KEGG   PATHWAY: som03018
Entry
som03018                    Pathway                                
Name
RNA degradation - Schizosaccharomyces osmophilus (fission yeast)
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
som03018  RNA degradation
som03018

Other DBs
GO: 0006401
Organism
Schizosaccharomyces osmophilus (fission yeast) [GN:som]
Gene
SOMG_00049  eno102; enolase [KO:K01689] [EC:4.2.1.11]
SOMG_00213  mpp6; nuclear exosome-associated RNA binding protein Mpp6 [KO:K12593]
SOMG_00323  rrp41; exosome subunit Rrp41 [KO:K11600]
SOMG_00363  exo2; exonuclease II Exo2 [KO:K12618] [EC:3.1.13.-]
SOMG_00389  ssc1; mitochondrial (2Fe-2S) cluster assembly chaperone Ssc1 [KO:K04043]
SOMG_00502  dis3; exosome 3'-5' exoribonuclease subunit Dis3 [KO:K12585] [EC:3.1.13.-]
SOMG_00546  mtr3; exosome subunit Mtr3 [KO:K12587]
SOMG_00703  ppk26; PAN complex protein phosphotransferase subunit Ppk26 [KO:K12572]
SOMG_00721  nhm1; m7G(5')PppN diphosphatase Nhm1 [KO:K12584] [EC:3.6.1.59]
SOMG_00760  dhp1; 5'-3' exoribonuclease Dhp1 [KO:K12619] [EC:3.1.13.-]
SOMG_00962  rrp43; exosome subunit Rrp43 [KO:K12586]
SOMG_00974  lsm5; Lsm2-8 complex subunit Lsm5 [KO:K12624]
SOMG_01025  ste13; ATP-dependent RNA helicase Ste13/Dhh1 [KO:K12614] [EC:3.6.4.13]
SOMG_01069  lsm4; Lsm2-8 complex subunit Lsm4 [KO:K12623]
SOMG_01293  lsm1; mRNA decapping complex subunit [KO:K12620]
SOMG_01430  air1; TRAMP complex zinc knuckle subunit Air1 [KO:K12597]
SOMG_01500  pfk1; 6-phosphofructokinase pfk1 [KO:K00850] [EC:2.7.1.11]
SOMG_01567  rrp6; exosome 3'-5' exoribonuclease subunit Rrp6 [KO:K12591] [EC:3.1.13.-]
SOMG_01586  rrp4; exosome subunit Rrp4 [KO:K03679]
SOMG_01654  pan2; PAN complex (poly(A)-specific ribonuclease) ubiquitin C-terminal hydrolase subunit Pan2 [KO:K12571] [EC:3.1.13.4]
SOMG_01678  mot2; CCR4-Not complex ubiquitin-protein ligase E3 subunit 4 [KO:K10643] [EC:2.3.2.27]
SOMG_01836  rrp40; exosome subunit Rrp40 [KO:K03681]
SOMG_01907  mtr4; TRAMP complex ATP-dependent RNA helicase subunit Mtr4 [KO:K12598] [EC:3.6.4.13]
SOMG_01929  not1; CCR4-Not complex scaffold subunit 1 [KO:K12604]
SOMG_01984  pabP; major poly(A) binding protein Pabp/Pab1 [KO:K13126]
SOMG_02126  edc3; enhancer of mRNA decapping Edc3 [KO:K12615]
SOMG_02214  eno101; enolase [KO:K01689] [EC:4.2.1.11]
SOMG_02302  rrp46; exosome subunit Rrp46 [KO:K12590]
SOMG_02432  rcd1; CCR4-Not complex RNA-binding protein subunit 9 [KO:K12606]
SOMG_02528  rrp45; exosome subunit Rrp45 [KO:K03678]
SOMG_02646  mtl1; MTREC (exosome adaptor) complex RNA helicase subunit Mtl1 [KO:K12598] [EC:3.6.4.13]
SOMG_02853  dcp2; mRNA decapping complex catalytic subunit Dcp2 [KO:K12613] [EC:3.6.1.62]
SOMG_03150  lsm3; Lsm2-8 complex subunit Lsm3 [KO:K12622]
SOMG_03199  pdc2; topoisomerase II-associated deadenylation-dependent mRNA-decapping factor Pdc2 [KO:K12617]
SOMG_03426  cid14; TRAMP complex poly(A) polymerase subunit Cid14 [KO:K03514] [EC:2.7.7.19]
SOMG_03512  not3; CCR4-Not complex NOT box subunit 3/5 [KO:K12580]
SOMG_03588  mcp60; mitochondrial heat shock protein Hsp60/Mcp60 [KO:K04077] [EC:5.6.1.7]
SOMG_03823  caf16; CCR4-Not complex ATPase subunit Caf16 [KO:K12608]
SOMG_03912  rrp42; exosome subunit Rrp42 [KO:K12589]
SOMG_04237  not2; CCR4-Not complex NOT box subunit 2 [KO:K12605]
SOMG_04319  ccr4; CCR4-Not complex 3'-5'-exoribonuclease subunit 6 [KO:K12603] [EC:3.1.13.4]
SOMG_04537  ski2; Ski complex RNA helicase Ski2 [KO:K12599] [EC:3.6.4.13]
SOMG_04620  lsm6; Lsm2-8 complex subunit Lsm6 [KO:K12625]
SOMG_04764  lsm7; Lsm2-8 complex Lsm7 [KO:K12626]
SOMG_04865  lsm2; Lsm2-8 complex subunit Lsm2 [KO:K12621]
SOMG_04895  caf1; CCR4-Not complex CAF1 family ribonuclease subunit 7/8 [KO:K12581]
SOMG_04929  cti1; exosome C1D family subunit Cti1 [KO:K12592]
SOMG_04941  ski3; Ski complex TPR repeat subunit Ski3 [KO:K12600]
SOMG_04945  lsm8; Lsm2-8 complex Lsm8 [KO:K12627]
SOMG_04946  csl4; exosome subunit Csl4 [KO:K07573]
SOMG_04994  rec14; Ski complex subunit Rec14 [KO:K12601]
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
som03015  mRNA surveillance pathway
KO pathway
ko03018   

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