KEGG   PATHWAY: gab03018
Entry
gab03018                    Pathway                                
Name
RNA degradation - Gossypium arboreum (tree cotton)
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
gab03018  RNA degradation
gab03018

Other DBs
GO: 0006401
Organism
Gossypium arboreum (tree cotton) [GN:gab]
Gene
108484409  exosome complex component RRP4 homolog [KO:K03679]
108466311  exosome complex component RRP4 homolog [KO:K03679]
108477402  putative exosome complex component rrp40 isoform X1 [KO:K03681]
108480752  exosome complex component RRP43-like [KO:K12586]
108466050  exosome complex component RRP43-like [KO:K12586]
108450595  exosome complex component RRP41-like [KO:K12587]
108458389  exosome complex component RRP42 [KO:K12589]
108472526  exosome complex component RRP41 homolog [KO:K11600]
108485168  exosome complex exonuclease RRP46 homolog [KO:K12590]
108462892  exosome complex exonuclease RRP46 homolog [KO:K12590]
108484464  exosome complex component RRP45A-like [KO:K03678]
108454706  exosome complex component RRP45B isoform X1 [KO:K03678]
108483498  exosome complex exonuclease RRP44 homolog A [KO:K12585] [EC:3.1.13.-]
108473652  protein RRP6-like 2 [KO:K12591] [EC:3.1.13.-]
108464428  protein RRP6-like 2 [KO:K12591] [EC:3.1.13.-]
108464429  protein RRP6-like 2 isoform X1 [KO:K12591] [EC:3.1.13.-]
108473365  nuclear nucleic acid-binding protein C1D [KO:K12592]
108483174  uncharacterized protein LOC108483174 [KO:K12593]
108451845  uncharacterized protein LOC108451845 [KO:K12593]
108480128  non-canonical poly(A) RNA polymerase PAPD7 [KO:K03514] [EC:2.7.7.19]
108486226  DExH-box ATP-dependent RNA helicase DExH9 [KO:K12598] [EC:5.6.2.6]
108464031  DExH-box ATP-dependent RNA helicase DExH10 [KO:K12598] [EC:5.6.2.6]
108483671  DExH-box ATP-dependent RNA helicase DExH11 isoform X1 [KO:K12599] [EC:5.6.2.6]
108453138  tetratricopeptide repeat protein SKI3 [KO:K12600]
108470958  WD repeat-containing protein VIP3-like [KO:K12602]
108471040  WD repeat-containing protein VIP3-like [KO:K12602]
108479324  carbon catabolite repressor protein 4 homolog 4 [KO:K12603] [EC:3.1.13.4]
108467209  carbon catabolite repressor protein 4 homolog 1-like [KO:K12603] [EC:3.1.13.4]
108457006  carbon catabolite repressor protein 4 homolog 1-like [KO:K12603] [EC:3.1.13.4]
108454513  carbon catabolite repressor protein 4 homolog 1-like [KO:K12603] [EC:3.1.13.4]
108452946  CCR4-NOT transcription complex subunit 1-like [KO:K12604]
108460381  CCR4-NOT transcription complex subunit 1-like isoform X1 [KO:K12604]
108470301  probable NOT transcription complex subunit VIP2 isoform X1 [KO:K12605]
108486448  probable NOT transcription complex subunit VIP2 isoform X1 [KO:K12605]
108453291  probable NOT transcription complex subunit VIP2 isoform X1 [KO:K12605]
108473762  CCR4-NOT transcription complex subunit 3-like isoform X1 [KO:K12580]
108465534  CCR4-NOT transcription complex subunit 3-like isoform X1 [KO:K12580]
108486105  uncharacterized protein LOC108486105 [KO:K10643] [EC:2.3.2.27]
108483087  uncharacterized protein LOC108483087 isoform X1 [KO:K10643] [EC:2.3.2.27]
108450777  uncharacterized protein LOC108450777 isoform X1 [KO:K10643] [EC:2.3.2.27]
108453512  uncharacterized protein LOC108453512 isoform X1 [KO:K10643] [EC:2.3.2.27]
108469684  LOW QUALITY PROTEIN: probable CCR4-associated factor 1 homolog 7 [KO:K12581]
108484441  probable CCR4-associated factor 1 homolog 6 [KO:K12581]
108474929  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
108474932  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
108470571  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
108468642  probable CCR4-associated factor 1 homolog 9 [KO:K12581]
108480176  probable CCR4-associated factor 1 homolog 6 [KO:K12581]
108471814  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
108475504  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
108473642  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
108468838  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
108455775  probable CCR4-associated factor 1 homolog 9 [KO:K12581]
108458950  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
108458954  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
108458955  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
108461167  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
108458817  probable CCR4-associated factor 1 homolog 6 [KO:K12581]
108474032  cell differentiation protein rcd1-like [KO:K12606]
108474046  cell differentiation protein RCD1 homolog [KO:K12606]
108452917  cell differentiation protein RCD1 homolog isoform X1 [KO:K12606]
108486130  cell differentiation protein RCD1 homolog [KO:K12606]
108486770  cell differentiation protein rcd1-like isoform X1 [KO:K12606]
108486637  cell differentiation protein rcd1-like [KO:K12606]
108484808  cell differentiation protein rcd1 [KO:K12606]
108469964  CCR4-NOT transcription complex subunit 10-like isoform X1 [KO:K12607]
108454759  CCR4-NOT transcription complex subunit 10-like isoform X1 [KO:K12607]
108464125  CCR4-NOT transcription complex subunit 10-like isoform X1 [KO:K12607]
108467481  ABC transporter I family member 21-like [KO:K12608]
108473683  ABC transporter I family member 20 [KO:K12608]
108456824  DExH-box ATP-dependent RNA helicase DExH5, mitochondrial isoform X1 [KO:K14442] [EC:5.6.2.6]
108457020  DExH-box ATP-dependent RNA helicase DExH3 [KO:K14442] [EC:5.6.2.6]
108460505  LOW QUALITY PROTEIN: DExH-box ATP-dependent RNA helicase DExH3 [KO:K14442] [EC:5.6.2.6]
108460507  DExH-box ATP-dependent RNA helicase DExH1 isoform X1 [KO:K14442] [EC:5.6.2.6]
108460536  DExH-box ATP-dependent RNA helicase DExH6 [KO:K14442] [EC:5.6.2.6]
108480388  poly(A)-specific ribonuclease PARN [KO:K01148] [EC:3.1.13.4]
108470929  uncharacterized CRM domain-containing protein At3g25440, chloroplastic isoform X1 [KO:K01148] [EC:3.1.13.4]
108473647  poly(A)-specific ribonuclease PARN-like [KO:K01148] [EC:3.1.13.4]
108483204  polyadenylate-binding protein 2-like [KO:K13126]
108486035  polyadenylate-binding protein 8-like [KO:K13126]
108475983  polyadenylate-binding protein 8-like [KO:K13126]
108489732  polyadenylate-binding protein 6-like isoform X1 [KO:K13126]
108452578  polyadenylate-binding protein 2-like [KO:K13126]
108472838  polyadenylate-binding protein 7-like [KO:K13126]
108456024  polyadenylate-binding protein 7-like [KO:K13126]
108485439  polyadenylate-binding protein 3 [KO:K13126]
108476934  30S ribosomal protein 2, chloroplastic [KO:K13126]
108486430  polyadenylate-binding protein 2-like [KO:K13126]
108483665  polyadenylate-binding protein 2-like isoform X1 [KO:K13126]
108467726  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
108457216  mRNA-decapping enzyme-like protein isoform X1 [KO:K12611] [EC:3.-.-.-]
108474183  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
108489564  mRNA-decapping enzyme subunit 2 [KO:K12613] [EC:3.6.1.62]
108469592  DEAD-box ATP-dependent RNA helicase 8-like [KO:K12614] [EC:5.6.2.7]
108467409  DEAD-box ATP-dependent RNA helicase 8 [KO:K12614] [EC:5.6.2.7]
108473420  DEAD-box ATP-dependent RNA helicase 8 [KO:K12614] [EC:5.6.2.7]
108455564  DEAD-box ATP-dependent RNA helicase 8-like [KO:K12614] [EC:5.6.2.7]
108469700  LOW QUALITY PROTEIN: enhancer of mRNA-decapping protein 4 [KO:K12616]
108456702  enhancer of mRNA-decapping protein 4-like isoform X1 [KO:K12616]
108476217  protein PAT1 homolog 1-like [KO:K12617]
108473532  uncharacterized protein LOC108473532 isoform X1 [KO:K12617]
108455165  protein PAT1 homolog 1-like [KO:K12617]
108453802  uncharacterized protein LOC108453802 [KO:K12617]
108463965  uncharacterized protein LOC108463965 isoform X1 [KO:K12617]
108463939  protein PAT1 homolog 1-like isoform X1 [KO:K12617]
108453346  5'-3' exoribonuclease 3-like isoform X1 [KO:K12619] [EC:3.1.13.-]
108483939  sm-like protein LSM1B isoform X1 [KO:K12620]
108487324  sm-like protein LSM1A [KO:K12620]
108452019  sm-like protein LSM1B [KO:K12620]
108453260  sm-like protein LSM1B [KO:K12620]
108473953  sm-like protein LSM2 [KO:K12621]
108461891  sm-like protein LSM2 [KO:K12621]
108480777  sm-like protein LSM3B [KO:K12622]
108487517  sm-like protein LSM3A [KO:K12622]
108479757  sm-like protein LSM4 [KO:K12623]
108467958  sm-like protein LSM4 [KO:K12623]
108488428  sm-like protein LSM5 [KO:K12624]
108482296  sm-like protein LSM5 [KO:K12624]
108474816  sm-like protein LSM36B isoform X1 [KO:K12625]
108454836  sm-like protein LSM36B [KO:K12625]
108467904  sm-like protein LSM7 [KO:K12626]
108480352  sm-like protein LSM8 [KO:K12627]
108478324  sm-like protein LSM8 isoform X1 [KO:K12627]
108467171  enolase [KO:K01689] [EC:4.2.1.11]
108473985  enolase 1, chloroplastic [KO:K01689] [EC:4.2.1.11]
108484057  cytosolic enolase 3 [KO:K01689] [EC:4.2.1.11]
108449952  enolase [KO:K01689] [EC:4.2.1.11]
108454026  enolase-like [KO:K01689] [EC:4.2.1.11]
108459500  enolase-like [KO:K01689] [EC:4.2.1.11]
108473383  probable polyribonucleotide nucleotidyltransferase 1, chloroplastic [KO:K00962] [EC:2.7.7.8]
108454078  polyribonucleotide nucleotidyltransferase 2, mitochondrial [KO:K00962] [EC:2.7.7.8]
108466449  ATP-dependent 6-phosphofructokinase 4, chloroplastic [KO:K00850] [EC:2.7.1.11]
108485440  ATP-dependent 6-phosphofructokinase 3 isoform X1 [KO:K00850] [EC:2.7.1.11]
108486422  ATP-dependent 6-phosphofructokinase 3-like [KO:K00850] [EC:2.7.1.11]
108486656  ATP-dependent 6-phosphofructokinase 3 [KO:K00850] [EC:2.7.1.11]
108461379  ATP-dependent 6-phosphofructokinase 5, chloroplastic [KO:K00850] [EC:2.7.1.11]
108462462  ATP-dependent 6-phosphofructokinase 3-like [KO:K00850] [EC:2.7.1.11]
108459956  ATP-dependent 6-phosphofructokinase 6-like [KO:K00850] [EC:2.7.1.11]
108453724  ATP-dependent 6-phosphofructokinase 2 [KO:K00850] [EC:2.7.1.11]
108479206  heat shock 70 kDa protein, mitochondrial isoform X1 [KO:K04043]
108479482  heat shock 70 kDa protein, mitochondrial-like [KO:K04043]
108454207  heat shock 70 kDa protein, mitochondrial-like [KO:K04043]
108456692  chaperonin CPN60-2, mitochondrial [KO:K04077] [EC:5.6.1.7]
108456693  chaperonin CPN60-2, mitochondrial-like [KO:K04077] [EC:5.6.1.7]
108489270  chaperonin 60 subunit beta 2, chloroplastic [KO:K04077] [EC:5.6.1.7]
108486980  chaperonin CPN60-2, mitochondrial-like [KO:K04077] [EC:5.6.1.7]
108460934  chaperonin 60 subunit beta 4, chloroplastic [KO:K04077] [EC:5.6.1.7]
108452251  chaperonin CPN60-like 2, mitochondrial [KO:K04077] [EC:5.6.1.7]
108453550  ruBisCO large subunit-binding protein subunit beta, chloroplastic-like [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
gab03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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