KEGG   PATHWAY: pale03018
Entry
pale03018                   Pathway                                
Name
RNA degradation - Pteropus alecto (black flying fox)
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
pale03018  RNA degradation
pale03018

Other DBs
GO: 0006401
Organism
Pteropus alecto (black flying fox) [GN:pale]
Gene
102877798  CNOT8; CCR4-NOT transcription complex subunit 8 isoform X1 [KO:K12581]
102878446  SKIV2L; helicase SKI2W isoform X1 [KO:K12599] [EC:3.6.4.13]
102878461  LSM6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
102878811  PAN2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X3 [KO:K12571] [EC:3.1.13.4]
102879340  DCPS; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
102879653  MTREX; exosome RNA helicase MTR4 [KO:K12598] [EC:3.6.4.13]
102879693  BTG2; protein BTG2 [KO:K14443]
102880629  LSM4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
102880866  LSM1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
102880885  PABPC1L; polyadenylate-binding protein 1-like [KO:K13126]
102880899  LSM2; U6 snRNA-associated Sm-like protein LSm2 [KO:K12621]
102880920  EDC4; enhancer of mRNA-decapping protein 4 isoform X3 [KO:K12616]
102881109  TENT4B; non-canonical poly(A) RNA polymerase PAPD5 isoform X1 [KO:K03514] [EC:2.7.7.19]
102881202  DCP2; m7GpppN-mRNA hydrolase isoform X1 [KO:K12613] [EC:3.6.1.62]
102881374  EXOSC5; exosome complex component RRP46 [KO:K12590]
102881544  PATL1; protein PAT1 homolog 1 [KO:K12617]
102882437  DCP1B; mRNA-decapping enzyme 1B isoform X1 [KO:K12611] [EC:3.-.-.-]
102882629  MPHOSPH6; M-phase phosphoprotein 6 isoform X1 [KO:K12593]
102882945  [KO:K13126]
102884068  LSM8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
102884576  CNOT4; CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
102884702  LSM7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
102885147  CNOT9; CCR4-NOT transcription complex subunit 9 isoform X1 [KO:K12606]
102885504  EXOSC10; LOW QUALITY PROTEIN: exosome component 10 [KO:K12591] [EC:3.1.13.-]
102885911  PNPT1; polyribonucleotide nucleotidyltransferase 1, mitochondrial isoform X1 [KO:K00962] [EC:2.7.7.8]
102885945  PABPC4L; polyadenylate-binding protein 4-like [KO:K13126]
102886089  PFKP; ATP-dependent 6-phosphofructokinase, platelet type isoform X3 [KO:K00850] [EC:2.7.1.11]
102886649  EXOSC3; exosome complex component RRP40 [KO:K03681]
102886722  CNOT3; CCR4-NOT transcription complex subunit 3 [KO:K12580]
102886881  EXOSC1; exosome complex component CSL4 [KO:K07573]
102886998  EXOSC4; exosome complex component RRP41 [KO:K11600]
102887035  PABPC5; polyadenylate-binding protein 5 [KO:K13126]
102887066  CNOT1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
102887122  BTG1; protein BTG1 [KO:K14443]
102887262  PNLDC1; poly(A)-specific ribonuclease PNLDC1 [KO:K01148] [EC:3.1.13.4]
102887265  EXOSC8; exosome complex component RRP43 [KO:K12586]
102887297  CNOT2; CCR4-NOT transcription complex subunit 2 isoform X1 [KO:K12605]
102887598  CNOT7; CCR4-NOT transcription complex subunit 7 [KO:K12581]
102888251  DDX6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:3.6.4.13]
102888326  ZCCHC7; zinc finger CCHC domain-containing protein 7 isoform X2 [KO:K12597]
102888505  EXOSC7; exosome complex component RRP42 [KO:K12589]
102888582  TTC37; tetratricopeptide repeat protein 37 [KO:K12600]
102888755  TENT4A; non-canonical poly(A) RNA polymerase PAPD7 isoform X1 [KO:K03514] [EC:2.7.7.19]
102889076  BTG4; protein BTG4 [KO:K14443]
102889090  XRN1; 5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
102890026  CNOT6; CCR4-NOT transcription complex subunit 6 isoform X1 [KO:K12603] [EC:3.1.13.4]
102890317  LSM5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
102890922  ENO3; beta-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
102891085  EDC3; enhancer of mRNA-decapping protein 3 [KO:K12615]
102891100  CNOT10; CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
102891220  ENO1; alpha-enolase [KO:K01689] [EC:4.2.1.11]
102891318  HSPD1; 60 kDa heat shock protein, mitochondrial [KO:K04077] [EC:5.6.1.7]
102891333  PAN3; PAN2-PAN3 deadenylation complex subunit PAN3 isoform X1 [KO:K12572]
102891676  NUDT16; U8 snoRNA-decapping enzyme [KO:K16855] [EC:3.6.1.62 3.6.1.64]
102891690  PARN; poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
102891712  TOB2; protein Tob2 [KO:K14443]
102892048  HSPA9; stress-70 protein, mitochondrial [KO:K04043]
102892196  DCP1A; mRNA-decapping enzyme 1A isoform X1 [KO:K12610] [EC:3.-.-.-]
102893321  DHX36; ATP-dependent RNA helicase DHX36 [KO:K14442] [EC:3.6.4.13]
102893608  XRN2; 5'-3' exoribonuclease 2 [KO:K12619] [EC:3.1.13.-]
102893676  PFKM; ATP-dependent 6-phosphofructokinase, muscle type isoform X1 [KO:K00850] [EC:2.7.1.11]
102893757  PABPC1; polyadenylate-binding protein 1 isoform X3 [KO:K13126]
102893843  EXOSC9; exosome complex component RRP45 isoform X1 [KO:K03678]
102894615  TOB1; protein Tob1 [KO:K14443]
102894946  PFKL; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
102895039  PABPC4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
102895065  LSM3; U6 snRNA-associated Sm-like protein LSm3 isoform X1 [KO:K12622]
102895152  ENO2; gamma-enolase [KO:K01689] [EC:4.2.1.11]
102895481  C1D; nuclear nucleic acid-binding protein C1D [KO:K12592]
102895681  EXOSC2; exosome complex component RRP4 isoform X1 [KO:K03679]
102896420  BTG3; protein BTG3 [KO:K14443]
102897611  DIS3L; DIS3-like exonuclease 1 isoform X1 [KO:K18681] [EC:3.1.13.-]
102897682  DIS3; exosome complex exonuclease RRP44 isoform X1 [KO:K12585] [EC:3.1.13.-]
102898411  CNOT6L; CCR4-NOT transcription complex subunit 6-like isoform X1 [KO:K12603] [EC:3.1.13.4]
102898636  WDR61; WD repeat-containing protein 61 [KO:K12602]
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
pale03015  mRNA surveillance pathway
KO pathway
ko03018   

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