KEGG   PATHWAY: clum03015
Entry
clum03015                   Pathway                                
Name
mRNA surveillance pathway - Cyclopterus lumpus (lumpfish)
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
clum03015  mRNA surveillance pathway
clum03015

Other DBs
GO: 0071028
Organism
Cyclopterus lumpus (lumpfish) [GN:clum]
Gene
117737542  nuclear cap-binding protein subunit 1 [KO:K12882]
117730098  ncbp2; nuclear cap-binding protein subunit 2 [KO:K12883]
117737266  upf3b; LOW QUALITY PROTEIN: regulator of nonsense transcripts 3B [KO:K14328]
117750995  upf3a; regulator of nonsense transcripts 3A isoform X1 [KO:K14328]
117728298  rbm8a; RNA-binding protein 8A isoform X1 [KO:K12876]
117729924  magoh; LOW QUALITY PROTEIN: protein mago nashi homolog [KO:K12877]
117734646  casc3; protein CASC3 [KO:K14323]
117729615  eif4a3; eukaryotic initiation factor 4A-III [KO:K13025] [EC:5.6.2.7]
117744118  sap18; histone deacetylase complex subunit SAP18 [KO:K14324]
117725129  pnn; pinin [KO:K13114]
117746690  acin1a; apoptotic chromatin condensation inducer in the nucleus [KO:K12875]
117747418  acin1b; apoptotic chromatin condensation inducer 1b isoform X1 [KO:K12875]
117734687  RNA-binding protein with serine-rich domain 1-like [KO:K14325]
117748964  RNA-binding protein with serine-rich domain 1-like [KO:K14325]
117735098  alyref; THO complex subunit 4 [KO:K12881]
117741699  THO complex subunit 4-A-like [KO:K12881]
117731215  ATP-dependent RNA helicase DDX19A-like [KO:K18655] [EC:5.6.2.7]
117733874  zgc:193690; ATP-dependent RNA helicase DDX19A [KO:K18655] [EC:5.6.2.7]
117735768  gle1; nucleoporin GLE1 [KO:K18723]
117737849  zgc:153681; nuclear RNA export factor 1 isoform X1 [KO:K14284]
117737093  nxt2; NTF2-related export protein 2 [KO:K14285]
117733858  pym1; LOW QUALITY PROTEIN: partner of Y14 and mago [KO:K14294]
117751259  srrm1; serine/arginine repetitive matrix protein 1 isoform X1 [KO:K13171]
117727358  rngtt; LOW QUALITY PROTEIN: mRNA-capping enzyme [KO:K13917] [EC:2.7.7.50 3.6.1.74]
117739570  rnmt; mRNA cap guanine-N7 methyltransferase [KO:K00565] [EC:2.1.1.56]
117734709  fus; RNA-binding protein FUS [KO:K13098]
117741080  taf15; LOW QUALITY PROTEIN: TATA-binding protein-associated factor 2N [KO:K13098]
117731299  tardbp; TAR DNA-binding protein 43 [KO:K23600]
117733399  tardbpl; TAR DNA binding protein, like isoform X1 [KO:K23600]
117749317  pabpn1; polyadenylate-binding protein 2 isoform X1 [KO:K14396]
117727685  pabpn1l; embryonic polyadenylate-binding protein 2 isoform X1 [KO:K14396]
117728614  nudt21; cleavage and polyadenylation specificity factor subunit 5 [KO:K14397]
117725963  cpsf6; cleavage and polyadenylation specificity factor subunit 6 isoform X1 [KO:K14398]
117743970  papolg; poly(A) polymerase gamma isoform X1 [KO:K14376] [EC:2.7.7.19]
117727757  poly(A) polymerase type 3-like [KO:K14376] [EC:2.7.7.19]
117737884  clp1; polyribonucleotide 5'-hydroxyl-kinase Clp1 [KO:K14399] [EC:2.7.1.78]
117742399  pcf11; pre-mRNA cleavage complex 2 protein Pcf11 [KO:K14400]
117739093  cpsf1; cleavage and polyadenylation specificity factor subunit 1 [KO:K14401]
117727616  cpsf2; cleavage and polyadenylation specificity factor subunit 2 [KO:K14402]
117725319  cleavage and polyadenylation specificity factor subunit 3-like [KO:K14403] [EC:3.1.27.-]
117727694  cleavage and polyadenylation specificity factor subunit 3 [KO:K14403] [EC:3.1.27.-]
117735319  cpsf4; cleavage and polyadenylation specificity factor subunit 4 [KO:K14404]
117734563  fip1l1b; LOW QUALITY PROTEIN: pre-mRNA 3'-end-processing factor FIP1 [KO:K14405]
117746013  wdr33; pre-mRNA 3' end processing protein WDR33 isoform X1 [KO:K15542]
117731525  wdr82; WD repeat-containing protein 82 [KO:K14962]
117736119  serine/threonine-protein phosphatase PP1-gamma catalytic subunit A [KO:K06269] [EC:3.1.3.16]
117749034  serine/threonine-protein phosphatase alpha-2 isoform-like [KO:K06269] [EC:3.1.3.16]
117727160  serine/threonine-protein phosphatase PP1-beta catalytic subunit-like [KO:K06269] [EC:3.1.3.16]
117751447  serine/threonine-protein phosphatase PP1-beta catalytic subunit-like [KO:K06269] [EC:3.1.3.16]
117734761  ppp1caa; protein phosphatase 1, catalytic subunit, alpha isozyme a [KO:K06269] [EC:3.1.3.16]
117747730  serine/threonine-protein phosphatase PP1-beta catalytic subunit [KO:K06269] [EC:3.1.3.16]
117730677  ssu72; RNA polymerase II subunit A C-terminal domain phosphatase SSU72 [KO:K15544] [EC:3.1.3.16]
117731279  cstf1; cleavage stimulation factor subunit 1 [KO:K14406]
117737418  cstf2; cleavage stimulation factor subunit 2 isoform X1 [KO:K14407]
117749337  cstf3; cleavage stimulation factor subunit 3 [KO:K14408]
117750093  sympk; symplekin [KO:K06100]
117736326  msi1b; RNA-binding protein Musashi homolog 1b [KO:K14411]
117742576  RNA-binding protein Musashi homolog 2 isoform X1 [KO:K14411]
117731222  RNA-binding protein Musashi homolog 1-like [KO:K14411]
117729487  dazap1; DAZ-associated protein 1 isoform X1 [KO:K14411]
117738658  polyadenylate-binding protein 1A-like isoform X1 [KO:K13126]
117728178  polyadenylate-binding protein 1A [KO:K13126]
117734006  embryonic polyadenylate-binding protein A-like [KO:K13126]
117751414  pabpc4; LOW QUALITY PROTEIN: polyadenylate-binding protein 4 [KO:K13126]
117737317  etf1a; eukaryotic peptide chain release factor subunit 1 isoform X1 [KO:K03265]
117748862  gspt1; eukaryotic peptide chain release factor GTP-binding subunit ERF3A [KO:K03267]
117734613  gspt1l; G1 to S phase transition 1, like [KO:K03267]
117729136  regulator of nonsense transcripts 1 isoform X1 [KO:K14326] [EC:5.6.2.5 5.6.2.3]
117746916  regulator of nonsense transcripts 1-like [KO:K14326] [EC:5.6.2.5 5.6.2.3]
117726051  upf2; regulator of nonsense transcripts 2 isoform X1 [KO:K14327]
117735644  smg1; serine/threonine-protein kinase SMG1 isoform X1 [KO:K08873] [EC:2.7.11.1]
117746425  smg7; protein SMG7 isoform X1 [KO:K14409]
117728034  smg5; protein SMG5 [KO:K11125]
117742391  smg6; telomerase-binding protein EST1A isoform X1 [KO:K11124] [EC:3.1.-.-]
117736039  serine/threonine-protein phosphatase 2A catalytic subunit beta isoform [KO:K04382] [EC:3.1.3.16]
117742883  ppp2cab; serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform [KO:K04382] [EC:3.1.3.16]
117737713  serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform-like [KO:K04382] [EC:3.1.3.16]
117741228  ppp2r1bb; serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform [KO:K03456]
117736251  ppp2r2aa; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform [KO:K04354]
117737350  ppp2r2ba; LOW QUALITY PROTEIN: serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B beta isoform [KO:K04354]
117737758  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B beta isoform isoform X1 [KO:K04354]
117743924  ppp2r2d; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform [KO:K04354]
117733363  ppp2r2ca; protein phosphatase 2, regulatory subunit B, gamma a [KO:K04354]
117740441  ppp2r2ab; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform isoform X1 [KO:K04354]
117750190  ppp2r3b; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X1 [KO:K11583]
117751263  ppp2r3c; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit gamma [KO:K11583]
117727017  ppp2r5cb; protein phosphatase 2, regulatory subunit B', gamma b isoform X1 [KO:K11584]
117727087  ppp2r5a; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform isoform X1 [KO:K11584]
117744089  ppp2r5d; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform isoform X1 [KO:K11584]
117751191  ppp2r5eb; protein phosphatase 2, regulatory subunit B', epsilon isoform X1 [KO:K11584]
117751271  ppp2r5ca; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform isoform X1 [KO:K11584]
117747693  ppp2r5b; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit beta isoform [KO:K11584]
117727902  hbs1l; HBS1-like protein isoform X1 [KO:K14416]
117749029  pelo; protein pelota homolog isoform X1 [KO:K06965]
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
clum03013  Nucleocytoplasmic transport
clum03018  RNA degradation
clum03040  Spliceosome
KO pathway
ko03015   
LinkDB

DBGET integrated database retrieval system