KEGG   PATHWAY: pmei03018
Entry
pmei03018                   Pathway                                
Name
RNA degradation - Poecilia mexicana (shortfin molly)
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
pmei03018  RNA degradation
pmei03018

Other DBs
GO: 0006401
Organism
Poecilia mexicana (shortfin molly) [GN:pmei]
Gene
106903403  pan3; PAB-dependent poly(A)-specific ribonuclease subunit PAN3 [KO:K12572]
106903717  btg3; protein BTG3 [KO:K14443]
106903761  [KO:K14443]
106903945  dis3l; DIS3-like exonuclease 1 [KO:K18681] [EC:3.1.13.-]
106904041  dis3; exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
106904638  eno3; beta-enolase [KO:K01689] [EC:4.2.1.11]
106905191  [KO:K00850] [EC:2.7.1.11]
106905303  pnpt1; polyribonucleotide nucleotidyltransferase 1, mitochondrial [KO:K00962] [EC:2.7.7.8]
106907118  mphosph6; M-phase phosphoprotein 6 [KO:K12593]
106907348  [KO:K13126]
106907586  pabpc1; polyadenylate-binding protein 1 [KO:K13126]
106907659  edc3; enhancer of mRNA-decapping protein 3 [KO:K12615]
106907762  pabpc4; polyadenylate-binding protein 4 [KO:K13126]
106908433  lsm2; U6 snRNA-associated Sm-like protein LSm2 [KO:K12621]
106908676  exosc1; exosome complex component CSL4 [KO:K07573]
106908812  [KO:K12605]
106909258  cnot10; CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
106909926  [KO:K12605]
106910354  hspa9; stress-70 protein, mitochondrial [KO:K04043]
106910518  dcp2; m7GpppN-mRNA hydrolase [KO:K12613] [EC:3.6.1.62]
106910531  patl1; protein PAT1 homolog 1 isoform X1 [KO:K12617]
106911081  xrn2; 5'-3' exoribonuclease 2 isoform X1 [KO:K12619] [EC:3.1.13.-]
106911645  [KO:K00850] [EC:2.7.1.11]
106912322  skiv2l2; superkiller viralicidic activity 2-like 2 [KO:K12598] [EC:3.6.4.13]
106914235  [KO:K12597]
106914931  [KO:K01689] [EC:4.2.1.11]
106915929  [KO:K12586]
106916307  rqcd1; cell differentiation protein RCD1 homolog isoform X1 [KO:K12606]
106916505  cnot8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
106916881  pan2; PAB-dependent poly(A)-specific ribonuclease subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
106917311  lsm8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
106917934  lsm3; U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
106917954  exosc5; exosome complex component RRP46 [KO:K12590]
106918536  [KO:K01689] [EC:4.2.1.11]
106918714  ttc37; tetratricopeptide repeat protein 37 [KO:K12600]
106918880  btg1; protein BTG1 [KO:K14443]
106919189  [KO:K14443]
106919608  [KO:K16855] [EC:3.6.1.62 3.6.1.64]
106919625  [KO:K12580]
106919922  [KO:K01689] [EC:4.2.1.11]
106920076  dcp1a; mRNA-decapping enzyme 1A [KO:K12610] [EC:3.-.-.-]
106920301  exosc10; exosome component 10 isoform X1 [KO:K12591] [EC:3.1.13.-]
106920569  exosc7; exosome complex component RRP42 isoform X1 [KO:K12589]
106920847  [KO:K12597]
106920869  [KO:K12603] [EC:3.1.13.4]
106921680  cnot1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
106922209  dcp1b; mRNA-decapping enzyme 1B isoform X1 [KO:K12611] [EC:3.-.-.-]
106922232  exosc8; exosome complex component RRP43 [KO:K12586]
106922732  lsm4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
106922899  exosc3; exosome complex component RRP40 [KO:K03681]
106923002  wdr61; WD repeat-containing protein 61 [KO:K12602]
106923644  [KO:K12614] [EC:3.6.4.13]
106923701  edc4; enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
106923756  lsm6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
106923917  exosc6; exosome complex component MTR3 [KO:K12587]
106924239  exosc2; exosome complex component RRP4 [KO:K03679]
106924386  [KO:K00850] [EC:2.7.1.11]
106924920  lsm7; U6 snRNA-associated Sm-like protein LSm7 isoform X1 [KO:K12626]
106925168  exosc9; exosome complex component RRP45 [KO:K03678]
106925375  cnot3; CCR4-NOT transcription complex subunit 3 isoform X1 [KO:K12580]
106926507  [KO:K14443]
106926900  [KO:K03514] [EC:2.7.7.19]
106927148  c1d; nuclear nucleic acid-binding protein C1D [KO:K12592]
106927338  papd5; non-canonical poly(A) RNA polymerase PAPD5 [KO:K03514] [EC:2.7.7.19]
106927885  pfkl; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
106927920  eno2; gamma-enolase [KO:K01689] [EC:4.2.1.11]
106928872  parn; poly(A)-specific ribonuclease PARN [KO:K01148] [EC:3.1.13.4]
106928928  dcps; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
106929088  cnot4; CCR4-NOT transcription complex subunit 4 [KO:K10643] [EC:2.3.2.27]
106930573  tob2; protein Tob2 [KO:K14443]
106930985  [KO:K12581]
106931030  exosc4; exosome complex component RRP41 [KO:K11600]
106931378  [KO:K00850] [EC:2.7.1.11]
106931538  dhx36; ATP-dependent RNA helicase DHX36 [KO:K14442] [EC:3.6.4.13]
106931601  skiv2l; helicase SKI2W [KO:K12599] [EC:3.6.4.13]
106932044  ddx6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:3.6.4.13]
106932341  tob1; protein Tob1 [KO:K14443]
106932471  hspd1; 60 kDa heat shock protein, mitochondrial [KO:K04077] [EC:5.6.1.7]
106932681  [KO:K13126]
106932852  papd7; non-canonical poly(A) RNA polymerase PAPD7 isoform X1 [KO:K03514] [EC:2.7.7.19]
106932988  xrn1; 5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
106933245  cnot6l; CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
106933823  lsm1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
106933890  lsm5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
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
pmei03015  mRNA surveillance pathway
KO pathway
ko03018   

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