KEGG   PATHWAY: apla03018
Entry
apla03018                   Pathway                                
Name
RNA degradation - Anas platyrhynchos (mallard)
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
apla03018  RNA degradation
apla03018

Other DBs
GO: 0006401
Organism
Anas platyrhynchos (mallard) [GN:apla]
Gene
101792448  DCPS; LOW QUALITY PROTEIN: m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
119717299  EXOSC1; exosome complex component CSL4 [KO:K07573]
101789948  EXOSC2; exosome complex component RRP4 [KO:K03679]
101803365  EXOSC3; exosome complex component RRP40 [KO:K03681]
101799603  EXOSC8; exosome complex component RRP43 [KO:K12586]
113844805  EXOSC6; LOW QUALITY PROTEIN: exosome complex component MTR3 [KO:K12587]
101791648  EXOSC7; exosome complex component RRP42 isoform X1 [KO:K12589]
101792563  EXOSC9; exosome complex component RRP45 [KO:K03678]
101790143  DIS3; exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
101793297  EXOSC10; exosome component 10 [KO:K12591] [EC:3.1.13.-]
101791064  C1D; nuclear nucleic acid-binding protein C1D isoform X1 [KO:K12592]
101792574  MPHOSPH6; M-phase phosphoprotein 6 [KO:K12593]
101789397  DIS3L; DIS3-like exonuclease 1 [KO:K18681] [EC:3.1.13.-]
101794381  TENT4B; LOW QUALITY PROTEIN: terminal nucleotidyltransferase 4B [KO:K03514] [EC:2.7.7.19]
101790626  TENT4A; LOW QUALITY PROTEIN: terminal nucleotidyltransferase 4A [KO:K03514] [EC:2.7.7.19]
101789729  ZCCHC7; zinc finger CCHC domain-containing protein 7 [KO:K12597]
101800697  MTREX; exosome RNA helicase MTR4 [KO:K12598] [EC:5.6.2.6]
101798127  TTC37; tetratricopeptide repeat protein 37 isoform X1 [KO:K12600]
101801412  WDR61; WD repeat-containing protein 61 [KO:K12602]
101798399  CNOT6; CCR4-NOT transcription complex subunit 6 isoform X1 [KO:K12603] [EC:3.1.13.4]
101800648  CNOT6L; CCR4-NOT transcription complex subunit 6-like isoform X1 [KO:K12603] [EC:3.1.13.4]
101803516  CNOT1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
101791062  CNOT2; CCR4-NOT transcription complex subunit 2 isoform X2 [KO:K12605]
101802687  CNOT4; CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
101803328  CNOT8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
113843488  CNOT7; CCR4-NOT transcription complex subunit 7 [KO:K12581]
101804561  CNOT9; CCR4-NOT transcription complex subunit 9 isoform X2 [KO:K12606]
101797115  CNOT10; CCR4-NOT transcription complex subunit 10 [KO:K12607]
101790929  DHX36; ATP-dependent DNA/RNA helicase DHX36 [KO:K14442] [EC:5.6.2.6]
101793853  PARN; poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
101795326  PNLDC1; poly(A)-specific ribonuclease PNLDC1 isoform X2 [KO:K01148] [EC:3.1.13.4]
101793601  BTG2; protein BTG2 [KO:K14443]
101795306  TOB2; protein Tob2 [KO:K14443]
101796375  BTG4; protein BTG4 [KO:K14443]
101802852  TOB1; protein Tob1 [KO:K14443]
101804984  BTG1; protein BTG1 [KO:K14443]
101802732  PABPC4; polyadenylate-binding protein 4 isoform X2 [KO:K13126]
101794091  PABPC1; polyadenylate-binding protein 1 isoform X1 [KO:K13126]
101790139  PABPC1L; polyadenylate-binding protein 1-like isoform X1 [KO:K13126]
119714629  PAN2; LOW QUALITY PROTEIN: PAN2-PAN3 deadenylation complex catalytic subunit PAN2 [KO:K12571] [EC:3.1.13.4]
101796427  PAN3; PAN2-PAN3 deadenylation complex subunit PAN3 isoform X1 [KO:K12572]
101791165  DCP1A; mRNA-decapping enzyme 1A isoform X2 [KO:K12610] [EC:3.-.-.-]
101791965  DCP1B; mRNA-decapping enzyme 1B [KO:K12611] [EC:3.-.-.-]
101801466  DCP2; m7GpppN-mRNA hydrolase isoform X2 [KO:K12613] [EC:3.6.1.62]
101798881  DDX6; probable ATP-dependent RNA helicase DDX6 isoform X1 [KO:K12614] [EC:5.6.2.7]
101793246  EDC3; enhancer of mRNA-decapping protein 3 [KO:K12615]
101801093  EDC4; enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
101799434  PATL1; LOW QUALITY PROTEIN: protein PAT1 homolog 1 [KO:K12617]
101794979  XRN1; 5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
101794687  XRN2; 5'-3' exoribonuclease 2 [KO:K12619] [EC:3.1.13.-]
101797025  LSM1; U6 snRNA-associated Sm-like protein LSm1 isoform X1 [KO:K12620]
101796253  LSM3; U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
106020318  LSM4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
101801966  LSM5; U6 snRNA-associated Sm-like protein LSm5 isoform X1 [KO:K12624]
101800680  LSM6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
101791716  LSM7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
101801164  LSM8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
101793724  ENO1; alpha-enolase [KO:K01689] [EC:4.2.1.11]
101790984  ENO2; gamma-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
101801777  PNPT1; polyribonucleotide nucleotidyltransferase 1, mitochondrial [KO:K00962] [EC:2.7.7.8]
101800081  PFKL; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
101804181  ATP-dependent 6-phosphofructokinase, platelet type isoform X2 [KO:K00850] [EC:2.7.1.11]
101803322  HSPA9; stress-70 protein, mitochondrial [KO:K04043]
101799191  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
apla03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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