ENTRY ko03018 Pathway 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 degradation PATHWAY_MAP ko03018 RNA degradation DBLINKS GO: 0006401 ORTHOLOGY K00850 pfkA, PFK; 6-phosphofructokinase 1 [EC:2.7.1.11] K00937 ppk1; polyphosphate kinase [EC:2.7.4.1] K00962 pnp, PNPT1; polyribonucleotide nucleotidyltransferase [EC:2.7.7.8] K00970 pcnB; poly(A) polymerase [EC:2.7.7.19] K01148 PARN, PNLDC1; poly(A)-specific ribonuclease [EC:3.1.13.4] K01689 ENO1_2_3, eno; enolase 1/2/3 [EC:4.2.1.11] K03514 PAPD5_7, TRF4; non-canonical poly(A) RNA polymerase PAPD5/7 [EC:2.7.7.19] K03628 rho; transcription termination factor Rho K03654 recQ; ATP-dependent DNA helicase RecQ [EC:5.6.2.4] 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 K03732 rhlB; ATP-dependent RNA helicase RhlB [EC:5.6.2.7] K04043 dnaK, HSPA9; molecular chaperone DnaK K04077 groEL, HSPD1, HSP60, CPN60, ths; chaperonin GroEL [EC:5.6.1.7] K05592 deaD, cshA; ATP-dependent RNA helicase DeaD [EC:5.6.2.7] K07573 CSL4, EXOSC1; exosome complex component CSL4 K08300 rne; ribonuclease E [EC:3.1.26.12] 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 K11927 rhlE; ATP-dependent RNA helicase RhlE [EC:5.6.2.7] 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 K12573 rnr, vacB; ribonuclease R [EC:3.1.13.1] 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 K12584 DCPS, DCS; m7GpppX diphosphatase [EC:3.6.1.59] 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 K12597 AIR1_2; protein AIR1/2 K12598 MTR4, SKIV2L2; ATP-dependent RNA helicase DOB1 [EC:5.6.2.6] K12599 SKI2, SKIV2L; antiviral helicase SKI2 [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 K12613 DCP2; mRNA-decapping enzyme subunit 2 [EC:3.6.1.62] 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] K14443 TOB; protein Tob/BTG K16855 NUDT16; U8 snoRNA-decapping enzyme [EC:3.6.1.62 3.6.1.64] K18681 DIS3L; DIS3-like exonuclease 1 [EC:3.1.13.-] K18682 rny; ribonucrease Y [EC:3.1.-.-] K22468 ppk2; polyphosphate kinase [EC:2.7.4.34] 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 REL_PATHWAY ko03015 mRNA surveillance pathway ///