KEGG   PATHWAY: osa03018
Entry
osa03018                    Pathway                                
Name
RNA degradation - Oryza sativa japonica (Japanese rice) (RefSeq)
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
osa03018  RNA degradation
osa03018

Other DBs
GO: 0006401
Organism
Oryza sativa japonica (Japanese rice) (RefSeq) [GN:osa]
Gene
4331133  exosome complex component csl4 [KO:K07573]
4336421  exosome complex component RRP4 homolog [KO:K03679]
4324917  putative exosome complex component rrp40 [KO:K03681]
4327851  putative exosome complex component rrp40 [KO:K03681]
4350355  exosome complex component RRP43 [KO:K12586]
4344519  exosome complex component RRP41-like [KO:K12587]
9269241  exosome complex component RRP41-like isoform X1 [KO:K12587]
4352037  exosome complex component RRP42 [KO:K12589]
4346519  exosome complex component RRP41 homolog [KO:K11600]
4334824  exosome complex exonuclease RRP46 homolog [KO:K12590]
4329627  exosome complex component RRP45A isoform X1 [KO:K03678]
4331494  exosome complex exonuclease RRP44 homolog A [KO:K12585] [EC:3.1.13.-]
4331677  protein RRP6-like 2 [KO:K12591] [EC:3.1.13.-]
9270208  protein RRP6-like 2 [KO:K12591] [EC:3.1.13.-]
4345136  nuclear nucleic acid-binding protein C1D [KO:K12592]
4325469  uncharacterized protein LOC4325469 [KO:K12593]
4325901  non-canonical poly(A) RNA polymerase PAPD5 [KO:K03514] [EC:2.7.7.19]
4349924  DExH-box ATP-dependent RNA helicase DExH10 [KO:K12598] [EC:3.6.4.13]
9268439  DExH-box ATP-dependent RNA helicase DExH9 [KO:K12598] [EC:3.6.4.13]
4328375  DExH-box ATP-dependent RNA helicase DExH11 [KO:K12599] [EC:3.6.4.13]
4349298  tetratricopeptide repeat protein SKI3 [KO:K12600]
4351059  WD repeat-containing protein VIP3 [KO:K12602]
4331740  carbon catabolite repressor protein 4 homolog 1 [KO:K12603] [EC:3.1.13.4]
4348610  carbon catabolite repressor protein 4 homolog 1 [KO:K12603] [EC:3.1.13.4]
4338672  carbon catabolite repressor protein 4 homolog 4 [KO:K12603] [EC:3.1.13.4]
9272729  CCR4-NOT transcription complex subunit 1 [KO:K12604]
4331296  CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
4330931  probable NOT transcription complex subunit VIP2 [KO:K12605]
4334027  probable NOT transcription complex subunit VIP2 isoform X1 [KO:K12605]
4339144  probable NOT transcription complex subunit VIP2 isoform X1 [KO:K12605]
4333598  general negative regulator of transcription subunit 3 isoform X1 [KO:K12580]
4351244  uncharacterized protein LOC4351244 isoform X1 [KO:K10643] [EC:2.3.2.27]
4349535  uncharacterized protein LOC4349535 [KO:K10643] [EC:2.3.2.27]
4325536  uncharacterized protein LOC4325536 [KO:K10643] [EC:2.3.2.27]
4347066  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
4337457  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
4331006  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
4345683  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
107277796  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
4336974  cell differentiation protein RCD1 homolog [KO:K12606]
4329079  cell differentiation protein rcd1 isoform X1 [KO:K12606]
4343622  cell differentiation protein RCD1 homolog [KO:K12606]
9272009  cell differentiation protein RCD1 homolog [KO:K12606]
107275860  cell differentiation protein RCD1 homolog [KO:K12606]
4346428  CCR4-NOT transcription complex subunit 10 [KO:K12607]
4331095  ABC transporter I family member 19 [KO:K12608]
4332655  ABC transporter I family member 20 [KO:K12608]
4325502  DExH-box ATP-dependent RNA helicase DExH6 [KO:K14442] [EC:3.6.4.13]
4326075  DExH-box ATP-dependent RNA helicase DExH3 [KO:K14442] [EC:3.6.4.13]
4334111  DExH-box ATP-dependent RNA helicase DExH3 [KO:K14442] [EC:3.6.4.13]
4345682  poly(A)-specific ribonuclease PARN-like [KO:K01148] [EC:3.1.13.4]
9268289  poly(A)-specific ribonuclease PARN [KO:K01148] [EC:3.1.13.4]
4336259  uncharacterized CRM domain-containing protein At3g25440, chloroplastic isoform X1 [KO:K01148] [EC:3.1.13.4]
4345242  polyadenylate-binding protein 2 [KO:K13126]
4346409  polyadenylate-binding protein 2 [KO:K13126]
4341408  polyadenylate-binding protein 4-like [KO:K13126]
4336331  polyadenylate-binding protein 2 [KO:K13126]
4337438  multiple RNA-binding domain-containing protein 1 [KO:K13126]
4332428  polyadenylate-binding protein 7 [KO:K13126]
4346605  30S ribosomal protein 2, chloroplastic [KO:K13126]
4342837  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
4351547  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
4334709  mRNA-decapping enzyme-like protein isoform X1 [KO:K12611] [EC:3.-.-.-]
4349816  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
4331069  mRNA-decapping enzyme subunit 2 [KO:K12613] [EC:3.6.1.62]
4336501  DEAD-box ATP-dependent RNA helicase 6 [KO:K12614] [EC:3.6.4.13]
4330120  DEAD-box ATP-dependent RNA helicase 8 [KO:K12614] [EC:3.6.4.13]
4349053  DEAD-box ATP-dependent RNA helicase 12 [KO:K12614] [EC:3.6.4.13]
4330568  enhancer of mRNA-decapping protein 4 [KO:K12616]
4340825  enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
4329076  protein PAT1 homolog 1 [KO:K12617]
9270665  protein PAT1 homolog 1 [KO:K12617]
4329480  protein PAT1 homolog 1 [KO:K12617]
4325594  uncharacterized protein LOC4325594 isoform X1 [KO:K12617]
4324952  5'-3' exoribonuclease 3 isoform X1 [KO:K12619] [EC:3.1.13.-]
4329368  5'-3' exoribonuclease 4 isoform X1 [KO:K12619] [EC:3.1.13.-]
4335963  sm-like protein LSM1B [KO:K12620]
4344686  sm-like protein LSM2 [KO:K12621]
4325074  sm-like protein LSM3A [KO:K12622]
4326227  probable U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
4338670  sm-like protein LSM5 [KO:K12624]
4329449  U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
4335668  U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
4344803  sm-like protein LSM7 [KO:K12626]
4339810  sm-like protein LSM8 [KO:K12627]
4340042  enolase 1 [KO:K01689] [EC:4.2.1.11]
4348176  enolase [KO:K01689] [EC:4.2.1.11]
4346906  enolase 1, chloroplastic [KO:K01689] [EC:4.2.1.11]
4332253  enolase-like [KO:K01689] [EC:4.2.1.11]
4332356  cytosolic enolase 3 [KO:K01689] [EC:4.2.1.11]
4342497  probable polyribonucleotide nucleotidyltransferase 1, chloroplastic [KO:K00962] [EC:2.7.7.8]
4329995  polyribonucleotide nucleotidyltransferase 2, mitochondrial [KO:K00962] [EC:2.7.7.8]
4344306  probable ATP-dependent DNA helicase RecQ isoform X1 [KO:K03654] [EC:5.6.2.4]
4339369  ATP-dependent 6-phosphofructokinase 6 [KO:K00850] [EC:2.7.1.11]
4327301  ATP-dependent 6-phosphofructokinase 6 [KO:K00850] [EC:2.7.1.11]
4348582  ATP-dependent 6-phosphofructokinase 5, chloroplastic [KO:K00850] [EC:2.7.1.11]
4347060  ATP-dependent 6-phosphofructokinase 5, chloroplastic isoform X1 [KO:K00850] [EC:2.7.1.11]
4347383  ATP-dependent 6-phosphofructokinase 2 [KO:K00850] [EC:2.7.1.11]
4336113  LOW QUALITY PROTEIN: ATP-dependent 6-phosphofructokinase 2 [KO:K00850] [EC:2.7.1.11]
4338034  ATP-dependent 6-phosphofructokinase 6 [KO:K00850] [EC:2.7.1.11]
4340153  ATP-dependent 6-phosphofructokinase 3 [KO:K00850] [EC:2.7.1.11]
4327196  ATP-dependent 6-phosphofructokinase 6 isoform X1 [KO:K00850] [EC:2.7.1.11]
4330888  heat shock 70 kDa protein, mitochondrial [KO:K04043]
4331379  heat shock 70 kDa protein, mitochondrial [KO:K04043]
9270165  heat shock 70 kDa protein, mitochondrial [KO:K04043]
4327993  ruBisCO large subunit-binding protein subunit beta, chloroplastic [KO:K04077]
4348824  chaperonin CPN60-2, mitochondrial [KO:K04077]
4331590  chaperonin CPN60-1, mitochondrial [KO:K04077]
4339466  chaperonin CPN60-like 2, mitochondrial [KO:K04077]
4339910  ruBisCO large subunit-binding protein subunit beta, chloroplastic [KO:K04077]
107275738  chaperonin 60 subunit beta 4, chloroplastic-like [KO:K04077]
107279834  LOW QUALITY PROTEIN: chaperonin 60 subunit beta 4, chloroplastic-like [KO:K04077]
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
Related
pathway
osa03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

DBGET integrated database retrieval system