KEGG   PATHWAY: sita03015
Entry
sita03015                   Pathway                                
Name
mRNA surveillance pathway - Setaria italica (foxtail millet)
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
sita03015  mRNA surveillance pathway
sita03015

Other DBs
GO: 0071028
Organism
Setaria italica (foxtail millet) [GN:sita]
Gene
101767718  LOW QUALITY PROTEIN: nuclear cap-binding protein subunit 1 [KO:K12882]
101783000  nuclear cap-binding protein subunit 2 [KO:K12883]
101781144  regulator of nonsense transcripts UPF3 [KO:K14328]
101774955  RNA-binding protein Y14A [KO:K12876]
101760799  RNA-binding protein Y14B [KO:K12876]
101779089  RNA-binding protein Y14A [KO:K12876]
101774134  protein mago nashi homolog 1 [KO:K12877]
101759099  protein mago nashi homolog 1 [KO:K12877]
101758423  eukaryotic initiation factor 4A-III homolog A [KO:K13025] [EC:5.6.2.7]
101777611  histone deacetylase complex subunit SAP18 [KO:K14324]
101782940  pinin [KO:K13114]
101758731  uncharacterized protein LOC101758731 isoform X1 [KO:K12875]
101756757  apoptotic chromatin condensation inducer in the nucleus [KO:K12875]
101765576  serine/arginine-rich splicing factor SR45 isoform X2 [KO:K14325]
101777845  THO complex subunit 4D isoform X1 [KO:K12881]
101757827  THO complex subunit 4A isoform X1 [KO:K12881]
101785030  THO complex subunit 4B [KO:K12881]
101753852  THO complex subunit 4D [KO:K12881]
101768390  THO complex subunit 4A [KO:K12881]
101768942  DEAD-box ATP-dependent RNA helicase 38 [KO:K18655] [EC:5.6.2.7]
101775435  protein GLE1 [KO:K18723]
101779223  DEAD-box ATP-dependent RNA helicase 15 [KO:K12812] [EC:5.6.2.7]
101753358  DEAD-box ATP-dependent RNA helicase 15 isoform X1 [KO:K12812] [EC:5.6.2.7]
101759209  partner of Y14 and mago [KO:K14294]
101767855  serine/arginine repetitive matrix protein 1 [KO:K13171]
101755911  mRNA-capping enzyme isoform X1 [KO:K13917] [EC:2.7.7.50 3.6.1.74]
101763425  mRNA cap guanine-N7 methyltransferase 1 [KO:K00565] [EC:2.1.1.56]
101776969  mRNA cap guanine-N7 methyltransferase 2 [KO:K00565] [EC:2.1.1.56]
111257411  LOW QUALITY PROTEIN: transcription initiation factor TFIID subunit 15b [KO:K13098]
101757345  polyadenylate-binding protein 2 [KO:K14396]
101767449  polyadenylate-binding protein 2 isoform X2 [KO:K14396]
101768004  polyadenylate-binding protein 1 isoform X1 [KO:K14396]
101784135  pre-mRNA cleavage factor Im 25 kDa subunit 2 [KO:K14397]
101780585  pre-mRNA cleavage factor Im 25 kDa subunit 1 [KO:K14397]
101773012  U1 small nuclear ribonucleoprotein 70 kDa [KO:K14398]
101760232  nuclear poly(A) polymerase 1 [KO:K14376] [EC:2.7.7.19]
101774058  nuclear poly(A) polymerase 3 isoform X1 [KO:K14376] [EC:2.7.7.19]
101768533  nuclear poly(A) polymerase 4 isoform X2 [KO:K14376] [EC:2.7.7.19]
101771822  LOW QUALITY PROTEIN: nuclear poly(A) polymerase 4-like [KO:K14376] [EC:2.7.7.19]
101779428  nuclear poly(A) polymerase 4 [KO:K14376] [EC:2.7.7.19]
101779504  nuclear poly(A) polymerase 4 [KO:K14376] [EC:2.7.7.19]
101765756  LOW QUALITY PROTEIN: nuclear poly(A) polymerase 3 [KO:K14376] [EC:2.7.7.19]
101758957  protein CLP1 homolog [KO:K14399] [EC:2.7.1.78]
101756392  polyadenylation and cleavage factor homolog 4 [KO:K14400]
101762925  probable cleavage and polyadenylation specificity factor subunit 1 [KO:K14401]
101764527  cleavage and polyadenylation specificity factor subunit 2 [KO:K14402]
101772119  cleavage and polyadenylation specificity factor subunit 3-I [KO:K14403] [EC:3.1.27.-]
101765271  zinc finger CCCH domain-containing protein 45 [KO:K14404]
101780563  flowering time control protein FY [KO:K15542]
101757146  protein ANTHESIS POMOTING FACTOR 1 [KO:K14962]
101761853  protein ANTHESIS POMOTING FACTOR 1 isoform X3 [KO:K14962]
101754784  serine/threonine-protein phosphatase PP1 [KO:K06269] [EC:3.1.3.16]
101785098  serine/threonine-protein phosphatase PP1 [KO:K06269] [EC:3.1.3.16]
101777876  serine/threonine-protein phosphatase PP1 [KO:K06269] [EC:3.1.3.16]
101778653  serine/threonine-protein phosphatase PP1 isozyme 1 [KO:K06269] [EC:3.1.3.16]
101775041  serine/threonine-protein phosphatase PP1 [KO:K06269] [EC:3.1.3.16]
101763111  LOW QUALITY PROTEIN: serine/threonine-protein phosphatase PP1 [KO:K06269] [EC:3.1.3.16]
101783713  serine/threonine-protein phosphatase PP1 [KO:K06269] [EC:3.1.3.16]
101766173  RNA polymerase II subunit A C-terminal domain phosphatase SSU72 [KO:K15544] [EC:3.1.3.16]
101785487  LOW QUALITY PROTEIN: cleavage stimulation factor subunit 50 [KO:K14406]
101762996  cleavage stimulating factor 64 [KO:K14407]
101758207  LOW QUALITY PROTEIN: cleavage stimulation factor subunit 2-like [KO:K14407]
101777805  LOW QUALITY PROTEIN: cleavage stimulating factor 64-like [KO:K14407]
101780017  cleavage stimulation factor subunit 77 [KO:K14408]
101783541  uncharacterized protein LOC101783541 [KO:K06100]
101757641  uncharacterized protein LOC101757641 [KO:K06100]
101769825  heterogeneous nuclear ribonucleoprotein 1 [KO:K14411]
101757070  RNA-binding protein Musashi homolog 2 [KO:K14411]
101771943  RNA-binding protein 1 [KO:K14411]
101766561  heterogeneous nuclear ribonucleoprotein 1 [KO:K14411]
101763753  heterogeneous nuclear ribonucleoprotein 1 [KO:K14411]
101769460  heterogeneous nuclear ribonucleoprotein D-like [KO:K14411]
101776600  heterogeneous nuclear ribonucleoprotein 1 [KO:K14411]
101768325  30S ribosomal protein 2, chloroplastic [KO:K13126]
101772489  polyadenylate-binding protein 8 [KO:K13126]
101756777  polyadenylate-binding protein 4-like [KO:K13126]
101769033  polyadenylate-binding protein 2 [KO:K13126]
101768678  LOW QUALITY PROTEIN: polyadenylate-binding protein 5-like [KO:K13126]
101780068  eukaryotic peptide chain release factor subunit 1-3 [KO:K03265]
101776581  eukaryotic peptide chain release factor subunit 1-2 [KO:K03265]
101781722  eukaryotic peptide chain release factor subunit 1-3 [KO:K03265]
101786486  eukaryotic peptide chain release factor GTP-binding subunit ERF3A [KO:K03267]
101763040  eukaryotic peptide chain release factor GTP-binding subunit ERF3A [KO:K03267]
101755895  regulator of nonsense transcripts 1 homolog [KO:K14326] [EC:5.6.2.5 5.6.2.3]
101757870  regulator of nonsense transcripts UPF2 [KO:K14327]
101768463  regulator of nonsense transcripts UPF2 isoform X1 [KO:K14327]
101758768  serine/threonine-protein kinase SMG1 [KO:K08873] [EC:2.7.11.1]
101780864  protein SMG7 [KO:K14409]
101759356  serine/threonine-protein phosphatase PP2A-1 catalytic subunit [KO:K04382] [EC:3.1.3.16]
101762976  serine/threonine-protein phosphatase PP2A-1 catalytic subunit [KO:K04382] [EC:3.1.3.16]
101778772  serine/threonine-protein phosphatase PP2A-2 catalytic subunit [KO:K04382] [EC:3.1.3.16]
101780683  serine/threonine-protein phosphatase PP2A-4 catalytic subunit [KO:K04382] [EC:3.1.3.16]
101774981  putative serine/threonine-protein phosphatase PP2A-4 catalytic subunit [KO:K04382] [EC:3.1.3.16]
101765054  serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform [KO:K03456]
101773428  serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform isoform X1 [KO:K03456]
101782451  serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B beta isoform [KO:K04354]
101763964  serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B beta isoform isoform X1 [KO:K04354]
101779476  serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform isoform X1 [KO:K04354]
101766110  serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B beta isoform isoform X1 [KO:K04354]
101761912  serine/threonine protein phosphatase 2A regulatory subunit B''beta [KO:K11583]
101763779  probable serine/threonine protein phosphatase 2A regulatory subunit B''delta [KO:K11583]
101762149  probable serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit TON2 [KO:K11583]
101770877  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' theta isoform [KO:K11584]
101756915  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' kappa isoform [KO:K11584]
101752870  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' kappa isoform [KO:K11584]
101761989  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' kappa isoform [KO:K11584]
101765639  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' kappa isoform [KO:K11584]
101786253  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' theta isoform isoform X1 [KO:K11584]
101762003  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' theta isoform [KO:K11584]
101770619  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' theta isoform [KO:K11584]
101756466  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' alpha isoform [KO:K11584]
101778612  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' alpha isoform [KO:K11584]
101766190  HBS1-like protein isoform X1 [KO:K14416]
101755671  HBS1-like protein [KO:K14416]
101766735  protein PELOTA 1 [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
sita03013  Nucleocytoplasmic transport
sita03018  RNA degradation
sita03040  Spliceosome
KO pathway
ko03015   
LinkDB

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