KEGG   PATHWAY: ccw03018
Entry
ccw03018                    Pathway                                
Name
RNA degradation - Corvus cornix (hooded crow)
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
ccw03018  RNA degradation
ccw03018

Other DBs
GO: 0006401
Organism
Corvus cornix (hooded crow) [GN:ccw]
Gene
104692219  DCPS; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
104695848  EXOSC1; exosome complex component CSL4 isoform X2 [KO:K07573]
104688473  EXOSC2; exosome complex component RRP4 [KO:K03679]
109144754  EXOSC3; exosome complex component RRP40 [KO:K03681]
104689994  EXOSC8; exosome complex component RRP43 isoform X1 [KO:K12586]
120410592  EXOSC6; LOW QUALITY PROTEIN: exosome complex component MTR3 [KO:K12587]
104689278  EXOSC7; exosome complex component RRP42 [KO:K12589]
120411567  EXOSC5; exosome complex component RRP46 isoform X1 [KO:K12590]
104693688  EXOSC9; exosome complex component RRP45 [KO:K03678]
104693128  DIS3; exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
104693231  EXOSC10; exosome component 10 [KO:K12591] [EC:3.1.13.-]
104696579  C1D; nuclear nucleic acid-binding protein C1D [KO:K12592]
104691829  MPHOSPH6; M-phase phosphoprotein 6 [KO:K12593]
104683881  DIS3L; DIS3-like exonuclease 1 isoform X2 [KO:K18681] [EC:3.1.13.-]
104685871  TENT4A; terminal nucleotidyltransferase 4A isoform X1 [KO:K03514] [EC:2.7.7.19]
104687453  TENT4B; LOW QUALITY PROTEIN: terminal nucleotidyltransferase 4B [KO:K03514] [EC:2.7.7.19]
104695820  ZCCHC7; zinc finger CCHC domain-containing protein 7 isoform X1 [KO:K12597]
104686770  MTREX; exosome RNA helicase MTR4 isoform X1 [KO:K12598] [EC:5.6.2.6]
104685236  TTC37; tetratricopeptide repeat protein 37 [KO:K12600]
104697463  WDR61; WD repeat-containing protein 61 [KO:K12602]
104689593  CNOT6; CCR4-NOT transcription complex subunit 6 isoform X1 [KO:K12603] [EC:3.1.13.4]
104696810  CNOT6L; CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
104687526  CNOT1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
104698384  CNOT2; CCR4-NOT transcription complex subunit 2 [KO:K12605]
104696411  CNOT4; CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
104690605  CNOT7; CCR4-NOT transcription complex subunit 7 [KO:K12581]
104689553  CNOT8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
104694196  CNOT9; CCR4-NOT transcription complex subunit 9 isoform X1 [KO:K12606]
104689290  CNOT10; CCR4-NOT transcription complex subunit 10 isoform X2 [KO:K12607]
104688091  DHX36; LOW QUALITY PROTEIN: ATP-dependent DNA/RNA helicase DHX36 [KO:K14442] [EC:5.6.2.6]
104684717  PARN; poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
104690370  PNLDC1; poly(A)-specific ribonuclease PNLDC1 isoform X4 [KO:K01148] [EC:3.1.13.4]
104692090  BTG4; protein BTG4 [KO:K14443]
104692522  BTG2; protein BTG2 [KO:K14443]
104696349  TOB2; protein Tob2 [KO:K14443]
104698442  BTG1; protein BTG1 [KO:K14443]
104694281  TOB1; protein Tob1 [KO:K14443]
120410663  protein BTG1-like [KO:K14443]
104692715  PABPC1; polyadenylate-binding protein 1 [KO:K13126]
104687757  PABPC1L; polyadenylate-binding protein 1-like [KO:K13126]
104689894  PAN3; PAN2-PAN3 deadenylation complex subunit PAN3 isoform X1 [KO:K12572]
104683256  DCP1A; mRNA-decapping enzyme 1A isoform X1 [KO:K12610] [EC:3.-.-.-]
104692244  DCP1B; mRNA-decapping enzyme 1B isoform X3 [KO:K12611] [EC:3.-.-.-]
104684172  DCP2; m7GpppN-mRNA hydrolase isoform X1 [KO:K12613] [EC:3.6.1.62]
104692040  DDX6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:5.6.2.7]
104697433  EDC3; enhancer of mRNA-decapping protein 3 [KO:K12615]
104691785  EDC4; enhancer of mRNA-decapping protein 4 [KO:K12616]
104684137  PATL1; LOW QUALITY PROTEIN: protein PAT1 homolog 1 [KO:K12617]
104693453  XRN1; 5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
104691474  XRN2; 5'-3' exoribonuclease 2 isoform X1 [KO:K12619] [EC:3.1.13.-]
120412188  U8 snoRNA-decapping enzyme-like isoform X1 [KO:K16855] [EC:3.6.1.62 3.6.1.64]
104694902  LSM1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
104683307  LSM3; U6 snRNA-associated Sm-like protein LSm3 isoform X1 [KO:K12622]
104697381  LSM4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
104690444  LSM5; U6 snRNA-associated Sm-like protein LSm5 isoform X1 [KO:K12624]
104697237  LSM6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
104696970  LSM7; U6 snRNA-associated Sm-like protein LSm7 isoform X1 [KO:K12626]
104698287  LSM8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
104687131  ENO2; gamma-enolase [KO:K01689] [EC:4.2.1.11]
104693328  ENO1; alpha-enolase [KO:K01689] [EC:4.2.1.11]
104691500  PNPT1; polyribonucleotide nucleotidyltransferase 1, mitochondrial [KO:K00962] [EC:2.7.7.8]
104686451  ATP-dependent 6-phosphofructokinase, platelet type isoform X2 [KO:K00850] [EC:2.7.1.11]
104696736  PFKL; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
104696046  HSPA9; stress-70 protein, mitochondrial isoform X1 [KO:K04043]
104693754  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
ccw03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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