KEGG   PATHWAY: hcg03018
Entry
hcg03018                    Pathway                                
Name
RNA degradation - Hemicordylus capensis (graceful crag lizard)
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
hcg03018  RNA degradation
hcg03018

Other DBs
GO: 0006401
Organism
Hemicordylus capensis (graceful crag lizard) [GN:hcg]
Gene
128334037  DCPS; m7GpppX diphosphatase isoform X1 [KO:K12584] [EC:3.6.1.59]
128352171  EXOSC1; exosome complex component CSL4 [KO:K07573]
128339089  EXOSC2; exosome complex component RRP4 isoform X1 [KO:K03679]
128350779  EXOSC3; exosome complex component RRP40 [KO:K03681]
128347089  EXOSC8; exosome complex component RRP43 [KO:K12586]
128338808  EXOSC6; exosome complex component MTR3 [KO:K12587]
128329330  EXOSC7; exosome complex component RRP42 [KO:K12589]
128324035  EXOSC4; exosome complex component RRP41 [KO:K11600]
128332617  EXOSC5; exosome complex component RRP46 isoform X1 [KO:K12590]
128328305  EXOSC9; exosome complex component RRP45 isoform X1 [KO:K03678]
128349915  DIS3; exosome complex exonuclease RRP44 isoform X1 [KO:K12585] [EC:3.1.13.-]
128338430  EXOSC10; exosome component 10 isoform X1 [KO:K12591] [EC:3.1.13.-]
128340398  C1D; nuclear nucleic acid-binding protein C1D isoform X1 [KO:K12592]
128334522  MPHOSPH6; M-phase phosphoprotein 6 [KO:K12593]
128334827  DIS3L; DIS3-like exonuclease 1 isoform X1 [KO:K18681] [EC:3.1.13.-]
128334275  TENT4B; terminal nucleotidyltransferase 4B [KO:K03514] [EC:2.7.7.19]
128324453  TENT4A; terminal nucleotidyltransferase 4A isoform X1 [KO:K03514] [EC:2.7.7.19]
128343006  ZCCHC7; zinc finger CCHC domain-containing protein 7 [KO:K12597]
128341742  MTREX; exosome RNA helicase MTR4 [KO:K12598] [EC:5.6.2.6]
128346777  SKIC2; SKI2 subunit of superkiller complex protein isoform X1 [KO:K12599] [EC:5.6.2.6]
128344895  SKIC3; SKI3 subunit of superkiller complex protein [KO:K12600]
128335104  SKIC8; SKI8 subunit of superkiller complex protein [KO:K12602]
128327060  CNOT6L; CCR4-NOT transcription complex subunit 6-like isoform X1 [KO:K12603] [EC:3.1.13.4]
128343526  CNOT6; CCR4-NOT transcription complex subunit 6 isoform X1 [KO:K12603] [EC:3.1.13.4]
128334277  CNOT1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
128326398  CNOT2; CCR4-NOT transcription complex subunit 2 isoform X1 [KO:K12605]
128329425  CNOT3; CCR4-NOT transcription complex subunit 3 isoform X1 [KO:K12580]
128327630  CNOT4; CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
128325746  CNOT7; CCR4-NOT transcription complex subunit 7 isoform X1 [KO:K12581]
128342945  CNOT8; CCR4-NOT transcription complex subunit 8 isoform X1 [KO:K12581]
128340932  CNOT9; CCR4-NOT transcription complex subunit 9 isoform X1 [KO:K12606]
128330321  CNOT10; CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
128350867  DHX36; ATP-dependent DNA/RNA helicase DHX36 isoform X1 [KO:K14442] [EC:5.6.2.6]
128344448  PNLDC1; poly(A)-specific ribonuclease PNLDC1 isoform X1 [KO:K01148] [EC:3.1.13.4]
128336713  PARN; poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
128324636  BTG2; protein BTG2 [KO:K14443]
128348205  protein BTG1-like [KO:K14443]
128333560  BTG4; protein BTG4 [KO:K14443]
128327228  TOB2; protein Tob2 [KO:K14443]
128327845  BTG1; protein BTG1 [KO:K14443]
128347229  TOB1; protein Tob1 [KO:K14443]
128332986  PABPC4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
128325261  PABPC1L; polyadenylate-binding protein 1-like isoform X1 [KO:K13126]
128321951  PABPC1; polyadenylate-binding protein 1 isoform X1 [KO:K13126]
128345232  PAN2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
128349438  PAN3; PAN2-PAN3 deadenylation complex subunit PAN3 isoform X1 [KO:K12572]
128345821  DCP1A; mRNA-decapping enzyme 1A isoform X1 [KO:K12610] [EC:3.-.-.-]
128326988  DCP1B; mRNA-decapping enzyme 1B isoform X1 [KO:K12611] [EC:3.-.-.-]
128344620  DCP2; m7GpppN-mRNA hydrolase isoform X1 [KO:K12613] [EC:3.6.1.62]
128333669  DDX6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:5.6.2.7]
128335113  EDC3; enhancer of mRNA-decapping protein 3 isoform X1 [KO:K12615]
128334525  EDC4; enhancer of mRNA-decapping protein 4 [KO:K12616]
128351595  PATL1; protein PAT1 homolog 1 isoform X1 [KO:K12617]
128349829  XRN1; 5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
128323293  XRN2; 5'-3' exoribonuclease 2 isoform X1 [KO:K12619] [EC:3.1.13.-]
128346821  U8 snoRNA-decapping enzyme-like [KO:K16855] [EC:3.6.1.62 3.6.1.64]
128333493  LSM1; U6 snRNA-associated Sm-like protein LSm1 isoform X1 [KO:K12620]
128347131  LSM2; U6 snRNA-associated Sm-like protein LSm2 [KO:K12621]
128344928  LSM3; U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
128343172  LSM4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
128331561  LSM5; U6 snRNA-associated Sm-like protein LSm5 isoform X1 [KO:K12624]
128327017  LSM6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
128345278  LSM7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
128326612  U6 snRNA-associated Sm-like protein LSm8 [KO:K12627]
128327014  U6 snRNA-associated Sm-like protein LSm8 [KO:K12627]
128342824  ENO2; gamma-enolase [KO:K01689] [EC:4.2.1.11]
128329053  ENO3; beta-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
128338409  ENO1; alpha-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
128323377  PNPT1; polyribonucleotide nucleotidyltransferase 1, mitochondrial isoform X1 [KO:K00962] [EC:2.7.7.8]
128342987  PFKM; ATP-dependent 6-phosphofructokinase, muscle type isoform X1 [KO:K00850] [EC:2.7.1.11]
128350866  PFKL; ATP-dependent 6-phosphofructokinase, liver type isoform X1 [KO:K00850] [EC:2.7.1.11]
128329527  PFKP; ATP-dependent 6-phosphofructokinase, platelet type isoform X1 [KO:K00850] [EC:2.7.1.11]
128340125  HSPA9; stress-70 protein, mitochondrial isoform X1 [KO:K04043]
128337047  HSPD1; 60 kDa heat shock protein, mitochondrial [KO:K04077] [EC:5.6.1.7]
Reference
PMID:19239894
  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
PMID:16968219
  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
PMID:16939780
  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
PMID:17471261
  Authors
Hartung S, Hopfner KP
  Title
The exosome, plugged.
  Journal
EMBO Rep 8:456-7 (2007)
DOI:10.1038/sj.embor.7400961
Reference
PMID:17447862
  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
PMID:16766188
  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
PMID:17560162
  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
hcg03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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