ENTRY       sly03018                    Pathway
NAME        RNA degradation - Solanum lycopersicum (tomato)
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 sly03018  RNA degradation
DBLINKS     GO: 0006401
ORGANISM    Solanum lycopersicum (tomato) [GN:sly]
GENE        101246918  exosome complex component CSL4 [KO:K07573]
            101267058  exosome complex component RRP4 homolog [KO:K03679]
            101262526  putative exosome complex component rrp40 isoform X1 [KO:K03681]
            101259053  exosome complex component RRP43-like isoform X1 [KO:K12586]
            101260939  exosome complex component RRP41-like [KO:K12587]
            101268414  exosome complex exonuclease RRP42 isoform X1 [KO:K12589]
            101250449  exosome complex component RRP41 homolog [KO:K11600]
            101256312  exosome complex exonuclease RRP46 homolog [KO:K12590]
            101263517  exosome complex component RRP45A [KO:K03678]
            101263664  exosome complex exonuclease RRP44 homolog A isoform X1 [KO:K12585] [EC:3.1.13.-]
            101243936  protein RRP6-like 2 [KO:K12591] [EC:3.1.13.-]
            101259554  nuclear nucleic acid-binding protein C1D [KO:K12592]
            101255403  uncharacterized protein LOC101255403 [KO:K12593]
            101268034  nucleotidyltransferase family protein [KO:K03514] [EC:2.7.7.19]
            101257307  DExH-box ATP-dependent RNA helicase DExH9 [KO:K12598] [EC:3.6.4.13]
            101262619  DExH-box ATP-dependent RNA helicase DExH10 [KO:K12598] [EC:3.6.4.13]
            101261492  DExH-box ATP-dependent RNA helicase DExH10-like isoform X1 [KO:K12598] [EC:3.6.4.13]
            101264125  DExH-box ATP-dependent RNA helicase DExH11 isoform X1 [KO:K12599] [EC:3.6.4.13]
            101247817  tetratricopeptide repeat protein SKI3 [KO:K12600]
            101246693  WD repeat-containing protein [KO:K12602]
            101260155  WD repeat-containing protein VIP3 [KO:K12602]
            101255473  carbon catabolite repressor protein 4 homolog 1-like [KO:K12603] [EC:3.1.13.4]
            101256818  carbon catabolite repressor protein 4 homolog 1 [KO:K12603] [EC:3.1.13.4]
            101260665  carbon catabolite repressor protein 4 homolog 4 isoform X1 [KO:K12603] [EC:3.1.13.4]
            101267935  CCR4-NOT transcription complex subunit 1 [KO:K12604]
            101258724  probable NOT transcription complex subunit VIP2 isoform X1 [KO:K12605]
            101256781  probable NOT transcription complex subunit VIP2 isoform X3 [KO:K12605]
            101245924  general negative regulator of transcription subunit 3 isoform X1 [KO:K12580]
            101251877  uncharacterized protein LOC101251877 isoform X1 [KO:K10643] [EC:2.3.2.27]
            101257555  uncharacterized protein LOC101257555 isoform X2 [KO:K10643] [EC:2.3.2.27]
            101252746  uncharacterized protein LOC101252746 isoform X3 [KO:K10643] [EC:2.3.2.27]
            101247127  uncharacterized protein LOC101247127 isoform X8 [KO:K10643] [EC:2.3.2.27]
            101254325  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
            101248416  probable CCR4-associated factor 1 homolog 9 [KO:K12581]
            101248130  probable CCR4-associated factor 1 homolog 9 [KO:K12581]
            101244756  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
            101268737  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
            101256741  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
            101258664  probable CCR4-associated factor 1 homolog 6 [KO:K12581]
            101258270  probable CCR4-associated factor 1 homolog 9 [KO:K12581]
            101264525  uncharacterized protein LOC101264525 [KO:K12606]
            101263614  CCR4-NOT transcription complex subunit 9-like [KO:K12606]
            104647600  CCR4-NOT transcription complex subunit 9-like isoform X1 [KO:K12606]
            101249588  CCR4-NOT transcription complex subunit 9-like [KO:K12606]
            101263473  CCR4-NOT transcription complex subunit 9 [KO:K12606]
            101260874  CCR4-NOT transcription complex subunit 9-like isoform X1 [KO:K12606]
            101265516  CCR4-NOT transcription complex subunit 9 [KO:K12606]
            112941881  CCR4-NOT transcription complex subunit 9-like [KO:K12606]
            112941882  CCR4-NOT transcription complex subunit 9-like [KO:K12606]
            101257283  CCR4-NOT transcription complex subunit 9-like [KO:K12606]
            101256990  CCR4-NOT transcription complex subunit 9-like [KO:K12606]
            104648404  cell differentiation protein rcd1-like [KO:K12606]
            101266237  CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
            101256419  ABC transporter I family member 20 [KO:K12608]
            101253419  ABC transporter I family member 21 [KO:K12608]
            101264453  DExH-box ATP-dependent RNA helicase DExH1 isoform X1 [KO:K14442] [EC:3.6.4.13]
            101264455  DExH-box ATP-dependent RNA helicase DExH3 [KO:K14442] [EC:3.6.4.13]
            101263393  DExH-box ATP-dependent RNA helicase DExH3 [KO:K14442] [EC:3.6.4.13]
            101261705  DExH-box ATP-dependent RNA helicase DExH5, mitochondrial isoform X1 [KO:K14442] [EC:3.6.4.13]
            101247633  DExH-box ATP-dependent RNA helicase DExH6 isoform X1 [KO:K14442] [EC:3.6.4.13]
            101264368  poly(A)-specific ribonuclease PARN-like [KO:K01148] [EC:3.1.13.4]
            101259346  uncharacterized CRM domain-containing protein At3g25440, chloroplastic [KO:K01148] [EC:3.1.13.4]
            101250035  poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
            101258105  polyadenylate-binding protein 8-like [KO:K13126]
            101248632  polyadenylate-binding protein 7-like [KO:K13126]
            101264108  polyadenylate-binding protein 3 isoform X2 [KO:K13126]
            101261596  polyadenylate-binding protein 2-like [KO:K13126]
            101266448  polyadenylate-binding protein 7 [KO:K13126]
            101247742  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
            101254498  mRNA-decapping enzyme-like protein isoform X2 [KO:K12611] [EC:3.-.-.-]
            101243815  mRNA-decapping enzyme-like protein isoform X2 [KO:K12611] [EC:3.-.-.-]
            101252182  mRNA-decapping enzyme subunit 2 [KO:K12613] [EC:3.6.1.62]
            101253227  DEAD-box ATP-dependent RNA helicase 8 [KO:K12614] [EC:3.6.4.13]
            101258459  DEAD-box ATP-dependent RNA helicase 8 [KO:K12614] [EC:3.6.4.13]
            101251630  DEAD-box ATP-dependent RNA helicase 8-like [KO:K12614] [EC:3.6.4.13]
            101268011  enhancer of mRNA-decapping protein 4-like [KO:K12616]
            101260608  protein PAT1 homolog 2 isoform X2 [KO:K12617]
            101253667  protein PAT1 homolog [KO:K12617]
            101257075  protein PAT1 homolog 1-like [KO:K12617]
            101254180  sm-like protein LSM1B [KO:K12620]
            101251854  sm-like protein LSM1B isoform X1 [KO:K12620]
            101252597  sm-like protein LSM1B [KO:K12620]
            104649355  sm-like protein LSM2 [KO:K12621]
            101250608  sm-like protein LSM2 [KO:K12621]
            101264277  sm-like protein LSM3A [KO:K12622]
            101255434  probable U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
            101256523  sm-like protein LSM5 [KO:K12624]
            101268815  sm-like protein LSM36B [KO:K12625]
            101258986  sm-like protein LSM7 isoform X1 [KO:K12626]
            101267415  sm-like protein LSM8 [KO:K12627]
            101267392  enolase 1, chloroplastic [KO:K01689] [EC:4.2.1.11]
            544068  PGH1; enolase [KO:K01689] [EC:4.2.1.11]
            101247482  enolase [KO:K01689] [EC:4.2.1.11]
            101262427  cytosolic enolase 3 [KO:K01689] [EC:4.2.1.11]
            101256146  polyribonucleotide nucleotidyltransferase 2, mitochondrial [KO:K00962] [EC:2.7.7.8]
            101245783  probable polyribonucleotide nucleotidyltransferase 1, chloroplastic [KO:K00962] [EC:2.7.7.8]
            101263933  uncharacterized protein LOC101263933 isoform X1 [KO:K03654] [EC:5.6.2.4]
            101266704  ATP-dependent 6-phosphofructokinase 4, chloroplastic isoform X1 [KO:K00850] [EC:2.7.1.11]
            101253771  ATP-dependent 6-phosphofructokinase 2 [KO:K00850] [EC:2.7.1.11]
            101245938  ATP-dependent 6-phosphofructokinase 5, chloroplastic-like [KO:K00850] [EC:2.7.1.11]
            101268752  ATP-dependent 6-phosphofructokinase 6-like isoform X1 [KO:K00850] [EC:2.7.1.11]
            101268243  ATP-dependent 6-phosphofructokinase 5, chloroplastic [KO:K00850] [EC:2.7.1.11]
            101245480  ATP-dependent 6-phosphofructokinase 6 [KO:K00850] [EC:2.7.1.11]
            101259840  ATP-dependent 6-phosphofructokinase 6-like [KO:K00850] [EC:2.7.1.11]
            101268121  ATP-dependent 6-phosphofructokinase 6 isoform X1 [KO:K00850] [EC:2.7.1.11]
            101244620  heat shock 70 kDa protein, mitochondrial [KO:K04043]
            101267273  heat shock 70 kDa protein, mitochondrial [KO:K04043]
            101253117  ruBisCO large subunit-binding protein subunit beta, chloroplastic [KO:K04077] [EC:5.6.1.7]
            101259035  ruBisCO large subunit-binding protein subunit beta, chloroplastic [KO:K04077] [EC:5.6.1.7]
            101265626  chaperonin CPN60-like 2, mitochondrial [KO:K04077] [EC:5.6.1.7]
            101250927  chaperonin CPN60-2, mitochondrial [KO:K04077] [EC:5.6.1.7]
            101263320  chaperonin CPN60-2, mitochondrial [KO:K04077] [EC:5.6.1.7]
            101250405  ruBisCO large subunit-binding protein subunit beta, chloroplastic isoform X1 [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 sly03015  mRNA surveillance pathway
KO_PATHWAY  ko03018
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