KEGG   PATHWAY: pcad03015
Entry
pcad03015                   Pathway                                
Name
mRNA surveillance pathway - Physeter catodon (sperm whale)
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
pcad03015  mRNA surveillance pathway
pcad03015

Other DBs
GO: 0071028
Organism
Physeter catodon (sperm whale) [GN:pcad]
Gene
102993683  NCBP1; nuclear cap-binding protein subunit 1 isoform X1 [KO:K12882]
102985544  NCBP2; nuclear cap-binding protein subunit 2 isoform X2 [KO:K12883]
112066142  NCBP2L; LOW QUALITY PROTEIN: nuclear cap-binding protein subunit 2-like [KO:K12883]
102980813  nuclear cap-binding protein subunit 2-like [KO:K12883]
102976918  UPF3B; regulator of nonsense transcripts 3B isoform X1 [KO:K14328]
102985235  UPF3A; LOW QUALITY PROTEIN: regulator of nonsense transcripts 3A [KO:K14328]
102981663  RBM8A; RNA-binding protein 8A isoform X1 [KO:K12876]
102983009  RNA-binding protein 8A-like [KO:K12876]
114483854  MAGOHB; protein mago nashi homolog 2 isoform X2 [KO:K12877]
102990179  MAGOH; protein mago nashi homolog [KO:K12877]
102986085  CASC3; protein CASC3 isoform X1 [KO:K14323]
102979387  eukaryotic initiation factor 4A-III [KO:K13025] [EC:5.6.2.7]
102988173  SAP18; histone deacetylase complex subunit SAP18 [KO:K14324]
102990934  PNN; pinin [KO:K13114]
102980214  ACIN1; apoptotic chromatin condensation inducer in the nucleus isoform X1 [KO:K12875]
102981144  RNPS1; RNA-binding protein with serine-rich domain 1 isoform X1 [KO:K14325]
102978259  LOW QUALITY PROTEIN: RNA-binding protein with serine-rich domain 1-like [KO:K14325]
102993393  ALYREF; THO complex subunit 4 [KO:K12881]
102988391  ATP-dependent RNA helicase DDX19B isoform X1 [KO:K18655] [EC:5.6.2.7]
102989045  ATP-dependent RNA helicase DDX19A [KO:K18655] [EC:5.6.2.7]
102980615  GLE1; mRNA export factor GLE1 isoform X3 [KO:K18723]
102977911  NXF1; nuclear RNA export factor 1 [KO:K14284]
102977204  nuclear RNA export factor 2 [KO:K14284]
114484661  LOW QUALITY PROTEIN: nuclear RNA export factor 2-like [KO:K14284]
102973772  LOW QUALITY PROTEIN: nuclear RNA export factor 3-like [KO:K14284]
102986802  nuclear RNA export factor 3-like [KO:K14284]
102994592  LOW QUALITY PROTEIN: nuclear RNA export factor 2-like [KO:K14284]
112066110  NTF2-related export protein 2-like [KO:K14285]
102976925  NTF2-related export protein 2-like [KO:K14285]
102996136  NXT1; NTF2-related export protein 1 [KO:K14285]
102978168  NTF2-related export protein 2 [KO:K14285]
102984110  DDX39B; spliceosome RNA helicase DDX39B [KO:K12812] [EC:5.6.2.7]
102994724  PYM1; partner of Y14 and mago [KO:K14294]
102980515  SRRM1; serine/arginine repetitive matrix protein 1 isoform X1 [KO:K13171]
102995880  RNGTT; mRNA-capping enzyme isoform X1 [KO:K13917] [EC:2.7.7.50 3.6.1.74]
102973220  RNMT; mRNA cap guanine-N7 methyltransferase isoform X2 [KO:K00565] [EC:2.1.1.56]
102986151  FUS; RNA-binding protein FUS isoform X1 [KO:K13098]
102992395  TARDBP; TAR DNA-binding protein 43 isoform X1 [KO:K23600]
102995347  embryonic polyadenylate-binding protein 2 isoform X1 [KO:K14396]
102975428  NUDT21; cleavage and polyadenylation specificity factor subunit 5 isoform X3 [KO:K14397]
102984616  LOW QUALITY PROTEIN: cleavage and polyadenylation specificity factor subunit 5-like [KO:K14397]
102990353  CPSF7; cleavage and polyadenylation specificity factor subunit 7 isoform X1 [KO:K14398]
102996967  CPSF6; cleavage and polyadenylation specificity factor subunit 6 isoform X1 [KO:K14398]
102976233  PAPOLA; poly(A) polymerase alpha isoform X1 [KO:K14376] [EC:2.7.7.19]
102989917  PAPOLB; poly(A) polymerase beta [KO:K14376] [EC:2.7.7.19]
102977323  PAPOLG; poly(A) polymerase gamma isoform X1 [KO:K14376] [EC:2.7.7.19]
102975489  CLP1; polyribonucleotide 5'-hydroxyl-kinase Clp1 isoform X2 [KO:K14399] [EC:2.7.1.78]
102986397  PCF11; pre-mRNA cleavage complex 2 protein Pcf11 isoform X1 [KO:K14400]
102995248  cleavage and polyadenylation specificity factor subunit 1 [KO:K14401]
102985688  CPSF2; cleavage and polyadenylation specificity factor subunit 2 [KO:K14402]
102977623  CPSF3; cleavage and polyadenylation specificity factor subunit 3 isoform X1 [KO:K14403] [EC:3.1.27.-]
102995601  CPSF4L; putative cleavage and polyadenylation specificity factor subunit 4-like protein [KO:K14404]
102996937  CPSF4; cleavage and polyadenylation specificity factor subunit 4 isoform X2 [KO:K14404]
102984231  FIP1L1; pre-mRNA 3'-end-processing factor FIP1 isoform X2 [KO:K14405]
102985139  WDR33; pre-mRNA 3' end processing protein WDR33 [KO:K15542]
102979577  WDR82; WD repeat-containing protein 82 [KO:K14962]
102991018  LOW QUALITY PROTEIN: WD repeat-containing protein 82-like [KO:K14962]
102981740  PPP1CA; serine/threonine-protein phosphatase PP1-alpha catalytic subunit [KO:K06269] [EC:3.1.3.16]
102992996  PPP1CB; serine/threonine-protein phosphatase PP1-beta catalytic subunit [KO:K06269] [EC:3.1.3.16]
102981359  PPP1CC; serine/threonine-protein phosphatase PP1-gamma catalytic subunit [KO:K06269] [EC:3.1.3.16]
102985060  SSU72; RNA polymerase II subunit A C-terminal domain phosphatase SSU72 [KO:K15544] [EC:3.1.3.16]
102996216  LOW QUALITY PROTEIN: RNA polymerase II subunit A C-terminal domain phosphatase SSU72 like protein 3-like [KO:K15544] [EC:3.1.3.16]
102994414  CSTF1; cleavage stimulation factor subunit 1 [KO:K14406]
102973701  CSTF2T; cleavage stimulation factor subunit 2 tau variant [KO:K14407]
102975355  CSTF2; cleavage stimulation factor subunit 2 isoform X1 [KO:K14407]
102987885  CSTF3; cleavage stimulation factor subunit 3 isoform X1 [KO:K14408]
102985779  SYMPK; symplekin [KO:K06100]
102990280  DAZAP1; DAZ-associated protein 1 isoform X3 [KO:K14411]
102994886  RNA-binding protein Musashi homolog 2 isoform X1 [KO:K14411]
102978204  MSI1; RNA-binding protein Musashi homolog 1 [KO:K14411]
114483957  RNA-binding protein Musashi homolog 2-like isoform X1 [KO:K14411]
102983303  PABPC5; polyadenylate-binding protein 5 [KO:K13126]
102979607  PABPC4L; polyadenylate-binding protein 4-like [KO:K13126]
102980694  PABPC4; polyadenylate-binding protein 4 [KO:K13126]
102993556  PABPC1L; polyadenylate-binding protein 1-like isoform X2 [KO:K13126]
102983711  PABPC1; polyadenylate-binding protein 1 isoform X1 [KO:K13126]
102976014  LOW QUALITY PROTEIN: polyadenylate-binding protein 4-like [KO:K13126]
102989536  PABPC1L2A; polyadenylate-binding protein 1-like 2 [KO:K13126]
102978330  LOW QUALITY PROTEIN: polyadenylate-binding protein 4-like [KO:K13126]
102982749  LOW QUALITY PROTEIN: polyadenylate-binding protein 4-like [KO:K13126]
102976626  ETF1; eukaryotic peptide chain release factor subunit 1 isoform X1 [KO:K03265]
102993302  GSPT1; eukaryotic peptide chain release factor GTP-binding subunit ERF3A isoform X3 [KO:K03267]
102984266  GSPT2; eukaryotic peptide chain release factor GTP-binding subunit ERF3B [KO:K03267]
102975873  UPF1; regulator of nonsense transcripts 1 isoform X1 [KO:K14326] [EC:5.6.2.5 5.6.2.3]
102984577  UPF2; regulator of nonsense transcripts 2 isoform X1 [KO:K14327]
102993856  SMG1; serine/threonine-protein kinase SMG1 isoform X3 [KO:K08873] [EC:2.7.11.1]
102984873  SMG7; nonsense-mediated mRNA decay factor SMG7 [KO:K14409]
102974695  SMG5; nonsense-mediated mRNA decay factor SMG5 [KO:K11125]
114483896  SMG6; telomerase-binding protein EST1A [KO:K11124] [EC:3.1.-.-]
102987480  telomerase-binding protein EST1A [KO:K11124] [EC:3.1.-.-]
102974912  PPP2CB; serine/threonine-protein phosphatase 2A catalytic subunit beta isoform [KO:K04382] [EC:3.1.3.16]
102993796  PPP2CA; serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform [KO:K04382] [EC:3.1.3.16]
102992184  PPP2R1A; serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform isoform X2 [KO:K03456]
102992659  PPP2R1B; serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform isoform X1 [KO:K03456]
102985759  PPP2R2C; protein phosphatase 2, regulatory subunit B, gamma isoform X1 [KO:K04354]
102982040  PPP2R2B; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B beta isoform isoform X1 [KO:K04354]
102976080  PPP2R2D; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform isoform X1 [KO:K04354]
102993492  PPP2R2A; serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform isoform X3 [KO:K04354]
102974323  PPP2R3C; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit gamma isoform X1 [KO:K11583]
102985008  PPP2R3A; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit alpha isoform X1 [KO:K11583]
102986162  PPP2R3B; serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta isoform X1 [KO:K11583]
102983421  PPP2R5A; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit alpha isoform [KO:K11584]
102994835  PPP2R5B; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit beta isoform isoform X1 [KO:K11584]
102984521  PPP2R5C; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform isoform X1 [KO:K11584]
102987078  PPP2R5E; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform isoform X1 [KO:K11584]
102996184  PPP2R5D; serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform [KO:K11584]
102983610  LOW QUALITY PROTEIN: serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform-like [KO:K11584]
102973257  HBS1L; HBS1-like protein isoform X1 [KO:K14416]
102977238  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
pcad03013  Nucleocytoplasmic transport
pcad03018  RNA degradation
pcad03040  Spliceosome
KO pathway
ko03015   
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