KEGG   PATHWAY: lco03015
Entry
lco03015                    Pathway                                
Name
mRNA surveillance pathway - Larimichthys crocea (large yellow croaker)
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
lco03015  mRNA surveillance pathway
lco03015

Other DBs
GO: 0071028
Organism
Larimichthys crocea (large yellow croaker) [GN:lco]
Gene
104938071  ncbp1; nuclear cap-binding protein subunit 1 [KO:K12882]
104938011  ncbp2; nuclear cap-binding protein subunit 2 [KO:K12883]
104926303  upf3a; regulator of nonsense transcripts 3A isoform X1 [KO:K14328]
104933365  rbm8a; RNA-binding protein 8A isoform X1 [KO:K12876]
104921747  protein mago nashi homolog [KO:K12877]
104937770  casc3; protein CASC3 [KO:K14323]
104935431  eif4a3; eukaryotic initiation factor 4A-III [KO:K13025] [EC:5.6.2.7]
104936898  sap18; histone deacetylase complex subunit SAP18 [KO:K14324]
104932906  apoptotic chromatin condensation inducer in the nucleus [KO:K12875]
104927977  apoptotic chromatin condensation inducer in the nucleus [KO:K12875]
104924145  RNA-binding protein with serine-rich domain 1-B [KO:K14325]
104933647  rnps1; RNA-binding protein with serine-rich domain 1 [KO:K14325]
104929524  alyref; THO complex subunit 4 [KO:K12881]
104920400  aly/REF export factor 2 isoform X1 [KO:K12881]
104938712  ATP-dependent RNA helicase DDX19B [KO:K18655] [EC:5.6.2.7]
104936306  ATP-dependent RNA helicase DDX19B [KO:K18655] [EC:5.6.2.7]
104934955  gle1; nucleoporin GLE1 [KO:K18723]
104925535  nxf1; nuclear RNA export factor 1 isoform X4 [KO:K14284]
104922445  nxt2; NTF2-related export protein 2 [KO:K14285]
104931065  spliceosome RNA helicase DDX39B isoform X1 [KO:K12812] [EC:5.6.2.7]
104919942  pym1; partner of Y14 and mago [KO:K14294]
104919315  srrm1; serine/arginine repetitive matrix protein 1 isoform X1 [KO:K13171]
104936194  rngtt; mRNA-capping enzyme [KO:K13917] [EC:2.7.7.50 3.6.1.74]
104931889  rnmt; mRNA cap guanine-N7 methyltransferase [KO:K00565] [EC:2.1.1.56]
109142515  fus; RNA-binding protein FUS [KO:K13098]
104924159  RNA-binding protein FUS [KO:K13098]
109137047  tardbp; TAR DNA-binding protein 43 [KO:K23600]
104922767  embryonic polyadenylate-binding protein 2-B [KO:K14396]
104927509  pabpn1; polyadenylate-binding protein 2 isoform X4 [KO:K14396]
104930373  nudt21; cleavage and polyadenylation specificity factor subunit 5 [KO:K14397]
104919233  cpsf7; cleavage and polyadenylation specificity factor subunit 7 [KO:K14398]
104940538  LOW QUALITY PROTEIN: cleavage and polyadenylation specificity factor subunit 6 [KO:K14398]
104925900  papolg; poly(A) polymerase gamma isoform X1 [KO:K14376] [EC:2.7.7.19]
104940282  poly(A) polymerase type 3 isoform X1 [KO:K14376] [EC:2.7.7.19]
104926119  pcf11; pre-mRNA cleavage complex 2 protein Pcf11 isoform X1 [KO:K14400]
104926991  cpsf1; cleavage and polyadenylation specificity factor subunit 1 [KO:K14401]
104930840  cpsf2; cleavage and polyadenylation specificity factor subunit 2 [KO:K14402]
104922138  cleavage and polyadenylation specificity factor subunit 3 [KO:K14403] [EC:3.1.27.-]
104938536  cleavage and polyadenylation specificity factor subunit 3 [KO:K14403] [EC:3.1.27.-]
104932071  cpsf4; cleavage and polyadenylation specificity factor subunit 4 [KO:K14404]
104919086  fip1l1; pre-mRNA 3'-end-processing factor FIP1 isoform X1 [KO:K14405]
104937414  pre-mRNA 3'-end-processing factor FIP1 isoform X1 [KO:K14405]
104936864  wdr33; pre-mRNA 3' end processing protein WDR33 isoform X1 [KO:K15542]
109136690  wdr82; WD repeat-containing protein 82 [KO:K14962]
104926366  ppp1cc; serine/threonine-protein phosphatase PP1-gamma catalytic subunit [KO:K06269] [EC:3.1.3.16]
104930710  serine/threonine-protein phosphatase alpha-2 isoform [KO:K06269] [EC:3.1.3.16]
104919667  serine/threonine-protein phosphatase PP1-beta catalytic subunit [KO:K06269] [EC:3.1.3.16]
104926887  serine/threonine-protein phosphatase alpha-2 isoform [KO:K06269] [EC:3.1.3.16]
104936456  serine/threonine-protein phosphatase PP1-beta catalytic subunit [KO:K06269] [EC:3.1.3.16]
104928004  ssu72; RNA polymerase II subunit A C-terminal domain phosphatase SSU72 [KO:K15544] [EC:3.1.3.16]
104929685  cstf1; cleavage stimulation factor subunit 1 [KO:K14406]
104928738  cstf2; cleavage stimulation factor subunit 2 isoform X1 [KO:K14407]
104927690  cstf3; cleavage stimulation factor subunit 3 [KO:K14408]
104925868  sympk; symplekin [KO:K06100]
104934384  msi2; RNA-binding protein Musashi homolog 2 isoform X4 [KO:K14411]
104928397  dazap1; DAZ-associated protein 1 isoform X5 [KO:K14411]
104937961  RNA-binding protein Musashi homolog 1 [KO:K14411]
104921056  msi1; RNA-binding protein Musashi homolog 1 isoform X1 [KO:K14411]
104935356  embryonic polyadenylate-binding protein A isoform X1 [KO:K13126]
104919307  pabpc4; polyadenylate-binding protein 4 [KO:K13126]
104931622  polyadenylate-binding protein 1 [KO:K13126]
104936343  pabpc1; polyadenylate-binding protein 1 isoform X1 [KO:K13126]
104934045  etf1; eukaryotic peptide chain release factor subunit 1 [KO:K03265]
104930119  eukaryotic peptide chain release factor GTP-binding subunit ERF3A [KO:K03267]
104918902  gspt1; eukaryotic peptide chain release factor GTP-binding subunit ERF3A [KO:K03267]
104920975  regulator of nonsense transcripts 1 [KO:K14326] [EC:5.6.2.5 5.6.2.3]
104930911  regulator of nonsense transcripts 1 [KO:K14326] [EC:5.6.2.5 5.6.2.3]
104927099  upf2; regulator of nonsense transcripts 2 isoform X1 [KO:K14327]
104938332  smg1; serine/threonine-protein kinase SMG1 isoform X2 [KO:K08873] [EC:2.7.11.1]
104937528  smg7; protein SMG7 isoform X1 [KO:K14409]
104929583  smg5; protein SMG5 [KO:K11125]
104925819  smg6; telomerase-binding protein EST1A [KO:K11124] [EC:3.1.-.-]
104938463  serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform [KO:K04382] [EC:3.1.3.16]
104935225  ppp2cb; serine/threonine-protein phosphatase 2A catalytic subunit beta isoform [KO:K04382] [EC:3.1.3.16]
104924365  ppp2ca; serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform [KO:K04382] [EC:3.1.3.16]
104918016  serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform [KO:K03456]
104929468  ppp2r2d; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform [KO:K04354]
104924353  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B gamma isoform [KO:K04354]
104923610  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform-like [KO:K04354]
104921711  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform [KO:K04354]
104922615  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B beta isoform isoform X1 [KO:K04354]
104924230  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B beta isoform isoform X2 [KO:K04354]
104935195  ppp2r3c; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit gamma [KO:K11583]
104920052  ppp2r3a; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit alpha isoform X1 [KO:K11583]
104926307  serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X1 [KO:K11583]
104937597  ppp2r5d; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform [KO:K11584]
104924693  serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform isoform X3 [KO:K11584]
104940385  serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform isoform X1 [KO:K11584]
104931237  ppp2r5a; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform isoform X1 [KO:K11584]
104929538  serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform isoform X4 [KO:K11584]
104918057  ppp2r5b; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit beta isoform [KO:K11584]
104925667  hbs1l; HBS1-like protein isoform X1 [KO:K14416]
104926888  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
lco03013  Nucleocytoplasmic transport
lco03018  RNA degradation
lco03040  Spliceosome
KO pathway
ko03015   
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