KEGG   PATHWAY: mcep03018
Entry
mcep03018                   Pathway                                
Name
RNA degradation - Mugil cephalus (flathead mullet)
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
mcep03018  RNA degradation
mcep03018

Other DBs
GO: 0006401
Organism
Mugil cephalus (flathead mullet) [GN:mcep]
Gene
125008146  dcpS; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
125003986  exosc1; exosome complex component CSL4 isoform X1 [KO:K07573]
124997130  exosc2; exosome complex component RRP4 [KO:K03679]
125007954  exosc3; exosome complex component RRP40 [KO:K03681]
125021378  exosc8; exosome complex component RRP43 [KO:K12586]
125014873  exosc6; exosome complex component MTR3 [KO:K12587]
125020275  exosc7; exosome complex component RRP42 [KO:K12589]
125010536  exosc4; exosome complex component RRP41 [KO:K11600]
125014020  exosc5; exosome complex component RRP46 [KO:K12590]
125004203  exosc9; exosome complex component RRP45 [KO:K03678]
125018482  dis3; LOW QUALITY PROTEIN: exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
124997782  exosc10; exosome component 10 [KO:K12591] [EC:3.1.13.-]
125018878  c1d; nuclear nucleic acid-binding protein C1D isoform X1 [KO:K12592]
125014943  M-phase phosphoprotein 6 [KO:K12593]
125005223  dis3l; DIS3-like exonuclease 1 isoform X1 [KO:K18681] [EC:3.1.13.-]
125020453  tent4a; terminal nucleotidyltransferase 4A isoform X1 [KO:K03514] [EC:2.7.7.19]
125016989  terminal nucleotidyltransferase 4A-like [KO:K03514] [EC:2.7.7.19]
125005161  tent4b; terminal nucleotidyltransferase 4B [KO:K03514] [EC:2.7.7.19]
125008039  zinc finger CCHC domain-containing protein 7-like isoform X1 [KO:K12597]
125004324  zcchc7; zinc finger CCHC domain-containing protein 7 [KO:K12597]
124996780  mtrex; exosome RNA helicase MTR4 [KO:K12598] [EC:5.6.2.6]
125019566  skiv2l; helicase SKI2W [KO:K12599] [EC:5.6.2.6]
125011621  ttc37; tetratricopeptide repeat protein 37 [KO:K12600]
125014883  wdr61; WD repeat-containing protein 61 [KO:K12602]
125011972  cnot6l; CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
125008073  CCR4-NOT transcription complex subunit 6 [KO:K12603] [EC:3.1.13.4]
125014438  cnot1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
125014762  cnot2; CCR4-NOT transcription complex subunit 2 isoform X1 [KO:K12605]
125000204  CCR4-NOT transcription complex subunit 2-like [KO:K12605]
125020472  cnot3b; CCR4-NOT transcription complex subunit 3b [KO:K12580]
125016167  cnot3a; CCR4-NOT transcription complex subunit 3a isoform X1 [KO:K12580]
125014966  cnot4a; CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
125021130  cnot8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
125008243  cnot7; CCR4-NOT transcription complex subunit 7 [KO:K12581]
125018030  CCR4-NOT transcription complex subunit 9-like [KO:K12606]
125000624  cnot9; CCR4-NOT transcription complex subunit 9 [KO:K12606]
125016646  cnot10; CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
125013148  dhx36; ATP-dependent DNA/RNA helicase DHX36 [KO:K14442] [EC:5.6.2.6]
125004605  parN; poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
125022279  protein Tob1-like [KO:K14443]
125021150  btg3; protein BTG3 [KO:K14443]
125021285  btg4; protein BTG4 [KO:K14443]
125016305  si:dkey-79d12.5; maternal B9.15 protein isoform X1 [KO:K14443]
125000181  btg1; protein BTG1 [KO:K14443]
124997639  protein Tob1-like [KO:K14443]
124998468  protein Tob2 [KO:K14443]
125023925  pabpc4; polyadenylate-binding protein 4 [KO:K13126]
125019657  polyadenylate-binding protein 1A-like isoform X1 [KO:K13126]
125016820  polyadenylate-binding protein 1A isoform X1 [KO:K13126]
125012609  pabpc1l; polyadenylate-binding protein 1-like isoform X1 [KO:K13126]
125006705  pan2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
124995990  pan3; PAN2-PAN3 deadenylation complex subunit PAN3 isoform X1 [KO:K12572]
125000736  dcp1a; mRNA-decapping enzyme 1A [KO:K12610] [EC:3.-.-.-]
124999864  dcp1b; mRNA-decapping enzyme 1B [KO:K12611] [EC:3.-.-.-]
124996923  dcp2; m7GpppN-mRNA hydrolase isoform X1 [KO:K12613] [EC:3.6.1.62]
125013201  ddx6; probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:5.6.2.7]
125020565  ddx61; probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:5.6.2.7]
125014697  edc3; enhancer of mRNA-decapping protein 3 [KO:K12615]
125005208  enhancer of mRNA-decapping protein 3-like [KO:K12615]
125015028  edc4; enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
125010691  xrn1; 5'-3' exoribonuclease 1 [KO:K12618] [EC:3.1.13.-]
124999144  xrn2; 5'-3' exoribonuclease 2 isoform X1 [KO:K12619] [EC:3.1.13.-]
125015508  zgc:103759; U8 snoRNA-decapping enzyme [KO:K16855] [EC:3.6.1.62 3.6.1.64]
125011844  lsm1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
125008970  smx5; smx5 [KO:K12621]
125007467  lsm3; snRNA-associated Sm-like protein LSm3 [KO:K12622]
125009062  lsm4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
124995919  lsm5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
125000371  lsm6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
125008836  lsm7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
124999813  lsm8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
125019851  gamma-enolase [KO:K01689] [EC:4.2.1.11]
125016884  gamma-enolase-like [KO:K01689] [EC:4.2.1.11]
125012896  eno1a; enolase 1a, (alpha) isoform X1 [KO:K01689] [EC:4.2.1.11]
125007174  eno1b; enolase 1b, (alpha) [KO:K01689] [EC:4.2.1.11]
125009300  eno3; beta-enolase [KO:K01689] [EC:4.2.1.11]
125019223  polyribonucleotide nucleotidyltransferase 1, mitochondrial [KO:K00962] [EC:2.7.7.8]
125017551  ATP-dependent 6-phosphofructokinase, muscle type-like [KO:K00850] [EC:2.7.1.11]
125017556  pfkla; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
125007239  pfkmb; phosphofructokinase, muscle B [KO:K00850] [EC:2.7.1.11]
124995550  pfkpa; ATP-dependent 6-phosphofructokinase, platelet type isoform X1 [KO:K00850] [EC:2.7.1.11]
125010337  ATP-dependent 6-phosphofructokinase, platelet type-like isoform X1 [KO:K00850] [EC:2.7.1.11]
125007872  hspa9; stress-70 protein, mitochondrial [KO:K04043]
125017471  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
mcep03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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