KEGG   PATHWAY: dsp03018
Entry
dsp03018                    Pathway                                
Name
RNA degradation - Dipodomys spectabilis (banner-tailed kangaroo rat)
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
dsp03018  RNA degradation
dsp03018

Other DBs
GO: 0006401
Organism
Dipodomys spectabilis (banner-tailed kangaroo rat) [GN:dsp]
Gene
122095262  Xrn1; 5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
122095644  Exosc7; exosome complex component RRP42 [KO:K12589]
122095738  Nudt16; U8 snoRNA-decapping enzyme [KO:K16855] [EC:3.6.1.62 3.6.1.64]
122096046  Xrn2; 5'-3' exoribonuclease 2 isoform X1 [KO:K12619] [EC:3.1.13.-]
122096061  Cnot10; CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
122096395  [KO:K13126]
122096396  [KO:K13126]
122097421  Exosc5; exosome complex component RRP46 [KO:K12590]
122098437  Edc3; enhancer of mRNA-decapping protein 3 isoform X1 [KO:K12615]
122098905  Exosc4; exosome complex component RRP41 [KO:K11600]
122099303  Lsm7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
122099547  Cnot4; CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
122100882  Lsm4; U6 snRNA-associated Sm-like protein LSm4 isoform X1 [KO:K12623]
122100917  Dcp2; m7GpppN-mRNA hydrolase [KO:K12613] [EC:3.6.1.62]
122101127  Mphosph6; M-phase phosphoprotein 6 [KO:K12593]
122101296  Pfkl; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
122101951  Eno2; gamma-enolase [KO:K01689] [EC:4.2.1.11]
122102235  Cnot1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
122102303  Pabpc1; polyadenylate-binding protein 1 [KO:K13126]
122102545  Dcp1b; mRNA-decapping enzyme 1B [KO:K12611] [EC:3.-.-.-]
122103160  [KO:K12592]
122103206  Tob1; protein Tob1 [KO:K14443]
122104200  Dcps; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
122105065  Patl1; protein PAT1 homolog 1 [KO:K12617]
122105550  Btg3; protein BTG3 [KO:K14443]
122106161  Pfkm; ATP-dependent 6-phosphofructokinase, muscle type isoform X1 [KO:K00850] [EC:2.7.1.11]
122106164  Pabpc4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
122106919  Cnot6l; CCR4-NOT transcription complex subunit 6-like isoform X1 [KO:K12603] [EC:3.1.13.4]
122107207  Pabpc5; polyadenylate-binding protein 5 [KO:K13126]
122107418  Cnot9; CCR4-NOT transcription complex subunit 9 [KO:K12606]
122107639  Lsm1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
122108017  Lsm3; U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
122108122  Dcp1a; mRNA-decapping enzyme 1A [KO:K12610] [EC:3.-.-.-]
122108471  [KO:K14443]
122108482  [KO:K14443]
122108484  [KO:K14443]
122108575  Eno3; beta-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
122108957  Exosc2; exosome complex component RRP4 [KO:K03679]
122109548  Btg2; protein BTG2 [KO:K14443]
122110216  Btg4; protein BTG4 [KO:K14443]
122110377  Ddx6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:3.6.4.13]
122110535  C1d; nuclear nucleic acid-binding protein C1D isoform X1 [KO:K12592]
122110668  Cnot3; CCR4-NOT transcription complex subunit 3 isoform X1 [KO:K12580]
122111103  Skiv2l; helicase SKI2W [KO:K12599] [EC:3.6.4.13]
122111289  Lsm2; U6 snRNA-associated Sm-like protein LSm2 [KO:K12621]
122112535  Exosc8; exosome complex component RRP43 isoform X1 [KO:K12586]
122112537  Pan3; PAN2-PAN3 deadenylation complex subunit PAN3 isoform X1 [KO:K12572]
122112569  Dhx36; ATP-dependent DNA/RNA helicase DHX36 [KO:K14442] [EC:3.6.4.13]
122112776  Dis3; exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
122113003  [KO:K00850] [EC:2.7.1.11]
122114512  Dis3l; DIS3-like exonuclease 1 [KO:K18681] [EC:3.1.13.-]
122115027  Hspd1; 60 kDa heat shock protein, mitochondrial [KO:K04077] [EC:5.6.1.7]
122115376  Cnot6; CCR4-NOT transcription complex subunit 6 isoform X1 [KO:K12603] [EC:3.1.13.4]
122115809  Exosc1; exosome complex component CSL4 isoform X1 [KO:K07573]
122116104  Pnldc1; poly(A)-specific ribonuclease PNLDC1 [KO:K01148] [EC:3.1.13.4]
122117125  Mtrex; exosome RNA helicase MTR4 [KO:K12598] [EC:3.6.4.13]
122117354  Ttc37; tetratricopeptide repeat protein 37 [KO:K12600]
122117447  Pnpt1; polyribonucleotide nucleotidyltransferase 1, mitochondrial [KO:K00962] [EC:2.7.7.8]
122118071  Hspa9; stress-70 protein, mitochondrial [KO:K04043]
122119060  Exosc9; exosome complex component RRP45 [KO:K03678]
122119125  Btg1; protein BTG1 [KO:K14443]
122119274  [KO:K12624]
122119368  Tent4b; terminal nucleotidyltransferase 4B isoform X1 [KO:K03514] [EC:2.7.7.19]
122120311  Pabpc1l; polyadenylate-binding protein 1-like isoform X1 [KO:K13126]
122120832  Lsm5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
122121005  Tent4a; terminal nucleotidyltransferase 4A isoform X1 [KO:K03514] [EC:2.7.7.19]
122121490  Exosc10; exosome component 10 [KO:K12591] [EC:3.1.13.-]
122121496  Eno1; alpha-enolase [KO:K01689] [EC:4.2.1.11]
122121564  Zcchc7; zinc finger CCHC domain-containing protein 7 isoform X1 [KO:K12597]
122121832  Lsm8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
122121944  Exosc3; exosome complex component RRP40 [KO:K03681]
122123273  Cnot8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
122123385  Wdr61; WD repeat-containing protein 61 isoform X1 [KO:K12602]
122123600  Tob2; protein Tob2 [KO:K14443]
122123871  Parn; poly(A)-specific ribonuclease PARN [KO:K01148] [EC:3.1.13.4]
122124041  Cnot2; CCR4-NOT transcription complex subunit 2 isoform X1 [KO:K12605]
122124064  Pan2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
122126076  Exosc6; exosome complex component MTR3 [KO:K12587]
122126143  Edc4; enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
122127140  Lsm6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
122127578  Cnot7; CCR4-NOT transcription complex subunit 7 isoform X1 [KO:K12581]
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
dsp03015  mRNA surveillance pathway
KO pathway
ko03018   

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