KEGG   PATHWAY: char03015
Entry
char03015                   Pathway                                
Name
mRNA surveillance pathway - Clupea harengus (Atlantic herring)
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
char03015  mRNA surveillance pathway
char03015

Other DBs
GO: 0071028
Organism
Clupea harengus (Atlantic herring) [GN:char]
Gene
105888632  [KO:K12882]
105888934  clp1; polyribonucleotide 5'-hydroxyl-kinase Clp1 isoform X2 [KO:K14399] [EC:2.7.1.78]
105889133  cstf3; cleavage stimulation factor subunit 3 [KO:K14408]
105889818  [KO:K06269] [EC:3.1.3.16]
105890435  [KO:K14411]
105890557  ppp2r2ab; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform [KO:K04354]
105891126  [KO:K14398]
105891552  eif4a3; eukaryotic initiation factor 4A-III [KO:K13025] [EC:5.6.2.7]
105891605  gle1; nucleoporin GLE1 isoform X1 [KO:K18723]
105891816  rbm8a; RNA-binding protein 8A isoform X1 [KO:K12876]
105891879  smg5; protein SMG5 [KO:K11125]
105892015  rnmt; mRNA cap guanine-N7 methyltransferase [KO:K00565] [EC:2.1.1.56]
105892357  cpsf6; cleavage and polyadenylation specificity factor subunit 6 isoform X1 [KO:K14398]
105892915  pabpn1l; embryonic polyadenylate-binding protein 2 [KO:K14396]
105893093  [KO:K03265]
105893104  cstf2; cleavage stimulation factor subunit 2 isoform X1 [KO:K14407]
105893210  ppp2cab; serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform [KO:K04382] [EC:3.1.3.16]
105893486  papolg; LOW QUALITY PROTEIN: poly(A) polymerase gamma [KO:K14376] [EC:2.7.7.19]
105894036  [KO:K06965]
105894037  [KO:K06269] [EC:3.1.3.16]
105894330  pym1; partner of Y14 and mago isoform X1 [KO:K14294]
105894467  ppp2r5a; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform [KO:K11584]
105894634  ppp2cb; serine/threonine-protein phosphatase 2A catalytic subunit beta isoform [KO:K04382] [EC:3.1.3.16]
105894670  hbs1l; HBS1-like protein isoform X1 [KO:K14416]
105895063  fip1l1a; pre-mRNA 3'-end-processing factor FIP1 [KO:K14405]
105895368  ppp2r1ba; protein phosphatase 2, regulatory subunit A, beta a [KO:K03456]
105895509  ppp2r5b; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit beta isoform [KO:K11584]
105895588  sympk; symplekin [KO:K06100]
105895947  wdr82; WD repeat-containing protein 82 [KO:K14962]
105896100  ppp2r2aa; LOW QUALITY PROTEIN: serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform [KO:K04354]
105896162  pabpc1a; polyadenylate-binding protein 1A isoform X1 [KO:K13126]
105896615  pabpc4; polyadenylate-binding protein 4 [KO:K13126]
105896704  srrm1; serine/arginine repetitive matrix protein 1 isoform X1 [KO:K13171]
105897062  cpsf3; cleavage and polyadenylation specificity factor subunit 3 [KO:K14403] [EC:3.1.27.-]
105897394  [KO:K11584]
105897413  [KO:K12881]
105897453  [KO:K14284]
105897688  ppp1caa; protein phosphatase 1, catalytic subunit, alpha isozyme a [KO:K06269] [EC:3.1.3.16]
105897767  ppp2r5ea; protein phosphatase 2, regulatory subunit B', epsilon [KO:K11584]
105897914  ssu72; RNA polymerase II subunit A C-terminal domain phosphatase SSU72 [KO:K15544] [EC:3.1.3.16]
105898138  ddx19b; ATP-dependent RNA helicase DDX19B [KO:K18655] [EC:5.6.2.7]
105898367  upf2; regulator of nonsense transcripts 2 isoform X1 [KO:K14327]
105899087  msi1b; RNA-binding protein Musashi homolog 1b isoform X1 [KO:K14411]
105899184  smg7; protein SMG7 isoform X1 [KO:K14409]
105899218  wdr33; LOW QUALITY PROTEIN: pre-mRNA 3' end processing protein WDR33 [KO:K15542]
105899638  ppp2r3c; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit gamma isoform X1 [KO:K11583]
105899669  pnn; pinin [KO:K13114]
105899954  smg1; serine/threonine-protein kinase SMG1 isoform X1 [KO:K08873] [EC:2.7.11.1]
105899964  gspt1l; G1 to S phase transition 1, like isoform X1 [KO:K03267]
105900387  nxf1b; nuclear RNA export factor 1 [KO:K14284]
105900883  [KO:K14326] [EC:5.6.2.5 5.6.2.3]
105900893  magoh; protein mago nashi homolog [KO:K12877]
105901871  tardbpb; TAR DNA-binding protein 43 isoform X1 [KO:K23600]
105902301  papola; poly(A) polymerase alpha [KO:K14376] [EC:2.7.7.19]
105902388  ppp2r2bb; protein phosphatase 2, regulatory subunit B, beta b isoform X1 [KO:K04354]
105902490  [KO:K14411]
105902522  ppp1cc; serine/threonine-protein phosphatase PP1-gamma catalytic subunit A [KO:K06269] [EC:3.1.3.16]
105902792  msi2b; RNA-binding protein Musashi homolog 2b isoform X1 [KO:K14411]
105903144  [KO:K06269] [EC:3.1.3.16]
105903320  ppp2r2d; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform isoform X1 [KO:K04354]
105903502  ppp2r2ca; protein phosphatase 2, regulatory subunit B, gamma a [KO:K04354]
105903575  fip1l1b; pre-mRNA 3'-end-processing factor FIP1 isoform X1 [KO:K14405]
105903801  ppp2r1bb; serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform [KO:K03456]
105904522  nudt21; cleavage and polyadenylation specificity factor subunit 5 [KO:K14397]
105904710  ddx39b; LOW QUALITY PROTEIN: DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B [KO:K12812] [EC:5.6.2.7]
105904942  cpsf1; cleavage and polyadenylation specificity factor subunit 1 [KO:K14401]
105904970  [KO:K12881]
105905021  taf15; TATA-binding protein-associated factor 2N isoform X1 [KO:K13098]
105905291  [KO:K14325]
105905426  [KO:K14325]
105905945  ppp2r3b; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X1 [KO:K11583]
105905952  upf3a; regulator of nonsense transcripts 3A isoform X1 [KO:K14328]
105905986  [KO:K03265]
105907049  upf1; regulator of nonsense transcripts 1 isoform X1 [KO:K14326] [EC:5.6.2.5 5.6.2.3]
105907307  cpsf2; cleavage and polyadenylation specificity factor subunit 2 [KO:K14402]
105907384  smg6; telomerase-binding protein EST1A [KO:K11124] [EC:3.1.-.-]
105907451  pcf11; pre-mRNA cleavage complex 2 protein Pcf11 isoform X1 [KO:K14400]
105907650  rngtt; mRNA-capping enzyme [KO:K13917] [EC:2.7.7.50 3.6.1.74]
105907709  pabpc1b; polyadenylate-binding protein 1b [KO:K13126]
105908323  ppp2r5ca; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform isoform X1 [KO:K11584]
105908490  ppp2r3a; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit alpha [KO:K11583]
105909583  ppp2r5cb; protein phosphatase 2, regulatory subunit B', gamma b isoform X1 [KO:K11584]
105909901  cstf1; cleavage stimulation factor subunit 1 [KO:K14406]
105910250  gspt1; eukaryotic peptide chain release factor GTP-binding subunit ERF3A [KO:K03267]
105911342  [KO:K11584]
105912710  ddx19a; ATP-dependent RNA helicase DDX19A isoform X2 [KO:K18655] [EC:5.6.2.7]
105912829  casc3; protein CASC3 isoform X1 [KO:K14323]
105912950  ncbp2; nuclear cap-binding protein subunit 2 [KO:K12883]
105913111  upf3b; regulator of nonsense transcripts 3B [KO:K14328]
105913270  sap18; histone deacetylase complex subunit SAP18 [KO:K14324]
116218716  alyref; THO complex subunit 4 [KO:K12881]
116223330  [KO:K11584]
116225174  nxt2; NTF2-related export protein 2 [KO:K14285]
122129255  [KO:K14411]
122129261  cpsf4; cleavage and polyadenylation specificity factor subunit 4 [KO:K14404]
122129456  [KO:K06269] [EC:3.1.3.16]
122129457  [KO:K06965]
122130257  [KO:K04382] [EC:3.1.3.16]
122130366  pabpn1; polyadenylate-binding protein 2 isoform X1 [KO:K14396]
122130840  tardbpa; TAR DNA binding protein, like isoform X1 [KO:K23600]
122132099  [KO:K13126]
122132530  dazap1; DAZ-associated protein 1 isoform X1 [KO:K14411]
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
char03013  Nucleocytoplasmic transport
char03018  RNA degradation
char03040  Spliceosome
KO pathway
ko03015   

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