KEGG   PATHWAY: oki03018
Entry
oki03018                    Pathway                                
Name
RNA degradation - Oncorhynchus kisutch (coho salmon)
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
oki03018  RNA degradation
oki03018

Other DBs
GO: 0006401
Organism
Oncorhynchus kisutch (coho salmon) [GN:oki]
Gene
109872891  dcps; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
116359032  exosome complex component CSL4-like isoform X1 [KO:K07573]
109880856  exosome complex component CSL4-like isoform X2 [KO:K07573]
109879866  exosome complex component RRP4 [KO:K03679]
109874281  exosome complex component RRP4-like [KO:K03679]
109864791  exosc3; exosome complex component RRP40 [KO:K03681]
109883872  exosc8; exosome complex component RRP43 [KO:K12586]
109867312  exosc6; exosome complex component MTR3 [KO:K12587]
109908480  exosc7; exosome complex component RRP42 [KO:K12589]
109872286  exosc4; exosome complex component RRP41 [KO:K11600]
109881684  exosc5; exosome complex component RRP46 [KO:K12590]
109884773  exosome complex component RRP45 isoform X2 [KO:K03678]
109881797  exosome complex exonuclease RRP44-like [KO:K12585] [EC:3.1.13.-]
116352981  LOW QUALITY PROTEIN: exosome complex exonuclease RRP44-like [KO:K12585] [EC:3.1.13.-]
109908024  exosc10; exosome component 10 isoform X1 [KO:K12591] [EC:3.1.13.-]
109885784  c1d; nuclear nucleic acid-binding protein C1D [KO:K12592]
109866806  mphosph6; M-phase phosphoprotein 6 [KO:K12593]
109887543  DIS3-like exonuclease 1 isoform X1 [KO:K18681] [EC:3.1.13.-]
109883802  DIS3-like exonuclease 1 isoform X1 [KO:K18681] [EC:3.1.13.-]
109889611  terminal nucleotidyltransferase 4B-like [KO:K03514] [EC:2.7.7.19]
109881361  terminal nucleotidyltransferase 4B-like [KO:K03514] [EC:2.7.7.19]
109881651  terminal nucleotidyltransferase 4B-like [KO:K03514] [EC:2.7.7.19]
109881129  terminal nucleotidyltransferase 4A isoform X2 [KO:K03514] [EC:2.7.7.19]
109907343  terminal nucleotidyltransferase 4A-like isoform X2 [KO:K03514] [EC:2.7.7.19]
109866802  terminal nucleotidyltransferase 4B isoform X1 [KO:K03514] [EC:2.7.7.19]
109905196  zinc finger CCHC domain-containing protein 7 isoform X2 [KO:K12597]
109886069  zinc finger CCHC domain-containing protein 7 [KO:K12597]
109868275  exosome RNA helicase MTR4 [KO:K12598] [EC:5.6.2.6]
109892374  exosome RNA helicase MTR4-like isoform X1 [KO:K12598] [EC:5.6.2.6]
109903721  helicase SKI2W-like isoform X1 [KO:K12599] [EC:5.6.2.6]
109907617  helicase SKI2W-like [KO:K12599] [EC:5.6.2.6]
109875838  ttc37; tetratricopeptide repeat protein 37 [KO:K12600]
109867600  wdr61; WD repeat-containing protein 61 [KO:K12602]
109905064  CCR4-NOT transcription complex subunit 6-like isoform X1 [KO:K12603] [EC:3.1.13.4]
109884067  LOW QUALITY PROTEIN: CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
109864629  CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
109872617  CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
109877878  CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
109889570  CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
109867006  CCR4-NOT transcription complex subunit 1-like isoform X1 [KO:K12604]
109897813  CCR4-NOT transcription complex subunit 2 isoform X9 [KO:K12605]
109886334  CCR4-NOT transcription complex subunit 2-like [KO:K12605]
109867346  CCR4-NOT transcription complex subunit 2-like isoform X1 [KO:K12605]
109883194  CCR4-NOT transcription complex subunit 3-like isoform X1 [KO:K12580]
109907564  CCR4-NOT transcription complex subunit 3 isoform X4 [KO:K12580]
109903641  CCR4-NOT transcription complex subunit 3 isoform X1 [KO:K12580]
109884478  CCR4-NOT transcription complex subunit 3-like isoform X1 [KO:K12580]
109889658  CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
109883097  CCR4-NOT transcription complex subunit 4-like isoform X1 [KO:K10643] [EC:2.3.2.27]
109867403  CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
109892763  CCR4-NOT transcription complex subunit 8 [KO:K12581]
109873129  CCR4-NOT transcription complex subunit 8 isoform X3 [KO:K12581]
109904984  CCR4-NOT transcription complex subunit 7 isoform X1 [KO:K12581]
109906683  CCR4-NOT transcription complex subunit 9 isoform X2 [KO:K12606]
109890645  CCR4-NOT transcription complex subunit 9 isoform X2 [KO:K12606]
109871131  cnot9; CCR4-NOT transcription complex subunit 9 [KO:K12606]
109900233  CCR4-NOT transcription complex subunit 10-like isoform X1 [KO:K12607]
109882790  CCR4-NOT transcription complex subunit 10-like isoform X1 [KO:K12607]
109908359  dhx36; ATP-dependent DNA/RNA helicase DHX36 [KO:K14442] [EC:5.6.2.6]
109883572  poly(A)-specific ribonuclease PARN-like [KO:K01148] [EC:3.1.13.4]
109885688  poly(A)-specific ribonuclease PARN [KO:K01148] [EC:3.1.13.4]
109876824  protein Tob1 [KO:K14443]
109878572  protein BTG1-like [KO:K14443]
109907131  protein BTG3 [KO:K14443]
109869527  protein BTG1 [KO:K14443]
109898520  protein Tob2-like [KO:K14443]
109898582  protein Tob2-like [KO:K14443]
109870184  protein Tob1 [KO:K14443]
109891307  protein BTG2-like [KO:K14443]
109891462  protein BTG1 [KO:K14443]
116375246  protein BTG1-like [KO:K14443]
109892734  protein BTG3 [KO:K14443]
109893040  protein BTG2 [KO:K14443]
109901813  maternal B9.15 protein-like [KO:K14443]
109872927  protein BTG3-like [KO:K14443]
116352716  protein Tob1-like [KO:K14443]
109874120  btg4; protein BTG4 [KO:K14443]
109882730  protein Tob1-like isoform X1 [KO:K14443]
109869850  embryonic polyadenylate-binding protein isoform X1 [KO:K13126]
109883393  polyadenylate-binding protein 1A isoform X1 [KO:K13126]
109886876  polyadenylate-binding protein 1A isoform X1 [KO:K13126]
109890670  polyadenylate-binding protein 4-like [KO:K13126]
109894590  polyadenylate-binding protein 4-like isoform X1 [KO:K13126]
116366029  polyadenylate-binding protein 1A isoform X1 [KO:K13126]
109903959  polyadenylate-binding protein 4 [KO:K13126]
109869113  pan2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
109909872  pan3; PAN2-PAN3 deadenylation complex subunit PAN3 [KO:K12572]
109899247  PAN2-PAN3 deadenylation complex subunit pan3-like isoform X3 [KO:K12572]
109869163  mRNA-decapping enzyme 1A isoform X1 [KO:K12610] [EC:3.-.-.-]
109907824  dcp1a; mRNA-decapping enzyme 1A isoform X1 [KO:K12610] [EC:3.-.-.-]
116360600  mRNA-decapping enzyme 1B-like [KO:K12611] [EC:3.-.-.-]
116361497  mRNA-decapping enzyme 1B-like [KO:K12611] [EC:3.-.-.-]
109887461  mRNA-decapping enzyme 1B isoform X1 [KO:K12611] [EC:3.-.-.-]
109867994  dcp2; m7GpppN-mRNA hydrolase isoform X1 [KO:K12613] [EC:3.6.1.62]
109887623  probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:5.6.2.7]
109907626  probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:5.6.2.7]
109883686  ddx6; LOW QUALITY PROTEIN: probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:5.6.2.7]
109881765  probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:5.6.2.7]
109903782  probable ATP-dependent RNA helicase ddx6 isoform X1 [KO:K12614] [EC:5.6.2.7]
109895320  enhancer of mRNA-decapping protein 3-like isoform X1 [KO:K12615]
109874919  enhancer of mRNA-decapping protein 3-like [KO:K12615]
109880937  enhancer of mRNA-decapping protein 3 [KO:K12615]
109889334  enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
109867368  enhancer of mRNA-decapping protein 4 isoform X2 [KO:K12616]
109901075  protein PAT1 homolog 1 [KO:K12617]
109894184  protein PAT1 homolog 1-like [KO:K12617]
109871810  LOW QUALITY PROTEIN: 5'-3' exoribonuclease 1 [KO:K12618] [EC:3.1.13.-]
109874616  5'-3' exoribonuclease 1-like isoform X6 [KO:K12618] [EC:3.1.13.-]
109900616  5'-3' exoribonuclease 2 isoform X1 [KO:K12619] [EC:3.1.13.-]
109866309  5'-3' exoribonuclease 2 [KO:K12619] [EC:3.1.13.-]
109870870  U8 snoRNA-decapping enzyme isoform X2 [KO:K16855] [EC:3.6.1.62 3.6.1.64]
109868827  U6 snRNA-associated Sm-like protein LSm1 isoform X1 [KO:K12620]
109882852  U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
109895154  U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
109881932  lsm2; U6 snRNA-associated Sm-like protein LSm2 [KO:K12621]
109879094  lsm3; U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
109889117  U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
109902375  U6 snRNA-associated Sm-like protein LSm4 isoform X2 [KO:K12623]
109899398  U6 snRNA-associated Sm-like protein LSm5 isoform X1 [KO:K12624]
109884279  U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
116374663  U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
109901303  U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
109872188  U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
109875069  lsm7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
116360623  U6 snRNA-associated Sm-like protein LSm8 [KO:K12627]
116366743  U6 snRNA-associated Sm-like protein LSm8 [KO:K12627]
109884890  enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
116353075  gamma-enolase-like [KO:K01689] [EC:4.2.1.11]
109900570  gamma-enolase-like [KO:K01689] [EC:4.2.1.11]
109881981  eno3; beta-enolase [KO:K01689] [EC:4.2.1.11]
109885655  beta-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
109893686  enolase [KO:K01689] [EC:4.2.1.11]
109907549  gamma-enolase-like isoform X1 [KO:K01689] [EC:4.2.1.11]
109903630  gamma-enolase isoform X2 [KO:K01689] [EC:4.2.1.11]
109908388  alpha-enolase isoform X2 [KO:K01689] [EC:4.2.1.11]
109890018  pnpt1; polyribonucleotide nucleotidyltransferase 1, mitochondrial isoform X1 [KO:K00962] [EC:2.7.7.8]
109899773  polyribonucleotide nucleotidyltransferase 1, mitochondrial [KO:K00962] [EC:2.7.7.8]
109910001  ATP-dependent 6-phosphofructokinase, platelet type isoform X3 [KO:K00850] [EC:2.7.1.11]
109869022  ATP-dependent 6-phosphofructokinase, muscle type-like isoform X2 [KO:K00850] [EC:2.7.1.11]
109891127  ATP-dependent 6-phosphofructokinase, muscle type-like [KO:K00850] [EC:2.7.1.11]
109874693  ATP-dependent 6-phosphofructokinase, platelet type-like isoform X1 [KO:K00850] [EC:2.7.1.11]
109870961  ATP-dependent 6-phosphofructokinase, liver type-like [KO:K00850] [EC:2.7.1.11]
109871622  ATP-dependent 6-phosphofructokinase, platelet type-like isoform X10 [KO:K00850] [EC:2.7.1.11]
109895819  ATP-dependent 6-phosphofructokinase, muscle type [KO:K00850] [EC:2.7.1.11]
109905047  stress-70 protein, mitochondrial [KO:K04043]
109864527  stress-70 protein, mitochondrial [KO:K04043]
109867907  60 kDa heat shock protein, mitochondrial [KO:K04077] [EC:5.6.1.7]
109870895  60 kDa heat shock protein, mitochondrial [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
oki03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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