KEGG PATHWAY: rno03018

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

Module

rno_M00390	Exosome, archaea [PATH:rno03018]
rno_M00391	Exosome, eukaryotes [PATH:rno03018]
rno_M00392	Ski complex [PATH:rno03018]
rno_M00393	TRAMP complex [PATH:rno03018]
rno_M00394	RNA degradosome [PATH:rno03018]
rno_M00395	Decapping complex [PATH:rno03018]
rno_M00396	Lsm 2-8 complex [PATH:rno03018]
rno_M00397	Lsm 1-7 complex [PATH:rno03018]

Other DBs

BSID:

117249

GO:

0006401

Organism

Rattus norvegicus (rat) [GN:rno]

Gene

266605	Dcps; decapping enzyme, scavenger [KO:K12584] [EC:3.-.-.-]
679140	similar to exosome component 1; K07573 exosome complex component CSL4 [KO:K07573]
366017	Exosc2; exosome component 2 [KO:K03679]
313243	Exosc3; exosome component 3 [KO:K03681]
306103	Dis3; DIS3 mitotic control homolog (S. cerevisiae) [KO:K12585] [EC:3.1.13.-]
295050	Exosc8; exosome component 8 [KO:K12586]
307850	Exosc6; exosome component 6 [KO:K12587]
316098	Exosc7; exosome component 7 [KO:K12589]
300045	Exosc4; exosome component 4 [KO:K11600]
308441	Exosc5; exosome component 5 [KO:K12590]
294975	Exosc9; exosome component 9 [KO:K03678]
313707	similar to exosome component 10; K12591 exosome complex exonuclease RRP6 [EC:3.1.13.-] [KO:K12591] [EC:3.1.13.-]
289810	C1d; C1D nuclear receptor co-repressor [KO:K12592]
100912037	nuclear nucleic acid-binding protein C1D-like; K12592 exosome complex protein LRP1 [KO:K12592]
299173	Mphosph6; M phase phosphoprotein 6 [KO:K12593]
686999	similar to M phase phosphoprotein 6; K12593 M-phase phosphoprotein 6, animal type [KO:K12593]
306672	Papd7; PAP associated domain containing 7 [KO:K03514] [EC:2.7.7.7]
298086	Zcchc7; zinc finger, CCHC domain containing 7 [KO:K12597]
365668	Skiv2l2; superkiller viralicidic activity 2-like 2 (S. cerevisiae) [KO:K12598] [EC:3.6.4.13]
294260	Skiv2l; superkiller viralicidic activity 2-like (S. cerevisiae ) [KO:K12599] [EC:3.6.4.-]
294595	Ttc37; tetratricopeptide repeat domain 37 [KO:K12600]
363064	Wdr61; WD repeat domain 61 [KO:K12602]
287249	Cnot6; CCR4-NOT transcription complex, subunit 6 [KO:K12603]
360917	Cnot6l; CCR4-NOT transcription complex, subunit 6-like [KO:K12603]
291841	Cnot1; CCR4-NOT transcription complex, subunit 1 [KO:K12604]
299805	Cnot2; CCR4-NOT transcription complex, subunit 2 [KO:K12605]
308311	Cnot3; CCR4-NOT transcription complex, subunit 3 [KO:K12580]
312227	Cnot4; CCR4-NOT transcription complex, subunit 4 [KO:K10643] [EC:6.3.2.19]
306492	Cnot7; CCR4-NOT transcription complex, subunit 7 [KO:K12581]
363603	Cnot8; CCR4-NOT transcription complex, subunit 8 [KO:K12581]
301513	Rqcd1; Rcd1 required for cell differentiation1 homolog (S. pombe) [KO:K12606]
316034	Cnot10; CCR4-NOT transcription complex, subunit 10 [KO:K12607]
310461	Dhx36; DEAH (Asp-Glu-Ala-His) box polypeptide 36 [KO:K14442] [EC:3.6.4.13]
360464	Parn; poly(A)-specific ribonuclease [KO:K01148] [EC:3.1.13.4]
170842	Tob1; transducer of ErbB-2.1 [KO:K14443]
29618	Btg1; B-cell translocation gene 1, anti-proliferative [KO:K14443]
29619	Btg2; BTG family, member 2 [KO:K14443]
298349	RGD1563150; similar to B-cell translocation gene 1 [KO:K14443]
315159	Tob2; transducer of ERBB2, 2 [KO:K14443]
315650	Btg4; B-cell translocation gene 4 [KO:K14443]
367975	similar to B-cell translocation gene 1; K14443 protein Tob/BTG [KO:K14443]
54230	Btg3; BTG family, member 3 [KO:K14443]
171350	Pabpc1; poly(A) binding protein, cytoplasmic 1 [KO:K13126]
688518	Pabpc5; poly A binding protein, cytoplasmic 5 [KO:K13126]
298510	Pabpc4; poly(A) binding protein, cytoplasmic 4 [KO:K13126]
296351	Pabpc1l; poly(A) binding protein, cytoplasmic 1-like [KO:K13126]
302405	Pabpc1l2a; poly(A) binding protein, cytoplasmic 1-like 2A [KO:K13126]
292295	Pabpc6; poly(A) binding protein, cytoplasmic 6 [KO:K13126]
295010	Pabpc4l; poly(A) binding protein, cytoplasmic 4-like [KO:K13126]
291615	Pabpc2; poly(A) binding protein, cytoplasmic 2 [KO:K13126]
408200	Pan2; PAN2 polyA specific ribonuclease subunit homolog (S. cerevisiae) [KO:K12571] [EC:3.1.13.4]
360760	Pan3; PAN3 polyA specific ribonuclease subunit homolog (S. cerevisiae) [KO:K12572]
361109	Dcp1a; DCP1 decapping enzyme homolog A (S. cerevisiae) [KO:K12610] [EC:3.-.-.-]
500305	Dcp1b; DCP1 decapping enzyme homolog b (S. cerevisiae) [KO:K12611] [EC:3.-.-.-]
291604	Dcp2; DCP2 decapping enzyme homolog (S. cerevisiae) [KO:K12613] [EC:3.6.1.62]
500988	Ddx6; DEAD (Asp-Glu-Ala-Asp) box helicase 6 [KO:K12614] [EC:3.6.4.13]
315708	Edc3; enhancer of mRNA decapping 3 homolog (S. cerevisiae) [KO:K12615]
361399	Edc4; enhancer of mRNA decapping 4 [KO:K12616]
361736	Patl1; protein associated with topoisomerase II homolog 1 (yeast) [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; nudix (nucleoside diphosphate linked moiety X)-type motif 16 [KO:K16855] [EC:3.6.1.64 3.6.1.62]
688828	similar to Nucleoside diphosphate-linked moiety X motif 16 (Nudix motif 16); K16855 U8 snoRNA-decapping enzyme [EC:3.6.1.62 3.6.1.64] [KO:K16855] [EC:3.6.1.64 3.6.1.62]
364624	Lsm1; LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae) [KO:K12620]
684148	Lsm2; LSM2 homolog, U6 small nuclear RNA associated (S. cerevisiae) [KO:K12621]
297455	Lsm3; LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) [KO:K12622]
290647	Lsm4; LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae) [KO:K12623]
679753	similar to LSM5 homolog; K12624 U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
306222	Lsm5; LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) [KO:K12624]
498934	Lsm6; LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae) [KO:K12625]
100360750	Sm protein F-like; K12625 U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
362829	Lsm7; LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) [KO:K12626]
690350	similar to LSM7 homolog; K12626 U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
296913	Naa38; N(alpha)-acetyltransferase 38, NatC auxiliary subunit [KO:K12627]
24333	Eno1; enolase 1, (alpha) [KO:K01689] [EC:4.2.1.11]
25438	Eno3; enolase 3, beta, muscle [KO:K01689] [EC:4.2.1.11]
24334	Eno2; enolase 2, gamma, neuronal [KO:K01689] [EC:4.2.1.11]
100911625	gamma-enolase-like; K01689 enolase [EC:4.2.1.11] [KO:K01689] [EC:4.2.1.11]
360992	Pnpt1; polyribonucleotide nucleotidyltransferase 1 [KO:K00962] [EC:2.7.7.8]
291671	Hspa9; heat shock protein 9 [KO:K04043]
63868	Hspd1; heat shock protein 1 (chaperonin) [KO:K04077]

Compound

C00201

Nucleoside triphosphate

Reference

PMID:19239894

Authors

Houseley J, Tollervey D

Title

The many pathways of RNA degradation.

Journal

Cell 136:763-76 (2009)

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)

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)

Reference

PMID:17471261

Authors

Hartung S, Hopfner KP

Title

The exosome, plugged.

Journal

EMBO Rep 8:456-7 (2007)

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)

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)

Reference

PMID:17560162

Authors

Condon C

Title

Maturation and degradation of RNA in bacteria.

Journal

Curr Opin Microbiol 10:271-8 (2007)

KO pathway

ko03018

All links

Pathway (8)   
   KEGG MODULE (7)   
   BioSystems (1)   
Genome (1)   
   KEGG GENOME (1)   
Gene (81)   
   KEGG GENES (81)   
All databases (90)   

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