KEGG   PATHWAY: pprm03018
Entry
pprm03018                   Pathway                                
Name
RNA degradation - Pimephales promelas (fathead minnow)
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
pprm03018  RNA degradation
pprm03018

Other DBs
GO: 0006401
Organism
Pimephales promelas (fathead minnow) [GN:pprm]
Gene
120482632  dcps; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
120488324  exosc1; exosome complex component CSL4 [KO:K07573]
120472390  exosc2; exosome complex component RRP4 [KO:K03679]
120460606  exosc3; exosome complex component RRP40 [KO:K03681]
120482151  exosc8; exosome complex component RRP43 [KO:K12586]
120473151  exosc6; exosome complex component MTR3 [KO:K12587]
120483430  exosc7; exosome complex component RRP42 [KO:K12589]
120461692  exosc4; exosome complex component RRP41 [KO:K11600]
120487571  exosc5; exosome complex component RRP46 [KO:K12590]
120493345  exosc9; exosome complex component RRP45 [KO:K03678]
120468835  dis3; exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
120488334  exosc10; exosome component 10 [KO:K12591] [EC:3.1.13.-]
120480723  c1d; nuclear nucleic acid-binding protein C1D [KO:K12592]
120468189  mphosph6; M-phase phosphoprotein 6 [KO:K12593]
120491059  dis3l; DIS3-like exonuclease 1 [KO:K18681] [EC:3.1.13.-]
120468774  tent4b; terminal nucleotidyltransferase 4B isoform X1 [KO:K03514] [EC:2.7.7.19]
120485326  tent4a; terminal nucleotidyltransferase 4A [KO:K03514] [EC:2.7.7.19]
120495107  terminal nucleotidyltransferase 4A-like isoform X1 [KO:K03514] [EC:2.7.7.19]
120493964  zcchc7; zinc finger CCHC domain-containing protein 7 isoform X1 [KO:K12597]
120481680  mtrex; exosome RNA helicase MTR4 [KO:K12598] [EC:5.6.2.6]
120485295  skiv2l; helicase SKI2W [KO:K12599] [EC:5.6.2.6]
120472230  tetratricopeptide repeat protein 37-like [KO:K12600]
120477801  wdr61; WD repeat-containing protein 61 [KO:K12602]
120461072  cnot6b; CCR4-NOT transcription complex, subunit 6b [KO:K12603] [EC:3.1.13.4]
120470068  cnot6l; CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
120494541  cnot6a; CCR4-NOT transcription complex subunit 6a [KO:K12603] [EC:3.1.13.4]
120459054  cnot1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
120469175  cnot2; CCR4-NOT transcription complex subunit 2 isoform X1 [KO:K12605]
120484467  cnot3a; CCR4-NOT transcription complex subunit 3a isoform X1 [KO:K12580]
120463178  cnot3b; CCR4-NOT transcription complex subunit 3b isoform X1 [KO:K12580]
120476839  cnot4b; CCR4-NOT transcription complex subunit 4 [KO:K10643] [EC:2.3.2.27]
120469108  cnot4a; CCR4-NOT transcription complex subunit 4 [KO:K10643] [EC:2.3.2.27]
120474985  cnot7; CCR4-NOT transcription complex subunit 7 isoform X1 [KO:K12581]
120483028  cnot8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
120486816  cnot9; CCR4-NOT transcription complex subunit 9 [KO:K12606]
120495104  cnot10; CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
120486020  dhx36; ATP-dependent DNA/RNA helicase DHX36 isoform X1 [KO:K14442] [EC:5.6.2.6]
120466918  parn; poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
120464370  tob1b; protein Tob1b [KO:K14443]
120490192  protein Tob2 [KO:K14443]
120482611  btg3; protein BTG3 [KO:K14443]
120477057  btg1; protein BTG1 [KO:K14443]
120484562  si:dkey-79d12.5; maternal B9.15 protein isoform X1 [KO:K14443]
120492804  si:dkey-42i9.4; protein BTG1 [KO:K14443]
120469953  protein Tob1-like [KO:K14443]
120486454  btg2; protein BTG2 [KO:K14443]
120472273  btg4; protein BTG4 [KO:K14443]
120473383  protein BTG1-like [KO:K14443]
120491085  embryonic polyadenylate-binding protein-like [KO:K13126]
120459309  pabpc4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
120485196  pabpc1b; polyadenylate-binding protein 1b isoform X1 [KO:K13126]
120471095  polyadenylate-binding protein 1-like [KO:K13126]
120471102  pabpc1a; polyadenylate-binding protein 1A [KO:K13126]
120462832  pan2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
120476080  pan3; PAN2-PAN3 deadenylation complex subunit PAN3 [KO:K12572]
120481335  dcp1a; mRNA-decapping enzyme 1A isoform X1 [KO:K12610] [EC:3.-.-.-]
120476945  dcp1b; mRNA-decapping enzyme 1B [KO:K12611] [EC:3.-.-.-]
120482216  dcp2; m7GpppN-mRNA hydrolase [KO:K12613] [EC:3.6.1.62]
120483518  probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:5.6.2.7]
120459947  ddx6; probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:5.6.2.7]
120484538  ddx61; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:5.6.2.7]
120469222  edc3; enhancer of mRNA-decapping protein 3 [KO:K12615]
120487695  edc4; enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
120489012  patl1; protein PAT1 homolog 1 [KO:K12617]
120482478  xrn1; 5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
120480919  xrn2; 5'-3' exoribonuclease 2 isoform X1 [KO:K12619] [EC:3.1.13.-]
120462816  zgc:103759; U8 snoRNA-decapping enzyme [KO:K16855] [EC:3.6.1.62 3.6.1.64]
120474870  lsm1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
120493068  smx5; smx5 [KO:K12621]
120479947  lsm3; snRNA-associated Sm-like protein LSm3 [KO:K12622]
120476364  lsm4; U6 snRNA-associated Sm-like protein LSm4 isoform X1 [KO:K12623]
120492937  lsm5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
120484962  U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
120461337  lsm6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
120486246  lsm7; U6 snRNA-associated Sm-like protein LSm7 isoform X1 [KO:K12626]
120476682  lsm8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
120491495  eno1b; enolase 1b, (alpha) [KO:K01689] [EC:4.2.1.11]
120484087  eno3; beta-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
120485625  eno2; gamma-enolase [KO:K01689] [EC:4.2.1.11]
120463680  eno1a; enolase 1a, (alpha) isoform X1 [KO:K01689] [EC:4.2.1.11]
120484218  polyribonucleotide nucleotidyltransferase 1, mitochondrial-like [KO:K00962] [EC:2.7.7.8]
120484233  polyribonucleotide nucleotidyltransferase 1, mitochondrial isoform X1 [KO:K00962] [EC:2.7.7.8]
120475803  pfkpa; ATP-dependent 6-phosphofructokinase, platelet type isoform X1 [KO:K00850] [EC:2.7.1.11]
120483116  pfkpb; ATP-dependent 6-phosphofructokinase, platelet type [KO:K00850] [EC:2.7.1.11]
120491374  pfkmb; phosphofructokinase, muscle b isoform X1 [KO:K00850] [EC:2.7.1.11]
120491957  pfklb; phosphofructokinase, liver b [KO:K00850] [EC:2.7.1.11]
120486984  pfkla; LOW QUALITY PROTEIN: ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
120462774  pfkma; phosphofructokinase, muscle a [KO:K00850] [EC:2.7.1.11]
120494839  hspa9; stress-70 protein, mitochondrial [KO:K04043]
120467267  hspd1; 60 kDa heat shock protein, mitochondrial [KO:K04077] [EC:5.6.1.7]
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
pprm03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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