KEGG   PATHWAY: rkg03015
Entry
rkg03015                    Pathway                                
Name
mRNA surveillance pathway - Rhinichthys klamathensis goyatoka (western speckled dace)
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
rkg03015  mRNA surveillance pathway
rkg03015

Other DBs
GO: 0071028
Organism
Rhinichthys klamathensis goyatoka (western speckled dace) [GN:rkg]
Gene
130072502  nuclear cap-binding protein subunit 1 [KO:K12882]
130075382  ncbp2; nuclear cap-binding protein subunit 2 [KO:K12883]
130072987  upf3b; regulator of nonsense transcripts 3B [KO:K14328]
130069245  upf3a; regulator of nonsense transcripts 3A isoform X1 [KO:K14328]
130077684  rbm8a; RNA-binding protein 8A [KO:K12876]
130086105  magoh; protein mago nashi homolog [KO:K12877]
130070272  casc3; protein CASC3 isoform X1 [KO:K14323]
130078641  eif4a3; eukaryotic initiation factor 4A-III [KO:K13025] [EC:5.6.2.7]
130076324  sap18; histone deacetylase complex subunit SAP18 [KO:K14324]
130102664  acin1b; apoptotic chromatin condensation inducer 1b [KO:K12875]
130076185  acin1a; apoptotic chromatin condensation inducer in the nucleus isoform X1 [KO:K12875]
130070996  rnps1; RNA-binding protein with serine-rich domain 1 [KO:K14325]
130085240  alyref; THO complex subunit 4 isoform X1 [KO:K12881]
130090588  ddx19a; ATP-dependent RNA helicase DDX19A [KO:K18655] [EC:5.6.2.7]
130071778  ddx19b; ATP-dependent RNA helicase DDX19B isoform X1 [KO:K18655] [EC:5.6.2.7]
130073991  nxf1b; nuclear RNA export factor 1 [KO:K14284]
130084735  nxf1a; nuclear RNA export factor 1 [KO:K14284]
130075593  nxt2; NTF2-related export protein 2 [KO:K14285]
130087926  ddx39b; DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B [KO:K12812] [EC:5.6.2.7]
130079455  pym1; partner of Y14 and mago [KO:K14294]
130097510  srrm1; serine/arginine repetitive matrix protein 1 [KO:K13171]
130082605  rngtt; mRNA-capping enzyme [KO:K13917] [EC:2.7.7.50 3.6.1.74]
130088021  rnmt; mRNA cap guanine-N7 methyltransferase [KO:K00565] [EC:2.1.1.56]
130104366  taf15; TATA-binding protein-associated factor 2N isoform X1 [KO:K13098]
130088465  fus; RNA-binding protein FUS isoform X1 [KO:K13098]
130074127  tardbpa; TAR DNA binding protein, like isoform X1 [KO:K23600]
130089095  tardbpb; TAR DNA-binding protein 43 [KO:K23600]
130070425  pabpn1l; embryonic polyadenylate-binding protein 2 [KO:K14396]
130087680  pabpn1; polyadenylate-binding protein 2 isoform X1 [KO:K14396]
130088475  nudt21; cleavage and polyadenylation specificity factor subunit 5 isoform X1 [KO:K14397]
130080004  cpsf6; cleavage and polyadenylation specificity factor subunit 6 isoform X1 [KO:K14398]
130089625  papolg; poly(A) polymerase gamma isoform X1 [KO:K14376] [EC:2.7.7.19]
130096011  papola; poly(A) polymerase alpha isoform X1 [KO:K14376] [EC:2.7.7.19]
130095679  clp1; polyribonucleotide 5'-hydroxyl-kinase Clp1 isoform X1 [KO:K14399] [EC:2.7.1.78]
130096508  pcf11; pre-mRNA cleavage complex 2 protein Pcf11 [KO:K14400]
130088002  cpsf1; cleavage and polyadenylation specificity factor subunit 1 [KO:K14401]
130096182  cpsf2; cleavage and polyadenylation specificity factor subunit 2 [KO:K14402]
130075456  cpsf3; cleavage and polyadenylation specificity factor subunit 3 [KO:K14403] [EC:3.1.27.-]
130095001  cpsf4; cleavage and polyadenylation specificity factor subunit 4 isoform X1 [KO:K14404]
130091748  fip1l1a; pre-mRNA 3'-end-processing factor FIP1 [KO:K14405]
130071388  fip1l1b; pre-mRNA 3'-end-processing factor FIP1 isoform X1 [KO:K14405]
130098480  wdr33; pre-mRNA 3' end processing protein WDR33 isoform X1 [KO:K15542]
130087462  wdr82; WD repeat-containing protein 82 [KO:K14962]
130101112  ppp1cc; serine/threonine-protein phosphatase PP1-gamma catalytic subunit A [KO:K06269] [EC:3.1.3.16]
130073454  ppp1cb; serine/threonine-protein phosphatase PP1-beta catalytic subunit [KO:K06269] [EC:3.1.3.16]
130079564  serine/threonine-protein phosphatase PP1-beta catalytic subunit-like [KO:K06269] [EC:3.1.3.16]
130097247  ppp1caa; protein phosphatase 1, catalytic subunit, alpha isozyme a [KO:K06269] [EC:3.1.3.16]
130082409  ppp1cab; protein phosphatase 1, catalytic subunit, alpha isozyme b [KO:K06269] [EC:3.1.3.16]
130072723  ssu72; RNA polymerase II subunit A C-terminal domain phosphatase SSU72 [KO:K15544] [EC:3.1.3.16]
130085575  cstf1; cleavage stimulation factor subunit 1 [KO:K14406]
130103956  cstf2; cleavage stimulation factor subunit 2 isoform X1 [KO:K14407]
130069956  cstf3; cleavage stimulation factor subunit 3 [KO:K14408]
130082466  sympk; symplekin isoform X1 [KO:K06100]
130100873  dazap1; DAZ-associated protein 1 isoform X1 [KO:K14411]
130104590  msi2b; RNA-binding protein Musashi homolog 2b isoform X1 [KO:K14411]
130105328  msi2a; RNA-binding protein Musashi homolog 2a isoform X1 [KO:K14411]
130088198  RNA-binding protein Musashi homolog 1 isoform X1 [KO:K14411]
130081849  msi1b; RNA-binding protein Musashi homolog 1b isoform X1 [KO:K14411]
130091542  polyadenylate-binding protein 1A [KO:K13126]
130091574  polyadenylate-binding protein 1A-like [KO:K13126]
130088006  pabpc1b; polyadenylate-binding protein 1b [KO:K13126]
130097502  pabpc4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
130081997  pabpc1l; polyadenylate-binding protein 1-like isoform X1 [KO:K13126]
130082941  etf1b; eukaryotic peptide chain release factor subunit 1b isoform X1 [KO:K03265]
130086551  etf1a; eukaryotic peptide chain release factor subunit 1-like [KO:K03265]
130075868  gspt1l; G1 to S phase transition 1, like [KO:K03267]
130088593  gspt1; eukaryotic peptide chain release factor GTP-binding subunit ERF3A [KO:K03267]
130075336  upf1; regulator of nonsense transcripts 1 isoform X1 [KO:K14326] [EC:5.6.2.5 5.6.2.3]
130080076  upf2; regulator of nonsense transcripts 2 [KO:K14327]
130097233  smg1; serine/threonine-protein kinase SMG1 isoform X1 [KO:K08873] [EC:2.7.11.1]
130071538  smg7; LOW QUALITY PROTEIN: nonsense-mediated mRNA decay factor SMG7 [KO:K14409]
130079557  nonsense-mediated mRNA decay factor SMG5 [KO:K11125]
130074124  smg6; telomerase-binding protein EST1A [KO:K11124] [EC:3.1.-.-]
130077501  ppp2cab; serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform [KO:K04382] [EC:3.1.3.16]
130095675  ppp2caa; protein phosphatase 2 catalytic subunit alpha a [KO:K04382] [EC:3.1.3.16]
130099760  ppp2cb; serine/threonine-protein phosphatase 2A catalytic subunit beta isoform [KO:K04382] [EC:3.1.3.16]
130086756  ppp2r1ba; protein phosphatase 2, regulatory subunit A, beta a [KO:K03456]
130096714  ppp2r1bb; serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform [KO:K03456]
130072497  ppp2r2ba; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B beta isoform isoform X1 [KO:K04354]
130090629  ppp2r2d; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform [KO:K04354]
130084774  ppp2r2cb; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B beta isoform [KO:K04354]
130095495  serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B beta isoform isoform X1 [KO:K04354]
130087068  ppp2r2ab; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform [KO:K04354]
130071383  ppp2r2ca; protein phosphatase 2, regulatory subunit B, gamma a [KO:K04354]
130069234  ppp2r3b; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X1 [KO:K11583]
130070893  ppp2r3a; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit alpha isoform X1 [KO:K11583]
130084507  ppp2r5d; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform isoform X1 [KO:K11584]
130102710  ppp2r5b; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit beta isoform [KO:K11584]
130096034  ppp2r5a; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform [KO:K11584]
130088230  ppp2r5eb; protein phosphatase 2, regulatory subunit B', epsilon [KO:K11584]
130097561  ppp2r5ea; protein phosphatase 2, regulatory subunit B', epsilon [KO:K11584]
130071828  ppp2r5ca; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform isoform X1 [KO:K11584]
130082328  ppp2r5cb; protein phosphatase 2, regulatory subunit B', gamma b isoform X1 [KO:K11584]
130075274  hbs1l; HBS1-like protein isoform X1 [KO:K14416]
130082408  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
rkg03013  Nucleocytoplasmic transport
rkg03018  RNA degradation
rkg03040  Spliceosome
KO pathway
ko03015   
LinkDB

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