KEGG   PATHWAY: char03018
Entry
char03018                   Pathway                                
Name
RNA degradation - Clupea harengus (Atlantic herring)
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
char03018  RNA degradation
char03018

Other DBs
GO: 0006401
Organism
Clupea harengus (Atlantic herring) [GN:char]
Gene
105888485  cnot4a; CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
105888627  exosc3; exosome complex component RRP40 [KO:K03681]
105888864  tob1b; protein Tob1b [KO:K14443]
105889213  eno1b; enolase 1b, (alpha) [KO:K01689] [EC:4.2.1.11]
105889978  lsm1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
105890032  ttc37; tetratricopeptide repeat protein 37 [KO:K12600]
105890271  pan3; PAN2-PAN3 deadenylation complex subunit PAN3 [KO:K12572]
105890529  cnot8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
105890644  [KO:K14443]
105891708  si:dkey-79d12.5; maternal B9.15 protein [KO:K14443]
105892018  eno2; gamma-enolase [KO:K01689] [EC:4.2.1.11]
105892019  tent4a; terminal nucleotidyltransferase 4A isoform X2 [KO:K03514] [EC:2.7.7.19]
105892103  btg4; protein BTG4 [KO:K14443]
105892175  wdr61; WD repeat-containing protein 61 [KO:K12602]
105892549  exosc6; exosome complex component MTR3 [KO:K12587]
105893449  c1d; nuclear nucleic acid-binding protein C1D [KO:K12592]
105893506  [KO:K14443]
105894127  zgc:103759; U8 snoRNA-decapping enzyme isoform X1 [KO:K16855] [EC:3.6.1.62 3.6.1.64]
105894631  mtrex; exosome RNA helicase MTR4 [KO:K12598] [EC:3.6.4.13]
105894644  dcp2; LOW QUALITY PROTEIN: m7GpppN-mRNA hydrolase [KO:K12613] [EC:3.6.1.62]
105895616  cnot1; CCR4-NOT transcription complex subunit 1 isoform X12 [KO:K12604]
105895656  mphosph6; M-phase phosphoprotein 6 [KO:K12593]
105895822  parn; poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
105896162  pabpc1a; polyadenylate-binding protein 1A isoform X1 [KO:K13126]
105896234  exosc8; exosome complex component RRP43 [KO:K12586]
105896294  exosc1; exosome complex component CSL4 [KO:K07573]
105896615  pabpc4; polyadenylate-binding protein 4 [KO:K13126]
105896643  dis3; exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
105896645  pfklb; phosphofructokinase, liver b [KO:K00850] [EC:2.7.1.11]
105897079  xrn2; 5'-3' exoribonuclease 2 isoform X1 [KO:K12619] [EC:3.1.13.-]
105897162  exosc5; exosome complex component RRP46 [KO:K12590]
105897335  pfkma; phosphofructokinase, muscle a [KO:K00850] [EC:2.7.1.11]
105897510  lsm8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
105897546  btg1; protein BTG1 [KO:K14443]
105897871  lsm3; snRNA-associated Sm-like protein LSm3 [KO:K12622]
105897989  [KO:K14443]
105899003  exosc10; exosome component 10 isoform X2 [KO:K12591] [EC:3.1.13.-]
105899007  eno1a; enolase 1a, (alpha) isoform X2 [KO:K01689] [EC:4.2.1.11]
105899061  dcp1a; mRNA-decapping enzyme 1A [KO:K12610] [EC:3.-.-.-]
105899162  exosc4; exosome complex component RRP41 [KO:K11600]
105899193  xrn1; 5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
105899390  hspd1; 60 kDa heat shock protein, mitochondrial [KO:K04077] [EC:5.6.1.7]
105899778  tent4b; terminal nucleotidyltransferase 4B [KO:K03514] [EC:2.7.7.19]
105900546  btg2; protein BTG2 [KO:K14443]
105900886  lsm4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
105900975  lsm7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
105901208  cnot6l; CCR4-NOT transcription complex subunit 6-like isoform X1 [KO:K12603] [EC:3.1.13.4]
105901657  [KO:K01689] [EC:4.2.1.11]
105901704  cnot3a; CCR4-NOT transcription complex subunit 3a isoform X1 [KO:K12580]
105901788  cnot9; CCR4-NOT transcription complex subunit 9 isoform X1 [KO:K12606]
105901945  cnot2; CCR4-NOT transcription complex subunit 2 [KO:K12605]
105902019  cnot3b; CCR4-NOT transcription complex subunit 3b isoform X1 [KO:K12580]
105902029  [KO:K12614] [EC:3.6.4.13]
105902171  patl1; protein PAT1 homolog 1 isoform X2 [KO:K12617]
105903270  pan2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
105903484  [KO:K12615]
105903530  zcchc7; zinc finger CCHC domain-containing protein 7 isoform X2 [KO:K12597]
105903534  lsm6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
105903663  exosc7; exosome complex component RRP42 [KO:K12589]
105903935  exosc9; LOW QUALITY PROTEIN: exosome complex component RRP45 [KO:K03678]
105904500  edc4; enhancer of mRNA-decapping protein 4 isoform X2 [KO:K12616]
105904565  eno3; beta-enolase [KO:K01689] [EC:4.2.1.11]
105904606  cnot6a; CCR4-NOT transcription complex subunit 6a [KO:K12603] [EC:3.1.13.4]
105904814  ddx6; probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:3.6.4.13]
105904817  dhx36; ATP-dependent DNA/RNA helicase DHX36 [KO:K14442] [EC:3.6.4.13]
105905238  lsm5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
105906164  pfkpa; ATP-dependent 6-phosphofructokinase, platelet type isoform X5 [KO:K00850] [EC:2.7.1.11]
105906561  dis3l; DIS3-like exonuclease 1 isoform X1 [KO:K18681] [EC:3.1.13.-]
105906673  [KO:K01689] [EC:4.2.1.11]
105906719  [KO:K12603] [EC:3.1.13.4]
105907709  pabpc1b; polyadenylate-binding protein 1b [KO:K13126]
105907727  skiv2l; helicase SKI2W [KO:K12599] [EC:3.6.4.13]
105909152  btg3; protein BTG3 isoform X1 [KO:K14443]
105910535  cnot10; CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
105910646  ddx61; probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:3.6.4.13]
105910971  tob1a; protein Tob1a [KO:K14443]
105911136  [KO:K00850] [EC:2.7.1.11]
105911366  dcp1b; mRNA-decapping enzyme 1B [KO:K12611] [EC:3.-.-.-]
105911975  [KO:K04077] [EC:5.6.1.7]
105912360  hspa9; stress-70 protein, mitochondrial [KO:K04043]
105912423  cnot4b; CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
105912429  [KO:K12605]
105912568  edc3; enhancer of mRNA-decapping protein 3 [KO:K12615]
105912658  pfkla; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
105912767  cnot7; CCR4-NOT transcription complex subunit 7 isoform X1 [KO:K12581]
105913086  exosc2; exosome complex component RRP4 [KO:K03679]
116220807  [KO:K14443]
116222779  [KO:K12598] [EC:3.6.4.13]
122129937  [KO:K14443]
122130814  smx5; smx5 [KO:K12621]
122131800  [KO:K00962] [EC:2.7.7.8]
122132060  dcps; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
122132099  [KO:K13126]
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
char03015  mRNA surveillance pathway
KO pathway
ko03018   

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