, Volume 21, Issue 6, pp 833–859 | Cite as

The rutin catabolic pathway with special emphasis on quercetinase

  • Sylvain Tranchimand
  • Pierre Brouant
  • Gilles IacazioEmail author
Review Paper


The aim of this review is to give a general account on the oxidative microbial degradation of flavonols. Since now 50 years, various research groups have deciphered the way microorganisms aerobically deal with this important class of flavonoids. Flavonols such as rutin and quercetin are abundantly found in vegetal tissues and exudates, and it was thus patent that various microorganisms will bear the enzymatic machinery necessary to cope with these vegetal secondary metabolites. After initial studies focussed on the general metabolic capacity of various microorganisms towards flavonols, the so called rutin catabolic pathway was rapidly established in moulds. Enzymes of the path as well as substrates and products were known at the beginning of the seventies. Then during 30 years, only sporadic studies were focused on this pathway, before a new burst of interest at the beginning of the new century arose with structural, genomic and theorical studies mainly conducted towards quercetinase. This is the goal of this work to relate this 50 years journey at the crossroads of microbiology, biochemistry, genetic and chemistry. Some mention of the potential usefulness of the enzymes of the path as well as micro-organisms bearing the whole rutin catabolic pathway is also discussed.


Rutin catabolic pathway Quercetinase Flavonol Flavonol biodegradation 



This work was supported in part by a grant (no. 10659) from the “Ministère Délégué à l’Enseignement Supérieur et à la Recherche” to Sylvain Tranchimand.


  1. Adams M, Jia Z (2005) Structural and biochemical analysis reveal pirins to possess quercetinase activity. J Biol Chem 280:28675–28682CrossRefPubMedGoogle Scholar
  2. Agarwall G, Rajavel M, Gopal B, Srinivasan N (2009) Structure-based phylogeny as a diagnostic for functional characterization of proteins with a cupin fold. PLoS ONE 4:e5736CrossRefGoogle Scholar
  3. Antonczak S, Fiorucci S, Golebiowski J, Cabrol-Bass D (2009) Theorical investigations of the role played by quercetinase enzymes upon the flavonoids oxygenolysis mechanism. Phys Chem Chem Phys 11:1491–1501CrossRefPubMedGoogle Scholar
  4. Armand-Fraysse D, Lebreton P (1969) Recherches physiologiques sur les champignons III. Transformation métabolique de la rutine par les champignons lignivores. Bull Soc Chim Biol 51:563–578PubMedGoogle Scholar
  5. Barney BM, Schaab MR, LoBrutto R, Francisco WA (2004) Evidence for a new metal in a known active site: purification and characterization of an iron-containing quercetin 2,3-dioxygenase from Bacillus subtilis. Protein Expr Purif 35:131–141CrossRefPubMedGoogle Scholar
  6. Barz W (1971) Uber den abbau aromatisher verbindungen durch Fusarium oxysporum Schlecht. Arch Mikrobiol 78:341–352CrossRefPubMedGoogle Scholar
  7. Bowater L, Fairhurst SA, Just VJ, Bornemann S (2004) Bacillus subtilis YxaG is a novel Fe-containing quercetin 2,3-dioxygenase. FEBS Lett 557:45–48CrossRefPubMedGoogle Scholar
  8. Braune A, Gutschow M, Engst W, Blaut M (2001) Degradation of quercetin and luteolin by Eubacterium ramulus. Appl Environ Microbiol 62:5558–5567CrossRefGoogle Scholar
  9. Brown SB, Rajananda V, Holroyd JA, Evans EGV (1982) A study of the mechanism of quercetin oxygenation by 18O labelling. Biochem J 205:239–244PubMedGoogle Scholar
  10. Child JJ, Simpson FJ, Westlake DWS (1963) Degradation of rutin by Aspergillus flavus. Factors affecting production of the enzyme system. Can J Microbiol 9:653–664CrossRefGoogle Scholar
  11. Child JJ, Oka T, Simpson FJ, Krishnamurty HG (1971) Purification and properties of a phenol carboxylic acid esterase from Aspergillus flavus. Can J Microbiol 17:1455–1463CrossRefPubMedGoogle Scholar
  12. Clissold PM, Ponting CP (2001) JmjC: cupin metalloenzyme-like domains in jumonji, hairless and phospholipase A2β. Trends Biochem Sci 26:7–9CrossRefPubMedGoogle Scholar
  13. Das S, Rosazza JPN (2006) Microbial and enzymatic transformations of flavonoids. J Nat Prod 69:499–508CrossRefPubMedGoogle Scholar
  14. Dunwell JM (1998) Cupins: a new superfamily of functionally-diverse proteins that include germins and plant seed storage proteins. Biotechnol Genet Eng 15:1–32Google Scholar
  15. Dunwell JM, Gane PJ (1998) Microbial relatives of the seed storage proteins of higher plants: conservation of motifs in a functionally diverse superfamilly of enzymes. J Mol Evol 46:147–154CrossRefPubMedGoogle Scholar
  16. Dunwell JM, Khuri S, Gane PJ (2000) Microbial relatives of the seed storage proteins of higher plants: conservation of structure and diversification of function during evolution of the cupin superfamily. Microbiol Mol Biol Rev 64:153–179CrossRefPubMedGoogle Scholar
  17. Dunwell JM, Culham A, Carter CE, Sosa-Aguirre CR, Goodenough PW (2001) Evolution of functional diversity in the cupin superfamily. Trends Biochem Sci 26:740–746CrossRefPubMedGoogle Scholar
  18. Dunwell JM, Purvis A, Khuri S (2004) Cupins: the most functionally diverse protein superfamily? Phytochemistry 65:1–17CrossRefGoogle Scholar
  19. Fiorucci S, Golebiowski J, Cabrol-Bass D, Antonczak S (2004) Oxygenolysis of flavonoid compounds: DFT description of the mechanism for quercetin. ChemPhysChem 5:1726–1733CrossRefPubMedGoogle Scholar
  20. Fiorucci S, Golebiowski J, Cabrol-Bass D, Antonczak S (2006) Molecular simulations reveal a new entry site in quercetin 2,3-dioxygenase. A pathway for dioxygen. Proteins 64:845–850CrossRefPubMedGoogle Scholar
  21. Fiorucci S, Golebiowski J, Cabrol-Bass D, Antonczak S (2007) Molecular simulations bring new insights into flavonoid/quercetinase interaction mode. Proteins 67:961–970CrossRefPubMedGoogle Scholar
  22. Fittipaldi M, Steiner RA, Matsushita M, Dijkstra BW, Groenen EJJ, Huber M (2003) Single-crystal EPR study at 95 Hz of the type 2 copper site of the inhibitor-bound quercetin 2,3-dioxygenase. Biophys J 85:4047–4054CrossRefPubMedGoogle Scholar
  23. Fusetti F, Schröter KH, Steiner RA, van Noort PI, Pijning T, Rozeboom HJ, Kalk KH, Egmond MR, Dijkstra BW (2002) Crystal structure of the copper-containing quercetin 2,3-dioxygenase from Aspergillus japonicus. Structure 10:259–268CrossRefPubMedGoogle Scholar
  24. Gallego MV, Pinaga F, Ramon D, Valles S (2001) Purification and characterization of an α-L-rhamnosidase from Aspergillus terreus of interest in wine making. J Food Sci 65:204–209CrossRefGoogle Scholar
  25. Gopal B, Madan LL, Betz SF, Kossiakoff AA (2005) The crystal structure of a quercetin 2,3-dioxygenase from Bacillus subtilis suggests modulation of enzyme activity by a change in the metal ion at the active site(s). Biochemistry 44:193–201CrossRefPubMedGoogle Scholar
  26. Haluk JP, Metche M (1970) Transformation microbiologique de la quercetine par Aspergillus niger Van Tieghem. Bull Soc Chim Biol 52:667–676PubMedGoogle Scholar
  27. Hattori S, Noguchi I (1959) Microbial degradation of rutin. Nature 184:1145–1146CrossRefPubMedGoogle Scholar
  28. Hay GW, Westlake DWS, Simpson FJ (1961) Microbial decomposition of rutin. Can J Microbiol 7:921–931CrossRefPubMedGoogle Scholar
  29. Hirooka K, Kunikane S, Matsuoka H, Yoshida K-I, Kunamoto K, Tojo S, Fujita Y (2007) Dual regulation of the Bacillus subtilis regulon comprising the lmrAB and yxaGH operons and yxaF gene by two transcriptional repressors, LmrA and YxaF, in response to flavonoids. J Bacteriol 189:5170–5182CrossRefPubMedGoogle Scholar
  30. Hund H-K, Breuer J, Lingans F, Hüttermann J, Kappel R, Fetzner S (1999) Flavonol 2,4-dioxygenase from Aspergillus niger DSM 821, a type 2 CuII-containing glycoprotein. Eur J Biochem 263:871–878CrossRefPubMedGoogle Scholar
  31. Iacazio G (2005) Increased quercetinase production by Penicillium olsonii using fractional factorial design. Process Biochem 40:379–384CrossRefGoogle Scholar
  32. Kaizer J, Balogh-Hergovich E, Czaun M, Csay T, Speier G (2006) Redox and non-redox metal assisted model systems with relevance to flavonol and 3-hydroxyquinolin-4(1H)-one 2,4-dioxygenase. Coord Chem Rev 250:2222–2233CrossRefGoogle Scholar
  33. Kooter IM, Steiner RA, Dijkstra BW, van Noort PI, Egmond MR, Huber M (2002) EPR characterization of the mononuclear Cu-containing Aspergillus japonicus quercetin 2,3-dioxygenase reveals dramatic changes upon anaerobic binding of substrates. Eur J Biochem 269:2971–2979CrossRefPubMedGoogle Scholar
  34. Krishnamachari V, Levine LH, Paré PW (2002) Flavonoid oxidation by the radical generator AIBN: a unified mechanism for quercetin radical scavenging. J Agric Food Chem 50:4357–4363CrossRefPubMedGoogle Scholar
  35. Krishnamurty HG, Simpson FJ (1970) Degradation of rutin by Aspergillus flavus. Studies with oxygen 18 on the action of a dioxygenase on quercetin. J Biol Chem 245:1467–1471PubMedGoogle Scholar
  36. Kurosawa Y, Ikeda K, Igami F (1973) Alpha-L-rhamnosidase of the liver of Turbo cornutus and Aspergillus niger. J Biochem 73:31–37PubMedGoogle Scholar
  37. Mamma D, Kalogeris E, Hatzinikolaou DG, Lekanidou A, Kekos D, Macris BJ, Christakopoulos P (2004) Biochemical characterization of the multi-enzyme system produced by Penicillium decumbens grown on rutin. Food Biotechnol 18:1–18CrossRefGoogle Scholar
  38. Manzanares P, de Graaf LH, Visser J (1997) Purification and characterization of an a-L-rhamnosidase from Aspergillus niger. FEMS Microbiol Lett 157:279–283CrossRefPubMedGoogle Scholar
  39. Manzanares P, Orejas M, Ibanez E, Valles S, Ramon D (2000) Purification and characterization of an α-L-rhamnosidase from Aspergillus nidulans. Lett Appl Microbiol 31:198–202CrossRefPubMedGoogle Scholar
  40. Manzanares P, van den Broeck HC, de Graaf LH, Visser J (2001) Purification and characterization of two different α-L-rhamnosidases, RhaA and RhaB, from Aspergillus aculeatus. Appl Environ Microbiol 67:2230–2234CrossRefPubMedGoogle Scholar
  41. Medina ML, Kiernan VA, Francisco WA (2004) Proteomic analysis of rutin-induced secreted proteins from Aspergillus flavus. Fungal Genet Biol 41:327–335CrossRefPubMedGoogle Scholar
  42. Medina ML, Haynes PA, Breci L, Francisco WA (2005) Analysis of secreted proteins from Aspergillus flavus. Proteomics 5:3153–3161CrossRefPubMedGoogle Scholar
  43. Merkens H, Fetzner S (2008) Transcriptional analysis of the queD gene coding for quercetinase of Streptomyces sp. FLA. FEMS Microbiol Lett 287:100–107CrossRefPubMedGoogle Scholar
  44. Merkens H, Sielker S, Rose K, Fetzner S (2007) A new monocupin quercetinase of Streptomyces sp. FLA: identification and heterologous expression of the queD gene and activity of the recombinant enzyme towards different flavonols. Arch Microbiol 187:475–487CrossRefPubMedGoogle Scholar
  45. Merkens H, Kappl R, Jakob RP, Schmid FX, Fetzner S (2008) Quercetinase QueD of Streptomyces sp. FLA, a monocupin dioxygenase with a preference for nickel and cobalt. Biochemistry 47:12185–12196CrossRefPubMedGoogle Scholar
  46. Mills ENC, Jenkins J, Marigheto N, Belton PS, Gunning AP, Morris VJ (2002) Allergens of the cupin superfamily. Biochem Soc Trans 30:925–929CrossRefPubMedGoogle Scholar
  47. Monti D, Pisvejcova A, Kren V, Lama M, Riva S (2004) Generation of an a-L-rhamnosidases library and its application for the selective derhamnosylation of natural products. Biotechnol Bioeng 87:763–771CrossRefPubMedGoogle Scholar
  48. Narikawa T, Karaki Y, Shinoyama H, Fujii T (1998) Rutin degradation by culture filtrates from Penicillia. Nippon Nogeik Kaishi 72:473–479Google Scholar
  49. Narikawa T, Shinoyama H, Fujii T (2000) A β-rutinosidase from Penicillium rugulosum IFO 7242 that is a peculiar flavonoid glycosidase. Biosci Biotechnol Biochem 64:1317–1319CrossRefPubMedGoogle Scholar
  50. Neznanov N, Kondratova A, Chumakov KM, Neznanova L, Kondratov R, Banerjee AK, Gudkov AV (2008) Quercetinase pirin makes poliovirus replication resistant to flavonoid quercetin. DNA Cell Biol 27:191–198CrossRefPubMedGoogle Scholar
  51. Noguchi I (1963) The degradation of flavonols by Pullularia fermentans var. candida. Bot Mag Tokyo 76:191–198Google Scholar
  52. Oka T, Simpson FJ (1971) Quercetinase: a dioxygenase containing copper. Biochem Biophys Res Commun 43:1–5CrossRefPubMedGoogle Scholar
  53. Oka T, Simpson FJ (1972) Degradation of rutin by Aspergillus flavus. Quercetinase: isolation of a low molecular weight form containing less carbohydrate. Can J Microbiol 18:1171–1175CrossRefPubMedGoogle Scholar
  54. Oka T, Simpson FJ, Child JJ, Mills SC (1971) Degradation of rutin by Aspergillus flavus. Purification of the dioxygenase, quercetinase. Can J Microbiol 17:111–118CrossRefPubMedGoogle Scholar
  55. Oka T, Simpson FJ, Krishnamurty HG (1972) Degradation of rutin by Aspergillus flavus. Studies on specificity, inhibition and possible reaction mechanism of quercetinase. Can J Microbiol 18:493–508CrossRefPubMedGoogle Scholar
  56. Omori T, Shiozawa K, Sekiya M, Minoda Y (1986) Formation of 2,4,6-trihydroxy-carboxylic acid and 2-protocatechuoylphloroglucinol carboxylic acid from rutin by bacteria. Agric Biol Chem Tokyo 50:779–780Google Scholar
  57. Padrn J, Grist KL, Clark JB, Wender SH (1960) Specificity studies on an extracellular enzyme preparation obtained from quercetin grown cells of Aspergillus. Biochem Biophys Res Commun 3:412–416CrossRefGoogle Scholar
  58. Pang H, Bartlam M, Zeng Q, Miyatake H, Hisano T, Miki K, Wong L, Gao GF, Rao Z (2004) Crystal structure of human pirin. J Biol Chem 279:1491–1498CrossRefPubMedGoogle Scholar
  59. Pietta P-G (2000) Flavonoids as antioxidants. J Nat Prod 63:1035–1042CrossRefPubMedGoogle Scholar
  60. Pillai BVS, Swarup S (2002) Elucidation of the flavonoid catabolism pathway in Pseudomonas putida PML2 by comparative metabolic profiling. Appl Environ Microbiol 68:143–151CrossRefPubMedGoogle Scholar
  61. Puti M, Kalra S (2005) Purification and characterization of naringinase from a newly isolated strain of Aspergillus niger 1344 for the transformation of flavonoids. World J Microbiol Biotechnol 21:753–758CrossRefGoogle Scholar
  62. Rajavel M, Kulkarni NN, Gopal B (2008) Conformational studies suggest that the double stranded β helix scaffold provides an optimal balance between protein stability and function. Protein Pept Lett 15:244–249CrossRefPubMedGoogle Scholar
  63. Rao JR, Cooper JE (1994) Rhizobia catabolize nod gene-inducing flavonoids via C-ring fission mechanisms. J Bacteriol 176:5409–5413PubMedGoogle Scholar
  64. Rao KV, Weisner NT (1981) Microbial transformation of quercetin by Bacillus cereus. Appl Environ Microbiol 42:450–452PubMedGoogle Scholar
  65. Rao JR, Sharma ND, Hamilton JTG, Boyd DR, Cooper JE (1991) Biotransformation of the pentahydroxy flavone quercetin by Rhizobium loti and Bradyrhizobium stains (Lotus). Appl Environ Microbiol 57:1563–1565PubMedGoogle Scholar
  66. Rose K, Fetzner S (2006) Identification of linear plasmid pAM1 in the flavonoid degrading strain Actinoplanes missouriensi T (DSM 43046). Plasmid 55:249–254CrossRefPubMedGoogle Scholar
  67. Schaab MR, Barney BM, Francisco WA (2006) Kinetic and spectroscopic studies on the quercetin 2,3-dioxygenase from Bacillus subtilis. Biochemistry 45:1009–1016CrossRefPubMedGoogle Scholar
  68. Schneider H, Blaut M (2000) Anaerobic degradation of flavonoids by Eubacterium ramulus. Arch Microbiol 173:71–75CrossRefPubMedGoogle Scholar
  69. Schoefer L, Mohan R, Schwiertz A, Braune A, Blaut M (2003) Anaerobic degradation of flavonoids by Clostridium orbiscindens. Appl Environ Microbiol 69:5849–5854CrossRefPubMedGoogle Scholar
  70. Siegbahn PEM (2004) Hybrid DFT study of the mechanism of quercetin 2,3-dioxygenase. Inorg Chem 43:5944–5953CrossRefPubMedGoogle Scholar
  71. Simpson FJ, Talbot G, Westlake DWS (1960) Production of carbon monoxide in the enzymatic degradation of rutin. Biochem Biophys Res Commun 2:15–18CrossRefPubMedGoogle Scholar
  72. Simpson FJ, Narasimhachari N, Westlake DWS (1963) Degradation of rutin by Aspergillus flavus. The carbon monoxide producing system. Can J Microbiol 9:15–25CrossRefGoogle Scholar
  73. Steiner RA, Kalk KH, Dijkstra BW (2002a) Anaerobic enzyme substrate structures provide insight into the reaction mechanism of the copper-dependent quercetin 2,3-dioxygenase. Proc Natl Acad Sci USA 99:16625–16630CrossRefPubMedGoogle Scholar
  74. Steiner RA, Kooter IM, Dijkstra BW (2002b) Functional analysis of the copper-dependent quercetin 2,3-dioxygenase. 1. Ligand-induced coordination changes probed by X-ray crystallography: inhibition, ordering effect, and mechanistic insights. Biochemistry 41:7955–7962CrossRefPubMedGoogle Scholar
  75. Steiner RA, Meyer-Klaucke W, Dijkstra BW (2002c) Functional analysis of the copper-dependent quercetin 2,3-dioxygenase. 2. X-ray absorption studies of native enzyme and anaerobic complexes with the substrates quercetin and myricetin. Biochemistry 41:7963–7968CrossRefPubMedGoogle Scholar
  76. Tranchimand S, Tron T, Gaudin C, Iacazio G (2005) Evaluation of phenolics and sugars as inducers of quercetinase activity in Penicillium olsonii. FEMS Microbiol Lett 253:289–294CrossRefPubMedGoogle Scholar
  77. Tranchimand S, Tron T, Gaudin C, Iacazio G (2006) First chemical synthesis of three natural depsides involved in flavonoid catabolism and related to quercetinase catalysis. Synth Commun 36:587–597CrossRefGoogle Scholar
  78. Tranchimand S, Ertel G, Gaydou V, Gaudin C, Tron T, Iacazio G (2008) Biochemical and molecular characterization of a quercetinase from Penicillium olsonii. Biochimie 90:781–789CrossRefPubMedGoogle Scholar
  79. van den Bosch M, Swart M, van Gunsteren WN, Canters GW (2004) Simulation of the substrate cavity dynamics of quercetinase. J Mol Biol 344:725–738CrossRefPubMedGoogle Scholar
  80. van der Heiden M, Nondmann DH, van der Helm MJ, Verrips CT, Swarthoff T, Smits A (1998) WO1997EP07138 19971210Google Scholar
  81. Westlake DWS (1963) Microbial degradation of quercitrin. Can J Microbiol 9:211–220CrossRefGoogle Scholar
  82. Westlake DWS, Simpson FJ (1961) Degradation of rutin by Aspergillus flavus. Factors affecting production of the enzyme system. Can J Microbiol 7:33–44CrossRefPubMedGoogle Scholar
  83. Westlake DWS, Spencer JFT (1966) The utilisation of flavonoid compounds by yeast and yeast like fungi. Can J Microbiol 12:165–174CrossRefPubMedGoogle Scholar
  84. Westlake DWS, Talbot G, Blakley ER, Simpson FJ (1959) Microbial decomposition of rutin. Can J Microbiol 5:621–629CrossRefPubMedGoogle Scholar
  85. Westlake DWS, Roxburgh JM, Talbot G (1961) Microbial production of carbon monoxide from flavonoids. Nature 189:510–511CrossRefPubMedGoogle Scholar
  86. Winter J, Moore LH, Dowell VR Jr, Bokkenheuser VD (1989) C-ring cleavage of flavonoids by human intestinal bacteria. Appl Environ Microbiol 55:1203–1208PubMedGoogle Scholar
  87. Yoshida K-I, Ohki Y-H, Murata M, Kinehara M, Matsuoka H, Satomura T, Ohki R, Kumano M, Yamane K, Kunamoto K, Fujita Y (2004) Bacillus subtilis LmrA is a repressor of the lmrAB and yxaGH operons: identification of its binding site and functional analysis of lmrB and yxaGH. J Bacteriol 186:5640–5648CrossRefPubMedGoogle Scholar

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© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • Sylvain Tranchimand
    • 1
  • Pierre Brouant
    • 1
  • Gilles Iacazio
    • 1
    Email author
  1. 1.BiosCiencesUMR 6263 ISM2, Université Paul Cézanne Aix-Marseille IIIMarseille Cedex 20France

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