Pathways Knowlegdes

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Pathway DOIs Note
trans-lycopene biosynthesis II (plants)

Accession ID: BioCyc:SYNEL_PWY-6475		 -
superpathway of carotenoid biosynthesis in plants

Accession ID: BioCyc:META_CAROTENOID-PWY
  • 10.1006/prep.1997.0730
  • 10.1007/bf00019013
  • 10.1007/s00203-003-0545-4
  • 10.1007/s00253-006-0426-2
  • 10.1007/s00425-004-1395-2
  • 10.1016/0014-5793(93)80980-9
  • 10.1016/s0005-2760(98)00029-0
  • 10.1016/s0014-5793(02)02453-5
  • 10.1016/s0167-4781(03)00017-4
  • 10.1016/s0167-4781(99)00088-3
  • 10.1016/s1369-5266(00)00163-1
  • 10.1042/bj2910687
  • 10.1046/j.1365-313x.1995.08030417.x
  • 10.1046/j.1432-1327.1998.2520229.x
  • 10.1046/j.1432-1327.1999.00746.x
  • 10.1073/pnas.051618398
  • 10.1073/pnas.0702984104
  • 10.1074/jbc.271.40.24349
  • 10.1074/jbc.272.10.6128
  • 10.1104/pp.123.4.1427
  • 10.1105/tpc.6.8.1107
  • 10.1111/j.1432-1033.1996.00115.x
  • 10.1146/annurev.arplant.57.032905.105248
 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.; Grotewold E. The genetics and biochemistry of floral pigments. Annu Rev Plant Biol. 2006;57():761–80. doi: 10.1146/annurev.arplant.57.032905.105248. PMID: 16669781.; 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.; Breitenbach J, Sandmann G. zeta-Carotene cis isomers as products and substrates in the plant poly-cis carotenoid biosynthetic pathway to lycopene. Planta. 2005 Mar;220(5):785–93. doi: 10.1007/s00425-004-1395-2. PMID: 15503129.; Stickforth P, Steiger S, Hess WR, Sandmann G. A novel type of lycopene epsilon-cyclase in the marine cyanobacterium Prochlorococcus marinus MED4. Arch Microbiol. 2003 Jun;179(6):409–15. doi: 10.1007/s00203-003-0545-4. PMID: 12712234.; 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.; 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.; Hirschberg J. Carotenoid biosynthesis in flowering plants. Curr Opin Plant Biol. 2001 Jun;4(3):210–8. doi: 10.1016/s1369-5266(00)00163-1. PMID: 11312131.; Cunningham FX, Gantt E. One ring or two? Determination of ring number in carotenoids by lycopene epsilon-cyclases. Proc Natl Acad Sci U S A. 2001 Feb 27;98(5):2905–10. PMID: 11226339; PMCID: PMC30238.; Josse EM, Simkin AJ, Gaffé J, Labouré AM, Kuntz M, Carol P. A plastid terminal oxidase associated with carotenoid desaturation during chromoplast differentiation. Plant Physiol. 2000 Aug;123(4):1427–36. PMID: 10938359; PMCID: PMC59099.; Breitenbach J, Kuntz M, Takaichi S, Sandmann G. Catalytic properties of an expressed and purified higher plant type?-carotene desaturase fromCapsicum annuum. European Journal of Biochemistry. 1999 Oct;265(1):376–83. doi: 10.1046/j.1432-1327.1999.00746.x.; 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.; Schneider C, Böger P, Sandmann G. Phytoene Desaturase: Heterologous Expression in an Active State, Purification, and Biochemical Properties. Protein Expression and Purification. 1997 Jul;10(2):175–9. doi: 10.1006/prep.1997.0730.; 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.; Albrecht M, Linden H, Sandmann G. Biochemical Characterization of Purified ?-Carotene Desaturase from Anabaena PCC 7120 after Expression in Escherichia coli. European Journal of Biochemistry. 1996 Feb;236(1):115–20. doi: 10.1111/j.1432-1033.1996.00115.x.; 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.; Fraser PD, Linden H, Sandmann G. Purification and reactivation of recombinant Synechococcus phytoene desaturase from an overexpressing strain of Escherichia coli. Biochem J. 1993 May 01;291 ( Pt 3)():687–92. PMID: 8489496; PMCID: PMC1132422.
trans-lycopene biosynthesis II (plants)

Accession ID: BioCyc:SCO_PWY-6475		 -
superpathway of carotenoid biosynthesis

Accession ID: BioCyc:SCO_CAROTENOID-PWY		 -
trans-lycopene biosynthesis II (oxygenic phototrophs and green sulfur bacteria)

Accession ID: BioCyc:META_PWY-6475
  • 10.1006/prep.1997.0730
  • 10.1007/s00425-004-1395-2
  • 10.1016/j.abb.2008.10.004
  • 10.1042/bj2910687
  • 10.1046/j.1432-1327.1999.00746.x
  • 10.1104/pp.104.052092
  • 10.1104/pp.107.098996
  • 10.1104/pp.110.153916
  • 10.1104/pp.123.4.1427
  • 10.1111/j.1432-1033.1996.00115.x
 Chen Y, Li F, Wurtzel ET. Isolation and Characterization of the Z-ISO Gene Encoding a Missing Component of Carotenoid Biosynthesis in Plants . 2010 Mar 24;153(1):66–79. doi: 10.1104/pp.110.153916.; Sandmann G. Evolution of carotene desaturation: The complication of a simple pathway. Archives of Biochemistry and Biophysics. 2009 Mar;483(2):169–74. doi: 10.1016/j.abb.2008.10.004.; Li F, Murillo C, Wurtzel ET. Maize Y9 Encodes a Product Essential for 15-cis-?-Carotene Isomerization. 2007 Apr 13;144(2):1181–9. doi: 10.1104/pp.107.098996.; Isaacson T, Ohad I, Beyer P, Hirschberg J. Analysis in vitro of the enzyme CRTISO establishes a poly-cis-carotenoid biosynthesis pathway in plants. Plant Physiol. 2004 Dec;136(4):4246–55. PMID: 15557094; PMCID: PMC535854.; Breitenbach J, Sandmann G. zeta-Carotene cis isomers as products and substrates in the plant poly-cis carotenoid biosynthetic pathway to lycopene. Planta. 2005 Mar;220(5):785–93. doi: 10.1007/s00425-004-1395-2. PMID: 15503129.; Josse EM, Simkin AJ, Gaffé J, Labouré AM, Kuntz M, Carol P. A plastid terminal oxidase associated with carotenoid desaturation during chromoplast differentiation. Plant Physiol. 2000 Aug;123(4):1427–36. PMID: 10938359; PMCID: PMC59099.; Breitenbach J, Kuntz M, Takaichi S, Sandmann G. Catalytic properties of an expressed and purified higher plant type?-carotene desaturase fromCapsicum annuum. European Journal of Biochemistry. 1999 Oct;265(1):376–83. doi: 10.1046/j.1432-1327.1999.00746.x.; Schneider C, Böger P, Sandmann G. Phytoene Desaturase: Heterologous Expression in an Active State, Purification, and Biochemical Properties. Protein Expression and Purification. 1997 Jul;10(2):175–9. doi: 10.1006/prep.1997.0730.; Albrecht M, Linden H, Sandmann G. Biochemical Characterization of Purified ?-Carotene Desaturase from Anabaena PCC 7120 after Expression in Escherichia coli. European Journal of Biochemistry. 1996 Feb;236(1):115–20. doi: 10.1111/j.1432-1033.1996.00115.x.; Fraser PD, Linden H, Sandmann G. Purification and reactivation of recombinant Synechococcus phytoene desaturase from an overexpressing strain of Escherichia coli. Biochem J. 1993 May 01;291 ( Pt 3)():687–92. PMID: 8489496; PMCID: PMC1132422.
trans-lycopene biosynthesis II (plants)

Accession ID: BioCyc:ARA_PWY-6475
  • 10.1007/s00425-004-1395-2
  • 10.1016/j.abb.2008.10.004
  • 10.1104/pp.104.052092
  • 10.1104/pp.107.098996
  • 10.1104/pp.110.153916
 Chen Y, Li F, Wurtzel ET. Isolation and Characterization of the Z-ISO Gene Encoding a Missing Component of Carotenoid Biosynthesis in Plants . 2010 Mar 24;153(1):66–79. doi: 10.1104/pp.110.153916.; Sandmann G. Evolution of carotene desaturation: The complication of a simple pathway. Archives of Biochemistry and Biophysics. 2009 Mar;483(2):169–74. doi: 10.1016/j.abb.2008.10.004.; Li F, Murillo C, Wurtzel ET. Maize Y9 Encodes a Product Essential for 15-cis-?-Carotene Isomerization. 2007 Apr 13;144(2):1181–9. doi: 10.1104/pp.107.098996.; Isaacson T, Ohad I, Beyer P, Hirschberg J. Analysis in vitro of the enzyme CRTISO establishes a poly-cis-carotenoid biosynthesis pathway in plants. Plant Physiol. 2004 Dec;136(4):4246–55. PMID: 15557094; PMCID: PMC535854.; Breitenbach J, Sandmann G. zeta-Carotene cis isomers as products and substrates in the plant poly-cis carotenoid biosynthetic pathway to lycopene. Planta. 2005 Mar;220(5):785–93. doi: 10.1007/s00425-004-1395-2. PMID: 15503129.
trans-lycopene biosynthesis II (oxygenic phototrophs and green sulfur bacteria)

Accession ID: PlantCyc:SOY_PWY-6475		 -
trans-lycopene biosynthesis II (oxygenic phototrophs and green sulfur bacteria)

Accession ID: PlantCyc:SPENNELLII_PWY-6475		 -
trans-lycopene biosynthesis II (oxygenic phototrophs and green sulfur bacteria)

Accession ID: PlantCyc:AHALLERI_PWY-6475		 -
trans-lycopene biosynthesis II (oxygenic phototrophs and green sulfur bacteria)

Accession ID: PlantCyc:SWITCHGRASS_PWY-6475		 -
trans-lycopene biosynthesis II (oxygenic phototrophs and green sulfur bacteria)

Accession ID: PlantCyc:TPARVULA_PWY-6475		 -
trans-lycopene biosynthesis II (oxygenic phototrophs and green sulfur bacteria)

Accession ID: PlantCyc:BANANA_PWY-6475		 -
trans-lycopene biosynthesis II (oxygenic phototrophs and green sulfur bacteria)

Accession ID: PlantCyc:WHEATD_PWY-6475		 -
trans-lycopene biosynthesis II (oxygenic phototrophs and green sulfur bacteria)

Accession ID: PlantCyc:CANNUUM_PWY-6475
  • 10.1007/s00425-004-1395-2
  • 10.1016/j.abb.2008.10.004
  • 10.1046/j.1432-1327.1999.00746.x
  • 10.1104/pp.104.052092
  • 10.1104/pp.107.098996
  • 10.1104/pp.110.153916
  • 10.1104/pp.123.4.1427
  • 10.1111/j.1432-1033.1996.00115.x
 Chen Y, Li F, Wurtzel ET. Isolation and characterization of the Z-ISO gene encoding a missing component of carotenoid biosynthesis in plants. Plant Physiol. 2010 May;153(1):66–79. PMID: 20335404; PMCID: PMC2862425.; Sandmann G. Evolution of carotene desaturation: The complication of a simple pathway. Archives of Biochemistry and Biophysics. 2009 Mar;483(2):169–74. doi: 10.1016/j.abb.2008.10.004.; Li F, Murillo C, Wurtzel ET. Maize Y9 encodes a product essential for 15-cis-zeta-carotene isomerization. Plant Physiol. 2007 Jun;144(2):1181–9. PMID: 17434985; PMCID: PMC1914175.; Isaacson T, Ohad I, Beyer P, Hirschberg J. Analysis in vitro of the enzyme CRTISO establishes a poly-cis-carotenoid biosynthesis pathway in plants. Plant Physiol. 2004 Dec;136(4):4246–55. PMID: 15557094; PMCID: PMC535854.; Breitenbach J, Sandmann G. zeta-Carotene cis isomers as products and substrates in the plant poly-cis carotenoid biosynthetic pathway to lycopene. Planta. 2005 Mar;220(5):785–93. doi: 10.1007/s00425-004-1395-2. PMID: 15503129.; Josse EM, Simkin AJ, Gaffé J, Labouré AM, Kuntz M, Carol P. A plastid terminal oxidase associated with carotenoid desaturation during chromoplast differentiation. Plant Physiol. 2000 Aug;123(4):1427–36. PMID: 10938359; PMCID: PMC59099.; Breitenbach J, Kuntz M, Takaichi S, Sandmann G. Catalytic properties of an expressed and purified higher plant type?-carotene desaturase fromCapsicum annuum. European Journal of Biochemistry. 1999 Oct;265(1):376–83. doi: 10.1046/j.1432-1327.1999.00746.x.; Albrecht M, Linden H, Sandmann G. Biochemical Characterization of Purified ?-Carotene Desaturase from Anabaena PCC 7120 after Expression in Escherichia coli. European Journal of Biochemistry. 1996 Feb;236(1):115–20. doi: 10.1111/j.1432-1033.1996.00115.x.
trans-lycopene biosynthesis II (oxygenic phototrophs and green sulfur bacteria)

Accession ID: PlantCyc:CARNATION_PWY-6475		 -
superpathway of carotenoid biosynthesis in plants

Accession ID: PlantCyc:SACREDLOTUS_CAROTENOID-PWY		 -
superpathway of carotenoid biosynthesis in plants

Accession ID: PlantCyc:SETARIA_CAROTENOID-PWY		 -
superpathway of carotenoid biosynthesis in plants

Accession ID: PlantCyc:SFALLAX_CAROTENOID-PWY		 -
superpathway of carotenoid biosynthesis in plants

Accession ID: PlantCyc:SOY_CAROTENOID-PWY		 -
trans-lycopene biosynthesis II (oxygenic phototrophs and green sulfur bacteria)

Accession ID: PlantCyc:CLEMENTINE_PWY-6475		 -