KEGG   PATHWAY: cqi03018
Entry
cqi03018                    Pathway                                
Name
RNA degradation - Chenopodium quinoa (quinoa)
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
cqi03018  RNA degradation
cqi03018

Other DBs
GO: 0006401
Organism
Chenopodium quinoa (quinoa) [GN:cqi]
Gene
110735878  uncharacterized protein LOC110735878 [KO:K07573]
110701406  exosome complex component CSL4 [KO:K07573]
110700920  exosome complex component RRP4 homolog [KO:K03679]
110711881  exosome complex component RRP4 homolog [KO:K03679]
110701550  exosome complex component RRP4 homolog [KO:K03679]
110700399  putative exosome complex component rrp40 [KO:K03681]
110686646  putative exosome complex component rrp40 [KO:K03681]
110707284  exosome complex component RRP43 [KO:K12586]
110738430  exosome complex component RRP41-like [KO:K12587]
110724951  exosome complex component RRP41-like [KO:K12587]
110714288  exosome complex component RRP42-like isoform X1 [KO:K12589]
110690772  exosome complex component RRP42-like [KO:K12589]
110725316  exosome complex component RRP42-like [KO:K12589]
110714286  exosome complex component RRP41 homolog [KO:K11600]
110725190  exosome complex component RRP41 homolog [KO:K11600]
110693344  exosome complex exonuclease RRP46 homolog [KO:K12590]
110705584  exosome complex exonuclease RRP46 homolog [KO:K12590]
110711414  exosome complex exonuclease RRP46 homolog [KO:K12590]
110735153  exosome complex component RRP45A-like isoform X1 [KO:K03678]
110738990  exosome complex component RRP45A-like isoform X1 [KO:K03678]
110702150  exosome complex component RRP45B-like [KO:K03678]
110705620  exosome complex component RRP45B-like isoform X1 [KO:K03678]
110682150  exosome complex exonuclease RRP44 homolog A-like [KO:K12585] [EC:3.1.13.-]
110703461  exosome complex exonuclease RRP44 homolog A-like [KO:K12585] [EC:3.1.13.-]
110739869  protein RRP6-like 2 [KO:K12591] [EC:3.1.13.-]
110705273  protein RRP6-like 1 [KO:K12591] [EC:3.1.13.-]
110721168  protein RRP6-like 2 isoform X1 [KO:K12591] [EC:3.1.13.-]
110728877  protein RRP6-like 2 [KO:K12591] [EC:3.1.13.-]
110712153  nuclear nucleic acid-binding protein C1D-like [KO:K12592]
110723061  nuclear nucleic acid-binding protein C1D-like [KO:K12592]
110688393  M-phase phosphoprotein 6-like [KO:K12593]
110684031  M-phase phosphoprotein 6-like [KO:K12593]
110720165  non-canonical poly(A) RNA polymerase PAPD5-like [KO:K03514] [EC:2.7.7.19]
110693272  non-canonical poly(A) RNA polymerase PAPD5-like [KO:K03514] [EC:2.7.7.19]
110683789  DExH-box ATP-dependent RNA helicase DExH10-like [KO:K12598] [EC:5.6.2.6]
110687913  DExH-box ATP-dependent RNA helicase DExH9-like [KO:K12598] [EC:5.6.2.6]
110706925  DExH-box ATP-dependent RNA helicase DExH9-like [KO:K12598] [EC:5.6.2.6]
110710326  DExH-box ATP-dependent RNA helicase DExH10-like [KO:K12598] [EC:5.6.2.6]
110683399  DExH-box ATP-dependent RNA helicase DExH11-like [KO:K12599] [EC:5.6.2.6]
110688325  DExH-box ATP-dependent RNA helicase DExH11-like [KO:K12599] [EC:5.6.2.6]
110685563  tetratricopeptide repeat protein SKI3-like isoform X1 [KO:K12600]
110699110  tetratricopeptide repeat protein SKI3-like [KO:K12600]
110724434  WD repeat-containing protein VIP3-like [KO:K12602]
110685481  WD repeat-containing protein VIP3-like [KO:K12602]
110739111  carbon catabolite repressor protein 4 homolog 1-like [KO:K12603] [EC:3.1.13.4]
110739113  carbon catabolite repressor protein 4 homolog 1-like isoform X1 [KO:K12603] [EC:3.1.13.4]
110706576  carbon catabolite repressor protein 4 homolog 1-like isoform X1 [KO:K12603] [EC:3.1.13.4]
110692776  carbon catabolite repressor protein 4 homolog 4-like isoform X1 [KO:K12603] [EC:3.1.13.4]
110732711  carbon catabolite repressor protein 4 homolog 4-like isoform X1 [KO:K12603] [EC:3.1.13.4]
110689191  carbon catabolite repressor protein 4 homolog 1-like [KO:K12603] [EC:3.1.13.4]
110704818  carbon catabolite repressor protein 4 homolog 1-like [KO:K12603] [EC:3.1.13.4]
110721506  CCR4-NOT transcription complex subunit 1-like isoform X1 [KO:K12604]
110713911  CCR4-NOT transcription complex subunit 1-like isoform X1 [KO:K12604]
110695089  probable NOT transcription complex subunit VIP2 isoform X1 [KO:K12605]
110729127  probable NOT transcription complex subunit VIP2 [KO:K12605]
110681926  probable NOT transcription complex subunit VIP2 isoform X1 [KO:K12605]
110696077  probable NOT transcription complex subunit VIP2 isoform X1 [KO:K12605]
110692457  general negative regulator of transcription subunit 3-like isoform X1 [KO:K12580]
110704747  general negative regulator of transcription subunit 3-like isoform X1 [KO:K12580]
110712010  uncharacterized protein LOC110712010 [KO:K10643] [EC:2.3.2.27]
110712112  uncharacterized protein LOC110712112 isoform X1 [KO:K10643] [EC:2.3.2.27]
110701595  uncharacterized protein LOC110701595 [KO:K10643] [EC:2.3.2.27]
110701601  uncharacterized protein LOC110701601 [KO:K10643] [EC:2.3.2.27]
110739958  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
110734611  putative CCR4-associated factor 1 homolog 8 [KO:K12581]
110733655  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
110684963  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
110682229  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
110683586  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
110688149  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
110732944  putative CCR4-associated factor 1 homolog 8 [KO:K12581]
110730152  probable CCR4-associated factor 1 homolog 9 [KO:K12581]
110688884  putative CCR4-associated factor 1 homolog 8 [KO:K12581]
110705864  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
110720926  CCR4-NOT transcription complex subunit 9-like [KO:K12606]
110723883  CCR4-NOT transcription complex subunit 9-like [KO:K12606]
110725591  CCR4-NOT transcription complex subunit 10-like [KO:K12607]
110707992  CCR4-NOT transcription complex subunit 10-like [KO:K12607]
110735121  ABC transporter I family member 19-like [KO:K12608]
110736536  ABC transporter I family member 20-like [KO:K12608]
110701207  ABC transporter I family member 20-like [KO:K12608]
110730685  ABC transporter I family member 19-like [KO:K12608]
110735396  LOW QUALITY PROTEIN: DExH-box ATP-dependent RNA helicase DExH1-like [KO:K14442] [EC:5.6.2.6]
110737393  DExH-box ATP-dependent RNA helicase DExH3-like [KO:K14442] [EC:5.6.2.6]
110681837  DExH-box ATP-dependent RNA helicase DExH6-like [KO:K14442] [EC:5.6.2.6]
110733840  DExH-box ATP-dependent RNA helicase DExH1-like [KO:K14442] [EC:5.6.2.6]
110703013  DExH-box ATP-dependent RNA helicase DExH3-like [KO:K14442] [EC:5.6.2.6]
110724579  DExH-box ATP-dependent RNA helicase DExH3-like [KO:K14442] [EC:5.6.2.6]
110694639  DExH-box ATP-dependent RNA helicase DExH6-like isoform X1 [KO:K14442] [EC:5.6.2.6]
110714001  DExH-box ATP-dependent RNA helicase DExH5, mitochondrial-like isoform X1 [KO:K14442] [EC:5.6.2.6]
110694503  DExH-box ATP-dependent RNA helicase DExH3-like [KO:K14442] [EC:5.6.2.6]
110715019  DExH-box ATP-dependent RNA helicase DExH5, mitochondrial-like isoform X1 [KO:K14442] [EC:5.6.2.6]
110738127  uncharacterized CRM domain-containing protein At3g25440, chloroplastic-like [KO:K01148] [EC:3.1.13.4]
110735515  poly(A)-specific ribonuclease PARN-like [KO:K01148] [EC:3.1.13.4]
110734208  uncharacterized CRM domain-containing protein At3g25440, chloroplastic-like [KO:K01148] [EC:3.1.13.4]
110727538  poly(A)-specific ribonuclease PARN-like [KO:K01148] [EC:3.1.13.4]
110700280  poly(A)-specific ribonuclease PARN-like [KO:K01148] [EC:3.1.13.4]
110707011  poly(A)-specific ribonuclease PARN-like isoform X1 [KO:K01148] [EC:3.1.13.4]
110682445  polyadenylate-binding protein 2-like [KO:K13126]
110690046  polyadenylate-binding protein 2-like [KO:K13126]
110691170  polyadenylate-binding protein 2-like [KO:K13126]
110718750  polyadenylate-binding protein 2-like [KO:K13126]
110735635  polyadenylate-binding protein 5-like [KO:K13126]
110714859  30S ribosomal protein 2, chloroplastic [KO:K13126]
110704177  polyadenylate-binding protein 5-like [KO:K13126]
110711649  30S ribosomal protein 2, chloroplastic-like [KO:K13126]
110683600  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
110688140  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
110695675  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
110729909  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
110735175  mRNA-decapping enzyme subunit 2-like [KO:K12613] [EC:3.6.1.62]
110738976  mRNA-decapping enzyme subunit 2-like [KO:K12613] [EC:3.6.1.62]
110714643  DEAD-box ATP-dependent RNA helicase 8-like [KO:K12614] [EC:5.6.2.7]
110719465  DEAD-box ATP-dependent RNA helicase 8-like [KO:K12614] [EC:5.6.2.7]
110685317  DEAD-box ATP-dependent RNA helicase 8-like isoform X1 [KO:K12614] [EC:5.6.2.7]
110702467  DEAD-box ATP-dependent RNA helicase 8-like [KO:K12614] [EC:5.6.2.7]
110685338  DEAD-box ATP-dependent RNA helicase 8-like isoform X1 [KO:K12614] [EC:5.6.2.7]
110707071  LOW QUALITY PROTEIN: enhancer of mRNA-decapping protein 4-like [KO:K12616]
110710979  enhancer of mRNA-decapping protein 4-like [KO:K12616]
110682752  protein PAT1 homolog 1-like [KO:K12617]
110724965  uncharacterized protein LOC110724965 [KO:K12617]
110696538  protein PAT1 homolog 1-like [KO:K12617]
110697711  uncharacterized protein LOC110697711 [KO:K12617]
110704248  5'-3' exoribonuclease 3-like isoform X1 [KO:K12619] [EC:3.1.13.-]
110715739  sm-like protein LSM1B [KO:K12620]
110684407  sm-like protein LSM1B [KO:K12620]
110688063  sm-like protein LSM1B [KO:K12620]
110734298  sm-like protein LSM2 [KO:K12621]
110733045  sm-like protein LSM2 [KO:K12621]
110735719  sm-like protein LSM3A [KO:K12622]
110725869  sm-like protein LSM3A [KO:K12622]
110739224  sm-like protein LSM4 [KO:K12623]
110727891  sm-like protein LSM4 [KO:K12623]
110716863  sm-like protein LSM5 isoform X1 [KO:K12624]
110712933  sm-like protein LSM5 [KO:K12624]
110717862  sm-like protein LSM36B [KO:K12625]
110738693  sm-like protein LSM36B [KO:K12625]
110732568  sm-like protein LSM7 [KO:K12626]
110730156  sm-like protein LSM7 [KO:K12626]
110721615  sm-like protein LSM8 [KO:K12627]
110709741  sm-like protein LSM8 [KO:K12627]
110712526  LOW QUALITY PROTEIN: sm-like protein LSM8 [KO:K12627]
110688333  cytosolic enolase 3-like [KO:K01689] [EC:4.2.1.11]
110729395  enolase-like [KO:K01689] [EC:4.2.1.11]
110683393  cytosolic enolase 3-like [KO:K01689] [EC:4.2.1.11]
110726083  enolase 1, chloroplastic-like [KO:K01689] [EC:4.2.1.11]
110709242  enolase [KO:K01689] [EC:4.2.1.11]
110735016  probable polyribonucleotide nucleotidyltransferase 1, chloroplastic [KO:K00962] [EC:2.7.7.8]
110707495  probable polyribonucleotide nucleotidyltransferase 1, chloroplastic [KO:K00962] [EC:2.7.7.8]
110692421  polyribonucleotide nucleotidyltransferase 2, mitochondrial-like [KO:K00962] [EC:2.7.7.8]
110734037  uncharacterized protein LOC110734037 isoform X1 [KO:K03654] [EC:5.6.2.4]
110740237  ATP-dependent 6-phosphofructokinase 6-like [KO:K00850] [EC:2.7.1.11]
110715485  ATP-dependent 6-phosphofructokinase 3-like [KO:K00850] [EC:2.7.1.11]
110713332  ATP-dependent 6-phosphofructokinase 2-like [KO:K00850] [EC:2.7.1.11]
110705518  LOW QUALITY PROTEIN: ATP-dependent 6-phosphofructokinase 3-like [KO:K00850] [EC:2.7.1.11]
110730405  ATP-dependent 6-phosphofructokinase 5, chloroplastic-like [KO:K00850] [EC:2.7.1.11]
110729895  ATP-dependent 6-phosphofructokinase 3-like [KO:K00850] [EC:2.7.1.11]
110690897  ATP-dependent 6-phosphofructokinase 6-like [KO:K00850] [EC:2.7.1.11]
110692674  ATP-dependent 6-phosphofructokinase 5, chloroplastic-like [KO:K00850] [EC:2.7.1.11]
110706292  ATP-dependent 6-phosphofructokinase 2-like [KO:K00850] [EC:2.7.1.11]
110723769  ATP-dependent 6-phosphofructokinase 5, chloroplastic-like [KO:K00850] [EC:2.7.1.11]
110692319  ATP-dependent 6-phosphofructokinase 6-like [KO:K00850] [EC:2.7.1.11]
110711464  uncharacterized protein LOC110711464 [KO:K00850] [EC:2.7.1.11]
110740048  heat shock 70 kDa protein, mitochondrial [KO:K04043]
110685064  heat shock 70 kDa protein, mitochondrial-like [KO:K04043]
110713474  heat shock 70 kDa protein, mitochondrial-like isoform X1 [KO:K04043]
110715360  ruBisCO large subunit-binding protein subunit beta, chloroplastic-like [KO:K04077] [EC:5.6.1.7]
110687897  ruBisCO large subunit-binding protein subunit beta, chloroplastic-like isoform X1 [KO:K04077] [EC:5.6.1.7]
110727366  chaperonin CPN60, mitochondrial [KO:K04077] [EC:5.6.1.7]
110729844  ruBisCO large subunit-binding protein subunit beta, chloroplastic-like [KO:K04077] [EC:5.6.1.7]
110684320  chaperonin CPN60-like 2, mitochondrial [KO:K04077] [EC:5.6.1.7]
110692481  chaperonin CPN60, mitochondrial-like [KO:K04077] [EC:5.6.1.7]
110715011  ruBisCO large subunit-binding protein subunit beta, chloroplastic [KO:K04077] [EC:5.6.1.7]
110711800  ruBisCO large subunit-binding protein subunit beta, chloroplastic [KO:K04077] [EC:5.6.1.7]
110726810  ruBisCO large subunit-binding protein subunit beta, chloroplastic-like isoform X1 [KO:K04077] [EC:5.6.1.7]
Reference
  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
  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
  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
  Authors
Hartung S, Hopfner KP
  Title
The exosome, plugged.
  Journal
EMBO Rep 8:456-7 (2007)
DOI:10.1038/sj.embor.7400961
Reference
  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
  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
  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
Related
pathway
cqi03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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