KEGG   PATHWAY: shf03018
Entry
shf03018                    Pathway                                
Name
RNA degradation - Shewanella sp. FDAARGOS_354
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
shf03018  RNA degradation
shf03018

Other DBs
GO: 0006401
Organism
Shewanella sp. FDAARGOS_354 [GN:shf]
Gene
CEQ32_09310  RNA pyrophosphohydrolase [KO:K08311] [EC:3.6.1.-]
CEQ32_02515  ribonuclease E [KO:K08300] [EC:3.1.26.12]
CEQ32_14065  ATP-dependent RNA helicase RhlB [KO:K03732] [EC:5.6.2.7]
CEQ32_21870  phosphopyruvate hydratase [KO:K01689] [EC:4.2.1.11]
CEQ32_10500  pnp; polyribonucleotide nucleotidyltransferase [KO:K00962] [EC:2.7.7.8]
CEQ32_20515  ATP-dependent RNA helicase [KO:K11927] [EC:5.6.2.7]
CEQ32_08635  RNA helicase [KO:K11927] [EC:5.6.2.7]
CEQ32_01185  ATP-dependent helicase [KO:K11927] [EC:5.6.2.7]
CEQ32_09040  RNA helicase [KO:K11927] [EC:5.6.2.7]
CEQ32_03925  DEAD/DEAH box helicase [KO:K11927] [EC:5.6.2.7]
CEQ32_10905  ATP-dependent helicase [KO:K11927] [EC:5.6.2.7]
CEQ32_22150  DEAD/DEAH box helicase [KO:K11927] [EC:5.6.2.7]
CEQ32_19910  ribonuclease R [KO:K12573] [EC:3.1.13.1]
CEQ32_19495  ATP-dependent RNA helicase [KO:K05592] [EC:5.6.2.7]
CEQ32_04730  RecQ family ATP-dependent DNA helicase [KO:K03654] [EC:5.6.2.4]
CEQ32_18565  recQ; DNA helicase RecQ [KO:K03654] [EC:5.6.2.4]
CEQ32_14075  rho; transcription termination factor Rho [KO:K03628]
CEQ32_10930  molecular chaperone DnaK [KO:K04043]
CEQ32_12850  groL; molecular chaperone GroEL [KO:K04077] [EC:5.6.1.7]
CEQ32_13090  RNA-binding protein Hfq [KO:K03666]
CEQ32_03295  ppk1; polyphosphate kinase 1 [KO:K00937] [EC:2.7.4.1]
CEQ32_12110  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   
LinkDB

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