KEGG   PATHWAY: cbor03015
Entry
cbor03015                   Pathway                                
Name
mRNA surveillance pathway - Calonectris borealis (Cory's shearwater)
Description
The mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go decay (NGD). NMD is a mechanism that eliminates mRNAs containing premature translation-termination codons (PTCs). In vertebrates, PTCs trigger efficient NMD when located upstream of an exon junction complex (EJC). Upf3, together with Upf1 and Upf2, may signal the presence of the PTC to the 5'end of the transcript, resulting in decapping and rapid exonucleolytic digestion of the mRNA. In the NSD pathway, which targets mRNAs lacking termination codons, the ribosome is believed to translate through the 3' untranslated region and stall at the end of the poly(A) tail. NSD involves an eRF3-like protein, Ski7p, which is hypothesized to bind the empty A site of the ribosome and recruit the exosome to degrade the mRNA from the 3' end. NGD targets mRNAs with stalls in translation elongation for endonucleolytic cleavage in a process involving the Dom34 and Hbs1 proteins.
Class
Genetic Information Processing; Translation
Pathway map
cbor03015  mRNA surveillance pathway
cbor03015

Other DBs
GO: 0071028
Organism
Calonectris borealis (Cory's shearwater) [GN:cbor]
Gene
142073537  SMG5; nonsense-mediated mRNA decay factor SMG5 isoform X1 [KO:K11125]
142073671  PYM1; partner of Y14 and mago isoform X1 [KO:K14294]
142073961  PPP2R3B; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X1 [KO:K11583]
142074042  SYMPK; symplekin isoform X1 [KO:K06100]
142074407  PPP2R1A; serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform isoform X1 [KO:K03456]
142074485  NXF1; LOW QUALITY PROTEIN: nuclear RNA export factor 1 [KO:K14284]
142074558  PABPN1; polyadenylate-binding protein 2 [KO:K14396]
142074629  FUS; RNA-binding protein FUS [KO:K13098]
142074881  [KO:K12882]
142075289  NCBP1; nuclear cap-binding protein subunit 1 isoform X1 [KO:K12882]
142075299  UPF3A; regulator of nonsense transcripts 3A isoform X1 [KO:K14328]
142075733  PELO; protein pelota homolog [KO:K06965]
142077607  [KO:K14401]
142077797  SAP18; histone deacetylase complex subunit SAP18 [KO:K14324]
142077901  PCF11; pre-mRNA cleavage complex 2 protein Pcf11 isoform X1 [KO:K14400]
142078598  PABPC1; polyadenylate-binding protein 1 [KO:K13126]
142078889  RNMT; mRNA cap guanine-N(7) methyltransferase isoform X1 [KO:K00565] [EC:2.1.1.56]
142079365  UPF2; regulator of nonsense transcripts 2 isoform X1 [KO:K14327]
142079774  [KO:K14401]
142080152  CPSF3; cleavage and polyadenylation specificity factor subunit 3 isoform X1 [KO:K14403] [EC:3.1.27.-]
142080296  RNGTT; mRNA-capping enzyme isoform X1 [KO:K13917] [EC:2.7.7.50 3.6.1.74]
142080469  HBS1L; HBS1-like protein isoform X1 [KO:K14416]
142080815  PPP1CB; serine/threonine-protein phosphatase PP1-beta catalytic subunit isoform X1 [KO:K06269] [EC:3.1.3.16]
142080869  PPP2R5A; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform isoform X1 [KO:K11584]
142081019  PPP2R5D; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform isoform X1 [KO:K11584]
142081046  EIF4A3; eukaryotic initiation factor 4A-III [KO:K13025] [EC:5.6.2.7]
142081152  PAPOLG; poly(A) polymerase gamma [KO:K14376] [EC:2.7.7.19]
142081717  PPP2R2C; protein phosphatase 2, regulatory subunit B, gamma isoform X1 [KO:K04354]
142081847  FIP1L1; pre-mRNA 3'-end-processing factor FIP1 isoform X1 [KO:K14405]
142082020  CPSF6; cleavage and polyadenylation specificity factor subunit 6 isoform X1 [KO:K14398]
142082289  PPP2CB; serine/threonine-protein phosphatase 2A catalytic subunit beta isoform [KO:K04382] [EC:3.1.3.16]
142082656  PPP2R5E; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform isoform X1 [KO:K11584]
142082720  PPP2R5C; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform isoform X1 [KO:K11584]
142082744  PAPOLA; poly(A) polymerase alpha isoform X1 [KO:K14376] [EC:2.7.7.19]
142082777  CPSF2; cleavage and polyadenylation specificity factor subunit 2 [KO:K14402]
142082893  PNN; pinin [KO:K13114]
142082912  PPP2R3C; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit gamma isoform X1 [KO:K11583]
142084501  PPP2R2D; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform isoform X1 [KO:K04354]
142084768  MAGOH; protein mago nashi homolog [KO:K12877]
142085172  SMG7; nonsense-mediated mRNA decay factor SMG7 isoform X1 [KO:K14409]
142085719  PPP2R3A; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit alpha [KO:K11583]
142085871  [KO:K12883]
142086272  WDR82; WD repeat-containing protein 82 [KO:K14962]
142087153  NUDT21; cleavage and polyadenylation specificity factor subunit 5 [KO:K14397]
142087291  PABPN1L; embryonic polyadenylate-binding protein 2 [KO:K14396]
142087609  CSTF2; cleavage stimulation factor subunit 2 isoform X1 [KO:K14407]
142087660  [KO:K12883]
142087757  UPF3B; regulator of nonsense transcripts 3B [KO:K14328]
142087796  NXT2; NTF2-related export protein 2 isoform X1 [KO:K14285]
142087827  [KO:K14405]
142088177  CSTF3; cleavage stimulation factor subunit 3 isoform X1 [KO:K14408]
142088273  PPP1CA; serine/threonine-protein phosphatase PP1-alpha catalytic subunit isoform X1 [KO:K06269] [EC:3.1.3.16]
142088308  CPSF7; cleavage and polyadenylation specificity factor subunit 7 isoform X1 [KO:K14398]
142088407  CLP1; polyribonucleotide 5'-hydroxyl-kinase Clp1 [KO:K14399] [EC:2.7.1.78]
142088602  ETF1; eukaryotic peptide chain release factor subunit 1 isoform X1 [KO:K03265]
142088767  PPP2R2B; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B beta isoform isoform X1 [KO:K04354]
142088820  [KO:K04382] [EC:3.1.3.16]
142089073  GSPT1; eukaryotic peptide chain release factor GTP-binding subunit ERF3A [KO:K03267]
142089085  SMG1; serine/threonine-protein kinase SMG1 isoform X1 [KO:K08873] [EC:2.7.11.1]
142089206  CPSF4; cleavage and polyadenylation specificity factor subunit 4 [KO:K14404]
142089349  RNPS1; RNA-binding protein with serine-rich domain 1 isoform X1 [KO:K14325]
142089685  PABPC1L; polyadenylate-binding protein 1-like isoform X1 [KO:K13126]
142089727  CSTF1; cleavage stimulation factor subunit 1 [KO:K14406]
142090058  MSI1; RNA-binding protein Musashi homolog 1 [KO:K14411]
142090169  PPP1CC; serine/threonine-protein phosphatase PP1-gamma catalytic subunit [KO:K06269] [EC:3.1.3.16]
142090440  MSI2; RNA-binding protein Musashi homolog 2 isoform X1 [KO:K14411]
142090585  SMG6; telomerase-binding protein EST1A isoform X1 [KO:K11124] [EC:3.1.-.-]
142090837  ALYREF; THO complex subunit 4 [KO:K12881]
142091191  CPSF4L; putative cleavage and polyadenylation specificity factor subunit 4-like protein [KO:K14404]
142091300  GLE1; mRNA export factor GLE1 [KO:K18723]
142091962  CASC3; protein CASC3 isoform X1 [KO:K14323]
142092347  SSU72; RNA polymerase II subunit A C-terminal domain phosphatase SSU72 [KO:K15544] [EC:3.1.3.16]
142092433  TARDBP; TAR DNA-binding protein 43 [KO:K23600]
142092490  [KO:K18655] [EC:5.6.2.7]
142092822  PABPC4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
142092851  SRRM1; serine/arginine repetitive matrix protein 1 isoform X1 [KO:K13171]
142093574  PPP2R2A; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform isoform X1 [KO:K04354]
142093900  DAZAP1; DAZ-associated protein 1 isoform X1 [KO:K14411]
142093917  UPF1; regulator of nonsense transcripts 1 isoform X1 [KO:K14326] [EC:5.6.2.5 5.6.2.3]
142094043  RBM8A; RNA-binding protein 8A [KO:K12876]
Reference
PMID:15040442
  Authors
Maquat LE
  Title
Nonsense-mediated mRNA decay: splicing, translation and mRNP dynamics.
  Journal
Nat Rev Mol Cell Biol 5:89-99 (2004)
DOI:10.1038/nrm1310
Reference
PMID:16723977
  Authors
Amrani N, Sachs MS, Jacobson A
  Title
Early nonsense: mRNA decay solves a translational problem.
  Journal
Nat Rev Mol Cell Biol 7:415-25 (2006)
DOI:10.1038/nrm1942
Reference
PMID:17183357
  Authors
Eulalio A, Behm-Ansmant I, Izaurralde E
  Title
P bodies: at the crossroads of post-transcriptional pathways.
  Journal
Nat Rev Mol Cell Biol 8:9-22 (2007)
DOI:10.1038/nrm2080
Reference
PMID:18158581
  Authors
Mandel CR, Bai Y, Tong L
  Title
Protein factors in pre-mRNA 3'-end processing.
  Journal
Cell Mol Life Sci 65:1099-122 (2008)
DOI:10.1007/s00018-007-7474-3
Reference
PMID:16715045
  Authors
Clement SL, Lykke-Andersen J
  Title
No mercy for messages that mess with the ribosome.
  Journal
Nat Struct Mol Biol 13:299-301 (2006)
DOI:10.1038/nsmb0406-299
Related
pathway
cbor03013  Nucleocytoplasmic transport
cbor03018  RNA degradation
cbor03040  Spliceosome
KO pathway
ko03015   

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