KEGG   PATHWAY: cclu03018
Entry
cclu03018                   Pathway                                
Name
RNA degradation - Coregonus clupeaformis (lake whitefish)
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
cclu03018  RNA degradation
cclu03018

Other DBs
GO: 0006401
Organism
Coregonus clupeaformis (lake whitefish) [GN:cclu]
Gene
121530764  [KO:K12603] [EC:3.1.13.4]
121531624  [KO:K10643] [EC:2.3.2.27]
121531713  [KO:K12605]
121531849  exosc6; exosome complex component MTR3 [KO:K12587]
121531876  [KO:K12616]
121532026  wdr61; WD repeat-containing protein 61 isoform X1 [KO:K12602]
121532163  [KO:K03514] [EC:2.7.7.19]
121532166  mphosph6; M-phase phosphoprotein 6 [KO:K12593]
121532321  [KO:K12604]
121532748  [KO:K12623]
121533673  [KO:K12597]
121534323  [KO:K07573]
121534648  [KO:K11600]
121535135  [KO:K12618] [EC:3.1.13.-]
121535168  [KO:K00850] [EC:2.7.1.11]
121535408  [KO:K12626]
121535801  [KO:K03514] [EC:2.7.7.19]
121536008  lsm6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
121537050  [KO:K04077] [EC:5.6.1.7]
121537552  [KO:K14443]
121537630  smx5; smx5 [KO:K12621]
121537740  eno1a; enolase 1a, (alpha) isoform X1 [KO:K01689] [EC:4.2.1.11]
121537841  pfkma; phosphofructokinase, muscle a [KO:K00850] [EC:2.7.1.11]
121538038  [KO:K12571] [EC:3.1.13.4]
121538132  [KO:K12610] [EC:3.-.-.-]
121538376  exosc10; exosome component 10 [KO:K12591] [EC:3.1.13.-]
121539180  pabpc4; polyadenylate-binding protein 4 [KO:K13126]
121540592  [KO:K12605]
121540792  [KO:K12615]
121541168  [KO:K03679]
121541295  btg4; protein BTG4 isoform X1 [KO:K14443]
121541969  [KO:K12603] [EC:3.1.13.4]
121542051  exosc8; exosome complex component RRP43 [KO:K12586]
121542157  exosc9; exosome complex component RRP45 [KO:K03678]
121542631  [KO:K12607]
121542812  [KO:K14443]
121542899  cnot3a; LOW QUALITY PROTEIN: CCR4-NOT transcription complex subunit 3a [KO:K12580]
121542977  [KO:K01689] [EC:4.2.1.11]
121543297  [KO:K12607]
121543423  [KO:K14443]
121543625  [KO:K12611] [EC:3.-.-.-]
121544673  [KO:K12603] [EC:3.1.13.4]
121544868  [KO:K04043]
121545008  [KO:K13126]
121545352  [KO:K14443]
121545353  pabpc1l; polyadenylate-binding protein 1-like isoform X1 [KO:K13126]
121545478  [KO:K12610] [EC:3.-.-.-]
121545707  [KO:K12571] [EC:3.1.13.4]
121545903  [KO:K00850] [EC:2.7.1.11]
121546155  [KO:K01689] [EC:4.2.1.11]
121546370  dis3l; LOW QUALITY PROTEIN: DIS3-like exonuclease 1 [KO:K18681] [EC:3.1.13.-]
121546371  [KO:K03681]
121547444  [KO:K14443]
121548053  [KO:K12592]
121549054  [KO:K12619] [EC:3.1.13.-]
121549612  [KO:K12626]
121549630  [KO:K14443]
121549699  [KO:K12626]
121549740  [KO:K12624]
121549841  pan3; PAN2-PAN3 deadenylation complex subunit PAN3 isoform X2 [KO:K12572]
121549939  pfkpa; ATP-dependent 6-phosphofructokinase, platelet type isoform X1 [KO:K00850] [EC:2.7.1.11]
121550920  [KO:K14443]
121551404  [KO:K14443]
121551420  [KO:K12606]
121552863  xrn2; 5'-3' exoribonuclease 2 isoform X1 [KO:K12619] [EC:3.1.13.-]
121553256  zgc:103759; U8 snoRNA-decapping enzyme [KO:K16855] [EC:3.6.1.62 3.6.1.64]
121553457  [KO:K00962] [EC:2.7.7.8]
121553481  [KO:K12605]
121554036  [KO:K01148] [EC:3.1.13.4]
121554274  [KO:K01689] [EC:4.2.1.11]
121554864  [KO:K04077] [EC:5.6.1.7]
121554874  [KO:K00850] [EC:2.7.1.11]
121555491  [KO:K13126]
121555785  [KO:K13126]
121556755  [KO:K12585] [EC:3.1.13.-]
121557525  [KO:K12626]
121558765  [KO:K12626]
121560298  [KO:K07573]
121560406  cnot4b; CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
121560773  patl1; protein PAT1 homolog 1 [KO:K12617]
121561471  [KO:K01689] [EC:4.2.1.11]
121562132  [KO:K01148] [EC:3.1.13.4]
121562327  [KO:K03514] [EC:2.7.7.19]
121566843  dhx36; ATP-dependent DNA/RNA helicase DHX36 [KO:K14442] [EC:3.6.4.13]
121567845  exosc5; exosome complex component RRP46 [KO:K12590]
121567860  ddx6; probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:3.6.4.13]
121568049  [KO:K12615]
121568074  [KO:K12606]
121568419  [KO:K12627]
121568832  [KO:K14443]
121569029  [KO:K14443]
121569253  [KO:K12572]
121569400  [KO:K12624]
121571384  [KO:K12614] [EC:3.6.4.13]
121571464  skiv2l; helicase SKI2W [KO:K12599] [EC:3.6.4.13]
121571529  [KO:K12580]
121571552  [KO:K01689] [EC:4.2.1.11]
121571705  [KO:K00962] [EC:2.7.7.8]
121571884  [KO:K03514] [EC:2.7.7.19]
121573492  [KO:K12598] [EC:3.6.4.13]
121573527  [KO:K12581]
121573570  [KO:K14443]
121575075  eno1b; enolase 1b, (alpha) [KO:K01689] [EC:4.2.1.11]
121575267  [KO:K00850] [EC:2.7.1.11]
121575414  [KO:K14443]
121575715  [KO:K14443]
121575772  [KO:K12622]
121576641  [KO:K12616]
121576888  [KO:K03514] [EC:2.7.7.19]
121576941  [KO:K12604]
121577063  [KO:K10643] [EC:2.3.2.27]
121577626  [KO:K00850] [EC:2.7.1.11]
121578128  [KO:K14443]
121578187  [KO:K01689] [EC:4.2.1.11]
121578592  si:dkey-42i9.4; protein BTG1 isoform X1 [KO:K14443]
121578598  [KO:K12622]
121579251  [KO:K12597]
121579256  dcps; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
121579420  [KO:K12581]
121579665  [KO:K12603] [EC:3.1.13.4]
121579842  [KO:K12603] [EC:3.1.13.4]
121580119  [KO:K14443]
121580293  [KO:K14443]
121580845  [KO:K12618] [EC:3.1.13.-]
121580876  [KO:K00850] [EC:2.7.1.11]
121581275  [KO:K12626]
121581528  [KO:K11600]
121581844  [KO:K12592]
121581960  dcp2; m7GpppN-mRNA hydrolase isoform X1 [KO:K12613] [EC:3.6.1.62]
121582834  [KO:K12598] [EC:3.6.4.13]
121583156  [KO:K12620]
121583205  [KO:K12620]
121583325  [KO:K03679]
121583596  [KO:K12615]
121584224  [KO:K12620]
121584449  ttc37; tetratricopeptide repeat protein 37 isoform X1 [KO:K12600]
121584466  [KO:K12603] [EC:3.1.13.4]
121585498  [KO:K01689] [EC:4.2.1.11]
121585755  [KO:K12599] [EC:3.6.4.13]
121585962  [KO:K13126]
121586122  [KO:K14443]
121586155  ddx61; probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:3.6.4.13]
121586278  [KO:K12614] [EC:3.6.4.13]
121586344  [KO:K12589]
121586413  [KO:K12580]
121586430  [KO:K01689] [EC:4.2.1.11]
121586595  tent4a; terminal nucleotidyltransferase 4A isoform X2 [KO:K03514] [EC:2.7.7.19]
121587173  cnot7; CCR4-NOT transcription complex subunit 7 isoform X1 [KO:K12581]
123484321  [KO:K12585] [EC:3.1.13.-]
123485030  [KO:K12627]
123491972  lsm4; U6 snRNA-associated Sm-like protein LSm4 isoform X1 [KO:K12623]
123492712  [KO:K03681]
123492849  [KO:K04043]
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
cclu03015  mRNA surveillance pathway
KO pathway
ko03018   

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