KEGG   PATHWAY: cyo03018
Entry
cyo03018                    Pathway                                
Name
RNA degradation - Citrobacter youngae
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
cyo03018  RNA degradation
cyo03018

Other DBs
GO: 0006401
Organism
Citrobacter youngae [GN:cyo]
Gene
CD187_04705  RNA pyrophosphohydrolase [KO:K08311] [EC:3.6.1.-]
CD187_14510  ribonuclease E [KO:K08300] [EC:3.1.26.12]
CD187_23830  ATP-dependent RNA helicase RhlB [KO:K03732] [EC:5.6.2.7]
CD187_04970  phosphopyruvate hydratase [KO:K01689] [EC:4.2.1.11]
CD187_02745  pnp; polyribonucleotide nucleotidyltransferase [KO:K00962] [EC:2.7.7.8]
CD187_16185  ATP-dependent RNA helicase RhlE [KO:K11927] [EC:5.6.2.7]
CD187_21605  rnr; ribonuclease R [KO:K12573] [EC:3.1.13.1]
CD187_02755  DEAD/DEAH family ATP-dependent RNA helicase [KO:K05592] [EC:5.6.2.7]
CD187_23645  ATP-dependent DNA helicase RecQ [KO:K03654] [EC:5.6.2.4]
CD187_23815  rho; transcription termination factor Rho [KO:K03628]
CD187_23120  pfkA; ATP-dependent 6-phosphofructokinase [KO:K00850] [EC:2.7.1.11]
CD187_20475  molecular chaperone DnaK [KO:K04043]
CD187_21795  groL; molecular chaperone GroEL [KO:K04077] [EC:5.6.1.7]
CD187_21640  RNA-binding protein Hfq [KO:K03666]
CD187_06855  ppk1; polyphosphate kinase 1 [KO:K00937] [EC:2.7.4.1]
CD187_19785  polynucleotide adenylyltransferase PcnB [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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