KEGG   PATHWAY: png03018
Entry
png03018                    Pathway                                
Name
RNA degradation - Pseudoalteromonas nigrifaciens
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
png03018  RNA degradation
png03018

Other DBs
GO: 0006401
Organism
Pseudoalteromonas nigrifaciens [GN:png]
Gene
PNIG_a0901  nudH; putative (di)nucleoside polyphosphate hydrolase [KO:K08311] [EC:3.6.1.-]
PNIG_a2439  rne; ribonuclease E [KO:K08300] [EC:3.1.26.12]
PNIG_a0136  rhlB; ATP-dependent RNA helicase RhlB [KO:K03732] [EC:5.6.2.7]
PNIG_a0898  eno; enolase [KO:K01689] [EC:4.2.1.11]
PNIG_a1210  pnp; polyribonucleotide nucleotidyltransferase [KO:K00962] [EC:2.7.7.8]
PNIG_a2591  rhlE; ATP-dependent RNA helicase RhlE [KO:K11927] [EC:5.6.2.7]
PNIG_a3786  hypothetical protein [KO:K11927] [EC:5.6.2.7]
PNIG_b0563  hypothetical protein [KO:K11927] [EC:5.6.2.7]
PNIG_a0767  hypothetical protein [KO:K11927] [EC:5.6.2.7]
PNIG_a3784  vacB; ribonuclease R [KO:K12573] [EC:3.1.13.1]
PNIG_a3164  vacB; ribonuclease R [KO:K12573] [EC:3.1.13.1]
PNIG_a1198  deaD; ATP-dependent RNA helicase DeaD [KO:K05592] [EC:5.6.2.7]
PNIG_a3281  recQ; ATP-dependent DNA helicase RecQ [KO:K03654] [EC:5.6.2.4]
PNIG_b0150  recQ; ATP-dependent DNA helicase RecQ [KO:K03654] [EC:5.6.2.4]
PNIG_a0134  rho; transcription termination factor Rho [KO:K03628]
PNIG_b0489  dnaK; molecular chaperone DnaK [KO:K04043]
PNIG_a0296  groEL; chaperonin GroEL [KO:K04077] [EC:5.6.1.7]
PNIG_a0311  hfq; host factor-I protein [KO:K03666]
PNIG_a0723  pcnB; poly(A) polymerase [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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