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
100360750  Lsm6l1; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
103693862  Lsm5l1; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
103694176  Hspd1l1; 60 kDa heat shock protein, mitochondrial-like [KO:K04077] [EC:5.6.1.7]
134479289  [KO:K12593]
134479437  [KO:K12593]
134479438  [KO:K12593]
134479439  [KO:K12593]
134479440  [KO:K12593]
134479441  [KO:K12593]
134479442  [KO:K12593]
134479443  [KO:K12593]
134479444  [KO:K12593]
134479504  [KO:K12624]
134484067  Pabpc1l2b; polyadenylate-binding protein 1-like 2 [KO:K13126]
170842  Tob1; protein Tob1 [KO:K14443]
171350  Pabpc1; polyadenylate-binding protein 1 [KO:K13126]
24333  Eno1; alpha-enolase [KO:K01689] [EC:4.2.1.11]
24334  Eno2; gamma-enolase [KO:K01689] [EC:4.2.1.11]
25438  Eno3; beta-enolase [KO:K01689] [EC:4.2.1.11]
25741  Pfkl; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
266605  Dcps; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
287249  Cnot6; CCR4-NOT transcription complex subunit 6 [KO:K12603] [EC:3.1.13.4]
289810  C1d; nuclear nucleic acid-binding protein C1D [KO:K12592]
290647  Lsm4; U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
291604  Dcp2; m7GpppN-mRNA hydrolase [KO:K12613] [EC:3.6.1.62]
291615  Pabpc2; poly(A) binding protein, cytoplasmic 2 [KO:K13126]
291671  Hspa9; stress-70 protein, mitochondrial [KO:K04043]
291841  Cnot1; CCR4-NOT transcription complex subunit 1 [KO:K12604]
292295  Pabpc6; poly(A) binding protein, cytoplasmic 6 [KO:K13126]
294260  Skic2; SKI2 subunit of superkiller complex protein [KO:K12599] [EC:5.6.2.6]
294595  Skic3; tetratricopeptide repeat protein 37 [KO:K12600]
294975  Exosc9; exosome complex component RRP45 [KO:K03678]
295010  Pabpc4l; polyadenylate-binding protein 4-like [KO:K13126]
295050  Exosc8; exosome complex component RRP43 [KO:K12586]
29618  Btg1; protein BTG1 [KO:K14443]
29619  Btg2; protein BTG2 [KO:K14443]
296351  Pabpc1l; polyadenylate-binding protein 1-like [KO:K13126]
296913  Lsm8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
297455  Lsm3; U6 snRNA-associated Sm-like protein LSm3 [KO:K12622]
298086  Zcchc7; zinc finger CCHC domain-containing protein 7 [KO:K12597]
298349  Btg1c; protein BTG1 [KO:K14443]
298510  Pabpc4; polyadenylate-binding protein 4 [KO:K13126]
299805  Cnot2; CCR4-NOT transcription complex subunit 2 Isoform 1 [KO:K12605]
300045  Exosc4; exosome complex component RRP41 [KO:K11600]
300944  Xrn1; 5'-3' exoribonuclease 1 [KO:K12618] [EC:3.1.13.-]
301513  Cnot9; CCR4-NOT transcription complex subunit 9 [KO:K12606]
302405  Pabpc1l2a; polyadenylate-binding protein 1-like 2 [KO:K13126]
306103  Dis3; exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
306222  Lsm5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
306492  Cnot7; CCR4-NOT transcription complex subunit 7 [KO:K12581]
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]
307850  Exosc6; exosome complex component MTR3 [KO:K12587]
308311  Cnot3; CCR4-NOT transcription complex subunit 3 [KO:K12580]
308441  Exosc5; exosome complex component RRP46 [KO:K12590]
310461  Dhx36; ATP-dependent DNA/RNA helicase DHX36 [KO:K14442] [EC:5.6.2.6]
312227  Cnot4; CCR4-NOT transcription complex subunit 4 [KO:K10643] [EC:2.3.2.27]
313243  Exosc3; exosome complex component RRP40 [KO:K03681]
313707  Exosc10; exosome complex component 10 [KO:K12591] [EC:3.1.13.-]
315159  Tob2; protein Tob2 [KO:K14443]
315650  Btg4; protein BTG4 isoform 2 [KO:K14443]
315708  Edc3; enhancer of mRNA-decapping protein 3 [KO:K12615]
316034  Cnot10; CCR4-NOT transcription complex subunit 10 [KO:K12607]
316098  Exosc7; exosome complex component RRP42 [KO:K12589]
360464  Parn; poly(A)-specific ribonuclease PARN [KO:K01148] [EC:3.1.13.4]
360760  Pan3; PAN2-PAN3 deadenylation complex subunit PAN3 [KO:K12572]
360917  Cnot6l; CCR4-NOT transcription complex subunit 6-like isoform 1 [KO:K12603] [EC:3.1.13.4]
360992  Pnpt1; polyribonucleotide nucleotidyltransferase 1, mitochondrial [KO:K00962] [EC:2.7.7.8]
361109  Dcp1a; mRNA-decapping enzyme 1A isoform 1 [KO:K12610] [EC:3.-.-.-]
361399  Edc4; enhancer of mRNA-decapping protein 4 [KO:K12616]
361478  Pnldc1; poly(A)-specific ribonuclease PNLDC1 [KO:K01148] [EC:3.1.13.4]
361736  Patl1; protein PAT1 homolog 1 [KO:K12617]
362229  Xrn2; 5'-3' exoribonuclease 2 [KO:K12619] [EC:3.1.13.-]
362829  Lsm7; U6 snRNA-associated Sm-like protein LSm7 isoform 1 [KO:K12626]
363064  Skic8; superkiller complex protein 8 [KO:K12602]
363077  Dis3l; DIS3-like exonuclease 1 [KO:K18681] [EC:3.1.13.-]
363129  Nudt16; U8 snoRNA-decapping enzyme [KO:K16855] [EC:3.6.1.62 3.6.1.64]
363603  Cnot8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
364624  Lsm1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
365668  Mtrex; exosome RNA helicase MTR4 [KO:K12598] [EC:5.6.2.6]
366017  Exosc2; exosome complex component RRP4 [KO:K03679]
367975  Btg1b; Protein BTG1-like [KO:K14443]
408200  Pan2; PAN2-PAN3 deadenylation complex catalytic subunit Pan2 isoform 1 [KO:K12571] [EC:3.1.13.4]
498934  Lsm6; U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
500305  Dcp1b; mRNA-decapping enzyme 1B isoform X2 [KO:K12611] [EC:3.-.-.-]
500988  Ddx6; probable ATP-dependent RNA helicase DDX6 [KO:K12614] [EC:5.6.2.7]
54230  Btg3; protein BTG3 [KO:K14443]
60416  Pfkp; ATP-dependent 6-phosphofructokinase, platelet type [KO:K00850] [EC:2.7.1.11]
63868  Hspd1; 60 kDa heat shock protein, mitochondrial [KO:K04077] [EC:5.6.1.7]
65152  Pfkm; ATP-dependent 6-phosphofructokinase, muscle type [KO:K00850] [EC:2.7.1.11]
679140  Exosc1; exosome complex component CSL4 [KO:K07573]
684148  Lsm2; U6 snRNA-associated Sm-like protein LSm2 isoform 1 [KO:K12621]
686999  Mphosph6; M-phase phosphoprotein 6 [KO:K12593]
688518  Pabpc5; polyadenylate-binding protein 5 [KO:K13126]
688828  Nudt16l2; uncharacterized protein LOC688828 [KO:K16855] [EC:3.6.1.62 3.6.1.64]
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   

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