KEGG   PATHWAY: caua03018
Entry
caua03018                   Pathway                                
Name
RNA degradation - Carassius auratus (goldfish)
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
caua03018  RNA degradation
caua03018

Other DBs
GO: 0006401
Organism
Carassius auratus (goldfish) [GN:caua]
Gene
113110030  dcps; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
113075094  exosome complex component CSL4-like isoform X1 [KO:K07573]
113056823  exosome complex component CSL4-like [KO:K07573]
113097626  exosome complex component CSL4-like isoform X1 [KO:K07573]
113084586  exosc2; exosome complex component RRP4 [KO:K03679]
113113864  exosome complex component RRP40-like [KO:K03681]
113054454  exosome complex component RRP43-like [KO:K12586]
113110043  exosome complex component RRP43-like [KO:K12586]
113049498  exosc6; exosome complex component MTR3 [KO:K12587]
113120295  exosc7; exosome complex component RRP42 [KO:K12589]
113046136  exosc4; exosome complex component RRP41 [KO:K11600]
113118791  exosome complex component RRP46-like isoform X1 [KO:K12590]
113061680  exosome complex component RRP46-like [KO:K12590]
113106511  exosome complex component RRP45-like [KO:K03678]
113097196  exosome complex component RRP45-like [KO:K03678]
113044196  exosc9; exosome complex component RRP45 [KO:K03678]
113044396  dis3; exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
113041075  exosc10; exosome component 10 isoform X1 [KO:K12591] [EC:3.1.13.-]
113113015  nuclear nucleic acid-binding protein C1D [KO:K12592]
113057276  nuclear nucleic acid-binding protein C1D-like [KO:K12592]
113067213  M-phase phosphoprotein 6-like [KO:K12593]
113106010  dis3l; DIS3-like exonuclease 1 [KO:K18681] [EC:3.1.13.-]
113119537  non-canonical poly(A) RNA polymerase PAPD7-like isoform X1 [KO:K03514] [EC:2.7.7.19]
113051419  non-canonical poly(A) RNA polymerase PAPD5-like [KO:K03514] [EC:2.7.7.19]
113090799  non-canonical poly(A) RNA polymerase PAPD7-like isoform X1 [KO:K03514] [EC:2.7.7.19]
113106062  non-canonical poly(A) RNA polymerase PAPD5-like [KO:K03514] [EC:2.7.7.19]
113076765  zinc finger CCHC domain-containing protein 7-like [KO:K12597]
113044241  zinc finger CCHC domain-containing protein 7-like [KO:K12597]
113110382  mtrex; exosome RNA helicase MTR4 [KO:K12598] [EC:5.6.2.6]
113119516  helicase SKI2W-like [KO:K12599] [EC:5.6.2.6]
113090773  helicase SKI2W-like isoform X1 [KO:K12599] [EC:5.6.2.6]
113079349  tetratricopeptide repeat protein 37-like [KO:K12600]
113066648  WD repeat-containing protein 61 [KO:K12602]
113066669  WD repeat-containing protein 61 [KO:K12602]
113043160  WD repeat-containing protein 61-like [KO:K12602]
113043192  WD repeat-containing protein 61-like [KO:K12602]
113049113  CCR4-NOT transcription complex subunit 6-like isoform X1 [KO:K12603] [EC:3.1.13.4]
113114024  CCR4-NOT transcription complex subunit 6-like isoform X1 [KO:K12603] [EC:3.1.13.4]
113049598  CCR4-NOT transcription complex subunit 6-like isoform X1 [KO:K12603] [EC:3.1.13.4]
113057587  CCR4-NOT transcription complex subunit 6-like isoform X1 [KO:K12603] [EC:3.1.13.4]
113063999  CCR4-NOT transcription complex subunit 6 [KO:K12603] [EC:3.1.13.4]
113038408  CCR4-NOT transcription complex subunit 6-like isoform X1 [KO:K12603] [EC:3.1.13.4]
113066724  CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
113043251  CCR4-NOT transcription complex subunit 1-like isoform X1 [KO:K12604]
113066962  CCR4-NOT transcription complex subunit 2-like [KO:K12605]
113043455  CCR4-NOT transcription complex subunit 2 [KO:K12605]
113120163  CCR4-NOT transcription complex subunit 3-like [KO:K12580]
113116045  CCR4-NOT transcription complex subunit 3-like isoform X1 [KO:K12580]
113099617  CCR4-NOT transcription complex subunit 3-like isoform X1 [KO:K12580]
113047800  CCR4-NOT transcription complex subunit 4-like [KO:K10643] [EC:2.3.2.27]
113066897  CCR4-NOT transcription complex subunit 4-like [KO:K10643] [EC:2.3.2.27]
113043316  CCR4-NOT transcription complex subunit 4-like [KO:K10643] [EC:2.3.2.27]
113078795  CCR4-NOT transcription complex subunit 4-like [KO:K10643] [EC:2.3.2.27]
113062934  CCR4-NOT transcription complex subunit 4-like isoform X1 [KO:K10643] [EC:2.3.2.27]
113087350  CCR4-NOT transcription complex subunit 4-like [KO:K10643] [EC:2.3.2.27]
113113998  CCR4-NOT transcription complex subunit 7 isoform X1 [KO:K12581]
113057927  CCR4-NOT transcription complex subunit 7-like isoform X1 [KO:K12581]
113038365  cnot8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
113064786  CCR4-NOT transcription complex subunit 9-like isoform X1 [KO:K12606]
113039468  CCR4-NOT transcription complex subunit 9 [KO:K12606]
113039562  CCR4-NOT transcription complex subunit 9 [KO:K12606]
113060105  CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
113116187  CCR4-NOT transcription complex subunit 10-like isoform X1 [KO:K12607]
113118537  dhx36; ATP-dependent RNA helicase DHX36 [KO:K14442] [EC:5.6.2.6]
113100633  poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
113090608  poly(A)-specific ribonuclease PARN-like isoform X1 [KO:K01148] [EC:3.1.13.4]
113048169  protein BTG1-like [KO:K14443]
113054355  protein BTG3-like [KO:K14443]
113048273  protein BTG1-like [KO:K14443]
113048670  protein Tob2-like [KO:K14443]
113060891  protein BTG1-like [KO:K14443]
113055228  protein Tob2-like [KO:K14443]
113076902  maternal B9.15 protein-like [KO:K14443]
113077412  protein BTG1-like [KO:K14443]
113067785  protein Tob2-like [KO:K14443]
113095816  maternal B9.15 protein-like [KO:K14443]
113050065  maternal B9.15 protein-like [KO:K14443]
113069149  protein BTG1-like [KO:K14443]
113079553  protein BTG1-like [KO:K14443]
113096630  protein BTG2-like [KO:K14443]
113097153  protein BTG3-like [KO:K14443]
113097684  protein BTG2-like [KO:K14443]
113081895  maternal B9.10 protein-like [KO:K14443]
113098997  LOW QUALITY PROTEIN: protein BTG2-like [KO:K14443]
113116715  protein BTG3-like isoform X1 [KO:K14443]
113052202  protein Tob1-like [KO:K14443]
113064718  protein BTG1-like [KO:K14443]
113046642  protein Tob1-like [KO:K14443]
113065443  protein BTG1-like [KO:K14443]
113112034  protein Tob1-like [KO:K14443]
113040245  protein BTG1-like [KO:K14443]
113119188  polyadenylate-binding protein 1 [KO:K13126]
113107325  embryonic polyadenylate-binding protein B-like isoform X1 [KO:K13126]
113068275  polyadenylate-binding protein 1-like isoform X1 [KO:K13126]
113115783  polyadenylate-binding protein 1-like [KO:K13126]
113115791  polyadenylate-binding protein 1-like [KO:K13126]
113070386  polyadenylate-binding protein 4-like isoform X1 [KO:K13126]
113070683  embryonic polyadenylate-binding protein-like isoform X1 [KO:K13126]
113117450  polyadenylate-binding protein 4-like isoform X1 [KO:K13126]
113059413  polyadenylate-binding protein 1-like [KO:K13126]
113041399  PAN2-PAN3 deadenylation complex catalytic subunit PAN2-like isoform X1 [KO:K12571] [EC:3.1.13.4]
113065607  PAN2-PAN3 deadenylation complex catalytic subunit PAN2-like isoform X1 [KO:K12571] [EC:3.1.13.4]
113066259  PAN2-PAN3 deadenylation complex subunit pan3-like [KO:K12572]
113041913  LOW QUALITY PROTEIN: PAN2-PAN3 deadenylation complex subunit pan3-like [KO:K12572]
113041934  PAN2-PAN3 deadenylation complex subunit pan3-like [KO:K12572]
113107805  dcp1a; mRNA-decapping enzyme 1A isoform X1 [KO:K12610] [EC:3.-.-.-]
113107873  mRNA-decapping enzyme 1A-like [KO:K12610] [EC:3.-.-.-]
113048095  mRNA-decapping enzyme 1B-like isoform X1 [KO:K12611] [EC:3.-.-.-]
113062351  mRNA-decapping enzyme 1B-like [KO:K12611] [EC:3.-.-.-]
113053983  m7GpppN-mRNA hydrolase-like isoform X1 [KO:K12613] [EC:3.6.1.62]
113109539  m7GpppN-mRNA hydrolase-like [KO:K12613] [EC:3.6.1.62]
113118691  probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:5.6.2.7]
113061772  ddx6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:5.6.2.7]
113120142  probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:5.6.2.7]
113062345  probable ATP-dependent RNA helicase DDX6 isoform X1 [KO:K12614] [EC:5.6.2.7]
113116669  probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:5.6.2.7]
113059081  probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:5.6.2.7]
113066912  enhancer of mRNA-decapping protein 3-like [KO:K12615]
113043346  enhancer of mRNA-decapping protein 3 isoform X1 [KO:K12615]
113061583  enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
113118425  enhancer of mRNA-decapping protein 4-like isoform X1 [KO:K12616]
113061380  protein PAT1 homolog 1-like isoform X1 [KO:K12617]
113044072  protein PAT1 homolog 1-like [KO:K12617]
113097575  protein PAT1 homolog 1 [KO:K12617]
113115476  5'-3' exoribonuclease 1-like isoform X1 [KO:K12618] [EC:3.1.13.-]
113045786  5'-3' exoribonuclease 1-like isoform X1 [KO:K12618] [EC:3.1.13.-]
113093348  5'-3' exoribonuclease 2-like [KO:K12619] [EC:3.1.13.-]
113120621  5'-3' exoribonuclease 2-like [KO:K12619] [EC:3.1.13.-]
113094762  U8 snoRNA-decapping enzyme-like [KO:K16855] [EC:3.6.1.62 3.6.1.64]
113069121  U8 snoRNA-decapping enzyme-like [KO:K16855] [EC:3.6.1.62 3.6.1.64]
113071070  U8 snoRNA-decapping enzyme-like [KO:K16855] [EC:3.6.1.62 3.6.1.64]
113107343  U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
113070698  U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
113050615  U6 snRNA-associated Sm-like protein LSm2 [KO:K12621]
113099037  U6 snRNA-associated Sm-like protein LSm2 [KO:K12621]
113070585  U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
113065102  U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
113055159  U6 snRNA-associated Sm-like protein LSm4 isoform X1 [KO:K12623]
113110698  U6 snRNA-associated Sm-like protein LSm4 isoform X1 [KO:K12623]
113110763  U6 snRNA-associated Sm-like protein LSm4 isoform X1 [KO:K12623]
113072464  U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
113112122  U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
113095008  lsm6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
113114229  U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
113079551  U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
113064741  U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
113040232  U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
113048302  U6 snRNA-associated Sm-like protein LSm8 [KO:K12627]
113059156  U6 snRNA-associated Sm-like protein LSm8 [KO:K12627]
113041673  beta-enolase [KO:K01689] [EC:4.2.1.11]
113119641  gamma-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
113119875  LOW QUALITY PROTEIN: gamma-enolase-like [KO:K01689] [EC:4.2.1.11]
113094895  enolase-like [KO:K01689] [EC:4.2.1.11]
113068400  alpha-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
113068891  enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
113062435  gamma-enolase-like [KO:K01689] [EC:4.2.1.11]
113062636  gamma-enolase-like [KO:K01689] [EC:4.2.1.11]
113065773  beta-enolase-like [KO:K01689] [EC:4.2.1.11]
113057341  pnpt1; polyribonucleotide nucleotidyltransferase 1, mitochondrial isoform X1 [KO:K00962] [EC:2.7.7.8]
113066058  ATP-dependent 6-phosphofructokinase, platelet type-like isoform X1 [KO:K00850] [EC:2.7.1.11]
113066314  ATP-dependent 6-phosphofructokinase, platelet type-like isoform X1 [KO:K00850] [EC:2.7.1.11]
113042198  ATP-dependent 6-phosphofructokinase, platelet type-like isoform X1 [KO:K00850] [EC:2.7.1.11]
113113690  ATP-dependent 6-phosphofructokinase, platelet type-like isoform X1 [KO:K00850] [EC:2.7.1.11]
113055573  ATP-dependent 6-phosphofructokinase, liver type-like [KO:K00850] [EC:2.7.1.11]
113094431  ATP-dependent 6-phosphofructokinase, muscle type-like [KO:K00850] [EC:2.7.1.11]
113050368  ATP-dependent 6-phosphofructokinase, muscle type-like isoform X1 [KO:K00850] [EC:2.7.1.11]
113070540  ATP-dependent 6-phosphofructokinase, muscle type-like isoform X1 [KO:K00850] [EC:2.7.1.11]
113045291  ATP-dependent 6-phosphofructokinase, platelet type-like isoform X1 [KO:K00850] [EC:2.7.1.11]
113045326  ATP-dependent 6-phosphofructokinase, platelet type-like isoform X1 [KO:K00850] [EC:2.7.1.11]
113084879  ATP-dependent 6-phosphofructokinase, liver type-like [KO:K00850] [EC:2.7.1.11]
113111267  ATP-dependent 6-phosphofructokinase, liver type-like isoform X1 [KO:K00850] [EC:2.7.1.11]
113111269  ATP-dependent 6-phosphofructokinase, liver type-like [KO:K00850] [EC:2.7.1.11]
113052924  ATP-dependent 6-phosphofructokinase, liver type-like [KO:K00850] [EC:2.7.1.11]
113113418  stress-70 protein, mitochondrial [KO:K04043]
113113553  stress-70 protein, mitochondrial-like [KO:K04043]
113108448  60 kDa heat shock protein, mitochondrial [KO:K04077] [EC:5.6.1.7]
113108638  60 kDa heat shock protein, mitochondrial-like [KO:K04077] [EC:5.6.1.7]
113053149  60 kDa heat shock protein, mitochondrial-like [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
caua03015  mRNA surveillance pathway
KO pathway
ko03018   
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