KEGG   PATHWAY: jcu03018
Entry
jcu03018                    Pathway                                
Name
RNA degradation - Jatropha curcas (Barbados nut)
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
jcu03018  RNA degradation
jcu03018

Other DBs
GO: 0006401
Organism
Jatropha curcas (Barbados nut) [GN:jcu]
Gene
105647870  uncharacterized protein LOC105647870 isoform X1 [KO:K07573]
105650044  exosome complex component RRP4 homolog [KO:K03679]
105640387  putative exosome complex component rrp40 [KO:K03681]
105645225  exosome complex component RRP43 [KO:K12586]
105628072  exosome complex component RRP41-like [KO:K12587]
105640895  exosome complex component RRP42 [KO:K12589]
105641504  exosome complex component RRP42 [KO:K12589]
105650443  exosome complex component RRP41 homolog [KO:K11600]
105648217  exosome complex exonuclease RRP46 homolog [KO:K12590]
105636306  exosome complex component RRP45A isoform X2 [KO:K03678]
105628925  exosome complex component RRP45B [KO:K03678]
105628581  exosome complex exonuclease RRP44 homolog A [KO:K12585] [EC:3.1.13.-]
105632591  protein RRP6-like 2 [KO:K12591] [EC:3.1.13.-]
105637544  uncharacterized protein LOC105637544 [KO:K12592]
105629952  uncharacterized protein LOC105629952 [KO:K12593]
105644267  inactive non-canonical poly(A) RNA polymerase protein Trf4-2 [KO:K03514] [EC:2.7.7.19]
105630976  DExH-box ATP-dependent RNA helicase DExH11 [KO:K12599] [EC:5.6.2.6]
105635143  tetratricopeptide repeat protein SKI3 [KO:K12600]
105637923  WD repeat-containing protein VIP3 [KO:K12602]
105648942  carbon catabolite repressor protein 4 homolog 1 [KO:K12603] [EC:3.1.13.4]
105643393  carbon catabolite repressor protein 4 homolog 4 [KO:K12603] [EC:3.1.13.4]
105643175  CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
105628189  probable NOT transcription complex subunit VIP2 isoform X1 [KO:K12605]
105650400  general negative regulator of transcription subunit 3 isoform X1 [KO:K12580]
105628163  uncharacterized protein LOC105628163 [KO:K10643] [EC:2.3.2.27]
105642163  uncharacterized protein LOC105642163 isoform X1 [KO:K10643] [EC:2.3.2.27]
105635844  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
105629080  putative CCR4-associated factor 1 homolog 8 [KO:K12581]
105630324  probable CCR4-associated factor 1 homolog 6 [KO:K12581]
105633493  probable CCR4-associated factor 1 homolog 6 [KO:K12581]
105637570  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
105649118  putative CCR4-associated factor 1 homolog 8 [KO:K12581]
105649120  putative CCR4-associated factor 1 homolog 8 [KO:K12581]
105643945  probable CCR4-associated factor 1 homolog 9 [KO:K12581]
105633494  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
105632997  CCR4-NOT transcription complex subunit 9 [KO:K12606]
105640826  CCR4-NOT transcription complex subunit 9 [KO:K12606]
105641287  CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
105636300  ABC transporter I family member 20 [KO:K12608]
105644518  ABC transporter I family member 21 [KO:K12608]
105636912  DExH-box ATP-dependent RNA helicase DExH5, mitochondrial isoform X1 [KO:K14442] [EC:5.6.2.6]
105637119  DExH-box ATP-dependent RNA helicase DExH3 [KO:K14442] [EC:5.6.2.6]
105635804  DExH-box ATP-dependent RNA helicase DExH1 isoform X1 [KO:K14442] [EC:5.6.2.6]
105640444  DExH-box ATP-dependent RNA helicase DExH3 [KO:K14442] [EC:5.6.2.6]
105645327  DExH-box ATP-dependent RNA helicase DExH6 [KO:K14442] [EC:5.6.2.6]
105644153  poly(A)-specific ribonuclease PARN-like isoform X1 [KO:K01148] [EC:3.1.13.4]
105645304  poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
105644861  uncharacterized CRM domain-containing protein At3g25440, chloroplastic isoform X1 [KO:K01148] [EC:3.1.13.4]
105635923  polyadenylate-binding protein 3 [KO:K13126]
105631520  polyadenylate-binding protein 6 isoform X1 [KO:K13126]
105642321  polyadenylate-binding protein 7 [KO:K13126]
105630930  LOW QUALITY PROTEIN: polyadenylate-binding protein 2 [KO:K13126]
105639743  polyadenylate-binding protein 4 [KO:K13126]
105639744  polyadenylate-binding protein 4 [KO:K13126]
105635881  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
105643012  DEAD-box ATP-dependent RNA helicase 8 [KO:K12614] [EC:5.6.2.7]
105642128  enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
105639151  enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
105646216  protein PAT1 homolog isoform X1 [KO:K12617]
105646218  protein PAT1 homolog isoform X1 [KO:K12617]
105650094  protein PAT1 homolog 2 [KO:K12617]
105635361  5'-3' exoribonuclease 3 isoform X1 [KO:K12619] [EC:3.1.13.-]
105631370  sm-like protein LSM1B [KO:K12620]
105637986  sm-like protein LSM1B [KO:K12620]
105650034  sm-like protein LSM2 [KO:K12621]
105629113  sm-like protein LSM3A [KO:K12622]
105642505  sm-like protein LSM4 [KO:K12623]
105647497  probable U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
105644417  sm-like protein LSM5 [KO:K12624]
105644477  sm-like protein LSM5 [KO:K12624]
105636672  sm-like protein LSM36B [KO:K12625]
105628682  sm-like protein LSM7 [KO:K12626]
105636398  sm-like protein LSM8 [KO:K12627]
105636400  sm-like protein LSM8 [KO:K12627]
105631045  cytosolic enolase 3 [KO:K01689] [EC:4.2.1.11]
105650621  enolase 1, chloroplastic [KO:K01689] [EC:4.2.1.11]
105648575  enolase [KO:K01689] [EC:4.2.1.11]
105648577  enolase [KO:K01689] [EC:4.2.1.11]
105632574  polyribonucleotide nucleotidyltransferase 1, chloroplastic isoform X1 [KO:K00962] [EC:2.7.7.8]
105641282  polyribonucleotide nucleotidyltransferase 2, mitochondrial [KO:K00962] [EC:2.7.7.8]
105638472  probable ATP-dependent DNA helicase RecQ [KO:K03654] [EC:5.6.2.4]
105636232  ATP-dependent 6-phosphofructokinase 2 [KO:K00850] [EC:2.7.1.11]
105631524  ATP-dependent 6-phosphofructokinase 6 isoform X1 [KO:K00850] [EC:2.7.1.11]
105641667  ATP-dependent 6-phosphofructokinase 5, chloroplastic [KO:K00850] [EC:2.7.1.11]
105637812  ATP-dependent 6-phosphofructokinase 7 [KO:K00850] [EC:2.7.1.11]
105638195  ATP-dependent 6-phosphofructokinase 6 [KO:K00850] [EC:2.7.1.11]
105648651  ATP-dependent 6-phosphofructokinase 4, chloroplastic isoform X1 [KO:K00850] [EC:2.7.1.11]
105636020  heat shock 70 kDa protein, mitochondrial [KO:K04043]
105639933  heat shock 70 kDa protein, mitochondrial [KO:K04043]
105638466  chaperonin CPN60-2, mitochondrial [KO:K04077] [EC:5.6.1.7]
105644437  chaperonin CPN60-2, mitochondrial [KO:K04077] [EC:5.6.1.7]
105640997  chaperonin 60 subunit beta 2, chloroplastic [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
jcu03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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