ENTRY       ath03018                    Pathway
NAME        RNA degradation - Arabidopsis thaliana (thale cress)
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 ath03018  RNA degradation
DBLINKS     GO: 0006401
ORGANISM    Arabidopsis thaliana (thale cress) [GN:ath]
GENE        AT5G38890  Nucleic acid-binding, OB-fold-like protein [KO:K07573]
            AT1G03360  RRP4; ribosomal RNA processing 4 [KO:K03679]
            AT2G25355  PNAS-3-like protein [KO:K03681]
            AT4G32175  PNAS-3-like protein [KO:K03681]
            AT1G60080  3'-5'-exoribonuclease family protein [KO:K12586]
            AT4G27490  RRP41L; 3'-5'-exoribonuclease family protein [KO:K12587]
            AT3G07750  3'-5'-exoribonuclease family protein [KO:K12589]
            AT3G61620  RRP41; 3'-5'-exoribonuclease family protein [KO:K11600]
            AT3G46210  Ribosomal protein S5 domain 2-like superfamily protein [KO:K12590]
            AT3G60500  CER7; 3'-5'-exoribonuclease family protein [KO:K03678]
            AT3G12990  RRP45a; ribonuclease PH45A [KO:K03678]
            AT2G17510  EMB2763; ribonuclease II family protein [KO:K12585] [EC:3.1.13.-]
            AT5G35910  Polynucleotidyl transferase, ribonuclease H fold protein with HRDC domain-containing protein [KO:K12591] [EC:3.1.13.-]
            AT1G54440  Polynucleotidyl transferase, ribonuclease H fold protein with HRDC domain-containing protein [KO:K12591] [EC:3.1.13.-]
            AT5G25080  Sas10/Utp3/C1D family [KO:K12592]
            AT5G59460  scarecrow-like transcription factor 11 (SCL11) [KO:K12593]
            AT5G53770  Nucleotidyltransferase family protein [KO:K03514] [EC:2.7.7.19]
            AT1G59760  MTR4; RNA helicase, ATP-dependent, SK12/DOB1 protein [KO:K12598] [EC:3.6.4.13]
            AT2G06990  HEN2; RNA helicase, ATP-dependent, SK12/DOB1 protein [KO:K12598] [EC:3.6.4.13]
            AT3G46960  RNA helicase, ATP-dependent, SK12/DOB1 protein [KO:K12599] [EC:3.6.4.13]
            AT1G76630  Tetratricopeptide repeat (TPR)-like superfamily protein [KO:K12600]
            AT4G29830  VIP3; Transducin/WD40 repeat-like superfamily protein [KO:K12602]
            AT3G58560  DNAse I-like superfamily protein [KO:K12603] [EC:3.1.13.4]
            AT3G58580  DNAse I-like superfamily protein [KO:K12603] [EC:3.1.13.4]
            AT1G31500  DNAse I-like superfamily protein [KO:K12603] [EC:3.1.13.4]
            AT1G31530  DNAse I-like superfamily protein [KO:K12603] [EC:3.1.13.4]
            AT1G02080  transcription regulator [KO:K12604]
            AT1G07705  NOT2 / NOT3 / NOT5 family [KO:K12605]
            AT5G59710  VIP2; VIRE2 interacting protein 2 [KO:K12605]
            AT5G18230  transcription regulator NOT2/NOT3/NOT5 family protein [KO:K12580]
            AT3G45630  RNA binding (RRM/RBD/RNP motifs) family protein [KO:K10643] [EC:2.3.2.27]
            AT5G60170  RNA binding (RRM/RBD/RNP motifs) family protein [KO:K10643] [EC:2.3.2.27]
            AT2G28540  RNA binding (RRM/RBD/RNP motifs) family protein [KO:K10643] [EC:2.3.2.27]
            AT1G80780  Polynucleotidyl transferase, ribonuclease H-like superfamily protein [KO:K12581]
            AT5G10960  Polynucleotidyl transferase, ribonuclease H-like superfamily protein [KO:K12581]
            AT1G06450  Polynucleotidyl transferase, ribonuclease H-like superfamily protein [KO:K12581]
            AT1G27890  Polynucleotidyl transferase, ribonuclease H-like superfamily protein [KO:K12581]
            AT3G44240  Polynucleotidyl transferase, ribonuclease H-like superfamily protein [KO:K12581]
            AT1G27820  Polynucleotidyl transferase, ribonuclease H-like superfamily protein [KO:K12581]
            AT1G61470  Polynucleotidyl transferase, ribonuclease H-like superfamily protein [KO:K12581]
            AT2G32070  Polynucleotidyl transferase, ribonuclease H-like superfamily protein [KO:K12581]
            AT1G15920  Polynucleotidyl transferase, ribonuclease H-like superfamily protein [KO:K12581]
            AT3G44260  CAF1a; Polynucleotidyl transferase, ribonuclease H-like superfamily protein [KO:K12581]
            AT5G22250  CAF1b; Polynucleotidyl transferase, ribonuclease H-like superfamily protein [KO:K12581]
            AT3G20800  Cell differentiation, Rcd1-like protein [KO:K12606]
            AT5G12980  Cell differentiation, Rcd1-like protein [KO:K12606]
            AT2G32550  Cell differentiation, Rcd1-like protein [KO:K12606]
            AT5G35430  Tetratricopeptide repeat (TPR)-like superfamily protein [KO:K12607]
            AT1G03905  ABCI19; P-loop containing nucleoside triphosphate hydrolases superfamily protein [KO:K12608]
            AT5G02270  ABCI20; non-intrinsic ABC protein 9 [KO:K12608]
            AT5G44110  ABCI21; P-loop containing nucleoside triphosphate hydrolases superfamily protein [KO:K12608]
            AT2G35920  RNA helicase family protein [KO:K14442] [EC:3.6.4.13]
            AT1G48650  DEA(D/H)-box RNA helicase family protein [KO:K14442] [EC:3.6.4.13]
            AT2G01130  DEA(D/H)-box RNA helicase family protein [KO:K14442] [EC:3.6.4.13]
            AT5G04895  ABO6; DEA(D/H)-box RNA helicase family protein [KO:K14442] [EC:3.6.4.13]
            AT1G06670  NIH; nuclear DEIH-boxhelicase [KO:K14442] [EC:3.6.4.13]
            AT2G30800  HVT1; helicase in vascular tissue and tapetum [KO:K14442] [EC:3.6.4.13]
            AT1G55870  AHG2; Polynucleotidyl transferase, ribonuclease H-like superfamily protein [KO:K01148] [EC:3.1.13.4]
            AT3G25430  Polynucleotidyl transferase, ribonuclease H-like superfamily protein [KO:K01148] [EC:3.1.13.4]
            AT3G25440  LOH1; RNA-binding CRS1 / YhbY (CRM) domain protein [KO:K01148] [EC:3.1.13.4]
            AT1G49760  PAB8; poly(A) binding protein 8 [KO:K13126]
            AT4G34110  PAB2; poly(A) binding protein 2 [KO:K13126]
            AT3G52150  PSRP2; RNA-binding (RRM/RBD/RNP motifs) family protein [KO:K13126]
            AT1G22760  PAB3; poly(A) binding protein 3 [KO:K13126]
            AT1G71770  PAB5; poly(A)-binding protein 5 [KO:K13126]
            AT2G23350  PAB4; poly(A) binding protein 4 [KO:K13126]
            AT1G34140  PAB1; poly(A) binding protein 1 [KO:K13126]
            AT2G36660  PAB7; poly(A) binding protein 7 [KO:K13126]
            AT3G16380  PAB6; poly(A) binding protein 6 [KO:K13126]
            AT1G08370  DCP1; decapping 1 [KO:K12611] [EC:3.-.-.-]
            AT5G13570  DCP2; decapping 2 [KO:K12613] [EC:3.6.1.62]
            AT3G61240  DEA(D/H)-box RNA helicase family protein [KO:K12614] [EC:3.6.4.13]
            AT2G45810  DEA(D/H)-box RNA helicase family protein [KO:K12614] [EC:3.6.4.13]
            AT4G00660  RH8; RNAhelicase-like 8 [KO:K12614] [EC:3.6.4.13]
            AT3G13300  VCS; Transducin/WD40 repeat-like superfamily protein [KO:K12616]
            AT3G13290  VCR; varicose-like protein [KO:K12616]
            AT1G79090  topoisomerase II-associated protein [KO:K12617]
            AT4G14990  Topoisomerase II-associated protein PAT1 [KO:K12617]
            AT3G22270  Topoisomerase II-associated protein PAT1 [KO:K12617]
            AT5G42540  XRN2; exoribonuclease 2 [KO:K12619] [EC:3.1.13.-]
            AT1G75660  XRN3; 5'-3' exoribonuclease 3 [KO:K12619] [EC:3.1.13.-]
            AT3G14080  LSM1B; Small nuclear ribonucleoprotein family protein [KO:K12620]
            AT1G19120  LSM1A; Small nuclear ribonucleoprotein family protein [KO:K12620]
            AT1G03330  LSM2; Small nuclear ribonucleoprotein family protein [KO:K12621]
            AT1G76860  LSM3B; Small nuclear ribonucleoprotein family protein [KO:K12622]
            AT1G21190  LSM3A; Small nuclear ribonucleoprotein family protein [KO:K12622]
            AT5G27720  emb1644; Small nuclear ribonucleoprotein family protein [KO:K12623]
            AT5G48870  SAD1; Small nuclear ribonucleoprotein family protein [KO:K12624]
            AT3G59810  LSM6A; Small nuclear ribonucleoprotein family protein [KO:K12625]
            AT2G43810  LSM6B; Small nuclear ribonucleoprotein family protein [KO:K12625]
            AT2G03870  EMB2816; Small nuclear ribonucleoprotein family protein [KO:K12626]
            AT1G65700  LSM8; Small nuclear ribonucleoprotein family protein [KO:K12627]
            AT1G74030  ENO1; enolase 1 [KO:K01689] [EC:4.2.1.11]
            AT2G36530  LOS2; Enolase [KO:K01689] [EC:4.2.1.11]
            AT2G29560  ENOC; cytosolic enolase [KO:K01689] [EC:4.2.1.11]
            AT5G14580  polyribonucleotide nucleotidyltransferase [KO:K00962] [EC:2.7.7.8]
            AT3G03710  RIF10; polyribonucleotide nucleotidyltransferase [KO:K00962] [EC:2.7.7.8]
            AT4G32840  PFK6; phosphofructokinase 6 [KO:K00850] [EC:2.7.1.11]
            AT5G56630  PFK7; phosphofructokinase 7 [KO:K00850] [EC:2.7.1.11]
            AT5G61580  PFK4; phosphofructokinase 4 [KO:K00850] [EC:2.7.1.11]
            AT4G29220  PFK1; phosphofructokinase 1 [KO:K00850] [EC:2.7.1.11]
            AT2G22480  PFK5; phosphofructokinase 5 [KO:K00850] [EC:2.7.1.11]
            AT4G26270  PFK3; phosphofructokinase 3 [KO:K00850] [EC:2.7.1.11]
            AT5G47810  PFK2; phosphofructokinase 2 [KO:K00850] [EC:2.7.1.11]
            AT4G37910  mtHsc70-1; mitochondrial heat shock protein 70-1 [KO:K04043]
            AT5G09590  MTHSC70-2; mitochondrial HSO70 2 [KO:K04043]
            AT2G33210  HSP60-2; heat shock protein 60-2 [KO:K04077] [EC:5.6.1.7]
            AT3G23990  HSP60; heat shock protein 60 [KO:K04077] [EC:5.6.1.7]
            AT3G13860  HSP60-3A; heat shock protein 60-3A [KO:K04077] [EC:5.6.1.7]
            AT3G13470  Cpn60beta2; TCP-1/cpn60 chaperonin family protein [KO:K04077] [EC:5.6.1.7]
            AT1G26230  Cpn60beta4; TCP-1/cpn60 chaperonin family protein [KO:K04077] [EC:5.6.1.7]
            AT1G55490  CPN60B; chaperonin 60 beta [KO:K04077] [EC:5.6.1.7]
            AT5G56500  Cpn60beta3; TCP-1/cpn60 chaperonin family protein [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
REL_PATHWAY ath03015  mRNA surveillance pathway
KO_PATHWAY  ko03018
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