KEGG   PATHWAY: cpic03018
Entry
cpic03018                   Pathway                                
Name
RNA degradation - Chrysemys picta (western painted turtle)
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
cpic03018  RNA degradation
cpic03018

Other DBs
GO: 0006401
Organism
Chrysemys picta (western painted turtle) [GN:cpic]
Gene
101942376  DCPS; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
101943367  EXOSC1; exosome complex component CSL4 [KO:K07573]
101935645  EXOSC2; exosome complex component RRP4 [KO:K03679]
101934130  EXOSC3; exosome complex component RRP40 [KO:K03681]
101947816  EXOSC8; exosome complex component RRP43 [KO:K12586]
101934253  EXOSC7; exosome complex component RRP42 [KO:K12589]
101944807  EXOSC4; exosome complex component RRP41 [KO:K11600]
101945065  EXOSC5; exosome complex component RRP46 [KO:K12590]
101941916  EXOSC9; exosome complex component RRP45 [KO:K03678]
101940775  DIS3; exosome complex exonuclease RRP44 isoform X1 [KO:K12585] [EC:3.1.13.-]
101950117  EXOSC10; exosome component 10 [KO:K12591] [EC:3.1.13.-]
101949435  C1D; nuclear nucleic acid-binding protein C1D [KO:K12592]
101932233  MPHOSPH6; M-phase phosphoprotein 6 [KO:K12593]
101950435  DIS3L; DIS3-like exonuclease 1 isoform X1 [KO:K18681] [EC:3.1.13.-]
101949816  TENT4B; terminal nucleotidyltransferase 4B isoform X1 [KO:K03514] [EC:2.7.7.19]
101952679  TENT4A; LOW QUALITY PROTEIN: terminal nucleotidyltransferase 4A [KO:K03514] [EC:2.7.7.19]
101937250  ZCCHC7; zinc finger CCHC domain-containing protein 7 [KO:K12597]
101933895  MTREX; exosome RNA helicase MTR4 [KO:K12598] [EC:5.6.2.6]
101946235  SKIV2L; helicase SKI2W [KO:K12599] [EC:5.6.2.6]
101931245  TTC37; tetratricopeptide repeat protein 37 isoform X2 [KO:K12600]
101950606  WDR61; WD repeat-containing protein 61 [KO:K12602]
101940954  CNOT6L; CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
101951072  CNOT6; CCR4-NOT transcription complex subunit 6 isoform X1 [KO:K12603] [EC:3.1.13.4]
101948832  CNOT1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
101943867  CNOT2; CCR4-NOT transcription complex subunit 2 isoform X2 [KO:K12605]
101939066  CNOT3; CCR4-NOT transcription complex subunit 3 isoform X4 [KO:K12580]
101949253  CNOT4; CCR4-NOT transcription complex subunit 4 isoform X2 [KO:K10643] [EC:2.3.2.27]
101949164  CNOT7; CCR4-NOT transcription complex subunit 7 isoform X1 [KO:K12581]
101931779  CNOT8; CCR4-NOT transcription complex subunit 8 isoform X1 [KO:K12581]
101950710  CNOT9; CCR4-NOT transcription complex subunit 9 isoform X1 [KO:K12606]
101933991  CNOT10; CCR4-NOT transcription complex subunit 10 isoform X3 [KO:K12607]
101932571  DHX36; ATP-dependent DNA/RNA helicase DHX36 [KO:K14442] [EC:5.6.2.6]
101945694  PARN; poly(A)-specific ribonuclease PARN isoform X2 [KO:K01148] [EC:3.1.13.4]
101944137  PNLDC1; poly(A)-specific ribonuclease PNLDC1 isoform X1 [KO:K01148] [EC:3.1.13.4]
101953478  protein BTG1-like [KO:K14443]
101942360  BTG4; protein BTG4 [KO:K14443]
101941502  TOB2; protein Tob2 [KO:K14443]
101935111  BTG1; protein BTG1 [KO:K14443]
101938878  BTG2; protein BTG2 [KO:K14443]
101953271  TOB1; protein Tob1 [KO:K14443]
101948320  PABPC4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
101951430  PABPC1L; polyadenylate-binding protein 1-like isoform X1 [KO:K13126]
101935964  PABPC1; polyadenylate-binding protein 1 isoform X1 [KO:K13126]
101938970  PAN2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
101943897  PAN3; PAN2-PAN3 deadenylation complex subunit PAN3 isoform X5 [KO:K12572]
101952415  DCP1A; mRNA-decapping enzyme 1A [KO:K12610] [EC:3.-.-.-]
101932401  mRNA-decapping enzyme 1B isoform X1 [KO:K12611] [EC:3.-.-.-]
101950053  DCP2; m7GpppN-mRNA hydrolase isoform X3 [KO:K12613] [EC:3.6.1.62]
101944918  DDX6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:5.6.2.7]
101945059  EDC3; enhancer of mRNA-decapping protein 3 [KO:K12615]
101935780  EDC4; enhancer of mRNA-decapping protein 4 [KO:K12616]
101950630  PATL1; protein PAT1 homolog 1 isoform X2 [KO:K12617]
101931509  XRN1; 5'-3' exoribonuclease 1 [KO:K12618] [EC:3.1.13.-]
101947639  XRN2; 5'-3' exoribonuclease 2 [KO:K12619] [EC:3.1.13.-]
101939820  U8 snoRNA-decapping enzyme [KO:K16855] [EC:3.6.1.62 3.6.1.64]
101948934  LSM3; U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
101943314  LSM4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
101950419  LSM5; U6 snRNA-associated Sm-like protein LSm5 isoform X1 [KO:K12624]
101946853  uncharacterized protein LOC101946853 [KO:K12624]
101940870  LSM6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
101947072  LSM7; U6 snRNA-associated Sm-like protein LSm7 isoform X1 [KO:K12626]
101933023  LSM8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
101940003  ENO2; gamma-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
101936895  ENO1; alpha-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
101947120  beta-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
101937008  PNPT1; polyribonucleotide nucleotidyltransferase 1, mitochondrial [KO:K00962] [EC:2.7.7.8]
101935728  ATP-dependent 6-phosphofructokinase, platelet type isoform X1 [KO:K00850] [EC:2.7.1.11]
101931604  PFKL; ATP-dependent 6-phosphofructokinase, liver type isoform X1 [KO:K00850] [EC:2.7.1.11]
101949044  PFKM; ATP-dependent 6-phosphofructokinase, muscle type isoform X1 [KO:K00850] [EC:2.7.1.11]
101942990  HSPA9; stress-70 protein, mitochondrial [KO:K04043]
101949322  HSPD1; 60 kDa heat shock protein, 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
cpic03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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