Pathways Knowlegdes
Biological pathway database
| Pathway | DOIs | Note |
|---|---|---|
| 5-deoxystrigol biosynthesis Accession ID: BioCyc:META_PWY-7101 |
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Alder A, Jamil M, Marzorati M, Bruno M, Vermathen M, Bigler P, Ghisla S, Bouwmeester H, Beyer P, Al-Babili S. The path from ß-carotene to carlactone, a strigolactone-like plant hormone. Science. 2012 Mar 16;335(6074):1348–51. doi: 10.1126/science.1218094. PMID: 22422982. |
| astaxanthin biosynthesis (flowering plants) Accession ID: BioCyc:META_PWY-7636 |
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Ambati RR, Phang SM, Ravi S, Aswathanarayana RG. Astaxanthin: sources, extraction, stability, biological activities and its commercial applications--a review. Mar Drugs. 2014 Jan 07;12(1):128–52. PMID: 24402174; PMCID: PMC3917265.; Tanaka T, Shnimizu M, Moriwaki H. Cancer chemoprevention by carotenoids. Molecules. 2012 Mar 14;17(3):3202–42. PMID: 22418926; PMCID: PMC6268471.; Cunningham FX, Gantt E. Elucidation of the pathway to astaxanthin in the flowers of Adonis aestivalis. Plant Cell. 2011 Aug;23(8):3055–69. PMID: 21862704; PMCID: PMC3180810.; Zhong Y-, Huang J-, Liu J, Li Y, Jiang Y, Xu Z-, Sandmann G, Chen F. Functional characterization of various algal carotenoid ketolases reveals that ketolating zeaxanthin efficiently is essential for high production of astaxanthin in transgenic Arabidopsis. Journal of Experimental Botany. 2011 Mar 11;62(10):3659–69. doi: 10.1093/jxb/err070.; Maoka T, Etoh T, Kishimoto S, Sakata S. Carotenoids and their fatty acid esters in the petals of Adonis aestivalis. J Oleo Sci. 2011;60(2):47–52. doi: 10.5650/jos.60.47. PMID: 21263199.; Schmidt I, Schewe H, Gassel S, Jin C, Buckingham J, Hümbelin M, Sandmann G, Schrader J. Biotechnological production of astaxanthin with Phaffia rhodozyma/Xanthophyllomyces dendrorhous. Applied Microbiology and Biotechnology. 2010 Nov 03;89(3):555–71. doi: 10.1007/s00253-010-2976-6.; Zhu C, Naqvi S, Capell T, Christou P. Metabolic engineering of ketocarotenoid biosynthesis in higher plants. Archives of Biochemistry and Biophysics. 2009 Mar;483(2):182–90. doi: 10.1016/j.abb.2008.10.029.; Gerjets T, Sandmann G. Ketocarotenoid formation in transgenic potato. Journal of Experimental Botany. 2006 Sep 06;57(14):3639–45. doi: 10.1093/jxb/erl103.; Cunningham FX, Gantt E. A study in scarlet: enzymes of ketocarotenoid biosynthesis in the flowers of Adonis aestivalis. The Plant Journal. 2005 Jan 11;41(3):478–92. doi: 10.1111/j.1365-313x.2004.02309.x.; Hix LM, Lockwood SF, Bertram JS. Bioactive carotenoids: potent antioxidants and regulators of gene expression. Redox Rep. 2004;9(4):181–91. doi: 10.1179/135100004225005967. PMID: 15479561.; Johnson EA. Phaffia rhodozyma : colorful odyssey. International Microbiology. 2003 Sep 01;6(3):169–74. doi: 10.1007/s10123-003-0130-3.; Nishino H, Murakoshi M, Ii T, Takemura M, Kuchide M, Kanazawa M, Yang Mou X, Wada S, Masuda M, Ohsaka Y, Yogosawa S, Satomi Y, Jinno K. Carotenoids in Cancer Chemoprevention. Cancer and Metastasis Reviews. 2002 Dec;21(3-4):257–64. doi: 10.1023/a:1021206826750.; Lorenz RT, Cysewski GR. Commercial potential for Haematococcus microalgae as a natural source of astaxanthin. Trends Biotechnol. 2000 Apr;18(4):160–7. doi: 10.1016/s0167-7799(00)01433-5. PMID: 10740262.; Eriksson CE, Na A. Antioxidant agents in raw materials and processed foods. Biochem Soc Symp. 1995;61():221–34. doi: 10.1042/bss0610221. PMID: 8660397.; Goodwin TW. Metabolism, nutrition, and function of carotenoids. Annu Rev Nutr. 1986;6():273–97. doi: 10.1146/annurev.nu.06.070186.001421. PMID: 3524619.; SEYBOLD A, GOODWIN TW. Occurrence of astaxanthin in the flower petals of Adonis annua L. Nature. 1959 Nov 28;184 (Suppl 22)():1714–5. doi: 10.1038/1841714a0. PMID: 14445279. |
| β-carotene biosynthesis (engineered) Accession ID: BioCyc:META_PWY-7393 |
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Stickforth P, Sandmann G. Structural and kinetics properties of a mutated phytoene desaturase from Rubrivivax gelatinosus with modified product specificity. Archives of Biochemistry and Biophysics. 2011 Jan;505(1):118–22. doi: 10.1016/j.abb.2010.09.021.; Iniesta AA, Cervantes M, Murillo FJ. Cooperation of two carotene desaturases in the production of lycopene in Myxococcus xanthus. The FEBS Journal. 2007 Jul 27;274(16):4306–14. doi: 10.1111/j.1742-4658.2007.05960.x.; Maresca JA, Graham JE, Wu M, Eisen JA, Bryant DA. Identification of a fourth family of lycopene cyclases in photosynthetic bacteria. Proc Natl Acad Sci U S A. 2007 Jul 10;104(28):11784–9. PMID: 17606904; PMCID: PMC1905924.; Hornero-Méndez D, Britton G. Involvement of NADPH in the cyclization reaction of carotenoid biosynthesis. FEBS Lett. 2002 Mar 27;515(1-3):133–6. doi: 10.1016/s0014-5793(02)02453-5. PMID: 11943208.; Wang C, Liao JC. Alteration of Product Specificity of Rhodobacter sphaeroides Phytoene Desaturase by Directed Evolution. Journal of Biological Chemistry. 2001 Nov;276(44):41161–4. doi: 10.1074/jbc.m105786200.; Ye X, Al-Babili S, Klöti A, Zhang J, Lucca P, Beyer P, Potrykus I. Engineering the provitamin A (beta-carotene) biosynthetic pathway into (carotenoid-free) rice endosperm. Science. 2000 Jan 14;287(5451):303–5. doi: 10.1126/science.287.5451.303. PMID: 10634784.; Raisig A, Bartley G, Scolnik P, Sandmann G. Purification in an Active State and Properties of the 3-Step Phytoene Desaturase from Rhodobacter capsulatus Overexpressed in Escherichia coil. Journal of Biochemistry. 1996 Mar 01;119(3):559–64. doi: 10.1093/oxfordjournals.jbchem.a021278.; Pecker I, Gabbay R, Cunningham FX, Hirschberg J. Cloning and characterization of the cDNA for lycopene beta-cyclase from tomato reveals decrease in its expression during fruit ripening. Plant Mol Biol. 1996 Feb;30(4):807–19. doi: 10.1007/bf00019013. PMID: 8624411.; Hugueney P, Badillo A, Chen H, Klein A, Hirschberg J, Camara B, Kuntz M. Metabolism of cyclic carotenoids: a model for the alteration of this biosynthetic pathway in Capsicum annuum chromoplasts. The Plant Journal. 1995 Sep;8(3):417–24. doi: 10.1046/j.1365-313x.1995.08030417.x.; Cunningham FX, Sun Z, Chamovitz D, Hirschberg J, Gantt E. Molecular structure and enzymatic function of lycopene cyclase from the cyanobacterium Synechococcus sp strain PCC7942. Plant Cell. 1994 Aug;6(8):1107–21. PMID: 7919981; PMCID: PMC160505.; Cunningham FX, Chamovitz D, Misawa N, Gantt E, Hirschberg J. Cloning and functional expression in Escherichia coli of a cyanobacterial gene for lycopene cyclase, the enzyme that catalyzes the biosynthesis of beta-carotene. FEBS Lett. 1993 Aug 09;328(1-2):130–8. doi: 10.1016/0014-5793(93)80980-9. PMID: 8344419. |
| β-carotene biosynthesis Accession ID: BioCyc:ARA_PWY-5943 |
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Cunningham FX, Pogson B, Sun Z, McDonald KA, DellaPenna D, Gantt E. Functional analysis of the beta and epsilon lycopene cyclase enzymes of Arabidopsis reveals a mechanism for control of cyclic carotenoid formation. Plant Cell. 1996 Sep;8(9):1613–26. PMID: 8837512; PMCID: PMC161302. |
| carotenoid cleavage Accession ID: BioCyc:ARA_PWY-6806 |
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Ilg A, Beyer P, Al-Babili S. Characterization of the rice carotenoid cleavage dioxygenase 1 reveals a novel route for geranial biosynthesis. FEBS J. 2009 Feb;276(3):736–47. doi: 10.1111/j.1742-4658.2008.06820.x. PMID: 19120446.; Schwartz SH, Qin X, Loewen MC. The Biochemical Characterization of Two Carotenoid Cleavage Enzymes from Arabidopsis Indicates That a Carotenoid-derived Compound Inhibits Lateral Branching. Journal of Biological Chemistry. 2004 Nov;279(45):46940–5. doi: 10.1074/jbc.m409004200.; Wyss A. Carotene Oxygenases: A New Family of Double Bond Cleavage Enzymes. The Journal of Nutrition. 2004 Jan;134(1):246S–250S. doi: 10.1093/jn/134.1.246s.; Schwartz SH, Qin X, Zeevaart JD. Characterization of a Novel Carotenoid Cleavage Dioxygenase from Plants. Journal of Biological Chemistry. 2001 Jan;276(27):25208–11. doi: 10.1074/jbc.m102146200.; Kiefer C, Hessel S, Lampert JM, Vogt K, Lederer MO, Breithaupt DE, von Lintig J. Identification and Characterization of a Mammalian Enzyme Catalyzing the Asymmetric Oxidative Cleavage of Provitamin A. Journal of Biological Chemistry. 2001 Apr;276(17):14110–6. doi: 10.1074/jbc.m011510200. |
| β-carotene biosynthesis Accession ID: BioCyc:SYNEL_PWY-5943 |
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| Gravitropism under normal or artificial gravity environments Accession ID: Plant Reactome:R-OSA-9826798 |
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| Shoot gravitropism: development, growth, and architecture of shoot in response to gravity Accession ID: Plant Reactome:R-OSA-9924422 |
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| Metabolism and regulation Accession ID: Plant Reactome:R-OAU-2744345 |
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| Secondary metabolism Accession ID: Plant Reactome:R-TAE-2744344 |
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| Carotenoid biosynthesis Accession ID: Plant Reactome:R-TAE-1119449 |
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| Metabolism and regulation Accession ID: Plant Reactome:R-MES-2744345 |
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| Hormone signaling, transport, and metabolism Accession ID: Plant Reactome:R-MES-2744341 |
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| Strigolactone biosynthesis Accession ID: Plant Reactome:R-MES-5367729 |
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Cardoso C, Zhang Y, Jamil M, Hepworth J, Charnikhova T, Dimkpa SON, Meharg C, Wright MH, Liu J, Meng X, Wang Y, Li J, McCouch SR, Leyser O, Price AH, Bouwmeester HJ, Ruyter-Spira C. Natural variation of rice strigolactone biosynthesis is associated with the deletion of two MAX1 orthologs. Proc. Natl. Acad. Sci. U.S.A. 2014 Jan 24;111(6):2379–84. doi: 10.1073/pnas.1317360111.; Challis RJ, Hepworth J, Mouchel C, Waites R, Leyser O. A Role forMORE AXILLARY GROWTH1(MAX1) in Evolutionary Diversity in Strigolactone Signaling Upstream ofMAX2 . 2013 Feb 19;161(4):1885–902. doi: 10.1104/pp.112.211383.; Ruyter-Spira C, Al-Babili S, van der Krol S, Bouwmeester H. The biology of strigolactones. Trends Plant Sci. 2013 Feb;18(2):72–83. doi: 10.1016/j.tplants.2012.10.003. PMID: 23182342. |
| Metabolism and regulation Accession ID: Plant Reactome:R-TDI-2744345 |
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| Hormone signaling, transport, and metabolism Accession ID: Plant Reactome:R-OGU-2744341 |
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| Strigolactone biosynthesis Accession ID: Plant Reactome:R-OGU-5367729 |
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Cardoso C, Zhang Y, Jamil M, Hepworth J, Charnikhova T, Dimkpa SON, Meharg C, Wright MH, Liu J, Meng X, Wang Y, Li J, McCouch SR, Leyser O, Price AH, Bouwmeester HJ, Ruyter-Spira C. Natural variation of rice strigolactone biosynthesis is associated with the deletion of two MAX1 orthologs. Proc. Natl. Acad. Sci. U.S.A. 2014 Jan 24;111(6):2379–84. doi: 10.1073/pnas.1317360111.; Challis RJ, Hepworth J, Mouchel C, Waites R, Leyser O. A Role forMORE AXILLARY GROWTH1(MAX1) in Evolutionary Diversity in Strigolactone Signaling Upstream ofMAX2 . 2013 Feb 19;161(4):1885–902. doi: 10.1104/pp.112.211383.; Ruyter-Spira C, Al-Babili S, van der Krol S, Bouwmeester H. The biology of strigolactones. Trends Plant Sci. 2013 Feb;18(2):72–83. doi: 10.1016/j.tplants.2012.10.003. PMID: 23182342. |
| Carotenoid biosynthesis Accession ID: Plant Reactome:R-OGU-1119449 |
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| Secondary metabolism Accession ID: Plant Reactome:R-GSU-2744344 |
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| Metabolism and regulation Accession ID: Plant Reactome:R-PTI-2744345 |
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