KEGG   PATHWAY: dle03018
Entry
dle03018                    Pathway                                
Name
RNA degradation - Delphinapterus leucas (beluga whale)
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
dle03018  RNA degradation
dle03018

Other DBs
GO: 0006401
Organism
Delphinapterus leucas (beluga whale) [GN:dle]
Gene
111165468  DCPS; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
111172446  EXOSC1; exosome complex component CSL4 isoform X1 [KO:K07573]
111177119  EXOSC2; exosome complex component RRP4 [KO:K03679]
111188050  EXOSC3; exosome complex component RRP40 [KO:K03681]
111175253  exosome complex component RRP43 [KO:K12586]
111175254  exosome complex component RRP43 [KO:K12586]
111179524  EXOSC6; exosome complex component MTR3 [KO:K12587]
111174494  EXOSC7; exosome complex component RRP42 isoform X1 [KO:K12589]
111165131  EXOSC4; exosome complex component RRP41 [KO:K11600]
111180822  EXOSC5; exosome complex component RRP46 isoform X1 [KO:K12590]
111186071  EXOSC9; exosome complex component RRP45 [KO:K03678]
111176494  DIS3; exosome complex exonuclease RRP44 isoform X1 [KO:K12585] [EC:3.1.13.-]
111187183  EXOSC10; exosome component 10 [KO:K12591] [EC:3.1.13.-]
111186546  C1D; nuclear nucleic acid-binding protein C1D [KO:K12592]
111179460  MPHOSPH6; M-phase phosphoprotein 6 isoform X1 [KO:K12593]
111177741  DIS3L; DIS3-like exonuclease 1 isoform X1 [KO:K18681] [EC:3.1.13.-]
111178555  TENT4A; terminal nucleotidyltransferase 4A [KO:K03514] [EC:2.7.7.19]
111165005  TENT4B; terminal nucleotidyltransferase 4B isoform X1 [KO:K03514] [EC:2.7.7.19]
111188000  ZCCHC7; zinc finger CCHC domain-containing protein 7 [KO:K12597]
111186665  MTREX; exosome RNA helicase MTR4 [KO:K12598] [EC:5.6.2.6]
111170702  SKIV2L; helicase SKI2W [KO:K12599] [EC:5.6.2.6]
111184251  TTC37; tetratricopeptide repeat protein 37 isoform X1 [KO:K12600]
111177874  WDR61; WD repeat-containing protein 61 [KO:K12602]
111187650  CNOT6L; CCR4-NOT transcription complex subunit 6-like isoform X1 [KO:K12603] [EC:3.1.13.4]
111170901  CNOT6; CCR4-NOT transcription complex subunit 6 isoform X1 [KO:K12603] [EC:3.1.13.4]
111165326  CNOT1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
111173748  CNOT2; CCR4-NOT transcription complex subunit 2 isoform X1 [KO:K12605]
111180977  CNOT3; CCR4-NOT transcription complex subunit 3 isoform X1 [KO:K12580]
111178031  CNOT4; CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
111183141  CNOT8; CCR4-NOT transcription complex subunit 8 isoform X1 [KO:K12581]
111173449  CNOT7; CCR4-NOT transcription complex subunit 7 [KO:K12581]
111171830  CNOT9; CCR4-NOT transcription complex subunit 9 [KO:K12606]
111164259  CNOT10; CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
111179327  DHX36; ATP-dependent DNA/RNA helicase DHX36 isoform X1 [KO:K14442] [EC:5.6.2.6]
111167578  PNLDC1; poly(A)-specific ribonuclease PNLDC1 [KO:K01148] [EC:3.1.13.4]
111163471  PARN; poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
111186334  TOB2; protein Tob2 [KO:K14443]
111175540  BTG3; protein BTG3 isoform X1 [KO:K14443]
111168052  BTG4; protein BTG4 [KO:K14443]
111166397  TOB1; protein Tob1 [KO:K14443]
111183874  protein Tob1-like [KO:K14443]
111184802  BTG2; protein BTG2 [KO:K14443]
111163579  BTG1; protein BTG1 [KO:K14443]
111165903  PABPC4L; polyadenylate-binding protein 4-like [KO:K13126]
111169266  LOW QUALITY PROTEIN: polyadenylate-binding protein 4-like [KO:K13126]
111178167  PABPC5; polyadenylate-binding protein 5 [KO:K13126]
111171014  polyadenylate-binding protein 1-like 2 [KO:K13126]
111175629  PABPC4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
111184143  polyadenylate-binding protein 1-like [KO:K13126]
111184272  polyadenylate-binding protein 1-like [KO:K13126]
111180377  PABPC1; polyadenylate-binding protein 1 [KO:K13126]
111173870  PAN2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
111175186  PAN3; PAN2-PAN3 deadenylation complex subunit PAN3 isoform X1 [KO:K12572]
111174282  DCP1A; mRNA-decapping enzyme 1A [KO:K12610] [EC:3.-.-.-]
111176596  DCP1B; mRNA-decapping enzyme 1B [KO:K12611] [EC:3.-.-.-]
111183706  DCP2; m7GpppN-mRNA hydrolase isoform X1 [KO:K12613] [EC:3.6.1.62]
111166863  DDX6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:5.6.2.7]
111177817  EDC3; enhancer of mRNA-decapping protein 3 [KO:K12615]
111179619  EDC4; enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
111183910  PATL1; protein PAT1 homolog 1 [KO:K12617]
111179267  XRN1; 5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
111185048  XRN2; 5'-3' exoribonuclease 2 [KO:K12619] [EC:3.1.13.-]
111168182  NUDT16; U8 snoRNA-decapping enzyme [KO:K16855] [EC:3.6.1.62 3.6.1.64]
111173512  LSM1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
111170689  LSM2; U6 snRNA-associated Sm-like protein LSm2 [KO:K12621]
111168813  LSM3; U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
111166678  LSM4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
111179949  LSM5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
111187730  LSM6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
111166191  LSM7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
111182416  LSM8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
111176699  ENO2; gamma-enolase [KO:K01689] [EC:4.2.1.11]
111185951  ENO3; beta-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
111187129  ENO1; alpha-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
111186513  PNPT1; polyribonucleotide nucleotidyltransferase 1, mitochondrial [KO:K00962] [EC:2.7.7.8]
111186309  PFKL; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
111174038  PFKM; ATP-dependent 6-phosphofructokinase, muscle type isoform X1 [KO:K00850] [EC:2.7.1.11]
111164750  PFKP; ATP-dependent 6-phosphofructokinase, platelet type isoform X1 [KO:K00850] [EC:2.7.1.11]
111182501  HSPA9; stress-70 protein, mitochondrial [KO:K04043]
111171694  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
dle03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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