KEGG   PATHWAY: ssen03018
Entry
ssen03018                   Pathway                                
Name
RNA degradation - Solea senegalensis (Senegalese sole)
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
ssen03018  RNA degradation
ssen03018

Other DBs
GO: 0006401
Organism
Solea senegalensis (Senegalese sole) [GN:ssen]
Gene
122758243  exosc2; exosome complex component RRP4 [KO:K03679]
122758410  mtrex; exosome RNA helicase MTR4 [KO:K12598] [EC:3.6.4.13]
122758692  dcp2; m7GpppN-mRNA hydrolase [KO:K12613] [EC:3.6.1.62]
122759037  hspa9; stress-70 protein, mitochondrial [KO:K04043]
122759045  cnot9; CCR4-NOT transcription complex subunit 9 [KO:K12606]
122759677  tob1b; protein Tob1b [KO:K14443]
122759882  [KO:K12614] [EC:3.6.4.13]
122760311  [KO:K12589]
122760727  edc3; enhancer of mRNA-decapping protein 3 [KO:K12615]
122761037  lsm8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
122761256  pabpc4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
122761366  [KO:K12584] [EC:3.6.1.59]
122762540  cnot10; CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
122762736  [KO:K14443]
122765084  pfkla; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
122765097  pfkpa; ATP-dependent 6-phosphofructokinase, platelet type isoform X1 [KO:K00850] [EC:2.7.1.11]
122765431  [KO:K14443]
122766057  eno3; beta-enolase [KO:K01689] [EC:4.2.1.11]
122766312  [KO:K12605]
122766613  btg1; protein BTG1 [KO:K14443]
122766761  xrn1; 5'-3' exoribonuclease 1 [KO:K12618] [EC:3.1.13.-]
122767005  dcp1b; mRNA-decapping enzyme 1B [KO:K12611] [EC:3.-.-.-]
122767705  lsm3; snRNA-associated Sm-like protein LSm3 [KO:K12622]
122768192  eno1b; enolase 1b, (alpha) [KO:K01689] [EC:4.2.1.11]
122768259  pfkmb; phosphofructokinase, muscle b [KO:K00850] [EC:2.7.1.11]
122769371  ttc37; tetratricopeptide repeat protein 37 [KO:K12600]
122769894  cnot6l; CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
122769987  lsm1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
122770443  lsm6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
122770465  [KO:K00850] [EC:2.7.1.11]
122770555  exosc9; exosome complex component RRP45 [KO:K03678]
122770957  [KO:K04043]
122771281  patl1; protein PAT1 homolog 1 [KO:K12617]
122771340  zcchc7; zinc finger CCHC domain-containing protein 7 [KO:K12597]
122771449  exosc1; exosome complex component CSL4 isoform X1 [KO:K07573]
122771581  parn; poly(A)-specific ribonuclease PARN [KO:K01148] [EC:3.1.13.4]
122772188  tent4b; terminal nucleotidyltransferase 4B [KO:K03514] [EC:2.7.7.19]
122772547  dis3l; DIS3-like exonuclease 1 [KO:K18681] [EC:3.1.13.-]
122772964  exosc5; exosome complex component RRP46 [KO:K12590]
122773408  ddx6; probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:3.6.4.13]
122773793  dhx36; ATP-dependent DNA/RNA helicase DHX36 [KO:K14442] [EC:3.6.4.13]
122774015  pan3; PAN2-PAN3 deadenylation complex subunit PAN3 isoform X1 [KO:K12572]
122774442  [KO:K03514] [EC:2.7.7.19]
122774531  cnot3a; CCR4-NOT transcription complex subunit 3a isoform X1 [KO:K12580]
122774567  si:dkey-79d12.5; protein BTG4 [KO:K14443]
122774764  [KO:K13126]
122775128  lsm5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
122775229  [KO:K01689] [EC:4.2.1.11]
122775402  mphosph6; M-phase phosphoprotein 6 [KO:K12593]
122775572  cnot1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
122775639  cnot2; CCR4-NOT transcription complex subunit 2 [KO:K12605]
122775692  exosc6; exosome complex component MTR3 [KO:K12587]
122775714  edc4; enhancer of mRNA-decapping protein 4 [KO:K12616]
122775824  exosc4; exosome complex component RRP41 [KO:K11600]
122776050  cnot4a; CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
122776147  wdr61; WD repeat-containing protein 61 [KO:K12602]
122776679  zgc:103759; U8 snoRNA-decapping enzyme isoform X1 [KO:K16855] [EC:3.6.1.62 3.6.1.64]
122777043  pan2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
122777079  [KO:K00850] [EC:2.7.1.11]
122777144  dcp1a; mRNA-decapping enzyme 1A [KO:K12610] [EC:3.-.-.-]
122777438  eno1a; enolase 1a, (alpha) isoform X1 [KO:K01689] [EC:4.2.1.11]
122777719  exosc10; exosome component 10 [KO:K12591] [EC:3.1.13.-]
122778134  cnot7; CCR4-NOT transcription complex subunit 7 [KO:K12581]
122778198  exosc3; exosome complex component RRP40 [KO:K03681]
122778300  [KO:K12597]
122778391  cnot6a; CCR4-NOT transcription complex subunit 6a [KO:K12603] [EC:3.1.13.4]
122778794  [KO:K12584] [EC:3.6.1.59]
122779582  btg4; protein BTG4 [KO:K14443]
122779619  [KO:K12586]
122779775  btg3; protein BTG3 [KO:K14443]
122779779  [KO:K12586]
122779994  cnot8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
122780412  lsm4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
122780444  smx5; smx5 [KO:K12621]
122780955  lsm7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
122781435  [KO:K00962] [EC:2.7.7.8]
122781869  dis3; exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
122782233  [KO:K12581]
122782325  c1d; nuclear nucleic acid-binding protein C1D [KO:K12592]
122783776  [KO:K14443]
122784340  xrn2; 5'-3' exoribonuclease 2 isoform X1 [KO:K12619] [EC:3.1.13.-]
122784499  [KO:K14443]
122785060  hspd1; 60 kDa heat shock protein, mitochondrial [KO:K04077] [EC:5.6.1.7]
122785642  [KO:K14443]
122785745  [KO:K14443]
122786012  tent4a; terminal nucleotidyltransferase 4A isoform X1 [KO:K03514] [EC:2.7.7.19]
122786215  [KO:K12614] [EC:3.6.4.13]
122786507  [KO:K12580]
122786541  [KO:K12589]
122786634  skiv2l; helicase SKI2W [KO:K12599] [EC:3.6.4.13]
122786657  [KO:K01689] [EC:4.2.1.11]
122786804  [KO:K13126]
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
ssen03015  mRNA surveillance pathway
KO pathway
ko03018   

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