KEGG   PATHWAY: bbel03018
Entry
bbel03018                   Pathway                                
Name
RNA degradation - Branchiostoma belcheri (Belcher's lancelet)
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
bbel03018  RNA degradation
bbel03018

Other DBs
GO: 0006401
Organism
Branchiostoma belcheri (Belcher's lancelet) [GN:bbel]
Gene
109484414  m7GpppX diphosphatase-like [KO:K12584] [EC:3.6.1.59]
109485263  exosome complex component CSL4-like [KO:K07573]
109462178  exosome complex component RRP4-like [KO:K03679]
109484415  exosome complex component RRP4-like [KO:K03679]
109486165  exosome complex component RRP40-like [KO:K03681]
109470630  exosome complex component RRP43-like [KO:K12586]
109465804  exosome complex component MTR3-like [KO:K12587]
109473873  exosome complex component RRP42-like [KO:K12589]
109473784  exosome complex component RRP41-like [KO:K11600]
109464126  exosome complex component RRP46-like [KO:K12590]
109467973  exosome complex component RRP45-like [KO:K03678]
109487685  exosome complex exonuclease RRP44-like [KO:K12585] [EC:3.1.13.-]
109479691  exosome component 10-like [KO:K12591] [EC:3.1.13.-]
109471030  nuclear nucleic acid-binding protein C1D-like isoform X1 [KO:K12592]
109473761  M-phase phosphoprotein 6-like [KO:K12593]
109480749  DIS3-like exonuclease 1 [KO:K18681] [EC:3.1.13.-]
109480527  non-canonical poly(A) RNA polymerase protein Trf4-1-like [KO:K03514] [EC:2.7.7.19]
109467068  superkiller viralicidic activity 2-like 2 isoform X1 [KO:K12598] [EC:5.6.2.6]
109467237  helicase SKI2W-like [KO:K12599] [EC:5.6.2.6]
109464379  LOW QUALITY PROTEIN: tetratricopeptide repeat protein 37-like [KO:K12600]
109468983  WD repeat-containing protein 61-like isoform X1 [KO:K12602]
109485467  CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
109480446  CCR4-NOT transcription complex subunit 1-like [KO:K12604]
109482742  CCR4-NOT transcription complex subunit 2-like isoform X1 [KO:K12605]
109462742  CCR4-NOT transcription complex subunit 3-like isoform X1 [KO:K12580]
109463394  LOW QUALITY PROTEIN: CCR4-NOT transcription complex subunit 4-like [KO:K10643] [EC:2.3.2.27]
109470718  CCR4-NOT transcription complex subunit 7-like [KO:K12581]
109478029  cell differentiation protein RCD1 homolog isoform X1 [KO:K12606]
109482138  CCR4-NOT transcription complex subunit 10-like [KO:K12607]
109472564  ATP-dependent RNA helicase DHX36-like [KO:K14442] [EC:5.6.2.6]
109483291  poly(A)-specific ribonuclease PARN-like [KO:K01148] [EC:3.1.13.4]
109484346  poly(A)-specific ribonuclease PARN-like domain-containing protein 1 [KO:K01148] [EC:3.1.13.4]
109461913  protein Tob1-like [KO:K14443]
109476271  maternal B9.15 protein-like [KO:K14443]
109476270  polyadenylate-binding protein 4-like isoform X1 [KO:K13126]
109474665  PAB-dependent poly(A)-specific ribonuclease subunit PAN2-like isoform X1 [KO:K12571] [EC:3.1.13.4]
109470712  PAB-dependent poly(A)-specific ribonuclease subunit PAN3-like isoform X1 [KO:K12572]
109469818  LOW QUALITY PROTEIN: mRNA-decapping enzyme 1A-like [KO:K12611] [EC:3.-.-.-]
109471865  m7GpppN-mRNA hydrolase-like isoform X1 [KO:K12613] [EC:3.6.1.62]
109484017  probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:5.6.2.7]
109471881  enhancer of mRNA-decapping protein 3-like [KO:K12615]
109473739  enhancer of mRNA-decapping protein 4-like isoform X1 [KO:K12616]
109479675  5'-3' exoribonuclease 1-like [KO:K12618] [EC:3.1.13.-]
109488193  5'-3' exoribonuclease 2-like [KO:K12619] [EC:3.1.13.-]
109477070  U8 snoRNA-decapping enzyme-like [KO:K16855] [EC:3.6.1.62 3.6.1.64]
109478584  U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
109482336  U6 snRNA-associated Sm-like protein LSm2 [KO:K12621]
109477262  U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
109472709  U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
109465342  U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
109480820  U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
109468902  U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
109477238  U6 snRNA-associated Sm-like protein LSm8 [KO:K12627]
109479939  enolase-like [KO:K01689] [EC:4.2.1.11]
109482807  polyribonucleotide nucleotidyltransferase 1, mitochondrial-like isoform X1 [KO:K00962] [EC:2.7.7.8]
109484809  probable Werner syndrome ATP-dependent helicase homolog 1 [KO:K03654] [EC:5.6.2.4]
109472075  LOW QUALITY PROTEIN: ATP-dependent DNA helicase Q-like SIM [KO:K03654] [EC:5.6.2.4]
109465538  ATP-dependent DNA helicase Q-like 3 [KO:K03654] [EC:5.6.2.4]
109483478  ATP-dependent DNA helicase Q-like SIM [KO:K03654] [EC:5.6.2.4]
109469398  ATP-dependent 6-phosphofructokinase, muscle type-like [KO:K00850] [EC:2.7.1.11]
109478517  stress-70 protein, mitochondrial-like [KO:K04043]
109478769  60 kDa heat shock protein, mitochondrial-like [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
bbel03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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