KEGG   PATHWAY: aqu03018
Entry
aqu03018                    Pathway                                
Name
RNA degradation - Amphimedon queenslandica (sponge)
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
aqu03018  RNA degradation
aqu03018

Other DBs
GO: 0006401
Organism
Amphimedon queenslandica (sponge) [GN:aqu]
Gene
100632526  m7GpppX diphosphatase-like [KO:K12584] [EC:3.6.1.59]
105316238  exosome complex component CSL4-like [KO:K07573]
100641417  exosome complex component RRP4-like [KO:K03679]
100638557  exosome complex component RRP40-like [KO:K03681]
109586972  exosome complex component RRP43-like [KO:K12586]
105311947  exosome complex component MTR3-like [KO:K12587]
100642061  exosome complex component RRP42-like [KO:K12589]
100641638  exosome complex component RRP41-like [KO:K11600]
100640546  exosome complex component RRP46-like [KO:K12590]
100639813  exosome complex component RRP45-like isoform X1 [KO:K03678]
100637401  exosome complex exonuclease RRP44-like [KO:K12585] [EC:3.1.13.-]
100633351  exosome component 10-like [KO:K12591] [EC:3.1.13.-]
100635318  nuclear nucleic acid-binding protein C1D-like isoform X2 [KO:K12592]
100641791  uncharacterized protein LOC100641791 [KO:K12593]
100632772  DIS3-like exonuclease 1 [KO:K18681] [EC:3.1.13.-]
100640371  DIS3-like exonuclease 1 [KO:K18681] [EC:3.1.13.-]
100634010  non-canonical poly(A) RNA polymerase PAPD5-like [KO:K03514] [EC:2.7.7.19]
100635506  zinc finger CCHC domain-containing protein 7-like [KO:K12597]
100632290  superkiller viralicidic activity 2-like 2 [KO:K12598] [EC:5.6.2.6]
100641382  helicase SKI2W [KO:K12599] [EC:5.6.2.6]
105312824  tetratricopeptide repeat protein 37-like isoform X1 [KO:K12600]
100639496  WD repeat-containing protein 61-like [KO:K12602]
100631616  CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
100636010  CCR4-NOT transcription complex subunit 1-like [KO:K12604]
100638394  CCR4-NOT transcription complex subunit 2-like [KO:K12605]
100637646  CCR4-NOT transcription complex subunit 2-like [KO:K12605]
100632597  CCR4-NOT transcription complex subunit 2-like [KO:K12605]
109583388  CCR4-NOT transcription complex subunit 2-like [KO:K12605]
100638414  CCR4-NOT transcription complex subunit 3-like [KO:K12580]
100632654  uncharacterized protein LOC100632654 isoform X1 [KO:K10643] [EC:2.3.2.27]
100640317  CCR4-NOT transcription complex subunit 7-like [KO:K12581]
100633543  cell differentiation protein RCD1 homolog [KO:K12606]
100631848  CCR4-NOT transcription complex subunit 10-like [KO:K12607]
100633205  ATP-dependent RNA helicase DHX36 [KO:K14442] [EC:5.6.2.6]
109580255  poly(A)-specific ribonuclease PARN-like domain-containing protein 1 [KO:K01148] [EC:3.1.13.4]
100638393  protein BTG2-like [KO:K14443]
100638044  polyadenylate-binding protein 4-like [KO:K13126]
100631763  polyadenylate-binding protein 1-like [KO:K13126]
100632976  m7GpppN-mRNA hydrolase-like [KO:K12613] [EC:3.6.1.62]
100640873  probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:5.6.2.7]
105312786  enhancer of mRNA-decapping protein 4-like [KO:K12616]
100641709  protein PAT1 homolog 1-like [KO:K12617]
100632707  5'-3' exoribonuclease 1-like [KO:K12618] [EC:3.1.13.-]
100640875  5'-3' exoribonuclease 2-like [KO:K12619] [EC:3.1.13.-]
100632565  U8 snoRNA-decapping enzyme-like [KO:K16855] [EC:3.6.1.62 3.6.1.64]
100642141  U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
100638662  U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
100636659  U6 snRNA-associated Sm-like protein LSm2 [KO:K12621]
100635851  U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
100639706  U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
100633302  U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
100636859  U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
100640003  U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
100634218  U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
100640983  U6 snRNA-associated Sm-like protein LSm8 [KO:K12627]
100633963  enolase-like [KO:K01689] [EC:4.2.1.11]
100639188  polyribonucleotide nucleotidyltransferase 1, mitochondrial-like [KO:K00962] [EC:2.7.7.8]
100636927  ATP-dependent DNA helicase Q-like SIM [KO:K03654] [EC:5.6.2.4]
100641194  ATP-dependent DNA helicase Q-like 3 [KO:K03654] [EC:5.6.2.4]
105316681  uncharacterized protein LOC105316681 [KO:K03654] [EC:5.6.2.4]
105313494  uncharacterized protein LOC105313494 [KO:K03654] [EC:5.6.2.4]
100639172  ATP-dependent DNA helicase Q-like SIM [KO:K03654] [EC:5.6.2.4]
100634020  ATP-dependent 6-phosphofructokinase, muscle type-like [KO:K00850] [EC:2.7.1.11]
100641128  stress-70 protein, mitochondrial-like isoform X1 [KO:K04043]
100634895  60 kDa heat shock protein, mitochondrial-like [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
aqu03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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