KEGG   PATHWAY: aly00900
Entry
aly00900                    Pathway                                
Name
Terpenoid backbone biosynthesis - Arabidopsis lyrata (lyrate rockcress)
Description
Terpenoids, also known as isoprenoids, are a large class of natural products consisting of isoprene (C5) units. There are two biosynthetic pathways, the mevalonate pathway [MD:M00095] and the non-mevalonate pathway or the MEP/DOXP pathway [MD:M00096], for the terpenoid building blocks: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). The action of prenyltransferases then generates higher-order building blocks: geranyl diphosphate (GPP), farsenyl diphosphate (FPP), and geranylgeranyl diphosphate (GGPP), which are the precursors of monoterpenoids (C10), sesquiterpenoids (C15), and diterpenoids (C20), respectively. Condensation of these building blocks gives rise to the precursors of sterols (C30) and carotenoids (C40). The MEP/DOXP pathway is absent in higher animals and fungi, but in green plants the MEP/DOXP and mevalonate pathways co-exist in separate cellular compartments. The MEP/DOXP pathway, operating in the plastids, is responsible for the formation of essential oil monoterpenes and linalyl acetate, some sesquiterpenes, diterpenes, and carotenoids and phytol. The mevalonate pathway, operating in the cytosol, gives rise to triterpenes, sterols, and most sesquiterpenes.
Class
Metabolism; Metabolism of terpenoids and polyketides
Pathway map
aly00900  Terpenoid backbone biosynthesis
aly00900

Module
aly_M00095  C5 isoprenoid biosynthesis, mevalonate pathway [PATH:aly00900]
aly_M00096  C5 isoprenoid biosynthesis, non-mevalonate pathway [PATH:aly00900]
aly_M00366  C10-C20 isoprenoid biosynthesis, plants [PATH:aly00900]
Other DBs
GO: 0009240 0016091
Organism
Arabidopsis lyrata (lyrate rockcress) [GN:aly]
Gene
9319377  1-deoxy-D-xylulose-5-phosphate synthase, chloroplastic [KO:K01662] [EC:2.2.1.7]
9304269  1-deoxy-D-xylulose-5-phosphate synthase, chloroplastic [KO:K01662] [EC:2.2.1.7]
9309577  1-deoxy-D-xylulose-5-phosphate synthase, chloroplastic isoform X2 [KO:K01662] [EC:2.2.1.7]
9300894  1-deoxy-D-xylulose 5-phosphate reductoisomerase, chloroplastic [KO:K00099] [EC:1.1.1.267]
9311200  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic [KO:K00991] [EC:2.7.7.60]
9315087  4-diphosphocytidyl-2-C-methyl-D-erythritol kinase, chloroplastic [KO:K00919] [EC:2.7.1.148]
9322439  2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, chloroplastic isoform X1 [KO:K01770] [EC:4.6.1.12]
9300770  4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (ferredoxin), chloroplastic [KO:K03526] [EC:1.17.7.1 1.17.7.3]
9305225  4-hydroxy-3-methylbut-2-enyl diphosphate reductase, chloroplastic [KO:K03527] [EC:1.17.7.4]
9299401  probable acetyl-CoA acetyltransferase, cytosolic 2 isoform X1 [KO:K00626] [EC:2.3.1.9]
9299957  acetyl-CoA acetyltransferase, cytosolic 1 [KO:K00626] [EC:2.3.1.9]
9308696  hydroxymethylglutaryl-CoA synthase [KO:K01641] [EC:2.3.3.10]
9320120  3-hydroxy-3-methylglutaryl-coenzyme A reductase 2 [KO:K00021] [EC:1.1.1.34]
9325151  3-hydroxy-3-methylglutaryl-coenzyme A reductase 1 [KO:K00021] [EC:1.1.1.34]
9308340  mevalonate kinase [KO:K00869] [EC:2.7.1.36]
9327018  phosphomevalonate kinase, peroxisomal [KO:K00938] [EC:2.7.4.2]
9315829  diphosphomevalonate decarboxylase MVD1, peroxisomal [KO:K01597] [EC:4.1.1.33]
9312318  diphosphomevalonate decarboxylase MVD2, peroxisomal [KO:K01597] [EC:4.1.1.33]
9329452  uncharacterized protein LOC9329452 [KO:K06981] [EC:2.7.4.26]
9307787  isopentenyl-diphosphate Delta-isomerase I, chloroplastic [KO:K01823] [EC:5.3.3.2]
9320405  isopentenyl-diphosphate Delta-isomerase II, chloroplastic [KO:K01823] [EC:5.3.3.2]
9306191  farnesyl pyrophosphate synthase 2 [KO:K00787] [EC:2.5.1.1 2.5.1.10]
9299444  farnesyl pyrophosphate synthase 1, mitochondrial [KO:K00787] [EC:2.5.1.1 2.5.1.10]
9315575  solanesyl diphosphate synthase 3, chloroplastic/mitochondrial isoform X1 [KO:K14066] [EC:2.5.1.1]
9321115  geranylgeranyl pyrophosphate synthase 3, chloroplastic [KO:K13789] [EC:2.5.1.1 2.5.1.10 2.5.1.29]
9322252  LOW QUALITY PROTEIN: geranylgeranyl pyrophosphate synthase 7, chloroplastic [KO:K13789] [EC:2.5.1.1 2.5.1.10 2.5.1.29]
9322253  geranylgeranyl pyrophosphate synthase 4 [KO:K13789] [EC:2.5.1.1 2.5.1.10 2.5.1.29]
9305092  heterodimeric geranylgeranyl pyrophosphate synthase large subunit 1, chloroplastic [KO:K13789] [EC:2.5.1.1 2.5.1.10 2.5.1.29]
9319299  geranylgeranyl pyrophosphate synthase 10, mitochondrial [KO:K13789] [EC:2.5.1.1 2.5.1.10 2.5.1.29]
9327578  geranylgeranyl pyrophosphate synthase 6, mitochondrial [KO:K13789] [EC:2.5.1.1 2.5.1.10 2.5.1.29]
9316595  heterodimeric geranylgeranyl pyrophosphate synthase large subunit 2 [KO:K13789] [EC:2.5.1.1 2.5.1.10 2.5.1.29]
9320214  geranylgeranyl pyrophosphate synthase 4 [KO:K13789] [EC:2.5.1.1 2.5.1.10 2.5.1.29]
9302872  heterodimeric geranylgeranyl pyrophosphate synthase small subunit, chloroplastic [KO:K13789] [EC:2.5.1.1 2.5.1.10 2.5.1.29]
9323808  solanesyl diphosphate synthase 1 isoform X1 [KO:K05356] [EC:2.5.1.84 2.5.1.85]
9304798  solanesyl diphosphate synthase 2, chloroplastic [KO:K05356] [EC:2.5.1.84 2.5.1.85]
110225373  solanesyl diphosphate synthase 2, chloroplastic [KO:K05356] [EC:2.5.1.84 2.5.1.85]
9316564  dehydrodolichyl diphosphate synthase 1 [KO:K11778] [EC:2.5.1.87]
9316565  dehydrodolichyl diphosphate synthase 1 isoform X1 [KO:K11778] [EC:2.5.1.87]
9322188  dehydrodolichyl diphosphate synthase 6 [KO:K11778] [EC:2.5.1.87]
9325958  dehydrodolichyl diphosphate synthase complex subunit NUS1 [KO:K11778] [EC:2.5.1.87]
110225902  dehydrodolichyl diphosphate synthase 7 [KO:K11778] [EC:2.5.1.87]
9302458  dehydrodolichyl diphosphate synthase 8 [KO:K11778] [EC:2.5.1.87]
9302365  dehydrodolichyl diphosphate synthase 2 [KO:K11778] [EC:2.5.1.87]
9300665  dehydrodolichyl diphosphate synthase 4 [KO:K11778] [EC:2.5.1.87]
9302366  dehydrodolichyl diphosphate synthase 5 [KO:K11778] [EC:2.5.1.87]
9325042  geranylgeranyl diphosphate reductase, chloroplastic [KO:K10960] [EC:1.3.1.83 1.3.1.111]
9306207  (E)-beta-ocimene synthase, chloroplastic [KO:K12742] [EC:4.2.3.27]
9314337  protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha [KO:K05955] [EC:2.5.1.58 2.5.1.59]
110226330  protein farnesyltransferase subunit beta [KO:K05954] [EC:2.5.1.58]
9317504  CAAX prenyl protease 2 [KO:K08658] [EC:3.4.26.1]
9311057  CAAX prenyl protease 1 homolog [KO:K06013] [EC:3.4.24.84]
9307390  protein-S-isoprenylcysteine O-methyltransferase B [KO:K00587] [EC:2.1.1.100]
9308120  protein-S-isoprenylcysteine O-methyltransferase A [KO:K00587] [EC:2.1.1.100]
9309814  isoprenylcysteine alpha-carbonyl methylesterase ICME [KO:K15889] [EC:3.1.1.-]
9318295  probable isoprenylcysteine alpha-carbonyl methylesterase ICMEL2 [KO:K15889] [EC:3.1.1.-]
9326739  probable isoprenylcysteine alpha-carbonyl methylesterase ICMEL1 [KO:K15889] [EC:3.1.1.-]
9302655  farnesylcysteine lyase [KO:K05906] [EC:1.8.3.5 1.8.3.6]
9305289  uncharacterized protein LOC9305289 [KO:K15891] [EC:1.1.1.354]
9302348  LOW QUALITY PROTEIN: farnesol kinase, chloroplastic [KO:K15892] [EC:2.7.1.216]
Compound
C00022  Pyruvate
C00024  Acetyl-CoA
C00118  D-Glyceraldehyde 3-phosphate
C00129  Isopentenyl diphosphate
C00235  Dimethylallyl diphosphate
C00332  Acetoacetyl-CoA
C00341  Geranyl diphosphate
C00353  Geranylgeranyl diphosphate
C00356  (S)-3-Hydroxy-3-methylglutaryl-CoA
C00418  (R)-Mevalonate
C00448  trans,trans-Farnesyl diphosphate
C01107  (R)-5-Phosphomevalonate
C01126  (2E,6E)-Farnesol
C01143  (R)-5-Diphosphomevalonate
C01230  all-trans-Hexaprenyl diphosphate
C02321  cis-1,4-Polyisoprene
C03461  2-trans,6-trans-Farnesal
C04145  all-trans-Nonaprenyl diphosphate
C04146  all-trans-Octaprenyl diphosphate
C04216  all-trans-Heptaprenyl diphosphate
C04506  Protein C-terminal S-farnesyl-L-cysteine
C04574  di-trans,poly-cis-Undecaprenyl diphosphate
C04748  Protein C-terminal S-farnesyl-L-cysteine methyl ester
C05427  Phytyl diphosphate
C05859  ditrans,polycis-Polyprenyl diphosphate
C06081  Polyprenol
C11434  2-C-Methyl-D-erythritol 4-phosphate
C11435  4-(Cytidine 5'-diphospho)-2-C-methyl-D-erythritol
C11436  2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol
C11437  1-Deoxy-D-xylulose 5-phosphate
C11453  2-C-Methyl-D-erythritol 2,4-cyclodiphosphate
C11811  1-Hydroxy-2-methyl-2-butenyl 4-diphosphate
C16521  Isoprene
C16826  2-cis,6-trans-Farnesyl diphosphate
C17432  all-trans-Decaprenyl diphosphate
C18321  trans,octacis-Decaprenyl diphosphate
C19691  Farnesylcysteine
C19760  2-cis,6-cis-Farnesyl diphosphate
C19852  tritrans,heptacis-Undecaprenyl diphosphate
C19853  trans,polycis-Polyprenyl diphosphate
C20120  S-Farnesyl protein
C20121  trans,trans-Farnesyl phosphate
C20345  Isopentenyl phosphate
C20847  (R)-Mevalonate 3-phosphate
C20848  (R)-Mevalonate 3,5-bisphosphate
C22453  trans-Anhydromevalonate 5-phosphate
Reference
  Authors
Lange BM, Ghassemian M.
  Title
Genome organization in Arabidopsis thaliana: a survey for genes involved in isoprenoid and chlorophyll metabolism.
  Journal
Plant Mol Biol 51:925-48 (2003)
DOI:10.1023/A:1023005504702
Reference
  Authors
Saiki R, Nagata A, Kainou T, Matsuda H, Kawamukai M
  Title
Characterization of solanesyl and decaprenyl diphosphate synthases in mice and humans.
  Journal
FEBS J 272:5606-22 (2005)
DOI:10.1111/j.1742-4658.2005.04956.x
Reference
PMID:9858571
  Authors
Sato M, Sato K, Nishikawa S, Hirata A, Kato J, Nakano A
  Title
The yeast RER2 gene, identified by endoplasmic reticulum protein localization mutations, encodes cis-prenyltransferase, a key enzyme in dolichol synthesis.
  Journal
Mol Cell Biol 19:471-83 (1999)
DOI:10.1128/MCB.19.1.471
Reference
  Authors
Vannice JC, Skaff DA, Keightley A, Addo JK, Wyckoff GJ, Miziorko HM
  Title
Identification in Haloferax volcanii of phosphomevalonate decarboxylase and isopentenyl phosphate kinase as catalysts of the terminal enzyme reactions in an  archaeal alternate mevalonate pathway.
  Journal
J Bacteriol 196:1055-63 (2014)
DOI:10.1128/JB.01230-13
Related
pathway
aly00010  Glycolysis / Gluconeogenesis
aly00100  Steroid biosynthesis
aly00130  Ubiquinone and other terpenoid-quinone biosynthesis
aly00270  Cysteine and methionine metabolism
aly00510  N-Glycan biosynthesis
aly00902  Monoterpenoid biosynthesis
aly00904  Diterpenoid biosynthesis
aly00906  Carotenoid biosynthesis
aly00908  Zeatin biosynthesis
aly00909  Sesquiterpenoid and triterpenoid biosynthesis
KO pathway
ko00900   
LinkDB

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