KEGG   PATHWAY: msam03018
Entry
msam03018                   Pathway                                
Name
RNA degradation - Micropterus salmoides (largemouth bass)
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
msam03018  RNA degradation
msam03018

Other DBs
GO: 0006401
Organism
Micropterus salmoides (largemouth bass) [GN:msam]
Gene
119881932  [KO:K16855] [EC:3.6.1.62 3.6.1.64]
119882291  dhx36; ATP-dependent DNA/RNA helicase DHX36 [KO:K14442] [EC:3.6.4.13]
119882891  ddx6; probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:3.6.4.13]
119883298  exosc5; exosome complex component RRP46 [KO:K12590]
119884115  exosc9; exosome complex component RRP45 [KO:K03678]
119884340  [KO:K03514] [EC:2.7.7.19]
119884474  [KO:K12581]
119884482  [KO:K12581]
119884489  [KO:K12611] [EC:3.-.-.-]
119884619  lsm7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
119884831  [KO:K14443]
119885484  [KO:K01689] [EC:4.2.1.11]
119886143  pfkmb; phosphofructokinase, muscle b [KO:K00850] [EC:2.7.1.11]
119886437  lsm3; snRNA-associated Sm-like protein LSm3 [KO:K12622]
119888110  tob1a; protein Tob1a [KO:K14443]
119888416  [KO:K12597]
119888487  hspa9; stress-70 protein, mitochondrial [KO:K04043]
119888591  cnot6a; CCR4-NOT transcription complex subunit 6a [KO:K12603] [EC:3.1.13.4]
119888649  cnot7; CCR4-NOT transcription complex subunit 7 [KO:K12581]
119888739  [KO:K03681]
119889013  exosc3; exosome complex component RRP40 [KO:K03681]
119889163  dcps; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
119889980  [KO:K18681] [EC:3.1.13.-]
119890090  tent4b; terminal nucleotidyltransferase 4B [KO:K03514] [EC:2.7.7.19]
119890212  [KO:K12615]
119891472  lsm1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
119891782  ttc37; tetratricopeptide repeat protein 37 [KO:K12600]
119892020  cnot6l; CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
119893261  cnot2; CCR4-NOT transcription complex subunit 2 isoform X1 [KO:K12605]
119893450  wdr61; LOW QUALITY PROTEIN: WD repeat-containing protein 61 [KO:K12602]
119893524  exosc6; exosome complex component MTR3 [KO:K12587]
119893718  mphosph6; M-phase phosphoprotein 6 [KO:K12593]
119893719  cnot4a; CCR4-NOT transcription complex subunit 4 [KO:K10643] [EC:2.3.2.27]
119894347  edc3; enhancer of mRNA-decapping protein 3 [KO:K12615]
119894403  cnot1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
119894459  edc4; enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
119895072  lsm8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
119895253  [KO:K12605]
119895398  exosc8; exosome complex component RRP43 [KO:K12586]
119895923  btg3; protein BTG3 [KO:K14443]
119896021  btg4; protein BTG4 [KO:K14443]
119896100  cnot8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
119896901  cnot10; CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
119897332  [KO:K12614] [EC:3.6.4.13]
119897422  [KO:K01689] [EC:4.2.1.11]
119897523  cnot3a; CCR4-NOT transcription complex subunit 3a isoform X1 [KO:K12580]
119897893  [KO:K03514] [EC:2.7.7.19]
119898081  [KO:K13126]
119898331  si:dkey-79d12.5; maternal B9.15 protein [KO:K14443]
119898688  parn; poly(A)-specific ribonuclease PARN [KO:K01148] [EC:3.1.13.4]
119898857  lsm6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
119899087  zcchc7; zinc finger CCHC domain-containing protein 7 [KO:K12597]
119899519  exosc1; exosome complex component CSL4 isoform X1 [KO:K07573]
119899808  patl1; protein PAT1 homolog 1 isoform X1 [KO:K12617]
119900494  lsm4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
119900686  [KO:K12626]
119901161  smx5; smx5 [KO:K12621]
119901704  [KO:K00850] [EC:2.7.1.11]
119902029  exosc4; exosome complex component RRP41 [KO:K11600]
119902571  xrn1; LOW QUALITY PROTEIN: 5'-3' exoribonuclease 1 [KO:K12618] [EC:3.1.13.-]
119903815  cnot9; CCR4-NOT transcription complex subunit 9 [KO:K12606]
119904003  pfkla; ATP-dependent 6-phosphofructokinase, liver type isoform X1 [KO:K00850] [EC:2.7.1.11]
119904561  hspd1; 60 kDa heat shock protein, mitochondrial [KO:K04077] [EC:5.6.1.7]
119904776  [KO:K01689] [EC:4.2.1.11]
119905201  pan2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
119905398  [KO:K13126]
119905512  pfkma; phosphofructokinase, muscle a [KO:K00850] [EC:2.7.1.11]
119905609  eno1a; enolase 1a, (alpha) isoform X1 [KO:K01689] [EC:4.2.1.11]
119906021  exosc10; exosome component 10 [KO:K12591] [EC:3.1.13.-]
119906765  pfkpa; ATP-dependent 6-phosphofructokinase, platelet type isoform X1 [KO:K00850] [EC:2.7.1.11]
119907011  cnot3b; CCR4-NOT transcription complex subunit 3b isoform X1 [KO:K12580]
119907164  [KO:K13126]
119907369  skiv2l; helicase SKI2W [KO:K12599] [EC:3.6.4.13]
119907669  tent4a; terminal nucleotidyltransferase 4A [KO:K03514] [EC:2.7.7.19]
119907926  [KO:K12614] [EC:3.6.4.13]
119908029  exosc7; exosome complex component RRP42 [KO:K12589]
119908079  [KO:K01689] [EC:4.2.1.11]
119908897  xrn2; LOW QUALITY PROTEIN: 5'-3' exoribonuclease 2 [KO:K12619] [EC:3.1.13.-]
119909772  pan3; PAN2-PAN3 deadenylation complex subunit PAN3 [KO:K12572]
119910343  pabpc4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
119912637  [KO:K01689] [EC:4.2.1.11]
119912906  lsm5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
119914231  exosc2; exosome complex component RRP4 [KO:K03679]
119914518  mtrex; exosome RNA helicase MTR4 [KO:K12598] [EC:3.6.4.13]
119914566  dcp2; m7GpppN-mRNA hydrolase isoform X1 [KO:K12613] [EC:3.6.1.62]
119915719  [KO:K14443]
119916776  [KO:K16855] [EC:3.6.1.62 3.6.1.64]
119916973  dis3; exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
119917596  [KO:K00962] [EC:2.7.7.8]
119917650  c1d; nuclear nucleic acid-binding protein C1D [KO:K12592]
119917956  btg1; protein BTG1 [KO:K14443]
119918401  cnot4b; CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
119918505  [KO:K16855] [EC:3.6.1.62 3.6.1.64]
119919222  [KO:K13126]
119919339  [KO:K12610] [EC:3.-.-.-]
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
msam03015  mRNA surveillance pathway
KO pathway
ko03018   

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