KEGG   PATHWAY: vpn03018
Entry
vpn03018                    Pathway                                
Name
RNA degradation - Virgibacillus dokdonensis
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
vpn03018  RNA degradation
vpn03018

Other DBs
GO: 0006401
Organism
Virgibacillus dokdonensis [GN:vpn]
Gene
A21D_00104  eno; Enolase [KO:K01689] [EC:4.2.1.11]
A21D_03601  pnp; Polyribonucleotide nucleotidyltransferase [KO:K00962] [EC:2.7.7.8]
A21D_00094  rnr; Ribonuclease R [KO:K12573] [EC:3.1.13.1]
A21D_02029  cshA; DEAD-box ATP-dependent RNA helicase CshA [KO:K05592] [EC:5.6.2.7]
A21D_01857  recQ_1; ATP-dependent DNA helicase RecQ [KO:K03654] [EC:5.6.2.4]
A21D_03346  recQ_2; ATP-dependent DNA helicase RecQ [KO:K03654] [EC:5.6.2.4]
A21D_00956  hypothetical protein [KO:K03628]
A21D_03575  rny; Ribonuclease Y [KO:K18682] [EC:3.1.-.-]
A21D_03799  rnjA; Ribonuclease J 1 [KO:K12574] [EC:3.1.-.-]
A21D_02965  pfkA; 6-phosphofructokinase [KO:K00850] [EC:2.7.1.11]
A21D_03180  dnaK; Chaperone protein DnaK [KO:K04043]
A21D_02080  groL; 60 kDa chaperonin [KO:K04077] [EC:5.6.1.7]
A21D_03565  hfq; RNA-binding protein Hfq [KO:K03666]
A21D_02802  ppk; Polyphosphate kinase [KO:K00937] [EC:2.7.4.1]
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
KO pathway
ko03018   
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