KEGG   PATHWAY: itr03018
Entry
itr03018                    Pathway                                
Name
RNA degradation - Ipomoea triloba (trilobed morning glory)
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
itr03018  RNA degradation
itr03018

Other DBs
GO: 0006401
Organism
Ipomoea triloba (trilobed morning glory) [GN:itr]
Gene
116022862  exosome complex component CSL4 [KO:K07573]
116017033  exosome complex component RRP4 homolog isoform X1 [KO:K03679]
116016124  exosome complex component RRP4 homolog [KO:K03679]
116016592  exosome complex component RRP4 homolog [KO:K03679]
116007162  putative exosome complex component rrp40 [KO:K03681]
116019767  exosome complex component RRP43 [KO:K12586]
116029455  exosome complex component RRP43-like [KO:K12586]
116025991  exosome complex component RRP41-like [KO:K12587]
116006006  exosome complex component RRP42 [KO:K12589]
116024743  exosome complex component RRP41 homolog [KO:K11600]
116012267  exosome complex component RRP41 homolog [KO:K11600]
116006679  exosome complex exonuclease RRP46 homolog [KO:K12590]
116003696  exosome complex component RRP45A-like isoform X1 [KO:K03678]
116024604  exosome complex component RRP45A-like [KO:K03678]
116020984  exosome complex exonuclease RRP44 homolog A isoform X1 [KO:K12585] [EC:3.1.13.-]
116006598  protein RRP6-like 1 isoform X1 [KO:K12591] [EC:3.1.13.-]
115998556  protein RRP6-like 2 [KO:K12591] [EC:3.1.13.-]
116021815  nuclear nucleic acid-binding protein C1D [KO:K12592]
116017576  uncharacterized protein LOC116017576 [KO:K12593]
116023254  terminal nucleotidyltransferase 4B [KO:K03514] [EC:2.7.7.19]
116012762  DExH-box ATP-dependent RNA helicase DExH10 [KO:K12598] [EC:5.6.2.6]
116029263  DExH-box ATP-dependent RNA helicase DExH9 [KO:K12598] [EC:5.6.2.6]
116004528  DExH-box ATP-dependent RNA helicase DExH11 isoform X1 [KO:K12599] [EC:5.6.2.6]
116022223  tetratricopeptide repeat protein SKI3 [KO:K12600]
115998211  WD repeat-containing protein VIP3 [KO:K12602]
116020997  carbon catabolite repressor protein 4 homolog 1-like [KO:K12603] [EC:3.1.13.4]
116027512  carbon catabolite repressor protein 4 homolog 4 [KO:K12603] [EC:3.1.13.4]
116029997  carbon catabolite repressor protein 4 homolog 1 [KO:K12603] [EC:3.1.13.4]
116017841  CCR4-NOT transcription complex subunit 1-like [KO:K12604]
116030009  CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
116003122  probable NOT transcription complex subunit VIP2 isoform X1 [KO:K12605]
116004688  probable NOT transcription complex subunit VIP2 [KO:K12605]
116006887  general negative regulator of transcription subunit 3 isoform X1 [KO:K12580]
116029992  general negative regulator of transcription subunit 3-like isoform X1 [KO:K12580]
116004519  uncharacterized protein LOC116004519 isoform X1 [KO:K10643] [EC:2.3.2.27]
116024485  uncharacterized protein LOC116024485 isoform X1 [KO:K10643] [EC:2.3.2.27]
115996715  uncharacterized protein LOC115996715 isoform X1 [KO:K10643] [EC:2.3.2.27]
116031500  probable CCR4-associated factor 1 homolog 6 [KO:K12581]
116018164  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
116007204  probable CCR4-associated factor 1 homolog 9 [KO:K12581]
115996308  probable CCR4-associated factor 1 homolog 6 [KO:K12581]
116011307  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
116014896  probable CCR4-associated factor 1 homolog 9 [KO:K12581]
116015518  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
116021083  CCR4-NOT transcription complex subunit 9-like [KO:K12606]
116009672  CCR4-NOT transcription complex subunit 9-like isoform X1 [KO:K12606]
116023779  cell differentiation protein rcd1-like [KO:K12606]
115996992  CCR4-NOT transcription complex subunit 9-like [KO:K12606]
116029153  cell differentiation protein rcd1-like [KO:K12606]
116001978  CCR4-NOT transcription complex subunit 10-like [KO:K12607]
116032205  CCR4-NOT transcription complex subunit 10-like [KO:K12607]
116022954  ABC transporter I family member 20 [KO:K12608]
116014760  ABC transporter I family member 19-like [KO:K12608]
116004506  DExH-box ATP-dependent RNA helicase DExH5, mitochondrial isoform X1 [KO:K14442] [EC:5.6.2.6]
116005713  DExH-box ATP-dependent RNA helicase DExH3-like [KO:K14442] [EC:5.6.2.6]
116006473  DExH-box ATP-dependent RNA helicase DExH3-like [KO:K14442] [EC:5.6.2.6]
116022334  DExH-box ATP-dependent RNA helicase DExH3 [KO:K14442] [EC:5.6.2.6]
116009851  DExH-box ATP-dependent RNA helicase DExH6-like [KO:K14442] [EC:5.6.2.6]
116029988  DExH-box ATP-dependent RNA helicase DExH1 isoform X1 [KO:K14442] [EC:5.6.2.6]
116002076  uncharacterized CRM domain-containing protein At3g25440, chloroplastic [KO:K01148] [EC:3.1.13.4]
116011196  poly(A)-specific ribonuclease PARN [KO:K01148] [EC:3.1.13.4]
116016247  poly(A)-specific ribonuclease PARN-like isoform X1 [KO:K01148] [EC:3.1.13.4]
116003570  uncharacterized protein DDB_G0290685-like isoform X1 [KO:K13126]
116004532  uncharacterized protein LOC116004532 [KO:K13126]
116004994  polyadenylate-binding protein 7-like [KO:K13126]
116022112  polyadenylate-binding protein 2-like [KO:K13126]
116022247  polyadenylate-binding protein 2-like [KO:K13126]
116007555  polyadenylate-binding protein 7 isoform X1 [KO:K13126]
116022920  polyadenylate-binding protein 3 [KO:K13126]
116010032  polyadenylate-binding protein 4-like [KO:K13126]
116023637  polyadenylate-binding protein 4-like [KO:K13126]
116027522  polyadenylate-binding protein 2-like [KO:K13126]
116014719  30S ribosomal protein 2, chloroplastic [KO:K13126]
116015456  polyadenylate-binding protein 8-like [KO:K13126]
116030133  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
116004676  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
116015493  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
116011176  mRNA-decapping enzyme subunit 2 [KO:K12613] [EC:3.6.1.62]
116002189  DEAD-box ATP-dependent RNA helicase 8-like [KO:K12614] [EC:5.6.2.7]
116030234  DEAD-box ATP-dependent RNA helicase 8-like [KO:K12614] [EC:5.6.2.7]
115995819  DEAD-box ATP-dependent RNA helicase 6-like [KO:K12614] [EC:5.6.2.7]
116027664  DEAD-box ATP-dependent RNA helicase 8-like [KO:K12614] [EC:5.6.2.7]
116009729  enhancer of mRNA-decapping protein 4-like [KO:K12616]
116001350  enhancer of mRNA-decapping protein 4-like [KO:K12616]
116023196  enhancer of mRNA-decapping protein 4-like [KO:K12616]
116020028  protein PAT1 homolog isoform X1 [KO:K12617]
116022280  protein PAT1 homolog 2-like [KO:K12617]
116009779  protein PAT1 homolog 1-like [KO:K12617]
116009780  protein PAT1 homolog 1-like [KO:K12617]
116020744  5'-3' exoribonuclease 3 isoform X1 [KO:K12619] [EC:3.1.13.-]
116003871  sm-like protein LSM1B [KO:K12620]
116022681  sm-like protein LSM1B [KO:K12620]
115996203  sm-like protein LSM1B [KO:K12620]
116024909  sm-like protein LSM2 [KO:K12621]
115998130  sm-like protein LSM3B [KO:K12622]
116032632  probable U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
116006071  probable U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
116001781  sm-like protein LSM5 [KO:K12624]
116002584  sm-like protein LSM5 [KO:K12624]
116006553  sm-like protein LSM36B [KO:K12625]
115997146  sm-like protein LSM7 [KO:K12626]
116001508  sm-like protein LSM7 [KO:K12626]
115999807  sm-like protein LSM8 [KO:K12627]
116007144  enolase [KO:K01689] [EC:4.2.1.11]
116022974  enolase 1, chloroplastic [KO:K01689] [EC:4.2.1.11]
116025370  cytosolic enolase 3 [KO:K01689] [EC:4.2.1.11]
115999929  polyribonucleotide nucleotidyltransferase 2, mitochondrial [KO:K00962] [EC:2.7.7.8]
116029385  probable polyribonucleotide nucleotidyltransferase 1, chloroplastic [KO:K00962] [EC:2.7.7.8]
116016897  uncharacterized protein LOC116016897 [KO:K03654] [EC:5.6.2.4]
116019016  ATP-dependent 6-phosphofructokinase 6-like [KO:K00850] [EC:2.7.1.11]
116019182  ATP-dependent 6-phosphofructokinase 5, chloroplastic-like [KO:K00850] [EC:2.7.1.11]
116019973  ATP-dependent 6-phosphofructokinase 4, chloroplastic-like [KO:K00850] [EC:2.7.1.11]
116006347  ATP-dependent 6-phosphofructokinase 6-like [KO:K00850] [EC:2.7.1.11]
116021671  ATP-dependent 6-phosphofructokinase 6-like [KO:K00850] [EC:2.7.1.11]
116007072  ATP-dependent 6-phosphofructokinase 3-like [KO:K00850] [EC:2.7.1.11]
116007525  ATP-dependent 6-phosphofructokinase 2 [KO:K00850] [EC:2.7.1.11]
115998165  ATP-dependent 6-phosphofructokinase 5, chloroplastic [KO:K00850] [EC:2.7.1.11]
116013693  ATP-dependent 6-phosphofructokinase 6-like [KO:K00850] [EC:2.7.1.11]
116013729  ATP-dependent 6-phosphofructokinase 6-like isoform X1 [KO:K00850] [EC:2.7.1.11]
116032616  heat shock 70 kDa protein, mitochondrial [KO:K04043]
116024565  heat shock 70 kDa protein, mitochondrial-like [KO:K04043]
116001959  chaperonin CPN60-2, mitochondrial [KO:K04077] [EC:5.6.1.7]
115996654  ruBisCO large subunit-binding protein subunit beta, chloroplastic-like [KO:K04077] [EC:5.6.1.7]
116024711  chaperonin 60 subunit beta 4, chloroplastic [KO:K04077] [EC:5.6.1.7]
115997350  chaperonin CPN60-like 2, mitochondrial [KO:K04077] [EC:5.6.1.7]
116025350  ruBisCO large subunit-binding protein subunit beta, chloroplastic [KO:K04077] [EC:5.6.1.7]
116015503  chaperonin CPN60, mitochondrial [KO:K04077] [EC:5.6.1.7]
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
itr03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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