Functional & Integrative Genomics

, Volume 11, Issue 1, pp 13–22

Structure, function, and engineering of enzymes in isoflavonoid biosynthesis

Review

Abstract

Isoflavonoids are a large group of plant natural products and play important roles in plant defense. They also possess valuable health-promoting activities with significant health benefits for animals and humans. The isoflavonoids are identified primarily in leguminous plants and are synthesized through the central phenylpropanoid pathway and the specific isoflavonoid branch pathways in legumes. Structural studies of some key enzymes in the central phenylpropanoid pathway shed light on the early stages of the (iso)flavonoid biosynthetic process. Significant impact has also been made on structural studies of enzymes in the isoflavonoid branch pathways. Structures of isoflavonoid-specific NADPH-dependent reductases revealed how the (iso)flavonoid backbones are modified by reduction reactions and how enzymes specifically recognize isoflavonoids and catalyze stereo-specific reductions. Structural studies of isoflavonoid methyltransferases and glycosyltransferases revealed how isoflavonoids are further decorated with methyl group and sugars in different methylation and glycosylation patterns that determine their bioactivities and functions. In combination with mutagenesis and biochemical studies, the detailed structural information of these enzymes provides a basis for understanding the complex biosynthetic process, enzyme catalytic mechanisms, and substrate specificities. Structure-based homology modeling facilitates the functional characterization of these large groups of biosynthetic enzymes and their homologs. Structure-based enzyme engineering is becoming a new strategy for synthesis of bioactive isoflavonoids and also facilitates plant metabolic engineering towards improvement of quality and production of crop plants.

Keywords

Isoflavonoid Plant natural product Biosynthesis Enzyme Crystal structure Engineering 

References

  1. Achnine L, Huhman DV, Farag MA, Sumner LW, Blount JW, Dixon RA (2005) Genomics-based selection and functional characterization of triterpene glycosyltransferases from the model legume Medicago truncatula. Plant J 41:875–887PubMedCrossRefGoogle Scholar
  2. Akashi T, Aoki T, Ayabe S (1999) Cloning and functional expression of a cytochrome P450 cDNA encoding 2-hydroxyisoflavanone synthase involved in biosynthesis of the isoflavonoid skeleton in licorice. Plant Physiol 121:821–828PubMedCrossRefGoogle Scholar
  3. Babiychuk E, Kushnir S, Belles-Boix E, Van Montagu M, Inzé D (1995) Arabidopsis thaliana NADPH oxidoreductase homologs confer tolerance of yeasts toward the thiol-oxidizing drug diamine. J Biol Chem 270:26224–26231PubMedCrossRefGoogle Scholar
  4. Banerjee S, Li Y, Wang Z, Sarkar FH (2008) Multi-targeted therapy of cancer by genistein. Cancer Lett 269:226–242PubMedCrossRefGoogle Scholar
  5. Barnes S, Kirk M, Coward L (1994) Isoflavones and their conjugates in soy foods: extraction conditions and analysis by HPLC mass spectrometry. J Agric Chem 42:2466–2474CrossRefGoogle Scholar
  6. Bomati EK, Austin MB, Bowman ME, Dixon RA, Noel JP (2005) Structural elucidation of chalcone reductase and implications for deoxychalcone biosynthesis. J Biol Chem 280:30496–30503PubMedCrossRefGoogle Scholar
  7. Bowles D, Lim EK, Poppenberger B, Vaistij FE (2006) Glycosyltransferases of lipophilic small molecules. Annu Rev Plant Biol 57:567–597PubMedCrossRefGoogle Scholar
  8. Calabrese JC, Jordan DB, Boodhoo A, Sariaslani S, Vannelli T (2004) Crystal structure of phenylalanine ammonia lyase: multiple helix dipoles implicated in catalysis. Biochemistry 43:11403–11416PubMedCrossRefGoogle Scholar
  9. Campbell JA, Davies GJ, Bulone V, Henrissat B (1997) A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities. Biochem J 326:929–939PubMedGoogle Scholar
  10. Coutinho PM, Deleury E, Davies GJ, Henrissat B (2003) An evolving hierarchical family classification for glycosyltransferases. J Mol Biol 328:307–317PubMedCrossRefGoogle Scholar
  11. Cruickshank IAM, Perrin DR (1960) Isolation of a phytoalexin from Pisum sativum L. Nature 187:799–800PubMedCrossRefGoogle Scholar
  12. Daniel S, Tiemann K, Wittkampf U, Bless W, Hinderer W, Barz W (1990) Elicitor-induced metabolic changes in cell cultures of chickpea (Cicer arietinum L.) cultivar resistant and susceptible to Ascochyta rabiei. Planta 182:270–278CrossRefGoogle Scholar
  13. Deavours BE, Dixon RA (2005) Metabolic engineering of isoflavonoid biosynthesis in alfalfa (Medicago sativa L.). Plant Physiol 138:2245–2259PubMedCrossRefGoogle Scholar
  14. Deavours BE, Liu CJ, Naoumkina MA, Tang Y, Farag MA, Sumner LW, Noel JP, Dixon RA (2006) Functional analysis of members of the isoflavone and isoflavanone O-methyltransferase enzyme families from the model legume Medicago truncatula. Plant Mol Biol 62:715–733PubMedCrossRefGoogle Scholar
  15. Dhaubhadel S, Farhangkhoee M, Chapman R (2008) Identification and characterization of isoflavonoid specific glycosyltransferase and malonyltransferase from soybean seeds. J Exp Bot 59:981–994PubMedCrossRefGoogle Scholar
  16. Dixon RA (1999) Isoflavonoids: biochemistry, molecular biology and biological functions. In: Sankawa U (ed) Comprehensive natural products chemistry. Elsevier, Oxford, pp 773–823CrossRefGoogle Scholar
  17. Dixon RA, Sumner LW (2003) Legume natural products: understanding and manipulating complex pathways for human and animal health. Plant Physiol 131:878–885PubMedCrossRefGoogle Scholar
  18. Dixon RA, Harrison MJ, Paiva NL (1995) The isoflavonoid phytoalexin pathway: from enzymes to genes to transcription factors. Physiol Plant 93:385–392CrossRefGoogle Scholar
  19. Ferrer JL, Jez JM, Bowman ME, Dixon RA, Noel JP (1999) Structure of chalcone synthase and the molecular basis of plant polyketide biosynthesis. Nat Struct Biol 6:775–784PubMedCrossRefGoogle Scholar
  20. Gargouri M, Manigand C, Maugé C, Granier T, Langlois d’Estaintot B, Cala O, Pianet I, Bathany K, Chaudière J, Gallois B (2009) Structure and epimerase activity of anthocyanidin reductase from Vitis vinifera. Acta Crystallogr D 65:989–1000PubMedCrossRefGoogle Scholar
  21. Guo L, Dixon RA, Paiva NL (1994) Conversion of vestitone to medicarpin in alfalfa (Medicago sativa L.) is catalyzed by two indenpendent enzymes. J Biol Chem 269:22372–22378PubMedGoogle Scholar
  22. He X, Reddy JT, Dixon RA (1998) Stress responses in alfalfa (Medicago sativa L). XXII. cDNA cloning and characterization of an elicitor-inducible isoflavone 7-O-methyltransferase. Plant Mol Biol 36:43–54PubMedCrossRefGoogle Scholar
  23. He X, Wang X, Dixon RA (2006) Mutational analysis of the Medicago glycosyltransferase UGT71G1 reveals residues that control regioselectivity for (iso)flavonoid glycosylation. J Biol Chem 281:34441–34447PubMedCrossRefGoogle Scholar
  24. He X, Li W, Blount JW, Dixon RA (2008) Regioselective synthesis of plant (iso)flavone glycosides in Escherichia coli. Appl Microbiol Biotechnol 80:253–260PubMedCrossRefGoogle Scholar
  25. Higgins VJ (1972) Role of the phytoalexin medicarpin in three leafspot diseases of alfalfa. Physiol Plant Pathol 2:289–300CrossRefGoogle Scholar
  26. Hughes J, Hughes MA (1994) Multiple secondary plant product UDP-glucose glucosyltransferase genes expressed in cassava (Manihot esculenta Crantz) cotyledons. DNA Seq 5:41–49PubMedGoogle Scholar
  27. Isin EM, Guengerich FP (2007) Complex reactions catalyzed by cytochrome P450 enzymes. Biochim Biophys Acta 1770:314–329PubMedGoogle Scholar
  28. Jez JM, Noel JP (2002) Reaction mechanism of chalcone isomerase. pH dependence, diffusion control, and product binding differences. J Biol Chem 277:1361–1369PubMedCrossRefGoogle Scholar
  29. Jez JM, Bowman ME, Dixon RA, Noel JP (2000) Structure and mechanism of the evolutionarily unique plant enzyme chalcone isomerase. Nat Struct Biol 7:786–791PubMedCrossRefGoogle Scholar
  30. Jones P, Vogt T (2001) Glycosyltransferases in secondary plant metabolism: tranquilizers and stimulant controllers. Planta 213:164–174PubMedCrossRefGoogle Scholar
  31. Karamloo F, Schmitz N, Scheurer S, Foetisch K, Hoffmann A, Haustein D, Vieths S (1999) Molecular cloning and characterization of a birch pollen minor allergen, Bet v 5, belonging to a family of isoflavone reductase-related proteins. J Allergy Clin Immunol 104:991–999PubMedCrossRefGoogle Scholar
  32. Lairson LL, Henrissat B, Davies GJ, Withers SG (2008) Glycosyltransferases: structures, functions, and mechanisms. Annu Rev Biochem 77:521–555PubMedCrossRefGoogle Scholar
  33. Lee DS, Nioche P, Hamberg M, Raman CS (2008) Structural insights into the evolutionary paths of oxylipin biosynthetic enzymes. Nature 455:363–368PubMedCrossRefGoogle Scholar
  34. Li Y, Baldauf S, Lim EK, Bowles DJ (2001) Phylogenetic analysis of the UDP-glycosyltransferase multigene family of Arabidopsis thaliana. J Biol Chem 276:4338–4343PubMedCrossRefGoogle Scholar
  35. Li L, Modolo LV, Escamilla-Trevino LL, Achnine L, Dixon RA, Wang X (2007) Crystal structure of Medicago truncatula UGT85H2—insights into the structural basis of a multifunctional (iso)flavonoid glycosyltransferase. J Mol Biol 370:951–963PubMedCrossRefGoogle Scholar
  36. Li L, Chang Z, Pan Z, Fu ZQ, Wang X (2008) Modes of heme binding and substrate access for cytochrome P450 CYP74A revealed by crystal structures of allene oxide synthase. Proc Natl Acad Sci USA 105:13883–13888PubMedCrossRefGoogle Scholar
  37. Lim EK, Ashford DA, Hou B, Jackson RG, Bowles DJ (2004) Arabidopsis glycosyltransferases as biocatalysts in fermentation for regioselective synthesis of diverse quercetin glucosides. Biotech Bioeng 87:623–631CrossRefGoogle Scholar
  38. Liu C, Blount JW, Steele CL, Dixon RA (2002) Bottlenecks for the metabolic engineering of isoflavone glycoconjugates in Arabidopsis. Proc Natl Acad Sci USA 99:14578–14583PubMedCrossRefGoogle Scholar
  39. Liu C, Deavours BE, Richard SB, Ferrer JL, Blount JW, Huhman D, Dixon RA, Noel JP (2006) Structural basis for dual functionality of isoflavonoid O-methyltransferases in the evolution of plant defense responses. Plant Cell 18:3656–3669PubMedCrossRefGoogle Scholar
  40. Maugé C, Granier T, d’Estaintot BL, Gargouri M, Manigand C, Schmitter JM, Chaudière J, Gallois B (2010) Crystal structure and catalytic mechanism of leucoanthocyanidin reductase from Vitis vinifera. J Mol Biol 397:1079–1091PubMedCrossRefGoogle Scholar
  41. Min T, Kasahara H, Bedgar DL, Youn B, Lawrence PK, Gang DR, Halls SC, Park H, Hilsenbeck JL, Davin LB, Lewis NG, Kang C (2003) Crystal structures of pinoresinol-lariciresinol and phenylcoumaran benzylic ether reductases and their relationship to isoflavone reductases. J Biol Chem 278:50714–50723PubMedCrossRefGoogle Scholar
  42. Modolo LV, E-T LL, Dixon RA, Wang X (2009a) Single amino acid mutations of Medicago glycosyltransferase UGT85H2 enhance activity and impart reversibility. FEBS Lett 583:2131–2135PubMedCrossRefGoogle Scholar
  43. Modolo LV, Li L, Dixon RA, Wang X (2009b) Crystal structures of glycosyltransferase UGT78G1 reveal the molecular basis for glycosylation and deglycosylation of (iso)flavonoids. J Mol Biol 392:1292–1302PubMedCrossRefGoogle Scholar
  44. Moffitt MC, Louie GV, Bowman ME, Pence J, Noel JP, Moore BS (2007) Discovery of two cyanobacterial phenylalanine ammonia lyases: kinetic and structural characterization. Biochemistry 46:1004–1012PubMedCrossRefGoogle Scholar
  45. Nagashima S, Inagaki R, Kubo A, Hirotani M, Yoshikawa T (2004) cDNA cloning and expression of isoflavonoid-specific glucosyltransferase from Glycyrrhiza echinata cell-suspension cultures. Planta 218:456–459PubMedCrossRefGoogle Scholar
  46. Noel J, Dixon RA, Pichersky E, Zubieta C, Ferrer J (2003) Structural, functional, and evolutionary basis for methylation of plant small molecules. Recent Adv Phytochem 37:37–58CrossRefGoogle Scholar
  47. Noguchi A, Saito A, Homma Y, Nakao M, Sasaki N, Nishino T, Takahashi S, Nakayama T (2007) A UDP-glucose:isoflavone 7-O-glucosyltransferase from the roots of soybean (Glycine max) seedlings—purification, gene cloning, phylogenetics, and an implication for an alternative strategy of enzyme catalysis. J Biol Chem 282:23581–23590PubMedCrossRefGoogle Scholar
  48. Noguchi A, Horikawa M, Fukui Y, Fukuchi-Mizutani M, Iuchi-Okada A, Ishiguro M, Kiso Y, Nakayama T, Ono E (2009) Local differentiation of sugar donor specificity of flavonoid glycosyltransferase in Lamiales. Plant Cell 21:1556–1572PubMedCrossRefGoogle Scholar
  49. Offen W, Martinez-Fleites C, Yang M, Kiat-Lim E, Davis BG, Tarling CA, Ford CM, Bowles DJ, Davies GJ (2006) Structure of a flavonoid glucosyltransferase reveals the basis for plant natural product modification. EMBO J 25:1396–1405PubMedCrossRefGoogle Scholar
  50. Osmani SA, Bak S, Imberty A, Olsen CE, Moller BL (2008) Catalytic key amino acids and UDP-sugar donor specificity of a plant glucuronosyltransferase, UGT94B1: molecular modeling substantiated by site-specific mutagenesis and biochemical analyses. Plant Physiol 148:1295–1308PubMedCrossRefGoogle Scholar
  51. Paiva NL, Edwards R, Sun Y, Hrazdina G, Dixon RA (1991) Stress responses in alfalfa (Medicago sativa L.). 11. Molecular cloning and expression of alfalfa isoflavone reductase, a key enzyme of isoflavonoid phytoalexin biosynthesis. Plant Mol Biol 17:653–667PubMedCrossRefGoogle Scholar
  52. Paquette SM, Bak S, Feyereisen R (2000) Intron-exon organization and phylogeny in a large superfamily, the paralogous cytochrome P450 genes of Arabidopsis thaliana. DNA Cell Biol 19:307–317PubMedCrossRefGoogle Scholar
  53. Petit P, Granier T, d’Estaintot BL, Manigand C, Bathany K, Schmitter JM, Lauvergeat V, Hamdi S, Gallois B (2007) Crystal structure of grape dihydroflavonol 4-reductase, a key enzyme in flavonoid biosynthesis. J Mol Biol 368:1345–1357PubMedCrossRefGoogle Scholar
  54. Petrucco S, Bolchi A, Foroni C, Percudani R, Rossi GL, Ottonello S (1996) A maize gene encoding an NADPH binding enzyme highly homologous to isoflavone reductases is activated in response to sulfur starvation. Plant Cell 8:69–80PubMedCrossRefGoogle Scholar
  55. Ritter H, Schulz GE (2004) Structural basis for the entrance into the phenylpropanoid metabolism catalyzed by phenylalanine ammonia-lyase. Plant Cell 16:3426–3436PubMedCrossRefGoogle Scholar
  56. Ross J, Li Y, Lim E, Bowles DJ (2001) Higher plant glycosyltransferases. Genome Biol 2:3004.3001–3004.3006CrossRefGoogle Scholar
  57. Sarkar FH, Li Y (2004) The role of isoflavones in cancer chemoprevention. Front Biosci 9:2714–2724PubMedCrossRefGoogle Scholar
  58. Schuler MA, Werck-Reichhart D (2003) Functional genomics of P450s. Annu Rev Plant Biol 54:629–667PubMedCrossRefGoogle Scholar
  59. Schwede TF, Retey J, Schulz GE (1999) Crystal structure of histidine ammonia-lyase revealing a novel polypeptide modification as the catalytic electrophile. Biochemistry 38:5355–5361PubMedCrossRefGoogle Scholar
  60. Shao H, He X, Achnine L, Blount JW, Dixon RA, Wang X (2005) Crystal structures of a multifunctional triterpene/flavonoid glycosyltransferase from Medicago truncatula. Plant Cell 17:3141–3154PubMedCrossRefGoogle Scholar
  61. Shao H, Dixon RA, Wang X (2007) Crystal structure of vestitone reductase from Alfalfa (Medicago sativa L.). J Mol Biol 369:265–276PubMedCrossRefGoogle Scholar
  62. Shoji T, Winz R, Iwase T, Keiji Nakajima K, Yamada Y, Hashimoto T (2002) Expression patterns of two tobacco isoflavone reductase-like genes and their possible roles in secondary metabolism in tobacco. Plant Mol Biol 50:427–440PubMedCrossRefGoogle Scholar
  63. Steele CL, Gijzen M, Qutob D, Dixon RA (1999) Molecular characterization of the enzyme catalyzing the aryl migration reaction of isoflavonoid biosynthesis in soybean. Arch Biochem Biophys 367:146–150PubMedCrossRefGoogle Scholar
  64. Wang X (2009) Structure, mechanism and engineering of plant natural product glycosyltransferases. FEBS Lett 583:3303–3309PubMedCrossRefGoogle Scholar
  65. Wang HJ, Murphy PA (1994) Isoflavone content of commercial soybean foods. J Agric Food Chem 42:1666–1673CrossRefGoogle Scholar
  66. Wang X, He X, Lin J, Shao H, Chang Z, Dixon RA (2006) Crystal structure of isoflavone reductase from Alfalfa (Medicago sativa L.). J Mol Biol 358:1341–1352PubMedCrossRefGoogle Scholar
  67. Winkel-Shirley B (2001) Flavonoid biosynthesis. A colorful model for genetics, biochemistry, cell biology, and biotechnology. Plant Physiol 126:485–493PubMedCrossRefGoogle Scholar
  68. Xie D, Sharma SB, Paiva NL, Ferreira D, Dixon RA (2003) BANYULS encodes anthocyanidin reductase active in plant flavonoid biosynthesis. Science 299:396–399PubMedCrossRefGoogle Scholar
  69. Zubieta C, Dixon RA, Noel JP (2001) Crystal structures of chalcone O-methyltransferase and isoflavone O-methyltransferase reveal the structural basis for substrate specificity in plant O-methyltransferases. Nat Struct Biol 8:271–279PubMedCrossRefGoogle Scholar
  70. Zubieta C, Ross JR, Koscheski P, Yang Y, Pichersky E, Noel JP (2003) Structural basis for substrate recognition in the salicylic acid carboxyl methyltransferase family. Plant Cell 15:1704–1716PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  1. 1.Plant Biology DivisionSamuel Roberts Noble FoundationArdmoreUSA

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