KEGG   PATHWAY: stow03018
Entry
stow03018                   Pathway                                
Name
RNA degradation - Sphaerodactylus townsendi (Townsend's least gecko)
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
stow03018  RNA degradation
stow03018

Other DBs
GO: 0006401
Organism
Sphaerodactylus townsendi (Townsend's least gecko) [GN:stow]
Gene
125441714  DCPS; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
125438120  EXOSC1; exosome complex component CSL4 [KO:K07573]
125442007  EXOSC2; exosome complex component RRP4 [KO:K03679]
125437394  EXOSC3; exosome complex component RRP40 [KO:K03681]
125436030  EXOSC8; exosome complex component RRP43 [KO:K12586]
125443249  EXOSC6; exosome complex component MTR3 [KO:K12587]
125441299  EXOSC7; exosome complex component RRP42 [KO:K12589]
125425135  EXOSC4; LOW QUALITY PROTEIN: exosome complex component RRP41 [KO:K11600]
125439891  EXOSC9; exosome complex component RRP45 [KO:K03678]
125431076  DIS3; LOW QUALITY PROTEIN: exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
125445986  EXOSC10; exosome component 10 [KO:K12591] [EC:3.1.13.-]
125435434  C1D; nuclear nucleic acid-binding protein C1D [KO:K12592]
125424882  MPHOSPH6; M-phase phosphoprotein 6 [KO:K12593]
125424626  DIS3L; DIS3-like exonuclease 1 [KO:K18681] [EC:3.1.13.-]
125443584  TENT4B; terminal nucleotidyltransferase 4B isoform X1 [KO:K03514] [EC:2.7.7.19]
125443662  TENT4A; terminal nucleotidyltransferase 4A isoform X1 [KO:K03514] [EC:2.7.7.19]
125436707  ZCCHC7; zinc finger CCHC domain-containing protein 7 isoform X1 [KO:K12597]
125436241  MTREX; LOW QUALITY PROTEIN: exosome RNA helicase MTR4 [KO:K12598] [EC:5.6.2.6]
125428528  SKIV2L; helicase SKI2W [KO:K12599] [EC:5.6.2.6]
125436375  TTC37; tetratricopeptide repeat protein 37 [KO:K12600]
125424438  WDR61; WD repeat-containing protein 61 [KO:K12602]
125428216  CNOT6; CCR4-NOT transcription complex subunit 6 [KO:K12603] [EC:3.1.13.4]
125439995  CNOT6L; CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
125443490  CNOT1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
125435926  CNOT2; CCR4-NOT transcription complex subunit 2 isoform X1 [KO:K12605]
125434823  CNOT4; CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
125440195  CNOT7; CCR4-NOT transcription complex subunit 7 [KO:K12581]
125429875  CNOT8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
125426683  CNOT9; CCR4-NOT transcription complex subunit 9 isoform X1 [KO:K12606]
125440882  CNOT10; CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
125437953  DHX36; ATP-dependent DNA/RNA helicase DHX36 [KO:K14442] [EC:5.6.2.6]
125428141  PNLDC1; poly(A)-specific ribonuclease PNLDC1 isoform X1 [KO:K01148] [EC:3.1.13.4]
125431469  PARN; poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
125434815  TOB2; protein Tob2 [KO:K14443]
125434965  protein BTG3-like [KO:K14443]
125435093  BTG1; protein BTG1 [KO:K14443]
125429571  TOB1; protein Tob1 [KO:K14443]
125429734  protein BTG1-like [KO:K14443]
125442047  BTG4; protein BTG4 [KO:K14443]
125433079  BTG2; protein BTG2 [KO:K14443]
125434407  PABPC4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
125432894  PABPC1L; polyadenylate-binding protein 1-like isoform X1 [KO:K13126]
125439505  PABPC1; polyadenylate-binding protein 1 [KO:K13126]
125429323  PAN2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
125430724  PAN3; PAN2-PAN3 deadenylation complex subunit PAN3 isoform X1 [KO:K12572]
125429236  DCP1A; mRNA-decapping enzyme 1A [KO:K12610] [EC:3.-.-.-]
125436399  DCP2; m7GpppN-mRNA hydrolase isoform X1 [KO:K12613] [EC:3.6.1.62]
125441646  DDX6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:5.6.2.7]
125446184  EDC3; LOW QUALITY PROTEIN: enhancer of mRNA-decapping protein 3 [KO:K12615]
125443561  EDC4; enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
125426084  PATL1; protein PAT1 homolog 1 isoform X1 [KO:K12617]
125437698  5'-3' exoribonuclease 1-like [KO:K12618] [EC:3.1.13.-]
125443413  XRN2; 5'-3' exoribonuclease 2 isoform X1 [KO:K12619] [EC:3.1.13.-]
125427638  U8 snoRNA-decapping enzyme-like isoform X1 [KO:K16855] [EC:3.6.1.62 3.6.1.64]
125441914  LSM1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
125434556  U6 snRNA-associated Sm-like protein LSm2 [KO:K12621]
125427645  LSM2; U6 snRNA-associated Sm-like protein LSm2 [KO:K12621]
125430150  LSM3; U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
125433782  LSM4; U6 snRNA-associated Sm-like protein LSm4 isoform X1 [KO:K12623]
125441106  LSM5; U6 snRNA-associated Sm-like protein LSm5 isoform X1 [KO:K12624]
125439713  LSM6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
125434041  LSM7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
125435080  LSM8; LSM8 homolog, U6 small nuclear RNA associated isoform X1 [KO:K12627]
125433397  U6 snRNA-associated Sm-like protein LSm8 [KO:K12627]
125445710  ENO1; enolase [KO:K01689] [EC:4.2.1.11]
125436188  ENO2; gamma-enolase [KO:K01689] [EC:4.2.1.11]
125437267  PNPT1; polyribonucleotide nucleotidyltransferase 1, mitochondrial [KO:K00962] [EC:2.7.7.8]
125441245  ATP-dependent 6-phosphofructokinase, platelet type isoform X1 [KO:K00850] [EC:2.7.1.11]
125430305  ATP-dependent 6-phosphofructokinase, muscle type isoform X1 [KO:K00850] [EC:2.7.1.11]
125437880  PFKL; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
125434517  HSPA9; stress-70 protein, mitochondrial [KO:K04043]
125425829  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
stow03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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