KEGG   PATHWAY: nasi03018
Entry
nasi03018                   Pathway                                
Name
RNA degradation - Neophocaena asiaeorientalis asiaeorientalis (Yangtze finless porpoise)
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
nasi03018  RNA degradation
nasi03018

Other DBs
GO: 0006401
Organism
Neophocaena asiaeorientalis asiaeorientalis (Yangtze finless porpoise) [GN:nasi]
Gene
112390940  BTG3; protein BTG3 isoform X1 [KO:K14443]
112391756  DCP1B; mRNA-decapping enzyme 1B isoform X1 [KO:K12611] [EC:3.-.-.-]
112391839  ENO2; gamma-enolase [KO:K01689] [EC:4.2.1.11]
112392030  [KO:K13126]
112392053  EDC4; enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
112392658  EXOSC3; exosome complex component RRP40 isoform X1 [KO:K03681]
112392731  NUDT16; U8 snoRNA-decapping enzyme [KO:K16855] [EC:3.6.1.62 3.6.1.64]
112392967  EXOSC1; exosome complex component CSL4 isoform X1 [KO:K07573]
112393114  DIS3L; DIS3-like exonuclease 1 isoform X1 [KO:K18681] [EC:3.1.13.-]
112393422  EXOSC6; exosome complex component MTR3 [KO:K12587]
112393492  MPHOSPH6; M-phase phosphoprotein 6 isoform X1 [KO:K12593]
112393762  LSM6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
112394227  PAN2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
112394253  ENO3; beta-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
112394262  CNOT2; CCR4-NOT transcription complex subunit 2 isoform X1 [KO:K12605]
112394271  PFKM; ATP-dependent 6-phosphofructokinase, muscle type [KO:K00850] [EC:2.7.1.11]
112394384  LSM5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
112394659  TOB2; protein Tob2 [KO:K14443]
112394942  CNOT4; CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
112395372  SKIV2L; helicase SKI2W [KO:K12599] [EC:3.6.4.13]
112395448  LSM2; U6 snRNA-associated Sm-like protein LSm2 [KO:K12621]
112395561  PABPC4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
112396437  LSM7; LOW QUALITY PROTEIN: U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
112396876  DCPS; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
112397081  EXOSC4; exosome complex component RRP41 [KO:K11600]
112397438  C1D; nuclear nucleic acid-binding protein C1D [KO:K12592]
112397877  PABPC5; polyadenylate-binding protein 5 [KO:K13126]
112397897  CNOT3; CCR4-NOT transcription complex subunit 3 [KO:K12580]
112398691  DCP2; m7GpppN-mRNA hydrolase isoform X1 [KO:K12613] [EC:3.6.1.62]
112398766  CNOT10; CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
112399395  PARN; poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
112399756  EXOSC9; exosome complex component RRP45 [KO:K03678]
112399758  PABPC4L; LOW QUALITY PROTEIN: polyadenylate-binding protein 4-like [KO:K13126]
112400161  TOB1; protein Tob1 [KO:K14443]
112400536  DCP1A; mRNA-decapping enzyme 1A isoform X1 [KO:K12610] [EC:3.-.-.-]
112400763  [KO:K13126]
112400854  PABPC1L; polyadenylate-binding protein 1-like isoform X1 [KO:K13126]
112400952  TTC37; tetratricopeptide repeat protein 37 [KO:K12600]
112401253  PAPD5; non-canonical poly(A) RNA polymerase PAPD5 [KO:K03514] [EC:2.7.7.19]
112401651  PNLDC1; poly(A)-specific ribonuclease PNLDC1 [KO:K01148] [EC:3.1.13.4]
112401995  [KO:K14443]
112402431  PATL1; protein PAT1 homolog 1 [KO:K12617]
112402695  ENO1; alpha-enolase [KO:K01689] [EC:4.2.1.11]
112402787  EXOSC10; exosome component 10 isoform X1 [KO:K12591] [EC:3.1.13.-]
112403199  CNOT1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
112403364  XRN2; 5'-3' exoribonuclease 2 isoform X1 [KO:K12619] [EC:3.1.13.-]
112403528  BTG2; protein BTG2 [KO:K14443]
112403938  DDX6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:3.6.4.13]
112404347  HSPA9; LOW QUALITY PROTEIN: stress-70 protein, mitochondrial [KO:K04043]
112404521  PAPD7; non-canonical poly(A) RNA polymerase PAPD7 isoform X1 [KO:K03514] [EC:2.7.7.19]
112404856  PNPT1; polyribonucleotide nucleotidyltransferase 1, mitochondrial [KO:K00962] [EC:2.7.7.8]
112405497  PFKP; ATP-dependent 6-phosphofructokinase, platelet type [KO:K00850] [EC:2.7.1.11]
112405512  DIS3; exosome complex exonuclease RRP44 isoform X1 [KO:K12585] [EC:3.1.13.-]
112405600  CNOT6L; CCR4-NOT transcription complex subunit 6-like isoform X1 [KO:K12603] [EC:3.1.13.4]
112405744  BTG4; protein BTG4 [KO:K14443]
112405769  WDR61; WD repeat-containing protein 61 [KO:K12602]
112405820  BTG1; protein BTG1 [KO:K14443]
112406528  EXOSC8; exosome complex component RRP43 [KO:K12586]
112406564  PAN3; PAN2-PAN3 deadenylation complex subunit PAN3 isoform X1 [KO:K12572]
112407308  PABPC1; polyadenylate-binding protein 1 isoform X1 [KO:K13126]
112407873  HSPD1; 60 kDa heat shock protein, mitochondrial [KO:K04077] [EC:5.6.1.7]
112408176  LSM8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
112408582  PFKL; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
112409702  CNOT7; CCR4-NOT transcription complex subunit 7 [KO:K12581]
112409798  CNOT8; CCR4-NOT transcription complex subunit 8 isoform X1 [KO:K12581]
112410888  EDC3; enhancer of mRNA-decapping protein 3 [KO:K12615]
112411454  EXOSC2; exosome complex component RRP4 [KO:K03679]
112411761  ZCCHC7; zinc finger CCHC domain-containing protein 7 [KO:K12597]
112411921  CNOT9; CCR4-NOT transcription complex subunit 9 [KO:K12606]
112412001  LSM3; U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
112413083  CNOT6; CCR4-NOT transcription complex subunit 6 isoform X1 [KO:K12603] [EC:3.1.13.4]
112413143  LSM1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
112413355  EXOSC7; exosome complex component RRP42 [KO:K12589]
112413392  MTREX; exosome RNA helicase MTR4 [KO:K12598] [EC:3.6.4.13]
112414928  LSM4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
112415406  EXOSC5; exosome complex component RRP46 isoform X1 [KO:K12590]
112415867  XRN1; 5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
112415878  DHX36; ATP-dependent RNA helicase DHX36 [KO:K14442] [EC:3.6.4.13]
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
nasi03015  mRNA surveillance pathway
KO pathway
ko03018   

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