KEGG   PATHWAY: pvir03018
Entry
pvir03018                   Pathway                                
Name
RNA degradation - Panicum virgatum (switchgrass)
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
pvir03018  RNA degradation
pvir03018

Other DBs
GO: 0006401
Organism
Panicum virgatum (switchgrass) [GN:pvir]
Gene
120657598  exosome complex component CSL4-like [KO:K07573]
120706235  exosome complex component CSL4-like isoform X1 [KO:K07573]
120642505  exosome complex component RRP4 homolog [KO:K03679]
120682686  exosome complex component RRP4 homolog [KO:K03679]
120642015  putative exosome complex component rrp40 isoform X1 [KO:K03681]
120672648  putative exosome complex component rrp40 [KO:K03681]
120672433  exosome complex component RRP43-like [KO:K12586]
120660099  exosome complex component RRP43-like [KO:K12586]
120661924  exosome complex component RRP41-like isoform X1 [KO:K12587]
120694584  exosome complex component RRP41-like [KO:K12587]
120696930  exosome complex component RRP42-like [KO:K12589]
120666638  exosome complex component RRP42-like [KO:K12589]
120711933  exosome complex component RRP42-like [KO:K12589]
120647297  exosome complex component RRP41 homolog [KO:K11600]
120692572  exosome complex component RRP41 homolog [KO:K11600]
120687432  exosome complex exonuclease RRP46 homolog [KO:K12590]
120649055  exosome complex exonuclease RRP46 homolog [KO:K12590]
120704245  exosome complex component RRP45A-like isoform X1 [KO:K03678]
120698007  exosome complex component RRP45A-like isoform X1 [KO:K03678]
120654506  exosome complex component RRP45A-like isoform X1 [KO:K03678]
120688309  exosome complex exonuclease RRP44 homolog A-like [KO:K12585] [EC:3.1.13.-]
120647439  exosome complex exonuclease RRP44 homolog A-like isoform X1 [KO:K12585] [EC:3.1.13.-]
120689587  protein RRP6-like 2 [KO:K12591] [EC:3.1.13.-]
120647248  protein RRP6-like 1 [KO:K12591] [EC:3.1.13.-]
120691351  protein RRP6-like 1 isoform X1 [KO:K12591] [EC:3.1.13.-]
120650969  protein RRP6-like 2 isoform X1 [KO:K12591] [EC:3.1.13.-]
120679083  nuclear nucleic acid-binding protein C1D-like [KO:K12592]
120711987  nuclear nucleic acid-binding protein C1D-like [KO:K12592]
120673850  uncharacterized protein LOC120673850 [KO:K12593]
120706008  uncharacterized protein LOC120706008 [KO:K12593]
120672134  terminal nucleotidyltransferase 4B-like [KO:K03514] [EC:2.7.7.19]
120707576  terminal nucleotidyltransferase 4B-like [KO:K03514] [EC:2.7.7.19]
120669807  DExH-box ATP-dependent RNA helicase DExH9-like [KO:K12598] [EC:5.6.2.6]
120685266  DExH-box ATP-dependent RNA helicase DExH10-like [KO:K12598] [EC:5.6.2.6]
120702330  DExH-box ATP-dependent RNA helicase DExH9-like [KO:K12598] [EC:5.6.2.6]
120643807  DExH-box ATP-dependent RNA helicase DExH10-like [KO:K12598] [EC:5.6.2.6]
120660943  DExH-box ATP-dependent RNA helicase DExH11-like [KO:K12599] [EC:5.6.2.6]
120687183  tetratricopeptide repeat protein SKI3-like isoform X1 [KO:K12600]
120651763  tetratricopeptide repeat protein SKI3-like isoform X1 [KO:K12600]
120685958  WD repeat-containing protein VIP3-like [KO:K12602]
120645183  WD repeat-containing protein VIP3-like [KO:K12602]
120688096  carbon catabolite repressor protein 4 homolog 1-like [KO:K12603] [EC:3.1.13.4]
120689569  carbon catabolite repressor protein 4 homolog 1-like [KO:K12603] [EC:3.1.13.4]
120647197  carbon catabolite repressor protein 4 homolog 1-like [KO:K12603] [EC:3.1.13.4]
120678513  carbon catabolite repressor protein 4 homolog 4-like [KO:K12603] [EC:3.1.13.4]
120651074  carbon catabolite repressor protein 4 homolog 1-like isoform X1 [KO:K12603] [EC:3.1.13.4]
120665628  carbon catabolite repressor protein 4 homolog 4-like isoform X1 [KO:K12603] [EC:3.1.13.4]
120698835  carbon catabolite repressor protein 4 homolog 4-like isoform X1 [KO:K12603] [EC:3.1.13.4]
120690437  CCR4-NOT transcription complex subunit 1-like isoform X1 [KO:K12604]
120651701  CCR4-NOT transcription complex subunit 1-like isoform X1 [KO:K12604]
120657393  probable NOT transcription complex subunit VIP2 isoform X1 [KO:K12605]
120644121  probable NOT transcription complex subunit VIP2 isoform X1 [KO:K12605]
120665118  probable NOT transcription complex subunit VIP2 isoform X1 [KO:K12605]
120698323  probable NOT transcription complex subunit VIP2 [KO:K12605]
120689607  general negative regulator of transcription subunit 3-like isoform X1 [KO:K12580]
120650213  CCR4-NOT transcription complex subunit 3-like isoform X1 [KO:K12580]
120705628  uncharacterized protein LOC120705628 [KO:K10643] [EC:2.3.2.27]
120675659  uncharacterized protein LOC120675659 isoform X1 [KO:K10643] [EC:2.3.2.27]
120679195  uncharacterized protein LOC120679195 [KO:K10643] [EC:2.3.2.27]
120679196  uncharacterized protein LOC120679196 [KO:K10643] [EC:2.3.2.27]
120679197  uncharacterized protein LOC120679197 isoform X1 [KO:K10643] [EC:2.3.2.27]
120712921  uncharacterized protein LOC120712921 [KO:K10643] [EC:2.3.2.27]
120712925  uncharacterized protein LOC120712925 [KO:K10643] [EC:2.3.2.27]
120712926  uncharacterized protein LOC120712926 isoform X1 [KO:K10643] [EC:2.3.2.27]
120669923  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
120685158  probable CCR4-associated factor 1 homolog 9 [KO:K12581]
120686599  probable CCR4-associated factor 1 homolog 9 [KO:K12581]
120700792  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
120642167  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
120702542  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
120657481  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
120689100  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
120645014  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
120660664  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
120660874  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
120648033  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
120663332  putative CCR4-associated factor 1 homolog 3 [KO:K12581]
120679585  probable CCR4-associated factor 1 homolog 6 [KO:K12581]
120694987  probable CCR4-associated factor 1 homolog 9 [KO:K12581]
120695646  probable CCR4-associated factor 1 homolog 7 [KO:K12581]
120653412  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
120712477  probable CCR4-associated factor 1 homolog 6 [KO:K12581]
120669268  probable CCR4-associated factor 1 homolog 11 [KO:K12581]
120656244  CCR4-NOT transcription complex subunit 9-like [KO:K12606]
120641758  CCR4-NOT transcription complex subunit 9-like [KO:K12606]
120656916  cell differentiation protein rcd1-like [KO:K12606]
120659150  CCR4-NOT transcription complex subunit 9-like [KO:K12606]
120659329  CCR4-NOT transcription complex subunit 9-like isoform X1 [KO:K12606]
120690836  CCR4-NOT transcription complex subunit 9-like [KO:K12606]
120661814  CCR4-NOT transcription complex subunit 9-like isoform X1 [KO:K12606]
120706664  CCR4-NOT transcription complex subunit 9-like [KO:K12606]
120649542  CCR4-NOT transcription complex subunit 9-like [KO:K12606]
120694958  CCR4-NOT transcription complex subunit 9-like [KO:K12606]
120683225  CCR4-NOT transcription complex subunit 9-like [KO:K12606]
120653599  uncharacterized protein LOC120653599 [KO:K12606]
120672979  CCR4-NOT transcription complex subunit 10-like [KO:K12607]
120660117  CCR4-NOT transcription complex subunit 10-like [KO:K12607]
120657562  ABC transporter I family member 19-like isoform X1 [KO:K12608]
120645831  ABC transporter I family member 19-like isoform X1 [KO:K12608]
120691775  ABC transporter I family member 20-like [KO:K12608]
120652568  ABC transporter I family member 20-like [KO:K12608]
120672150  DExH-box ATP-dependent RNA helicase DExH3-like [KO:K14442] [EC:5.6.2.6]
120689751  DExH-box ATP-dependent RNA helicase DExH1 isoform X1 [KO:K14442] [EC:5.6.2.6]
120690104  DExH-box ATP-dependent RNA helicase DExH3-like [KO:K14442] [EC:5.6.2.6]
120674992  DExH-box ATP-dependent RNA helicase DExH6-like [KO:K14442] [EC:5.6.2.6]
120706185  DExH-box ATP-dependent RNA helicase DExH3-like [KO:K14442] [EC:5.6.2.6]
120708174  DExH-box ATP-dependent RNA helicase DExH6-like [KO:K14442] [EC:5.6.2.6]
120649767  DExH-box ATP-dependent RNA helicase DExH3-like [KO:K14442] [EC:5.6.2.6]
120641193  poly(A)-specific ribonuclease PARN-like [KO:K01148] [EC:3.1.13.4]
120679231  poly(A)-specific ribonuclease PARN-like isoform X1 [KO:K01148] [EC:3.1.13.4]
120682905  poly(A)-specific ribonuclease PARN-like [KO:K01148] [EC:3.1.13.4]
120712476  poly(A)-specific ribonuclease PARN-like isoform X1 [KO:K01148] [EC:3.1.13.4]
120642149  polyadenylate-binding protein 4-like [KO:K13126]
120642395  polyadenylate-binding protein 2-like [KO:K13126]
120672940  polyadenylate-binding protein 8-like [KO:K13126]
120689301  polyadenylate-binding protein 4-like [KO:K13126]
120674249  30S ribosomal protein 2, chloroplastic-like [KO:K13126]
120705199  polyadenylate-binding protein 5-like [KO:K13126]
120660199  polyadenylate-binding protein 2-like [KO:K13126]
120660219  30S ribosomal protein 2, chloroplastic-like [KO:K13126]
120648840  polyadenylate-binding protein 4-like [KO:K13126]
120682619  polyadenylate-binding protein 2-like [KO:K13126]
120659713  mRNA-decapping enzyme-like protein isoform X1 [KO:K12611] [EC:3.-.-.-]
120690987  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
120649173  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
120663615  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
120696749  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
120666293  mRNA-decapping enzyme-like protein [KO:K12611] [EC:3.-.-.-]
120657545  mRNA-decapping enzyme subunit 2-like [KO:K12613] [EC:3.6.1.62]
120645584  mRNA-decapping enzyme subunit 2-like isoform X1 [KO:K12613] [EC:3.6.1.62]
120656604  DEAD-box ATP-dependent RNA helicase 8 [KO:K12614] [EC:5.6.2.7]
120692870  DEAD-box ATP-dependent RNA helicase 12 [KO:K12614] [EC:5.6.2.7]
120650582  DEAD-box ATP-dependent RNA helicase 12-like [KO:K12614] [EC:5.6.2.7]
120681240  DEAD-box ATP-dependent RNA helicase 8-like [KO:K12614] [EC:5.6.2.7]
120710526  DEAD-box ATP-dependent RNA helicase 8-like [KO:K12614] [EC:5.6.2.7]
120640223  enhancer of mRNA-decapping protein 4-like isoform X1 [KO:K12616]
120701969  enhancer of mRNA-decapping protein 4-like [KO:K12616]
120657076  enhancer of mRNA-decapping protein 4-like isoform X1 [KO:K12616]
120668457  LOW QUALITY PROTEIN: enhancer of mRNA-decapping protein 4-like [KO:K12616]
120655488  protein PAT1 homolog isoform X1 [KO:K12617]
120673578  protein PAT1 homolog 1-like isoform X1 [KO:K12617]
120708181  protein PAT1 homolog 1-like [KO:K12617]
120709105  protein PAT1 homolog [KO:K12617]
120664965  protein PAT1 homolog 1-like [KO:K12617]
120698157  protein PAT1 homolog 1-like [KO:K12617]
120643625  5'-3' exoribonuclease 3-like [KO:K12619] [EC:3.1.13.-]
120706403  5'-3' exoribonuclease 3-like isoform X1 [KO:K12619] [EC:3.1.13.-]
120676453  5'-3' exoribonuclease 3-like isoform X1 [KO:K12619] [EC:3.1.13.-]
120677783  5'-3' exoribonuclease 3-like isoform X1 [KO:K12619] [EC:3.1.13.-]
120711623  5'-3' exoribonuclease 3-like isoform X1 [KO:K12619] [EC:3.1.13.-]
120684339  5'-3' exoribonuclease 3-like [KO:K12619] [EC:3.1.13.-]
120641134  sm-like protein LSM1B [KO:K12620]
120683083  sm-like protein LSM1B [KO:K12620]
120678890  sm-like protein LSM2 isoform X1 [KO:K12621]
120711430  sm-like protein LSM2 isoform X1 [KO:K12621]
120676186  sm-like protein LSM3B [KO:K12622]
120708784  sm-like protein LSM3B [KO:K12622]
120665354  sm-like protein LSM3A [KO:K12622]
120698562  sm-like protein LSM3B [KO:K12622]
120706388  probable U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
120676549  probable U6 snRNA-associated Sm-like protein LSm4 isoform X1 [KO:K12623]
120665631  sm-like protein LSM5 [KO:K12624]
120698836  sm-like protein LSM5 [KO:K12624]
120640746  U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
120655832  U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
120702475  U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
120682934  U6 snRNA-associated Sm-like protein LSm6 [KO:K12625]
120641912  sm-like protein LSM7 [KO:K12626]
120682954  sm-like protein LSM7 [KO:K12626]
120700417  sm-like protein LSM8 [KO:K12627]
120664402  sm-like protein LSM8 [KO:K12627]
120669837  enolase 1 [KO:K01689] [EC:4.2.1.11]
120702522  enolase 1 [KO:K01689] [EC:4.2.1.11]
120702524  enolase 1-like [KO:K01689] [EC:4.2.1.11]
120660531  enolase 1, chloroplastic-like [KO:K01689] [EC:4.2.1.11]
120678259  enolase 1, chloroplastic-like [KO:K01689] [EC:4.2.1.11]
120693134  cytosolic enolase 3-like [KO:K01689] [EC:4.2.1.11]
120665998  enolase 2 [KO:K01689] [EC:4.2.1.11]
120652901  cytosolic enolase 3-like isoform X1 [KO:K01689] [EC:4.2.1.11]
120669627  enolase 1-like [KO:K01689] [EC:4.2.1.11]
120699236  enolase-like [KO:K01689] [EC:4.2.1.11]
120656465  polyribonucleotide nucleotidyltransferase 2, mitochondrial-like [KO:K00962] [EC:2.7.7.8]
120659431  probable polyribonucleotide nucleotidyltransferase 1, chloroplastic isoform X1 [KO:K00962] [EC:2.7.7.8]
120662893  probable polyribonucleotide nucleotidyltransferase 1, chloroplastic [KO:K00962] [EC:2.7.7.8]
120708848  polyribonucleotide nucleotidyltransferase 2, mitochondrial-like [KO:K00962] [EC:2.7.7.8]
120662191  probable ATP-dependent DNA helicase RecQ [KO:K03654] [EC:5.6.2.4]
120694869  probable ATP-dependent DNA helicase RecQ [KO:K03654] [EC:5.6.2.4]
120669871  ATP-dependent 6-phosphofructokinase 6-like [KO:K00850] [EC:2.7.1.11]
120641203  ATP-dependent 6-phosphofructokinase 2-like [KO:K00850] [EC:2.7.1.11]
120702644  ATP-dependent 6-phosphofructokinase 6-like [KO:K00850] [EC:2.7.1.11]
120673810  ATP-dependent 6-phosphofructokinase 6-like [KO:K00850] [EC:2.7.1.11]
120660656  ATP-dependent 6-phosphofructokinase 5, chloroplastic-like [KO:K00850] [EC:2.7.1.11]
120675562  ATP-dependent 6-phosphofructokinase 6-like [KO:K00850] [EC:2.7.1.11]
120690830  ATP-dependent 6-phosphofructokinase 5, chloroplastic-like isoform X1 [KO:K00850] [EC:2.7.1.11]
120705727  ATP-dependent 6-phosphofructokinase 6-like [KO:K00850] [EC:2.7.1.11]
120707976  ATP-dependent 6-phosphofructokinase 6-like [KO:K00850] [EC:2.7.1.11]
120664342  ATP-dependent 6-phosphofructokinase 6-like [KO:K00850] [EC:2.7.1.11]
120664868  ATP-dependent 6-phosphofructokinase 6-like [KO:K00850] [EC:2.7.1.11]
120695637  ATP-dependent 6-phosphofructokinase 5, chloroplastic-like isoform X1 [KO:K00850] [EC:2.7.1.11]
120651108  ATP-dependent 6-phosphofructokinase 5, chloroplastic-like isoform X1 [KO:K00850] [EC:2.7.1.11]
120697647  ATP-dependent 6-phosphofructokinase 6-like [KO:K00850] [EC:2.7.1.11]
120698069  ATP-dependent 6-phosphofructokinase 6-like [KO:K00850] [EC:2.7.1.11]
120712465  ATP-dependent 6-phosphofructokinase 5, chloroplastic-like [KO:K00850] [EC:2.7.1.11]
120639492  ATP-dependent 6-phosphofructokinase-like isoform X1 [KO:K00850] [EC:2.7.1.11]
120683436  ATP-dependent 6-phosphofructokinase 2-like [KO:K00850] [EC:2.7.1.11]
120688413  heat shock 70 kDa protein, mitochondrial-like [KO:K04043]
120660774  heat shock 70 kDa protein, mitochondrial [KO:K04043]
120661092  heat shock 70 kDa protein, mitochondrial-like [KO:K04043]
120679889  heat shock 70 kDa protein, mitochondrial-like [KO:K04043]
120683327  heat shock 70 kDa protein, mitochondrial-like [KO:K04043]
120641102  chaperonin 60 subunit beta 4, chloroplastic-like [KO:K04077] [EC:5.6.1.7]
120702394  ruBisCO large subunit-binding protein subunit beta, chloroplastic-like [KO:K04077] [EC:5.6.1.7]
120689842  chaperonin CPN60-2, mitochondrial [KO:K04077] [EC:5.6.1.7]
120646736  uncharacterized protein LOC120646736 isoform X1 [KO:K04077] [EC:5.6.1.7]
120647334  chaperonin CPN60-1, mitochondrial-like isoform X1 [KO:K04077] [EC:5.6.1.7]
120664785  chaperonin CPN60-like 2, mitochondrial [KO:K04077] [EC:5.6.1.7]
120650859  chaperonin CPN60-2, mitochondrial-like [KO:K04077] [EC:5.6.1.7]
120650954  ruBisCO large subunit-binding protein subunit beta, chloroplastic-like [KO:K04077] [EC:5.6.1.7]
120654355  ruBisCO large subunit-binding protein subunit beta, chloroplastic-like [KO:K04077] [EC:5.6.1.7]
120668805  ruBisCO large subunit-binding protein subunit beta, chloroplastic [KO:K04077] [EC:5.6.1.7]
120683706  ruBisCO large subunit-binding protein subunit beta, chloroplastic-like isoform X1 [KO:K04077] [EC:5.6.1.7]
120683708  chaperonin 60 subunit beta 4, chloroplastic-like [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
Related
pathway
pvir03015  mRNA surveillance pathway
KO pathway
ko03018   
LinkDB

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