KEGG   PATHWAY: pfor03018
Entry
pfor03018                   Pathway                                
Name
RNA degradation - Poecilia formosa (Amazon 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
pfor03018  RNA degradation
pfor03018

Other DBs
GO: 0006401
Organism
Poecilia formosa (Amazon molly) [GN:pfor]
Gene
103149293  dcps; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
103150556  exosc1; exosome complex component CSL4 [KO:K07573]
103149545  exosc2; exosome complex component RRP4 [KO:K03679]
103155972  exosc3; exosome complex component RRP40 [KO:K03681]
103140081  exosome complex component RRP43-like [KO:K12586]
103140161  exosc8; exosome complex component RRP43 isoform X1 [KO:K12586]
103148666  exosc6; exosome complex component MTR3 [KO:K12587]
103144442  exosc7; exosome complex component RRP42 [KO:K12589]
103135794  exosc4; exosome complex component RRP41 [KO:K11600]
103138249  exosc5; exosome complex component RRP46 [KO:K12590]
103132873  exosc9; exosome complex component RRP45 [KO:K03678]
103133588  dis3; exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
103138927  exosc10; exosome component 10 isoform X1 [KO:K12591] [EC:3.1.13.-]
103137375  c1d; nuclear nucleic acid-binding protein C1D [KO:K12592]
103130840  mphosph6; M-phase phosphoprotein 6 [KO:K12593]
103151145  DIS3-like exonuclease 1 [KO:K18681] [EC:3.1.13.-]
103138066  papd5; non-canonical poly(A) RNA polymerase PAPD5 [KO:K03514] [EC:2.7.7.19]
103150776  non-canonical poly(A) RNA polymerase PAPD7-like isoform X1 [KO:K03514] [EC:2.7.7.19]
103146019  papd7; non-canonical poly(A) RNA polymerase PAPD7 isoform X1 [KO:K03514] [EC:2.7.7.19]
103137927  zinc finger CCHC domain-containing protein 7-like isoform X2 [KO:K12597]
103147498  zinc finger CCHC domain-containing protein 7-like isoform X1 [KO:K12597]
103142779  superkiller viralicidic activity 2-like 2 [KO:K12598] [EC:5.6.2.6]
103154562  skiv2l; helicase SKI2W [KO:K12599] [EC:5.6.2.6]
103145402  ttc37; tetratricopeptide repeat protein 37 [KO:K12600]
103134528  wdr61; WD repeat-containing protein 61 [KO:K12602]
103134923  cnot6l; CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
103135533  CCR4-NOT transcription complex subunit 6 [KO:K12603] [EC:3.1.13.4]
103138894  cnot1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
103144404  cnot2; CCR4-NOT transcription complex subunit 2 isoform X1 [KO:K12605]
103140179  CCR4-NOT transcription complex subunit 2-like isoform X1 [KO:K12605]
103146427  CCR4-NOT transcription complex subunit 3-like [KO:K12580]
103136644  cnot3; CCR4-NOT transcription complex subunit 3 isoform X1 [KO:K12580]
103134414  cnot4; CCR4-NOT transcription complex subunit 4 [KO:K10643] [EC:2.3.2.27]
103152877  CCR4-NOT transcription complex subunit 8 [KO:K12581]
103139883  CCR4-NOT transcription complex subunit 7 [KO:K12581]
103138132  cnot9; cell differentiation protein RCD1 homolog isoform X1 [KO:K12606]
103132260  cnot10; CCR4-NOT transcription complex subunit 10 isoform X2 [KO:K12607]
103148059  dhx36; ATP-dependent RNA helicase DHX36 [KO:K14442] [EC:5.6.2.6]
103136437  parn; poly(A)-specific ribonuclease PARN [KO:K01148] [EC:3.1.13.4]
103144242  protein Tob1-like [KO:K14443]
103145458  tob1; protein Tob1 [KO:K14443]
103146241  btg1; protein BTG1 [KO:K14443]
103152890  maternal B9.10 protein-like [KO:K14443]
103153420  tob2; protein Tob2 [KO:K14443]
103142104  btg3; protein BTG3 [KO:K14443]
103143130  maternal B9.15 protein-like [KO:K14443]
103145056  embryonic polyadenylate-binding protein B-like isoform X2 [KO:K13126]
103151587  LOW QUALITY PROTEIN: polyadenylate-binding protein 1-like [KO:K13126]
103153373  pabpc4; polyadenylate-binding protein 4 [KO:K13126]
103136982  pabpc1; polyadenylate-binding protein 1 [KO:K13126]
103139124  pan2; PAB-dependent poly(A)-specific ribonuclease subunit PAN2 [KO:K12571] [EC:3.1.13.4]
103139731  pan3; PAB-dependent poly(A)-specific ribonuclease subunit PAN3 [KO:K12572]
103156030  dcp1a; mRNA-decapping enzyme 1A [KO:K12610] [EC:3.-.-.-]
103146497  dcp1b; mRNA-decapping enzyme 1B isoform X1 [KO:K12611] [EC:3.-.-.-]
103153228  dcp2; m7GpppN-mRNA hydrolase [KO:K12613] [EC:3.6.1.62]
103138207  ddx6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:5.6.2.7]
103143484  probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:5.6.2.7]
103150248  edc3; enhancer of mRNA-decapping protein 3 [KO:K12615]
103138849  edc4; enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
103156427  patl1; protein PAT1 homolog 1 isoform X1 [KO:K12617]
103138350  xrn1; 5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
103156411  xrn2; 5'-3' exoribonuclease 2 isoform X1 [KO:K12619] [EC:3.1.13.-]
103151327  U8 snoRNA-decapping enzyme-like isoform X1 [KO:K16855] [EC:3.6.1.62 3.6.1.64]
103146580  lsm1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
103151356  lsm2; U6 snRNA-associated Sm-like protein LSm2 [KO:K12621]
103143240  lsm3; U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
103143825  lsm4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
103146936  lsm5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
103144838  lsm6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
103138523  lsm7; U6 snRNA-associated Sm-like protein LSm7 isoform X1 [KO:K12626]
103154281  lsm8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
103137853  alpha-enolase-like [KO:K01689] [EC:4.2.1.11]
103151087  enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
103146450  gamma-enolase [KO:K01689] [EC:4.2.1.11]
103136757  eno2; gamma-enolase [KO:K01689] [EC:4.2.1.11]
103129607  beta-enolase [KO:K01689] [EC:4.2.1.11]
103137430  pnpt1; polyribonucleotide nucleotidyltransferase 1, mitochondrial [KO:K00962] [EC:2.7.7.8]
103137958  ATP-dependent 6-phosphofructokinase, platelet type-like isoform X7 [KO:K00850] [EC:2.7.1.11]
103138027  ATP-dependent 6-phosphofructokinase, platelet type-like isoform X1 [KO:K00850] [EC:2.7.1.11]
103141185  ATP-dependent 6-phosphofructokinase, muscle type-like [KO:K00850] [EC:2.7.1.11]
103147648  ATP-dependent 6-phosphofructokinase, muscle type-like [KO:K00850] [EC:2.7.1.11]
103155779  pfkl; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
103143367  ATP-dependent 6-phosphofructokinase, platelet type-like isoform X6 [KO:K00850] [EC:2.7.1.11]
103131840  hspa9; stress-70 protein, mitochondrial [KO:K04043]
103156731  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
pfor03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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