KEGG   PATHWAY: biu03018
Entry
biu03018                    Pathway                                
Name
RNA degradation - Bos indicus (zebu cattle)
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
biu03018  RNA degradation
biu03018

Other DBs
GO: 0006401
Organism
Bos indicus (zebu cattle) [GN:biu]
Gene
109553021  EXOSC1; exosome complex component CSL4 isoform X1 [KO:K07573]
109566552  EXOSC2; exosome complex component RRP4 isoform X1 [KO:K03679]
109563048  EXOSC3; exosome complex component RRP40 [KO:K03681]
109566768  EXOSC8; exosome complex component RRP43 [KO:K12586]
109576186  EXOSC7; exosome complex component RRP42 [KO:K12589]
109568394  EXOSC4; exosome complex component RRP41 [KO:K11600]
109572634  EXOSC5; exosome complex component RRP46 [KO:K12590]
109560206  EXOSC9; exosome complex component RRP45 isoform X1 [KO:K03678]
109567065  DIS3; exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
109570605  EXOSC10; exosome component 10 [KO:K12591] [EC:3.1.13.-]
109566224  C1D; nuclear nucleic acid-binding protein C1D [KO:K12592]
109572928  MPHOSPH6; M-phase phosphoprotein 6 [KO:K12593]
109564695  DIS3L; DIS3-like exonuclease 1 isoform X1 [KO:K18681] [EC:3.1.13.-]
109572643  PAPD5; non-canonical poly(A) RNA polymerase PAPD5 isoform X1 [KO:K03514] [EC:2.7.7.19]
109574906  PAPD7; non-canonical poly(A) RNA polymerase PAPD7 isoform X1 [KO:K03514] [EC:2.7.7.19]
109563040  ZCCHC7; zinc finger CCHC domain-containing protein 7 [KO:K12597]
109574776  SKIV2L2; superkiller viralicidic activity 2-like 2 [KO:K12598] [EC:5.6.2.6]
109576931  LOW QUALITY PROTEIN: helicase SKI2W-like [KO:K12599] [EC:5.6.2.6]
109561138  TTC37; tetratricopeptide repeat protein 37 [KO:K12600]
109575413  WDR61; WD repeat-containing protein 61 [KO:K12602]
109571706  LOW QUALITY PROTEIN: WD repeat-containing protein 61-like [KO:K12602]
109560613  CNOT6L; CCR4-NOT transcription complex subunit 6-like isoform X1 [KO:K12603] [EC:3.1.13.4]
109561328  CNOT6; CCR4-NOT transcription complex subunit 6 isoform X1 [KO:K12603] [EC:3.1.13.4]
109572255  CNOT1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
109559226  CNOT2; LOW QUALITY PROTEIN: CCR4-NOT transcription complex subunit 2 [KO:K12605]
109572043  CNOT3; CCR4-NOT transcription complex subunit 3 isoform X1 [KO:K12580]
109557665  CNOT4; CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
109553420  CNOT7; CCR4-NOT transcription complex subunit 7 [KO:K12581]
109561108  CCR4-NOT transcription complex subunit 8-like [KO:K12581]
109562236  CCR4-NOT transcription complex subunit 8 [KO:K12581]
109570620  CNOT9; cell differentiation protein RCD1 homolog [KO:K12606]
109576353  CNOT10; CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
109559117  DHX36; ATP-dependent RNA helicase DHX36 [KO:K14442] [EC:5.6.2.6]
109563599  PNLDC1; poly(A)-specific ribonuclease PARN-like domain-containing protein 1 [KO:K01148] [EC:3.1.13.4]
109578580  PARN; poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
109560043  BTG3; protein BTG3 [KO:K14443]
109574239  protein Tob1 [KO:K14443]
109559859  TOB2; protein Tob2 [KO:K14443]
109570024  BTG4; protein BTG4 [KO:K14443]
109570512  BTG2; protein BTG2 [KO:K14443]
109573591  protein Tob1-like [KO:K14443]
109558972  BTG1; protein BTG1 [KO:K14443]
109555542  polyadenylate-binding protein 1-like 2 [KO:K13126]
109567705  PABPC1L; polyadenylate-binding protein 1-like [KO:K13126]
109571504  PABPC4L; polyadenylate-binding protein 4-like [KO:K13126]
109555516  PABPC5; polyadenylate-binding protein 5 [KO:K13126]
109556465  PABPC4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
109559360  PAN2; PAB-dependent poly(A)-specific ribonuclease subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
109566824  PAN3; PAB-dependent poly(A)-specific ribonuclease subunit PAN3 isoform X1 [KO:K12572]
109576220  DCP1A; mRNA-decapping enzyme 1A [KO:K12610] [EC:3.-.-.-]
109558614  DCP1B; mRNA-decapping enzyme 1B [KO:K12611] [EC:3.-.-.-]
109564602  DCP2; m7GpppN-mRNA hydrolase [KO:K12613] [EC:3.6.1.62]
109569564  DDX6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:5.6.2.7]
109575393  EDC3; enhancer of mRNA-decapping protein 3 [KO:K12615]
109572686  EDC4; enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
109569656  PATL1; protein PAT1 homolog 1 isoform X1 [KO:K12617]
109559563  XRN1; 5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
109568047  XRN2; 5'-3' exoribonuclease 2 isoform X1 [KO:K12619] [EC:3.1.13.-]
109553458  LSM1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
109576432  LSM3; U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
109561411  LSM4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
109557468  LSM5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
109571462  LSM6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
109561793  LSM7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
109557928  LSM8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
109573780  ENO3; beta-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
109570481  ENO1; alpha-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
109558913  ENO2; gamma-enolase [KO:K01689] [EC:4.2.1.11]
109566088  PNPT1; polyribonucleotide nucleotidyltransferase 1, mitochondrial isoform X1 [KO:K00962] [EC:2.7.7.8]
109559166  PFKM; ATP-dependent 6-phosphofructokinase, muscle type [KO:K00850] [EC:2.7.1.11]
109568096  PFKP; ATP-dependent 6-phosphofructokinase, platelet type [KO:K00850] [EC:2.7.1.11]
109561060  PFKL; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
109562068  HSPA9; stress-70 protein, mitochondrial [KO:K04043]
109569043  HSPD1; 60 kDa heat shock protein, mitochondrial isoform X1 [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
biu03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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