KEGG   PATHWAY: caua03018
Entry
caua03018                   Pathway                                
Name
RNA degradation - Carassius auratus (goldfish)
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
caua03018  RNA degradation
caua03018

Other DBs
GO: 0006401
Organism
Carassius auratus (goldfish) [GN:caua]
Gene
113038365  cnot8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
113038408  [KO:K12603] [EC:3.1.13.4]
113039468  [KO:K12606]
113039562  [KO:K12606]
113040232  [KO:K12626]
113040245  [KO:K14443]
113041075  exosc10; exosome component 10 isoform X1 [KO:K12591] [EC:3.1.13.-]
113041399  [KO:K12571] [EC:3.1.13.4]
113041673  [KO:K01689] [EC:4.2.1.11]
113041913  [KO:K12572]
113041934  [KO:K12572]
113042198  [KO:K00850] [EC:2.7.1.11]
113043160  [KO:K12602]
113043192  [KO:K12602]
113043251  [KO:K12604]
113043316  [KO:K10643] [EC:2.3.2.27]
113043346  [KO:K12615]
113043455  [KO:K12605]
113044072  [KO:K12617]
113044196  exosc9; exosome complex component RRP45 [KO:K03678]
113044241  [KO:K12597]
113044396  dis3; exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
113045291  [KO:K00850] [EC:2.7.1.11]
113045326  [KO:K00850] [EC:2.7.1.11]
113045786  [KO:K12618] [EC:3.1.13.-]
113046136  exosc4; exosome complex component RRP41 [KO:K11600]
113046642  [KO:K14443]
113047800  [KO:K10643] [EC:2.3.2.27]
113048095  [KO:K12611] [EC:3.-.-.-]
113048169  [KO:K14443]
113048273  [KO:K14443]
113048302  [KO:K12627]
113048670  [KO:K14443]
113049113  [KO:K12603] [EC:3.1.13.4]
113049498  exosc6; exosome complex component MTR3 [KO:K12587]
113049598  [KO:K12603] [EC:3.1.13.4]
113050065  [KO:K14443]
113050368  [KO:K00850] [EC:2.7.1.11]
113050615  [KO:K12621]
113051419  [KO:K03514] [EC:2.7.7.19]
113052202  [KO:K14443]
113052924  [KO:K00850] [EC:2.7.1.11]
113053149  [KO:K04077] [EC:5.6.1.7]
113053983  [KO:K12613] [EC:3.6.1.62]
113054355  [KO:K14443]
113054454  [KO:K12586]
113055159  [KO:K12623]
113055228  [KO:K14443]
113055573  [KO:K00850] [EC:2.7.1.11]
113056823  [KO:K07573]
113057276  [KO:K12592]
113057341  pnpt1; polyribonucleotide nucleotidyltransferase 1, mitochondrial isoform X1 [KO:K00962] [EC:2.7.7.8]
113057587  [KO:K12603] [EC:3.1.13.4]
113057927  [KO:K12581]
113059081  [KO:K12614] [EC:3.6.4.13]
113059156  [KO:K12627]
113059413  [KO:K13126]
113060105  [KO:K12607]
113060891  [KO:K14443]
113061380  [KO:K12617]
113061583  [KO:K12616]
113061680  [KO:K12590]
113061772  ddx6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:3.6.4.13]
113062345  [KO:K12614] [EC:3.6.4.13]
113062351  [KO:K12611] [EC:3.-.-.-]
113062435  [KO:K01689] [EC:4.2.1.11]
113062636  [KO:K01689] [EC:4.2.1.11]
113062934  [KO:K10643] [EC:2.3.2.27]
113063999  [KO:K12603] [EC:3.1.13.4]
113064718  [KO:K14443]
113064741  [KO:K12626]
113064786  [KO:K12606]
113065102  [KO:K12622]
113065443  [KO:K14443]
113065607  [KO:K12571] [EC:3.1.13.4]
113065773  [KO:K01689] [EC:4.2.1.11]
113066058  [KO:K00850] [EC:2.7.1.11]
113066259  [KO:K12572]
113066314  [KO:K00850] [EC:2.7.1.11]
113066648  [KO:K12602]
113066669  [KO:K12602]
113066724  [KO:K12604]
113066897  [KO:K10643] [EC:2.3.2.27]
113066912  [KO:K12615]
113066962  [KO:K12605]
113067213  [KO:K12593]
113067785  [KO:K14443]
113068275  [KO:K13126]
113068400  [KO:K01689] [EC:4.2.1.11]
113068891  [KO:K01689] [EC:4.2.1.11]
113069121  [KO:K16855] [EC:3.6.1.62 3.6.1.64]
113069149  [KO:K14443]
113070386  [KO:K13126]
113070540  [KO:K00850] [EC:2.7.1.11]
113070585  [KO:K12622]
113070683  [KO:K13126]
113070698  [KO:K12620]
113071070  [KO:K16855] [EC:3.6.1.62 3.6.1.64]
113072464  [KO:K12624]
113075094  [KO:K07573]
113076765  [KO:K12597]
113076902  [KO:K14443]
113077412  [KO:K14443]
113078795  [KO:K10643] [EC:2.3.2.27]
113079349  [KO:K12600]
113079551  [KO:K12626]
113079553  [KO:K14443]
113081895  [KO:K14443]
113084586  exosc2; exosome complex component RRP4 [KO:K03679]
113084879  [KO:K00850] [EC:2.7.1.11]
113087350  [KO:K10643] [EC:2.3.2.27]
113090608  [KO:K01148] [EC:3.1.13.4]
113090773  [KO:K12599] [EC:3.6.4.13]
113090799  [KO:K03514] [EC:2.7.7.19]
113093348  [KO:K12619] [EC:3.1.13.-]
113094431  [KO:K00850] [EC:2.7.1.11]
113094762  [KO:K16855] [EC:3.6.1.62 3.6.1.64]
113094895  [KO:K01689] [EC:4.2.1.11]
113095008  lsm6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
113095816  [KO:K14443]
113096630  [KO:K14443]
113097153  [KO:K14443]
113097196  [KO:K03678]
113097575  [KO:K12617]
113097626  [KO:K07573]
113097684  [KO:K14443]
113098997  [KO:K14443]
113099037  [KO:K12621]
113099617  [KO:K12580]
113100633  [KO:K01148] [EC:3.1.13.4]
113106010  dis3l; DIS3-like exonuclease 1 [KO:K18681] [EC:3.1.13.-]
113106062  [KO:K03514] [EC:2.7.7.19]
113106511  [KO:K03678]
113107325  [KO:K13126]
113107343  [KO:K12620]
113107805  dcp1a; mRNA-decapping enzyme 1A isoform X1 [KO:K12610] [EC:3.-.-.-]
113107873  [KO:K12610] [EC:3.-.-.-]
113108448  [KO:K04077] [EC:5.6.1.7]
113108638  [KO:K04077] [EC:5.6.1.7]
113109539  [KO:K12613] [EC:3.6.1.62]
113110030  dcps; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
113110043  [KO:K12586]
113110382  mtrex; exosome RNA helicase MTR4 [KO:K12598] [EC:3.6.4.13]
113110698  [KO:K12623]
113110763  [KO:K12623]
113111267  [KO:K00850] [EC:2.7.1.11]
113111269  [KO:K00850] [EC:2.7.1.11]
113112034  [KO:K14443]
113112122  [KO:K12624]
113113015  [KO:K12592]
113113418  [KO:K04043]
113113553  [KO:K04043]
113113690  [KO:K00850] [EC:2.7.1.11]
113113864  [KO:K03681]
113113998  [KO:K12581]
113114024  [KO:K12603] [EC:3.1.13.4]
113114229  [KO:K12625]
113115476  [KO:K12618] [EC:3.1.13.-]
113115783  [KO:K13126]
113115791  [KO:K13126]
113116045  [KO:K12580]
113116187  [KO:K12607]
113116669  [KO:K12614] [EC:3.6.4.13]
113116715  [KO:K14443]
113117450  [KO:K13126]
113118425  [KO:K12616]
113118537  dhx36; ATP-dependent RNA helicase DHX36 [KO:K14442] [EC:3.6.4.13]
113118691  [KO:K12614] [EC:3.6.4.13]
113118791  [KO:K12590]
113119188  [KO:K13126]
113119516  [KO:K12599] [EC:3.6.4.13]
113119537  [KO:K03514] [EC:2.7.7.19]
113119641  [KO:K01689] [EC:4.2.1.11]
113119875  [KO:K01689] [EC:4.2.1.11]
113120142  [KO:K12614] [EC:3.6.4.13]
113120163  [KO:K12580]
113120295  exosc7; exosome complex component RRP42 [KO:K12589]
113120621  [KO:K12619] [EC:3.1.13.-]
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
caua03015  mRNA surveillance pathway
KO pathway
ko03018   

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