KEGG   PATHWAY: gra03018
Entry
gra03018                    Pathway                                
Name
RNA degradation - Gossypium raimondii
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
gra03018  RNA degradation
gra03018

Other DBs
GO: 0006401
Organism
Gossypium raimondii [GN:gra]
Gene
105782559  uncharacterized protein LOC105782559 [KO:K07573]
105785382  exosome complex component RRP4 homolog [KO:K03679]
105777669  exosome complex component RRP4 homolog [KO:K03679]
105794144  uncharacterized protein LOC105794144 [KO:K03681]
105773471  LOW QUALITY PROTEIN: uncharacterized protein LOC105773471 [KO:K12586]
105783619  uncharacterized protein LOC105783619 [KO:K12586]
105767927  exosome complex component RRP41-like [KO:K12587]
105780770  uncharacterized protein LOC105780770 [KO:K12589]
105802766  exosome complex component RRP41 homolog [KO:K11600]
105774485  exosome complex exonuclease RRP46 homolog isoform X1 [KO:K12590]
105784099  exosome complex exonuclease RRP46 homolog [KO:K12590]
105787930  exosome complex component RRP45A isoform X1 [KO:K03678]
105799383  exosome complex component RRP45B [KO:K03678]
105800686  exosome complex exonuclease RRP44 homolog A [KO:K12585] [EC:3.1.13.-]
105783258  protein RRP6-like 2 isoform X1 [KO:K12591] [EC:3.1.13.-]
105783321  protein RRP6-like 2 isoform X1 [KO:K12591] [EC:3.1.13.-]
105804420  protein RRP6-like 2 [KO:K12591] [EC:3.1.13.-]
105768374  uncharacterized protein LOC105768374 [KO:K12592]
105788809  uncharacterized protein LOC105788809 [KO:K12593]
105770854  uncharacterized protein LOC105770854 [KO:K12593]
105779107  uncharacterized protein LOC105779107 [KO:K03514] [EC:2.7.7.19]
105773245  DExH-box ATP-dependent RNA helicase DExH9 [KO:K12598] [EC:5.6.2.6]
105782109  DExH-box ATP-dependent RNA helicase DExH10 [KO:K12598] [EC:5.6.2.6]
105788733  DExH-box ATP-dependent RNA helicase DExH11 isoform X1 [KO:K12599] [EC:5.6.2.6]
105768756  tetratricopeptide repeat protein SKI3 [KO:K12600]
105794320  WD repeat-containing protein VIP3 [KO:K12602]
105774037  WD repeat-containing protein VIP3 [KO:K12602]
105786258  carbon catabolite repressor protein 4 homolog 1 isoform X1 [KO:K12603] [EC:3.1.13.4]
105764920  carbon catabolite repressor protein 4 homolog 4 [KO:K12603] [EC:3.1.13.4]
105766561  carbon catabolite repressor protein 4 homolog 1 isoform X1 [KO:K12603] [EC:3.1.13.4]
105799566  carbon catabolite repressor protein 4 homolog 1 [KO:K12603] [EC:3.1.13.4]
105763730  uncharacterized protein LOC105763730 isoform X1 [KO:K12604]
105802567  uncharacterized protein LOC105802567 isoform X1 [KO:K12604]
105789958  probable NOT transcription complex subunit VIP2 isoform X1 [KO:K12605]
105782809  probable NOT transcription complex subunit VIP2 isoform X1 [KO:K12605]
105767823  probable NOT transcription complex subunit VIP2 isoform X1 [KO:K12605]
105782729  general negative regulator of transcription subunit 3 isoform X1 [KO:K12580]
105804746  uncharacterized protein LOC105804746 isoform X1 [KO:K12580]
105790805  uncharacterized protein LOC105790805 isoform X1 [KO:K10643] [EC:2.3.2.27]
105789947  uncharacterized protein LOC105789947 isoform X1 [KO:K10643] [EC:2.3.2.27]
105782867  uncharacterized protein LOC105782867 [KO:K10643] [EC:2.3.2.27]
105769348  uncharacterized protein LOC105769348 isoform X1 [KO:K10643] [EC:2.3.2.27]
105773080  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
105767142  uncharacterized protein LOC105767142 isoform X1 [KO:K12581]
105792889  probable CCR4-associated factor 1 homolog 9 [KO:K12581]
105790035  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
105796010  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
105795299  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
105796231  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
105773890  probable CCR4-associated factor 1 homolog 6 [KO:K12581]
105774189  probable CCR4-associated factor 1 homolog 6 [KO:K12581]
105779138  LOW QUALITY PROTEIN: probable CCR4-associated factor 1 homolog 11 [KO:K12581]
105779139  LOW QUALITY PROTEIN: probable CCR4-associated factor 1 homolog 11 [KO:K12581]
105779142  LOW QUALITY PROTEIN: probable CCR4-associated factor 1 homolog 11 [KO:K12581]
105775744  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
105768961  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
105773639  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
105799243  probable CCR4-associated factor 1 homolog 9 [KO:K12581]
105761724  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
128031856  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
105802340  cell differentiation protein rcd1 [KO:K12606]
105802366  cell differentiation protein rcd1 isoform X2 [KO:K12606]
105764354  cell differentiation protein rcd1 [KO:K12606]
105773866  uncharacterized protein LOC105773866 isoform X1 [KO:K12606]
105783189  uncharacterized protein LOC105783189 isoform X1 [KO:K12606]
128042481  uncharacterized protein LOC128042481 [KO:K12606]
105791028  uncharacterized protein LOC105791028 isoform X3 [KO:K12607]
105773327  uncharacterized protein LOC105773327 isoform X1 [KO:K12607]
105783076  uncharacterized protein LOC105783076 isoform X1 [KO:K12607]
105767860  ABC transporter I family member 21 [KO:K12608]
105761826  ABC transporter I family member 20 [KO:K12608]
105794788  DExH-box ATP-dependent RNA helicase DExH5, mitochondrial isoform X1 [KO:K14442] [EC:5.6.2.6]
105766574  DExH-box ATP-dependent RNA helicase DExH1 isoform X1 [KO:K14442] [EC:5.6.2.6]
105780208  DExH-box ATP-dependent RNA helicase DExH3 isoform X1 [KO:K14442] [EC:5.6.2.6]
105801732  DExH-box ATP-dependent RNA helicase DExH3 isoform X1 [KO:K14442] [EC:5.6.2.6]
105779903  DExH-box ATP-dependent RNA helicase DExH6 [KO:K14442] [EC:5.6.2.6]
105781864  poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
105803347  poly(A)-specific ribonuclease PARN-like [KO:K01148] [EC:3.1.13.4]
105795234  polyadenylate-binding protein 8 [KO:K13126]
105797316  polyadenylate-binding protein 2 [KO:K13126]
105761788  polyadenylate-binding protein 7 [KO:K13126]
105802224  polyadenylate-binding protein 2 isoform X1 [KO:K13126]
105770406  30S ribosomal protein 2, chloroplastic [KO:K13126]
105777381  polyadenylate-binding protein 6 [KO:K13126]
105773928  polyadenylate-binding protein 3 [KO:K13126]
105769251  polyadenylate-binding protein 2 [KO:K13126]
105782111  polyadenylate-binding protein 8 [KO:K13126]
105773252  polyadenylate-binding protein 2 [KO:K13126]
105767704  polyadenylate-binding protein 7 [KO:K13126]
105790032  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
105799646  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
105761733  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
105776314  mRNA-decapping enzyme subunit 2 [KO:K12613] [EC:3.6.1.62]
105797129  DEAD-box ATP-dependent RNA helicase 8 [KO:K12614] [EC:5.6.2.7]
105791593  DEAD-box ATP-dependent RNA helicase 8 [KO:K12614] [EC:5.6.2.7]
105790346  DEAD-box ATP-dependent RNA helicase 8 [KO:K12614] [EC:5.6.2.7]
105802677  DEAD-box ATP-dependent RNA helicase 8 [KO:K12614] [EC:5.6.2.7]
105776106  DEAD-box ATP-dependent RNA helicase 8 isoform X1 [KO:K12614] [EC:5.6.2.7]
105790253  enhancer of mRNA-decapping protein 4 [KO:K12616]
105798918  enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
105789562  protein PAT1 homolog 1 [KO:K12617]
105802053  protein PAT1 homolog 1 [KO:K12617]
105792791  protein PAT1 homolog [KO:K12617]
105782399  protein PAT1 homolog [KO:K12617]
105803499  protein PAT1 homolog 1 isoform X1 [KO:K12617]
105786644  protein PAT1 homolog [KO:K12617]
105770030  5'-3' exoribonuclease 3 isoform X1 [KO:K12619] [EC:3.1.13.-]
105796685  sm-like protein LSM1B [KO:K12620]
105773306  sm-like protein LSM1B [KO:K12620]
105770412  sm-like protein LSM1A [KO:K12620]
105768782  sm-like protein LSM1B [KO:K12620]
105790755  sm-like protein LSM2 [KO:K12621]
105803082  sm-like protein LSM2 [KO:K12621]
105777443  sm-like protein LSM3A [KO:K12622]
105770582  sm-like protein LSM3B [KO:K12622]
105790442  sm-like protein LSM4 [KO:K12623]
105764124  sm-like protein LSM4 [KO:K12623]
105798958  sm-like protein LSM5 [KO:K12624]
105803269  sm-like protein LSM5 [KO:K12624]
105796326  sm-like protein LSM36B [KO:K12625]
105800464  sm-like protein LSM36B [KO:K12625]
105790282  sm-like protein LSM7 [KO:K12626]
105780461  sm-like protein LSM8 isoform X2 [KO:K12627]
105761192  sm-like protein LSM8 [KO:K12627]
105783435  enolase [KO:K01689] [EC:4.2.1.11]
105786370  enolase [KO:K01689] [EC:4.2.1.11]
105788505  enolase 1, chloroplastic [KO:K01689] [EC:4.2.1.11]
105783640  cytosolic enolase 3 isoform X2 [KO:K01689] [EC:4.2.1.11]
105799708  enolase [KO:K01689] [EC:4.2.1.11]
105798341  polyribonucleotide nucleotidyltransferase 2, mitochondrial [KO:K00962] [EC:2.7.7.8]
105804403  polyribonucleotide nucleotidyltransferase 1, chloroplastic [KO:K00962] [EC:2.7.7.8]
105785371  ATP-dependent 6-phosphofructokinase 4, chloroplastic isoform X1 [KO:K00850] [EC:2.7.1.11]
105761110  ATP-dependent 6-phosphofructokinase 6 isoform X1 [KO:K00850] [EC:2.7.1.11]
105787828  ATP-dependent 6-phosphofructokinase 5, chloroplastic [KO:K00850] [EC:2.7.1.11]
105789522  LOW QUALITY PROTEIN: ATP-dependent 6-phosphofructokinase 3 [KO:K00850] [EC:2.7.1.11]
105773468  ATP-dependent 6-phosphofructokinase 3 [KO:K00850] [EC:2.7.1.11]
105783109  ATP-dependent 6-phosphofructokinase 3 [KO:K00850] [EC:2.7.1.11]
105769427  ATP-dependent 6-phosphofructokinase 2 [KO:K00850] [EC:2.7.1.11]
105773620  ATP-dependent 6-phosphofructokinase 3 [KO:K00850] [EC:2.7.1.11]
105769815  ATP-dependent 6-phosphofructokinase 3 [KO:K00850] [EC:2.7.1.11]
105762747  heat shock 70 kDa protein, mitochondrial [KO:K04043]
105762749  heat shock 70 kDa protein, mitochondrial isoform X2 [KO:K04043]
128031964  LOW QUALITY PROTEIN: heat shock 70 kDa protein, mitochondrial-like [KO:K04043]
105764858  uncharacterized protein LOC105764858 [KO:K04077] [EC:5.6.1.7]
105767572  chaperonin 60 subunit beta 4, chloroplastic [KO:K04077] [EC:5.6.1.7]
105767724  chaperonin CPN60-like 2, mitochondrial [KO:K04077] [EC:5.6.1.7]
105769476  ruBisCO large subunit-binding protein subunit beta, chloroplastic [KO:K04077] [EC:5.6.1.7]
105776172  chaperonin 60 subunit beta 2, chloroplastic [KO:K04077] [EC:5.6.1.7]
105800341  chaperonin CPN60-2, mitochondrial isoform X1 [KO:K04077] [EC:5.6.1.7]
105803260  chaperonin CPN60-2, 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
gra03015  mRNA surveillance pathway
KO pathway
ko03018   
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