KEGG   PATHWAY: malb03018
Entry
malb03018                   Pathway                                
Name
RNA degradation - Monopterus albus (swamp eel)
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
malb03018  RNA degradation
malb03018

Other DBs
GO: 0006401
Organism
Monopterus albus (swamp eel) [GN:malb]
Gene
109957539  dcps; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
109957813  exosc1; exosome complex component CSL4 isoform X1 [KO:K07573]
109960681  exosc2; exosome complex component RRP4 [KO:K03679]
109956749  exosc3; exosome complex component RRP40 [KO:K03681]
109971911  exosc8; exosome complex component RRP43 [KO:K12586]
109962524  exosc6; exosome complex component MTR3 [KO:K12587]
109958739  exosc7; exosome complex component RRP42 [KO:K12589]
109957689  exosc4; exosome complex component RRP41 [KO:K11600]
109963216  exosc5; exosome complex component RRP46 [KO:K12590]
109957920  exosc9; exosome complex component RRP45 [KO:K03678]
109960138  dis3; exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
109971039  exosc10; exosome component 10 isoform X1 [KO:K12591] [EC:3.1.13.-]
109961136  c1d; nuclear nucleic acid-binding protein C1D [KO:K12592]
109969154  mphosph6; M-phase phosphoprotein 6 [KO:K12593]
109951240  dis3l; DIS3-like exonuclease 1 [KO:K18681] [EC:3.1.13.-]
109958283  non-canonical poly(A) RNA polymerase PAPD7-like isoform X1 [KO:K03514] [EC:2.7.7.19]
109955849  papd5; non-canonical poly(A) RNA polymerase PAPD5 [KO:K03514] [EC:2.7.7.19]
109971724  papd7; non-canonical poly(A) RNA polymerase PAPD7 isoform X1 [KO:K03514] [EC:2.7.7.19]
109974146  zcchc7; zinc finger CCHC domain-containing protein 7 [KO:K12597]
109972309  skiv2l2; superkiller viralicidic activity 2-like 2 [KO:K12598] [EC:5.6.2.6]
109958622  skiv2l; helicase SKI2W [KO:K12599] [EC:5.6.2.6]
109956929  ttc37; tetratricopeptide repeat protein 37 [KO:K12600]
109972313  wdr61; WD repeat-containing protein 61 [KO:K12602]
109957331  cnot6l; CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
109973146  cnot6; CCR4-NOT transcription complex subunit 6 isoform X1 [KO:K12603] [EC:3.1.13.4]
109962521  cnot1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
109967889  CCR4-NOT transcription complex subunit 2 [KO:K12605]
109967706  cnot2; CCR4-NOT transcription complex subunit 2 isoform X1 [KO:K12605]
109968885  CCR4-NOT transcription complex subunit 3-like [KO:K12580]
109970197  cnot3; CCR4-NOT transcription complex subunit 3 isoform X1 [KO:K12580]
109973034  cnot4; CCR4-NOT transcription complex subunit 4 [KO:K10643] [EC:2.3.2.27]
109957528  CCR4-NOT transcription complex subunit 7 [KO:K12581]
109952160  cnot8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
109972628  cnot9; cell differentiation protein RCD1 homolog isoform X1 [KO:K12606]
109973037  cnot10; CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
109968984  dhx36; LOW QUALITY PROTEIN: ATP-dependent RNA helicase DHX36 [KO:K14442] [EC:5.6.2.6]
109973316  parn; poly(A)-specific ribonuclease PARN [KO:K01148] [EC:3.1.13.4]
109952645  tob2; protein Tob2 [KO:K14443]
109964920  protein BTG4-like [KO:K14443]
109952303  protein Tob1-like [KO:K14443]
109959845  btg1; protein BTG1 [KO:K14443]
109959182  maternal B9.10 protein-like [KO:K14443]
109967056  btg3; protein BTG3 [KO:K14443]
109969517  LOW QUALITY PROTEIN: protein Tob1-like [KO:K14443]
109963864  pabpc1; polyadenylate-binding protein 1 [KO:K13126]
109964645  embryonic polyadenylate-binding protein-like isoform X1 [KO:K13126]
109964928  polyadenylate-binding protein 4-like isoform X1 [KO:K13126]
109958607  LOW QUALITY PROTEIN: polyadenylate-binding protein 1-like [KO:K13126]
109970328  pan2; PAB-dependent poly(A)-specific ribonuclease subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
109960159  pan3; PAB-dependent poly(A)-specific ribonuclease subunit PAN3 isoform X1 [KO:K12572]
109971956  dcp1a; mRNA-decapping enzyme 1A [KO:K12610] [EC:3.-.-.-]
109959790  dcp1b; mRNA-decapping enzyme 1B [KO:K12611] [EC:3.-.-.-]
109960699  dcp2; m7GpppN-mRNA hydrolase isoform X1 [KO:K12613] [EC:3.6.1.62]
109954660  probable ATP-dependent RNA helicase ddx6 isoform X1 [KO:K12614] [EC:5.6.2.7]
109958632  probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:5.6.2.7]
109968454  ddx6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:5.6.2.7]
109973623  edc3; enhancer of mRNA-decapping protein 3 [KO:K12615]
109962519  edc4; enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
109952113  patl1; protein PAT1 homolog 1 [KO:K12617]
109971310  xrn2; 5'-3' exoribonuclease 2 isoform X1 [KO:K12619] [EC:3.1.13.-]
109970390  U8 snoRNA-decapping enzyme-like [KO:K16855] [EC:3.6.1.62 3.6.1.64]
109954930  lsm1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
109965740  lsm2; U6 snRNA-associated Sm-like protein LSm2 [KO:K12621]
109972402  lsm3; U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
109966843  lsm4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
109959970  lsm5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
109955533  lsm6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
109967458  lsm7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
109974614  lsm8; LSM8 homolog, U6 small nuclear RNA associated isoform X1 [KO:K12627]
109959072  enolase-like [KO:K01689] [EC:4.2.1.11]
109952449  beta-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
109968883  gamma-enolase [KO:K01689] [EC:4.2.1.11]
109966147  eno2; gamma-enolase [KO:K01689] [EC:4.2.1.11]
109970496  eno1; alpha-enolase [KO:K01689] [EC:4.2.1.11]
109961890  LOW QUALITY PROTEIN: polyribonucleotide nucleotidyltransferase 1, mitochondrial-like [KO:K00962] [EC:2.7.7.8]
109961188  pnpt1; polyribonucleotide nucleotidyltransferase 1, mitochondrial [KO:K00962] [EC:2.7.7.8]
109956115  ATP-dependent 6-phosphofructokinase, muscle type-like [KO:K00850] [EC:2.7.1.11]
109957147  pfkl; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
109965124  ATP-dependent 6-phosphofructokinase, platelet type-like isoform X1 [KO:K00850] [EC:2.7.1.11]
109967100  ATP-dependent 6-phosphofructokinase, platelet type-like [KO:K00850] [EC:2.7.1.11]
109971225  ATP-dependent 6-phosphofructokinase, muscle type-like isoform X1 [KO:K00850] [EC:2.7.1.11]
109966420  hspa9; stress-70 protein, mitochondrial [KO:K04043]
109972694  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
malb03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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