KEGG   PATHWAY: pdab03015
Entry
pdab03015                   Pathway                                
Name
mRNA surveillance pathway - Paramisgurnus dabryanus (large-scale loach)
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
pdab03015  mRNA surveillance pathway
pdab03015

Other DBs
GO: 0071028
Organism
Paramisgurnus dabryanus (large-scale loach) [GN:pdab]
Gene
135718857  cstf1; cleavage stimulation factor subunit 1 [KO:K14406]
135719155  ddx19b; ATP-dependent RNA helicase DDX19B [KO:K18655] [EC:5.6.2.7]
135719204  dazap1; DAZ-associated protein 1 isoform X1 [KO:K14411]
135720382  gspt1; eukaryotic peptide chain release factor GTP-binding subunit ERF3A [KO:K03267]
135720508  pelo; protein pelota homolog [KO:K06965]
135720510  ppp1cab; protein phosphatase 1, catalytic subunit, alpha isozyme b [KO:K06269] [EC:3.1.3.16]
135720521  clp1; polyribonucleotide 5'-hydroxyl-kinase Clp1 [KO:K14399] [EC:2.7.1.78]
135721021  ssu72; RNA polymerase II subunit A C-terminal domain phosphatase SSU72 [KO:K15544] [EC:3.1.3.16]
135729283  magoh; protein mago nashi homolog [KO:K12877]
135729697  pabpc1l; polyadenylate-binding protein 1-like [KO:K13126]
135730199  pym1; partner of Y14 and mago isoform X1 [KO:K14294]
135730348  ppp2r2aa; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform [KO:K04354]
135730390  gle1; mRNA export factor GLE1 [KO:K18723]
135730776  acin1b; apoptotic chromatin condensation inducer 1b [KO:K12875]
135730819  ppp2r5b; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit beta isoform isoform X1 [KO:K11584]
135731026  sap18; histone deacetylase complex subunit SAP18 [KO:K14324]
135731552  ppp1cbl; protein phosphatase 1, catalytic subunit, beta isoform, like [KO:K06269] [EC:3.1.3.16]
135732779  ppp1cc; serine/threonine-protein phosphatase PP1-gamma catalytic subunit A [KO:K06269] [EC:3.1.3.16]
135732838  [KO:K14411]
135732934  ppp2r5d; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform [KO:K11584]
135733396  ppp2r3b; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X1 [KO:K11583]
135733402  upf3a; regulator of nonsense transcripts 3A isoform X1 [KO:K14328]
135733943  casc3; protein CASC3 isoform X1 [KO:K14323]
135734251  [KO:K14325]
135734404  pnn; pinin [KO:K13114]
135734469  ppp2r3c; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit gamma [KO:K11583]
135735846  ppp2r2ca; protein phosphatase 2, regulatory subunit B, gamma a [KO:K04354]
135735849  fip1l1b; pre-mRNA 3'-end-processing factor FIP1 isoform X1 [KO:K14405]
135738403  ppp2r5cb; protein phosphatase 2, regulatory subunit B', gamma b isoform X1 [KO:K11584]
135738470  cpsf2; cleavage and polyadenylation specificity factor subunit 2 [KO:K14402]
135738768  cpsf3; cleavage and polyadenylation specificity factor subunit 3 [KO:K14403] [EC:3.1.27.-]
135738945  fip1l1a; pre-mRNA 3'-end-processing factor FIP1 [KO:K14405]
135738978  ppp2r5ea; protein phosphatase 2, regulatory subunit B', epsilon [KO:K11584]
135740738  eif4a3; eukaryotic initiation factor 4A-III [KO:K13025] [EC:5.6.2.7]
135740933  ncbp2; nuclear cap-binding protein subunit 2 isoform X1 [KO:K12883]
135741445  msi1b; RNA-binding protein Musashi homolog 1b isoform X1 [KO:K14411]
135742272  smg6; telomerase-binding protein EST1A isoform X1 [KO:K11124] [EC:3.1.-.-]
135743116  msi2a; RNA-binding protein Musashi homolog 2a isoform X1 [KO:K14411]
135743851  pabpn1l; embryonic polyadenylate-binding protein 2 [KO:K14396]
135744232  upf1; regulator of nonsense transcripts 1 isoform X2 [KO:K14326] [EC:5.6.2.5 5.6.2.3]
135744408  ppp2r2d; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform [KO:K04354]
135745532  [KO:K14284]
135745608  ppp2r2ba; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B beta isoform isoform X1 [KO:K04354]
135745622  [KO:K12882]
135746120  cpsf4; cleavage and polyadenylation specificity factor subunit 4 [KO:K14404]
135748363  ppp2r2cb; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B gamma isoform [KO:K04354]
135748432  nxt2; NTF2-related export protein 2 [KO:K14285]
135749080  srrm1; serine/arginine repetitive matrix protein 1 isoform X1 [KO:K13171]
135750025  papola; poly(A) polymerase alpha [KO:K14376] [EC:2.7.7.19]
135750051  rngtt; mRNA-capping enzyme [KO:K13917] [EC:2.7.7.50 3.6.1.74]
135750098  ppp2r5a; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform [KO:K11584]
135752146  [KO:K13126]
135752187  pabpc1a; polyadenylate-binding protein 1A isoform X1 [KO:K13126]
135753711  ppp2cb; serine/threonine-protein phosphatase 2A catalytic subunit beta isoform [KO:K04382] [EC:3.1.3.16]
135754864  gspt1l; G1 to S phase transition 1, like [KO:K03267]
135757042  upf3b; regulator of nonsense transcripts 3B [KO:K14328]
135758699  cstf2; cleavage stimulation factor subunit 2 isoform X1 [KO:K14407]
135758714  upf2; regulator of nonsense transcripts 2 [KO:K14327]
135758762  cpsf6; cleavage and polyadenylation specificity factor subunit 6 isoform X1 [KO:K14398]
135760165  ppp1caa; protein phosphatase 1, catalytic subunit, alpha isozyme a [KO:K06269] [EC:3.1.3.16]
135760884  ppp2caa; protein phosphatase 2 catalytic subunit alpha a [KO:K04382] [EC:3.1.3.16]
135761044  ppp2r5ca; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform isoform X1 [KO:K11584]
135761378  etf1a; eukaryotic peptide chain release factor subunit 1-like [KO:K03265]
135766027  wdr33; pre-mRNA 3' end processing protein WDR33 isoform X1 [KO:K15542]
135766850  ppp2r3a; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit alpha isoform X1 [KO:K11583]
135767046  smg7; nonsense-mediated mRNA decay factor SMG7 isoform X1 [KO:K14409]
135767348  acin1a; uncharacterized protein acin1a isoform X2 [KO:K12875]
135767728  fus; RNA-binding protein FUS [KO:K13098]
135768718  smg1; serine/threonine-protein kinase SMG1 isoform X1 [KO:K08873] [EC:2.7.11.1]
135770098  tardbpb; TAR DNA-binding protein 43 [KO:K23600]
135770155  wdr82; WD repeat-containing protein 82 [KO:K14962]
135770947  msi2b; RNA-binding protein Musashi homolog 2b isoform X1 [KO:K14411]
135771137  ppp2r1bb; serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform [KO:K03456]
135771518  taf15; TATA-binding protein-associated factor 2N isoform X1 [KO:K13098]
135773205  nudt21; cleavage and polyadenylation specificity factor subunit 5 [KO:K14397]
135773333  cstf3; cleavage stimulation factor subunit 3 [KO:K14408]
135774207  ppp2r1ba; protein phosphatase 2, regulatory subunit A, beta a [KO:K03456]
135774236  sympk; symplekin isoform X1 [KO:K06100]
135775357  hbs1l; HBS1-like protein isoform X1 [KO:K14416]
135775412  tardbpa; TAR DNA binding protein, like isoform X1 [KO:K23600]
135776025  ddx19a; ATP-dependent RNA helicase DDX19A isoform X1 [KO:K18655] [EC:5.6.2.7]
135776302  pcf11; pre-mRNA cleavage complex 2 protein Pcf11 [KO:K14400]
135776388  nxf1b; nuclear RNA export factor 1 [KO:K14284]
135776484  ppp2r2bb; protein phosphatase 2, regulatory subunit B, beta b isoform X1 [KO:K04354]
135776732  ppp2cab; serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform [KO:K04382] [EC:3.1.3.16]
135777902  pabpc4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
135777918  [KO:K06269] [EC:3.1.3.16]
135779679  ppp2r2ab; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform isoform X2 [KO:K04354]
135779714  etf1b; eukaryotic peptide chain release factor subunit 1b isoform X1 [KO:K03265]
135782659  rnmt; mRNA cap guanine-N(7) methyltransferase [KO:K00565] [EC:2.1.1.56]
135782725  pabpc1b; polyadenylate-binding protein 1b [KO:K13126]
135782781  cpsf1; cleavage and polyadenylation specificity factor subunit 1 [KO:K14401]
135783089  alyref; THO complex subunit 4 [KO:K12881]
135783415  ddx39b; DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B [KO:K12812] [EC:5.6.2.7]
135785493  pabpn1; polyadenylate-binding protein 2 isoform X1 [KO:K14396]
135786751  ppp2r5eb; protein phosphatase 2, regulatory subunit B', epsilon isoform X1 [KO:K11584]
135787016  papolg; poly(A) polymerase gamma isoform X1 [KO:K14376] [EC:2.7.7.19]
135789147  smg5; nonsense-mediated mRNA decay factor SMG5 [KO:K11125]
135789151  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
pdab03013  Nucleocytoplasmic transport
pdab03018  RNA degradation
pdab03040  Spliceosome
KO pathway
ko03015   

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