ENTRY       gmx03018                    Pathway
NAME        RNA degradation - Glycine max (soybean)
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 gmx03018  RNA degradation
DBLINKS     GO: 0006401
ORGANISM    Glycine max (soybean) [GN:gmx]
GENE        100796154  exosome complex component CSL4-like [KO:K07573]
            100809857  exosome complex component CSL4 [KO:K07573]
            100776358  exosome complex component RRP4 homolog [KO:K03679]
            100791930  putative exosome complex component rrp40 [KO:K03681]
            100778661  putative exosome complex component rrp40 [KO:K03681]
            100809941  uncharacterized protein LOC100809941 [KO:K03681]
            100776087  exosome complex component RRP43 [KO:K12586]
            100812139  uncharacterized protein LOC100812139 [KO:K12586]
            100812232  exosome complex component RRP43 isoform X2 [KO:K12586]
            100819105  exosome complex component RRP41-like [KO:K12587]
            100816271  exosome complex component RRP41-like [KO:K12587]
            100806953  exosome complex component RRP42 [KO:K12589]
            100818134  exosome complex component RRP42 [KO:K12589]
            100782953  exosome complex component RRP41 homolog [KO:K11600]
            100818324  exosome complex component RRP41 homolog [KO:K11600]
            100815140  exosome complex exonuclease RRP46 homolog [KO:K12590]
            100790116  exosome complex exonuclease RRP46 homolog [KO:K12590]
            100801484  exosome complex exonuclease RRP46 homolog [KO:K12590]
            100780196  exosome complex component RRP45A [KO:K03678]
            100802751  exosome complex component RRP45A [KO:K03678]
            100806652  exosome complex exonuclease RRP44 homolog A isoform X1 [KO:K12585] [EC:3.1.13.-]
            100782456  exosome complex exonuclease RRP44 homolog A isoform X1 [KO:K12585] [EC:3.1.13.-]
            100798683  exosome complex exonuclease RRP44 homolog A isoform X2 [KO:K12585] [EC:3.1.13.-]
            100819332  protein RRP6-like 2 isoform X1 [KO:K12591] [EC:3.1.13.-]
            100815329  protein RRP6-like 2 [KO:K12591] [EC:3.1.13.-]
            100800470  protein RRP6-like 2 [KO:K12591] [EC:3.1.13.-]
            100804872  protein RRP6-like 2 isoform X2 [KO:K12591] [EC:3.1.13.-]
            100795174  nuclear nucleic acid-binding protein C1D [KO:K12592]
            100500667  uncharacterized protein LOC100500667 [KO:K12592]
            100500463  uncharacterized protein LOC100500463 [KO:K12593]
            100500671  uncharacterized protein LOC100500671 [KO:K12593]
            100811320  terminal nucleotidyltransferase 4A [KO:K03514] [EC:2.7.7.19]
            100785694  DExH-box ATP-dependent RNA helicase DExH10 [KO:K12598] [EC:3.6.4.13]
            100804792  DExH-box ATP-dependent RNA helicase DExH9 [KO:K12598] [EC:3.6.4.13]
            100788432  DExH-box ATP-dependent RNA helicase DExH11 [KO:K12599] [EC:3.6.4.13]
            100779830  tetratricopeptide repeat protein SKI3 isoform X1 [KO:K12600]
            100790793  WD repeat-containing protein VIP3 [KO:K12602]
            100791764  WD repeat-containing protein VIP3 [KO:K12602]
            100808935  carbon catabolite repressor protein 4 homolog 1 [KO:K12603] [EC:3.1.13.4]
            100819402  carbon catabolite repressor protein 4 homolog 1 [KO:K12603] [EC:3.1.13.4]
            100775932  carbon catabolite repressor protein 4 homolog 4 isoform X2 [KO:K12603] [EC:3.1.13.4]
            100775270  carbon catabolite repressor protein 4 homolog 1 [KO:K12603] [EC:3.1.13.4]
            100803794  CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
            100818196  CCR4-NOT transcription complex subunit 1 [KO:K12604]
            100783935  CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
            100783662  probable NOT transcription complex subunit VIP2 isoform X2 [KO:K12605]
            100806559  probable NOT transcription complex subunit VIP2 isoform X2 [KO:K12605]
            100807026  probable NOT transcription complex subunit VIP2 isoform X1 [KO:K12605]
            100776413  probable NOT transcription complex subunit VIP2 isoform X1 [KO:K12605]
            100783415  CCR4-NOT transcription complex subunit 3 isoform X2 [KO:K12580]
            100819202  general negative regulator of transcription subunit 3 [KO:K12580]
            100780204  CCR4-NOT transcription complex subunit 3 isoform X1 [KO:K12580]
            100785965  general negative regulator of transcription subunit 3 isoform X1 [KO:K12580]
            100813427  uncharacterized protein LOC100813427 isoform X4 [KO:K10643] [EC:2.3.2.27]
            100805811  uncharacterized protein LOC100805811 isoform X3 [KO:K10643] [EC:2.3.2.27]
            100807521  uncharacterized protein LOC100807521 isoform X1 [KO:K10643] [EC:2.3.2.27]
            100780302  uncharacterized protein LOC100780302 isoform X3 [KO:K10643] [EC:2.3.2.27]
            100801880  uncharacterized protein LOC100801880 isoform X1 [KO:K10643] [EC:2.3.2.27]
            100796804  uncharacterized protein LOC100796804 isoform X1 [KO:K10643] [EC:2.3.2.27]
            100789409  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
            100799461  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
            100785970  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
            100798365  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
            100781759  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
            100817875  CCR4 associated factor 1-related protein precursor [KO:K12581]
            100500357  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
            100811298  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
            100805583  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
            100790027  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
            100801266  CCR4-NOT transcription complex subunit 9 [KO:K12606]
            100792784  CCR4-NOT transcription complex subunit 9 [KO:K12606]
            100792752  CCR4-NOT transcription complex subunit 9 [KO:K12606]
            100784529  CCR4-NOT transcription complex subunit 9 [KO:K12606]
            100812215  CCR4-NOT transcription complex subunit 10 isoform X2 [KO:K12607]
            100802507  CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
            100782386  ABC transporter I family member 20 [KO:K12608]
            100788503  ABC transporter I family member 21 [KO:K12608]
            100791006  DExH-box ATP-dependent RNA helicase DExH3 [KO:K14442] [EC:3.6.4.13]
            100792823  DExH-box ATP-dependent RNA helicase DExH1 isoform X1 [KO:K14442] [EC:3.6.4.13]
            100806141  DExH-box ATP-dependent RNA helicase DExH3 [KO:K14442] [EC:3.6.4.13]
            100798684  DExH-box ATP-dependent RNA helicase DExH5, mitochondrial isoform X1 [KO:K14442] [EC:3.6.4.13]
            100808902  DExH-box ATP-dependent RNA helicase DExH5, mitochondrial isoform X1 [KO:K14442] [EC:3.6.4.13]
            100782189  DExH-box ATP-dependent RNA helicase DExH6 [KO:K14442] [EC:3.6.4.13]
            100810272  DExH-box ATP-dependent RNA helicase DExH6 [KO:K14442] [EC:3.6.4.13]
            100792410  DExH-box ATP-dependent RNA helicase DExH3 [KO:K14442] [EC:3.6.4.13]
            100792623  DExH-box ATP-dependent RNA helicase DExH1 isoform X1 [KO:K14442] [EC:3.6.4.13]
            100786049  LOW QUALITY PROTEIN: DExH-box ATP-dependent RNA helicase DExH3 [KO:K14442] [EC:3.6.4.13]
            100784997  poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
            100803008  poly(A)-specific ribonuclease PARN-like [KO:K01148] [EC:3.1.13.4]
            100775770  uncharacterized CRM domain-containing protein At3g25440, chloroplastic isoform X1 [KO:K01148] [EC:3.1.13.4]
            100808217  poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
            100790692  uncharacterized CRM domain-containing protein At3g25440, chloroplastic isoform X1 [KO:K01148] [EC:3.1.13.4]
            100811385  polyadenylate-binding protein 2 [KO:K13126]
            100778879  polyadenylate-binding protein 8 [KO:K13126]
            100799386  polyadenylate-binding protein 8 isoform X1 [KO:K13126]
            100798998  polyadenylate-binding protein 3 [KO:K13126]
            100807057  polyadenylate-binding protein 7 [KO:K13126]
            100798828  polyadenylate-binding protein 7 isoform X1 [KO:K13126]
            100804671  polyadenylate-binding protein 7 [KO:K13126]
            100779547  polyadenylate-binding protein 7 [KO:K13126]
            100811197  uncharacterized protein LOC100811197 [KO:K13126]
            100780329  polyadenylate-binding protein 2 [KO:K13126]
            100783567  uncharacterized protein LOC100783567 [KO:K13126]
            100784442  polyadenylate-binding protein 2 [KO:K13126]
            100813735  polyadenylate-binding protein 2 [KO:K13126]
            100783163  polyadenylate-binding protein 3 [KO:K13126]
            100808877  polyadenylate-binding protein 2 [KO:K13126]
            100814161  mRNA-decapping enzyme-like protein isoform X2 [KO:K12611] [EC:3.-.-.-]
            100783361  uncharacterized protein LOC100783361 [KO:K12611] [EC:3.-.-.-]
            100786833  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
            100780081  mRNA-decapping enzyme-like protein isoform X2 [KO:K12611] [EC:3.-.-.-]
            100807659  uncharacterized protein LOC100807659 [KO:K12613] [EC:3.6.1.62]
            100784829  uncharacterized protein LOC100784829 [KO:K12613] [EC:3.6.1.62]
            100800861  DEAD-box ATP-dependent RNA helicase 8 isoform X1 [KO:K12614] [EC:3.6.4.13]
            100801402  DEAD-box ATP-dependent RNA helicase 8 [KO:K12614] [EC:3.6.4.13]
            100818905  DEAD-box ATP-dependent RNA helicase 8 [KO:K12614] [EC:3.6.4.13]
            100788032  DEAD-box ATP-dependent RNA helicase 8 [KO:K12614] [EC:3.6.4.13]
            106794117  DEAD-box ATP-dependent RNA helicase 8 [KO:K12614] [EC:3.6.4.13]
            100802374  enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
            100797699  enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
            100798228  enhancer of mRNA-decapping protein 4 [KO:K12616]
            100812450  protein PAT1 homolog 1 isoform X2 [KO:K12617]
            100779096  protein PAT1 homolog isoform X1 [KO:K12617]
            100787112  protein PAT1 homolog [KO:K12617]
            100787648  protein PAT1 homolog 1 [KO:K12617]
            100805313  protein PAT1 homolog [KO:K12617]
            100306352  uncharacterized protein LOC100306352 [KO:K12620]
            100812441  sm-like protein LSM1B [KO:K12620]
            100305778  Sm_like superfamily protein [KO:K12621]
            102665888  sm-like protein LSM2 [KO:K12621]
            100306547  uncharacterized protein LOC100306547 [KO:K12622]
            100499782  uncharacterized protein LOC100499782 [KO:K12622]
            100786834  small nuclear RNP family protein [KO:K12623]
            100795851  sm-like protein LSM4 isoform X2 [KO:K12623]
            100500134  small nuclear ribonucleoprotein family protein [KO:K12623]
            100815676  putative sm-like protein LSM4 [KO:K12623]
            100306359  sm-like protein LSM5 isoform X2 [KO:K12624]
            100527929  sm-like protein LSM5 [KO:K12624]
            100306112  uncharacterized protein LOC100306112 [KO:K12625]
            100797765  sm-like protein LSM6A [KO:K12625]
            100807381  sm-like protein LSM7 [KO:K12626]
            100306498  uncharacterized protein LOC100306498 [KO:K12626]
            100789536  sm-like protein LSM7 [KO:K12626]
            100305829  uncharacterized protein LOC100305829 [KO:K12627]
            100809048  sm-like protein LSM8 [KO:K12627]
            100811084  enolase [KO:K01689] [EC:4.2.1.11]
            100789125  cytosolic enolase 3-like [KO:K01689] [EC:4.2.1.11]
            100803925  enolase [KO:K01689] [EC:4.2.1.11]
            100811302  enolase 1, chloroplastic [KO:K01689] [EC:4.2.1.11]
            547752  enolase [KO:K01689] [EC:4.2.1.11]
            100787451  enolase 1, chloroplastic [KO:K01689] [EC:4.2.1.11]
            100806538  cytosolic enolase 3 [KO:K01689] [EC:4.2.1.11]
            100809646  enolase 1, chloroplastic [KO:K01689] [EC:4.2.1.11]
            100787663  enolase [KO:K01689] [EC:4.2.1.11]
            100816982  polyribonucleotide nucleotidyltransferase 2, mitochondrial [KO:K00962] [EC:2.7.7.8]
            100819741  polyribonucleotide nucleotidyltransferase 1, chloroplastic [KO:K00962] [EC:2.7.7.8]
            100785430  LOW QUALITY PROTEIN: probable polyribonucleotide nucleotidyltransferase 1, chloroplastic [KO:K00962] [EC:2.7.7.8]
            100797777  probable ATP-dependent DNA helicase RecQ [KO:K03654] [EC:5.6.2.4]
            100804673  probable ATP-dependent DNA helicase RecQ [KO:K03654] [EC:5.6.2.4]
            100820495  ATP-dependent 6-phosphofructokinase 4, chloroplastic isoform X1 [KO:K00850] [EC:2.7.1.11]
            100794539  ATP-dependent 6-phosphofructokinase 5, chloroplastic [KO:K00850] [EC:2.7.1.11]
            100803139  ATP-dependent 6-phosphofructokinase 6 [KO:K00850] [EC:2.7.1.11]
            100818755  ATP-dependent 6-phosphofructokinase 6 [KO:K00850] [EC:2.7.1.11]
            100795344  ATP-dependent 6-phosphofructokinase 7 [KO:K00850] [EC:2.7.1.11]
            100798766  ATP-dependent 6-phosphofructokinase 3 [KO:K00850] [EC:2.7.1.11]
            100780164  ATP-dependent 6-phosphofructokinase 5, chloroplastic [KO:K00850] [EC:2.7.1.11]
            100793844  ATP-dependent 6-phosphofructokinase 3 isoform X1 [KO:K00850] [EC:2.7.1.11]
            100815278  ATP-dependent 6-phosphofructokinase 3 [KO:K00850] [EC:2.7.1.11]
            100776597  ATP-dependent 6-phosphofructokinase 3 isoform X1 [KO:K00850] [EC:2.7.1.11]
            100796769  ATP-dependent 6-phosphofructokinase 3 [KO:K00850] [EC:2.7.1.11]
            100782166  ATP-dependent 6-phosphofructokinase 3 [KO:K00850] [EC:2.7.1.11]
            100796614  ATP-dependent 6-phosphofructokinase 3 [KO:K00850] [EC:2.7.1.11]
            100807957  ATP-dependent 6-phosphofructokinase 2 [KO:K00850] [EC:2.7.1.11]
            100793883  ATP-dependent 6-phosphofructokinase 5, chloroplastic [KO:K00850] [EC:2.7.1.11]
            100796791  heat shock 70 kDa protein, mitochondrial [KO:K04043]
            100804559  Hsp 70 family protein [KO:K04043]
            100811003  heat shock 70 kDa protein, mitochondrial [KO:K04043]
            100814039  heat shock 70 kDa protein, mitochondrial [KO:K04043]
            100818544  chaperonin CPN60-2, mitochondrial [KO:K04077] [EC:5.6.1.7]
            100788248  chaperonin CPN60-2, mitochondrial [KO:K04077] [EC:5.6.1.7]
            100820546  chaperonin CPN60-2, mitochondrial [KO:K04077] [EC:5.6.1.7]
            100811995  chaperonin CPN60-2, mitochondrial [KO:K04077] [EC:5.6.1.7]
            100778935  chaperonin CPN60-like 2, mitochondrial isoform X1 [KO:K04077] [EC:5.6.1.7]
            100787285  chaperonin CPN60-like 2, mitochondrial [KO:K04077] [EC:5.6.1.7]
            100819369  ruBisCO large subunit-binding protein subunit beta, chloroplastic [KO:K04077] [EC:5.6.1.7]
            100777674  ruBisCO large subunit-binding protein subunit beta, chloroplastic isoform X2 [KO:K04077] [EC:5.6.1.7]
            100785937  ruBisCO large subunit-binding protein subunit beta, chloroplastic isoform X1 [KO:K04077] [EC:5.6.1.7]
            100796464  ruBisCO large subunit-binding protein subunit beta, chloroplastic isoform X1 [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 gmx03015  mRNA surveillance pathway
KO_PATHWAY  ko03018
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