PATHWAY: ko03018 Help
Entry Name RNA degradation
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 degradationBRITE hierarchy
Pathway map Other DBs Orthology K00962 pnp, PNPT1; polyribonucleotide nucleotidyltransferase [EC:2.7.7.8 ]
K03514 PAPD5_7, TRF4; non-canonical poly(A) RNA polymerase PAPD5/7 [EC:2.7.7.19 ]
K03628 rho; transcription termination factor Rho
K03666 hfq; host factor-I protein
K03678 RRP45, EXOSC9; exosome complex component RRP45
K03679 RRP4, EXOSC2; exosome complex component RRP4
K03681 RRP40, EXOSC3; exosome complex component RRP40
K04043 dnaK, HSPA9; molecular chaperone DnaK
K07573 CSL4, EXOSC1; exosome complex component CSL4
K08311 nudH; putative (di)nucleoside polyphosphate hydrolase [EC:3.6.1.-]
K10643 CNOT4, NOT4, MOT2; CCR4-NOT transcription complex subunit 4 [EC:2.3.2.27 ]
K11600 RRP41, EXOSC4, SKI6; exosome complex component RRP41
K12571 PAN2; PAB-dependent poly(A)-specific ribonuclease subunit 2 [EC:3.1.13.4 ]
K12572 PAN3; PAB-dependent poly(A)-specific ribonuclease subunit 3
K12574 rnj; ribonuclease J [EC:3.1.-.-]
K12580 CNOT3, NOT3; CCR4-NOT transcription complex subunit 3
K12581 CNOT7_8, CAF1, POP2; CCR4-NOT transcription complex subunit 7/8
K12585 DIS3, RRP44; exosome complex exonuclease DIS3/RRP44 [EC:3.1.13.-]
K12586 RRP43, EXOSC8, OIP2; exosome complex component RRP43
K12587 MTR3, EXOSC6; exosome complex component MTR3
K12589 RRP42, EXOSC7; exosome complex component RRP42
K12590 RRP46, EXOSC5; exosome complex component RRP46
K12591 RRP6, EXOSC10; exosome complex exonuclease RRP6 [EC:3.1.13.-]
K12592 C1D, LRP1; exosome complex protein LRP1
K12593 MPHOSPH6, MPP6; M-phase phosphoprotein 6, animal type
K12594 MPP6; M-phase phosphoprotein 6, fungi type
K12595 SKI7; superkiller protein 7
K12596 TRF5; poly(A) RNA polymerase
K12598 MTR4, SKIV2L2; ATP-dependent RNA helicase DOB1 [EC:5.6.2.6 ]
K12600 SKI3, TTC37; superkiller protein 3
K12601 SKI8; superkiller protein 8
K12602 WDR61, REC14, SKI8; WD repeat-containing protein 61
K12603 CNOT6, CCR4; CCR4-NOT transcription complex subunit 6 [EC:3.1.13.4 ]
K12604 CNOT1, NOT1; CCR4-NOT transcription complex subunit 1
K12605 CNOT2, NOT2; CCR4-NOT transcription complex subunit 2
K12606 RCD1, CNOT9, CAF40; CCR4-NOT transcription complex subunit 9
K12607 CNOT10; CCR4-NOT transcription complex subunit 10
K12608 CAF16; CCR4-NOT complex subunit CAF16
K12609 CAF120; CCR4-NOT transcriptional complex subunit CAF120
K12610 DCP1A; mRNA-decapping enzyme 1A [EC:3.-.-.-]
K12611 DCP1B; mRNA-decapping enzyme 1B [EC:3.-.-.-]
K12612 DCP1; mRNA-decapping enzyme subunit 1
K12614 DDX6, RCK, DHH1; ATP-dependent RNA helicase DDX6/DHH1 [EC:5.6.2.7 ]
K12615 EDC3; enhancer of mRNA-decapping protein 3
K12616 EDC4; enhancer of mRNA-decapping protein 4
K12617 PATL1, PAT1; DNA topoisomerase 2-associated protein PAT1
K12618 XRN1, SEP1, KEM1; 5'-3' exoribonuclease 1 [EC:3.1.13.-]
K12619 XRN2, RAT1; 5'-3' exoribonuclease 2 [EC:3.1.13.-]
K12620 LSM1; U6 snRNA-associated Sm-like protein LSm1
K12621 LSM2; U6 snRNA-associated Sm-like protein LSm2
K12622 LSM3; U6 snRNA-associated Sm-like protein LSm3
K12623 LSM4; U6 snRNA-associated Sm-like protein LSm4
K12624 LSM5; U6 snRNA-associated Sm-like protein LSm5
K12625 LSM6; U6 snRNA-associated Sm-like protein LSm6
K12626 LSM7; U6 snRNA-associated Sm-like protein LSm7
K12627 LSM8; U6 snRNA-associated Sm-like protein LSm8
K13126 PABPC; polyadenylate-binding protein
K14442 DHX36, RHAU; ATP-dependent RNA helicase DHX36 [EC:5.6.2.6 ]
K18681 DIS3L; DIS3-like exonuclease 1 [EC:3.1.13.-]
K18682 rny; ribonucrease Y [EC:3.1.-.-]
Reference Authors Houseley J, Tollervey D
Title The many pathways of RNA degradation.
Journal Reference Authors Buttner K, Wenig K, Hopfner KP
Title The exosome: a macromolecular cage for controlled RNA degradation.
Journal 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 Reference Authors Hartung S, Hopfner KP
Title The exosome, plugged.
Journal Reference Authors Carpousis AJ
Title The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E.
Journal 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 Reference Authors Condon C
Title Maturation and degradation of RNA in bacteria.
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