940 (Uniprot-TrEMBL)
PAIP1 ProteinQ9H074 (Uniprot-TrEMBL)
PAIP1ProteinQ9H074 (Uniprot-TrEMBL)
PAN2 ProteinQ504Q3 (Uniprot-TrEMBL)
PAN2-PAN3 ComplexComplexREACT_20697 (Reactome)
PAN3ProteinQ58A45 (Uniprot-TrEMBL)
PARN ProteinO95453 (Uniprot-TrEMBL)
PARN homodimerComplexREACT_21052 (Reactome) Structural analysis has shown that PARN forms homodimers.
PATL1 ProteinQ86TB9 (Uniprot-TrEMBL)
Partially Deadenylated mRNA ComplexComplexREACT_20682 (Reactome)
RQCD1 ProteinQ92600 (Uniprot-TrEMBL)
TNKS1BP1 ProteinQ9C0C2 (Uniprot-TrEMBL)
Translatable mRNA ComplexComplexREACT_21129 (Reactome) mRNA's that are ready for translation have a circular structure caused by interaction between PABP bound to the 3' poly(A) tail and the eIF4E-eIF4G-PAIP complex bound to the 7-methylguanosine cap. The interaction between poly(A)-PABP and the eIF4G-eIF4E complex stimulates affinity of eIF4E for the cap and improves translation.
UMPMetaboliteCHEBI:16695 (ChEBI)
XRN1ProteinQ8IZH2 (Uniprot-TrEMBL)
capped oligoribonucleotideREACT_20913 (Reactome)
eIF4AProteinREACT_21151 (Reactome)
mature mRNA REACT_20743 (Reactome) After deadenylation, mRNAs have 10-15 3' adenosine residues remaining of about 200 initial adenosine residues.
oligoribonucleotide with a 5'-diphosphateREACT_20778 (Reactome)

Annotated Interactions

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SourceTargetTypeDatabase referenceComment
7-MeGDPArrowREACT_20560 (Reactome)
7-MeGMPArrowREACT_20556 (Reactome)
AMPArrowREACT_20533 (Reactome)
AMPArrowREACT_20588 (Reactome)
AMPArrowREACT_20606 (Reactome)
AMPArrowREACT_20651 (Reactome)
AMPArrowREACT_20662 (Reactome)
CCR4-NOT ComplexREACT_20651 (Reactome)
CMPArrowREACT_20533 (Reactome)
CMPArrowREACT_20588 (Reactome)
DCP1-DCP2 Decapping ComplexREACT_20560 (Reactome)
DCPSREACT_20556 (Reactome)
Deadenylated mRNA Lsm1-7 ComplexREACT_20560 (Reactome)
Decapped mRNA LSM1-7 ComplexArrowREACT_20560 (Reactome)
Decapped mRNA LSM1-7 ComplexREACT_20533 (Reactome)
EIF4BArrowREACT_20651 (Reactome)
EIF4BArrowREACT_20662 (Reactome)
EIF4EArrowREACT_20651 (Reactome)
EIF4EArrowREACT_20662 (Reactome)
EIF4G1ArrowREACT_20651 (Reactome)
EIF4G1ArrowREACT_20662 (Reactome)
Exosome ComplexREACT_20588 (Reactome)
GMPArrowREACT_20533 (Reactome)
GMPArrowREACT_20588 (Reactome)
H2OREACT_20533 (Reactome)
H2OREACT_20556 (Reactome)
H2OREACT_20560 (Reactome)
H2OREACT_20588 (Reactome)
H2OREACT_20606 (Reactome)
H2OREACT_20651 (Reactome)
H2OREACT_20662 (Reactome)
Lsm1-7 ComplexArrowREACT_20533 (Reactome)
Lsm1-7 ComplexREACT_20540 (Reactome)
PABPC1ArrowREACT_20651 (Reactome)
PABPC1ArrowREACT_20662 (Reactome)
PAIP1ArrowREACT_20651 (Reactome)
PAIP1ArrowREACT_20662 (Reactome)
PAN2-PAN3 ComplexREACT_20606 (Reactome)
PARN homodimerREACT_20662 (Reactome)
Partially Deadenylated mRNA ComplexArrowREACT_20606 (Reactome)
Partially Deadenylated mRNA ComplexREACT_20651 (Reactome)
Partially Deadenylated mRNA ComplexREACT_20662 (Reactome)
REACT_20533 (Reactome) The XRN1 exoribonuclease hydrolyzes decapped mRNA from 5' to 3' and yields ribonucleotides having 5'-monophosphates. In yeast Xrn1 associates with the Lsm1-7 complex.
REACT_20540 (Reactome) The Lsm1-7 complex forms a heptameric ring that binds the 3' oligoadenylated ends of mRNAs that have been deadenylated. The bound Lsm1-7 may prevent access of the exosome (a 3' to 5' exonuclease) to the 3' end and thereby direct the mRNA to the 5' to 3' exonuclease pathway. The yeast Lsm1-7 complex has a preference for oligoadenylated RNA compared to polyadenylated RNA, however other determinants of binding by Lsm1-7 are unknown.
REACT_20556 (Reactome) The scavenging nuclease DCPS hydrolyzes the triphosphate bond between the 7-methylguanosine cap and the remaining oligoribonucleotide body of the mRNA. The products are 7-methylguanosine 5'-monophosphate and an oligoribonucleotide with a 5'-diphosphate.
REACT_20560 (Reactome) The DCP1-DCP2 decapping complex binds the 7-methylguanosine cap of mRNA and hydrolyzes the triphosphate bond to yield 7-methylguanosine 5'-diphosphate and RNA with 5'-monophosphate. The DCP2 subunit of the complex catalyzes the hydrolysis. DCP2 has higher affinity for some subsets of mRNA.
REACT_20588 (Reactome) The exosome complex hydrolyzes capped, deadenylated mRNA from 3' to 5' and yields ribonucleotides having 5'-monophosphates. In yeast the Ski2-Ski3-Ski8 complex assists degradation by the exosome complex, however little is known about the function of the homologous Ski complex in mammals. Although many exosomal components contain exonuclease signatures, only two components have been shown to degrade RNA. Rrp6/PMSCL-100 has been shown to be involved in the 3’-5’ decay of nuclear mRNAs in yeast. Rrp6 may also function in the absence of the core exosomal components. The Rrp44/dDis3 component of the core exosome has been shown to possess both 3’-5’ exonuclease activity along with endonuclease activity via its PIN domain.
REACT_20606 (Reactome) The PAN2-PAN3 exoribonuclease complex hydrolyzes the poly(A) tail of a mRNA, shortening the tail from about 200 adenosine residues to about 80 adenosine residues and yielding adenosine 5'-monophosphate. PAN2 is the exoribonuclease component of the complex; PAN3 is required for cellular localization. The poly(A)-binding protein (PABP) interacts with PAN3 and recruits the PAN2-PAN3 complex to mRNA.
REACT_20651 (Reactome) The CCR4-NOT complex hydrolyzes adenosine residues at the 3' end of polyadenylated mRNA, shortening the number of adenosine residues to about 10-15 residues and yielding adenosine 5'-monophosphate. CNOT6 and CNOT6L are the exoribonucleases responsible for hydrolysis. Activity of the CCR4-NOT complex is inhibited by PABP bound to the poly(A) tail of the mRNA. The trigger for activation of deadenylation by the CCR4-NOT complex is unknown. Complexes containing CNOT7 rather than CNOT8 appear to be responsible for cytoplasmic mRNA decay.
REACT_20662 (Reactome) The PARN exoribonuclease hydrolyzes adenosine residues at the 3' ends of polyadenylated mRNA, shortening the poly(A) tail from about 80 adenosine residues to about 10-15 residues and yielding adenosine 5'-monophosphate. PARN interacts simultaneously with the poly(A) tail and with the 7-methylguanosine cap of the mRNA, therefore it is believed that PARN displaces the eIF4F cap-binding complex. The trigger for deadenylation by PARN is unknown. PARN is also part of a complex that regulates poly(A) tail length and hence translation in developing oocytes.
Translatable mRNA ComplexREACT_20606 (Reactome)
UMPArrowREACT_20533 (Reactome)
UMPArrowREACT_20588 (Reactome)
XRN1REACT_20533 (Reactome)
capped oligoribonucleotideArrowREACT_20588 (Reactome)
capped oligoribonucleotideREACT_20556 (Reactome)
eIF4AArrowREACT_20651 (Reactome)
eIF4AArrowREACT_20662 (Reactome)
mature mRNA ArrowREACT_20651 (Reactome)
mature mRNA ArrowREACT_20662 (Reactome)
mature mRNA REACT_20540 (Reactome)
mature mRNA REACT_20588 (Reactome)
oligoribonucleotide with a 5'-diphosphateArrowREACT_20556 (Reactome)
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