KEGG   PATHWAY: vfi03018
Entry
vfi03018                    Pathway                                
Name
RNA degradation - Aliivibrio fischeri ES114
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
vfi03018  RNA degradation
vfi03018

Other DBs
GO: 0006401
Organism
Aliivibrio fischeri ES114 [GN:vfi]
Gene
VF_0456  nudH; nucleotide hydrolase [KO:K08311] [EC:3.6.1.-]
VF_1748  rne; rne [KO:K08300] [EC:3.1.26.12]
VF_0056  rhlB; ATP-dependent RNA helicase [KO:K03732] [EC:5.6.2.7]
VF_2075  eno; enolase [KO:K01689] [EC:4.2.1.11]
VF_0490  pnp; polynucleotide phosphorylase (PNPase) [KO:K00962] [EC:2.7.7.8]
VF_A0374  ATP-dependent RNA helicase [KO:K11927] [EC:5.6.2.7]
VF_A0151  rhlE; RNA helicase [KO:K11927] [EC:5.6.2.7]
VF_1790  ATP-dependent RNA helicase [KO:K11927] [EC:5.6.2.7]
VF_2314  rnr; exoribonuclease R, RNase R [KO:K12573] [EC:3.1.13.1]
VF_A0384  deaD; ATP-dependent RNA helicase [KO:K05592] [EC:5.6.2.7]
VF_0070  recQ; ATP-dependent DNA helicase [KO:K03654] [EC:5.6.2.4]
VF_A1156  ATP-dependent DNA helicase RecQ [KO:K03654] [EC:5.6.2.4]
VF_0058  rho; transcription termination factor [KO:K03628]
VF_2340  pfkA; 6-phosphofructokinase I [KO:K00850] [EC:2.7.1.11]
VF_1994  dnaK; chaperone Hsp70/DnaK, co-chaperone with DnaJ [KO:K04043]
VF_1467  chaperone, DnaK-like protein [KO:K04043]
VF_0205  groL; Cpn60 chaperonin GroEL, large subunit of GroESL [KO:K04077] [EC:5.6.1.7]
VF_2323  hfq; RNA chaperone Hfq (HF-I) [KO:K03666]
VF_2166  pcnB; poly(A) polymerase I [KO:K00970] [EC:2.7.7.19]
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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