ENTRY       mtr03015                    Pathway
NAME        mRNA surveillance pathway - Medicago truncatula (barrel medic)
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 mtr03015  mRNA surveillance pathway
DBLINKS     GO: 0071028
ORGANISM    Medicago truncatula (barrel medic) [GN:mtr]
GENE        11429115  nuclear cap-binding protein subunit 1 [KO:K12882]
            25487697  nuclear cap-binding protein subunit 2 [KO:K12883]
            11430328  regulator of nonsense transcripts UPF3 isoform X1 [KO:K14328]
            11419393  regulator of nonsense transcripts UPF3 isoform X2 [KO:K14328]
            11427477  RNA-binding protein Y14A [KO:K12876]
            11423378  protein mago nashi homolog [KO:K12877]
            11421539  protein mago nashi homolog [KO:K12877]
            25488222  eukaryotic initiation factor 4A-3 [KO:K13025] [EC:3.6.4.13]
            25500995  histone deacetylase complex subunit SAP18 [KO:K14324]
            11421161  pinin [KO:K13114]
            11439947  actin cytoskeleton-regulatory complex protein PAN1 [KO:K12875]
            11408942  formin-like protein 5 [KO:K12875]
            11406805  serine/arginine-rich splicing factor SR45 [KO:K14325]
            11406653  THO complex subunit 4D [KO:K12881]
            25492480  THO complex subunit 4A [KO:K12881]
            11446087  THO complex subunit 4B [KO:K12881]
            25492156  LOW QUALITY PROTEIN: DEAD-box ATP-dependent RNA helicase 38 [KO:K18655] [EC:3.6.4.13]
            11434133  DEAD-box ATP-dependent RNA helicase 38 [KO:K18655] [EC:3.6.4.13]
            11414779  protein GLE1 isoform X1 [KO:K18723]
            11431965  DEAD-box ATP-dependent RNA helicase 15 [KO:K12812] [EC:3.6.4.13]
            25491302  DEAD-box ATP-dependent RNA helicase 15 isoform X1 [KO:K12812] [EC:3.6.4.13]
            11424505  DEAD-box ATP-dependent RNA helicase 15 isoform X1 [KO:K12812] [EC:3.6.4.13]
            11423581  partner of Y14 and mago [KO:K14294]
            11427645  serine/arginine repetitive matrix protein 1 [KO:K13171]
            25498713  mRNA-capping enzyme [KO:K13917] [EC:2.7.7.50 3.6.1.74]
            11416372  mRNA-capping enzyme isoform X1 [KO:K13917] [EC:2.7.7.50 3.6.1.74]
            11442053  mRNA cap guanine-N7 methyltransferase 1 isoform X1 [KO:K00565] [EC:2.1.1.56]
            11443469  mRNA cap guanine-N7 methyltransferase 2 [KO:K00565] [EC:2.1.1.56]
            25495070  mRNA cap guanine-N7 methyltransferase 1 isoform X1 [KO:K00565] [EC:2.1.1.56]
            11409261  transcription initiation factor TFIID subunit 15b isoform X1 [KO:K13098]
            11433289  polyadenylate-binding protein 1 isoform X1 [KO:K14396]
            25501878  polyadenylate-binding protein 2 isoform X1 [KO:K14396]
            11406230  polyadenylate-binding protein 2 [KO:K14396]
            25483206  polyadenylate-binding protein 2 [KO:K14396]
            25484152  polyadenylate-binding protein 2 [KO:K14396]
            25485080  pre-mRNA cleavage factor Im 25 kDa subunit 2 [KO:K14397]
            25486436  pre-mRNA cleavage factor Im 25 kDa subunit 1 [KO:K14397]
            25489148  uncharacterized PE-PGRS family protein PE_PGRS54 [KO:K14398]
            25489149  uncharacterized PE-PGRS family protein PE_PGRS54 [KO:K14398]
            11414390  nuclear poly(A) polymerase 1 isoform X1 [KO:K14376] [EC:2.7.7.19]
            25490147  nuclear poly(A) polymerase 4 isoform X1 [KO:K14376] [EC:2.7.7.19]
            11434036  nuclear poly(A) polymerase 4-like [KO:K14376] [EC:2.7.7.19]
            11422260  nuclear poly(A) polymerase 1 [KO:K14376] [EC:2.7.7.19]
            11428339  protein CLP1 homolog [KO:K14399] [EC:2.7.1.78]
            11435271  uncharacterized protein LOC11435271 isoform X1 [KO:K14400]
            25495279  polyadenylation and cleavage factor homolog 4 [KO:K14400]
            25483891  uncharacterized protein LOC25483891 [KO:K14400]
            25497136  cleavage and polyadenylation specificity factor subunit 1 [KO:K14401]
            25483257  cleavage and polyadenylation specificity factor subunit 2 [KO:K14402]
            11424192  cleavage and polyadenylation specificity factor subunit 3-I [KO:K14403] [EC:3.1.27.-]
            25486300  30-kDa cleavage and polyadenylation specificity factor 30 [KO:K14404]
            25486959  putative uncharacterized protein DDB_G0286901 isoform X1 [KO:K14404]
            11443981  flowering time control protein FY [KO:K15542]
            25501403  protein ANTHESIS POMOTING FACTOR 1 isoform X1 [KO:K14962]
            25495223  protein ANTHESIS POMOTING FACTOR 1 [KO:K14962]
            11432243  serine/threonine-protein phosphatase PP1 [KO:K06269] [EC:3.1.3.16]
            11425683  serine/threonine-protein phosphatase PP1 [KO:K06269] [EC:3.1.3.16]
            11413712  serine/threonine-protein phosphatase PP1 isozyme 1 [KO:K06269] [EC:3.1.3.16]
            25502117  serine/threonine-protein phosphatase PP1 [KO:K06269] [EC:3.1.3.16]
            11406064  serine/threonine-protein phosphatase PP1 isozyme 4 [KO:K06269] [EC:3.1.3.16]
            11419847  serine/threonine-protein phosphatase PP1 isozyme 3 isoform X1 [KO:K06269] [EC:3.1.3.16]
            11424441  serine/threonine-protein phosphatase PP1 isozyme 3 [KO:K06269] [EC:3.1.3.16]
            11431740  serine/threonine-protein phosphatase PP1 isoform X2 [KO:K06269] [EC:3.1.3.16]
            25480900  RNA polymerase II subunit A C-terminal domain phosphatase SSU72 [KO:K15544] [EC:3.1.3.16]
            112418104  putative ubiquitin-conjugating enzyme E2 38 [KO:K15544] [EC:3.1.3.16]
            11419557  cleavage stimulation factor subunit 50 [KO:K14406]
            25485016  cleavage stimulating factor 64 [KO:K14407]
            11408840  cleavage stimulation factor subunit 77 [KO:K14408]
            25491448  symplekin [KO:K06100]
            25490161  uncharacterized protein LOC25490161 isoform X1 [KO:K06100]
            11416649  heterogeneous nuclear ribonucleoprotein 1 [KO:K14411]
            11438007  heterogeneous nuclear ribonucleoprotein 1 [KO:K14411]
            120577404  RNA-binding protein Musashi homolog 2-like isoform X1 [KO:K14411]
            11410929  RNA-binding protein Musashi homolog 2 [KO:K14411]
            25489991  heterogeneous nuclear ribonucleoprotein 1 [KO:K14411]
            11424064  heterogeneous nuclear ribonucleoprotein 1 [KO:K14411]
            25484388  heterogeneous nuclear ribonucleoprotein 1 [KO:K14411]
            11440749  30S ribosomal protein 2, chloroplastic [KO:K13126]
            120575892  polyadenylate-binding protein 3-like [KO:K13126]
            25496270  LOW QUALITY PROTEIN: polyadenylate-binding protein 2 [KO:K13126]
            11434760  polyadenylate-binding protein 7 [KO:K13126]
            11429679  polyadenylate-binding protein 2 [KO:K13126]
            11445084  polyadenylate-binding protein 8 [KO:K13126]
            120580863  polyadenylate-binding protein 3-like [KO:K13126]
            112422765  polyadenylate-binding protein 3-like [KO:K13126]
            120580892  polyadenylate-binding protein 3-like [KO:K13126]
            120580893  polyadenylate-binding protein 3-like [KO:K13126]
            11419187  polyadenylate-binding protein 2 [KO:K13126]
            11420789  polyadenylate-binding protein 7 [KO:K13126]
            25485028  polyadenylate-binding protein 3 [KO:K13126]
            11413561  eukaryotic peptide chain release factor subunit 1-3 [KO:K03265]
            25497360  eukaryotic peptide chain release factor subunit 1-3 [KO:K03265]
            11427620  eukaryotic peptide chain release factor subunit 1-3 [KO:K03265]
            11409629  eukaryotic peptide chain release factor GTP-binding subunit ERF3A isoform X1 [KO:K03267]
            25496771  eukaryotic peptide chain release factor GTP-binding subunit ERF3A isoform X1 [KO:K03267]
            11422854  regulator of nonsense transcripts UPF2 isoform X1 [KO:K14327]
            11414460  serine/threonine-protein kinase SMG1 [KO:K08873] [EC:2.7.11.1]
            25480553  protein SMG7 [KO:K14409]
            11431860  protein SMG7 [KO:K14409]
            11416610  serine/threonine-protein phosphatase PP2A catalytic subunit [KO:K04382] [EC:3.1.3.16]
            11426573  serine/threonine-protein phosphatase PP2A-4 catalytic subunit [KO:K04382] [EC:3.1.3.16]
            25499560  serine/threonine-protein phosphatase PP2A catalytic subunit [KO:K04382] [EC:3.1.3.16]
            11406603  serine/threonine-protein phosphatase PP2A catalytic subunit [KO:K04382] [EC:3.1.3.16]
            25496859  protein phosphatase PP2A regulatory subunit A [KO:K03456]
            25485524  serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform [KO:K03456]
            11425778  serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B beta isoform isoform X1 [KO:K04354]
            25500415  serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B beta isoform isoform X1 [KO:K04354]
            11419844  serine/threonine protein phosphatase 2A 55 kDa regulatory subunit B beta isoform [KO:K04354]
            11424481  probable serine/threonine protein phosphatase 2A regulatory subunit B''delta [KO:K11583]
            11409007  probable serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit TON2 [KO:K11583]
            11434607  serine/threonine protein phosphatase 2A regulatory subunit B''beta [KO:K11583]
            11435115  probable serine/threonine protein phosphatase 2A regulatory subunit B''delta [KO:K11583]
            25485642  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' beta isoform [KO:K11584]
            11432697  serine/threonine protein phosphatase 2A 59 kDa regulatory subunit B' gamma isoform [KO:K11584]
            11446412  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' theta isoform [KO:K11584]
            11431523  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' kappa isoform [KO:K11584]
            25499334  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' beta isoform [KO:K11584]
            25495704  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' theta isoform [KO:K11584]
            11441590  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' kappa isoform [KO:K11584]
            11429629  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' kappa isoform [KO:K11584]
            25483949  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' beta isoform [KO:K11584]
            25485546  serine/threonine protein phosphatase 2A 57 kDa regulatory subunit B' beta isoform [KO:K11584]
            11406169  elongation factor 1-alpha isoform X2 [KO:K14416]
            11432958  protein PELOTA 1 [KO:K06965]
            25484607  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 mtr03013  Nucleocytoplasmic transport
            mtr03018  RNA degradation
            mtr03040  Spliceosome
KO_PATHWAY  ko03015
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