KEGG   PATHWAY: opi03018
Entry
opi03018                    Pathway                                
Name
RNA degradation - Ochotona princeps (American pika)
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
opi03018  RNA degradation
opi03018

Other DBs
GO: 0006401
Organism
Ochotona princeps (American pika) [GN:opi]
Gene
101528582  DCPS; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
101519177  EXOSC1; exosome complex component CSL4 isoform X1 [KO:K07573]
101517430  EXOSC2; exosome complex component RRP4 isoform X1 [KO:K03679]
101525018  EXOSC3; exosome complex component RRP40 [KO:K03681]
101526618  EXOSC8; exosome complex component RRP43 isoform X2 [KO:K12586]
101533002  EXOSC7; exosome complex component RRP42 [KO:K12589]
101532904  EXOSC5; exosome complex component RRP46 [KO:K12590]
101530880  EXOSC9; exosome complex component RRP45 isoform X1 [KO:K03678]
101525154  DIS3; exosome complex exonuclease RRP44 isoform X1 [KO:K12585] [EC:3.1.13.-]
101530729  EXOSC10; exosome component 10 isoform X1 [KO:K12591] [EC:3.1.13.-]
101516893  C1D; nuclear nucleic acid-binding protein C1D [KO:K12592]
101526651  MPHOSPH6; M-phase phosphoprotein 6 isoform X1 [KO:K12593]
101529161  TENT4A; terminal nucleotidyltransferase 4A [KO:K03514] [EC:2.7.7.19]
101518059  TENT4B; terminal nucleotidyltransferase 4B isoform X2 [KO:K03514] [EC:2.7.7.19]
101516729  ZCCHC7; zinc finger CCHC domain-containing protein 7 isoform X1 [KO:K12597]
101527638  MTREX; exosome RNA helicase MTR4 [KO:K12598] [EC:5.6.2.6]
101518914  SKIV2L; helicase SKI2W [KO:K12599] [EC:5.6.2.6]
101530698  TTC37; tetratricopeptide repeat protein 37 [KO:K12600]
101522174  WDR61; WD repeat-containing protein 61 [KO:K12602]
101524216  CNOT6; CCR4-NOT transcription complex subunit 6 isoform X1 [KO:K12603] [EC:3.1.13.4]
101536620  CNOT6L; CCR4-NOT transcription complex subunit 6-like isoform X2 [KO:K12603] [EC:3.1.13.4]
101526963  CNOT1; CCR4-NOT transcription complex subunit 1 [KO:K12604]
101521545  CNOT2; CCR4-NOT transcription complex subunit 2 isoform X1 [KO:K12605]
101533209  CNOT3; CCR4-NOT transcription complex subunit 3 [KO:K12580]
101533204  CNOT4; CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
101534998  CNOT7; CCR4-NOT transcription complex subunit 7 isoform X2 [KO:K12581]
101528229  CNOT8; CCR4-NOT transcription complex subunit 8 isoform X1 [KO:K12581]
101520961  LOW QUALITY PROTEIN: CCR4-NOT transcription complex subunit 7-like [KO:K12581]
101519400  CNOT9; CCR4-NOT transcription complex subunit 9 isoform X1 [KO:K12606]
101532623  CNOT10; CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
101518259  DHX36; ATP-dependent DNA/RNA helicase DHX36 [KO:K14442] [EC:5.6.2.6]
101533100  PARN; poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
101516220  PNLDC1; poly(A)-specific ribonuclease PNLDC1 [KO:K01148] [EC:3.1.13.4]
101516649  BTG1; protein BTG1 [KO:K14443]
101520274  TOB1; protein Tob1 isoform X1 [KO:K14443]
101535281  BTG4; protein BTG4 [KO:K14443]
101520881  BTG2; protein BTG2 [KO:K14443]
101522054  BTG3; protein BTG3 [KO:K14443]
101518075  TOB2; protein Tob2 [KO:K14443]
101518548  PABPC1L; polyadenylate-binding protein 1-like [KO:K13126]
101522141  PABPC4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
101534722  LOW QUALITY PROTEIN: polyadenylate-binding protein 4-like [KO:K13126]
101520182  PABPC4L; polyadenylate-binding protein 4-like [KO:K13126]
101535963  PABPC5; polyadenylate-binding protein 5 [KO:K13126]
101522701  PABPC1; polyadenylate-binding protein 1 isoform X1 [KO:K13126]
105942464  polyadenylate-binding protein 1-like [KO:K13126]
101535175  polyadenylate-binding protein 1-like 2 [KO:K13126]
101521001  PAN2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
101534101  PAN3; LOW QUALITY PROTEIN: PAN2-PAN3 deadenylation complex subunit PAN3 [KO:K12572]
101525256  DCP1A; mRNA-decapping enzyme 1A isoform X1 [KO:K12610] [EC:3.-.-.-]
101521124  DCP1B; mRNA-decapping enzyme 1B [KO:K12611] [EC:3.-.-.-]
101526810  DCP2; m7GpppN-mRNA hydrolase [KO:K12613] [EC:3.6.1.62]
101533564  DDX6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:5.6.2.7]
101534164  EDC3; enhancer of mRNA-decapping protein 3 [KO:K12615]
101526150  EDC4; enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
101531582  PATL1; protein PAT1 homolog 1 [KO:K12617]
101519646  XRN1; 5'-3' exoribonuclease 1 [KO:K12618] [EC:3.1.13.-]
101525994  XRN2; 5'-3' exoribonuclease 2 isoform X1 [KO:K12619] [EC:3.1.13.-]
101526244  U8 snoRNA-decapping enzyme-like [KO:K16855] [EC:3.6.1.62 3.6.1.64]
101526489  U8 snoRNA-decapping enzyme-like [KO:K16855] [EC:3.6.1.62 3.6.1.64]
101534031  LSM1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
101516553  LSM2; U6 snRNA-associated Sm-like protein LSm2 [KO:K12621]
101535190  LSM3; U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
101524907  LSM4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
101529030  LSM5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
101533221  LOW QUALITY PROTEIN: U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
101525491  U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
101520431  LSM6; LOW QUALITY PROTEIN: U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
101520618  LSM7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
101532702  U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
101530092  U6 snRNA-associated Sm-like protein LSm8 [KO:K12627]
101520684  LSM8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
101523073  ENO3; beta-enolase isoform X2 [KO:K01689] [EC:4.2.1.11]
101520871  LOW QUALITY PROTEIN: alpha-enolase-like [KO:K01689] [EC:4.2.1.11]
101517104  ENO2; gamma-enolase [KO:K01689] [EC:4.2.1.11]
101535241  ENO1; alpha-enolase [KO:K01689] [EC:4.2.1.11]
101530174  PNPT1; polyribonucleotide nucleotidyltransferase 1, mitochondrial [KO:K00962] [EC:2.7.7.8]
101518346  PFKM; ATP-dependent 6-phosphofructokinase, muscle type [KO:K00850] [EC:2.7.1.11]
101519802  PFKL; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
101529809  ATP-dependent 6-phosphofructokinase, platelet type isoform X1 [KO:K00850] [EC:2.7.1.11]
118759108  ATP-dependent 6-phosphofructokinase, platelet type [KO:K00850] [EC:2.7.1.11]
101519685  HSPA9; stress-70 protein, mitochondrial [KO:K04043]
101526281  HSPD1; 60 kDa heat shock protein, mitochondrial isoform X1 [KO:K04077] [EC:5.6.1.7]
101520309  60 kDa heat shock protein, mitochondrial-like [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
opi03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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