KEGG   PATHWAY: cery03018
Entry
cery03018                   Pathway                                
Name
RNA degradation - Chanodichthys erythropterus (predatory carp)
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
cery03018  RNA degradation
cery03018

Other DBs
GO: 0006401
Organism
Chanodichthys erythropterus (predatory carp) [GN:cery]
Gene
137002107  eno2; gamma-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
137002226  exosc7; exosome complex component RRP42 isoform X1 [KO:K12589]
137002939  exosc4; exosome complex component RRP41 [KO:K11600]
137003040  xrn1; 5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
137003122  pfkpb; ATP-dependent 6-phosphofructokinase, platelet type isoform X1 [KO:K00850] [EC:2.7.1.11]
137006325  pabpc4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
137007798  lsm5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
137007989  tob1b; protein Tob1b [KO:K14443]
137008689  pfkma; phosphofructokinase, muscle a [KO:K00850] [EC:2.7.1.11]
137008989  exosc10; exosome component 10 isoform X1 [KO:K12591] [EC:3.1.13.-]
137009174  eno3; beta-enolase [KO:K01689] [EC:4.2.1.11]
137009201  pan2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
137009227  eno1a; enolase 1a, (alpha) isoform X1 [KO:K01689] [EC:4.2.1.11]
137009476  zgc:103759; U8 snoRNA-decapping enzyme isoform X1 [KO:K16855] [EC:3.6.1.62 3.6.1.64]
137011317  smx5; smx5 [KO:K12621]
137011662  eno1b; enolase 1b, (alpha) [KO:K01689] [EC:4.2.1.11]
137011697  pfkmb; phosphofructokinase, muscle b isoform X1 [KO:K00850] [EC:2.7.1.11]
137012151  cnot8; CCR4-NOT transcription complex subunit 8 isoform X1 [KO:K12581]
137012497  cnot6a; CCR4-NOT transcription complex subunit 6a [KO:K12603] [EC:3.1.13.4]
137014338  pan3; PAN2-PAN3 deadenylation complex subunit PAN3 isoform X1 [KO:K12572]
137014368  pfkpa; ATP-dependent 6-phosphofructokinase, platelet type isoform X1 [KO:K00850] [EC:2.7.1.11]
137014744  cnot4a; CCR4-NOT transcription complex subunit 4 [KO:K10643] [EC:2.3.2.27]
137014880  cnot2; CCR4-NOT transcription complex subunit 2 isoform X1 [KO:K12605]
137014889  cnot1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
137014940  mphosph6; M-phase phosphoprotein 6 [KO:K12593]
137014941  edc3; enhancer of mRNA-decapping protein 3 isoform X1 [KO:K12615]
137015253  skic8; superkiller complex protein 8 [KO:K12602]
137017138  [KO:K14443]
137017326  tob1a; protein Tob1a [KO:K14443]
137017585  exosc3; exosome complex component RRP40 [KO:K03681]
137019213  xrn2; 5'-3' exoribonuclease 2 [KO:K12619] [EC:3.1.13.-]
137020492  cnot7; CCR4-NOT transcription complex subunit 7 isoform X1 [KO:K12581]
137020751  c1d; nuclear nucleic acid-binding protein C1D [KO:K12592]
137020832  pnpt1; polyribonucleotide nucleotidyltransferase 1, mitochondrial isoform X1 [KO:K00962] [EC:2.7.7.8]
137021333  pfklb; phosphofructokinase, liver b isoform X1 [KO:K00850] [EC:2.7.1.11]
137021715  lsm4; U6 snRNA-associated Sm-like protein LSm4 isoform X1 [KO:K12623]
137022406  cnot6b; CCR4-NOT transcription complex, subunit 6b isoform X1 [KO:K12603] [EC:3.1.13.4]
137023091  ddx6; probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:5.6.2.7]
137023151  dhx36; ATP-dependent DNA/RNA helicase DHX36 [KO:K14442] [EC:5.6.2.6]
137023386  edc4; enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
137023452  exosc5; exosome complex component RRP46 [KO:K12590]
137023803  lsm8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
137023936  hspa9; stress-70 protein, mitochondrial [KO:K04043]
137024363  cnot4b; CCR4-NOT transcription complex subunit 4 [KO:K10643] [EC:2.3.2.27]
137024420  btg1; protein BTG1 [KO:K14443]
137024510  dcp1b; mRNA-decapping enzyme 1B [KO:K12611] [EC:3.-.-.-]
137024663  [KO:K03514] [EC:2.7.7.19]
137024769  cnot10; CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
137026595  lsm1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
137026712  dcp1a; mRNA-decapping enzyme 1A [KO:K12610] [EC:3.-.-.-]
137026735  pabpc1l; polyadenylate-binding protein 1-like [KO:K13126]
137027385  si:dkey-79d12.5; maternal B9.15 protein [KO:K14443]
137028305  btg2; protein BTG2 [KO:K14443]
137028668  exosc8; exosome complex component RRP43 [KO:K12586]
137028717  btg3; protein BTG3 [KO:K14443]
137028858  mtrex; exosome RNA helicase MTR4 [KO:K12598] [EC:5.6.2.6]
137028950  dcp2; m7GpppN-mRNA hydrolase [KO:K12613] [EC:3.6.1.62]
137029025  lsm3; snRNA-associated Sm-like protein LSm3 [KO:K12622]
137029058  cnot9; CCR4-NOT transcription complex subunit 9 [KO:K12606]
137029228  lsm7; U6 snRNA-associated Sm-like protein LSm7 isoform X1 [KO:K12626]
137029237  si:dkey-42i9.4; protein BTG1 [KO:K14443]
137029518  dcps; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
137029647  [KO:K13126]
137030425  dis3l; DIS3-like exonuclease 1 [KO:K18681] [EC:3.1.13.-]
137030493  exosc6; exosome complex component MTR3 [KO:K12587]
137031339  tent4b; terminal nucleotidyltransferase 4B isoform X1 [KO:K03514] [EC:2.7.7.19]
137031653  parn; poly(A)-specific ribonuclease PARN [KO:K01148] [EC:3.1.13.4]
137031745  dis3; exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
137031812  patl1; protein PAT1 homolog 1 isoform X1 [KO:K12617]
137031898  exosc1; exosome complex component CSL4 [KO:K07573]
137032044  lsm6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
137032222  exosc9; exosome complex component RRP45 [KO:K03678]
137032589  zcchc7; zinc finger CCHC domain-containing protein 7 [KO:K12597]
137033623  cnot6l; CCR4-NOT transcription complex subunit 6-like isoform X1 [KO:K12603] [EC:3.1.13.4]
137033833  cnot3a; CCR4-NOT transcription complex subunit 3a isoform X1 [KO:K12580]
137034009  exosc2; exosome complex component RRP4 [KO:K03679]
137034480  btg4; protein BTG4 [KO:K14443]
137034493  [KO:K14443]
137034556  skic3; tetratricopeptide repeat protein 37 [KO:K12600]
137035329  hspd1; 60 kDa heat shock protein, mitochondrial [KO:K04077] [EC:5.6.1.7]
137035407  ddx61; probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:5.6.2.7]
137036509  pfkla; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
137037241  pabpc1a; polyadenylate-binding protein 1A [KO:K13126]
137037334  cnot3b; CCR4-NOT transcription complex subunit 3b [KO:K12580]
137037368  skic2; helicase SKI2W isoform X1 [KO:K12599] [EC:5.6.2.6]
137037415  pabpc1b; polyadenylate-binding protein 1b [KO:K13126]
137037675  [KO:K12614] [EC:5.6.2.7]
137037937  tent4a; terminal nucleotidyltransferase 4A isoform X1 [KO:K03514] [EC:2.7.7.19]
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
cery03015  mRNA surveillance pathway
KO pathway
ko03018   

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