ENTRY       zma03018                    Pathway
NAME        RNA degradation - Zea mays (maize)
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 zma03018  RNA degradation
DBLINKS     GO: 0006401
ORGANISM    Zea mays (maize) [GN:zma]
GENE        100281965  uncharacterized protein LOC100281965 [KO:K07573]
            100216860  uncharacterized protein LOC100216860 [KO:K03679]
            100282437  exosome complex exonuclease RRP40 [KO:K03681]
            103651400  putative exosome complex component rrp40 [KO:K03681]
            100193137  exosome complex exonuclease RRP43 [KO:K12586]
            100282327  exosome complex exonuclease RRP43 [KO:K12586]
            100382718  uncharacterized protein LOC100382718 [KO:K12587]
            100856959  exosome complex exonuclease RRP42 [KO:K12589]
            103626486  exosome complex component RRP42-like [KO:K12589]
            118471885  LOW QUALITY PROTEIN: exosome complex component RRP42-like [KO:K12589]
            100192964  uncharacterized protein LOC100192964 [KO:K11600]
            100280057  exosome complex exonuclease RRP46 [KO:K12590]
            100384304  uncharacterized protein LOC100384304 [KO:K03678]
            103638336  exosome complex component RRP45A [KO:K03678]
            100194408  uncharacterized protein LOC100194408 [KO:K12585] [EC:3.1.13.-]
            100384536  uncharacterized protein LOC100384536 [KO:K12591] [EC:3.1.13.-]
            103642577  protein RRP6-like 2 [KO:K12591] [EC:3.1.13.-]
            100383056  uncharacterized protein LOC100383056 [KO:K12591] [EC:3.1.13.-]
            100277089  uncharacterized protein LOC100277089 [KO:K12592]
            100277744  uncharacterized protein LOC100277744 [KO:K12593]
            103651371  terminal nucleotidyltransferase 4B [KO:K03514] [EC:2.7.7.19]
            103634889  DExH-box ATP-dependent RNA helicase DExH10 [KO:K12598] [EC:3.6.4.13]
            103638180  DExH-box ATP-dependent RNA helicase DExH9 [KO:K12598] [EC:3.6.4.13]
            100383871  uncharacterized protein LOC100383871 [KO:K12599] [EC:3.6.4.13]
            103644768  tetratricopeptide repeat protein SKI3 isoform X1 [KO:K12600]
            100192788  uncharacterized protein LOC100192788 [KO:K12602]
            100279626  uncharacterized protein LOC100279626 [KO:K12603] [EC:3.1.13.4]
            100280629  CCR4-NOT transcription complex subunit 6 [KO:K12603] [EC:3.1.13.4]
            100279717  uncharacterized protein LOC100279717 [KO:K12603] [EC:3.1.13.4]
            100282428  uncharacterized protein LOC100282428 [KO:K12603] [EC:3.1.13.4]
            100502409  CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
            100383837  uncharacterized protein LOC100383837 [KO:K12604]
            100281429  uncharacterized protein LOC100281429 [KO:K12605]
            100381661  uncharacterized protein LOC100381661 [KO:K12605]
            100193927  uncharacterized protein LOC100193927 [KO:K12580]
            103643788  CCR4-NOT transcription complex subunit 3 isoform X1 [KO:K12580]
            103647171  uncharacterized protein LOC103647171 [KO:K10643] [EC:2.3.2.27]
            100381591  uncharacterized protein LOC100381591 isoform X1 [KO:K10643] [EC:2.3.2.27]
            100384257  uncharacterized protein LOC100384257 [KO:K10643] [EC:2.3.2.27]
            103649602  uncharacterized protein LOC103649602 [KO:K10643] [EC:2.3.2.27]
            100216888  uncharacterized protein LOC100216888 [KO:K12581]
            100193739  CCR4-NOT transcription complex subunit 7 [KO:K12581]
            103631117  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
            103631416  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
            103640413  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
            103642973  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
            103638105  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
            103639806  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
            103639808  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
            103639812  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
            103639813  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
            103639817  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
            103639820  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
            100193751  uncharacterized protein LOC100193751 [KO:K12581]
            100193030  CCR4-NOT transcription complex subunit 8 [KO:K12581]
            100272282  uncharacterized protein LOC100272282 [KO:K12581]
            100282279  CCR4-NOT transcription complex subunit 7 [KO:K12581]
            100193338  uncharacterized protein LOC100193338 isoform 2 [KO:K12606]
            100284434  uncharacterized protein LOC100284434 [KO:K12606]
            100383212  uncharacterized protein LOC100383212 [KO:K12607]
            118472932  CCR4-NOT transcription complex subunit 10-like [KO:K12607]
            100191337  uncharacterized protein LOC100191337 [KO:K12608]
            100282925  uncharacterized protein LOC100282925 [KO:K12608]
            100384291  DExH-box ATP-dependent RNA helicase DExH6 isoform X1 [KO:K14442] [EC:3.6.4.13]
            103643471  DExH-box ATP-dependent RNA helicase DExH1 isoform X1 [KO:K14442] [EC:3.6.4.13]
            103649879  DExH-box ATP-dependent RNA helicase DExH3 [KO:K14442] [EC:3.6.4.13]
            100279262  uncharacterized protein LOC100279262 [KO:K14442] [EC:3.6.4.13]
            100193495  uncharacterized protein LOC100193495 [KO:K01148] [EC:3.1.13.4]
            100383372  uncharacterized protein LOC100383372 [KO:K01148] [EC:3.1.13.4]
            100383807  uncharacterized protein LOC100383807 [KO:K01148] [EC:3.1.13.4]
            100285420  uncharacterized protein LOC100285420 [KO:K13126]
            100282980  uncharacterized protein LOC100282980 [KO:K13126]
            100502035  uncharacterized protein LOC100502035 [KO:K13126]
            100381531  uncharacterized protein LOC100381531 [KO:K13126]
            103639307  polyadenylate-binding protein 7 [KO:K13126]
            103641822  polyadenylate-binding protein 2 [KO:K13126]
            100383542  uncharacterized protein LOC100383542 [KO:K13126]
            100279265  Dcp1-like decapping family [KO:K12611] [EC:3.-.-.-]
            100282788  uncharacterized protein LOC100282788 [KO:K12611] [EC:3.-.-.-]
            100191586  uncharacterized protein LOC100191586 [KO:K12611] [EC:3.-.-.-]
            100194374  uncharacterized protein LOC100194374 [KO:K12611] [EC:3.-.-.-]
            100216708  uncharacterized protein LOC100216708 [KO:K12611] [EC:3.-.-.-]
            100283962  mRNA decapping enzyme 2 [KO:K12613] [EC:3.6.1.62]
            103633816  uncharacterized protein LOC103633816 [KO:K12613] [EC:3.6.1.62]
            103631561  uncharacterized protein LOC103631561 [KO:K12613] [EC:3.6.1.62]
            100272835  putative DEAD-box ATP-dependent RNA helicase family protein [KO:K12614] [EC:3.6.4.13]
            100282580  ATP-dependent RNA helicase dhh1 [KO:K12614] [EC:3.6.4.13]
            100194030  uncharacterized protein LOC100194030 [KO:K12614] [EC:3.6.4.13]
            103654004  enhancer of mRNA-decapping protein 4-like [KO:K12616]
            103627664  enhancer of mRNA-decapping protein 4 [KO:K12616]
            100279503  uncharacterized protein LOC100279503 [KO:K12617]
            100272651  uncharacterized protein LOC100272651 isoform 1 [KO:K12617]
            103630584  protein PAT1 homolog 1 isoform X1 [KO:K12617]
            100383823  uncharacterized protein LOC100383823 [KO:K12617]
            103649964  5'-3' exoribonuclease 3 isoform X1 [KO:K12619] [EC:3.1.13.-]
            100280518  small nuclear ribonucleoprotein LSM1 [KO:K12620]
            100280029  uncharacterized protein LOC100280029 [KO:K12620]
            100286339  snRNP core Sm protein Sm-X5-like protein [KO:K12621]
            100276999  sm-like protein LSM2 [KO:K12621]
            100194361  uncharacterized protein LOC100194361 [KO:K12622]
            100285873  U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
            118473076  probable U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
            100283319  sm-like protein LSM5 [KO:K12624]
            100286213  SAD1 [KO:K12624]
            100192719  Small nuclear ribonucleoprotein F [KO:K12625]
            100282349  LSM7-like [KO:K12626]
            100285982  LSM7-like [KO:K12626]
            100284021  uncharacterized protein LOC100284021 [KO:K12627]
            732811  enolase 1 [KO:K01689] [EC:4.2.1.11]
            542316  eno2; enolase 2 [KO:K01689] [EC:4.2.1.11]
            100274470  uncharacterized protein LOC100274470 [KO:K01689] [EC:4.2.1.11]
            100283280  enolase [KO:K01689] [EC:4.2.1.11]
            103631112  enolase 1-like [KO:K01689] [EC:4.2.1.11]
            100502326  enolase [KO:K01689] [EC:4.2.1.11]
            100279772  uncharacterized protein LOC100279772 [KO:K00962] [EC:2.7.7.8]
            103631988  probable polyribonucleotide nucleotidyltransferase 1, chloroplastic [KO:K00962] [EC:2.7.7.8]
            103633568  uncharacterized protein 103633568 [KO:K03654] [EC:5.6.2.4]
            100279231  uncharacterized protein LOC100279231 [KO:K00850] [EC:2.7.1.11]
            100281464  6-phosphofructokinase isoform 2 [KO:K00850] [EC:2.7.1.11]
            100281585  6-phosphofructokinase 2 [KO:K00850] [EC:2.7.1.11]
            100285548  6-phosphofructokinase [KO:K00850] [EC:2.7.1.11]
            100192478  uncharacterized protein LOC100192478 isoform 1 [KO:K00850] [EC:2.7.1.11]
            100281688  6-phosphofructokinase 2 [KO:K00850] [EC:2.7.1.11]
            100280694  pyrophosphate--fructose 6-phosphate 1-phosphotransferase [KO:K00850] [EC:2.7.1.11]
            100191982  uncharacterized protein LOC100191982 [KO:K00850] [EC:2.7.1.11]
            103647427  ATP-dependent 6-phosphofructokinase 5, chloroplastic isoform X1 [KO:K00850] [EC:2.7.1.11]
            103629493  ATP-dependent 6-phosphofructokinase 7 [KO:K00850] [EC:2.7.1.11]
            103630144  ATP-dependent 6-phosphofructokinase 6 [KO:K00850] [EC:2.7.1.11]
            103630633  ATP-dependent 6-phosphofructokinase 6 [KO:K00850] [EC:2.7.1.11]
            100191408  uncharacterized protein LOC100191408 [KO:K04043]
            100285374  heat shock 70 kDa protein [KO:K04043]
            100286241  heat shock 70 kDa protein [KO:K04043]
            542736  chaperonin CPN60-1, mitochondrial precursor [KO:K04077] [EC:5.6.1.7]
            542707  chaperonin CPN60-2, mitochondrial precursor [KO:K04077] [EC:5.6.1.7]
            100272259  uncharacterized protein LOC100272259 [KO:K04077] [EC:5.6.1.7]
            100280498  ruBisCO large subunit-binding protein subunit beta [KO:K04077] [EC:5.6.1.7]
            542185  ruBisCO large subunit-binding protein subunit beta, chloroplastic [KO:K04077] [EC:5.6.1.7]
            103633537  ruBisCO large subunit-binding protein subunit beta, chloroplastic [KO:K04077] [EC:5.6.1.7]
            103629384  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 zma03015  mRNA surveillance pathway
KO_PATHWAY  ko03018
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