KEGG   PATHWAY: rno03018
Entry
rno03018                    Pathway                                
Name
RNA degradation - Rattus norvegicus (rat)
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
rno03018  RNA degradation
rno03018

Other DBs
GO: 0006401
Organism
Rattus norvegicus (rat) [GN:rno]
Gene
266605  Dcps; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
679140  Exosc1; exosome complex component CSL4 [KO:K07573]
366017  Exosc2; exosome complex component RRP4 [KO:K03679]
313243  Exosc3; exosome complex component RRP40 [KO:K03681]
295050  Exosc8; exosome complex component RRP43 [KO:K12586]
307850  Exosc6; exosome complex component MTR3 [KO:K12587]
316098  Exosc7; exosome complex component RRP42 [KO:K12589]
300045  Exosc4; exosome complex component RRP41 [KO:K11600]
308441  Exosc5; exosome complex component RRP46 [KO:K12590]
294975  Exosc9; exosome complex component RRP45 [KO:K03678]
306103  Dis3; exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
313707  Exosc10; exosome complex component 10 [KO:K12591] [EC:3.1.13.-]
289810  C1d; nuclear nucleic acid-binding protein C1D [KO:K12592]
686999  Mphosph6; M-phase phosphoprotein 6 [KO:K12593]
363077  Dis3l; DIS3-like exonuclease 1 [KO:K18681] [EC:3.1.13.-]
306672  Tent4a; terminal nucleotidyltransferase 4A isoform 2 [KO:K03514] [EC:2.7.7.19]
307745  Tent4b; terminal nucleotidyltransferase 4B isoform 2 [KO:K03514] [EC:2.7.7.19]
298086  Zcchc7; zinc finger CCHC domain-containing protein 7 [KO:K12597]
365668  Mtrex; exosome RNA helicase MTR4 [KO:K12598] [EC:5.6.2.6]
294260  Skic2; SKI2 subunit of superkiller complex protein [KO:K12599] [EC:5.6.2.6]
294595  Skic3; tetratricopeptide repeat protein 37 [KO:K12600]
363064  Skic8; superkiller complex protein 8 [KO:K12602]
287249  Cnot6; CCR4-NOT transcription complex subunit 6 [KO:K12603] [EC:3.1.13.4]
360917  Cnot6l; CCR4-NOT transcription complex subunit 6-like isoform 1 [KO:K12603] [EC:3.1.13.4]
291841  Cnot1; CCR4-NOT transcription complex subunit 1 [KO:K12604]
299805  Cnot2; CCR4-NOT transcription complex subunit 2 Isoform 1 [KO:K12605]
308311  Cnot3; CCR4-NOT transcription complex subunit 3 [KO:K12580]
312227  Cnot4; CCR4-NOT transcription complex subunit 4 [KO:K10643] [EC:2.3.2.27]
306492  Cnot7; CCR4-NOT transcription complex subunit 7 [KO:K12581]
363603  Cnot8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
301513  Cnot9; CCR4-NOT transcription complex subunit 9 [KO:K12606]
316034  Cnot10; CCR4-NOT transcription complex subunit 10 [KO:K12607]
310461  Dhx36; ATP-dependent DNA/RNA helicase DHX36 [KO:K14442] [EC:5.6.2.6]
360464  Parn; poly(A)-specific ribonuclease PARN [KO:K01148] [EC:3.1.13.4]
361478  Pnldc1; poly(A)-specific ribonuclease PNLDC1 [KO:K01148] [EC:3.1.13.4]
170842  Tob1; protein Tob1 [KO:K14443]
29618  Btg1; protein BTG1 [KO:K14443]
29619  Btg2; protein BTG2 [KO:K14443]
315159  Tob2; protein Tob2 [KO:K14443]
315650  Btg4; protein BTG4 isoform 2 [KO:K14443]
367975  Btg1b; Protein BTG1-like [KO:K14443]
54230  Btg3; protein BTG3 [KO:K14443]
298349  Btg1c; protein BTG1 [KO:K14443]
171350  Pabpc1; polyadenylate-binding protein 1 [KO:K13126]
688518  Pabpc5; polyadenylate-binding protein 5 [KO:K13126]
298510  Pabpc4; polyadenylate-binding protein 4 [KO:K13126]
296351  Pabpc1l; polyadenylate-binding protein 1-like [KO:K13126]
302405  Pabpc1l2a; polyadenylate-binding protein 1-like 2 [KO:K13126]
292295  Pabpc6; poly(A) binding protein, cytoplasmic 6 [KO:K13126]
295010  Pabpc4l; polyadenylate-binding protein 4-like [KO:K13126]
291615  Pabpc2; poly(A) binding protein, cytoplasmic 2 [KO:K13126]
134484067  Pabpc1l2b; polyadenylate-binding protein 1-like 2 [KO:K13126]
408200  Pan2; PAN2-PAN3 deadenylation complex catalytic subunit Pan2 isoform 1 [KO:K12571] [EC:3.1.13.4]
360760  Pan3; PAN2-PAN3 deadenylation complex subunit PAN3 [KO:K12572]
361109  Dcp1a; mRNA-decapping enzyme 1A isoform 1 [KO:K12610] [EC:3.-.-.-]
500305  Dcp1b; mRNA-decapping enzyme 1B isoform X2 [KO:K12611] [EC:3.-.-.-]
291604  Dcp2; m7GpppN-mRNA hydrolase [KO:K12613] [EC:3.6.1.62]
500988  Ddx6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:5.6.2.7]
315708  Edc3; enhancer of mRNA-decapping protein 3 [KO:K12615]
361399  Edc4; enhancer of mRNA-decapping protein 4 [KO:K12616]
361736  Patl1; protein PAT1 homolog 1 [KO:K12617]
300944  Xrn1; 5'-3' exoribonuclease 1 [KO:K12618] [EC:3.1.13.-]
362229  Xrn2; 5'-3' exoribonuclease 2 [KO:K12619] [EC:3.1.13.-]
363129  Nudt16; U8 snoRNA-decapping enzyme [KO:K16855] [EC:3.6.1.62 3.6.1.64]
688828  Nudt16l2; uncharacterized protein LOC688828 [KO:K16855] [EC:3.6.1.62 3.6.1.64]
364624  Lsm1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
684148  Lsm2; U6 snRNA-associated Sm-like protein LSm2 isoform 1 [KO:K12621]
297455  Lsm3; U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
290647  Lsm4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
306222  Lsm5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
103693862  Lsm5l1; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
134479504  U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
498934  Lsm6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
100360750  Lsm6l1; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
362829  Lsm7; U6 snRNA-associated Sm-like protein LSm7 isoform 1 [KO:K12626]
296913  Lsm8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
24333  Eno1; alpha-enolase [KO:K01689] [EC:4.2.1.11]
25438  Eno3; beta-enolase [KO:K01689] [EC:4.2.1.11]
24334  Eno2; gamma-enolase [KO:K01689] [EC:4.2.1.11]
360992  Pnpt1; polyribonucleotide nucleotidyltransferase 1, mitochondrial [KO:K00962] [EC:2.7.7.8]
65152  Pfkm; ATP-dependent 6-phosphofructokinase, muscle type [KO:K00850] [EC:2.7.1.11]
25741  Pfkl; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
60416  Pfkp; ATP-dependent 6-phosphofructokinase, platelet type [KO:K00850] [EC:2.7.1.11]
291671  Hspa9; stress-70 protein, mitochondrial [KO:K04043]
63868  Hspd1; 60 kDa heat shock protein, mitochondrial [KO:K04077] [EC:5.6.1.7]
103694176  Hspd1l1; 60 kDa heat shock protein, mitochondrial-like [KO:K04077] [EC:5.6.1.7]
Reference
PMID:19239894
  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
PMID:16968219
  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
PMID:16939780
  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
PMID:17471261
  Authors
Hartung S, Hopfner KP
  Title
The exosome, plugged.
  Journal
EMBO Rep 8:456-7 (2007)
DOI:10.1038/sj.embor.7400961
Reference
PMID:17447862
  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
PMID:16766188
  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
PMID:17560162
  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
rno03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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