KEGG   PATHWAY: omy03015
Entry
omy03015                    Pathway                                
Name
mRNA surveillance pathway - Oncorhynchus mykiss (rainbow trout)
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
omy03015  mRNA surveillance pathway
omy03015

Other DBs
GO: 0071028
Organism
Oncorhynchus mykiss (rainbow trout) [GN:omy]
Gene
100136054  [KO:K12881]
100136137  [KO:K14376] [EC:2.7.7.19]
100301754  nxt2; NTF2-related export protein 2 [KO:K14285]
100301863  cpsf5; cleavage and polyadenylation specificity factor subunit 5 [KO:K14397]
100305168  [KO:K12876]
100305325  wdr82; WD repeat-containing protein 82 [KO:K14962]
110485929  [KO:K12881]
110486084  [KO:K13025] [EC:5.6.2.7]
110486181  [KO:K14323]
110486660  [KO:K06269] [EC:3.1.3.16]
110486741  [KO:K03267]
110486981  [KO:K14325]
110487146  [KO:K08873] [EC:2.7.11.1]
110487670  rbm8a; RNA-binding protein 8A isoform X1 [KO:K12876]
110487700  [KO:K04354]
110487742  smg5; protein SMG5 [KO:K11125]
110487804  rnmt; mRNA cap guanine-N7 methyltransferase [KO:K00565] [EC:2.1.1.56]
110488198  [KO:K14401]
110488703  [KO:K03265]
110488732  cstf2; cleavage stimulation factor subunit 2 isoform X1 [KO:K14407]
110488835  [KO:K14399] [EC:2.7.1.78]
110488875  [KO:K12882]
110488971  upf3b; regulator of nonsense transcripts 3B [KO:K14328]
110489078  zgc:153681; nuclear RNA export factor 1 isoform X1 [KO:K14284]
110489177  [KO:K04382] [EC:3.1.3.16]
110489347  pabpc1b; polyadenylate-binding protein 1b isoform X1 [KO:K13126]
110489775  pabpn1; polyadenylate-binding protein 2-B isoform X1 [KO:K14396]
110490094  pcf11; pre-mRNA cleavage complex 2 protein Pcf11 isoform X1 [KO:K14400]
110490193  [KO:K14327]
110491457  [KO:K14325]
110491766  pelo; protein pelota homolog isoform X1 [KO:K06965]
110491770  ppp1cab; protein phosphatase 1, catalytic subunit, alpha isozyme b [KO:K06269] [EC:3.1.3.16]
110491896  [KO:K23600]
110492074  [KO:K18655] [EC:5.6.2.7]
110492123  [KO:K14294]
110492327  [KO:K14326] [EC:5.6.2.5 5.6.2.3]
110492471  pabpc1l; polyadenylate-binding protein 1-like [KO:K13126]
110492806  smg6; telomerase-binding protein EST1A isoform X1 [KO:K11124] [EC:3.1.-.-]
110493654  [KO:K12881]
110493798  [KO:K13025] [EC:5.6.2.7]
110494131  [KO:K14411]
110494370  ssu72; RNA polymerase II subunit A C-terminal domain phosphatase SSU72 [KO:K15544] [EC:3.1.3.16]
110494662  [KO:K23600]
110494764  ddx19; ATP-dependent RNA helicase DDX19B [KO:K18655] [EC:5.6.2.7]
110494845  cstf1; cleavage stimulation factor subunit 1 [KO:K14406]
110494976  [KO:K14962]
110495638  [KO:K14324]
110495709  ppp2r3a; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit alpha isoform X1 [KO:K11583]
110495874  [KO:K14411]
110495915  [KO:K13126]
110496377  [KO:K14401]
110496721  ddx39b; spliceosome RNA helicase DDX39B [KO:K12812] [EC:5.6.2.7]
110497069  [KO:K11583]
110497722  [KO:K13114]
110497830  [KO:K11584]
110498014  srrm1; serine/arginine repetitive matrix protein 1 isoform X1 [KO:K13171]
110498021  pabpc4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
110498183  ppp2r5ca; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform isoform X1 [KO:K11584]
110499084  gspt1; eukaryotic peptide chain release factor GTP-binding subunit ERF3A [KO:K03267]
110499704  [KO:K14398]
110500263  [KO:K14327]
110500325  [KO:K11584]
110500490  [KO:K12875]
110500690  [KO:K06269] [EC:3.1.3.16]
110500955  [KO:K14398]
110501261  upf3a; regulator of nonsense transcripts 3A isoform X1 [KO:K14328]
110501265  ppp2r3b; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X1 [KO:K11583]
110502361  [KO:K11584]
110502483  [KO:K04354]
110502883  [KO:K03267]
110503518  taf15; TATA-binding protein-associated factor 2N isoform X1 [KO:K13098]
110503528  [KO:K03456]
110504066  msi1a; RNA-binding protein Musashi homolog 2 isoform X1 [KO:K14411]
110504529  [KO:K04382] [EC:3.1.3.16]
110504850  [KO:K04354]
110504899  [KO:K03265]
110504931  [KO:K14407]
110505041  [KO:K14399] [EC:2.7.1.78]
110505072  [KO:K12882]
110505181  [KO:K14328]
110505199  [KO:K11584]
110505429  [KO:K13126]
110505433  [KO:K13171]
110505634  [KO:K11584]
110505737  ppp2r3c; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit gamma [KO:K11583]
110505740  pnn; pinin [KO:K13114]
110506194  cstf3; cleavage stimulation factor subunit 3 [KO:K14408]
110506414  [KO:K14396]
110506663  [KO:K14398]
110507354  [KO:K13098]
110507360  ppp2r1bb; serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform [KO:K03456]
110507900  [KO:K14411]
110508482  acin1a; apoptotic chromatin condensation inducer in the nucleus [KO:K12875]
110508759  smg7; protein SMG7 isoform X1 [KO:K14409]
110508900  [KO:K14326] [EC:5.6.2.5 5.6.2.3]
110509534  [KO:K04382] [EC:3.1.3.16]
110509872  [KO:K04354]
110509974  [KO:K14284]
110510045  sympk; symplekin isoform X1 [KO:K06100]
110510097  [KO:K14405]
110510236  [KO:K11124] [EC:3.1.-.-]
110510589  [KO:K14376] [EC:2.7.7.19]
110512931  [KO:K14404]
110513555  [KO:K14405]
110515194  [KO:K11125]
110515636  [KO:K14405]
110515783  pabpc1a; polyadenylate-binding protein 1A isoform X1 [KO:K13126]
110516989  [KO:K04354]
110517086  [KO:K04354]
110518374  [KO:K14404]
110519445  [KO:K08873] [EC:2.7.11.1]
110519597  ppp2r5b; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit beta isoform [KO:K11584]
110519965  [KO:K14328]
110520308  [KO:K14397]
110521087  [KO:K14402]
110521668  fip1l1a; pre-mRNA 3'-end-processing factor FIP1 isoform X1 [KO:K14405]
110521779  [KO:K12877]
110522027  [KO:K11584]
110522061  cpsf3; cleavage and polyadenylation specificity factor subunit 3 [KO:K14403] [EC:3.1.27.-]
110522104  rngtt; mRNA-capping enzyme [KO:K13917] [EC:2.7.7.50 3.6.1.74]
110522490  ppp2r5cb; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform isoform X1 [KO:K11584]
110522515  [KO:K06269] [EC:3.1.3.16]
110522579  [KO:K14376] [EC:2.7.7.19]
110523185  ppp2cb; serine/threonine-protein phosphatase 2A catalytic subunit beta isoform [KO:K04382] [EC:3.1.3.16]
110523658  ppp2r2ab; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform [KO:K04354]
110524138  [KO:K14326] [EC:5.6.2.5 5.6.2.3]
110524168  [KO:K14411]
110524693  magoh; protein mago nashi homolog [KO:K12877]
110524821  ncbp2; nuclear cap-binding protein subunit 2 [KO:K12883]
110525529  [KO:K06269] [EC:3.1.3.16]
110525548  [KO:K14411]
110525620  [KO:K04354]
110526131  [KO:K04382] [EC:3.1.3.16]
110526299  pabpn1l; embryonic polyadenylate-binding protein 2-B isoform X1 [KO:K14396]
110526442  [KO:K14397]
110526532  [KO:K14398]
110527312  [KO:K14324]
110527436  [KO:K11584]
110527705  [KO:K18655] [EC:5.6.2.7]
110527802  [KO:K23600]
110528064  [KO:K15544] [EC:3.1.3.16]
110528278  [KO:K14411]
110529206  [KO:K04354]
110529414  ppp2r5a; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform [KO:K11584]
110529774  [KO:K14402]
110529802  [KO:K06269] [EC:3.1.3.16]
110529847  [KO:K11584]
110529960  wdr33; pre-mRNA 3' end processing protein WDR33 isoform X1 [KO:K15542]
110530135  [KO:K14326] [EC:5.6.2.5 5.6.2.3]
110530300  [KO:K14409]
110530602  [KO:K12875]
110531487  papolg; poly(A) polymerase gamma [KO:K14376] [EC:2.7.7.19]
110531579  [KO:K04354]
110531633  acin1b; apoptotic chromatin condensation inducer in the nucleus isoform X1 [KO:K12875]
110531833  [KO:K06269] [EC:3.1.3.16]
110532324  tardbpl; TAR DNA binding protein, like isoform X2 [KO:K23600]
110532539  [KO:K14294]
110532588  [KO:K18655] [EC:5.6.2.7]
110532856  [KO:K14416]
110532938  [KO:K04354]
110533330  [KO:K04354]
110533384  [KO:K04382] [EC:3.1.3.16]
110533864  [KO:K14411]
110533894  [KO:K03265]
110533985  [KO:K14284]
110535217  [KO:K14396]
110535889  gle1; nucleoporin GLE1 isoform X1 [KO:K18723]
110535906  [KO:K06269] [EC:3.1.3.16]
110535923  msi1b; RNA-binding protein Musashi homolog 1 isoform X1 [KO:K14411]
110535982  [KO:K04354]
110537225  [KO:K03265]
110537258  [KO:K14411]
110537728  [KO:K04382] [EC:3.1.3.16]
110537784  ppp2r2bb; protein phosphatase 2, regulatory subunit B, beta b isoform X1 [KO:K04354]
110538103  [KO:K14323]
110538528  [KO:K12881]
110538620  ppp1caa; protein phosphatase 1, catalytic subunit, alpha isozyme a [KO:K06269] [EC:3.1.3.16]
110538689  [KO:K03267]
110538821  [KO:K14325]
110539084  fus; RNA-binding protein FUS isoform X1 [KO:K13098]
118938226  [KO:K12812] [EC:5.6.2.7]
118938227  [KO:K12812] [EC:5.6.2.7]
118938717  [KO:K04354]
118946024  [KO:K04354]
118946056  [KO:K04354]
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
omy03013  Nucleocytoplasmic transport
omy03018  RNA degradation
omy03040  Spliceosome
KO pathway
ko03015   

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