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

Enzyme View:

Pathway diagram: trans-lycopene biosynthesis I (bacteria)

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 : Gloeobacter violaceus PCC 7421, Myxococcus xanthus, Neurospora crassa, Pantoea ananatis, Pantoea stewartii, Rubrivivax gelatinosus, Xanthophyllomyces dendrorhous

Expected Taxonomic Range: Archaea, Bacteria , Fungi

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. 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). The plant pathway is described in trans-lycopene biosynthesis II (plants).

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

About This Pathway

Two types of enzymes have been described in bacteria that produce all-trans-lycopene. In many organisms, such as Pantoea ananatis, a single FAD-containing enzyme, CrtI, catalyzes the initial isomerization and the four subsequent desaturation reactions necessary to convert 15-cis-phytoene to all-trans-lycopene, via the intermediate all-trans phytofluene, all-trans-ζ-carotene and all-trans neurosporene. In the bacterium Myxococcus xanthus, on the other hand, two enzymes are required for this process. The first one, CrtIa, catalyzes the initial isomerization and the first two desaturation steps, while the second one, CrtIb, catalyzes the two desaturation steps from all-trans-ζ-carotene to all-trans-lycopene.

The pathway has been documented in several organisms including the bacteria Pantoea ananatis and Rubrivivax gelatinosus [Bartley99, Harada01] and the fungus Neurospora crassa [Hausmann00]

Superpathways: β-carotene biosynthesis (engineered)

Subpathways: neurosporene biosynthesis

Variants: trans-lycopene biosynthesis II (plants)

Created 30-Mar-2010 by Caspi R, SRI International
Revised 21-Mar-2011 by Caspi R, SRI International


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

Harada01: Harada J, Nagashima KV, Takaichi S, Misawa N, Matsuura K, Shimada K (2001). "Phytoene desaturase, CrtI, of the purple photosynthetic bacterium, Rubrivivax gelatinosus, produces both neurosporene and lycopene." Plant Cell Physiol 42(10);1112-8. PMID: 11673627

Hausmann00: Hausmann A, Sandmann G (2000). "A single five-step desaturase is involved in the carotenoid biosynthesis pathway to beta-carotene and torulene in Neurospora crassa." Fungal Genet Biol 30(2);147-53. PMID: 11017770

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

Bartley90: Bartley GE, Schmidhauser TJ, Yanofsky C, Scolnik PA (1990). "Carotenoid desaturases from Rhodobacter capsulatus and Neurospora crassa are structurally and functionally conserved and contain domains homologous to flavoprotein disulfide oxidoreductases." J Biol Chem 265(26);16020-4. PMID: 2144293

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

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

Botella95: Botella JA, Murillo FJ, Ruiz-Vazquez R (1995). "A cluster of structural and regulatory genes for light-induced carotenogenesis in Myxococcus xanthus." Eur J Biochem 233(1);238-48. PMID: 7588751

Chen10a: 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

Cunningham98: 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

Fontes93: Fontes M, Ruiz-Vazquez R, Murillo FJ (1993). "Growth phase dependence of the activation of a bacterial gene for carotenoid synthesis by blue light." EMBO J 12(4);1265-75. PMID: 8467787

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.

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

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

Linden91: Linden H, Misawa N, Chamovitz D, Pecker I, Hirschberg J, Sandmann G (1991). "Functional complementation in Escherichia coli of different phytoene desaturase genes and analysis of accumulated carotenes." Z Naturforsch C 46(11-12);1045-51. PMID: 1817513

Lodato07: Lodato P, Alcaino J, Barahona S, Niklitschek M, Carmona M, Wozniak A, Baeza M, Jimenez A, Cifuentes V (2007). "Expression of the carotenoid biosynthesis genes in Xanthophyllomyces dendrorhous." Biol Res 40(1);73-84. PMID: 17657357

Maresca08: Maresca JA, Graham JE, Bryant DA (2008). "The biochemical basis for structural diversity in the carotenoids of chlorophototrophic bacteria." Photosynth Res 97(2);121-40. PMID: 18535920

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

Misawa90: Misawa N, Nakagawa M, Kobayashi K, Yamano S, Izawa Y, Nakamura K, Harashima K (1990). "Elucidation of the Erwinia uredovora carotenoid biosynthetic pathway by functional analysis of gene products expressed in Escherichia coli." J Bacteriol 172(12);6704-12. PMID: 2254247

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

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

Pinta03: Pinta V, Ouchane S, Picaud M, Takaichi S, Astier C, Reiss-Husson F (2003). "Characterization of unusual hydroxy- and ketocarotenoids in Rubrivivax gelatinosus: involvement of enzyme CrtF or CrtA." Arch Microbiol 179(5);354-62. PMID: 12664193

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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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