KEGG   PATHWAY: omy03018
Entry
omy03018                    Pathway                                
Name
RNA degradation - Oncorhynchus mykiss (rainbow trout)
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
omy03018  RNA degradation
omy03018

Other DBs
GO: 0006401
Organism
Oncorhynchus mykiss (rainbow trout) [GN:omy]
Gene
100301700  si:dkey-42i9.4; protein BTG1 [KO:K14443]
100305176  btg3; protein BTG3 [KO:K14443]
100499608  eno1a; enolase 1a, (alpha) isoform X1 [KO:K01689] [EC:4.2.1.11]
110485357  [KO:K01148] [EC:3.1.13.4]
110486417  [KO:K14443]
110486783  [KO:K14443]
110487504  [KO:K01148] [EC:3.1.13.4]
110488105  tent4a; terminal nucleotidyltransferase 4A isoform X1 [KO:K03514] [EC:2.7.7.19]
110488376  [KO:K01689] [EC:4.2.1.11]
110488558  [KO:K04043]
110488610  [KO:K12603] [EC:3.1.13.4]
110488862  [KO:K03681]
110489260  [KO:K12580]
110489347  pabpc1b; polyadenylate-binding protein 1b isoform X1 [KO:K13126]
110489660  [KO:K12572]
110489836  [KO:K12624]
110490579  [KO:K14443]
110490589  [KO:K12605]
110491163  [KO:K01689] [EC:4.2.1.11]
110491295  c1d; nuclear nucleic acid-binding protein C1D [KO:K12592]
110491299  [KO:K14443]
110491424  wdr61; WD repeat-containing protein 61 [KO:K12602]
110491922  [KO:K00850] [EC:2.7.1.11]
110492120  pan2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 [KO:K12571] [EC:3.1.13.4]
110492332  [KO:K12610] [EC:3.-.-.-]
110492471  pabpc1l; polyadenylate-binding protein 1-like [KO:K13126]
110492473  [KO:K14443]
110492606  [KO:K12623]
110493282  [KO:K12605]
110493413  [KO:K07573]
110494047  [KO:K14443]
110494130  eno1b; enolase 1b, (alpha) [KO:K01689] [EC:4.2.1.11]
110494332  pfkmb; phosphofructokinase, muscle b [KO:K00850] [EC:2.7.1.11]
110494646  exosc6; exosome complex component MTR3 [KO:K12587]
110495093  [KO:K12616]
110495907  [KO:K12606]
110495915  [KO:K13126]
110496037  exosc7; exosome complex component RRP42 [KO:K12589]
110496082  [KO:K12614] [EC:5.6.2.7]
110496103  [KO:K12599] [EC:5.6.2.6]
110496201  [KO:K01689] [EC:4.2.1.11]
110496469  [KO:K03514] [EC:2.7.7.19]
110496811  cnot3b; CCR4-NOT transcription complex subunit 3b isoform X1 [KO:K12580]
110497369  [KO:K12625]
110498021  pabpc4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
110498438  [KO:K12604]
110498679  [KO:K12617]
110498870  [KO:K14443]
110499252  [KO:K03514] [EC:2.7.7.19]
110499279  mphosph6; M-phase phosphoprotein 6 [KO:K12593]
110499743  [KO:K12605]
110499807  [KO:K12627]
110499881  [KO:K14443]
110500101  [KO:K10643] [EC:2.3.2.27]
110500739  edc3; enhancer of mRNA-decapping protein 3 [KO:K12615]
110500814  [KO:K01689] [EC:4.2.1.11]
110501384  zgc:103759; U8 snoRNA-decapping enzyme [KO:K16855] [EC:3.6.1.62 3.6.1.64]
110501568  [KO:K12606]
110501838  [KO:K04077] [EC:5.6.1.7]
110501986  pfkla; ATP-dependent 6-phosphofructokinase, liver type isoform X1 [KO:K00850] [EC:2.7.1.11]
110502562  [KO:K00962] [EC:2.7.7.8]
110503283  exosc5; exosome complex component RRP46 [KO:K12590]
110503440  ddx6; probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:5.6.2.7]
110504709  cnot7; CCR4-NOT transcription complex subunit 7 isoform X1 [KO:K12581]
110504772  [KO:K04043]
110504819  [KO:K12603] [EC:3.1.13.4]
110505024  [KO:K12597]
110505429  [KO:K13126]
110506702  [KO:K12615]
110506730  [KO:K03514] [EC:2.7.7.19]
110507515  [KO:K12607]
110508055  dhx36; ATP-dependent DNA/RNA helicase DHX36 [KO:K14442] [EC:5.6.2.6]
110508313  [KO:K12626]
110508617  exosc4; exosome complex component RRP41 [KO:K11600]
110508656  cnot3a; CCR4-NOT transcription complex subunit 3a isoform X1 [KO:K12580]
110508777  [KO:K00850] [EC:2.7.1.11]
110508810  xrn1; 5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
110509600  [KO:K01689] [EC:4.2.1.11]
110509797  [KO:K03679]
110510175  [KO:K12614] [EC:5.6.2.7]
110510202  [KO:K12603] [EC:3.1.13.4]
110510259  exosc8; exosome complex component RRP43 [KO:K12586]
110510314  btg4; protein BTG4 [KO:K14443]
110510472  [KO:K10643] [EC:2.3.2.27]
110510755  [KO:K14443]
110513025  [KO:K03678]
110513705  [KO:K03678]
110515118  [KO:K12599] [EC:5.6.2.6]
110515783  pabpc1a; polyadenylate-binding protein 1A isoform X1 [KO:K13126]
110516566  [KO:K12611] [EC:3.-.-.-]
110517393  [KO:K12611] [EC:3.-.-.-]
110518117  [KO:K12607]
110518478  [KO:K12627]
110518779  [KO:K12585] [EC:3.1.13.-]
110520236  [KO:K04077] [EC:5.6.1.7]
110520482  [KO:K12616]
110521383  cnot2; CCR4-NOT transcription complex subunit 2 isoform X1 [KO:K12605]
110522080  [KO:K12619] [EC:3.1.13.-]
110523163  dcp2; m7GpppN-mRNA hydrolase isoform X1 [KO:K12613] [EC:3.6.1.62]
110523325  [KO:K12620]
110523512  cnot1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
110523588  [KO:K03679]
110523912  [KO:K12598] [EC:5.6.2.6]
110524139  [KO:K12623]
110524212  [KO:K03514] [EC:2.7.7.19]
110524813  [KO:K10643] [EC:2.3.2.27]
110525304  ttc37; tetratricopeptide repeat protein 37 [KO:K12600]
110525941  [KO:K12620]
110526571  [KO:K12615]
110526595  tent4b; terminal nucleotidyltransferase 4B [KO:K03514] [EC:2.7.7.19]
110526820  [KO:K18681] [EC:3.1.13.-]
110527160  [KO:K12585] [EC:3.1.13.-]
110527522  [KO:K12606]
110528103  [KO:K00850] [EC:2.7.1.11]
110528374  [KO:K14443]
110528593  lsm3; snRNA-associated Sm-like protein LSm3 [KO:K12622]
110529465  [KO:K12619] [EC:3.1.13.-]
110530078  [KO:K00962] [EC:2.7.7.8]
110530214  [KO:K12618] [EC:3.1.13.-]
110530255  [KO:K00850] [EC:2.7.1.11]
110530780  lsm7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
110531058  [KO:K12614] [EC:5.6.2.7]
110531329  eno3; beta-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
110532066  [KO:K12610] [EC:3.-.-.-]
110532077  smx5; smx5 [KO:K12621]
110532316  exosc10; exosome component 10 [KO:K12591] [EC:3.1.13.-]
110532739  [KO:K00850] [EC:2.7.1.11]
110533428  dcps; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
110533615  cnot8; CCR4-NOT transcription complex subunit 8 isoform X1 [KO:K12581]
110533653  [KO:K14443]
110534192  cnot6a; CCR4-NOT transcription complex subunit 6a [KO:K12603] [EC:3.1.13.4]
110534339  patl1; protein PAT1 homolog 1 [KO:K12617]
110534533  [KO:K12625]
110535190  [KO:K12624]
110535339  pan3; PAN2-PAN3 deadenylation complex subunit pan3 [KO:K12572]
110535533  pfkpa; ATP-dependent 6-phosphofructokinase, platelet type isoform X2 [KO:K00850] [EC:2.7.1.11]
110536320  [KO:K12620]
110536456  cnot6l; CCR4-NOT transcription complex subunit 6-like isoform X1 [KO:K12603] [EC:3.1.13.4]
110536748  [KO:K12580]
110536793  [KO:K12598] [EC:5.6.2.6]
110537439  [KO:K01689] [EC:4.2.1.11]
110537512  [KO:K12581]
110537882  [KO:K12614] [EC:5.6.2.7]
110538306  [KO:K14443]
110538370  [KO:K14443]
110538731  [KO:K14443]
118936596  [KO:K18681] [EC:3.1.13.-]
118936868  [KO:K12597]
118938866  [KO:K10643] [EC:2.3.2.27]
118940029  [KO:K07573]
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
omy03015  mRNA surveillance pathway
KO pathway
ko03018   

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