KEGG   PATHWAY: dre03018
Entry
dre03018                    Pathway                                
Name
RNA degradation - Danio rerio (zebrafish)
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
dre03018  RNA degradation
dre03018

Other DBs
GO: 0006401
Organism
Danio rerio (zebrafish) [GN:dre]
Gene
100003553  dis3; exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
100007313  ddx61; probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:5.6.2.7]
100007655  tob2; protein Tob2 isoform X1 [KO:K14443]
100009659  patl1; protein PAT1 homolog 1 [KO:K12617]
100037372  cnot2; CCR4-NOT transcription complex subunit 2 [KO:K12605]
100126012  pan3; PAN2-PAN3 deadenylation complex subunit PAN3 [KO:K12572]
100332172  skic3; superkiller complex protein 3 [KO:K12600]
100535720  lsm3; U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
100538016  si:dkey-79d12.5; protein BTG3 isoform X1 [KO:K14443]
100750260  pnpt1; polyribonucleotide nucleotidyltransferase 1, mitochondrial [KO:K00962] [EC:2.7.7.8]
114432  btg1; protein BTG1 [KO:K14443]
282676  hspd1; 60 kDa heat shock protein, mitochondrial [KO:K04077] [EC:5.6.1.7]
30079  btg2; protein BTG2 [KO:K14443]
317641  zcchc7; zinc finger CCHC domain-containing protein 7 [KO:K12597]
321035  pabpc4; polyadenylate-binding protein 4 [KO:K13126]
321940  xrn2; 5'-3' exoribonuclease 2 [KO:K12619] [EC:3.1.13.-]
323016  exosc8; exosome complex component RRP43 [KO:K12586]
324048  cnot6a; CCR4-NOT transcription complex subunit 6a isoform X2 [KO:K12603] [EC:3.1.13.4]
326786  exosc6; exosome complex component MTR3 [KO:K12587]
327625  pabpc1l; polyadenylate-binding protein 1-like isoform X1 [KO:K13126]
327627  cnot3b; CCR4-NOT transcription complex subunit 3b [KO:K12580]
334116  eno1a; enolase 1a, (alpha) [KO:K01689] [EC:4.2.1.11]
360153  dcp1a; mRNA-decapping enzyme 1A [KO:K12610] [EC:3.-.-.-]
373085  hspa9; stress-70 protein, mitochondrial [KO:K04043]
378946  btg4; protein BTG4 [KO:K14443]
378963  eno3; beta-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
386629  tob1a; protein Tob1a [KO:K14443]
393121  dcp2; m7GpppN-mRNA hydrolase [KO:K12613] [EC:3.6.1.62]
393668  eno1b; enolase 1b, (alpha) [KO:K01689] [EC:4.2.1.11]
393669  lsm4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
393712  exosc4; exosome complex component RRP41 [KO:K11600]
393827  skic8; superkiller complex protein 8 [KO:K12602]
393856  pabpc1b; polyadenylate-binding protein 1B [KO:K13126]
394008  xrn1; 5'-3' exoribonuclease 1 [KO:K12618] [EC:3.1.13.-]
394064  exosc10; exosome complex component 10 [KO:K12591] [EC:3.1.13.-]
394144  cnot4b; uncharacterized protein LOC394144 [KO:K10643] [EC:2.3.2.27]
402850  dcpS; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
402874  eno2; gamma-enolase [KO:K01689] [EC:4.2.1.11]
406245  tob1b; protein Tob1b [KO:K14443]
406632  cnot9; CCR4-NOT transcription complex subunit 9 [KO:K12606]
406788  cnot8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
406795  mtrex; exosome RNA helicase MTR4 [KO:K12598] [EC:5.6.2.6]
415167  lsm6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
445157  lsm1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
445224  [KO:K12593]
447836  pfkma; phosphofructokinase, muscle A [KO:K00850] [EC:2.7.1.11]
448949  cnot1; CCR4-NOT transcription complex subunit 1 [KO:K12604]
449540  cnot3a; CCR4-NOT transcription complex subunit 3a [KO:K12580]
449918  cnot10; CCR4-NOT transcription complex subunit 10 [KO:K12607]
449987  zgc:103759; U8 snoRNA-decapping enzyme [KO:K16855] [EC:3.6.1.62 3.6.1.64]
450057  exosc9; exosome complex component RRP45 [KO:K03678]
474329  c1d; nuclear nucleic acid-binding protein C1D isoform X1 [KO:K12592]
492479  btg3; protein BTG3 isoform 2 [KO:K14443]
492503  si:dkey-42i9.4; uncharacterized protein LOC492503 [KO:K14443]
504054  edc3; enhancer of mRNA-decapping protein 3 [KO:K12615]
550234  exosc2; exosome complex component RRP4 [KO:K03679]
550247  exosc7; exosome complex component RRP42 [KO:K12589]
550259  pfklb; phosphofructokinase, liver B [KO:K00850] [EC:2.7.1.11]
553665  cnot6l; CCR4-NOT transcription complex subunit 6-like isoform X1 [KO:K12603] [EC:3.1.13.4]
557829  tent4a; terminal nucleotidyltransferase 4A isoform X4 [KO:K03514] [EC:2.7.7.19]
558857  exosc1; exosome complex component CSL4 [KO:K07573]
559653  skic2; superkiller complex protein 2 [KO:K12599] [EC:5.6.2.6]
560362  dis3l; DIS3-like exonuclease 1 [KO:K18681] [EC:3.1.13.-]
560386  cnot6b; CCR4-NOT transcription complex, subunit 6b [KO:K12603] [EC:3.1.13.4]
560944  pfkpa; ATP-dependent 6-phosphofructokinase, platelet type isoform X4 [KO:K00850] [EC:2.7.1.11]
561416  pfkpb; ATP-dependent 6-phosphofructokinase, platelet type isoform X1 [KO:K00850] [EC:2.7.1.11]
563948  lsm5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
564633  ddx6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:5.6.2.7]
565000  exosc3; exosome complex component RRP40 [KO:K03681]
565659  edc4; enhancer of mRNA-decapping protein 4 [KO:K12616]
566017  lsm8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
568001  pfkmb; phosphofructokinase, muscle b isoform 2 [KO:K00850] [EC:2.7.1.11]
568176  dcp1b; mRNA-decapping enzyme 1B isoform X1 [KO:K12611] [EC:3.-.-.-]
568678  tent4b; terminal nucleotidyltransferase 4B [KO:K03514] [EC:2.7.7.19]
569055  cnot4a; CCR4-NOT transcription complex subunit 4 [KO:K10643] [EC:2.3.2.27]
569072  dhx36; ATP-dependent DNA/RNA helicase DHX36 [KO:K14442] [EC:5.6.2.6]
570106  pfkla; ATP-dependent 6-phosphofructokinase, liver type isoform X2 [KO:K00850] [EC:2.7.1.11]
573047  lsm7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
57924  smx5; smx5 [KO:K12621]
606498  pabpc1a; polyadenylate-binding protein 1A isoform X1 [KO:K13126]
751632  exosc5; exosome complex component RRP46 [KO:K12590]
768119  cnot7; CCR4-NOT transcription complex subunit 7 [KO:K12581]
791461  parN; poly(A)-specific ribonuclease PARN isoform 1 [KO:K01148] [EC:3.1.13.4]
792831  pan2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X2 [KO:K12571] [EC:3.1.13.4]
Reference
PMID:19239894
  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
PMID:16968219
  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
PMID:16939780
  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
PMID:17471261
  Authors
Hartung S, Hopfner KP
  Title
The exosome, plugged.
  Journal
EMBO Rep 8:456-7 (2007)
DOI:10.1038/sj.embor.7400961
Reference
PMID:17447862
  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
PMID:16766188
  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
PMID:17560162
  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
dre03015  mRNA surveillance pathway
KO pathway
ko03018   

DBGET integrated database retrieval system