KEGG   PATHWAY: oma03018
Entry
oma03018                    Pathway                                
Name
RNA degradation - Oenanthe melanoleuca (Eastern black-eared wheatear)
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
oma03018  RNA degradation
oma03018

Other DBs
GO: 0006401
Organism
Oenanthe melanoleuca (Eastern black-eared wheatear) [GN:oma]
Gene
130248307  LSM8; LSM8 homolog, U6 small nuclear RNA associated isoform X1 [KO:K12627]
130248517  ENO2; gamma-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
130248651  BTG1; protein BTG1 [KO:K14443]
130248763  PABPC1; polyadenylate-binding protein 1 [KO:K13126]
130248971  DIS3; exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
130249095  CNOT10; CCR4-NOT transcription complex subunit 10 [KO:K12607]
130249145  EXOSC7; exosome complex component RRP42 [KO:K12589]
130249957  TENT4A; terminal nucleotidyltransferase 4A isoform X1 [KO:K03514] [EC:2.7.7.19]
130250300  EXOSC4; exosome complex component RRP41 [KO:K11600]
130250301  [KO:K11600]
130250398  PFKP; ATP-dependent 6-phosphofructokinase, platelet type isoform X1 [KO:K00850] [EC:2.7.1.11]
130250569  PNPT1; polyribonucleotide nucleotidyltransferase 1, mitochondrial [KO:K00962] [EC:2.7.7.8]
130250740  XRN2; 5'-3' exoribonuclease 2 isoform X1 [KO:K12619] [EC:3.1.13.-]
130251218  C1D; nuclear nucleic acid-binding protein C1D [KO:K12592]
130251413  PAN3; PAN2-PAN3 deadenylation complex subunit PAN3 isoform X1 [KO:K12572]
130251454  PNLDC1; poly(A)-specific ribonuclease PNLDC1 isoform X1 [KO:K01148] [EC:3.1.13.4]
130251980  LSM6; U6 snRNA-associated Sm-like protein LSm6 isoform X1 [KO:K12625]
130252444  EXOSC9; exosome complex component RRP45 [KO:K03678]
130252493  CNOT6L; LOW QUALITY PROTEIN: CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
130252864  CNOT7; CCR4-NOT transcription complex subunit 7 [KO:K12581]
130254011  PATL1; protein PAT1 homolog 1 isoform X1 [KO:K12617]
130255054  EXOSC1; exosome complex component CSL4 [KO:K07573]
130255096  EXOSC3; exosome complex component RRP40 [KO:K03681]
130255370  HSPD1; 60 kDa heat shock protein, mitochondrial [KO:K04077] [EC:5.6.1.7]
130255381  CNOT9; CCR4-NOT transcription complex subunit 9 [KO:K12606]
130256647  XRN1; 5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
130256759  DHX36; ATP-dependent DNA/RNA helicase DHX36 [KO:K14442] [EC:3.6.4.13]
130257025  PFKL; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
130257285  SKIC8; SKI8 subunit of superkiller complex protein [KO:K12602]
130257315  EDC3; enhancer of mRNA-decapping protein 3 isoform X1 [KO:K12615]
130257383  DIS3L; DIS3-like exonuclease 1 isoform X1 [KO:K18681] [EC:3.1.13.-]
130257623  CNOT1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
130257671  EXOSC6; exosome complex component MTR3 [KO:K12587]
130257726  MPHOSPH6; M-phase phosphoprotein 6 [KO:K12593]
130257852  TENT4B; terminal nucleotidyltransferase 4B [KO:K03514] [EC:2.7.7.19]
130257864  EDC4; enhancer of mRNA-decapping protein 4 [KO:K12616]
130258227  [KO:K14443]
130258352  LSM3; U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
130258482  DCP1A; mRNA-decapping enzyme 1A [KO:K12610] [EC:3.-.-.-]
130258610  CNOT6; CCR4-NOT transcription complex subunit 6 isoform X1 [KO:K12603] [EC:3.1.13.4]
130258628  HSPA9; stress-70 protein, mitochondrial [KO:K04043]
130258960  CNOT8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
130259474  PARN; poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
130260148  EXOSC2; exosome complex component RRP4 [KO:K03679]
130260528  TOB1; protein Tob1 [KO:K14443]
130260775  EXOSC8; exosome complex component RRP43 [KO:K12586]
130261327  PABPC1L; polyadenylate-binding protein 1-like [KO:K13126]
130261627  EXOSC10; exosome component 10 isoform X1 [KO:K12591] [EC:3.1.13.-]
130261673  ENO1; alpha-enolase [KO:K01689] [EC:4.2.1.11]
130262028  [KO:K12620]
130262210  PABPC4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
130262401  BTG4; protein BTG4 [KO:K14443]
130262412  DDX6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:3.6.4.13]
130262570  DCPS; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
130263578  DCP1B; mRNA-decapping enzyme 1B [KO:K12611] [EC:3.-.-.-]
130263743  BTG2; protein BTG2 [KO:K14443]
130264354  LSM7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
130264526  LSM4; U6 snRNA-associated Sm-like protein LSm4 isoform X1 [KO:K12623]
130264667  ZCCHC7; zinc finger CCHC domain-containing protein 7 [KO:K12597]
130264788  EXOSC5; exosome complex component RRP46 [KO:K12590]
130264889  MTREX; exosome RNA helicase MTR4 [KO:K12598] [EC:3.6.4.13]
130264936  DCP2; m7GpppN-mRNA hydrolase isoform X1 [KO:K12613] [EC:3.6.1.62]
130265378  LSM5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
130265618  SKIC3; SKI3 subunit of superkiller complex protein [KO:K12600]
130265669  PFKM; ATP-dependent 6-phosphofructokinase, muscle type isoform X1 [KO:K00850] [EC:2.7.1.11]
130265680  PAN2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
130266595  [KO:K12620]
130266830  TOB2; protein Tob2 isoform X1 [KO:K14443]
130266962  CNOT4; CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
130267018  CNOT2; CCR4-NOT transcription complex subunit 2 [KO:K12605]
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
oma03015  mRNA surveillance pathway
KO pathway
ko03018   

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