KEGG   PATHWAY: ko03018Help
Entry
ko03018                     Pathway                                

Name
RNA degradation
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
BRITE hierarchy
Pathway map
RNA degradation
ko03018

All organismsOrtholog table
Module
M00390  
Exosome, archaea [PATH:ko03018]
M00391  
Exosome, eukaryotes [PATH:ko03018]
M00392  
Ski complex [PATH:ko03018]
M00393  
TRAMP complex [PATH:ko03018]
M00394  
RNA degradosome [PATH:ko03018]
M00395  
Decapping complex [PATH:ko03018]
M00396  
Lsm 2-8 complex [PATH:ko03018]
M00397  
Lsm 1-7 complex [PATH:ko03018]
Other DBs
BSID: 
GO: 
Orthology
K12584  
scavenger mRNA-decapping enzyme DcpS [EC:3.-.-.-]
K07573  
exosome complex component CSL4
K03679  
exosome complex component RRP4
K03681  
exosome complex component RRP40
K12585  
exosome complex exonuclease DIS3/RRP44 [EC:3.1.13.-]
K12586  
exosome complex component RRP43
K12587  
exosome complex component MTR3
K12589  
exosome complex component RRP42
K11600  
exosome complex component RRP41
K12590  
exosome complex component RRP46
K03678  
exosome complex component RRP45
K12591  
exosome complex exonuclease RRP6 [EC:3.1.13.-]
K12592  
exosome complex protein LRP1
K12593  
M-phase phosphoprotein 6, animal type
K12594  
M-phase phosphoprotein 6, fungi type
K12595  
superkiller protein 7
K03514  
DNA polymerase sigma [EC:2.7.7.7]
K12596  
poly(A) RNA polymerase
K12597  
protein AIR1/2
K12598  
ATP-dependent RNA helicase DOB1 [EC:3.6.4.13]
K12599  
antiviral helicase SKI2 [EC:3.6.4.-]
K12600  
superkiller protein 3
K12601  
superkiller protein 8
K12602  
WD repeat-containing protein 61
K12603  
CCR4-NOT transcription complex subunit 6
K12604  
CCR4-NOT transcription complex subunit 1
K12605  
CCR4-NOT transcription complex subunit 2
K12580  
CCR4-NOT transcription complex subunit 3
K10643  
CCR4-NOT transcription complex subunit 4 [EC:6.3.2.19]
K12581  
CCR4-NOT transcription complex subunit 7/8
K12606  
CCR4-NOT transcription complex subunit 9
K12607  
CCR4-NOT transcription complex subunit 10
K12608  
CCR4-NOT complex subunit CAF16
K12609  
CCR4-NOT transcriptional complex subunit CAF120
K14442  
ATP-dependent RNA helicase DHX36 [EC:3.6.4.13]
K01148  
poly(A)-specific ribonuclease [EC:3.1.13.4]
K14443  
protein Tob/BTG
K13126  
polyadenylate-binding protein
K12571  
PAB-dependent poly(A)-specific ribonuclease subunit 2 [EC:3.1.13.4]
K12572  
PAB-dependent poly(A)-specific ribonuclease subunit 3
K12610  
mRNA-decapping enzyme 1A [EC:3.-.-.-]
K12611  
mRNA-decapping enzyme 1B [EC:3.-.-.-]
K12612  
mRNA-decapping enzyme subunit 1
K12613  
mRNA-decapping enzyme subunit 2 [EC:3.6.1.62]
K12614  
ATP-dependent RNA helicase DDX6/DHH1 [EC:3.6.4.13]
K12615  
enhancer of mRNA-decapping protein 3
K12616  
enhancer of mRNA-decapping protein 4
K12617  
DNA topoisomerase 2-associated protein PAT1
K12618  
5'-3' exoribonuclease 1 [EC:3.1.13.-]
K12619  
5'-3' exoribonuclease 2 [EC:3.1.13.-]
K16855  
U8 snoRNA-decapping enzyme [EC:3.6.1.64 3.6.1.62]
K12620  
U6 snRNA-associated Sm-like protein LSm1
K12621  
U6 snRNA-associated Sm-like protein LSm2
K12622  
U6 snRNA-associated Sm-like protein LSm3
K12623  
U6 snRNA-associated Sm-like protein LSm4
K12624  
U6 snRNA-associated Sm-like protein LSm5
K12625  
U6 snRNA-associated Sm-like protein LSm6
K12626  
U6 snRNA-associated Sm-like protein LSm7
K12627  
U6 snRNA-associated Sm-like protein LSm8
K08311  
putative (di)nucleoside polyphosphate hydrolase [EC:3.6.1.-]
K08300  
ribonuclease E [EC:3.1.26.12]
K03732  
ATP-dependent RNA helicase RhlB [EC:3.6.4.13]
K01689  
enolase [EC:4.2.1.11]
K00962  
polyribonucleotide nucleotidyltransferase [EC:2.7.7.8]
K11927  
ATP-dependent RNA helicase RhlE [EC:3.6.4.13]
K12573  
ribonuclease R [EC:3.1.-.-]
K05592  
ATP-dependent RNA helicase DeaD [EC:3.6.4.13]
K03654  
ATP-dependent DNA helicase RecQ [EC:3.6.4.12]
K03628  
transcription termination factor Rho
K12574  
ribonuclease J [EC:3.1.-.-]
K04043  
molecular chaperone DnaK
K04077  
chaperonin GroEL
K03666  
host factor-I protein
K00937  
polyphosphate kinase [EC:2.7.4.1]
K00970  
poly(A) polymerase [EC:2.7.7.19]
Compound
C00201  
Nucleoside triphosphate
Reference
  Authors
Houseley J, Tollervey D
  Title
The many pathways of RNA degradation.
  Journal
Cell 136:763-76 (2009)
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)
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)
Reference
  Authors
Hartung S, Hopfner KP
  Title
The exosome, plugged.
  Journal
EMBO Rep 8:456-7 (2007)
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)
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)
Reference
  Authors
Condon C
  Title
Maturation and degradation of RNA in bacteria.
  Journal
Curr Opin Microbiol 10:271-8 (2007)

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