KEGG   PATHWAY: slal03015
Entry
slal03015                   Pathway                                
Name
mRNA surveillance pathway - Seriola lalandi dorsalis (Yellowtail amberjack)
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
slal03015  mRNA surveillance pathway
slal03015

Other DBs
GO: 0071028
Organism
Seriola lalandi dorsalis (Yellowtail amberjack) [GN:slal]
Gene
111644638  ncbp1; nuclear cap-binding protein subunit 1 [KO:K12882]
111671779  ncbp2; nuclear cap-binding protein subunit 2 [KO:K12883]
111648320  upf3b; regulator of nonsense transcripts 3B [KO:K14328]
111653837  upf3a; regulator of nonsense transcripts 3A isoform X1 [KO:K14328]
111655643  rbm8a; RNA-binding protein 8A isoform X1 [KO:K12876]
111671961  protein mago nashi homolog [KO:K12877]
111652915  casc3; protein CASC3 [KO:K14323]
111651352  eif4a3; eukaryotic initiation factor 4A-III [KO:K13025] [EC:5.6.2.7]
111646043  sap18; histone deacetylase complex subunit SAP18 [KO:K14324]
111673730  pnn; pinin [KO:K13114]
111647173  apoptotic chromatin condensation inducer in the nucleus-like [KO:K12875]
111647202  apoptotic chromatin condensation inducer in the nucleus-like isoform X1 [KO:K12875]
111666578  apoptotic chromatin condensation inducer in the nucleus-like [KO:K12875]
111657730  RNA-binding protein with serine-rich domain 1-like [KO:K14325]
111654585  RNA-binding protein with serine-rich domain 1-like [KO:K14325]
111660396  THO complex subunit 4-like [KO:K12881]
111647521  alyref; THO complex subunit 4 isoform X1 [KO:K12881]
111667741  ATP-dependent RNA helicase DDX19A [KO:K18655] [EC:5.6.2.7]
111669362  ATP-dependent RNA helicase DDX19A-like [KO:K18655] [EC:5.6.2.7]
111645676  gle1; nucleoporin GLE1 [KO:K18723]
111655825  nxf1; nuclear RNA export factor 1 isoform X1 [KO:K14284]
111651837  NTF2-related export protein 2-like [KO:K14285]
111646479  NTF2-related export protein 2-like [KO:K14285]
111653987  NTF2-related export protein 2-like [KO:K14285]
111645609  spliceosome RNA helicase DDX39B [KO:K12812] [EC:5.6.2.7]
111661926  pym1; partner of Y14 and mago [KO:K14294]
111644559  serine/arginine repetitive matrix protein 1-like [KO:K13171]
111650095  srrm1; serine/arginine repetitive matrix protein 1 isoform X1 [KO:K13171]
111661520  rngtt; mRNA-capping enzyme [KO:K13917] [EC:2.7.7.50 3.6.1.74]
111659054  rnmt; mRNA cap guanine-N7 methyltransferase [KO:K00565] [EC:2.1.1.56]
111651163  fus; RNA-binding protein FUS [KO:K13098]
111655313  RNA-binding protein FUS-like [KO:K13098]
111670674  tardbp; TAR DNA-binding protein 43 isoform X1 [KO:K23600]
111653824  TAR DNA-binding protein 43-like isoform X1 [KO:K23600]
111648218  pabpn1; polyadenylate-binding protein 2 isoform X1 [KO:K14396]
111668278  pabpn1l; embryonic polyadenylate-binding protein 2 [KO:K14396]
111646235  nudt21; cleavage and polyadenylation specificity factor subunit 5 isoform X1 [KO:K14397]
111654824  cleavage and polyadenylation specificity factor subunit 7-like [KO:K14398]
111663652  cpsf6; cleavage and polyadenylation specificity factor subunit 6 isoform X1 [KO:K14398]
111646340  papolb; poly(A) polymerase beta [KO:K14376] [EC:2.7.7.19]
111669495  papolg; poly(A) polymerase gamma isoform X1 [KO:K14376] [EC:2.7.7.19]
111662733  clp1; polyribonucleotide 5'-hydroxyl-kinase Clp1 [KO:K14399] [EC:2.7.1.78]
111653007  pcf11; pre-mRNA cleavage complex 2 protein Pcf11 [KO:K14400]
111671455  cpsf1; cleavage and polyadenylation specificity factor subunit 1 [KO:K14401]
111661506  cpsf2; cleavage and polyadenylation specificity factor subunit 2 [KO:K14402]
111644788  cpsf3; cleavage and polyadenylation specificity factor subunit 3 [KO:K14403] [EC:3.1.27.-]
111672593  cleavage and polyadenylation specificity factor subunit 3-like [KO:K14403] [EC:3.1.27.-]
111647589  cpsf4; cleavage and polyadenylation specificity factor subunit 4 [KO:K14404]
111664557  fip1l1; pre-mRNA 3'-end-processing factor FIP1 isoform X1 [KO:K14405]
111666656  pre-mRNA 3'-end-processing factor FIP1-like [KO:K14405]
111666556  pre-mRNA 3'-end-processing factor FIP1-like [KO:K14405]
111659197  pre-mRNA 3' end processing protein WDR33-like [KO:K15542]
111667234  pre-mRNA 3' end processing protein WDR33-like [KO:K15542]
111653822  WD repeat-containing protein 82 [KO:K14962]
111660802  WD repeat-containing protein 82-like [KO:K14962]
111652244  serine/threonine-protein phosphatase alpha-2 isoform-like [KO:K06269] [EC:3.1.3.16]
111665361  serine/threonine-protein phosphatase PP1-gamma catalytic subunit B-like [KO:K06269] [EC:3.1.3.16]
111670459  serine/threonine-protein phosphatase PP1-beta catalytic subunit [KO:K06269] [EC:3.1.3.16]
111647878  ppp1cc; serine/threonine-protein phosphatase PP1-gamma catalytic subunit [KO:K06269] [EC:3.1.3.16]
111661496  serine/threonine-protein phosphatase PP1-beta catalytic subunit-like [KO:K06269] [EC:3.1.3.16]
111660545  serine/threonine-protein phosphatase alpha-2 isoform-like [KO:K06269] [EC:3.1.3.16]
111651017  serine/threonine-protein phosphatase PP1-beta catalytic subunit-like [KO:K06269] [EC:3.1.3.16]
111660812  ssu72; RNA polymerase II subunit A C-terminal domain phosphatase SSU72 [KO:K15544] [EC:3.1.3.16]
111668596  cstf1; cleavage stimulation factor subunit 1 [KO:K14406]
111652579  cstf2; cleavage stimulation factor subunit 2 isoform X1 [KO:K14407]
111645908  cstf3; cleavage stimulation factor subunit 3 isoform X1 [KO:K14408]
111667457  sympk; symplekin [KO:K06100]
111654308  RNA-binding protein Musashi homolog 2-like [KO:K14411]
111644938  msi1; RNA-binding protein Musashi homolog 1 [KO:K14411]
111663827  msi2; RNA-binding protein Musashi homolog 2 isoform X1 [KO:K14411]
111669991  dazap1; DAZ-associated protein 1 isoform X1 [KO:K14411]
111670985  RNA-binding protein Musashi homolog 1-like [KO:K14411]
111668731  RNA-binding protein Musashi homolog 2-like [KO:K14411]
111664133  polyadenylate-binding protein 1-like [KO:K13126]
111667171  embryonic polyadenylate-binding protein-like [KO:K13126]
111659242  polyadenylate-binding protein 1 isoform X1 [KO:K13126]
111650094  pabpc4; polyadenylate-binding protein 4 [KO:K13126]
111646642  etf1; eukaryotic peptide chain release factor subunit 1 [KO:K03265]
111646112  gspt1; eukaryotic peptide chain release factor GTP-binding subunit ERF3A [KO:K03267]
111667218  eukaryotic peptide chain release factor GTP-binding subunit ERF3A isoform X1 [KO:K03267]
111649927  regulator of nonsense transcripts 1 isoform X1 [KO:K14326] [EC:5.6.2.5 5.6.2.3]
111671095  regulator of nonsense transcripts 1-like [KO:K14326] [EC:5.6.2.5 5.6.2.3]
111657667  upf2; regulator of nonsense transcripts 2 isoform X1 [KO:K14327]
111647790  smg1; serine/threonine-protein kinase SMG1 [KO:K08873] [EC:2.7.11.1]
111649846  smg7; protein SMG7 [KO:K14409]
111655678  smg5; protein SMG5 [KO:K11125]
111662657  smg6; telomerase-binding protein EST1A isoform X1 [KO:K11124] [EC:3.1.-.-]
111670703  serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform-like [KO:K04382] [EC:3.1.3.16]
111659986  ppp2ca; serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform [KO:K04382] [EC:3.1.3.16]
111651955  serine/threonine-protein phosphatase 2A catalytic subunit beta isoform-like [KO:K04382] [EC:3.1.3.16]
111652704  serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform-like [KO:K04382] [EC:3.1.3.16]
111670499  serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform-like [KO:K04382] [EC:3.1.3.16]
111649884  serine/threonine-protein phosphatase 2A catalytic subunit beta isoform-like [KO:K04382] [EC:3.1.3.16]
111655990  ppp2r1b; serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform [KO:K03456]
111650154  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform [KO:K04354]
111649550  ppp2r2d; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform [KO:K04354]
111662795  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B beta isoform isoform X1 [KO:K04354]
111664507  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B gamma isoform-like [KO:K04354]
111645047  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform-like [KO:K04354]
111664661  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B beta isoform isoform X1 [KO:K04354]
111665844  ppp2r3a; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit alpha isoform X1 [KO:K11583]
111673724  ppp2r3c; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit gamma [KO:K11583]
111665785  serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta-like isoform X1 [KO:K11583]
111653839  serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta-like isoform X1 [KO:K11583]
111654333  ppp2r5e; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform isoform X1 [KO:K11584]
111661463  ppp2r5a; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform isoform X1 [KO:K11584]
111672623  serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform-like isoform X1 [KO:K11584]
111666431  ppp2r5b; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit beta isoform [KO:K11584]
111646209  serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform [KO:K11584]
111658894  serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform isoform X1 [KO:K11584]
111651217  hbs1l; HBS1-like protein isoform X1 [KO:K14416]
111652243  pelo; protein pelota homolog [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
slal03013  Nucleocytoplasmic transport
slal03018  RNA degradation
slal03040  Spliceosome
KO pathway
ko03015   
LinkDB

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