ENTRY       osa03015                    Pathway
NAME        mRNA surveillance pathway - Oryza sativa japonica (Japanese rice) (RefSeq)
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 osa03015  mRNA surveillance pathway
DBLINKS     GO: 0071028
ORGANISM    Oryza sativa japonica (Japanese rice) (RefSeq) [GN:osa]
GENE        4332822  LOW QUALITY PROTEIN: nuclear cap-binding protein subunit 1-like [KO:K12882]
            4329963  nuclear cap-binding protein subunit 2 [KO:K12883]
            4335928  regulator of nonsense transcripts UPF3 isoform X1 [KO:K14328]
            4337757  RNA-binding protein 8A [KO:K12876]
            4334528  RNA-binding protein 8A [KO:K12876]
            4351998  protein mago nashi homolog [KO:K12877]
            4344462  protein mago nashi homolog isoform X2 [KO:K12877]
            4326580  DEAD-box ATP-dependent RNA helicase 2 [KO:K13025] [EC:3.6.4.13]
            4333273  DEAD-box ATP-dependent RNA helicase 34 [KO:K13025] [EC:3.6.4.13]
            4328127  histone deacetylase complex subunit SAP18 [KO:K14324]
            4333834  pinin [KO:K13114]
            4343967  protein starmaker isoform X1 [KO:K12875]
            4332988  apoptotic chromatin condensation inducer in the nucleus [KO:K12875]
            4325394  serine/arginine-rich splicing factor SR45 isoform X1 [KO:K14325]
            4337561  serine/arginine-rich splicing factor SR45 isoform X1 [KO:K14325]
            4332426  THO complex subunit 4A [KO:K12881]
            4349526  THO complex subunit 4A isoform X1 [KO:K12881]
            4342793  THO complex subunit 4A isoform X1 [KO:K12881]
            4340675  THO complex subunit 4D [KO:K12881]
            4345621  THO complex subunit 4D isoform X1 [KO:K12881]
            4351236  THO complex subunit 4A isoform X1 [KO:K12881]
            4331680  DEAD-box ATP-dependent RNA helicase 38 [KO:K18655] [EC:3.6.4.13]
            4329863  protein GLE1 isoform X1 [KO:K18723]
            4326193  DEAD-box ATP-dependent RNA helicase 15 isoform X1 [KO:K12812] [EC:3.6.4.13]
            4326192  DEAD-box ATP-dependent RNA helicase 56 isoform X1 [KO:K12812] [EC:3.6.4.13]
            4332324  partner of Y14 and mago isoform X1 [KO:K14294]
            4332383  serine/arginine repetitive matrix protein 1 isoform X1 [KO:K13171]
            4351709  mRNA-capping enzyme [KO:K13917] [EC:2.7.7.50 3.6.1.74]
            4350086  mRNA-capping enzyme [KO:K13917] [EC:2.7.7.50 3.6.1.74]
            4344818  mRNA cap guanine-N7 methyltransferase 1 [KO:K00565] [EC:2.1.1.56]
            4330921  mRNA cap guanine-N7 methyltransferase 2 [KO:K00565] [EC:2.1.1.56]
            4324412  transcription initiation factor TFIID subunit 15b isoform X1 [KO:K13098]
            4340509  polyadenylate-binding protein 2 [KO:K14396]
            4330785  polyadenylate-binding protein 2 isoform X1 [KO:K14396]
            4337444  pre-mRNA cleavage factor Im 25 kDa subunit 2 [KO:K14397]
            4345502  pre-mRNA cleavage factor Im 25 kDa subunit 1 [KO:K14397]
            4345901  cleavage and polyadenylation specificity factor subunit 6 [KO:K14398]
            4347363  death-inducer obliterator 1 [KO:K14398]
            4340886  nuclear poly(A) polymerase 1 isoform X1 [KO:K14376] [EC:2.7.7.19]
            9268632  nuclear poly(A) polymerase 4 isoform X1 [KO:K14376] [EC:2.7.7.19]
            4328790  nuclear poly(A) polymerase 4 [KO:K14376] [EC:2.7.7.19]
            9272301  nuclear poly(A) polymerase 3 [KO:K14376] [EC:2.7.7.19]
            4344356  nuclear poly(A) polymerase 3 [KO:K14376] [EC:2.7.7.19]
            4324242  nuclear poly(A) polymerase 4 [KO:K14376] [EC:2.7.7.19]
            107275815  nuclear poly(A) polymerase 4-like [KO:K14376] [EC:2.7.7.19]
            4328733  protein CLP1 homolog [KO:K14399] [EC:2.7.1.78]
            4347878  polyadenylation and cleavage factor homolog 4 [KO:K14400]
            4344833  polyadenylation and cleavage factor homolog 4 isoform X1 [KO:K14400]
            9266269  probable cleavage and polyadenylation specificity factor subunit 1 isoform X1 [KO:K14401]
            4347905  cleavage and polyadenylation specificity factor subunit 2 [KO:K14402]
            4334816  cleavage and polyadenylation specificity factor subunit 3-I [KO:K14403] [EC:3.1.27.-]
            4341840  zinc finger CCCH domain-containing protein 45 [KO:K14404]
            4325772  flowering time control protein FY [KO:K15542]
            4339488  WD repeat-containing protein 82 [KO:K14962]
            4343770  WD repeat-containing protein 82-B [KO:K14962]
            4331166  serine/threonine-protein phosphatase PP1 [KO:K06269] [EC:3.1.3.16]
            4332369  LOW QUALITY PROTEIN: serine/threonine-protein phosphatase PP1-like [KO:K06269] [EC:3.1.3.16]
            4345748  serine/threonine-protein phosphatase PP1 isozyme 2 isoform X1 [KO:K06269] [EC:3.1.3.16]
            4326473  serine/threonine-protein phosphatase PP1 [KO:K06269] [EC:3.1.3.16]
            4340228  serine/threonine-protein phosphatase PP1 [KO:K06269] [EC:3.1.3.16]
            4351607  RNA polymerase II subunit A C-terminal domain phosphatase SSU72 [KO:K15544] [EC:3.1.3.16]
            4334149  cleavage stimulation factor subunit 50 [KO:K14406]
            4349923  cleavage stimulating factor 64 [KO:K14407]
            4341950  cleavage stimulating factor 64 [KO:K14407]
            4352587  cleavage stimulation factor subunit 77 isoform X1 [KO:K14408]
            4344390  uncharacterized protein LOC4344390 isoform X1 [KO:K06100]
            4323885  uncharacterized protein LOC4323885 isoform X1 [KO:K06100]
            4350986  heterogeneous nuclear ribonucleoprotein 1 [KO:K14411]
            4348867  heterogeneous nuclear ribonucleoprotein 1 [KO:K14411]
            4325826  RNA-binding protein Musashi homolog 2 isoform X1 [KO:K14411]
            4342307  RNA-binding protein Musashi homolog Rbp6 [KO:K14411]
            4343740  heterogeneous nuclear ribonucleoprotein 1 [KO:K14411]
            4345242  polyadenylate-binding protein 2 [KO:K13126]
            4346409  polyadenylate-binding protein 2 [KO:K13126]
            4341408  polyadenylate-binding protein 4-like [KO:K13126]
            4336331  polyadenylate-binding protein 2 [KO:K13126]
            4337438  multiple RNA-binding domain-containing protein 1 [KO:K13126]
            4332428  polyadenylate-binding protein 7 [KO:K13126]
            4346605  30S ribosomal protein 2, chloroplastic [KO:K13126]
            4338603  eukaryotic peptide chain release factor subunit 1-2 [KO:K03265]
            4333840  eukaryotic peptide chain release factor subunit 1-3 [KO:K03265]
            4326511  eukaryotic peptide chain release factor subunit 1-3 [KO:K03265]
            4343757  eukaryotic peptide chain release factor subunit 1-3 [KO:K03265]
            4335338  eukaryotic peptide chain release factor GTP-binding subunit ERF3A [KO:K03267]
            4329282  eukaryotic peptide chain release factor GTP-binding subunit ERF3A isoform X1 [KO:K03267]
            4343292  regulator of nonsense transcripts 1 homolog isoform X1 [KO:K14326] [EC:3.6.4.13 5.6.2.3]
            4330058  regulator of nonsense transcripts UPF2 [KO:K14327]
            4334045  serine/threonine-protein kinase SMG1 [KO:K08873] [EC:2.7.11.1]
            4345227  protein SMG7 isoform X1 [KO:K14409]
            4341364  serine/threonine-protein phosphatase PP2A-1 catalytic subunit [KO:K04382] [EC:3.1.3.16]
            4328734  serine/threonine-protein phosphatase PP2A-3 catalytic subunit [KO:K04382] [EC:3.1.3.16]
            4331747  serine/threonine-protein phosphatase PP2A-4 catalytic subunit-like [KO:K04382] [EC:3.1.3.16]
            4334494  serine/threonine-protein phosphatase PP2A-2 catalytic subunit [KO:K04382] [EC:3.1.3.16]
            4348601  serine/threonine-protein phosphatase PP2A-4 catalytic subunit [KO:K04382] [EC:3.1.3.16]
            4346507  serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform isoform X1 [KO:K03456]
            4341313  serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform isoform X2 [KO:K04354]
            4328769  serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B beta isoform isoform X1 [KO:K04354]
            9270873  serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B beta isoform-like [KO:K04354]
            9266142  serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B beta isoform isoform X1 [KO:K04354]
            4328580  serine/threonine protein phosphatase 2A regulatory subunit B''beta [KO:K11583]
            4337821  probable serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit TON2 [KO:K11583]
            4348893  probable serine/threonine protein phosphatase 2A regulatory subunit B''delta [KO:K11583]
            4334757  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' theta isoform [KO:K11584]
            4337970  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' iota isoform [KO:K11584]
            4336207  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' theta isoform [KO:K11584]
            4339558  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' iota isoform [KO:K11584]
            4342912  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' theta isoform [KO:K11584]
            4344549  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' theta isoform [KO:K11584]
            4333730  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' beta isoform [KO:K11584]
            4347742  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' alpha isoform [KO:K11584]
            4323870  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' iota isoform [KO:K11584]
            4336848  HBS1-like protein isoform X1 [KO:K14416]
            4337409  HBS1-like protein [KO:K14416]
            4326095  HBS1-like protein isoform X1 [KO:K14416]
            9269039  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
REL_PATHWAY osa03013  Nucleocytoplasmic transport
            osa03018  RNA degradation
            osa03040  Spliceosome
KO_PATHWAY  ko03015
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