Pathways Knowlegdes

Biological pathway database

Pathway DOIs Note
nicotine biosynthesis

Accession ID: BioCyc:META_PWY-5316
  • 10.1007/s11103-004-3352-7
  • 10.1073/pnas.0506581102
 Siminszky B, Gavilano L, Bowen SW, Dewey RE. Conversion of nicotine to nornicotine in Nicotiana tabacum is mediated by CYP82E4, a cytochrome P450 monooxygenase. Proc. Natl. Acad. Sci. U.S.A. 2005 Sep 28;102(41):14919–24. doi: 10.1073/pnas.0506581102.; Heim WG, Jelesko JG. Association of diamine oxidase and S-adenosylhomocysteine hydrolase in Nicotiana tabacum extracts. Plant Mol Biol. 2004 Sep;56(2):299–308. doi: 10.1007/s11103-004-3352-7. PMID: 15604745.
superpathway of nicotine biosynthesis

Accession ID: BioCyc:META_PWY-7342
  • 10.1007/s11103-004-3352-7
  • 10.1073/pnas.0506581102
  • 10.1093/pcp/pcn096
 Shoji T, Hashimoto T. Why does anatabine, but not nicotine, accumulate in jasmonate-elicited cultured tobacco BY-2 cells? Plant Cell Physiol. 2008 Aug;49(8):1209–16. doi: 10.1093/pcp/pcn096. PMID: 18567891.; Siminszky B, Gavilano L, Bowen SW, Dewey RE. Conversion of nicotine to nornicotine in Nicotiana tabacum is mediated by CYP82E4, a cytochrome P450 monooxygenase. Proc. Natl. Acad. Sci. U.S.A. 2005 Sep 28;102(41):14919–24. doi: 10.1073/pnas.0506581102.; Heim WG, Jelesko JG. Association of diamine oxidase and S-adenosylhomocysteine hydrolase in Nicotiana tabacum extracts. Plant Mol Biol. 2004 Sep;56(2):299–308. doi: 10.1007/s11103-004-3352-7. PMID: 15604745.
calystegine biosynthesis

Accession ID: BioCyc:META_PWY-5318
  • 10.1023/a:1013315110746
  • 10.1073/pnas.90.20.9591
  • 10.1104/pp.100.2.836
 Keiner R, Kaiser H, Nakajima K, Hashimoto T, Dräger B. Molecular cloning, expression and characterization of tropinone reductase II, an enzyme of the SDR family in Solanum tuberosum (L.). Plant Mol Biol. 2002 Feb 01;48(3):299–308. doi: 10.1023/a:1013315110746. PMID: 11855731.; Nakajima K, Hashimoto T, Yamada Y. Two tropinone reductases with different stereospecificities are short-chain dehydrogenases evolved from a common ancestor. Proc. Natl. Acad. Sci. U.S.A. 1993 Oct 15;90(20):9591–5. doi: 10.1073/pnas.90.20.9591.; Hashimoto T, Nakajima K, Ongena G, Yamada Y. Two Tropinone Reductases with Distinct Stereospecificities from Cultured Roots of Hyoscyamus niger. Plant Physiol. 1992 Oct 01;100(2):836–45. doi: 10.1104/pp.100.2.836.
cocaine biosynthesis

Accession ID: BioCyc:META_PWY-5843
  • 10.1016/0031-9422(95)00667-2
  • 10.1039/b001713m
  • 10.1055/s-2006-960979
 Humphrey AJ, O'Hagan D. Tropane alkaloid biosynthesis. A century old problem unresolved. Nat Prod Rep. 2001 Oct;18(5):494–502. doi: 10.1039/b001713m. PMID: 11699882.; Huang MN, Abraham TW, Kim SH, Leete E. 1-Methylpyrrolidine-2-acetic Acid is not a Precursor of Tropane Alkaloids. Phytochemistry. 1996 Feb;41(3):767–73. doi: 10.1016/0031-9422(95)00667-2. PMID: 8835455.; Leete E. Recent developments in the biosynthesis of the tropane alkaloids. Planta Med. 1990 Aug;56(4):339–52. doi: 10.1055/s-2006-960979. PMID: 2236285.
hyoscyamine and scopolamine biosynthesis

Accession ID: BioCyc:META_PWY-5317
  • 10.1016/s0021-9258(18)92843-7
  • 10.1021/np010612c
  • 10.1073/pnas.90.20.9591
  • 10.1093/oxfordjournals.pcp.a029494
  • 10.1104/pp.100.2.836
 Lanoue A, Boitel-Conti M, Portais J, Laberche J, Barbotin J, Christen P, Sangwan-Norreel B. Kinetic Study of Littorine Rearrangement inDaturainnoxiaHairy Roots by13C NMR Spectroscopy. J. Nat. Prod. 2002 Jul 11;65(8):1131–5. doi: 10.1021/np010612c.; Nakajima K, Hashimoto T. Two tropinone reductases, that catalyze opposite stereospecific reductions in tropane alkaloid biosynthesis, are localized in plant root with different cell-specific patterns. Plant Cell Physiol. 1999 Nov;40(11):1099–107. doi: 10.1093/oxfordjournals.pcp.a029494. PMID: 10635114.; Nakajima K, Hashimoto T, Yamada Y. Two tropinone reductases with different stereospecificities are short-chain dehydrogenases evolved from a common ancestor. Proc. Natl. Acad. Sci. U.S.A. 1993 Oct 15;90(20):9591–5. doi: 10.1073/pnas.90.20.9591.; Hashimoto T, Nakajima K, Ongena G, Yamada Y. Two Tropinone Reductases with Distinct Stereospecificities from Cultured Roots of Hyoscyamus niger. Plant Physiol. 1992 Oct 01;100(2):836–45. doi: 10.1104/pp.100.2.836.; Matsuda J, Okabe S, Hashimoto T, Yamada Y. Molecular cloning of hyoscyamine 6 beta-hydroxylase, a 2-oxoglutarate-dependent dioxygenase, from cultured roots of Hyoscyamus niger. Journal of Biological Chemistry. 1991 May;266(15):9460–4. doi: 10.1016/s0021-9258(18)92843-7.
N-methyl-Δ1-pyrrolinium cation biosynthesis

Accession ID: BioCyc:META_PWY-5315
  • 10.1007/s11103-004-3352-7
  • 10.1073/pnas.0401391101
  • 10.1093/pcp/pcn096
  • 10.1104/pp.100.2.826
  • 10.1104/pp.93.1.216
 Shoji T, Hashimoto T. Why does anatabine, but not nicotine, accumulate in jasmonate-elicited cultured tobacco BY-2 cells? Plant Cell Physiol. 2008 Aug;49(8):1209–16. doi: 10.1093/pcp/pcn096. PMID: 18567891.; Heim WG, Jelesko JG. Association of diamine oxidase and S-adenosylhomocysteine hydrolase in Nicotiana tabacum extracts. Plant Mol Biol. 2004 Sep;56(2):299–308. doi: 10.1007/s11103-004-3352-7. PMID: 15604745.; Zhang L, Ding R, Chai Y, Bonfill M, Moyano E, Oksman-Caldentey K, Xu T, Pi Y, Wang Z, Zhang H, Kai G, Liao Z, Sun X, Tang K. Engineering tropane biosynthetic pathway in Hyoscyamus niger hairy root cultures. Proc. Natl. Acad. Sci. U.S.A. 2004 Apr 14;101(17):6786–91. doi: 10.1073/pnas.0401391101.; Nadim MK, Brenner BM. Glomerular normalcy and pathosis: a 'fin de millénaire' perspective. J Nephrol. 1999 Jul;12 Suppl 2():S16–28. PMID: 10688399.; Hibi N, Fujita T, Hatano M, Hashimoto T, Yamada Y. Putrescine N-Methyltransferase in Cultured Roots of Hyoscyamus albus: n-Butylamine as a Potent Inhibitor of the Transferase both in Vitro and in Vivo. Plant Physiol. 1992 Oct;100(2):826–35. PMID: 16653064; PMCID: PMC1075632.; Hashimoto T, Mitani A, Yamada Y. Diamine Oxidase from Cultured Roots of Hyoscyamus niger: Its Function in Tropane Alkaloid Biosynthesis. Plant Physiol. 1990 May;93(1):216–21. PMID: 16667438; PMCID: PMC1062491.
hyoscyamine and scopolamine biosynthesis

Accession ID: BioCyc:THAPS_PWY-5317		 -
superpathway of hyoscyamine and scopolamine biosynthesis

Accession ID: BioCyc:META_PWY-7341
  • 10.1016/s0021-9258(18)92843-7
  • 10.1021/np010612c
  • 10.1073/pnas.90.20.9591
  • 10.1093/oxfordjournals.pcp.a029494
  • 10.1104/pp.100.2.836
 Lanoue A, Boitel-Conti M, Portais J, Laberche J, Barbotin J, Christen P, Sangwan-Norreel B. Kinetic Study of Littorine Rearrangement inDaturainnoxiaHairy Roots by13C NMR Spectroscopy. J. Nat. Prod. 2002 Jul 11;65(8):1131–5. doi: 10.1021/np010612c.; Nakajima K, Hashimoto T. Two tropinone reductases, that catalyze opposite stereospecific reductions in tropane alkaloid biosynthesis, are localized in plant root with different cell-specific patterns. Plant Cell Physiol. 1999 Nov;40(11):1099–107. doi: 10.1093/oxfordjournals.pcp.a029494. PMID: 10635114.; Nakajima K, Hashimoto T, Yamada Y. Two tropinone reductases with different stereospecificities are short-chain dehydrogenases evolved from a common ancestor. Proc. Natl. Acad. Sci. U.S.A. 1993 Oct 15;90(20):9591–5. doi: 10.1073/pnas.90.20.9591.; Hashimoto T, Nakajima K, Ongena G, Yamada Y. Two Tropinone Reductases with Distinct Stereospecificities from Cultured Roots of Hyoscyamus niger. Plant Physiol. 1992 Oct 01;100(2):836–45. doi: 10.1104/pp.100.2.836.; Matsuda J, Okabe S, Hashimoto T, Yamada Y. Molecular cloning of hyoscyamine 6 beta-hydroxylase, a 2-oxoglutarate-dependent dioxygenase, from cultured roots of Hyoscyamus niger. Journal of Biological Chemistry. 1991 May;266(15):9460–4. doi: 10.1016/s0021-9258(18)92843-7.
calystegine biosynthesis

Accession ID: PlantCyc:SPENNELLII_PWY-5318		 -
superpathway of nicotine biosynthesis

Accession ID: PlantCyc:SPENNELLII_PWY-7342		 -
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis

Accession ID: PlantCyc:SPENNELLII_PWY-7341		 -
nicotine biosynthesis

Accession ID: PlantCyc:TOMATO_PWY-5316		 -
calystegine biosynthesis

Accession ID: PlantCyc:TOMATO_PWY-5318		 -
1-methylpyrrolinium biosynthesis

Accession ID: PlantCyc:CANNUUM_PWY-5315		 -
superpathway of nicotine biosynthesis

Accession ID: PlantCyc:EGGPLANT_PWY-7342		 -
1-methylpyrrolinium biosynthesis

Accession ID: PlantCyc:EGGPLANT_PWY-5315		 -
nicotine biosynthesis

Accession ID: PlantCyc:NTABACUM_TN90_PWY-5316
  • 10.1007/s11103-004-3352-7
  • 10.1073/pnas.0506581102
 Siminszky B, Gavilano L, Bowen SW, Dewey RE. Conversion of nicotine to nornicotine in Nicotiana tabacum is mediated by CYP82E4, a cytochrome P450 monooxygenase. Proc. Natl. Acad. Sci. U.S.A. 2005 Sep 28;102(41):14919–24. doi: 10.1073/pnas.0506581102.; Heim WG, Jelesko JG. Association of diamine oxidase and S-adenosylhomocysteine hydrolase in Nicotiana tabacum extracts. Plant Mol Biol. 2004 Sep;56(2):299–308. doi: 10.1007/s11103-004-3352-7. PMID: 15604745.
hyoscyamine and scopolamine biosynthesis

Accession ID: PlantCyc:CARROT_PWY-5317		 -
tropane alkaloids biosynthesis

Accession ID: PlantCyc:PAXILLARIS_PWY-5317		 -
superpathway of nicotine biosynthesis

Accession ID: PlantCyc:POTATO_PWY-7342		 -