intramolecular lyases


Summary: Enzymes of the isomerase class that catalyze reactions in which a group can be regarded as eliminated from one part of a molecule, leaving a double bond, while remaining covalently attached to the molecule. (From Enzyme Nomenclature, 1992) EC 5.5.

Top Publications

  1. Blas A, Ming R, Liu Z, Veatch O, Paull R, Moore P, et al. Cloning of the papaya chromoplast-specific lycopene beta-cyclase, CpCYC-b, controlling fruit flesh color reveals conserved microsynteny and a recombination hot spot. Plant Physiol. 2010;152:2013-22 pubmed publisher
    ..Our results enhanced our understanding of papaya flesh color inheritance and generated new tools for papaya improvement...
  2. Shirley B, Hanley S, Goodman H. Effects of ionizing radiation on a plant genome: analysis of two Arabidopsis transparent testa mutations. Plant Cell. 1992;4:333-47 pubmed
    ..The chromosome rearrangements found in these mutants have important implications for the use of ionizing radiation-induced alleles in classical and molecular genetic experiments in plants. ..
  3. Hamma T, Ferré D Amaré A. Pseudouridine synthases. Chem Biol. 2006;13:1125-35 pubmed
  4. Ahrazem O, Rubio Moraga A, López R, Gomez Gomez L. The expression of a chromoplast-specific lycopene beta cyclase gene is involved in the high production of saffron's apocarotenoid precursors. J Exp Bot. 2010;61:105-19 pubmed publisher
    ..goulimyi and C. cancellatus, the absence of transcripts suggests that transcriptional regulation of CstLcyB2a is responsible for the low apocarotenoid content in these species...
  5. Yu B, Lydiate D, Young L, Schäfer U, Hannoufa A. Enhancing the carotenoid content of Brassica napus seeds by downregulating lycopene epsilon cyclase. Transgenic Res. 2008;17:573-85 pubmed
  6. Vidhyavathi R, Venkatachalam L, Sarada R, Ravishankar G. Regulation of carotenoid biosynthetic genes expression and carotenoid accumulation in the green alga Haematococcus pluvialis under nutrient stress conditions. J Exp Bot. 2008;59:1409-18 pubmed publisher
    ..The induction of general carotenoid synthesis genes was independent of cytoplasmic protein synthesis while BKT gene expression was dependent on de novo protein synthesis. ..
  7. Kato M, Ikoma Y, Matsumoto H, Sugiura M, Hyodo H, Yano M. Accumulation of carotenoids and expression of carotenoid biosynthetic genes during maturation in citrus fruit. Plant Physiol. 2004;134:824-37 pubmed
  8. Phannachet K, Elias Y, Huang R. Dissecting the roles of a strictly conserved tyrosine in substrate recognition and catalysis by pseudouridine 55 synthase. Biochemistry. 2005;44:15488-94 pubmed publisher
  9. Steinbrenner J, Linden H. Light induction of carotenoid biosynthesis genes in the green alga Haematococcus pluvialis: regulation by photosynthetic redox control. Plant Mol Biol. 2003;52:343-56 pubmed
    ..These results suggested that in Haematococcus not only the specific astaxanthin pathway but also general carotenoid biosynthesis is subject to photosynthetic redox control. ..

More Information


  1. Diretto G, Tavazza R, Welsch R, Pizzichini D, Mourgues F, Papacchioli V, et al. Metabolic engineering of potato tuber carotenoids through tuber-specific silencing of lycopene epsilon cyclase. BMC Plant Biol. 2006;6:13 pubmed
    ..Potato tubers contain low levels of carotenoids, composed mainly of the xanthophylls lutein, antheraxanthin, violaxanthin, and of xanthophyll esters. None of these carotenoids have provitamin A activity...
  2. Stickforth P, Steiger S, Hess W, Sandmann G. A novel type of lycopene epsilon-cyclase in the marine cyanobacterium Prochlorococcus marinus MED4. Arch Microbiol. 2003;179:409-15 pubmed
    ..Consequently, we suggest that multiple gene duplications followed by functional diversification resulted several times, and in independent lineages, in the appearance of enzymes for the biosynthesis of cyclic carotenoids. ..
  3. Wurbs D, Ruf S, Bock R. Contained metabolic engineering in tomatoes by expression of carotenoid biosynthesis genes from the plastid genome. Plant J. 2007;49:276-88 pubmed
    ..Our results demonstrate the feasibility of engineering nutritionally important biochemical pathways in non-green plastids by transformation of the chloroplast genome. ..
  4. Dharmapuri S, Rosati C, Pallara P, Aquilani R, Bouvier F, Camara B, et al. Metabolic engineering of xanthophyll content in tomato fruits. FEBS Lett. 2002;519:30-4 pubmed
    ..The transgenes and the phenotype are inherited in a dominant Mendelian fashion. This is the first example of successful metabolic engineering of xanthophyll content in tomato fruits. ..
  5. Beyer P, Al Babili S, Ye X, Lucca P, Schaub P, Welsch R, et al. Golden Rice: introducing the beta-carotene biosynthesis pathway into rice endosperm by genetic engineering to defeat vitamin A deficiency. J Nutr. 2002;132:506S-510S pubmed
    ..Various institutional arrangements for disseminating Golden Rice to research institutes in developing countries also are discussed. ..
  6. Ramos A, Coesel S, Marques A, Rodrigues M, Baumgartner A, Noronha J, et al. Isolation and characterization of a stress-inducible Dunaliella salina Lcy-beta gene encoding a functional lycopene beta-cyclase. Appl Microbiol Biotechnol. 2008;79:819-28 pubmed publisher
    ..The results presented here suggest that nutrient availability is a key factor influencing carotenogenesis as well as carotenoid biosynthesis-related gene expression in D. salina. ..
  7. Cunningham F, Pogson B, Sun Z, McDonald K, DellaPenna D, Gantt E. Functional analysis of the beta and epsilon lycopene cyclase enzymes of Arabidopsis reveals a mechanism for control of cyclic carotenoid formation. Plant Cell. 1996;8:1613-26 pubmed publisher
  8. Komatsu M, Tsuda M, Omura S, Oikawa H, Ikeda H. Identification and functional analysis of genes controlling biosynthesis of 2-methylisoborneol. Proc Natl Acad Sci U S A. 2008;105:7422-7 pubmed publisher
    ..We concluded that the biosynthetic pathway involves the methylation of GPP by GPP methyltransferase and its subsequent cyclization by monoterpene cyclase to 2-MIB. ..
  9. Aharoni A, Giri A, Verstappen F, Bertea C, Sevenier R, Sun Z, et al. Gain and loss of fruit flavor compounds produced by wild and cultivated strawberry species. Plant Cell. 2004;16:3110-31 pubmed publisher
    ..The findings shed light on the molecular evolutionary mechanisms resulting in different flavor profiles that are eventually selected for in domesticated species...
  10. Schwab W, Williams D, Davis E, Croteau R. Mechanism of monoterpene cyclization: stereochemical aspects of the transformation of noncyclizable substrate analogs by recombinant (-)-limonene synthase, (+)-bornyl diphosphate synthase, and (-)-pinene synthase. Arch Biochem Biophys. 2001;392:123-36 pubmed
  11. Ampomah Dwamena C, McGhie T, Wibisono R, Montefiori M, Hellens R, Allan A. The kiwifruit lycopene beta-cyclase plays a significant role in carotenoid accumulation in fruit. J Exp Bot. 2009;60:3765-79 pubmed publisher
    ..This indicates that the accumulation of beta-carotene, the major carotenoid in these kiwifruit species, appears to be controlled by the level of expression of LCY-beta gene...
  12. Jez J, Bowman M, Noel J. Role of hydrogen bonds in the reaction mechanism of chalcone isomerase. Biochemistry. 2002;41:5168-76 pubmed
    ..Conservation of these residues in CHIs from other plant species implies a common reaction mechanism for enzyme-catalyzed flavanone formation in all plants. ..
  13. Hirschberg J. Carotenoid biosynthesis in flowering plants. Curr Opin Plant Biol. 2001;4:210-8 pubmed
    ..Recent data on the biochemistry of carotenogenesis and its regulation in vivo present the possibility of genetically manipulating this pathway in crop plants. ..
  14. Diretto G, Al Babili S, Tavazza R, Papacchioli V, Beyer P, Giuliano G. Metabolic engineering of potato carotenoid content through tuber-specific overexpression of a bacterial mini-pathway. PLoS ONE. 2007;2:e350 pubmed
    ..Assuming a beta-carotene to retinol conversion of 6ratio1, this is sufficient to provide 50% of the Recommended Daily Allowance of Vitamin A with 250 gms (fresh weight) of "golden" potatoes. ..
  15. Verdoes J, Krubasik K, Sandmann G, van Ooyen A. Isolation and functional characterisation of a novel type of carotenoid biosynthetic gene from Xanthophyllomyces dendrorhous. Mol Gen Genet. 1999;262:453-61 pubmed
    ..coli with various deletion derivatives of the crtYB gene, the regions responsible for phytoene synthesis and lycopene cyclisation were localised within the protein. ..
  16. Giorio G, Stigliani A, D Ambrosio C. Agronomic performance and transcriptional analysis of carotenoid biosynthesis in fruits of transgenic HighCaro and control tomato lines under field conditions. Transgenic Res. 2007;16:15-28 pubmed
  17. Bai L, Kim E, DellaPenna D, Brutnell T. Novel lycopene epsilon cyclase activities in maize revealed through perturbation of carotenoid biosynthesis. Plant J. 2009;59:588-99 pubmed publisher
    ..The implications of these findings with respect to breeding for carotenoid composition in maize grain are discussed...
  18. Pecker I, Gabbay R, Cunningham F, 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;30:807-19 pubmed
    ..This conclusion supports the hypothesis that transcriptional regulation of gene expression is a predominant mechanism of regulating carotenogenesis...
  19. Devitt L, Fanning K, Dietzgen R, Holton T. Isolation and functional characterization of a lycopene beta-cyclase gene that controls fruit colour of papaya (Carica papaya L.). J Exp Bot. 2010;61:33-9 pubmed publisher
  20. Bouvier F, Suire C, d Harlingue A, Backhaus R, Camara B. Molecular cloning of geranyl diphosphate synthase and compartmentation of monoterpene synthesis in plant cells. Plant J. 2000;24:241-52 pubmed
    ..These data provide new information as to how monoterpene biosynthesis is compartmentalized and induced de novo in response to biotic and abiotic stress in diverse plants...
  21. Arrach N, Fern ndez Mart n R, Cerd Olmedo E, Avalos J. A single gene for lycopene cyclase, phytoene synthase, and regulation of carotene biosynthesis in Phycomyces. Proc Natl Acad Sci U S A. 2001;98:1687-92 pubmed publisher
  22. Cunningham F, Gantt E. One ring or two? Determination of ring number in carotenoids by lycopene epsilon-cyclases. Proc Natl Acad Sci U S A. 2001;98:2905-10 pubmed publisher
  23. Seemann M, Zhai G, de Kraker J, Paschall C, Christianson D, Cane D. Pentalenene synthase. Analysis of active site residues by site-directed mutagenesis. J Am Chem Soc. 2002;124:7681-9 pubmed
    ..Finally, the F77Y mutant had a k(cat)/K(m) which was reduced by 20-fold compared to that of the wild-type synthase. ..
  24. Ohara K, Ujihara T, Endo T, Sato F, Yazaki K. Limonene production in tobacco with Perilla limonene synthase cDNA. J Exp Bot. 2003;54:2635-42 pubmed
    ..The possibility of genetically engineering monoterpene production is discussed...
  25. Sanz C, Benito E, Orejas M, Alvarez M, Eslava A. Protein-DNA interactions in the promoter region of the Phycomyces carB and carRA genes correlate with the kinetics of their mRNA accumulation in response to light. Fungal Genet Biol. 2010;47:773-81 pubmed publisher
    ..In contrast, protein extracts from phototropic mutants formed dark retardation complexes identical to that of the wild type. ..
  26. Cunningham F, 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;6:1107-21 pubmed
    ..Preliminary results from DNA gel blot hybridization experiments suggest that, like two earlier genes in the pathway, the Synechococcus gene encoding lycopene cyclase is homologous to plant and algal genes encoding this enzyme. ..
  27. Pan H, Agarwalla S, Moustakas D, Finer Moore J, Stroud R. Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit. Proc Natl Acad Sci U S A. 2003;100:12648-53 pubmed publisher
  28. Arrach N, Schmidhauser T, Avalos J. Mutants of the carotene cyclase domain of al-2 from Neurospora crassa. Mol Genet Genomics. 2002;266:914-21 pubmed
  29. Bohlmann J, Martin D, Oldham N, Gershenzon J. Terpenoid secondary metabolism in Arabidopsis thaliana: cDNA cloning, characterization, and functional expression of a myrcene/(E)-beta-ocimene synthase. Arch Biochem Biophys. 2000;375:261-9 pubmed
  30. Hornero Méndez D, Britton G. Involvement of NADPH in the cyclization reaction of carotenoid biosynthesis. FEBS Lett. 2002;515:133-6 pubmed
    ..No hydrogen is transferred from NADPH, which is therefore not involved directly in the cyclization reaction, but must play an indirect role, e.g. as an allosteric activator. ..
  31. Saslowsky D, Winkel Shirley B. Localization of flavonoid enzymes in Arabidopsis roots. Plant J. 2001;27:37-48 pubmed
    ..Staining of flavonoid endproducts with DPBA was consistent with expression of CHS and CHI in these seedlings. ..
  32. Hoang C, Ferr D Amar A. Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme. Cell. 2001;107:929-39 pubmed
    ..It accesses its substrate uridyl residue by flipping out the nucleotide and disrupts the tertiary structure of tRNA. Structural comparisons with TruB demonstrate that all Psi synthases are descended from a common molecular ancestor...
  33. Gensheimer M, Mushegian A. Chalcone isomerase family and fold: no longer unique to plants. Protein Sci. 2004;13:540-4 pubmed
    ..At the same time, fungal and bacterial species that have chalcone isomerase-like genes tend to lack the orthologs of the upstream enzyme chalcone synthase, suggesting a novel variation of the pathway in these species. ..
  34. Rink R, Kluskens L, Kuipers A, Driessen A, Kuipers O, Moll G. NisC, the cyclase of the lantibiotic nisin, can catalyze cyclization of designed nonlantibiotic peptides. Biochemistry. 2007;46:13179-89 pubmed
    ..Taken together the data demonstrate that NisC can be widely applied for the cyclization and stabilization of nonlantibiotic peptides. ..
  35. Maresca J, Graham J, Wu M, Eisen J, Bryant D. Identification of a fourth family of lycopene cyclases in photosynthetic bacteria. Proc Natl Acad Sci U S A. 2007;104:11784-9 pubmed publisher
    ..Identification of these cyclases fills a major gap in the carotenoid biosynthetic pathways of green sulfur bacteria and cyanobacteria...
  36. Alqu zar B, Zacar as L, Rodrigo M. Molecular and functional characterization of a novel chromoplast-specific lycopene beta-cyclase from Citrus and its relation to lycopene accumulation. J Exp Bot. 2009;60:1783-97 pubmed publisher
  37. Sandmann G, Zhu C, Krubasik P, Fraser P. The biotechnological potential of the al-2 gene from Neurospora [correction of Neurospra] crassa for the production of monocyclic keto hydroxy carotenoids. Biochim Biophys Acta. 2006;1761:1085-92 pubmed
    ..Among them all the monocyclic gamma-carotene derivatives with 9 conjugated double bonds were not found naturally before. Furthermore, 2-HO-4-keto-torulene with 10 conjugated double bonds is another novel carotenoid. ..
  38. Nurse K, Wrzesinski J, Bakin A, Lane B, Ofengand J. Purification, cloning, and properties of the tRNA psi 55 synthase from Escherichia coli. RNA. 1995;1:102-12 pubmed
    ..Stoichiometric formation of psi occurred with no requirement for an external source of energy, indicating that psi synthesis is thermodynamically favored. ..
  39. Clotault J, Peltier D, Berruyer R, Thomas M, Briard M, Geoffriau E. Expression of carotenoid biosynthesis genes during carrot root development. J Exp Bot. 2008;59:3563-73 pubmed publisher
  40. Harjes C, Rocheford T, Bai L, Brutnell T, Kandianis C, Sowinski S, et al. Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification. Science. 2008;319:330-3 pubmed publisher
    ..Selection of favorable lcyE alleles with inexpensive molecular markers will now enable developing-country breeders to more effectively produce maize grain with higher provitamin A levels. ..
  41. Al Babili S, Ye X, Lucca P, Potrykus I, Beyer P. Biosynthesis of beta-carotene (provitamin A) in rice endosperm achieved by genetic engineering. Novartis Found Symp. 2001;236:219-28; discussion 228-32 pubmed
    ..pseudonarcissus as a model system, a likely hypothesis can be developed that trans lycopene or a trans lycopene derivative acts as an inductor in a kind of feedback mechanism stimulating endogenous carotenogenic genes. ..
  42. Li T, Shi C, Gan Z, Shi X. [Cloning and analysis of the gene encoding lycopene epsilon cyclase in Chlorella protothecoides CS-41]. Wei Sheng Wu Xue Bao. 2009;49:1180-9 pubmed
    ..protothecoides CS-41 and C. reinhardtii among the listed organisms. Finally, the expression product of the LCYE gene cloned in the study was confirmed to hold the function and activity of lycopene epsilon cyclase. ..
  43. Martin D, Tholl D, Gershenzon J, Bohlmann J. Methyl jasmonate induces traumatic resin ducts, terpenoid resin biosynthesis, and terpenoid accumulation in developing xylem of Norway spruce stems. Plant Physiol. 2002;129:1003-18 pubmed
  44. Whittington D, Wise M, Urbansky M, Coates R, Croteau R, Christianson D. Bornyl diphosphate synthase: structure and strategy for carbocation manipulation by a terpenoid cyclase. Proc Natl Acad Sci U S A. 2002;99:15375-80 pubmed
    ..Structures of complexes with aza analogues of substrate and carbocation intermediates, as well as complexes with pyrophosphate and bornyl diphosphate, provide "snapshots" of the terpene cyclization cascade. ..
  45. Fäldt J, Arimura G, Gershenzon J, Takabayashi J, Bohlmann J. Functional identification of AtTPS03 as (E)-beta-ocimene synthase: a monoterpene synthase catalyzing jasmonate- and wound-induced volatile formation in Arabidopsis thaliana. Planta. 2003;216:745-51 pubmed
    ..AtTPS03 provides an important gene for probing plant-insect and possibly plant-plant interactions mediated by terpenoid volatiles. ..
  46. Singh M, Lewis P, Hardeman K, Bai L, Rose J, Mazourek M, et al. Activator mutagenesis of the pink scutellum1/viviparous7 locus of maize. Plant Cell. 2003;15:874-84 pubmed
    ..This study demonstrates the utility of an Ac mutagenesis program to efficiently generate allelic diversity at closely linked loci in maize. ..
  47. Skelton R, Yu Q, Srinivasan R, Manshardt R, Moore P, Ming R. Tissue differential expression of lycopene beta-cyclase gene in papaya. Cell Res. 2006;16:731-9 pubmed
    ..Further expression analyses of cpLCY-B showed that its expression levels were seven- and three-fold higher in leaves and, respectively, flowers than in fruits, suggesting that cpLCY-B is down-regulated during the fruit ripening process. ..
  48. Dudareva N, Martin D, Kish C, Kolosova N, Gorenstein N, Fäldt J, et al. (E)-beta-ocimene and myrcene synthase genes of floral scent biosynthesis in snapdragon: function and expression of three terpene synthase genes of a new terpene synthase subfamily. Plant Cell. 2003;15:1227-41 pubmed
    ..Analyses of tissue-specific, developmental, and rhythmic expression of these monoterpene synthase genes in snapdragon flowers revealed coordinated regulation of phenylpropanoid and isoprenoid scent production...
  49. Jez J, Noel J. Reaction mechanism of chalcone isomerase. pH dependence, diffusion control, and product binding differences. J Biol Chem. 2002;277:1361-9 pubmed
  50. Apel W, Bock R. Enhancement of carotenoid biosynthesis in transplastomic tomatoes by induced lycopene-to-provitamin A conversion. Plant Physiol. 2009;151:59-66 pubmed publisher
    ..Our results provide new insights into the regulation of carotenoid biosynthesis and demonstrate the potential of plastids genome engineering for the nutritional enhancement of food crops. ..
  51. Hegeman C, Good L, Grabau E. Expression of D-myo-inositol-3-phosphate synthase in soybean. Implications for phytic acid biosynthesis. Plant Physiol. 2001;125:1941-8 pubmed
    ..The GmMIPS1 expression pattern suggested that it encodes a MIPS isoform that functions in seeds to generate D-myo-inositol-3-phosphate as a substrate for phytic acid biosynthesis...
  52. Yu Q, Schaub P, Ghisla S, Al Babili S, Krieger Liszkay A, Beyer P. The lycopene cyclase CrtY from Pantoea ananatis (formerly Erwinia uredovora) catalyzes an FADred-dependent non-redox reaction. J Biol Chem. 2010;285:12109-20 pubmed publisher
    ..Lycopene cyclase, thus, ranks among the novel class of non-redox flavoproteins, such as isopentenyl diphosphate:dimethylallyl diphosphate isomerase type 2 (IDI-2) that requires the reduced form of the cofactor...
  53. Laemmli C, Werlen C, van der Meer J. Mutation analysis of the different tfd genes for degradation of chloroaromatic compounds in Ralstonia eutropha JMP134. Arch Microbiol. 2004;181:112-21 pubmed
    ..In contrast, insertion mutation of tfdDII resulted in better growth of R. eutropha JMP134 on 3-CBA, which is most likely due to the prevention of toxic metabolite production in the absence of TfdDII activity. ..
  54. Punyasiri P, Abeysinghe I, Kumar V, Treutter D, Duy D, Gosch C, et al. Flavonoid biosynthesis in the tea plant Camellia sinensis: properties of enzymes of the prominent epicatechin and catechin pathways. Arch Biochem Biophys. 2004;431:22-30 pubmed
    ..Together with the enzyme activities and substrate specificities of the preceding enzymatic reactions, the biosynthesis of the most prominent flavonoids of tea is elucidated. ..