Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| luteolin glycosides biosynthesis Accession ID: PlantCyc:CROSEUS_PWY-6239 |
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Masada S, Terasaka K, Oguchi Y, Okazaki S, Mizushima T, Mizukami H. Functional and structural characterization of a flavonoid glucoside 1,6-glucosyltransferase from Catharanthus roseus. Plant Cell Physiol. 2009 Aug;50(8):1401–15. doi: 10.1093/pcp/pcp088. PMID: 19561332. |
| oryzalexin D and E biosynthesis Accession ID: PlantCyc:PLANT_PWY-7478 |
|
Wu Y, Wang Q, Hillwig ML, Peters RJ. Picking sides: distinct roles for CYP76M6 and CYP76M8 in rice oryzalexin biosynthesis. Biochem J. 2013 Sep 01;454(2):209–16. PMID: 23795884; PMCID: PMC3787970.; Sang T, Ge S. Understanding rice domestication and implications for cultivar improvement. Curr Opin Plant Biol. 2013 May;16(2):139–46. doi: 10.1016/j.pbi.2013.03.003. PMID: 23545218.; Wang Q, Hillwig ML, Okada K, Yamazaki K, Wu Y, Swaminathan S, Yamane H, Peters RJ. Characterization of CYP76M5–8 Indicates Metabolic Plasticity within a Plant Biosynthetic Gene Cluster. Journal of Biological Chemistry. 2012 Feb;287(9):6159–68. doi: 10.1074/jbc.m111.305599.; Wang Q, Hillwig ML, Wu Y, Peters RJ. CYP701A8: a rice ent-kaurene oxidase paralog diverted to more specialized diterpenoid metabolism. Plant Physiol. 2012 Mar;158(3):1418–25. PMID: 22247270; PMCID: PMC3291257.; Osbourn A. Gene clusters for secondary metabolic pathways: an emerging theme in plant biology. Plant Physiol. 2010 Oct;154(2):531–5. PMID: 20921179; PMCID: PMC2949040.; Hasegawa M, Mitsuhara I, Seo S, Imai T, Koga J, Okada K, Yamane H, Ohashi Y. Phytoalexin accumulation in the interaction between rice and the blast fungus. Mol Plant Microbe Interact. 2010 Aug;23(8):1000–11. doi: 10.1094/mpmi-23-8-1000. PMID: 20615111.; Osbourn AE, Field B. Operons. Cellular and Molecular Life Sciences. 2009 Aug 07;66(23):3755–75. doi: 10.1007/s00018-009-0114-3.; Fischbach MA, Walsh CT, Clardy J. The evolution of gene collectives: How natural selection drives chemical innovation. Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4601–8. PMID: 18216259; PMCID: PMC2290807.; Cyr A, Wilderman PR, Determan M, Peters RJ. A modular approach for facile biosynthesis of labdane-related diterpenes. J Am Chem Soc. 2007 May 30;129(21):6684–5. PMID: 17480080; PMCID: PMC2518946.; Xu M, Wilderman PR, Peters RJ. Following evolution's lead to a single residue switch for diterpene synthase product outcome. Proc Natl Acad Sci U S A. 2007 May 01;104(18):7397–401. PMID: 17456599; PMCID: PMC1855280.; Xu M, Wilderman PR, Morrone D, Xu J, Roy A, Margis-Pinheiro M, Upadhyaya NM, Coates RM, Peters RJ. Functional characterization of the rice kaurene synthase-like gene family. Phytochemistry. 2007 Feb;68(3):312–26. doi: 10.1016/j.phytochem.2006.10.016. PMID: 17141283.; Peters RJ. Uncovering the complex metabolic network underlying diterpenoid phytoalexin biosynthesis in rice and other cereal crop plants. Phytochemistry. 2006 Nov;67(21):2307–17. doi: 10.1016/j.phytochem.2006.08.009. PMID: 16956633.; Prisic S, Xu M, Wilderman PR, Peters RJ. Rice contains two disparate ent-copalyl diphosphate synthases with distinct metabolic functions. Plant Physiol. 2004 Dec;136(4):4228–36. PMID: 15542489; PMCID: PMC535852.; Otomo K, Kenmoku H, Oikawa H, König WA, Toshima H, Mitsuhashi W, Yamane H, Sassa T, Toyomasu T. Biological functions of ent- and syn-copalyl diphosphate synthases in rice: key enzymes for the branch point of gibberellin and phytoalexin biosynthesis. The Plant Journal. 2004 Jul 30;39(6):886–93. doi: 10.1111/j.1365-313x.2004.02175.x. |
| rosmarinic acid biosynthesis I Accession ID: PlantCyc:PLANT_PWY-5048 |
|
Vogelsang K, Schneider B, Petersen M. Production of rosmarinic acid and a new rosmarinic acid 3'-O-beta-D-glucoside in suspension cultures of the hornwort Anthoceros agrestis Paton. Planta. 2006 Jan;223(2):369–73. doi: 10.1007/s00425-005-0089-8. PMID: 16133208.; Kim KH, Janiak V, Petersen M. Purification, cloning and functional expression of hydroxyphenylpyruvate reductase involved in rosmarinic acid biosynthesis in cell cultures of Coleus blumei. Plant Mol Biol. 2004 Feb;54(3):311–23. doi: 10.1023/b:plan.0000036367.03056.b2. PMID: 15284489.; Petersen M. Cinnamic acid 4-hydroxylase from cell cultures of the hornwort Anthoceros agrestis. Planta. 2003 May;217(1):96–101. doi: 10.1007/s00425-002-0960-9. PMID: 12721853.; Petersen M, Simmonds MS. Rosmarinic acid. Phytochemistry. 2003 Jan;62(2):121–5. doi: 10.1016/s0031-9422(02)00513-7. PMID: 12482446.; Matsuno M, Nagatsu A, Ogihara Y, Ellis BE, Mizukami H. CYP98A6 from Lithospermum erythrorhizon encodes 4-coumaroyl-4'-hydroxyphenyllactic acid 3-hydroxylase involved in rosmarinic acid biosynthesis1. FEBS Letters. 2002 Mar 13;514(2-3):219–24. doi: 10.1016/s0014-5793(02)02368-2.; Ellis BE, Towers GH. Biogenesis of rosmarinic acid in Mentha. Biochem J. 1970 Jun;118(2):291–7. PMID: 5484678; PMCID: PMC1179116. |
| kaempferol gentiobioside biosynthesis Accession ID: PlantCyc:PLANT_PWY-7143 |
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Lei Y, Chen J, Zhang W, Fu W, Wu G, Wei H, Wang Q, Ruan J. In vivo investigation on the potential of galangin, kaempferol and myricetin for protection of D-galactose-induced cognitive impairment. Food Chem. 2012 Dec 15;135(4):2702–7. doi: 10.1016/j.foodchem.2012.07.043. PMID: 22980861.; Luo H, Jiang B, Li B, Li Z, Jiang BH, Chen YC. Kaempferol nanoparticles achieve strong and selective inhibition of ovarian cancer cell viability. Int J Nanomedicine. 2012;7():3951–9. PMID: 22866004; PMCID: PMC3410694.; Liu L, Xie Y, Song Z, Shang S, Chen X. Influence of dietary flavonoids on the glycation of plasma proteins. Mol Biosyst. 2012 Aug;8(8):2183–7. doi: 10.1039/c2mb25038a. PMID: 22710272.; Guo AJ, Choi RC, Zheng KY, Chen VP, Dong TT, Wang Z, Vollmer G, Lau DT, Tsim KW. Kaempferol as a flavonoid induces osteoblastic differentiation via estrogen receptor signaling. Chinese Medicine. 2012 Apr 30;7(1):10. doi: 10.1186/1749-8546-7-10.; Saito N, Tatsuzawa F, Toki K, Shinoda K, Shigihara A, Honda T. The blue anthocyanin pigments from the blue flowers of Heliophila coronopifolia L. (Brassicaceae). Phytochemistry. 2011 Dec;72(17):2219–29. doi: 10.1016/j.phytochem.2011.07.020. PMID: 21903230.; Bollina V, Kushalappa AC, Choo TM, Dion Y, Rioux S. Identification of metabolites related to mechanisms of resistance in barley against Fusarium graminearum, based on mass spectrometry. Plant Mol Biol. 2011 Nov;77(4-5):355–70. doi: 10.1007/s11103-011-9815-8. PMID: 21830145.; Iwashina T, Yamaguchi M, Nakayama M, Onozaki T, Yoshida H, Kawanobu S, Ono H, Okamura M. Kaempferol Glycosides in the Flowers of Carnation and their Contribution to the Creamy White Flower Color. Natural Product Communications. 2010 Dec;5(12). doi: 10.1177/1934578x1000501213.; Owens DK, McIntosh CA. Identification, recombinant expression, and biochemical characterization of a flavonol 3-O-glucosyltransferase clone from Citrus paradisi. Phytochemistry. 2009 Jul;70(11-12):1382–91. doi: 10.1016/j.phytochem.2009.07.027. PMID: 19733370.; Masada S, Terasaka K, Oguchi Y, Okazaki S, Mizushima T, Mizukami H. Functional and structural characterization of a flavonoid glucoside 1,6-glucosyltransferase from Catharanthus roseus. Plant Cell Physiol. 2009 Aug;50(8):1401–15. doi: 10.1093/pcp/pcp088. PMID: 19561332.; Oguchi Y, Masada S, Kondo T, Terasaka K, Mizukami H. Purification and characterization of UDP-glucose : curcumin glucoside 1,6-glucosyltransferase from Catharanthus roseus cell suspension cultures. Plant Cell Physiol. 2007 Nov;48(11):1635–43. doi: 10.1093/pcp/pcm138. PMID: 17940060.; TAHARA S. A Journey of Twenty-Five Years through the Ecological Biochemistry of Flavonoids. Bioscience, Biotechnology, and Biochemistry. 2007 Jun 23;71(6):1387–404. doi: 10.1271/bbb.70028.; Martens S, Mithöfer A. Flavones and flavone synthases. Phytochemistry. 2005 Oct;66(20):2399–407. doi: 10.1016/j.phytochem.2005.07.013. PMID: 16137727. |
| superpathway of rosmarinic acid biosynthesis Accession ID: PlantCyc:PLANT_PWY-5071 |
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Kim KH, Janiak V, Petersen M. Purification, cloning and functional expression of hydroxyphenylpyruvate reductase involved in rosmarinic acid biosynthesis in cell cultures of Coleus blumei. Plant Mol Biol. 2004 Feb;54(3):311–23. doi: 10.1023/b:plan.0000036367.03056.b2. PMID: 15284489.; Petersen M. Cinnamic acid 4-hydroxylase from cell cultures of the hornwort Anthoceros agrestis. Planta. 2003 May;217(1):96–101. doi: 10.1007/s00425-002-0960-9. PMID: 12721853.; Petersen M, Simmonds MS. Rosmarinic acid. Phytochemistry. 2003 Jan;62(2):121–5. doi: 10.1016/s0031-9422(02)00513-7. PMID: 12482446.; Matsuno M, Nagatsu A, Ogihara Y, Ellis BE, Mizukami H. CYP98A6 from Lithospermum erythrorhizon encodes 4-coumaroyl-4'-hydroxyphenyllactic acid 3-hydroxylase involved in rosmarinic acid biosynthesis1. FEBS Letters. 2002 Mar 13;514(2-3):219–24. doi: 10.1016/s0014-5793(02)02368-2.; Ellis BE, Towers GH. Biogenesis of rosmarinic acid in Mentha. Biochem J. 1970 Jun;118(2):291–7. PMID: 5484678; PMCID: PMC1179116. |
| curcumin glucoside biosynthesis Accession ID: PlantCyc:PLANT_PWY-4421 |
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Masada S, Terasaka K, Oguchi Y, Okazaki S, Mizushima T, Mizukami H. Functional and structural characterization of a flavonoid glucoside 1,6-glucosyltransferase from Catharanthus roseus. Plant Cell Physiol. 2009 Aug;50(8):1401–15. doi: 10.1093/pcp/pcp088. PMID: 19561332.; Kaminaga Y, Sahin FP, Mizukami H. Molecular cloning and characterization of a glucosyltransferase catalyzing glucosylation of curcumin in cultured Catharanthus roseus cells. FEBS Lett. 2004 Jun 04;567(2-3):197–202. doi: 10.1016/j.febslet.2004.04.056. PMID: 15178322.; Kaminaga Y, Nagatsu A, Akiyama T, Sugimoto N, Yamazaki T, Maitani T, Mizukami H. Production of unnatural glucosides of curcumin with drastically enhanced water solubility by cell suspension cultures of Catharanthus roseus. FEBS Lett. 2003 Dec 04;555(2):311–6. doi: 10.1016/s0014-5793(03)01265-1. PMID: 14644434.; Tønnesen HH, Másson M, Loftsson T. Studies of curcumin and curcuminoids. XXVII. Cyclodextrin complexation: solubility, chemical and photochemical stability. International Journal of Pharmaceutics. 2002 Sep;244(1-2):127–35. doi: 10.1016/s0378-5173(02)00323-x.; Gomes Dde C, Alegrio LV, de Lima ME, Leon LL, Araújo CA. Synthetic derivatives of curcumin and their activity against Leishmania amazonensis. Arzneimittelforschung. 2002;52(2):120–4. PMID: 11878200. |
| phytocassanes biosynthesis, shared reactions Accession ID: PlantCyc:PLANT_PWY-7484 |
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Wu Y, Wang Q, Hillwig ML, Peters RJ. Picking sides: distinct roles for CYP76M6 and CYP76M8 in rice oryzalexin biosynthesis. Biochem J. 2013 Sep 01;454(2):209–16. PMID: 23795884; PMCID: PMC3787970.; Wang Q, Hillwig ML, Okada K, Yamazaki K, Wu Y, Swaminathan S, Yamane H, Peters RJ. Characterization of CYP76M5–8 Indicates Metabolic Plasticity within a Plant Biosynthetic Gene Cluster. Journal of Biological Chemistry. 2012 Feb;287(9):6159–68. doi: 10.1074/jbc.m111.305599.; Wang Q, Hillwig ML, Wu Y, Peters RJ. CYP701A8: a rice ent-kaurene oxidase paralog diverted to more specialized diterpenoid metabolism. Plant Physiol. 2012 Mar;158(3):1418–25. PMID: 22247270; PMCID: PMC3291257.; Wu Y, Hillwig ML, Wang Q, Peters RJ. Parsing a multifunctional biosynthetic gene cluster from rice: Biochemical characterization of CYP71Z6 & 7. FEBS Lett. 2011 Nov 04;585(21):3446–51. PMID: 21985968; PMCID: PMC3227696.; Osbourn A. Gene clusters for secondary metabolic pathways: an emerging theme in plant biology. Plant Physiol. 2010 Oct;154(2):531–5. PMID: 20921179; PMCID: PMC2949040.; Swaminathan S, Morrone D, Wang Q, Fulton DB, Peters RJ. CYP76M7 is an ent-cassadiene C11alpha-hydroxylase defining a second multifunctional diterpenoid biosynthetic gene cluster in rice. Plant Cell. 2009 Oct;21(10):3315–25. PMID: 19825834; PMCID: PMC2782285.; Osbourn AE, Field B. Operons. Cellular and Molecular Life Sciences. 2009 Aug 07;66(23):3755–75. doi: 10.1007/s00018-009-0114-3.; Fischbach MA, Walsh CT, Clardy J. The evolution of gene collectives: How natural selection drives chemical innovation. Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4601–8. PMID: 18216259; PMCID: PMC2290807.; Okada A, Shimizu T, Okada K, Kuzuyama T, Koga J, Shibuya N, Nojiri H, Yamane H. Elicitor induced activation of the methylerythritol phosphate pathway toward phytoalexins biosynthesis in rice. Plant Mol Biol. 2007 Sep;65(1-2):177–87. doi: 10.1007/s11103-007-9207-2. PMID: 17634747.; Cyr A, Wilderman PR, Determan M, Peters RJ. A modular approach for facile biosynthesis of labdane-related diterpenes. J Am Chem Soc. 2007 May 30;129(21):6684–5. PMID: 17480080; PMCID: PMC2518946.; Xu M, Wilderman PR, Morrone D, Xu J, Roy A, Margis-Pinheiro M, Upadhyaya NM, Coates RM, Peters RJ. Functional characterization of the rice kaurene synthase-like gene family. Phytochemistry. 2007 Feb;68(3):312–26. doi: 10.1016/j.phytochem.2006.10.016. PMID: 17141283.; Peters RJ. Uncovering the complex metabolic network underlying diterpenoid phytoalexin biosynthesis in rice and other cereal crop plants. Phytochemistry. 2006 Nov;67(21):2307–17. doi: 10.1016/j.phytochem.2006.08.009. PMID: 16956633.; Prisic S, Xu M, Wilderman PR, Peters RJ. Rice contains two disparate ent-copalyl diphosphate synthases with distinct metabolic functions. Plant Physiol. 2004 Dec;136(4):4228–36. PMID: 15542489; PMCID: PMC535852.; Otomo K, Kenmoku H, Oikawa H, König WA, Toshima H, Mitsuhashi W, Yamane H, Sassa T, Toyomasu T. Biological functions of ent- and syn-copalyl diphosphate synthases in rice: key enzymes for the branch point of gibberellin and phytoalexin biosynthesis. The Plant Journal. 2004 Jul 30;39(6):886–93. doi: 10.1111/j.1365-313x.2004.02175.x. |