Pathways Knowlegdes
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| Pathway | DOIs | Note |
|---|---|---|
| astaxanthin biosynthesis (bacteria, fungi, algae) Accession ID: BioCyc:META_PWY-5288 |
|
Makino T, Harada H, Ikenaga H, Matsuda S, Takaichi S, Shindo K, Sandmann G, Ogata T, Misawa N. Characterization of cyanobacterial carotenoid ketolase CrtW and hydroxylase CrtR by complementation analysis in Escherichia coli. Plant Cell Physiol. 2008 Dec;49(12):1867–78. doi: 10.1093/pcp/pcn169. PMID: 18987067.; Choi SK, Matsuda S, Hoshino T, Peng X, Misawa N. Characterization of bacterial beta-carotene 3,3'-hydroxylases, CrtZ, and P450 in astaxanthin biosynthetic pathway and adonirubin production by gene combination in Escherichia coli. Appl Microbiol Biotechnol. 2006 Oct;72(6):1238–46. doi: 10.1007/s00253-006-0426-2. PMID: 16614859.; 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.; Zhu C, Yamamura S, Nishihara M, Koiwa H, Sandmann G. cDNAs for the synthesis of cyclic carotenoids in petals of Gentiana lutea and their regulation during flower development. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression. 2003 Feb;1625(3):305–8. doi: 10.1016/s0167-4781(03)00017-4.; Linden H. Carotenoid hydroxylase from Haematococcus pluvialis: cDNA sequence, regulation and functional complementation. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression. 1999 Sep;1446(3):203–12. doi: 10.1016/s0167-4781(99)00088-3.; Bouvier F, Keller Y, d'Harlingue A, Camara B. Xanthophyll biosynthesis: molecular and functional characterization of carotenoid hydroxylases from pepper fruits (Capsicum annuum L.). Biochimica et Biophysica Acta (BBA) - Lipids and Lipid Metabolism. 1998 Apr;1391(3):320–8. doi: 10.1016/s0005-2760(98)00029-0.; Fraser PD, Shimada H, Misawa N. Enzymic confirmation of reactions involved in routes to astaxanthin formation, elucidated using a direct substrate in vitro assay. European Journal of Biochemistry. 1998 Mar;252(2):229–36. doi: 10.1046/j.1432-1327.1998.2520229.x.; Fraser PD, Miura Y, Misawa N. In Vitro Characterization of Astaxanthin Biosynthetic Enzymes. Journal of Biological Chemistry. 1997 Mar;272(10):6128–35. doi: 10.1074/jbc.272.10.6128.; Sun Z, Gantt E, Cunningham FX. Cloning and functional analysis of the beta-carotene hydroxylase of Arabidopsis thaliana. J Biol Chem. 1996 Oct 04;271(40):24349–52. doi: 10.1074/jbc.271.40.24349. PMID: 8798688.; 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. |
| 2,2'-dihydroxyketocarotenoids biosynthesis Accession ID: BioCyc:META_PWY-7637 |
|
Takemura M, Maoka T, Misawa N. Biosynthetic routes of hydroxylated carotenoids (xanthophylls) in Marchantia polymorpha, and production of novel and rare xanthophylls through pathway engineering in Escherichia coli. Planta. 2015 Mar;241(3):699–710. doi: 10.1007/s00425-014-2213-0. PMID: 25467956.; Zhu L, Wu X, Li O, Qian C, Gao H. Cloning and Characterization of Genes Involved in Nostoxanthin Biosynthesis of Sphingomonas elodea ATCC 31461. PLoS ONE. 2012 Apr 11;7(4):e35099. doi: 10.1371/journal.pone.0035099.; Osawa A, Harada H, Choi SK, Misawa N, Shindo K. Production of caloxanthin 3'-ß-D-glucoside, zeaxanthin 3,3'-ß-D-diglucoside, and nostoxanthin in a recombinant Escherichia coli expressing system harboring seven carotenoid biosynthesis genes, including crtX and crtG. Phytochemistry. 2011 Jun;72(8):711–6. doi: 10.1016/j.phytochem.2011.02.017. PMID: 21429538.; Misawa N. Carotenoid ß-ring hydroxylase and ketolase from marine bacteria-promiscuous enzymes for synthesizing functional xanthophylls. Mar Drugs. 2011;9(5):757–71. PMID: 21673887; PMCID: PMC3111180.; Iwai M, Maoka T, Ikeuchi M, Takaichi S. 2,2'-beta-hydroxylase (CrtG) is involved in carotenogenesis of both nostoxanthin and 2-hydroxymyxol 2'-fucoside in Thermosynechococcus elongatus strain BP-1. Plant Cell Physiol. 2008 Nov;49(11):1678–87. doi: 10.1093/pcp/pcn142. PMID: 18794175.; Tao L, Rouvière PE, Cheng Q. A carotenoid synthesis gene cluster from a non-marine Brevundimonas that synthesizes hydroxylated astaxanthin. Gene. 2006 Sep 01;379():101–8. doi: 10.1016/j.gene.2006.04.017. PMID: 16781830.; Nishida Y, Adachi K, Kasai H, Shizuri Y, Shindo K, Sawabe A, Komemushi S, Miki W, Misawa N. Elucidation of a Carotenoid Biosynthesis Gene Cluster Encoding a Novel Enzyme, 2,2'-ß-Hydroxylase, from Brevundimonas sp. Strain SD212 and Combinatorial Biosynthesis of New or Rare Xanthophylls. Appl Environ Microbiol. 2005 Aug;71(8):4286–96. doi: 10.1128/aem.71.8.4286-4296.2005.; Iwamoto T, Hosoda K, Hirano R, Kurata H, Matsumoto A, Miki W, Kamiyama M, Itakura H, Yamamoto S, Kondo K. Inhibition of low-density lipoprotein oxidation by astaxanthin. J Atheroscler Thromb. 2000;7(4):216–22. doi: 10.5551/jat1994.7.216. PMID: 11521685. |
| canthaxanthin biosynthesis Accession ID: BioCyc:META_PWY-5291 |
|
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. |
| astaxanthin biosynthesis (flowering plants) Accession ID: BioCyc:META_PWY-7636 |
|
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. |
| astaxanthin biosynthesis (bacteria, fungi, algae) Accession ID: PlantCyc:CHLAMY_PWY-5288 |
|
Choi SK, Matsuda S, Hoshino T, Peng X, Misawa N. Characterization of bacterial beta-carotene 3,3'-hydroxylases, CrtZ, and P450 in astaxanthin biosynthetic pathway and adonirubin production by gene combination in Escherichia coli. Appl Microbiol Biotechnol. 2006 Oct;72(6):1238–46. doi: 10.1007/s00253-006-0426-2. PMID: 16614859.; 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.; Zhu C, Yamamura S, Nishihara M, Koiwa H, Sandmann G. cDNAs for the synthesis of cyclic carotenoids in petals of Gentiana lutea and their regulation during flower development. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression. 2003 Feb;1625(3):305–8. doi: 10.1016/s0167-4781(03)00017-4.; Linden H. Carotenoid hydroxylase from Haematococcus pluvialis: cDNA sequence, regulation and functional complementation. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression. 1999 Sep;1446(3):203–12. doi: 10.1016/s0167-4781(99)00088-3.; Bouvier F, Keller Y, d'Harlingue A, Camara B. Xanthophyll biosynthesis: molecular and functional characterization of carotenoid hydroxylases from pepper fruits (Capsicum annuum L.). Biochimica et Biophysica Acta (BBA) - Lipids and Lipid Metabolism. 1998 Apr;1391(3):320–8. doi: 10.1016/s0005-2760(98)00029-0.; Fraser PD, Shimada H, Misawa N. Enzymic confirmation of reactions involved in routes to astaxanthin formation, elucidated using a direct substrate in vitro assay. European Journal of Biochemistry. 1998 Mar;252(2):229–36. doi: 10.1046/j.1432-1327.1998.2520229.x.; Fraser PD, Miura Y, Misawa N. In Vitro Characterization of Astaxanthin Biosynthetic Enzymes. Journal of Biological Chemistry. 1997 Mar;272(10):6128–35. doi: 10.1074/jbc.272.10.6128.; Sun Z, Gantt E, Cunningham FX. Cloning and functional analysis of the beta-carotene hydroxylase of Arabidopsis thaliana. J Biol Chem. 1996 Oct 04;271(40):24349–52. doi: 10.1074/jbc.271.40.24349. PMID: 8798688.; 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. |
| canthaxanthin biosynthesis Accession ID: PlantCyc:PLANT_PWY-5291 |
|
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. |
| astaxanthin biosynthesis (bacteria, fungi, algae) Accession ID: PlantCyc:PLANT_PWY-5288 |
|
Choi SK, Matsuda S, Hoshino T, Peng X, Misawa N. Characterization of bacterial beta-carotene 3,3'-hydroxylases, CrtZ, and P450 in astaxanthin biosynthetic pathway and adonirubin production by gene combination in Escherichia coli. Appl Microbiol Biotechnol. 2006 Oct;72(6):1238–46. doi: 10.1007/s00253-006-0426-2. PMID: 16614859.; 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.; Zhu C, Yamamura S, Nishihara M, Koiwa H, Sandmann G. cDNAs for the synthesis of cyclic carotenoids in petals of Gentiana lutea and their regulation during flower development. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression. 2003 Feb;1625(3):305–8. doi: 10.1016/s0167-4781(03)00017-4.; Linden H. Carotenoid hydroxylase from Haematococcus pluvialis: cDNA sequence, regulation and functional complementation. Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression. 1999 Sep;1446(3):203–12. doi: 10.1016/s0167-4781(99)00088-3.; Bouvier F, Keller Y, d'Harlingue A, Camara B. Xanthophyll biosynthesis: molecular and functional characterization of carotenoid hydroxylases from pepper fruits (Capsicum annuum L.). Biochimica et Biophysica Acta (BBA) - Lipids and Lipid Metabolism. 1998 Apr;1391(3):320–8. doi: 10.1016/s0005-2760(98)00029-0.; Fraser PD, Shimada H, Misawa N. Enzymic confirmation of reactions involved in routes to astaxanthin formation, elucidated using a direct substrate in vitro assay. European Journal of Biochemistry. 1998 Mar;252(2):229–36. doi: 10.1046/j.1432-1327.1998.2520229.x.; Fraser PD, Miura Y, Misawa N. In Vitro Characterization of Astaxanthin Biosynthetic Enzymes. Journal of Biological Chemistry. 1997 Mar;272(10):6128–35. doi: 10.1074/jbc.272.10.6128.; Sun Z, Gantt E, Cunningham FX. Cloning and functional analysis of the beta-carotene hydroxylase of Arabidopsis thaliana. J Biol Chem. 1996 Oct 04;271(40):24349–52. doi: 10.1074/jbc.271.40.24349. PMID: 8798688.; 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. |
| astaxanthin biosynthesis (flowering plants) Accession ID: PlantCyc:PLANT_PWY-7636 |
|
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. |
| astaxanthin biosynthesis (bacteria, fungi, algae) Accession ID: PlantCyc:VCARTERI_PWY-5288 |
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| Retinol metabolism Accession ID: WikiPathways:WP1259 |
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Sturgeon SR, Ziegler RG, Brinton LA, Nasca PC, Mallin K, Gridley G. Diet and the risk of vulvar cancer. Ann Epidemiol. 1991 Aug;1(5):427–37. doi: 10.1016/1047-2797(91)90012-2. PMID: 1669523. |
| Vitamin A and carotenoid metabolism Accession ID: WikiPathways:WP1038 |
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Sies H, Stahl W, Sundquist AR. Antioxidant functions of vitamins. Vitamins E and C, beta-carotene, and other carotenoids. Ann N Y Acad Sci. 1992 Sep 30;669():7–20. doi: 10.1111/j.1749-6632.1992.tb17085.x. PMID: 1444060. |
| Retinol metabolism Accession ID: WikiPathways:WP1297 |
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Huet F, Semama D, Maingueneau C, Charavel A, Nivelon J-. Vitamin A deficiency and nocturnal vision in teenagers with cystic fibrosis. European Journal of Pediatrics. 1997 Nov 20;156(12):949–51. doi: 10.1007/s004310050749. |
| Vitamin A and carotenoid metabolism Accession ID: WikiPathways:WP716 |
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Waagmeester A, Pezik P, Coort S, Tourniaire F, Evelo C, Rebholz-Schuhmann D. Pathway Enrichment Based on Text Mining and Its Validation on Carotenoid and Vitamin A Metabolism. OMICS: A Journal of Integrative Biology. 2009 Oct;13(5):367–79. doi: 10.1089/omi.2009.0029. |
| Retinol metabolism Accession ID: WikiPathways:WP805 |
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Botilsrud M, Holmberg I, Wathne KO, Blomhoff HK, Norum KR, Blomhoff R. Effect of retinoids and 1,25(OH)2 vitamin D3 bound to their plasma transport proteins on growth and differentiation of HL-60 cells. Scand. J. of Clinical & Lab Investigation. 1990 May 01;50(3):309–17. doi: 10.3109/00365519009091584. |
| Vitamin A and carotenoid metabolism Accession ID: WikiPathways:WP3843 |
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Micozzi M, Brown E, Edwards B, Bieri J, Taylor P, Khachik F, Beecher G, Smith J. Plasma carotenoid response to chronic intake of selected foods and ß-carotene supplements in men. The American Journal of Clinical Nutrition. 1992 Jun;55(6):1120–5. doi: 10.1093/ajcn/55.6.1120. |