KEGG   PATHWAY: afb03018
Entry
afb03018                    Pathway                                
Name
RNA degradation - Anoplopoma fimbria (sablefish)
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
afb03018  RNA degradation
afb03018

Other DBs
GO: 0006401
Organism
Anoplopoma fimbria (sablefish) [GN:afb]
Gene
129089169  exosc4; exosome complex component RRP41 [KO:K11600]
129089726  cnot6a; CCR4-NOT transcription complex subunit 6a [KO:K12603] [EC:3.1.13.4]
129089990  cnot7; CCR4-NOT transcription complex subunit 7 [KO:K12581]
129090047  hspa9; stress-70 protein, mitochondrial [KO:K04043]
129090260  [KO:K12597]
129090317  [KO:K03681]
129090339  dcps; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
129090342  [KO:K03681]
129091323  tob1b; protein Tob1b [KO:K14443]
129092154  [KO:K00962] [EC:2.7.7.8]
129092329  dis3; LOW QUALITY PROTEIN: exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
129092509  c1d; nuclear nucleic acid-binding protein C1D [KO:K12592]
129093293  exosc5; exosome complex component RRP46 [KO:K12590]
129093696  eno3; beta-enolase [KO:K01689] [EC:4.2.1.11]
129094197  lsm7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
129094433  smx5; smx5 [KO:K12621]
129094449  xrn1; LOW QUALITY PROTEIN: 5'-3' exoribonuclease 1 [KO:K12618] [EC:3.1.13.-]
129094862  lsm4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
129094994  ddx6; probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:3.6.4.13]
129095598  parn; LOW QUALITY PROTEIN: poly(A)-specific ribonuclease PARN [KO:K01148] [EC:3.1.13.4]
129095678  patl1; protein PAT1 homolog 1 [KO:K12617]
129095821  zcchc7; zinc finger CCHC domain-containing protein 7 [KO:K12597]
129096038  exosc1; exosome complex component CSL4 [KO:K07573]
129096151  lsm6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
129096160  exosc9; exosome complex component RRP45 [KO:K03678]
129096819  skic2; LOW QUALITY PROTEIN: helicase SKI2W [KO:K12599] [EC:3.6.4.13]
129096839  [KO:K12580]
129096881  [KO:K01689] [EC:4.2.1.11]
129096987  [KO:K12614] [EC:3.6.4.13]
129097076  [KO:K13126]
129097472  tent4a; LOW QUALITY PROTEIN: terminal nucleotidyltransferase 4A [KO:K03514] [EC:2.7.7.19]
129097541  exosc7; exosome complex component RRP42 [KO:K12589]
129098398  [KO:K14443]
129098838  [KO:K14443]
129099333  pan2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
129099382  pfkma; phosphofructokinase, muscle a [KO:K00850] [EC:2.7.1.11]
129099549  eno1a; enolase 1a, (alpha) [KO:K01689] [EC:4.2.1.11]
129099677  exosc10; exosome component 10 [KO:K12591] [EC:3.1.13.-]
129099775  dcp1a; mRNA-decapping enzyme 1A [KO:K12610] [EC:3.-.-.-]
129100264  zgc:103759; LOW QUALITY PROTEIN: U8 snoRNA-decapping enzyme [KO:K16855] [EC:3.6.1.62 3.6.1.64]
129100426  pabpc1l; polyadenylate-binding protein 1-like [KO:K13126]
129100849  skic3; tetratricopeptide repeat protein 37 [KO:K12600]
129100987  cnot6l; CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
129101605  lsm1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
129101880  dis3l; LOW QUALITY PROTEIN: DIS3-like exonuclease 1 [KO:K18681] [EC:3.1.13.-]
129102351  dcp2; m7GpppN-mRNA hydrolase isoform X1 [KO:K12613] [EC:3.6.1.62]
129102493  exosc2; exosome complex component RRP4 [KO:K03679]
129102684  [KO:K12615]
129102898  mtrex; exosome RNA helicase MTR4 [KO:K12598] [EC:3.6.4.13]
129103358  pabpc4; polyadenylate-binding protein 4 [KO:K13126]
129104251  hspd1; 60 kDa heat shock protein, mitochondrial [KO:K04077] [EC:5.6.1.7]
129105029  pfkla; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
129105046  cnot9; CCR4-NOT transcription complex subunit 9 [KO:K12606]
129105245  eno1b; enolase 1b, (alpha) [KO:K01689] [EC:4.2.1.11]
129105989  lsm3; snRNA-associated Sm-like protein LSm3 [KO:K12622]
129106006  dhx36; ATP-dependent DNA/RNA helicase DHX36 isoform X1 [KO:K14442] [EC:3.6.4.13]
129106485  pfkmb; phosphofructokinase, muscle b isoform X1 [KO:K00850] [EC:2.7.1.11]
129106832  tent4b; terminal nucleotidyltransferase 4B [KO:K03514] [EC:2.7.7.19]
129106926  xrn2; LOW QUALITY PROTEIN: 5'-3' exoribonuclease 2 [KO:K12619] [EC:3.1.13.-]
129107813  cnot2; CCR4-NOT transcription complex subunit 2 isoform X1 [KO:K12605]
129108363  edc3; enhancer of mRNA-decapping protein 3 [KO:K12615]
129108461  cnot1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
129108482  exosc6; exosome complex component MTR3 [KO:K12587]
129108548  skic8; SKI8 subunit of superkiller complex protein [KO:K12602]
129108584  cnot4a; LOW QUALITY PROTEIN: CCR4-NOT transcription complex subunit 4 [KO:K10643] [EC:2.3.2.27]
129108658  mphosph6; M-phase phosphoprotein 6 [KO:K12593]
129108673  edc4; enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
129109054  cnot10; CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
129109466  [KO:K13126]
129109483  cnot3a; CCR4-NOT transcription complex subunit 3a isoform X1 [KO:K12580]
129109552  [KO:K01689] [EC:4.2.1.11]
129109593  [KO:K03514] [EC:2.7.7.19]
129109724  ddx61; probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:3.6.4.13]
129110155  si:dkey-79d12.5; maternal B9.15 protein [KO:K14443]
129110455  pfkpa; ATP-dependent 6-phosphofructokinase, platelet type isoform X1 [KO:K00850] [EC:2.7.1.11]
129110615  pan3; PAN2-PAN3 deadenylation complex subunit PAN3 isoform X1 [KO:K12572]
129110933  lsm5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
129112271  [KO:K12605]
129112504  dcp1b; mRNA-decapping enzyme 1B [KO:K12611] [EC:3.-.-.-]
129112531  btg1; protein BTG1 [KO:K14443]
129112614  lsm8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
129113526  exosc8; exosome complex component RRP43 [KO:K12586]
129113559  cnot8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
129113851  btg3; protein BTG3 [KO:K14443]
129113853  btg4; protein BTG4 [KO:K14443]
129116238  [KO:K00850] [EC:2.7.1.11]
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
afb03015  mRNA surveillance pathway
KO pathway
ko03018   

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