KEGG   PATHWAY: hsp03018
Entry
hsp03018                    Pathway                                
Name
RNA degradation - Hippoglossus stenolepis (Pacific halibut)
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
hsp03018  RNA degradation
hsp03018

Other DBs
GO: 0006401
Organism
Hippoglossus stenolepis (Pacific halibut) [GN:hsp]
Gene
118112809  dcps; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
118118685  exosc1; exosome complex component CSL4 [KO:K07573]
118126044  exosc2; exosome complex component RRP4 [KO:K03679]
118112114  exosc3; exosome complex component RRP40 [KO:K03681]
118121925  exosc8; exosome complex component RRP43 [KO:K12586]
118110088  exosc6; exosome complex component MTR3 [KO:K12587]
118124511  exosc7; exosome complex component RRP42 [KO:K12589]
118117871  exosc4; exosome complex component RRP41 [KO:K11600]
118106124  exosc5; exosome complex component RRP46 [KO:K12590]
118100404  exosc9; exosome complex component RRP45 isoform X1 [KO:K03678]
118118730  dis3; exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
118111351  exosc10; exosome component 10 [KO:K12591] [EC:3.1.13.-]
118118948  c1d; nuclear nucleic acid-binding protein C1D [KO:K12592]
118110217  mphosph6; M-phase phosphoprotein 6 [KO:K12593]
118107992  dis3l; DIS3-like exonuclease 1 [KO:K18681] [EC:3.1.13.-]
118106551  tent4b; terminal nucleotidyltransferase 4B [KO:K03514] [EC:2.7.7.19]
118114283  terminal nucleotidyltransferase 4A isoform X1 [KO:K03514] [EC:2.7.7.19]
118125099  tent4a; terminal nucleotidyltransferase 4A [KO:K03514] [EC:2.7.7.19]
118100578  zcchc7; zinc finger CCHC domain-containing protein 7 isoform X1 [KO:K12597]
118112258  zinc finger CCHC domain-containing protein 7 [KO:K12597]
118098167  mtrex; exosome RNA helicase MTR4 [KO:K12598] [EC:5.6.2.6]
118125024  skiv2l; helicase SKI2W [KO:K12599] [EC:5.6.2.6]
118115290  ttc37; tetratricopeptide repeat protein 37 isoform X1 [KO:K12600]
118109322  wdr61; WD repeat-containing protein 61 [KO:K12602]
118115477  cnot6l; CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
118112145  CCR4-NOT transcription complex subunit 6 [KO:K12603] [EC:3.1.13.4]
118109188  cnot1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
118109135  cnot2; CCR4-NOT transcription complex subunit 2 isoform X1 [KO:K12605]
118101599  CCR4-NOT transcription complex subunit 2 isoform X1 [KO:K12605]
118113597  cnot3a; CCR4-NOT transcription complex subunit 3a isoform X1 [KO:K12580]
118124579  cnot3b; CCR4-NOT transcription complex subunit 3b isoform X1 [KO:K12580]
118109847  cnot4a; CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
118122018  cnot8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
118111948  cnot7; CCR4-NOT transcription complex subunit 7 [KO:K12581]
118119841  cnot9; CCR4-NOT transcription complex subunit 9 [KO:K12606]
118113621  cnot10; CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
118105933  dhx36; ATP-dependent DNA/RNA helicase DHX36 [KO:K14442] [EC:5.6.2.6]
118125567  parn; poly(A)-specific ribonuclease PARN [KO:K01148] [EC:3.1.13.4]
118121737  btg3; protein BTG3 [KO:K14443]
118123705  protein Tob2 [KO:K14443]
118100519  tob1b; protein Tob1b [KO:K14443]
118123247  tob1a; protein Tob1a [KO:K14443]
118101780  btg1; protein BTG1 [KO:K14443]
118113504  si:dkey-79d12.5; maternal B9.15 protein [KO:K14443]
118122264  btg4; protein BTG4 [KO:K14443]
118116287  pabpc4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
118111374  embryonic polyadenylate-binding protein isoform X1 [KO:K13126]
118114401  polyadenylate-binding protein 1A [KO:K13126]
118124805  polyadenylate-binding protein 1 isoform X1 [KO:K13126]
118111381  pan2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
118098303  pan3; PAN2-PAN3 deadenylation complex subunit PAN3 isoform X1 [KO:K12572]
118111331  dcp1a; mRNA-decapping enzyme 1A [KO:K12610] [EC:3.-.-.-]
118101736  dcp1b; mRNA-decapping enzyme 1B isoform X1 [KO:K12611] [EC:3.-.-.-]
118126048  dcp2; m7GpppN-mRNA hydrolase isoform X1 [KO:K12613] [EC:3.6.1.62]
118113560  ddx61; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:5.6.2.7]
118105831  ddx6; probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:5.6.2.7]
118124521  probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:5.6.2.7]
118106585  enhancer of mRNA-decapping protein 3 [KO:K12615]
118109568  edc3; enhancer of mRNA-decapping protein 3 [KO:K12615]
118109741  edc4; enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
118118881  patl1; protein PAT1 homolog 1 isoform X1 [KO:K12617]
118117616  xrn1; 5'-3' exoribonuclease 1 [KO:K12618] [EC:3.1.13.-]
118099444  xrn2; 5'-3' exoribonuclease 2 isoform X1 [KO:K12619] [EC:3.1.13.-]
118111677  zgc:103759; U8 snoRNA-decapping enzyme isoform X1 [KO:K16855] [EC:3.6.1.62 3.6.1.64]
118114859  lsm1; U6 snRNA-associated Sm-like protein LSm1 isoform X1 [KO:K12620]
118120910  smx5; smx5 [KO:K12621]
118105278  lsm3; snRNA-associated Sm-like protein LSm3 [KO:K12622]
118121470  lsm4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
118098449  lsm5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
118116840  lsm6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
118121139  lsm7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
118102014  lsm8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
118110852  eno1a; enolase 1a, (alpha) isoform X1 [KO:K01689] [EC:4.2.1.11]
118102548  eno3; beta-enolase [KO:K01689] [EC:4.2.1.11]
118113208  gamma-enolase-like [KO:K01689] [EC:4.2.1.11]
118105386  eno1b; enolase 1b, (alpha) [KO:K01689] [EC:4.2.1.11]
118124644  gamma-enolase [KO:K01689] [EC:4.2.1.11]
118119395  polyribonucleotide nucleotidyltransferase 1, mitochondrial [KO:K00962] [EC:2.7.7.8]
118098576  pfkpa; ATP-dependent 6-phosphofructokinase, platelet type isoform X1 [KO:K00850] [EC:2.7.1.11]
118117329  ATP-dependent 6-phosphofructokinase, platelet type isoform X1 [KO:K00850] [EC:2.7.1.11]
118110861  ATP-dependent 6-phosphofructokinase, muscle type [KO:K00850] [EC:2.7.1.11]
118104968  pfkmb; phosphofructokinase, muscle b [KO:K00850] [EC:2.7.1.11]
118120339  pfkla; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
118112129  hspa9; stress-70 protein, mitochondrial [KO:K04043]
118119983  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
hsp03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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