KEGG   PATHWAY: egr03018
Entry
egr03018                    Pathway                                
Name
RNA degradation - Eucalyptus grandis (rose gum)
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
egr03018  RNA degradation
egr03018

Other DBs
GO: 0006401
Organism
Eucalyptus grandis (rose gum) [GN:egr]
Gene
104432552  exosome complex component CSL4 [KO:K07573]
104457036  exosome complex component RRP4 homolog [KO:K03679]
104418660  putative exosome complex component rrp40 [KO:K03681]
104432537  exosome complex component RRP43 [KO:K12586]
104432145  LOW QUALITY PROTEIN: exosome complex component RRP43 [KO:K12586]
120292641  LOW QUALITY PROTEIN: exosome complex component RRP43-like [KO:K12586]
104421643  exosome complex component RRP41-like [KO:K12587]
104454005  exosome complex component RRP42 [KO:K12589]
104450961  exosome complex component RRP41 homolog isoform X1 [KO:K11600]
104437777  exosome complex exonuclease RRP46 homolog [KO:K12590]
104414033  LOW QUALITY PROTEIN: exosome complex component RRP45A [KO:K03678]
120287570  exosome complex component RRP45A-like isoform X1 [KO:K03678]
104421073  exosome complex exonuclease RRP44 homolog A [KO:K12585] [EC:3.1.13.-]
104443185  protein RRP6-like 2 isoform X1 [KO:K12591] [EC:3.1.13.-]
104437564  nuclear nucleic acid-binding protein C1D [KO:K12592]
104432711  uncharacterized protein LOC104432711 [KO:K12593]
104448435  terminal nucleotidyltransferase 4B [KO:K03514] [EC:2.7.7.19]
104435888  DExH-box ATP-dependent RNA helicase DExH10 [KO:K12598] [EC:5.6.2.6]
104452464  LOW QUALITY PROTEIN: DExH-box ATP-dependent RNA helicase DExH9 [KO:K12598] [EC:5.6.2.6]
104432671  LOW QUALITY PROTEIN: DExH-box ATP-dependent RNA helicase DExH11 [KO:K12599] [EC:5.6.2.6]
104450366  LOW QUALITY PROTEIN: tetratricopeptide repeat protein SKI3 [KO:K12600]
104438065  WD repeat-containing protein VIP3 [KO:K12602]
104446230  carbon catabolite repressor protein 4 homolog 1 [KO:K12603] [EC:3.1.13.4]
104442335  carbon catabolite repressor protein 4 homolog 4 [KO:K12603] [EC:3.1.13.4]
104425511  carbon catabolite repressor protein 4 homolog 1 [KO:K12603] [EC:3.1.13.4]
104444451  CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
104422534  LOW QUALITY PROTEIN: probable NOT transcription complex subunit VIP2 [KO:K12605]
104442756  general negative regulator of transcription subunit 3 isoform X1 [KO:K12580]
104425248  CCR4-NOT transcription complex subunit 3-like [KO:K12580]
104432833  uncharacterized protein LOC104432833 isoform X1 [KO:K10643] [EC:2.3.2.27]
104422543  uncharacterized protein LOC104422543 isoform X2 [KO:K10643] [EC:2.3.2.27]
104447225  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
104437559  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
104436979  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
104436985  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
104433950  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
104437158  LOW QUALITY PROTEIN: probable CCR4-associated factor 1 homolog 7 [KO:K12581]
104450622  probable CCR4-associated factor 1 homolog 6 [KO:K12581]
104421334  LOW QUALITY PROTEIN: probable CCR4-associated factor 1 homolog 11 [KO:K12581]
104436006  uncharacterized protein LOC104436006 [KO:K12606]
104448204  CCR4-NOT transcription complex subunit 9 [KO:K12606]
104436827  CCR4-NOT transcription complex subunit 10 [KO:K12607]
104431810  ABC transporter I family member 19 [KO:K12608]
104456885  ABC transporter I family member 20 [KO:K12608]
104421971  DExH-box ATP-dependent RNA helicase DExH3 isoform X1 [KO:K14442] [EC:5.6.2.6]
104454062  DExH-box ATP-dependent RNA helicase DExH3 [KO:K14442] [EC:5.6.2.6]
104425567  DExH-box ATP-dependent RNA helicase DExH1 isoform X2 [KO:K14442] [EC:5.6.2.6]
104453748  DExH-box ATP-dependent RNA helicase DExH5, mitochondrial [KO:K14442] [EC:5.6.2.6]
104442350  DExH-box ATP-dependent RNA helicase DExH6 isoform X1 [KO:K14442] [EC:5.6.2.6]
104449117  poly(A)-specific ribonuclease PARN [KO:K01148] [EC:3.1.13.4]
104425678  uncharacterized CRM domain-containing protein At3g25440, chloroplastic isoform X1 [KO:K01148] [EC:3.1.13.4]
104423590  30S ribosomal protein 2, chloroplastic [KO:K13126]
104418709  polyadenylate-binding protein 2 [KO:K13126]
104447874  polyadenylate-binding protein 2 [KO:K13126]
104438776  polyadenylate-binding protein 7 [KO:K13126]
104449933  polyadenylate-binding protein 6 [KO:K13126]
104433958  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
104447428  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
104421790  mRNA-decapping enzyme subunit 2 [KO:K12613] [EC:3.6.1.62]
104442084  DEAD-box ATP-dependent RNA helicase 8 [KO:K12614] [EC:5.6.2.7]
104449088  enhancer of mRNA-decapping protein 4 [KO:K12616]
104425160  protein PAT1 homolog 1 [KO:K12617]
104450018  protein PAT1 homolog [KO:K12617]
104448827  5'-3' exoribonuclease 3 isoform X1 [KO:K12619] [EC:3.1.13.-]
104449390  sm-like protein LSM1B [KO:K12620]
104422972  sm-like protein LSM1B [KO:K12620]
104426693  sm-like protein LSM2 [KO:K12621]
104449601  sm-like protein LSM3B [KO:K12622]
104426751  probable U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
104414977  sm-like protein LSM5 isoform X1 [KO:K12624]
104453287  sm-like protein LSM36B [KO:K12625]
104453285  sm-like protein LSM36B [KO:K12625]
104453291  sm-like protein LSM36B [KO:K12625]
104440627  sm-like protein LSM36B [KO:K12625]
104425185  sm-like protein LSM7 [KO:K12626]
104432840  sm-like protein LSM8 [KO:K12627]
104448228  sm-like protein LSM8 isoform X2 [KO:K12627]
104438557  enolase-like [KO:K01689] [EC:4.2.1.11]
104438537  enolase 1 isoform X1 [KO:K01689] [EC:4.2.1.11]
104421210  enolase 1, chloroplastic [KO:K01689] [EC:4.2.1.11]
104422419  cytosolic enolase 3 [KO:K01689] [EC:4.2.1.11]
104443314  LOW QUALITY PROTEIN: probable polyribonucleotide nucleotidyltransferase 1, chloroplastic [KO:K00962] [EC:2.7.7.8]
104422623  polyribonucleotide nucleotidyltransferase 2, mitochondrial [KO:K00962] [EC:2.7.7.8]
104449962  ATP-dependent 6-phosphofructokinase 4, chloroplastic isoform X1 [KO:K00850] [EC:2.7.1.11]
104437807  ATP-dependent 6-phosphofructokinase 6 [KO:K00850] [EC:2.7.1.11]
104436270  ATP-dependent 6-phosphofructokinase 6 [KO:K00850] [EC:2.7.1.11]
104436541  LOW QUALITY PROTEIN: ATP-dependent 6-phosphofructokinase 3 [KO:K00850] [EC:2.7.1.11]
104440310  ATP-dependent 6-phosphofructokinase 3 [KO:K00850] [EC:2.7.1.11]
104441179  ATP-dependent 6-phosphofructokinase 2 [KO:K00850] [EC:2.7.1.11]
104418330  ATP-dependent 6-phosphofructokinase 5, chloroplastic [KO:K00850] [EC:2.7.1.11]
104419853  LOW QUALITY PROTEIN: heat shock 70 kDa protein, mitochondrial [KO:K04043]
104452953  heat shock 70 kDa protein, mitochondrial [KO:K04043]
120288266  LOW QUALITY PROTEIN: heat shock 70 kDa protein, mitochondrial-like [KO:K04043]
104433762  chaperonin 60 subunit beta 2, chloroplastic [KO:K04077] [EC:5.6.1.7]
104449971  chaperonin CPN60-like 2, mitochondrial [KO:K04077] [EC:5.6.1.7]
104453858  chaperonin 60 subunit beta 4, chloroplastic [KO:K04077] [EC:5.6.1.7]
104414388  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
egr03015  mRNA surveillance pathway
KO pathway
ko03018   

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