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MetaCyc Pathway: superpathway of carotenoid biosynthesis

If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Superclasses: Biosynthesis Secondary Metabolites Biosynthesis Terpenoids Biosynthesis Carotenoids Biosynthesis
Superpathways

Some taxa known to possess this pathway include ? : Arabidopsis thaliana col , Capsicum annuum , Lactuca sativa romaine , Solanum lycopersicum , Solanum tuberosum , Xanthophyllomyces dendrorhous

Expected Taxonomic Range: Cyanobacteria , Fungi , Rhodophyta , Viridiplantae

Summary:
General Background

Carotenoids with cyclic ends are integral constituents of plants, algae and cyanobacteria photosynthetic reaction centers [Goodwin80, Young93]. Animals, including humans, cannot synthesize carotenoids, although they are an essential source of retinoids and vitamin A. These isoprenoids pigments are lipid-soluble and are involved in a variety of functions including: protection against photooxidative stress through energy-dissipation of excess light absorbed by the antenna pigments; light-harvest for photosynthesis; the prominent lutein, as well as zeaxanthin, are involved in the reduction of cataract and macular degeneration; others are exploited as coloring agents in flowers and fruits to attract pollinators (and in industry as food colorant) and agents of seed dispersal; finally they are precursors for the plant growth hormone abscisic acid and vitamin A (for a succinct review of the applications of carotenoids, see [Cunningham98b]).

Carotenoids are C40 isoprenoids which consist of eight isoprene units and can be divided in two major groups: carotene and xanthophylls. Carotenes are linear or cyclized hydrocarbons such as lycopene, α-carotene and β-carotene. Xanthophylls are oxygenated derivatives (epoxy, keto or hydroxyl groups) of carotenes; for example: lutein, zeaxanthin. The carotenoid composition varies from species to species; the concentration and composition of xanthophylls are affected by light intensity and the accumulation of specific carotenoids in fruit and flower chromoplasts is a highly, developmentally regulated process [Fraser94, Giuliano93]. Important carotenoids variations are observed during fruit ripening (for review, see [Ronen99]). Higher plant chloroplasts typically accumulate lutein, β-carotene, violaxanthin and neoxanthin in the thylakoid membrane-bound photosystems [Peter91, Ryberg93]. β-Carotene is generally found in the reaction center where it plays a critical photoprotective role by quenching triplet chlorophyll and singlet oxygen, and can undergo rapid degradation during photooxidation [Young93a]. Adjacent to the reaction centers, in the core complex proteins, β-carotene and lutein can be found [Peter91, Bassi93]. Finally, the surrounding antenna complexes contain xanthophylls (lutein, violaxanthin and neoxanthin) [Peter91, Bassi93]. In the chromoplasts of ripening fruits and flower petals, and in the chloroplasts of senescing leaves, the carotenoids are found in membranes or in oil bodies or other structures within the stroma.

About This Pathway

The carotenoid pigments are synthesized in the plastids of plants where it is derived from the pathways of isoprenoid biosynthesis (for review, see [Cunningham98b]). More specifically, the first committed step of carotenoid biosynthesis is that of the formation of phytoene from geranylgeranyl diphosphate, obtained from the superpathway of geranylgeranyl diphosphate biosynthesis II (via MEP). This conversion is in fact a two-step reaction catalyzed by the enzyme phytoene synthase. Phytoene then undergoes a series of four desaturation reactions leading to the formation of all-trans-lycopene via all-trans phytofluene, all-trans-ζ-carotene, all-trans neurosporene. Although the desaturation steps use all-trans compounds in bacteria, plants accumulate small amounts of cis-carotenes indicative of additional cis-to-trans isomerization steps (see note below). An important branch-point in the biosynthesis of carotenoids lies in the cyclization of the linear, pink all-trans-lycopene into carotenes with all-β-, all-ε- or mixed β and ε rings. Carotenoids with two ε rings are, however, rarely observed in plants and algae, and, when detected, are usually found in trace amounts [Goodwin80]; lettuce is a rare example of plants known to accumulate substantial amounts of bicyclic ε ring carotenoids (see lactucaxanthin biosynthesis). The cyclization reaction are catalyzed by lycopene β- or ε-cyclases. These cyclases all share an amino acid sequence signature that is conserved in those enzymes and binds dinucleotides such as FAD and NADP [Cunningham96], but otherwise share little resemblance. The formation of α-carotene from lycopene is likely to proceed by the addition of a β-ring to δ-carotene. The alternative route (addition of an ε-ring to γ-carotene) appears unlikely as the ε-cyclase does not seem to be able to add a second ε ring to the monocyclic δ-carotene [Cunningham96].

Finally, the carotenes are oxygenated in various ways (hydroxylation, epoxydation, de-epoxidation) to form xanthophylls which comprise most of the carotenoid pigments in the thylakoid membrane of plants. Hydroxylations play an important role in the oxygenation of carotenes and are catalyzed by hydroxylases acting specifically onto β or ε rings.

It has been postulated that the regulation of ε-cyclase, possibly through control of gene expression, determines xanthophylls composition in leaves and other plant tissues, since its products (δ-carotene) is destined to the α-carotene branch [Ronen99].

In photosynthetic tissues, carotenoids generally occur as their stable trans configuration. For neoxanthin, however, it would appear that the 9'-cis isomer: 9'-cis-neoxanthin, is favored in photosynthetic tissues, while trans-neoxanthin preferentially accumulates in non-photosynthetic plant tissues or plants grown in the dark or under low light conditions [Bouvier00]. It has been postulated that a Δ9'-neoxanthin isomerase may exist in spinach [Strand00a]; moreover, while both isomers were detected during the characterization of the tomato neoxanthin synthase, the authors deemed the isomerization unlikely to be due to the activity of the enzyme per se [Bouvier00].

Citations: [Hirschberg01]

Subpathways: zeaxanthin, antheraxanthin and violaxanthin interconversion , trans-lycopene biosynthesis II (plants) , zeaxanthin biosynthesis , lutein biosynthesis , δ-carotene biosynthesis , β-carotene biosynthesis

Unification Links: AraCyc:CAROTENOID-PWY

Credits:
Created 10-Sep-2002 by Mueller L , TAIR
Revised 28-Jul-2006 by Tissier C , TAIR


References

Bassi93: Bassi R, Pineau B, Dainese P, Marquardt J (1993). "Carotenoid-binding proteins of photosystem II." Eur J Biochem 212(2);297-303. PMID: 8444169

Bouvier00: Bouvier F, D'harlingue A, Backhaus RA, Kumagai MH, Camara B (2000). "Identification of neoxanthin synthase as a carotenoid cyclase paralog." Eur J Biochem 267(21);6346-52. PMID: 11029576

Cunningham96: Cunningham FX, Pogson B, Sun Z, McDonald KA, DellaPenna D, Gantt E (1996). "Functional analysis of the β and ε lycopene cyclase enzymes of Arabidopsis reveals a mechanism for control of cyclic carotenoid formation." Plant Cell 8(9);1613-26. PMID: 8837512

Cunningham98b: Cunningham FX, Gantt E (1998). "Genes and enzymes of carotenoid biosynthesis in plants." Annu Rev Plant Physiol Plant Mol Biol 49;557-583. PMID: 15012246

Fraser94: Fraser PD, Truesdale MR, Bird CR, Schuch W, Bramley PM (1994). "Carotenoid Biosynthesis during Tomato Fruit Development (Evidence for Tissue-Specific Gene Expression)." Plant Physiol 105(1);405-413. PMID: 12232210

Giuliano93: Giuliano G, Bartley GE, Scolnik PA (1993). "Regulation of carotenoid biosynthesis during tomato development." Plant Cell 5(4);379-87. PMID: 8485401

Goodwin80: Goodwin, T.W. (1980). "The biochemistry of carotenoids." 2nd Edition, Vol. 1 (London: Chapman and Hall), pp. 261-320.

Grotewold06: Grotewold E (2006). "The genetics and biochemistry of floral pigments." Annu Rev Plant Biol 57;761-80. PMID: 16669781

Hirschberg01: Hirschberg J (2001). "Carotenoid biosynthesis in flowering plants." Curr Opin Plant Biol 2001;4(3);210-8. PMID: 11312131

Peter91: Peter GF, Thornber JP (1991). "Biochemical composition and organization of higher plant photosystem II light-harvesting pigment-proteins." J Biol Chem 266(25);16745-54. PMID: 1885603

Ronen99: Ronen G, Cohen M, Zamir D, Hirschberg J (1999). "Regulation of carotenoid biosynthesis during tomato fruit development: expression of the gene for lycopene epsilon-cyclase is down-regulated during ripening and is elevated in the mutant Delta." Plant J 17(4);341-51. PMID: 10205893

Ryberg93: Ryberg, H., Ryberg, M., Sundqvist, C. (1993). "Plastid ultrastructure and development." In "Pigment-protein complexes in plastids: synthesis and assembly', C.Sundqvist and M. Ryberg, eds, London: Academic Press, pp. 25-62.

Strand00a: Strand A, Kvernberg K, M Karlsen A , Liaaen-Jensen S (2000). "Geometrical E/Z isomers of (6R)- and (6S)-neoxanthin and biological implications." Biochem Syst Ecol 28(5);443-455. PMID: 10725601

Young93: Young, A. (1993). "Occurence and distribution of carotenoids in photosynthetic systems." Carotenoids in Photosynthesis, eds. Young, A.J. & Britton, G. (Chapman & Hall, London), pp. 16-71.

Young93a: Young AJ (1993). "Factors that affect the carotenoid composition of higer plants and algae." In 'Carotenoids in photosynthesis' A.J. Young and G. Britton, eds, London: Chapman and Hall, pp. 161-205.

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

Alvarez06: Alvarez V, Rodriguez-Saiz M, de la Fuente JL, Gudina EJ, Godio RP, Martin JF, Barredo JL (2006). "The crtS gene of Xanthophyllomyces dendrorhous encodes a novel cytochrome-P450 hydroxylase involved in the conversion of beta-carotene into astaxanthin and other xanthophylls." Fungal Genet Biol 43(4);261-72. PMID: 16455271

Baroli03: Baroli I, Do AD, Yamane T, Niyogi KK (2003). "Zeaxanthin accumulation in the absence of a functional xanthophyll cycle protects Chlamydomonas reinhardtii from photooxidative stress." Plant Cell 15(4);992-1008. PMID: 12671093

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

Bonk97: Bonk M, Hoffmann B, Von Lintig J, Schledz M, Al-Babili S, Hobeika E, Kleinig H, Beyer P (1997). "Chloroplast import of four carotenoid biosynthetic enzymes in vitro reveals differential fates prior to membrane binding and oligomeric assembly." Eur J Biochem 247(3);942-50. PMID: 9288918

Bouvier96: Bouvier F, d'Harlingue A, Hugueney P, Marin E, Marion-Poll A, Camara B (1996). "Xanthophyll biosynthesis. Cloning, expression, functional reconstitution, and regulation of beta-cyclohexenyl carotenoid epoxidase from pepper (Capsicum annuum)." J Biol Chem 271(46);28861-7. PMID: 8910532

Bouvier98a: Bouvier F, Keller Y, d'Harlingue A, Camara B (1998). "Xanthophyll biosynthesis: molecular and functional characterization of carotenoid hydroxylases from pepper fruits (Capsicum annuum L.)." Biochim Biophys Acta 1391(3);320-8. PMID: 9555077

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

Bugos96: Bugos RC, Yamamoto HY (1996). "Molecular cloning of violaxanthin de-epoxidase from romaine lettuce and expression in Escherichia coli." Proc Natl Acad Sci U S A 93(13);6320-5. PMID: 8692813

Chae11: Chae, Lee (2011). "The functional annotation of protein sequences was performed by the in-house Ensemble Enzyme Prediction Pipeline (E2P2, version 1.0). E2P2 systematically integrates results from three molecular function annotation algorithms using an ensemble classification scheme. For a given genome, all protein sequences are submitted as individual queries against the base-level annotation methods. The individual methods rely on homology transfer to annotate protein sequences, using single sequence (BLAST, E-value cutoff <= 1e-30, subset of SwissProt 15.3) and multiple sequence (Priam, November 2010; CatFam, version 2.0, 1% FDR profile library) models of enzymatic functions. The base-level predictions are then integrated into a final set of annotations using an average weighted integration algorithm, where the weight of each prediction from each individual method was determined via a 0.632 bootstrap process over 1000 rounds of testing. The training and testing data for E2P2 and the BLAST reference database were drawn from protein sequences with experimental support of existence, compiled from SwissProt release 15.3."

Chen10c: 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. PMID: 20335404

Choi06: Choi SK, Matsuda S, Hoshino T, Peng X, Misawa N (2006). "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 72(6);1238-46. PMID: 16614859

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

Cunningham01: Cunningham FX, Gantt E (2001). "One ring or two? Determination of ring number in carotenoids by lycopene ε-cyclases." Proc Natl Acad Sci U S A 2001;98(5);2905-10. PMID: 11226339

Cunningham93a: Cunningham FX, Chamovitz D, Misawa N, Gantt E, Hirschberg J (1993). "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 328(1-2);130-8. PMID: 8344419

Cunningham94: Cunningham FX, Sun Z, Chamovitz D, Hirschberg J, Gantt E (1994). "Molecular structure and enzymatic function of lycopene cyclase from the cyanobacterium Synechococcus sp strain PCC7942." Plant Cell 6(8);1107-21. PMID: 7919981

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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
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