ENTRY       sly03015                    Pathway
NAME        mRNA surveillance pathway - Solanum lycopersicum (tomato)
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 sly03015  mRNA surveillance pathway
DBLINKS     GO: 0071028
ORGANISM    Solanum lycopersicum (tomato) [GN:sly]
GENE        101249122  nuclear cap-binding protein subunit 1 [KO:K12882]
            101268545  nuclear cap-binding protein subunit 2 [KO:K12883]
            101264766  regulator of nonsense transcripts UPF3 [KO:K14328]
            101263168  regulator of nonsense transcripts UPF3-like isoform X3 [KO:K14328]
            101248886  RNA-binding protein 8A-like [KO:K12876]
            101268456  protein mago nashi homolog [KO:K12877]
            101256152  eukaryotic initiation factor 4A-3 [KO:K13025] [EC:3.6.4.13]
            101260232  histone deacetylase complex subunit SAP18 [KO:K14324]
            101248146  pinin [KO:K13114]
            101245055  apoptotic chromatin condensation inducer in the nucleus [KO:K12875]
            101257116  serine/arginine-rich splicing factor SR45 isoform X2 [KO:K14325]
            101268859  THO complex subunit 4D-like isoform X2 [KO:K12881]
            101256343  THO complex subunit 4D [KO:K12881]
            101262878  THO complex subunit 4A [KO:K12881]
            101266904  RNA-binding (RRM/RBD/RNP motifs) family protein [KO:K12881]
            101252541  DEAD-box ATP-dependent RNA helicase 38 [KO:K18655] [EC:3.6.4.13]
            101243705  DEAD-box ATP-dependent RNA helicase 38 [KO:K18655] [EC:3.6.4.13]
            101248103  protein GLE1 isoform X1 [KO:K18723]
            101261336  DEAD-box ATP-dependent RNA helicase 56 isoform X1 [KO:K12812] [EC:3.6.4.13]
            101259772  DEAD-box ATP-dependent RNA helicase 56 isoform X1 [KO:K12812] [EC:3.6.4.13]
            101261756  partner of Y14 and mago [KO:K14294]
            101263053  serine/arginine repetitive matrix protein 1 [KO:K13171]
            101258480  mRNA-capping enzyme-like isoform X2 [KO:K13917] [EC:2.7.7.50 3.6.1.74]
            101267011  mRNA cap guanine-N7 methyltransferase 1-like [KO:K00565] [EC:2.1.1.56]
            101253413  mRNA cap guanine-N7 methyltransferase 1 [KO:K00565] [EC:2.1.1.56]
            101256441  mRNA cap guanine-N7 methyltransferase 2 isoform X1 [KO:K00565] [EC:2.1.1.56]
            101251999  transcription initiation factor TFIID subunit 15b [KO:K13098]
            101247002  polyadenylate-binding protein 1 [KO:K14396]
            101248758  polyadenylate-binding protein 1-like isoform X1 [KO:K14396]
            104646444  polyadenylate-binding protein 1 [KO:K14396]
            101268437  polyadenylate-binding protein 2 [KO:K14396]
            101260498  polyadenylate-binding protein 2 isoform X1 [KO:K14396]
            101268710  pre-mRNA cleavage factor Im 25 kDa subunit 2 [KO:K14397]
            101268418  pre-mRNA cleavage factor Im 25 kDa subunit 2 [KO:K14397]
            101249048  pre-mRNA cleavage factor Im 25 kDa subunit 2 [KO:K14397]
            101261536  pre-mRNA cleavage factor Im 25 kDa subunit 1 isoform X1 [KO:K14397]
            104649492  uncharacterized protein LOC104649492 [KO:K14398]
            101251182  LOW QUALITY PROTEIN: cleavage and polyadenylation specificity factor subunit 6 [KO:K14398]
            101251491  cleavage and polyadenylation specificity factor subunit 6 [KO:K14398]
            101251795  cleavage and polyadenylation specificity factor subunit 6-like [KO:K14398]
            101244314  nuclear poly(A) polymerase 3 [KO:K14376] [EC:2.7.7.19]
            101266027  nuclear poly(A) polymerase 1 [KO:K14376] [EC:2.7.7.19]
            101243972  nuclear poly(A) polymerase 3-like [KO:K14376] [EC:2.7.7.19]
            101268462  nuclear poly(A) polymerase 4 isoform X1 [KO:K14376] [EC:2.7.7.19]
            101247241  nuclear poly(A) polymerase 4-like isoform X3 [KO:K14376] [EC:2.7.7.19]
            101249197  protein CLP1 homolog [KO:K14399] [EC:2.7.1.78]
            101244024  polyadenylation and cleavage factor homolog 4 [KO:K14400]
            101246003  polyadenylation and cleavage factor homolog 4 [KO:K14400]
            101252266  polyadenylation and cleavage factor homolog 4 isoform X2 [KO:K14400]
            101246111  cleavage and polyadenylation specificity factor subunit 1 [KO:K14401]
            101254167  cleavage and polyadenylation specificity factor subunit 2 [KO:K14402]
            101265747  cleavage and polyadenylation specificity factor subunit 3-I [KO:K14403] [EC:3.1.27.-]
            101263950  30-kDa cleavage and polyadenylation specificity factor 30 [KO:K14404]
            101254355  30-kDa cleavage and polyadenylation specificity factor 30 isoform X1 [KO:K14404]
            101251819  GATA zinc finger domain-containing protein 14 isoform X1 [KO:K14404]
            101252128  E3 ubiquitin ligase PQT3-like [KO:K15541]
            101263044  flowering time control protein FY isoform X2 [KO:K15542]
            101250377  protein ANTHESIS POMOTING FACTOR 1 isoform X1 [KO:K14962]
            101258611  ubiquitin ligase complex subunit 1-like [KO:K14962]
            101258308  serine/threonine-protein phosphatase PP1 [KO:K06269] [EC:3.1.3.16]
            101251329  serine/threonine-protein phosphatase PP1 [KO:K06269] [EC:3.1.3.16]
            101249363  serine/threonine-protein phosphatase PP1 [KO:K06269] [EC:3.1.3.16]
            101249463  serine/threonine-protein phosphatase PP1 isozyme 2 [KO:K06269] [EC:3.1.3.16]
            101260053  serine/threonine-protein phosphatase PP1 isozyme 1 [KO:K06269] [EC:3.1.3.16]
            101243716  serine/threonine-protein phosphatase PP1 isozyme 2 [KO:K06269] [EC:3.1.3.16]
            101254698  serine/threonine-protein phosphatase PP1 isozyme 3 [KO:K06269] [EC:3.1.3.16]
            101248465  RNA polymerase II subunit A C-terminal domain phosphatase SSU72 [KO:K15544] [EC:3.1.3.16]
            101264599  cleavage stimulation factor subunit 50 isoform X2 [KO:K14406]
            101252047  cleavage stimulating factor 64 [KO:K14407]
            101254235  cleavage stimulating factor 64 [KO:K14407]
            101249869  cleavage stimulation factor subunit 77 isoform X5 [KO:K14408]
            101249356  uncharacterized protein LOC101249356 [KO:K06100]
            101252517  uncharacterized protein LOC101252517 [KO:K06100]
            101267485  RNA-binding protein 1 [KO:K14411]
            101264892  heterogeneous nuclear ribonucleoprotein 1-like [KO:K14411]
            101267666  heterogeneous nuclear ribonucleoprotein A0 [KO:K14411]
            101254896  RNA-binding protein 1 [KO:K14411]
            101260528  heterogeneous nuclear ribonucleoprotein 1 [KO:K14411]
            101261462  heterogeneous nuclear ribonucleoprotein 1 [KO:K14411]
            101266100  heterogeneous nuclear ribonucleoprotein 1 [KO:K14411]
            101256558  heterogeneous nuclear ribonucleoprotein 1 [KO:K14411]
            101260293  heterogeneous nuclear ribonucleoprotein 1 [KO:K14411]
            101250612  heterogeneous nuclear ribonucleoprotein 1 isoform X2 [KO:K14411]
            101247161  heterogeneous nuclear ribonucleoprotein 1 isoform X1 [KO:K14411]
            101260765  heterogeneous nuclear ribonucleoprotein 1 [KO:K14411]
            101258105  polyadenylate-binding protein 8-like [KO:K13126]
            101248632  polyadenylate-binding protein 7-like [KO:K13126]
            101264108  polyadenylate-binding protein 3 isoform X2 [KO:K13126]
            101261596  polyadenylate-binding protein 2-like [KO:K13126]
            101266448  polyadenylate-binding protein 7 [KO:K13126]
            101246720  eukaryotic peptide chain release factor subunit 1-3 [KO:K03265]
            101251066  eukaryotic peptide chain release factor subunit 1-3 [KO:K03265]
            101261770  eukaryotic peptide chain release factor subunit 1-3 [KO:K03265]
            101255309  eukaryotic peptide chain release factor subunit 1-3-like [KO:K03265]
            101268089  LOW QUALITY PROTEIN: eukaryotic peptide chain release factor GTP-binding subunit ERF3A [KO:K03267]
            101244963  eukaryotic peptide chain release factor GTP-binding subunit ERF3A isoform X1 [KO:K03267]
            101253276  regulator of nonsense transcripts UPF2 isoform X1 [KO:K14327]
            101268042  serine/threonine-protein kinase SMG1-like [KO:K08873] [EC:2.7.11.1]
            101244332  protein SMG7-like [KO:K14409]
            101247106  protein SMG7-like [KO:K14409]
            101257003  serine/threonine-protein phosphatase PP2A catalytic subunit [KO:K04382] [EC:3.1.3.16]
            101245881  serine/threonine-protein phosphatase PP2A-5 catalytic subunit [KO:K04382] [EC:3.1.3.16]
            101252803  serine/threonine-protein phosphatase PP2A catalytic subunit [KO:K04382] [EC:3.1.3.16]
            544183  PP2Ac1; protein phosphatase 2A catalytic subunit [KO:K04382] [EC:3.1.3.16]
            544262  PP2Ac2; protein phosphatase 2A catalytic subunit [KO:K04382] [EC:3.1.3.16]
            101248570  serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform-like isoform X1 [KO:K03456]
            101267244  protein phosphatase 2A subunit A [KO:K03456]
            101259540  serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform isoform X1 [KO:K03456]
            101246329  serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B beta isoform isoform X2 [KO:K04354]
            101251957  serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B beta isoform isoform X2 [KO:K04354]
            101260240  serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B beta isoform [KO:K04354]
            101256096  serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B beta isoform isoform X1 [KO:K04354]
            101244115  probable serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit TON2 [KO:K11583]
            101251680  serine/threonine protein phosphatase 2A regulatory subunit B''beta isoform X2 [KO:K11583]
            101245749  calcium-binding EF-hand family protein [KO:K11583]
            101256045  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' beta isoform-like [KO:K11584]
            101251646  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' theta isoform [KO:K11584]
            101250942  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' theta isoform [KO:K11584]
            101264630  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' beta isoform isoform X1 [KO:K11584]
            101257402  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' beta isoform [KO:K11584]
            101268818  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' beta isoform [KO:K11584]
            101244838  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' kappa isoform-like [KO:K11584]
            101243899  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' iota isoform [KO:K11584]
            101257170  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' theta isoform [KO:K11584]
            101246839  serine/threonine protein phosphatase 2A 59 kDa regulatory subunit B' gamma isoform [KO:K11584]
            101264306  HBS1-like protein isoform X1 [KO:K14416]
            101256564  HBS1-like protein isoform X1 [KO:K14416]
            101246581  protein PELOTA 1-like [KO:K06965]
            101251671  PELOTA; 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
REL_PATHWAY sly03013  Nucleocytoplasmic transport
            sly03018  RNA degradation
            sly03040  Spliceosome
KO_PATHWAY  ko03015
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