KEGG   PATHWAY: asyl03018
Entry
asyl03018                   Pathway                                
Name
RNA degradation - Apodemus sylvaticus (European woodmouse)
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
asyl03018  RNA degradation
asyl03018

Other DBs
GO: 0006401
Organism
Apodemus sylvaticus (European woodmouse) [GN:asyl]
Gene
127663720  Hspa9; stress-70 protein, mitochondrial [KO:K04043]
127663934  [KO:K13126]
127664057  Dcp2; m7GpppN-mRNA hydrolase isoform X1 [KO:K12613] [EC:3.6.1.62]
127664629  Pfkp; ATP-dependent 6-phosphofructokinase, platelet type isoform X1 [KO:K00850] [EC:2.7.1.11]
127665225  [KO:K13126]
127665227  [KO:K13126]
127665228  [KO:K13126]
127665229  [KO:K13126]
127665230  [KO:K13126]
127665231  [KO:K13126]
127665232  [KO:K13126]
127665850  Btg3; protein BTG3 [KO:K14443]
127666599  Tent4a; terminal nucleotidyltransferase 4A isoform X1 [KO:K03514] [EC:2.7.7.19]
127666637  Skic3; SKI3 subunit of superkiller complex protein [KO:K12600]
127666720  Mtrex; exosome RNA helicase MTR4 [KO:K12598] [EC:5.6.2.6]
127667288  Pabpc1; polyadenylate-binding protein 1 [KO:K13126]
127667667  Exosc4; exosome complex component RRP41 [KO:K11600]
127667713  Tob2; protein Tob2 [KO:K14443]
127668040  Pfkm; ATP-dependent 6-phosphofructokinase, muscle type isoform X1 [KO:K00850] [EC:2.7.1.11]
127668408  Lsm1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
127668688  Lsm4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
127668922  Cnot7; CCR4-NOT transcription complex subunit 7 isoform X1 [KO:K12581]
127669523  Lsm2; U6 snRNA-associated Sm-like protein LSm2 isoform X1 [KO:K12621]
127669965  Pfkl; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
127670070  Skic2; SKI2 subunit of superkiller complex protein [KO:K12599] [EC:5.6.2.6]
127670453  Pan2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
127670689  Btg1; protein BTG1 [KO:K14443]
127670835  Lsm7; U6 snRNA-associated Sm-like protein LSm7 isoform X1 [KO:K12626]
127671153  Cnot2; CCR4-NOT transcription complex subunit 2 isoform X1 [KO:K12605]
127671471  Exosc6; exosome complex component MTR3 [KO:K12587]
127671521  Tent4b; terminal nucleotidyltransferase 4B isoform X1 [KO:K03514] [EC:2.7.7.19]
127671662  Edc4; enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
127671797  Lsm6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
127671854  Mphosph6; M-phase phosphoprotein 6 [KO:K12593]
127671870  Cnot1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
127673029  Pan3; PAN2-PAN3 deadenylation complex subunit PAN3 isoform X1 [KO:K12572]
127673133  Exosc5; exosome complex component RRP46 [KO:K12590]
127673921  Pnldc1; poly(A)-specific ribonuclease PNLDC1 [KO:K01148] [EC:3.1.13.4]
127673988  [KO:K13126]
127674616  Cnot3; CCR4-NOT transcription complex subunit 3 isoform X1 [KO:K12580]
127675286  Pabpc5; polyadenylate-binding protein 5 [KO:K13126]
127675514  [KO:K13126]
127675554  Pabpc1l2b; polyadenylate-binding protein 1-like 2 [KO:K13126]
127675612  [KO:K14443]
127675620  [KO:K14443]
127677560  [KO:K13126]
127678381  Lsm8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
127678467  Cnot4; CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
127678655  Lsm5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
127678959  Lsm3; U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
127679107  Dcp1b; mRNA-decapping enzyme 1B isoform X1 [KO:K12611] [EC:3.-.-.-]
127679189  Eno2; gamma-enolase [KO:K01689] [EC:4.2.1.11]
127679821  [KO:K07573]
127680741  Zcchc7; zinc finger CCHC domain-containing protein 7 [KO:K12597]
127680757  Exosc3; exosome complex component RRP40 [KO:K03681]
127681233  Pabpc4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
127681665  Exosc10; exosome component 10 [KO:K12591] [EC:3.1.13.-]
127681697  Eno1; alpha-enolase [KO:K01689] [EC:4.2.1.11]
127682368  Pabpc4l; polyadenylate-binding protein 4-like [KO:K13126]
127683301  Dhx36; ATP-dependent DNA/RNA helicase DHX36 [KO:K14442] [EC:5.6.2.6]
127683348  Exosc8; exosome complex component RRP43 isoform X1 [KO:K12586]
127683407  Exosc9; exosome complex component RRP45 [KO:K03678]
127685207  Exosc2; exosome complex component RRP4 [KO:K03679]
127686017  Xrn2; 5'-3' exoribonuclease 2 isoform X1 [KO:K12619] [EC:3.1.13.-]
127686223  Pabpc1l; polyadenylate-binding protein 1-like [KO:K13126]
127687345  Exosc1; exosome complex component CSL4 [KO:K07573]
127688342  Exosc7; exosome complex component RRP42 isoform X1 [KO:K12589]
127688436  Cnot10; CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
127688623  [KO:K16855] [EC:3.6.1.62 3.6.1.64]
127688624  [KO:K16855] [EC:3.6.1.62 3.6.1.64]
127688706  Xrn1; 5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
127688920  Dis3l; LOW QUALITY PROTEIN: DIS3-like exonuclease 1 [KO:K18681] [EC:3.1.13.-]
127688995  Edc3; enhancer of mRNA-decapping protein 3 [KO:K12615]
127689051  Skic8; SKI8 subunit of superkiller complex protein [KO:K12602]
127689169  Ddx6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:5.6.2.7]
127689260  Dcps; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
127689611  Patl1; protein PAT1 homolog 1 [KO:K12617]
127690036  Btg4; protein BTG4 [KO:K14443]
127690555  Dcp1a; mRNA-decapping enzyme 1A isoform X1 [KO:K12610] [EC:3.-.-.-]
127691212  Dis3; exosome complex exonuclease RRP44 isoform X1 [KO:K12585] [EC:3.1.13.-]
127693042  Cnot9; CCR4-NOT transcription complex subunit 9 [KO:K12606]
127693048  Hspd1; 60 kDa heat shock protein, mitochondrial [KO:K04077] [EC:5.6.1.7]
127693679  Parn; LOW QUALITY PROTEIN: poly(A)-specific ribonuclease PARN [KO:K01148] [EC:3.1.13.4]
127693705  Cnot6; CCR4-NOT transcription complex subunit 6 isoform X1 [KO:K12603] [EC:3.1.13.4]
127694929  Tob1; protein Tob1 [KO:K14443]
127695084  Eno3; beta-enolase [KO:K01689] [EC:4.2.1.11]
127695457  Cnot8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
127696177  Pnpt1; polyribonucleotide nucleotidyltransferase 1, mitochondrial [KO:K00962] [EC:2.7.7.8]
127696668  Cnot6l; CCR4-NOT transcription complex subunit 6-like isoform X1 [KO:K12603] [EC:3.1.13.4]
127696994  Btg2; protein BTG2 [KO:K14443]
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
asyl03015  mRNA surveillance pathway
KO pathway
ko03018   

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