KEGG   PATHWAY: ccae03018
Entry
ccae03018                   Pathway                                
Name
RNA degradation - Cyanistes caeruleus (blue tit)
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
ccae03018  RNA degradation
ccae03018

Other DBs
GO: 0006401
Organism
Cyanistes caeruleus (blue tit) [GN:ccae]
Gene
111939373  DCPS; m7GpppX diphosphatase isoform X1 [KO:K12584] [EC:3.6.1.59]
111931235  EXOSC1; exosome complex component CSL4 isoform X1 [KO:K07573]
111937003  EXOSC2; exosome complex component RRP4 [KO:K03679]
111943247  EXOSC8; exosome complex component RRP43 [KO:K12586]
111923586  EXOSC7; exosome complex component RRP42 [KO:K12589]
111941579  EXOSC5; exosome complex component RRP46 [KO:K12590]
111929036  EXOSC9; exosome complex component RRP45 [KO:K03678]
111923381  DIS3; exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
111938577  EXOSC10; exosome component 10 [KO:K12591] [EC:3.1.13.-]
111926514  C1D; nuclear nucleic acid-binding protein C1D [KO:K12592]
111934449  MPHOSPH6; M-phase phosphoprotein 6 [KO:K12593]
111933967  DIS3L; DIS3-like exonuclease 1 [KO:K18681] [EC:3.1.13.-]
111934616  PAPD5; non-canonical poly(A) RNA polymerase PAPD5 [KO:K03514] [EC:2.7.7.19]
111925393  PAPD7; non-canonical poly(A) RNA polymerase PAPD7 isoform X1 [KO:K03514] [EC:2.7.7.19]
111941623  ZCCHC7; zinc finger CCHC domain-containing protein 7 [KO:K12597]
111941442  MTREX; exosome RNA helicase MTR4 isoform X1 [KO:K12598] [EC:5.6.2.6]
111941540  TTC37; tetratricopeptide repeat protein 37 isoform X1 [KO:K12600]
111934230  WDR61; WD repeat-containing protein 61 isoform X1 [KO:K12602]
111929501  CNOT6L; CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
111935560  CNOT6; CCR4-NOT transcription complex subunit 6 isoform X1 [KO:K12603] [EC:3.1.13.4]
111934526  CNOT1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
111932798  CNOT2; CCR4-NOT transcription complex subunit 2 isoform X1 [KO:K12605]
111944370  CNOT3; CCR4-NOT transcription complex subunit 3 [KO:K12580]
111930365  CNOT4; CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
111935501  CNOT8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
111927998  CNOT7; CCR4-NOT transcription complex subunit 7 [KO:K12581]
111932189  CNOT9; CCR4-NOT transcription complex subunit 9 isoform X1 [KO:K12606]
111923885  CNOT10; CCR4-NOT transcription complex subunit 10 [KO:K12607]
111933583  DHX36; ATP-dependent RNA helicase DHX36 [KO:K14442] [EC:5.6.2.6]
111927668  PNLDC1; poly(A)-specific ribonuclease PNLDC1 isoform X1 [KO:K01148] [EC:3.1.13.4]
111935952  PARN; poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
111935333  protein BTG1-like [KO:K14443]
111933546  BTG1; protein BTG1 [KO:K14443]
111934516  TOB2; protein Tob2 [KO:K14443]
111939695  BTG2; protein BTG2 [KO:K14443]
111937363  TOB1; protein Tob1 [KO:K14443]
111939402  BTG4; protein BTG4 isoform X1 [KO:K14443]
111924496  PABPC1; polyadenylate-binding protein 1 [KO:K13126]
111938248  PABPC1L; polyadenylate-binding protein 1-like isoform X1 [KO:K13126]
111939136  PABPC4; polyadenylate-binding protein 4 [KO:K13126]
111940524  PAN2-PAN3 deadenylation complex catalytic subunit PAN2-like [KO:K12571] [EC:3.1.13.4]
111943862  PAN2-PAN3 deadenylation complex catalytic subunit PAN2-like [KO:K12571] [EC:3.1.13.4]
111923189  PAN3; PAN2-PAN3 deadenylation complex subunit PAN3 isoform X1 [KO:K12572]
111935130  DCP1A; mRNA-decapping enzyme 1A isoform X1 [KO:K12610] [EC:3.-.-.-]
111928011  DCP1B; mRNA-decapping enzyme 1B isoform X1 [KO:K12611] [EC:3.-.-.-]
111941736  DCP2; m7GpppN-mRNA hydrolase [KO:K12613] [EC:3.6.1.62]
111939207  DDX6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:5.6.2.7]
111934278  EDC3; enhancer of mRNA-decapping protein 3 [KO:K12615]
111934752  EDC4; enhancer of mRNA-decapping protein 4 [KO:K12616]
111944007  PATL1; protein PAT1 homolog 1 [KO:K12617]
111933509  XRN1; 5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
111926373  XRN2; 5'-3' exoribonuclease 2 [KO:K12619] [EC:3.1.13.-]
111938843  LSM1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
111935055  LSM3; U6 snRNA-associated Sm-like protein LSm3 isoform X1 [KO:K12622]
111940319  LSM4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
111941295  LSM5; U6 snRNA-associated Sm-like protein LSm5 isoform X1 [KO:K12624]
111928836  LSM6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
111942232  LSM7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
111931519  LSM8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
111938676  ENO1; alpha-enolase [KO:K01689] [EC:4.2.1.11]
111938227  ENO2; gamma-enolase [KO:K01689] [EC:4.2.1.11]
111926406  PNPT1; polyribonucleotide nucleotidyltransferase 1, mitochondrial isoform X1 [KO:K00962] [EC:2.7.7.8]
111924068  PFKP; ATP-dependent 6-phosphofructokinase, platelet type isoform X1 [KO:K00850] [EC:2.7.1.11]
111941974  PFKL; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
111940514  PFKM; ATP-dependent 6-phosphofructokinase, muscle type [KO:K00850] [EC:2.7.1.11]
111935689  HSPA9; stress-70 protein, mitochondrial isoform X1 [KO:K04043]
111931960  HSPD1; 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
ccae03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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