KEGG   PATHWAY: rtd03018
Entry
rtd03018                    Pathway                                
Name
RNA degradation - Rissa tridactyla (black-legged kittiwake)
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
rtd03018  RNA degradation
rtd03018

Other DBs
GO: 0006401
Organism
Rissa tridactyla (black-legged kittiwake) [GN:rtd]
Gene
128900348  BTG2; protein BTG2 [KO:K14443]
128900489  LSM7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
128900741  LSM4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
128901309  PFKM; ATP-dependent 6-phosphofructokinase, muscle type [KO:K00850] [EC:2.7.1.11]
128902380  MTREX; exosome RNA helicase MTR4 [KO:K12598] [EC:3.6.4.13]
128902440  SKIC3; SKI3 subunit of superkiller complex protein isoform X1 [KO:K12600]
128902480  ZCCHC7; zinc finger CCHC domain-containing protein 7 [KO:K12597]
128902772  DCP2; m7GpppN-mRNA hydrolase isoform X1 [KO:K12613] [EC:3.6.1.62]
128903203  PAN2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
128903643  EXOSC5; LOW QUALITY PROTEIN: exosome complex component RRP46 [KO:K12590]
128903873  EXOSC4; exosome complex component RRP41 [KO:K11600]
128904219  ENO2; gamma-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
128904670  EXOSC8; exosome complex component RRP43 isoform X1 [KO:K12586]
128904915  TENT4A; terminal nucleotidyltransferase 4A isoform X1 [KO:K03514] [EC:2.7.7.19]
128904945  CNOT10; CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
128905195  EXOSC7; exosome complex component RRP42 [KO:K12589]
128905205  PABPC1; polyadenylate-binding protein 1 isoform X1 [KO:K13126]
128905705  PFKP; ATP-dependent 6-phosphofructokinase, platelet type isoform X1 [KO:K00850] [EC:2.7.1.11]
128905930  CNOT2; CCR4-NOT transcription complex subunit 2 isoform X1 [KO:K12605]
128906140  LSM5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
128906826  CNOT4; CCR4-NOT transcription complex subunit 4 isoform X1 [KO:K10643] [EC:2.3.2.27]
128906950  XRN2; 5'-3' exoribonuclease 2 [KO:K12619] [EC:3.1.13.-]
128907656  PNLDC1; poly(A)-specific ribonuclease PNLDC1 isoform X1 [KO:K01148] [EC:3.1.13.4]
128907663  PNPT1; polyribonucleotide nucleotidyltransferase 1, mitochondrial [KO:K00962] [EC:2.7.7.8]
128907994  C1D; nuclear nucleic acid-binding protein C1D [KO:K12592]
128908156  CNOT1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
128908265  DIS3; exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
128908450  TENT4B; terminal nucleotidyltransferase 4B [KO:K03514] [EC:2.7.7.19]
128908557  MPHOSPH6; M-phase phosphoprotein 6 [KO:K12593]
128908584  EDC4; enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
128909001  EXOSC6; exosome complex component MTR3 [KO:K12587]
128909171  PATL1; protein PAT1 homolog 1 isoform X1 [KO:K12617]
128909744  DCP1B; mRNA-decapping enzyme 1B isoform X1 [KO:K12611] [EC:3.-.-.-]
128910142  CNOT7; CCR4-NOT transcription complex subunit 7 isoform X1 [KO:K12581]
128910199  LSM8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
128910348  EXOSC9; exosome complex component RRP45 [KO:K03678]
128910628  LSM6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
128910714  CNOT6L; CCR4-NOT transcription complex subunit 6-like isoform X1 [KO:K12603] [EC:3.1.13.4]
128910784  XRN1; 5'-3' exoribonuclease 1 isoform X1 [KO:K12618] [EC:3.1.13.-]
128910864  EXOSC1; exosome complex component CSL4 [KO:K07573]
128910886  EXOSC3; exosome complex component RRP40 isoform X1 [KO:K03681]
128911517  DHX36; ATP-dependent DNA/RNA helicase DHX36 [KO:K14442] [EC:3.6.4.13]
128911759  PFKL; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
128912805  HSPD1; 60 kDa heat shock protein, mitochondrial [KO:K04077] [EC:5.6.1.7]
128912879  CNOT9; CCR4-NOT transcription complex subunit 9 isoform X1 [KO:K12606]
128913521  BTG1; protein BTG1 [KO:K14443]
128913620  PARN; poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
128914456  SKIC8; SKI8 subunit of superkiller complex protein [KO:K12602]
128914569  EDC3; enhancer of mRNA-decapping protein 3 [KO:K12615]
128914898  DIS3L; DIS3-like exonuclease 1 isoform X1 [KO:K18681] [EC:3.1.13.-]
128915458  DCP1A; mRNA-decapping enzyme 1A isoform X1 [KO:K12610] [EC:3.-.-.-]
128915492  [KO:K14443]
128915505  LSM3; U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
128915928  CNOT8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
128916038  HSPA9; stress-70 protein, mitochondrial isoform X1 [KO:K04043]
128916095  CNOT6; CCR4-NOT transcription complex subunit 6 isoform X1 [KO:K12603] [EC:3.1.13.4]
128916426  TOB2; protein Tob2 [KO:K14443]
128916543  PABPC1L; polyadenylate-binding protein 1-like [KO:K13126]
128916944  PAN3; PAN2-PAN3 deadenylation complex subunit PAN3 isoform X1 [KO:K12572]
128917585  EXOSC2; exosome complex component RRP4 isoform X1 [KO:K03679]
128918000  TOB1; protein Tob1 [KO:K14443]
128918268  ENO1; alpha-enolase isoform X1 [KO:K01689] [EC:4.2.1.11]
128918366  EXOSC10; exosome component 10 [KO:K12591] [EC:3.1.13.-]
128918536  DCPS; LOW QUALITY PROTEIN: m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
128918582  DDX6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:3.6.4.13]
128918664  BTG4; protein BTG4 [KO:K14443]
128918885  PABPC4; polyadenylate-binding protein 4 isoform X1 [KO:K13126]
128919668  LSM1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
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
rtd03015  mRNA surveillance pathway
KO pathway
ko03018   

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