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Flavin-dependent halogenases involved in secondary metabolism in bacteria

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Abstract

The understanding of biological halogenation has increased during the last few years. While haloperoxidases were the only halogenating enzymes known until 1997, it is now clear that haloperoxidases are hardly, if at all, involved in biosynthesis of more complex halogenated compounds in microorganisms. A novel type of halogenating enzymes, flavin-dependent halogenases, has been identified as a major player in the introduction of chloride and bromide into activated organic molecules. Flavin-dependent halogenases require the activity of a flavin reductase for the production of reduced flavin, required by the actual halogenase. A number of flavin-dependent tryptophan halogenases have been investigated in some detail, and the first three-dimensional structure of a member of this enzyme subfamily, tryptophan 7-halogenase, has been elucidated. This structure suggests a mechanism involving the formation of hypohalous acid, which is used inside the enzyme for regioselective halogenation of the respective substrate. The introduction of halogen atoms into non-activated alkyl groups is catalysed by non-heme FeII α-ketoglutarate- and O2-dependent halogenases. Examples for the use of flavin-dependent halogenases for the formation of novel halogenated compounds in in vitro and in vivo reactions promise a bright future for the application of biological halogenation reactions.

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References

  • Bister B, Bischoff D, Nicholson GJ, Stockert S, Wink J, Brunati C, Donadio S, Pelzer S, Wohlleben W, Süssmuth RD (2003) Bromobalhimycin and chlorobromobalhimycins—illuminating the potential of halogenases in glycopeptide antibiotic biosyntheses. Chembiochem 4:658–662

    CAS  PubMed  Google Scholar 

  • Chang Z, Flatt P, Gerwick WH, Nguyen V-A, Willis CL, Sherman DH (2002) The barbamide biosynthetic gene cluster: a novel cyanobacterial system of mixed polyketide synthase (PKS)–non-ribosomal peptide synthetase (NRPS) origin involving an unusual trichloroleucyl starter unit. Gene 296:235–247

    CAS  PubMed  Google Scholar 

  • Dairi T, Nakano T, Aisaka K, Katsumata R, Hasegawa M (1995) Cloning and nucleotide sequence of the gene responsible for chlorination of tetracycline. Biosci Biotechnol Biochem 59:1099–1106

    CAS  PubMed  Google Scholar 

  • Doerschuk AP, McCormick JRD, Goodman JJ, Szumski SA, Growich JA, Miller PA, Bitler BA, Jensen ER, Matrishin M, Petty MA, Phelps AS (1959) Biosynthesis of tetracyclines. I. The halide metabolism of Streptomyces aureofaciens mutants. The preparation and characterization of tetracycline, 7-chloro36-tetracycline and 7-bromotetracycline. J Am Chem Soc 81:3069–3075

    CAS  Google Scholar 

  • Dong C, Kotzsch A, Dorward M, van Pée K-H, Naismith JH (2004a) Crystallization and x-ray diffraction of a halogenating enzyme, tryptophan 7-halogenase, from Pseudomonas fluorescens. Acta Crystallogr D Biol Crystallogr 60:1438–1440

    PubMed  Google Scholar 

  • Dong C, Huang F, Deng H, Schaffrath C, Spencer JB, O’Hagan D, Naismith JH (2004b) Crystal structure and mechanism of a bacterial fluorinating enzyme. Nature 427:561–565

    CAS  PubMed  Google Scholar 

  • Dong C, Flecks F, Unversucht S, Haupt C, van Pée K-H, Naismith JH (2005) Tryptophan 7-halogenase (PrnA) structure suggests a mechanism for regioselective chlorination. Science 306:2216–2219

    Google Scholar 

  • Dorrestein PC, Yeh E, Garncau-Tsodikova S, Kelleher NL, Walsh CT (2005) Dichlorination of pyrrolyl-S-carrier protein by FADH2-dependent halogenase PltA during pyoluteorin biosynthesis. Proc Natl Acad Sci USA 102:13843–13848

    CAS  PubMed  PubMed Central  Google Scholar 

  • Eustaquio AS, Gust B, Luft T, Li S-M, Chater KF, Heide L (2003) Clorobiocin biosynthesis in Streptomyces: identification of the halogenase and generation of structural analogs. Chem Biol 10:279–288

    CAS  PubMed  Google Scholar 

  • Eustaquio AS, Gust B, Li S-M, Pelzer S, Wohlleben W, Chater KF, Heide L (2004) Production of 8’-halogenated and 8’-unsubstituted novobiocin derivatives in genetically engineered Streptomyces coelicolor strains. Chem Biol 11:1561–1572

    CAS  PubMed  Google Scholar 

  • Galan B, Diaz E, Prieto MA, Garcia JL (2000) Functional analysis of the small component of the 4-hydroxyphenylacetate 3-monooxygenase of Escherichia coli W: a prototype of a new flavin: NAD(P)H reductase subfamily. J Bacteriol 182:627–636

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gribble GW (2003) The diversity of naturally produced organohalogens. In: Gribble GW (ed) Natural production of organohalogen compounds. Springer, Berlin Heidelberg New York, pp 1–15

    Google Scholar 

  • Hammer PE, Hill, DS, Lam ST, van Pée K-H, Ligon JM (1997) Four genes from Pseudomonas fluorescens that encode the biosynthesis of pyrrolnitrin. Appl Environ Microbiol 63:2147–2154

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hohaus K, Altmann A, Burd W, Fischer I, Hammer PE, Hill DS, Ligon JM, van Pée K-H (1997) NADH-dependent halogenases are more likely to be involved in halometabolite biosynthesis than haloperoxidases. Angew Chem Int Ed Engl 36:2012–2013

    CAS  Google Scholar 

  • Hölzer M, Burd W, Reiβig H-U, van Pée K-H (2001) Substrate specificity and regioselectivity of tryptophan 7-halogenase from Pseudomonas flourescens BL915. Adv Syn Catal 343:591–595

    Google Scholar 

  • Jiménez JI, Scheuer PJ (2001) New lipopeptides from the Caribbean cyanobacterium Lyngbya majuscula. J Nat Prod 64:200–203

    PubMed  Google Scholar 

  • Keller S, Wage T, Hohaus K, Hölzer M, Eichhorn E, van Pée K-H (2000) Purification and partial characterization of tryptophan 7-halogenase (PrnA) from Pseudomonas fluorescens. Angew Chem Int Ed Engl 39:2300–2302

    CAS  PubMed  Google Scholar 

  • Kendall EC (1919) Isolation of the iodine compound which occurs in the thyroid. J Biol Chem 39:125–147

    CAS  Google Scholar 

  • Kirchner U, Westphal AH, Müller R, van Berkel WJH (2003) Phenol hydroxylase from Bacillus thermoglucosidans A7: a two-protein-component monooxygenase with a dual role for FAD. J Biol Chem 278:47545–47553

    CAS  PubMed  Google Scholar 

  • Kling E, Schmid C, Unversucht S, Wage T, Zehner S, van Pée K-H (2005) Enzymatic incorporation of halogen atoms into natural compounds. In: Wohlleben W, Spellig T, Müller-Tiemann B (eds) Biocombinatorial approaches for drug finding. Springer, Berlin Heidelberg New York, pp 165–194

    Google Scholar 

  • Louie TM, Webster CM, Xun L (2002) Genetic and biochemical characterization of 2,4,6-trichlorophenol degradation pathway in Ralstonia eutropha JMP134. J Bacteriol 184:3492–3500

    CAS  PubMed  PubMed Central  Google Scholar 

  • Louie TM, Xie XS, Xun L (2003) Coordinated production and utilization of FADH2 by NAD(P)H-flavin oxidoreductase and 4-hydroxyphenylacetate 3-monooxygenase. Biochemistry 42:7509–7517

    CAS  PubMed  Google Scholar 

  • Low JC, Tu SC (2003) Energy transfer evidence for in vitro and in vivo complexes of Vibrio harveyi flavin reductase P and luciferase. Photochem Photobiol 77:446–452

    CAS  PubMed  Google Scholar 

  • Morris HR, Taylor GW, Masento MS, Jermyn KA, Kay RR (1987) Chemical structure of the morphogen differentiation inducing factor from Dictyostelium discoideum. Nature 328:811–814

    CAS  PubMed  Google Scholar 

  • Morton GO, Lancaster JE, Van Lear GE, Fulmor W, Meyer WE (1969) The structure of nucleocidin. III. A new structure. J Am Chem Soc 91:1535–1537

    CAS  PubMed  Google Scholar 

  • Oelrichs PB, McEwan T (1961) Isolation of the toxic principle in Acacia georginae. Nature 190:808–809

    CAS  PubMed  Google Scholar 

  • O'Hagan D, Schaffrath C, Cobb SL, Hamilton JTG, Murphy CD (2002) Biosynthesis of an organofluorine molecule. Nature 416:279

    PubMed  Google Scholar 

  • Otsuka M, Ichinose K, Fujii I, Ebizuka Y (2004) Cloning, sequencing, and functional analysis of an iterative type I polyketide synthase gene cluster for biosynthesis of the antitumor chlorinated polyenone neocarzilin in “Streptomyces carzinostaticus”. Antimicrob Agents Chemother 48:3468–3476

    CAS  PubMed  PubMed Central  Google Scholar 

  • Otto K, Hofstetter K, Röthlisberger M, Witholt B, Schmid A (2004) Biochemical characterization of StyAB from Pseudomonas sp. strain VLB120 as a two-component flavin-diffusible monooxygenase. J Bacteriol 186:5292–5302

    CAS  PubMed  PubMed Central  Google Scholar 

  • Paulsen IT, Press CM, Ravel J, Kobayashi DY, Myers GSA, Mavrodi DV, DeBoy RT, Seshadri R, Ren Q, Madupu R, Dodson RJ, Durkin AS, Brinkac LM, Daugherty SC, Sullivan SA, Rosovitz MJ, Gwinn ML, Zhou L, Schneider DJ, Cartinhour SW, Nelson WC, Weidman J, Watkins K, Tran K, Khouri H, Pierson EA, Pierson III LS, Thomashaw LS, Loper JE (2005) Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nat Biotechnol 23:873–878

    CAS  PubMed  PubMed Central  Google Scholar 

  • Piraee M, Vining LC (2002) Use of degenerate primers and touch-down PCR to amplify a halogenase gene fragment from Streptomyces venezuelae ISP5230. J Ind Microbiol Biotechnol 29:1–5

    CAS  PubMed  Google Scholar 

  • Piraee M, White R, Vining LC (2004) Biosynthesis of the dichloroacetyl component of chloramphenicol in Streptomyces venezuelae ISP5230: genes required for halogenation. Microbiology 150:85–94

    CAS  PubMed  Google Scholar 

  • Puk O, Huber P, Bischoff D, Recktenwald J, Jung G, Süßmuth RD, van Pée K-H, Wohlleben W, Pelzer S (2002) Glycopeptide biosynthesis in Amycolatopsis mediterranei DSM5908: function of a halogenase and a haloperoxidase/perhydrolase. Chem Biol 9:225–235

    CAS  PubMed  Google Scholar 

  • Puk O, Bischoff D, Kittel C, Pelzer S, Weist S, Stegmann E, Süssmuth RD, Wohlleben W (2004) Biosynthesis of chloro-β-hydroxytyrosine, a nonproteinogenic amino acid of the peptidic backbone of glycopeptide antibiotics. J Bacteriol 186:6093–6100

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ridley CP, Bergquist PR, Harper MK, Faulkner DJ, Hooper JNA, Haygood MG (2005) Speciation and biosynthetic variation in four dictyoceratid sponges and their cyanobacterial symbiont, Oscillatoria spongeliae. Chem Biol 12:397–406

    CAS  PubMed  Google Scholar 

  • Sanada M, Miyano T, Iwadare S, Williamson JM, Arison BH, Smith JL, Douglas AW, Liesch JM, Inamine E (1986) Biosynthesis of fluorothreonine and fluoroacetic acid by the thienamycin producer Streptomyces cattleya. J Antibiot 39:259–265

    CAS  Google Scholar 

  • Sanchez C, Butovich IA, Brana AF, Rohr J, Mendez C, Salas JA (2002). The biosynthetic gene cluster for the antitumor rebeccamycin. Characterization and generation of indolocarbazole derivatives. Chem Biol 9:519–531

    CAS  PubMed  Google Scholar 

  • Sanchez C, Zhu L, Brana AF, Salas AP, Rohr J, Mendez C, Salas JA (2005) Combinatorial biosynthesis of antitumor indolocarbazole compounds. Proc Natl Acad Sci U S A 102:461–466

    CAS  PubMed  Google Scholar 

  • Shaw PD, Hager LP (1959) Biological chlorination. IV. Peroxidative nature of enzymatic chlorination. J Am Chem Soc 81:6527–6528

    CAS  Google Scholar 

  • Smith GG (1958) Effect of halogen on the chloramphenicol fermentation. J Bacteriol 75:577–583

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sundaramoorthy M, Terner J, Poulos TL (1998) Stereochemistry of chloroperoxidase active site: crystallographic and molecular-modeling studies. Chem Biol 5:461–473

    CAS  PubMed  Google Scholar 

  • Trimurtulu G, Ohtani I, Patterson GML, Moore RE, Corbett TH, Valeriote FA, Demchik L (1994) Total structures of cryptophycins, potent antitumor depsipeptides from the blue-green alga Nostoc sp. strain GSV 224. J Am Chem Soc 116:4729–4737

    CAS  Google Scholar 

  • Unson MD, Rose CB, Faulkner DJ, Brinen LS, Steiner JR, Clardy J (1993) New polychlorinated amino acid derivatives from the marine sponge Dysidea herbacea. J Org Chem 58:6336–6343

    CAS  Google Scholar 

  • Unversucht S, Hollmann F, Schmid A, van Pée K-H (2005) FADH2-dependence of tryptophan 7-halogenase. Adv Synth Catal 347:1163–1167

    CAS  Google Scholar 

  • Vaillancourt FH, Yin J, Walsh CT (2005a) SyrB in syringomycin E biosynthesis is a nonheme FeII α-ketoglutarate- and O2-dependent halogenase. Proc Natl Acad Sci U S A 102:10111–10116

    CAS  PubMed  PubMed Central  Google Scholar 

  • Vaillancourt FH, Yeh E, Vosburg DA, O’Connor SE, Walsh CT (2005b) Cryptic chlorination by a non-haem iron enzyme during cyclopropyl amino acid biosynthesis. Nature 436:1191–1194

    CAS  PubMed  Google Scholar 

  • van Pée K-H (1996) Biosynthesis of halogenated metabolites by bacteria. Annu Rev Microbiol 50:375–399

    PubMed  Google Scholar 

  • van Pée K-H, Unversucht S (2003) Biological dehalogenation and halogenation reactions. Chemosphere 52:299–312

    PubMed  Google Scholar 

  • van Pée K-H, Zehner S (2003) Enzymology and molecular genetics of biological halogenation. In: Gribble G (ed) Natural production of organohalogen compounds. Springer, Berlin Heidelberg New York, pp 171–199

    Google Scholar 

  • van Pée K-H, Salcher O, Fischer P, Bokel M, Lingens F (1983) The biosynthesis of brominated pyrrolnitrin derivatives by Pseudomonas aureofaciens. J Antibiot 36:1735–1742

    Google Scholar 

  • Walsh CT (2003) Antibiotics: actions, origins, resistance. ASM Press, Washington

    Google Scholar 

  • Williams DH, Bardsley B (1999) The vancomycin group of antibiotics and the fight against resistant bacteria. Angew Chem Int Ed 38:1172–1193

    Google Scholar 

  • Wever R, Hemrika W (1998) Vanadium enzymes. In: Nriagu JO (ed) Vanadium in the environment. Part 1: chemistry and biochemistry. Wiley, New York, pp 285–305

    Google Scholar 

  • Wu W, Chen Y, d’Avignon A, Hazen SL (1999) 3-Bromotyrosine and 3,5-dibromotyrosine are major products of protein oxidation by eosinophil peroxidase: potential markers for eosinophil-dependent tissue injury in vivo. Biochemistry 38:3538–3548

    CAS  PubMed  Google Scholar 

  • Wynands I, van Pée K-H (2004) A novel halogenase gene from the pentachloropseudilin producer Actinoplanes sp. ATCC 33002 and detection of in vitro halogenase activity. FEMS Microbiol Lett 237:363–367

    CAS  PubMed  Google Scholar 

  • Yeh E, Garneau S, Walsh CT (2005) Robust in vitro activity of RebF and RebH, a two-component reductase/halogenase, generating 7-chlorotryptophan during rebeccamycin biosynthesis. Proc Natl Acad Sci U S A 102:3960–3965

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zehner S, Bister B, Süssmuth RD, Méndez C, Salas JA, van Pée K-H (2005) A regioselective tryptophan 5-halogenase is involved in pyrroindomycin biosynthesis in Streptomyces rugosporus LL-42D005. Chem Biol 12:445–452

    CAS  PubMed  Google Scholar 

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Acknowledgements

The work described in this review, which was performed in the laboratory of K.H. v. P., was supported by the Deutsche Forschungsgemeinschaft (DFG), the Sächsische Staatsministerium für Umwelt und Landwirtschaft and the Max-Buchner-Forschungsstiftung.

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van Pée, KH., Patallo, E.P. Flavin-dependent halogenases involved in secondary metabolism in bacteria. Appl Microbiol Biotechnol 70, 631–641 (2006). https://doi.org/10.1007/s00253-005-0232-2

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