KEGG   PATHWAY: ath03018
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
ath03018

Other DBs
GO: 0006401
Organism
Arabidopsis thaliana (thale cress) [GN:ath]
Gene
AT1G02080  [KO:K12604]
AT1G03330  LSM2; Small nuclear ribonucleoprotein family protein [KO:K12621]
AT1G03360  RRP4; ribosomal RNA processing 4 [KO:K03679]
AT1G03905  ABCI19; P-loop containing nucleoside triphosphate hydrolases superfamily protein [KO:K12608]
AT1G06450  [KO:K12581]
AT1G06670  NIH; nuclear DEIH-boxhelicase [KO:K14442] [EC:5.6.2.6]
AT1G07705  [KO:K12605]
AT1G08370  DCP1; decapping 1 [KO:K12611] [EC:3.-.-.-]
AT1G15920  [KO:K12581]
AT1G19120  LSM1A; Small nuclear ribonucleoprotein family protein [KO:K12620]
AT1G21190  LSM3A; Small nuclear ribonucleoprotein family protein [KO:K12622]
AT1G22760  PAB3; poly(A) binding protein 3 [KO:K13126]
AT1G26230  Cpn60beta4; TCP-1/cpn60 chaperonin family protein [KO:K04077] [EC:5.6.1.7]
AT1G27820  [KO:K12581]
AT1G27890  [KO:K12581]
AT1G31500  [KO:K12603] [EC:3.1.13.4]
AT1G31530  [KO:K12603] [EC:3.1.13.4]
AT1G34140  PAB1; poly(A) binding protein 1 [KO:K13126]
AT1G48650  [KO:K14442] [EC:5.6.2.6]
AT1G49760  PAB8; poly(A) binding protein 8 [KO:K13126]
AT1G54440  [KO:K12591] [EC:3.1.13.-]
AT1G55490  CPN60B; chaperonin 60 beta [KO:K04077] [EC:5.6.1.7]
AT1G55870  AHG2; Polynucleotidyl transferase, ribonuclease H-like superfamily protein [KO:K01148] [EC:3.1.13.4]
AT1G59760  MTR4; RNA helicase, ATP-dependent, SK12/DOB1 protein [KO:K12598] [EC:5.6.2.6]
AT1G60080  [KO:K12586]
AT1G61470  [KO:K12581]
AT1G65700  LSM8; Small nuclear ribonucleoprotein family protein [KO:K12627]
AT1G71770  PAB5; poly(A)-binding protein 5 [KO:K13126]
AT1G74030  ENO1; enolase 1 [KO:K01689] [EC:4.2.1.11]
AT1G75660  XRN3; 5'-3' exoribonuclease 3 [KO:K12619] [EC:3.1.13.-]
AT1G76630  [KO:K12600]
AT1G76860  LSM3B; Small nuclear ribonucleoprotein family protein [KO:K12622]
AT1G79090  [KO:K12617]
AT1G80780  [KO:K12581]
AT2G01130  [KO:K14442] [EC:5.6.2.6]
AT2G03870  EMB2816; Small nuclear ribonucleoprotein family protein [KO:K12626]
AT2G06990  HEN2; RNA helicase, ATP-dependent, SK12/DOB1 protein [KO:K12598] [EC:5.6.2.6]
AT2G17510  EMB2763; ribonuclease II family protein [KO:K12585] [EC:3.1.13.-]
AT2G22480  PFK5; phosphofructokinase 5 [KO:K00850] [EC:2.7.1.11]
AT2G23350  PAB4; poly(A) binding protein 4 [KO:K13126]
AT2G25355  [KO:K03681]
AT2G28000  CPN60A; chaperonin-60alpha [KO:K04077] [EC:5.6.1.7]
AT2G28540  [KO:K10643] [EC:2.3.2.27]
AT2G29560  ENOC; cytosolic enolase [KO:K01689] [EC:4.2.1.11]
AT2G30800  HVT1; helicase in vascular tissue and tapetum [KO:K14442] [EC:5.6.2.6]
AT2G32070  [KO:K12581]
AT2G32550  [KO:K12606]
AT2G33210  HSP60-2; heat shock protein 60-2 [KO:K04077] [EC:5.6.1.7]
AT2G35920  [KO:K14442] [EC:5.6.2.6]
AT2G36530  LOS2; Enolase [KO:K01689] [EC:4.2.1.11]
AT2G36660  PAB7; poly(A) binding protein 7 [KO:K13126]
AT2G43810  LSM6B; Small nuclear ribonucleoprotein family protein [KO:K12625]
AT2G45810  [KO:K12614] [EC:5.6.2.7]
AT3G03710  RIF10; polyribonucleotide nucleotidyltransferase [KO:K00962] [EC:2.7.7.8]
AT3G07750  [KO:K12589]
AT3G12990  RRP45a; ribonuclease PH45A [KO:K03678]
AT3G13290  VCR; varicose-like protein [KO:K12616]
AT3G13300  VCS; Transducin/WD40 repeat-like superfamily protein [KO:K12616]
AT3G13470  Cpn60beta2; TCP-1/cpn60 chaperonin family protein [KO:K04077] [EC:5.6.1.7]
AT3G13860  HSP60-3A; heat shock protein 60-3A [KO:K04077] [EC:5.6.1.7]
AT3G14080  LSM1B; Small nuclear ribonucleoprotein family protein [KO:K12620]
AT3G16380  PAB6; poly(A) binding protein 6 [KO:K13126]
AT3G20800  [KO:K12606]
AT3G22270  [KO:K12617]
AT3G23990  HSP60; heat shock protein 60 [KO:K04077] [EC:5.6.1.7]
AT3G25430  [KO:K01148] [EC:3.1.13.4]
AT3G44240  [KO:K12581]
AT3G44260  CAF1a; Polynucleotidyl transferase, ribonuclease H-like superfamily protein [KO:K12581]
AT3G45630  [KO:K10643] [EC:2.3.2.27]
AT3G46210  [KO:K12590]
AT3G46960  [KO:K12599] [EC:5.6.2.6]
AT3G52150  PSRP2; RNA-binding (RRM/RBD/RNP motifs) family protein [KO:K13126]
AT3G58560  [KO:K12603] [EC:3.1.13.4]
AT3G58580  [KO:K12603] [EC:3.1.13.4]
AT3G59810  LSM6A; Small nuclear ribonucleoprotein family protein [KO:K12625]
AT3G60500  CER7; 3'-5'-exoribonuclease family protein [KO:K03678]
AT3G61240  [KO:K12614] [EC:5.6.2.7]
AT3G61620  RRP41; 3'-5'-exoribonuclease family protein [KO:K11600]
AT4G00660  RH8; RNAhelicase-like 8 [KO:K12614] [EC:5.6.2.7]
AT4G14990  [KO:K12617]
AT4G26270  PFK3; phosphofructokinase 3 [KO:K00850] [EC:2.7.1.11]
AT4G27490  RRP41L; 3'-5'-exoribonuclease family protein [KO:K12587]
AT4G29220  PFK1; phosphofructokinase 1 [KO:K00850] [EC:2.7.1.11]
AT4G29830  VIP3; Transducin/WD40 repeat-like superfamily protein [KO:K12602]
AT4G32175  [KO:K03681]
AT4G32840  PFK6; phosphofructokinase 6 [KO:K00850] [EC:2.7.1.11]
AT4G34110  PAB2; poly(A) binding protein 2 [KO:K13126]
AT4G37910  mtHsc70-1; mitochondrial heat shock protein 70-1 [KO:K04043]
AT5G02270  ABCI20; non-intrinsic ABC protein 9 [KO:K12608]
AT5G04895  ABO6; DEA(D/H)-box RNA helicase family protein [KO:K14442] [EC:5.6.2.6]
AT5G09590  MTHSC70-2; mitochondrial HSO70 2 [KO:K04043]
AT5G10960  [KO:K12581]
AT5G12980  [KO:K12606]
AT5G13570  DCP2; decapping 2 [KO:K12613] [EC:3.6.1.62]
AT5G14580  [KO:K00962] [EC:2.7.7.8]
AT5G18230  [KO:K12580]
AT5G18820  Cpn60alpha2; TCP-1/cpn60 chaperonin family protein [KO:K04077] [EC:5.6.1.7]
AT5G22250  CAF1b; Polynucleotidyl transferase, ribonuclease H-like superfamily protein [KO:K12581]
AT5G25080  [KO:K12592]
AT5G27720  emb1644; Small nuclear ribonucleoprotein family protein [KO:K12623]
AT5G35430  [KO:K12607]
AT5G35910  [KO:K12591] [EC:3.1.13.-]
AT5G38890  [KO:K07573]
AT5G42540  XRN2; exoribonuclease 2 [KO:K12619] [EC:3.1.13.-]
AT5G44110  ABCI21; P-loop containing nucleoside triphosphate hydrolases superfamily protein [KO:K12608]
AT5G47810  PFK2; phosphofructokinase 2 [KO:K00850] [EC:2.7.1.11]
AT5G48870  SAD1; Small nuclear ribonucleoprotein family protein [KO:K12624]
AT5G53770  [KO:K03514] [EC:2.7.7.19]
AT5G56500  Cpn60beta3; TCP-1/cpn60 chaperonin family protein [KO:K04077] [EC:5.6.1.7]
AT5G56630  PFK7; phosphofructokinase 7 [KO:K00850] [EC:2.7.1.11]
AT5G59460  [KO:K12593]
AT5G59710  VIP2; VIRE2 interacting protein 2 [KO:K12605]
AT5G60170  [KO:K10643] [EC:2.3.2.27]
AT5G61580  PFK4; phosphofructokinase 4 [KO:K00850] [EC:2.7.1.11]
Reference
  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
  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
  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
  Authors
Hartung S, Hopfner KP
  Title
The exosome, plugged.
  Journal
EMBO Rep 8:456-7 (2007)
DOI:10.1038/sj.embor.7400961
Reference
  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
  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
  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
ath03015  mRNA surveillance pathway
KO pathway
ko03018   

DBGET integrated database retrieval system