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MetaCyc Pathway: trans-lycopene biosynthesis II (plants)
Traceable author statement to experimental supportInferred from experiment

Enzyme View:

Pathway diagram: trans-lycopene biosynthesis II (plants)

This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Superclasses: BiosynthesisSecondary Metabolites BiosynthesisTerpenoids BiosynthesisCarotenoids BiosynthesisLycopene biosynthesis

Some taxa known to possess this pathway include : Arabidopsis thaliana col, Capsicum annuum, Lactuca sativa romaine, Solanum lycopersicum, Solanum tuberosum, Synechococcus elongatus PCC 7942, Zea mays

Expected Taxonomic Range: Cyanobacteria, Rhodophyta, Viridiplantae

General Background

All-trans-lycopene is a bright red carotenoid pigment and phytochemical found in many photosynthetic organisms. Its name is derived from the name of the tomato plant, Solanum lycopersicum, in which it is found in large amounts. All-trans-lycopene is an important intermediate in the biosynthesis of many carotenoids, which are responsible for pigmentation, photosynthesis, and photo-protection in plants, algae, and other photosynthetic organisms.

The first committed step of carotenoid biosynthesis is that of the formation of 15-cis-phytoene from geranylgeranyl diphosphate. This conversion is in fact a two-step reaction catalyzed by the enzyme phytoene synthase.

In general, bacteria, fungi and plants differ in their conversion of 15-cis-phytoene to all-trans-lycopene. In noncyanobacterial bacteria and fungi the pathway starts with the isomerization of 15-cis-phytoene to all-trans-phytoene, and the rest of the pathway proceeds via exclusively trans isomers (see trans-lycopene biosynthesis I (bacteria)). In plants, algae and cyanobacteria, on the other hand, the pathway proceeeds via cis isomers, and the conversion from cis to trans occurs at the very end of the pathway, where prolycopene is converted to all-trans-lycopene by the dedicated enzyme carotenoid isomerase (CrtQ in cyanobacteria).

It should be noted that exceptions do occur - for example, the cyanobacterium Gloeobacter violaceus PCC 7421 utilizes the bacterial pathway [Tsuchiya05].

About This Pathway

In plants, algae and cyanobacteria 15-cis-phytoene undergoes a series of four desaturation reactions leading to the formation of all-trans-lycopene via 9,15,9'-tri-cis-ζ-carotene, 9,9'-di-cis-ζ-carotene and prolycopene. To catalyze this transofrmation, plants and cyanobacteria require two phylogenetically related desaturases and two isomerases, encoded by PDS, Z-ISO, ZDS and CRTISO.

The first desaturase, 15-cis-phytoene desaturase ( PDS), removes two hydrogens and introduces trans double bonds at 11 and 11', along with a cis bond at the 9 and 9' double bond positions, producing 9,15,9'-tri-cis-ζ-carotene which is isomerized at the 15-cis double bond to 9,9'-di-cis-ζ-carotene by ζ-carotene isomerase ( Z-ISO).

The downstream steps in the pathway are still under investigation. In one proposed route for all-trans-lycopene formation, the second desaturase, ζ-carotene desaturase ( ZDS), removes two hydrogens and introduces cis double bonds at the 7 and 7' positions, leading to formation of conjugated cis double bonds at 7,9 and 7', 9'. Finally, the second isomerase, carotenoid isomerase ( CRTISO), isomerizes the cis double bonds at 7,9 and 7', 9', producing all-trans-lycopene [Sandmann09, Chen10]. The accumulation of prolycopene in tangerine tomato mutants [Isaacson04], as well as the biochemical activities tested for CRTISO and ZDS support the existence of this branch of the pathway [Sandmann09, Isaacson04].

However, in vitro enzymatic assays reveal that carotenoid isomerase ( CRTISO) can also act directly on 7,9,9'-cis-neurosporene indicating that an isomerization of this intermediate might precede the second desaturation. If this is the case, then the following reaction from 9'-cis-neurosporene to 7',9'-cis-lycopene would be expected to be catalyzed by a ZDS enzyme. The final proposed step in this pathway has not been experimentally verified but researchers hypothesize that CRTISO would catalyze this alternate reaction that leads to the production of all-trans-lycopene [Isaacson04].

Additional assays revealed that plants use oxidized plastoquinones as electron acceptors in the desaturation sequence.

Further research will be required to determine whether different plant species use one or more of these alternative routes for producing all-trans-lycopene in vivo.

Superpathways: superpathway of carotenoid biosynthesis

Variants: trans-lycopene biosynthesis I (bacteria)

Unification Links: PlantCyc:PWY-6475

Created 29-May-2008 by Caspi R, SRI International
Revised 21-Mar-2011 by Caspi R, SRI International


Chen10: Chen Y, Li F, Wurtzel ET (2010). "Isolation and characterization of the Z-ISO gene encoding a missing component of carotenoid biosynthesis in plants." Plant Physiol 153(1);66-79. PMID: 20335404

Isaacson04: Isaacson T, Ohad I, Beyer P, Hirschberg J (2004). "Analysis in vitro of the enzyme CRTISO establishes a poly-cis-carotenoid biosynthesis pathway in plants." Plant Physiol 136(4);4246-55. PMID: 15557094

Li07b: Li F, Murillo C, Wurtzel ET (2007). "Maize Y9 encodes a product essential for 15-cis-zeta-carotene isomerization." Plant Physiol 144(2);1181-9. PMID: 17434985

Sandmann09: Sandmann G (2009). "Evolution of carotene desaturation: the complication of a simple pathway." Arch Biochem Biophys 483(2);169-74. PMID: 18948076

Tsuchiya05: Tsuchiya T, Takaichi S, Misawa N, Maoka T, Miyashita H, Mimuro M (2005). "The cyanobacterium Gloeobacter violaceus PCC 7421 uses bacterial-type phytoene desaturase in carotenoid biosynthesis." FEBS Lett 579(10);2125-9. PMID: 15811329

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Albrecht96: Albrecht M, Linden H, Sandmann G (1996). "Biochemical characterization of purified zeta-carotene desaturase from Anabaena PCC 7120 after expression in Escherichia coli." Eur J Biochem 236(1);115-20. PMID: 8617254

Bartley92: Bartley GE, Viitanen PV, Bacot KO, Scolnik PA (1992). "A tomato gene expressed during fruit ripening encodes an enzyme of the carotenoid biosynthesis pathway." J Biol Chem 267(8);5036-9. PMID: 1544888

Bartley99: Bartley GE, Scolnik PA, Beyer P (1999). "Two Arabidopsis thaliana carotene desaturases, phytoene desaturase and zeta-carotene desaturase, expressed in Escherichia coli, catalyze a poly-cis pathway to yield pro-lycopene." Eur J Biochem 1999;259(1-2);396-403. PMID: 9914519

Beyer91: Beyer P, Kroncke U, Nievelstein V (1991). "On the mechanism of the lycopene isomerase/cyclase reaction in Narcissus pseudonarcissus L. chromoplasts." J Biol Chem 266(26);17072-8. PMID: 1894603

Breitenbach01: Breitenbach J, Zhu C, Sandmann G (2001). "Bleaching herbicide norflurazon inhibits phytoene desaturase by competition with the cofactors." J Agric Food Chem 49(11);5270-2. PMID: 11714315

Breitenbach05: Breitenbach J, Sandmann G (2005). "zeta-Carotene cis isomers as products and substrates in the plant poly-cis carotenoid biosynthetic pathway to lycopene." Planta 220(5);785-93. PMID: 15503129

Breitenbach99: Breitenbach J, Kuntz M, Takaichi S, Sandmann G (1999). "Catalytic properties of an expressed and purified higher plant type zeta-carotene desaturase from Capsicum annuum." Eur J Biochem 265(1);376-83. PMID: 10491195

Buckner90: Buckner B, Kelson TL, Robertson DS (1990). "Cloning of the y1 Locus of Maize, a Gene Involved in the Biosynthesis of Carotenoids." Plant Cell 2(9);867-876. PMID: 12354969

Buckner96: Buckner B, Miguel PS, Janick-Buckner D, Bennetzen JL (1996). "The y1 gene of maize codes for phytoene synthase." Genetics 143(1);479-88. PMID: 8722797

Collins81: Collins MD, Jones D (1981). "Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication." Microbiol Rev 45(2);316-54. PMID: 7022156

Fraser93: Fraser PD, Linden H, Sandmann G (1993). "Purification and reactivation of recombinant Synechococcus phytoene desaturase from an overexpressing strain of Escherichia coli." Biochem J 291 ( Pt 3);687-92. PMID: 8489496

Iniesta07: Iniesta AA, Cervantes M, Murillo FJ (2007). "Cooperation of two carotene desaturases in the production of lycopene in Myxococcus xanthus." FEBS J 274(16);4306-14. PMID: 17662111

Isaacson02: Isaacson T, Ronen G, Zamir D, Hirschberg J (2002). "Cloning of tangerine from tomato reveals a carotenoid isomerase essential for the production of beta-carotene and xanthophylls in plants." Plant Cell 14(2);333-42. PMID: 11884678

Josse00: Josse EM, Simkin AJ, Gaffe J, Laboure AM, Kuntz M, Carol P (2000). "A plastid terminal oxidase associated with carotenoid desaturation during chromoplast differentiation." Plant Physiol 123(4);1427-36. PMID: 10938359

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Lindgren03: Lindgren LO, Stalberg KG, Hoglund AS (2003). "Seed-specific overexpression of an endogenous Arabidopsis phytoene synthase gene results in delayed germination and increased levels of carotenoids, chlorophyll, and abscisic acid." Plant Physiol 132(2);779-85. PMID: 12805607

MartinezLaborda90: Martinez-Laborda A, Balsalobre JM, Fontes M, Murillo FJ (1990). "Accumulation of carotenoids in structural and regulatory mutants of the bacterium Myxococcus xanthus." Mol Gen Genet 223(2);205-10. PMID: 2123519

Matthews03: Matthews PD, Luo R, Wurtzel ET (2003). "Maize phytoene desaturase and zeta-carotene desaturase catalyse a poly-Z desaturation pathway: implications for genetic engineering of carotenoid content among cereal crops." J Exp Bot 54(391);2215-30. PMID: 14504297

Paine05: Paine JA, Shipton CA, Chaggar S, Howells RM, Kennedy MJ, Vernon G, Wright SY, Hinchliffe E, Adams JL, Silverstone AL, Drake R (2005). "Improving the nutritional value of Golden Rice through increased pro-vitamin A content." Nat Biotechnol 23(4);482-7. PMID: 15793573

Park02: Park H, Kreunen SS, Cuttriss AJ, DellaPenna D, Pogson BJ (2002). "Identification of the carotenoid isomerase provides insight into carotenoid biosynthesis, prolamellar body formation, and photomorphogenesis." Plant Cell 14(2);321-32. PMID: 11884677

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by Pathway Tools version 19.5 (software by SRI International) on Sat Apr 30, 2016, biocyc13.