KEGG   PATHWAY: phi03018
Entry
phi03018                    Pathway                                
Name
RNA degradation - Pseudopodoces humilis (Tibetan ground-tit)
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
phi03018  RNA degradation
phi03018

Other DBs
GO: 0006401
Organism
Pseudopodoces humilis (Tibetan ground-tit) [GN:phi]
Gene
102099168  EXOSC2; exosome complex component RRP4 [KO:K03679]
102099286  PABPC4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
102099530  BTG2; protein BTG2 [KO:K14443]
102099718  DCP2; m7GpppN-mRNA hydrolase [KO:K12613] [EC:3.6.1.62]
102099780  PAN2; PAB-dependent poly(A)-specific ribonuclease subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
102099821  PABPC1L; polyadenylate-binding protein 1-like [KO:K13126]
102099933  RQCD1; cell differentiation protein RCD1 homolog [KO:K12606]
102100017  PFKP; ATP-dependent 6-phosphofructokinase, platelet type isoform X1 [KO:K00850] [EC:2.7.1.11]
102100419  PARN; poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
102100928  PATL1; protein PAT1 homolog 1 isoform X4 [KO:K12617]
102101345  EDC4; enhancer of mRNA-decapping protein 4 [KO:K12616]
102101646  WDR61; WD repeat-containing protein 61 isoform X2 [KO:K12602]
102101751  DIS3; exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
102102269  EXOSC6; exosome complex component MTR3 [KO:K12587]
102102282  ENO1; alpha-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
102102330  MPHOSPH6; M-phase phosphoprotein 6 [KO:K12593]
102102364  CNOT2; CCR4-NOT transcription complex subunit 2 [KO:K12605]
102102373  CNOT8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
102102431  [KO:K14443]
102102643  DCPS; m7GpppX diphosphatase isoform X2 [KO:K12584] [EC:3.6.1.59]
102102897  ZCCHC7; zinc finger CCHC domain-containing protein 7 [KO:K12597]
102103166  EXOSC4; exosome complex component RRP41 [KO:K11600]
102103485  DCP1A; mRNA-decapping enzyme 1A isoform X1 [KO:K12610] [EC:3.-.-.-]
102103701  CNOT6L; CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
102103805  PNPT1; polyribonucleotide nucleotidyltransferase 1, mitochondrial [KO:K00962] [EC:2.7.7.8]
102104007  HSPA9; stress-70 protein, mitochondrial [KO:K04043]
102104124  LSM4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
102104179  BTG4; protein BTG4 [KO:K14443]
102104476  TOB2; protein Tob2 [KO:K14443]
102104540  TTC37; tetratricopeptide repeat protein 37 isoform X1 [KO:K12600]
102104864  PNLDC1; poly(A)-specific ribonuclease PARN-like domain-containing protein 1 isoform X1 [KO:K01148] [EC:3.1.13.4]
102105089  LSM1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
102105112  CNOT4; CCR4-NOT transcription complex subunit 4 isoform X3 [KO:K10643] [EC:2.3.2.27]
102105952  EXOSC9; exosome complex component RRP45 [KO:K03678]
102106657  [KO:K12580]
102106843  PABPC1; polyadenylate-binding protein 1 [KO:K13126]
102107384  SKIV2L2; superkiller viralicidic activity 2-like 2 [KO:K12598] [EC:3.6.4.13]
102107484  CNOT6; CCR4-NOT transcription complex subunit 6 isoform X1 [KO:K12603] [EC:3.1.13.4]
102107832  LSM3; U6 snRNA-associated Sm-like protein LSm3 isoform X3 [KO:K12622]
102107852  EXOSC10; exosome component 10 [KO:K12591] [EC:3.1.13.-]
102107871  PAN3; PAB-dependent poly(A)-specific ribonuclease subunit PAN3 isoform X1 [KO:K12572]
102107881  EXOSC7; exosome complex component RRP42 [KO:K12589]
102107942  HSPD1; 60 kDa heat shock protein, mitochondrial [KO:K04077] [EC:5.6.1.7]
102108757  XRN2; 5'-3' exoribonuclease 2 isoform X2 [KO:K12619] [EC:3.1.13.-]
102109362  PAPD5; non-canonical poly(A) RNA polymerase PAPD5 [KO:K03514] [EC:2.7.7.19]
102109389  LSM2; U6 snRNA-associated Sm-like protein LSm2 [KO:K12621]
102109441  PFKL; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
102109721  DIS3L; DIS3-like exonuclease 1 [KO:K18681] [EC:3.1.13.-]
102109729  XRN1; 5'-3' exoribonuclease 1 [KO:K12618] [EC:3.1.13.-]
102109972  TOB1; protein Tob1 [KO:K14443]
102110112  PAPD7; non-canonical poly(A) RNA polymerase PAPD7 isoform X1 [KO:K03514] [EC:2.7.7.19]
102110183  CNOT7; CCR4-NOT transcription complex subunit 7 [KO:K12581]
102110517  DHX36; ATP-dependent RNA helicase DHX36 [KO:K14442] [EC:3.6.4.13]
102110764  EDC3; enhancer of mRNA-decapping protein 3 isoform X1 [KO:K12615]
102110895  ENO2; gamma-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
102111611  PFKM; ATP-dependent 6-phosphofructokinase, muscle type [KO:K00850] [EC:2.7.1.11]
102111655  LSM5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
102111715  C1D; nuclear nucleic acid-binding protein C1D [KO:K12592]
102112073  CNOT1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
102112266  DDX6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:3.6.4.13]
102112798  EXOSC3; exosome complex component RRP40 [KO:K03681]
102113193  LSM6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
102113237  CNOT10; CCR4-NOT transcription complex subunit 10 [KO:K12607]
102113240  BTG1; protein BTG1 [KO:K14443]
102113698  EXOSC5; exosome complex component RRP46 [KO:K12590]
102113719  EXOSC8; exosome complex component RRP43 [KO:K12586]
102113733  EXOSC1; exosome complex component CSL4 isoform X1 [KO:K07573]
102114166  LSM8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
102114395  SKIV2L; helicase SKI2W [KO:K12599] [EC:3.6.4.13]
102114693  LSM7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
106628574  DCP1B; mRNA-decapping enzyme 1B [KO:K12611] [EC:3.-.-.-]
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
phi03015  mRNA surveillance pathway
KO pathway
ko03018   

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