ENTRY       mtr03018                    Pathway
NAME        RNA degradation - Medicago truncatula (barrel medic)
DESCRIPTION The correct processing, quality control and turnover of cellular RNA molecules are critical to many aspects in the expression of genetic information. In eukaryotes, two major pathways of mRNA decay exist and both pathways are initiated by poly(A) shortening of the mRNA. In the 5' to 3' pathway, this is followed by decapping which then permits the 5' to 3' exonucleolytic degradation of transcripts. In the 3' to 5' pathway, the exosome, a large multisubunit complex, plays a key role. The exosome exists in archaeal cells, too. In bacteria, endoribonuclease E, a key enzyme involved in RNA decay and processing, organizes a protein complex called degradosome. RNase E or R interacts with the phosphate-dependent exoribonuclease polynucleotide phosphorylase, DEAD-box helicases, and additional factors in the RNA-degrading complex.
CLASS       Genetic Information Processing; Folding, sorting and degradation
PATHWAY_MAP mtr03018  RNA degradation
DBLINKS     GO: 0006401
ORGANISM    Medicago truncatula (barrel medic) [GN:mtr]
GENE        25484620  exosome complex component CSL4 [KO:K07573]
            11418314  exosome complex component RRP4 homolog [KO:K03679]
            11422163  putative exosome complex component rrp40 [KO:K03681]
            11420842  exosome complex component RRP43 [KO:K12586]
            11410037  exosome complex component RRP41-like [KO:K12587]
            11406638  exosome complex component RRP42 [KO:K12589]
            25482505  exosome complex component RRP42 [KO:K12589]
            11431768  exosome complex component RRP41 homolog [KO:K11600]
            11422609  exosome complex component RRP41 homolog isoform X1 [KO:K11600]
            11436468  exosome complex exonuclease RRP46 homolog [KO:K12590]
            11441855  exosome complex component RRP45A [KO:K03678]
            25483959  exosome complex component RRP45B [KO:K03678]
            11424636  exosome complex exonuclease RRP44 homolog A isoform X1 [KO:K12585] [EC:3.1.13.-]
            25495837  protein RRP6-like 2 [KO:K12591] [EC:3.1.13.-]
            11432643  protein RRP6-like 2 isoform X1 [KO:K12591] [EC:3.1.13.-]
            11431486  nuclear nucleic acid-binding protein C1D [KO:K12592]
            11432979  uncharacterized protein LOC11432979 [KO:K12592]
            11417386  uncharacterized protein LOC11417386 [KO:K12593]
            25487346  terminal nucleotidyltransferase 4A [KO:K03514] [EC:2.7.7.19]
            11442176  DExH-box ATP-dependent RNA helicase DExH10 [KO:K12598] [EC:3.6.4.13]
            11408570  DExH-box ATP-dependent RNA helicase DExH10 [KO:K12598] [EC:3.6.4.13]
            11442551  DExH-box ATP-dependent RNA helicase DExH9 [KO:K12598] [EC:3.6.4.13]
            25490766  DExH-box ATP-dependent RNA helicase DExH11 isoform X1 [KO:K12599] [EC:3.6.4.13]
            25494462  tetratricopeptide repeat protein SKI3 isoform X2 [KO:K12600]
            25494198  WD repeat-containing protein VIP3 [KO:K12602]
            25499554  carbon catabolite repressor protein 4 homolog 1-like isoform X2 [KO:K12603] [EC:3.1.13.4]
            25483569  carbon catabolite repressor protein 4 homolog 2 [KO:K12603] [EC:3.1.13.4]
            11416580  carbon catabolite repressor protein 4 homolog 4 [KO:K12603] [EC:3.1.13.4]
            25483567  carbon catabolite repressor protein 4 homolog 2 [KO:K12603] [EC:3.1.13.4]
            25483579  carbon catabolite repressor protein 4 homolog 2 isoform X1 [KO:K12603] [EC:3.1.13.4]
            11429926  CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
            11418070  probable NOT transcription complex subunit VIP2 isoform X1 [KO:K12605]
            25492462  probable NOT transcription complex subunit VIP2 isoform X2 [KO:K12605]
            11437872  CCR4-NOT transcription complex subunit 3 isoform X1 [KO:K12580]
            11417361  uncharacterized protein LOC11417361 isoform X2 [KO:K10643] [EC:2.3.2.27]
            11406476  uncharacterized protein LOC11406476 isoform X2 [KO:K10643] [EC:2.3.2.27]
            25484052  uncharacterized protein LOC25484052 isoform X2 [KO:K10643] [EC:2.3.2.27]
            112420417  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
            112416242  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
            112421400  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
            112416797  CCR4-NOT transcription complex subunit 9-like isoform X1 [KO:K12606]
            11421578  CCR4-NOT transcription complex subunit 9 [KO:K12606]
            11424425  CCR4-NOT transcription complex subunit 9 isoform X1 [KO:K12606]
            11407593  CCR4-NOT transcription complex subunit 9 [KO:K12606]
            11423385  CCR4-NOT transcription complex subunit 9 [KO:K12606]
            25488987  CCR4-NOT transcription complex subunit 9 [KO:K12606]
            11420285  CCR4-NOT transcription complex subunit 9 [KO:K12606]
            11444960  LOW QUALITY PROTEIN: CCR4-NOT transcription complex subunit 10 [KO:K12607]
            25484242  ABC transporter I family member 21 [KO:K12608]
            11410061  ABC transporter I family member 20 [KO:K12608]
            25485451  DExH-box ATP-dependent RNA helicase DExH5, mitochondrial [KO:K14442] [EC:3.6.4.13]
            11410150  DExH-box ATP-dependent RNA helicase DExH3 [KO:K14442] [EC:3.6.4.13]
            25501139  DExH-box ATP-dependent RNA helicase DExH3 [KO:K14442] [EC:3.6.4.13]
            11429946  DExH-box ATP-dependent RNA helicase DExH6 isoform X1 [KO:K14442] [EC:3.6.4.13]
            11424426  DExH-box ATP-dependent RNA helicase DExH1 isoform X1 [KO:K14442] [EC:3.6.4.13]
            11429426  uncharacterized CRM domain-containing protein At3g25440, chloroplastic isoform X1 [KO:K01148] [EC:3.1.13.4]
            112416806  poly(A)-specific ribonuclease PARN-like [KO:K01148] [EC:3.1.13.4]
            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]
            11414400  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
            25499412  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
            25495945  mRNA-decapping enzyme subunit 2 [KO:K12613] [EC:3.6.1.62]
            11427502  DEAD-box ATP-dependent RNA helicase 8 isoform X1 [KO:K12614] [EC:3.6.4.13]
            11436932  DEAD-box ATP-dependent RNA helicase 8 [KO:K12614] [EC:3.6.4.13]
            11444866  enhancer of mRNA-decapping protein 4 [KO:K12616]
            120577294  protein PAT1 homolog 1-like [KO:K12617]
            25487016  protein PAT1 homolog [KO:K12617]
            25487017  protein PAT1 homolog [KO:K12617]
            11421251  sm-like protein LSM1B [KO:K12620]
            11444969  sm-like protein LSM1B [KO:K12620]
            25499092  sm-like protein LSM2 [KO:K12621]
            11442020  sm-like protein LSM2 [KO:K12621]
            11446185  sm-like protein LSM3A [KO:K12622]
            11426059  sm-like protein LSM4 [KO:K12623]
            11430696  sm-like protein LSM4 [KO:K12623]
            25493392  sm-like protein LSM5 [KO:K12624]
            11420271  sm-like protein LSM6A [KO:K12625]
            25501029  sm-like protein LSM7 [KO:K12626]
            11407370  sm-like protein LSM7 [KO:K12626]
            25493016  sm-like protein LSM8 [KO:K12627]
            11446699  enolase [KO:K01689] [EC:4.2.1.11]
            25499389  enolase [KO:K01689] [EC:4.2.1.11]
            11442340  cytosolic enolase 3 [KO:K01689] [EC:4.2.1.11]
            25486813  enolase 1, chloroplastic [KO:K01689] [EC:4.2.1.11]
            11434901  polyribonucleotide nucleotidyltransferase 2, mitochondrial [KO:K00962] [EC:2.7.7.8]
            11438450  probable polyribonucleotide nucleotidyltransferase 1, chloroplastic [KO:K00962] [EC:2.7.7.8]
            25489175  probable ATP-dependent DNA helicase RecQ [KO:K03654] [EC:5.6.2.4]
            11423706  ATP-dependent 6-phosphofructokinase 5, chloroplastic [KO:K00850] [EC:2.7.1.11]
            11430664  ATP-dependent 6-phosphofructokinase 7 [KO:K00850] [EC:2.7.1.11]
            11415742  ATP-dependent 6-phosphofructokinase 3 [KO:K00850] [EC:2.7.1.11]
            11405809  ATP-dependent 6-phosphofructokinase 5, chloroplastic [KO:K00850] [EC:2.7.1.11]
            25494344  LOW QUALITY PROTEIN: ATP-dependent 6-phosphofructokinase 2 [KO:K00850] [EC:2.7.1.11]
            25490151  ATP-dependent 6-phosphofructokinase 6 [KO:K00850] [EC:2.7.1.11]
            11438579  ATP-dependent 6-phosphofructokinase 3 [KO:K00850] [EC:2.7.1.11]
            11410489  ATP-dependent 6-phosphofructokinase 4, chloroplastic isoform X1 [KO:K00850] [EC:2.7.1.11]
            11434343  heat shock 70 kDa protein, mitochondrial [KO:K04043]
            11406812  heat shock 70 kDa protein, mitochondrial [KO:K04043]
            11421237  chaperonin CPN60-like 2, mitochondrial [KO:K04077] [EC:5.6.1.7]
            120580586  chaperonin 60 subunit beta 4, chloroplastic-like [KO:K04077] [EC:5.6.1.7]
            25482039  ruBisCO large subunit-binding protein subunit beta, chloroplastic [KO:K04077] [EC:5.6.1.7]
            25482040  ruBisCO large subunit-binding protein subunit beta, chloroplastic [KO:K04077] [EC:5.6.1.7]
            11417778  chaperonin CPN60-2, mitochondrial [KO:K04077] [EC:5.6.1.7]
            11417779  chaperonin CPN60-2, mitochondrial [KO:K04077] [EC:5.6.1.7]
REFERENCE   PMID:19239894
  AUTHORS   Houseley J, Tollervey D
  TITLE     The many pathways of RNA degradation.
  JOURNAL   Cell 136:763-76 (2009)
            DOI:10.1016/j.cell.2009.01.019
REFERENCE   PMID:16968219
  AUTHORS   Buttner K, Wenig K, Hopfner KP
  TITLE     The exosome: a macromolecular cage for controlled RNA degradation.
  JOURNAL   Mol Microbiol 61:1372-9 (2006)
            DOI:10.1111/j.1365-2958.2006.05331.x
REFERENCE   PMID:16939780
  AUTHORS   Schilders G, van Dijk E, Raijmakers R, Pruijn GJ
  TITLE     Cell and molecular biology of the exosome: how to make or break an RNA.
  JOURNAL   Int Rev Cytol 251:159-208 (2006)
            DOI:10.1016/S0074-7696(06)51005-8
REFERENCE   PMID:17471261
  AUTHORS   Hartung S, Hopfner KP
  TITLE     The exosome, plugged.
  JOURNAL   EMBO Rep 8:456-7 (2007)
            DOI:10.1038/sj.embor.7400961
REFERENCE   PMID:17447862
  AUTHORS   Carpousis AJ
  TITLE     The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E.
  JOURNAL   Annu Rev Microbiol 61:71-87 (2007)
            DOI:10.1146/annurev.micro.61.080706.093440
REFERENCE   PMID:16766188
  AUTHORS   Marcaida MJ, DePristo MA, Chandran V, Carpousis AJ, Luisi BF
  TITLE     The RNA degradosome: life in the fast lane of adaptive molecular evolution.
  JOURNAL   Trends Biochem Sci 31:359-65 (2006)
            DOI:10.1016/j.tibs.2006.05.005
REFERENCE   PMID:17560162
  AUTHORS   Condon C
  TITLE     Maturation and degradation of RNA in bacteria.
  JOURNAL   Curr Opin Microbiol 10:271-8 (2007)
            DOI:10.1016/j.mib.2007.05.008
REL_PATHWAY mtr03015  mRNA surveillance pathway
KO_PATHWAY  ko03018
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