KEGG   PATHWAY: nle03018
Entry
nle03018                    Pathway                                
Name
RNA degradation - Nomascus leucogenys (northern white-cheeked gibbon)
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
nle03018  RNA degradation
nle03018

Other DBs
GO: 0006401
Organism
Nomascus leucogenys (northern white-cheeked gibbon) [GN:nle]
Gene
100601639  DCPS; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
100587202  EXOSC1; exosome complex component CSL4 isoform X1 [KO:K07573]
100597051  EXOSC2; exosome complex component RRP4 [KO:K03679]
100580602  EXOSC3; exosome complex component RRP40 isoform X1 [KO:K03681]
100585514  EXOSC8; exosome complex component RRP43 [KO:K12586]
100594136  LOW QUALITY PROTEIN: exosome complex component MTR3 [KO:K12587]
115838603  EXOSC6; exosome complex component MTR3 [KO:K12587]
100602463  EXOSC7; exosome complex component RRP42 isoform X1 [KO:K12589]
100599803  EXOSC4; exosome complex component RRP41 isoform X2 [KO:K11600]
100579732  EXOSC5; exosome complex component RRP46 [KO:K12590]
100587975  EXOSC9; exosome complex component RRP45 [KO:K03678]
100595908  DIS3; exosome complex exonuclease RRP44 isoform X1 [KO:K12585] [EC:3.1.13.-]
100593954  EXOSC10; exosome component 10 [KO:K12591] [EC:3.1.13.-]
100591403  C1D; nuclear nucleic acid-binding protein C1D [KO:K12592]
100589089  MPHOSPH6; M-phase phosphoprotein 6 [KO:K12593]
100607354  DIS3L; DIS3-like exonuclease 1 isoform X1 [KO:K18681] [EC:3.1.13.-]
100588374  TENT4B; terminal nucleotidyltransferase 4B isoform X1 [KO:K03514] [EC:2.7.7.19]
100579823  TENT4A; terminal nucleotidyltransferase 4A [KO:K03514] [EC:2.7.7.19]
100584256  ZCCHC7; zinc finger CCHC domain-containing protein 7 isoform X2 [KO:K12597]
100605886  MTREX; exosome RNA helicase MTR4 isoform X1 [KO:K12598] [EC:5.6.2.6]
100607619  SKIV2L; helicase SKI2W isoform X1 [KO:K12599] [EC:5.6.2.6]
100599679  TTC37; tetratricopeptide repeat protein 37 isoform X1 [KO:K12600]
100607534  WDR61; WD repeat-containing protein 61 [KO:K12602]
100582571  CNOT6; CCR4-NOT transcription complex subunit 6 isoform X1 [KO:K12603] [EC:3.1.13.4]
100606122  CNOT6L; CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
100589604  CNOT1; CCR4-NOT transcription complex subunit 1 isoform X4 [KO:K12604]
100580472  CNOT2; CCR4-NOT transcription complex subunit 2 isoform X1 [KO:K12605]
100605061  CNOT3; CCR4-NOT transcription complex subunit 3 isoform X1 [KO:K12580]
100590159  CNOT4; CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
100584332  CNOT8; CCR4-NOT transcription complex subunit 8 isoform X1 [KO:K12581]
100604269  CNOT7; CCR4-NOT transcription complex subunit 7 isoform X1 [KO:K12581]
100602877  CNOT9; CCR4-NOT transcription complex subunit 9 isoform X4 [KO:K12606]
100583778  CNOT10; CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
100587338  DHX36; ATP-dependent DNA/RNA helicase DHX36 [KO:K14442] [EC:5.6.2.6]
100598246  PARN; poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
100586640  PNLDC1; poly(A)-specific ribonuclease PNLDC1 isoform X2 [KO:K01148] [EC:3.1.13.4]
100597059  BTG1; protein BTG1 [KO:K14443]
100597985  TOB2; protein Tob2 [KO:K14443]
100580263  BTG3; protein BTG3 [KO:K14443]
100591230  TOB1; protein Tob1 [KO:K14443]
100603682  BTG4; protein BTG4 isoform X3 [KO:K14443]
100601505  BTG2; protein BTG2 [KO:K14443]
100607129  PABPC4L; polyadenylate-binding protein 4-like [KO:K13126]
100604028  PABPC4; polyadenylate-binding protein 4 isoform X3 [KO:K13126]
100594852  PABPC1L; polyadenylate-binding protein 1-like isoform X1 [KO:K13126]
100581403  PABPC3; polyadenylate-binding protein 3 [KO:K13126]
100588478  polyadenylate-binding protein 1-like 2 [KO:K13126]
100600602  PABPC5; polyadenylate-binding protein 5 [KO:K13126]
100595778  PABPC1; polyadenylate-binding protein 1 [KO:K13126]
100585062  PAN2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
100589516  PAN3; PAN2-PAN3 deadenylation complex subunit PAN3 isoform X1 [KO:K12572]
100591367  DCP1A; mRNA-decapping enzyme 1A isoform X1 [KO:K12610] [EC:3.-.-.-]
100599283  DCP1B; mRNA-decapping enzyme 1B [KO:K12611] [EC:3.-.-.-]
100588130  DCP2; m7GpppN-mRNA hydrolase isoform X1 [KO:K12613] [EC:3.6.1.62]
100589759  DDX6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:5.6.2.7]
100596650  EDC3; enhancer of mRNA-decapping protein 3 [KO:K12615]
100588939  EDC4; enhancer of mRNA-decapping protein 4 [KO:K12616]
100581759  PATL1; protein PAT1 homolog 1 isoform X1 [KO:K12617]
100597889  XRN1; 5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
100593111  XRN2; 5'-3' exoribonuclease 2 isoform X1 [KO:K12619] [EC:3.1.13.-]
100607601  NUDT16; U8 snoRNA-decapping enzyme isoform X2 [KO:K16855] [EC:3.6.1.62 3.6.1.64]
100599147  LSM1; U6 snRNA-associated Sm-like protein LSm1 isoform X2 [KO:K12620]
100594047  LSM2; U6 snRNA-associated Sm-like protein LSm2 isoform X1 [KO:K12621]
100589617  LSM3; U6 snRNA-associated Sm-like protein LSm3 isoform X4 [KO:K12622]
100600323  LSM4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
100579279  LSM5; U6 snRNA-associated Sm-like protein LSm5 isoform X1 [KO:K12624]
100580341  LSM6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
100580561  LSM7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
100602163  LSM8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
100590148  ENO3; beta-enolase [KO:K01689] [EC:4.2.1.11]
100602229  ENO1; alpha-enolase [KO:K01689] [EC:4.2.1.11]
100600313  ENO2; gamma-enolase [KO:K01689] [EC:4.2.1.11]
100593778  LOW QUALITY PROTEIN: alpha-enolase [KO:K01689] [EC:4.2.1.11]
100594439  PNPT1; polyribonucleotide nucleotidyltransferase 1, mitochondrial isoform X1 [KO:K00962] [EC:2.7.7.8]
100587636  PFKM; ATP-dependent 6-phosphofructokinase, muscle type [KO:K00850] [EC:2.7.1.11]
100582114  ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
100601116  PFKP; ATP-dependent 6-phosphofructokinase, platelet type isoform X1 [KO:K00850] [EC:2.7.1.11]
115833153  PFKL; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
100590864  HSPA9; stress-70 protein, mitochondrial [KO:K04043]
100604694  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
nle03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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