KEGG   PATHWAY: asn03018
Entry
asn03018                    Pathway                                
Name
RNA degradation - Alligator sinensis (Chinese alligator)
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
asn03018  RNA degradation
asn03018

Other DBs
GO: 0006401
Organism
Alligator sinensis (Chinese alligator) [GN:asn]
Gene
102367882  EXOSC8; exosome complex component RRP43 [KO:K12586]
102367939  ZCCHC7; zinc finger CCHC domain-containing protein 7 isoform X2 [KO:K12597]
102368126  EXOSC2; exosome complex component RRP4 [KO:K03679]
102368199  LSM8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
102368349  EXOSC7; exosome complex component RRP42 isoform X1 [KO:K12589]
102368846  DIS3; exosome complex exonuclease RRP44 isoform X1 [KO:K12585] [EC:3.1.13.-]
102369082  ENO1; alpha-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
102369135  CNOT6L; CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
102369243  PAN2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
102369498  [KO:K14443]
102369834  BTG1; protein BTG1 [KO:K14443]
102370080  PAN3; LOW QUALITY PROTEIN: PAN2-PAN3 deadenylation complex subunit PAN3 [KO:K12572]
102370215  DCP1A; mRNA-decapping enzyme 1A isoform X1 [KO:K12610] [EC:3.-.-.-]
102370358  HSPA9; stress-70 protein, mitochondrial [KO:K04043]
102371039  LSM6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
102371132  CNOT4; CCR4-NOT transcription complex subunit 4 isoform X2 [KO:K10643] [EC:2.3.2.27]
102371140  TOB2; protein Tob2 [KO:K14443]
102371698  EXOSC10; exosome component 10 isoform X1 [KO:K12591] [EC:3.1.13.-]
102372324  PFKM; ATP-dependent 6-phosphofructokinase, muscle type [KO:K00850] [EC:2.7.1.11]
102372424  EDC4; enhancer of mRNA-decapping protein 4 [KO:K12616]
102372557  PFKP; ATP-dependent 6-phosphofructokinase, platelet type isoform X5 [KO:K00850] [EC:2.7.1.11]
102373084  [KO:K16855] [EC:3.6.1.62 3.6.1.64]
102373465  DIS3L; DIS3-like exonuclease 1 isoform X1 [KO:K18681] [EC:3.1.13.-]
102373513  HSPD1; 60 kDa heat shock protein, mitochondrial [KO:K04077] [EC:5.6.1.7]
102373528  PABPC1L; polyadenylate-binding protein 1-like isoform X1 [KO:K13126]
102373713  TOB1; protein Tob1 [KO:K14443]
102373949  LSM2; LOW QUALITY PROTEIN: U6 snRNA-associated Sm-like protein LSm2 [KO:K12621]
102374177  PATL1; protein PAT1 homolog 1 isoform X1 [KO:K12617]
102374361  XRN2; 5'-3' exoribonuclease 2 [KO:K12619] [EC:3.1.13.-]
102374395  LSM1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
102375094  LSM7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
102375418  ENO2; gamma-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
102375620  CNOT6; CCR4-NOT transcription complex subunit 6 isoform X1 [KO:K12603] [EC:3.1.13.4]
102376189  LSM5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
102376452  C1D; nuclear nucleic acid-binding protein C1D [KO:K12592]
102376466  MPHOSPH6; M-phase phosphoprotein 6 isoform X2 [KO:K12593]
102378208  PNLDC1; poly(A)-specific ribonuclease PNLDC1 isoform X3 [KO:K01148] [EC:3.1.13.4]
102378235  [KO:K01689] [EC:4.2.1.11]
102379100  TTC37; tetratricopeptide repeat protein 37 isoform X1 [KO:K12600]
102379438  DCP2; m7GpppN-mRNA hydrolase [KO:K12613] [EC:3.6.1.62]
102379688  CNOT2; CCR4-NOT transcription complex subunit 2 isoform X1 [KO:K12605]
102379771  TENT4A; non-canonical poly(A) RNA polymerase PAPD7 isoform X1 [KO:K03514] [EC:2.7.7.19]
102379879  CNOT7; CCR4-NOT transcription complex subunit 7 [KO:K12581]
102379982  PARN; poly(A)-specific ribonuclease PARN isoform X2 [KO:K01148] [EC:3.1.13.4]
102380319  CNOT1; LOW QUALITY PROTEIN: CCR4-NOT transcription complex subunit 1 [KO:K12604]
102380393  EDC3; enhancer of mRNA-decapping protein 3 isoform X1 [KO:K12615]
102380424  XRN1; 5'-3' exoribonuclease 1 [KO:K12618] [EC:3.1.13.-]
102380776  SKIV2L; LOW QUALITY PROTEIN: helicase SKI2W [KO:K12599] [EC:3.6.4.13]
102380833  PABPC1; polyadenylate-binding protein 1 isoform X2 [KO:K13126]
102380862  DHX36; ATP-dependent RNA helicase DHX36 [KO:K14442] [EC:3.6.4.13]
102381752  PFKL; ATP-dependent 6-phosphofructokinase, liver type isoform X1 [KO:K00850] [EC:2.7.1.11]
102381998  CNOT10; CCR4-NOT transcription complex subunit 10 isoform X2 [KO:K12607]
102382217  DCP1B; LOW QUALITY PROTEIN: mRNA-decapping enzyme 1B [KO:K12611] [EC:3.-.-.-]
102383214  BTG2; protein BTG2 [KO:K14443]
102383571  EXOSC1; exosome complex component CSL4 [KO:K07573]
102384078  EXOSC9; exosome complex component RRP45 isoform X2 [KO:K03678]
102384340  PNPT1; polyribonucleotide nucleotidyltransferase 1, mitochondrial isoform X3 [KO:K00962] [EC:2.7.7.8]
102384700  WDR61; WD repeat-containing protein 61 isoform X2 [KO:K12602]
102384846  DCPS; m7GpppX diphosphatase isoform X1 [KO:K12584] [EC:3.6.1.59]
102385002  MTREX; exosome RNA helicase MTR4 [KO:K12598] [EC:3.6.4.13]
102386068  DDX6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:3.6.4.13]
102386133  CNOT3; CCR4-NOT transcription complex subunit 3 isoform X2 [KO:K12580]
102386577  PABPC4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
102386899  LSM3; U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
102386913  CNOT8; CCR4-NOT transcription complex subunit 8 isoform X2 [KO:K12581]
102387363  LSM4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
102387695  BTG4; protein BTG4 [KO:K14443]
102387872  TENT4B; non-canonical poly(A) RNA polymerase PAPD5 [KO:K03514] [EC:2.7.7.19]
102388694  [KO:K14443]
106723000  CNOT9; CCR4-NOT transcription complex subunit 9 [KO:K12606]
112547872  EXOSC3; exosome complex component RRP40 [KO:K03681]
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
asn03015  mRNA surveillance pathway
KO pathway
ko03018   

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