KEGG   PATHWAY: msam03015
Entry
msam03015                   Pathway                                
Name
mRNA surveillance pathway - Micropterus salmoides (largemouth bass)
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
msam03015  mRNA surveillance pathway
msam03015

Other DBs
GO: 0071028
Organism
Micropterus salmoides (largemouth bass) [GN:msam]
Gene
119882311  ppp2r1bb; serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform [KO:K03456]
119882993  taf15; TATA-binding protein-associated factor 2N [KO:K13098]
119884135  ppp2r5d; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform [KO:K11584]
119885040  [KO:K18655] [EC:5.6.2.7]
119885441  cpsf4; cleavage and polyadenylation specificity factor subunit 4 [KO:K14404]
119886172  alyref; LOW QUALITY PROTEIN: THO complex subunit 4 [KO:K12881]
119886228  ssu72; RNA polymerase II subunit A C-terminal domain phosphatase SSU72 [KO:K15544] [EC:3.1.3.16]
119886351  tardbpb; TAR DNA-binding protein 43 isoform X1 [KO:K23600]
119886444  wdr82; WD repeat-containing protein 82 [KO:K14962]
119886530  cstf1; cleavage stimulation factor subunit 1 [KO:K14406]
119886609  [KO:K18655] [EC:5.6.2.7]
119886681  [KO:K14411]
119887373  [KO:K11584]
119888259  [KO:K12882]
119888321  nxf1a; nuclear RNA export factor 1 isoform X1 [KO:K14284]
119888346  cstf2; LOW QUALITY PROTEIN: cleavage stimulation factor subunit 2 [KO:K14407]
119888548  [KO:K04354]
119888694  [KO:K04354]
119888745  upf3b; regulator of nonsense transcripts 3B [KO:K14328]
119888900  clp1; LOW QUALITY PROTEIN: polyribonucleotide 5'-hydroxyl-kinase Clp1 [KO:K14399] [EC:2.7.1.78]
119888909  [KO:K04382] [EC:3.1.3.16]
119889055  nxt2; NTF2-related export protein 2 [KO:K14285]
119889151  [KO:K03265]
119889946  pabpn1l; embryonic polyadenylate-binding protein 2 [KO:K14396]
119889982  [KO:K14325]
119890023  [KO:K14397]
119890186  cstf3; cleavage stimulation factor subunit 3 isoform X1 [KO:K14408]
119890722  [KO:K14398]
119891592  [KO:K04382] [EC:3.1.3.16]
119891775  ppp2r2aa; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform [KO:K04354]
119892165  ppp1cc; serine/threonine-protein phosphatase PP1-gamma catalytic subunit A [KO:K06269] [EC:3.1.3.16]
119892223  msi1b; RNA-binding protein Musashi homolog 1b isoform X1 [KO:K14411]
119892253  gle1; nucleoporin GLE1 [KO:K18723]
119893886  ppp1caa; protein phosphatase 1, catalytic subunit, alpha isozyme a [KO:K06269] [EC:3.1.3.16]
119895164  pcf11; pre-mRNA cleavage complex 2 protein Pcf11 [KO:K14400]
119895231  fus; LOW QUALITY PROTEIN: RNA-binding protein FUS [KO:K13098]
119895350  smg6; telomerase-binding protein EST1A isoform X1 [KO:K11124] [EC:3.1.-.-]
119895668  [KO:K14323]
119895758  ppp2cab; serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform [KO:K04382] [EC:3.1.3.16]
119895799  msi2b; RNA-binding protein Musashi homolog 2b isoform X1 [KO:K14411]
119896016  upf2; regulator of nonsense transcripts 2 isoform X1 [KO:K14327]
119896787  [KO:K14397]
119897106  smg5; protein SMG5 [KO:K11125]
119897109  rbm8a; RNA-binding protein 8A isoform X1 [KO:K12876]
119898081  [KO:K13126]
119899113  ppp2r2ca; protein phosphatase 2, regulatory subunit B, gamma a [KO:K04354]
119899142  fip1l1b; pre-mRNA 3'-end-processing factor FIP1 isoform X1 [KO:K14405]
119899749  [KO:K12881]
119899889  eif4a3; eukaryotic initiation factor 4A-III [KO:K13025] [EC:5.6.2.7]
119900153  [KO:K18723]
119900359  ncbp2; nuclear cap-binding protein subunit 2 [KO:K12883]
119900490  [KO:K14326] [EC:5.6.2.5 5.6.2.3]
119900508  dazap1; DAZ-associated protein 1 isoform X1 [KO:K14411]
119901068  fip1l1a; pre-mRNA 3'-end-processing factor FIP1 isoform X1 [KO:K14405]
119901229  magoh; protein mago nashi homolog [KO:K12877]
119901558  sap18; histone deacetylase complex subunit SAP18 [KO:K14324]
119902228  [KO:K14326] [EC:5.6.2.5 5.6.2.3]
119902741  smg7; protein SMG7 isoform X1 [KO:K14409]
119902794  wdr33; pre-mRNA 3' end processing protein WDR33 isoform X1 [KO:K15542]
119902995  acin1a; uncharacterized protein acin1a [KO:K12875]
119903431  sympk; symplekin [KO:K06100]
119904377  upf3a; regulator of nonsense transcripts 3A isoform X1 [KO:K14328]
119904389  ppp2r3b; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X1 [KO:K11583]
119905398  [KO:K13126]
119906066  zgc:193690; ATP-dependent RNA helicase DDX19A [KO:K18655] [EC:5.6.2.7]
119906101  pym1; partner of Y14 and mago [KO:K14294]
119907164  [KO:K13126]
119907282  rnmt; mRNA cap guanine-N7 methyltransferase [KO:K00565] [EC:2.1.1.56]
119907435  cpsf1; cleavage and polyadenylation specificity factor subunit 1 [KO:K14401]
119907542  pabpn1; polyadenylate-binding protein 2 isoform X1 [KO:K14396]
119908506  ppp2r5a; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform isoform X1 [KO:K11584]
119908532  [KO:K06269] [EC:3.1.3.16]
119908686  ppp2r5cb; protein phosphatase 2, regulatory subunit B', gamma b isoform X1 [KO:K11584]
119908807  cpsf2; cleavage and polyadenylation specificity factor subunit 2 [KO:K14402]
119908973  hbs1l; HBS1-like protein isoform X1 [KO:K14416]
119909240  [KO:K14376] [EC:2.7.7.19]
119909395  [KO:K14403] [EC:3.1.27.-]
119909597  rngtt; mRNA-capping enzyme [KO:K13917] [EC:2.7.7.50 3.6.1.74]
119910005  ppp2r5eb; protein phosphatase 2, regulatory subunit B', epsilon isoform X1 [KO:K11584]
119910097  ppp2r5ca; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform isoform X1 [KO:K11584]
119910106  srrm1; serine/arginine repetitive matrix protein 1 isoform X1 [KO:K13171]
119910282  ppp2r3a; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit alpha isoform X1 [KO:K11583]
119910321  [KO:K06269] [EC:3.1.3.16]
119910343  pabpc4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
119910410  [KO:K14403] [EC:3.1.27.-]
119910731  ppp2r3c; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit gamma [KO:K11583]
119911017  pnn; pinin [KO:K13114]
119911460  acin1b; apoptotic chromatin condensation inducer 1b [KO:K12875]
119911738  ppp2r5b; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit beta isoform [KO:K11584]
119911846  [KO:K06269] [EC:3.1.3.16]
119915047  [KO:K04354]
119915271  [KO:K14323]
119915501  gspt1; eukaryotic peptide chain release factor GTP-binding subunit ERF3A [KO:K03267]
119915533  pelo; protein pelota homolog [KO:K06965]
119915534  ppp1cab; protein phosphatase 1, catalytic subunit, alpha isozyme b [KO:K06269] [EC:3.1.3.16]
119916032  [KO:K14325]
119917136  ppp2r2d; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform [KO:K04354]
119917377  papolg; poly(A) polymerase gamma isoform X1 [KO:K14376] [EC:2.7.7.19]
119917393  [KO:K14376] [EC:2.7.7.19]
119917949  cpsf6; LOW QUALITY PROTEIN: cleavage and polyadenylation specificity factor subunit 6 [KO:K14398]
119918350  smg1; serine/threonine-protein kinase SMG1 isoform X1 [KO:K08873] [EC:2.7.11.1]
119918475  gspt1l; G1 to S phase transition 1, like [KO:K03267]
119919222  [KO:K13126]
119919335  tardbpa; TAR DNA binding protein, like isoform X1 [KO:K23600]
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
msam03013  Nucleocytoplasmic transport
msam03018  RNA degradation
msam03040  Spliceosome
KO pathway
ko03015   

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