Purification and characterization of a novel bacterial non-heme chloroperoxidase from Pseudomonas pyrrocinia

New Insights into Pseudomonas spp.-Produced Antibiotics: Genetic Regulation of Biosynthesis and Implementation in Biotechnology

Pseudomonas bacteria are renowned for their remarkable capacity to synthesize antibiotics, namely mupirocin, gluconic acid, pyrrolnitrin, and 2,4-diacetylphloroglucinol (DAPG). While these substances are extensively employed in agricultural biotechnology to safeguard plants against harmful bacteria and fungi, their potential for human medicine and healthcare remains highly promising for common science. However, the challenge of obtaining stable producers that yield higher quantities of these antibiotics continues to be a pertinent concern in modern biotechnology. Although the interest in antibiotics of Pseudomonas bacteria has persisted over the past century, many uncertainties still surround the regulation of the biosynthetic pathways of these compounds. Thus, the present review comprehensively studies the genetic organization and regulation of the biosynthesis of these antibiotics and provides a comprehensive summary of the genetic organization of antibiotic biosynthesis pathways in pseudomonas strains, appealing to both molecular biologists and biotechnologists. In addition, attention is also paid to the application of antibiotics in plant protection.

Halogenation in Fungi: What Do We Know and What Remains to Be Discovered?

In nature, living organisms produce a wide variety of specialized metabolites to perform many biological functions. Among these specialized metabolites, some carry halogen atoms on their structure, which can modify their chemical characteristics. Research into this type of molecule has focused on how organisms incorporate these atoms into specialized metabolites. Several families of enzymes have been described gathering metalloenzymes, flavoproteins, or S-adenosyl-L-methionine (SAM) enzymes that can incorporate these atoms into different types of chemical structures. However, even though the first halogenation enzyme was discovered in a fungus, this clade is still lagging behind other clades such as bacteria, where many enzymes have been discovered. This review will therefore focus on all halogenation enzymes that have been described in fungi and their associated metabolites by searching for proteins available in databases, but also by using all the available fungal genomes. In the second part of the review, the chemical diversity of halogenated molecules found in fungi will be discussed. This will allow the highlighting of halogenation mechanisms that are still unknown today, therefore, highlighting potentially new unknown halogenation enzymes.

A flavin-dependent halogenase from metagenomic analysis prefers bromination over chlorination

Flavin-dependent halogenases catalyse halogenation of aromatic compounds. In most cases, this reaction proceeds with high regioselectivity and requires only the presence of FADH2, oxygen, and halide salts. Since marine habitats contain high concentrations of halides, organisms populating the oceans might be valuable sources of yet undiscovered halogenases. A new Hidden-Markov-Model (HMM) based on the PFAM tryptophan halogenase model was used for the analysis of marine metagenomes. Eleven metagenomes were screened leading to the identification of 254 complete or partial putative flavin-dependent halogenase genes. One predicted halogenase gene (brvH) was selected, codon optimised for E. coli, and overexpressed. Substrate screening revealed that this enzyme represents an active flavin-dependent halogenase able to convert indole to 3-bromoindole. Remarkably, bromination prevails also in a large excess of chloride. The BrvH crystal structure is very similar to that of tryptophan halogenases but reveals a substrate binding site that is open to the solvent instead of being covered by a loop.

Silica Sol-Gel Entrapment of the Enzyme Chloroperoxidase

The enzyme chloroperoxidase (CPO) was immobilized in silica sol-gel beads prepared from tetramethoxysilane. The average pore diameter of the silica host structure (~3 nm) was smaller than the globular CPO diameter (~6 nm) and the enzyme remained entrapped after sol-gel maturation. The catalytic performance of the entrapped enzyme was assessed via the pyrogallol peroxidation reaction. Sol-gel beads loaded with 4 μg CPO per mL sol solution reached 9–12% relative activity compared to free CPO in solution. Enzyme kinetic analysis revealed a decrease inkcatbut no changes inKMorKI. Product release or enzyme damage might thus limit catalytic performance. Yet circular dichroism and visible absorption spectra of transparent CPO sol-gel sheets did not indicate enzyme damage. Activity decline due to methanol exposure was shown to be reversible in solution. To improve catalytic performance the sol-gel protocol was modified. The incorporation of 5, 20, or 40% methyltrimethoxysilane resulted in more brittle sol-gel beads but the catalytic performance increased to 14% relative to free CPO in solution. The use of more acidic casting buffers (pH 4.5 or 5.5 instead of 6.5) resulted in a more porous silica host reaching up to 18% relative activity.

Expression of chloroperoxidase from Pseudomonas pyrrocinia in tobacco plastids for fungal resistance

The chloroperoxidase (cpo) gene from Pseudomonas pyrrocinia was transformed into the plastid genome (plastome) of Nicotiana tabacum var. Petit Havana and transplastomic lines were compared with a nuclear transformant for the same gene. Southern analysis confirmed integration in the plastome and western blotting confirmed the presence of the chloroperoxidase protein (CPO) in higher abundance in transplastomic plants than in cpo nuclear transformants. Northern analysis of primary plastome transformants for cpo showed 15-fold higher transcript abundance than in the nuclear transformant, yet this extent of enhancement was not observed in western blot, enzyme or bioassay, indicating a bottleneck at the post-transcriptional level. Representative plants from the two transplastomic lines showed resistance to fungal pathogens in vitro (Aspergillus flavus, Fusarium verticillioides, and Verticillium dahliae) and in planta (Alternaria alternata).

Cloning and Characterization of a Novel Esterase from Rhodococcus sp. for Highly Enantioselective Synthesis of a Chiral Cilastatin Precursor

A novel nonheme chloroperoxidase (RhEst1), with promiscuous esterase activity for enantioselective hydrolysis of ethyl (S)-2,2-dimethylcyclopropanecarboxylate, was identified from a shotgun library of Rhodococcus sp. strain ECU1013. RhEst1 was overexpressed in Escherichia coli BL21(DE3), purified to homogeneity, and functionally characterized. Fingerprinting analysis revealed that RhEst1 prefers para-nitrophenyl (pNP) esters of short-chain acyl groups. pNP esters with a cyclic acyl moiety, especially that with a cyclobutanyl group, were also substrates for RhEst1. The Km values for methyl 2,2-dimethylcyclopropanecarboxylate (DmCpCm) and ethyl 2,2-dimethylcyclopropane carboxylate (DmCpCe) were 0.25 and 0.43 mM, respectively. RhEst1 could serve as an efficient hydrolase for the bioproduction of optically pure (S)-2,2-dimethyl cyclopropane carboxylic acid (DmCpCa), which is an important chiral building block for cilastatin. As much as 0.5 M DmCpCe was enantioselectively hydrolyzed into (S)-DmCpCa, with a molar yield of 47.8% and an enantiomeric excess (ee) of 97.5%, indicating an extremely high enantioselectivity (E = 240) of this novel and unique biocatalyst for green manufacturing of highly valuable chiral chemicals.

Biocatalysed halogenation of nucleobase analogues

The synthesis of halogenated nucleosides and nucleobases is of interest due to their chemical and pharmacological applications. Herein, the enzymatic halogenation of nucleobases and analogues catalysed by microorganisms and by chloroperoxidase from Caldariomyces fumago has been studied. This latter enzyme catalysed the chlorination and bromination of indoline and uracil. Pseudomonas, Citrobacter, Aeromonas, Streptomyces, Xanthomonas, and Bacillus genera catalysed the chlorination and/or bromination of indole and indoline. Different products were obtained depending on the substrate, the biocatalyst and the halide used. In particular, 85% conversion from indole to 5-bromoindole was achieved using Streptomyces cetonii.

Antifungal Activity in Transgenic Peanut (Arachis hypogaea L.) Conferred by a Nonheme Chloroperoxidase Gene

A nonheme chloroperoxidase gene (cpo-p) from Pseudomonas pyrrocinia, a growth inhibitor of mycotoxin-producing fungi, was introduced into peanut via particle bombardment. The expression of the cpo-p gene is predicted to increase pathogen defense in peanut. Embryogenic peanut tissues were bombarded with gold particles coated with plasmid pRT66 carrying the cpo-p and hygromycin phosphotransferase (hph) genes, under the control of a double CaMV 35S and a single CaMV 35S promoter, respectively. Selection for hygromycin-resistant somatic embryos was performed on a liquid medium containing 10–20 mg/L hygromycin 3–4 days after bombardment. The integration and expression of the cpo-p gene was confirmed by Southern, Northern and Western blot analyses. In vitro bioassay using crude protein extracts from transgenic T0, T1, and T4 plants showed inhibition of Aspergillus flavus hyphal growth, which could translate to a reduction in aflatoxin contamination of peanut seed.

The transcriptional repressor protein NsrR senses nitric oxide directly via a [2Fe-2S] cluster

The regulatory protein NsrR, a member of the Rrf2 family of transcription repressors, is specifically dedicated to sensing nitric oxide (NO) in a variety of pathogenic and non-pathogenic bacteria. It has been proposed that NO directly modulates NsrR activity by interacting with a predicted [Fe-S] cluster in the NsrR protein, but no experimental evidence has been published to support this hypothesis. Here we report the purification of NsrR from the obligate aerobe Streptomyces coelicolor. We demonstrate using UV-visible, near UV CD and EPR spectroscopy that the protein contains an NO-sensitive [2Fe-2S] cluster when purified from E. coli. Upon exposure of NsrR to NO, the cluster is nitrosylated, which results in the loss of DNA binding activity as detected by bandshift assays. Removal of the [2Fe-2S] cluster to generate apo-NsrR also resulted in loss of DNA binding activity. This is the first demonstration that NsrR contains an NO-sensitive [2Fe-2S] cluster that is required for DNA binding activity.

Hydrolase-catalysed synthesis of peroxycarboxylic acids: Biocatalytic promiscuity for practical applications

The enzymatic promiscuity concept involves the possibility that one active site of an enzyme can catalyse several different chemical transformations. A rational understanding of the mechanistic reasons for this catalytic performance could lead to new practical applications. The capability of certain hydrolases to perform the perhydrolysis was described more than a decade ago, and recently its molecular basis has been elucidated. Remarkably, a similarity between perhydrolases (cofactor-free haloperoxidases) and serine hydrolases was found, with both groups of enzymes sharing a common catalytic triad, which suggests an evolution from a common ancestor. On the other hand, several biotechnological applications derived from the capability of hydrolases to catalyse the synthesis of peracids have been reported: the use of hydrolases as bleaching agents via in situ generation of peracids; (self)-epoxidation of unsaturated fatty acids, olefins, or plant oils, via Prileshajev epoxidation; Baeyer-Villiger reactions. In the present review, the molecular basis for this promiscuous hydrolase capability, as well as identified applications are reviewed and described in detail.

Molecular cloning and expression of perhydrolase genes from Pseudomonas aeruginosa and Burkholderia cepacia in Escherichia coli

Two bacterial perhydrolase genes, perPA and perBC, were cloned from Pseudomonas aeruginosa and Burkholderia cepacia, respectively, using PCR amplification with primers designed to be specific for conserved amino acid sequences of the already-known perhydrolases. The amino acid sequence of PerPA was identical to a putative perhydrolase of P. aeruginosa PAO1 genome sequences, whereas PerBC of B. cepacia was a novel bacterial perhydrolase showing similarity of less than 80% with all other existing perhydrolases. Most importantly, the perPA gene was expressed as a soluble intracellular form to an extent of more than 50% of the total protein content in Escherichia coli. Two perhydrolase enzymes were confirmed to exhibit the halogenation activity towards Phenol Red and monochlorodimedone. These results suggested that we successfully obtained the newly identified members of the bacterial perhydrolase family, expanding the pool of available perhydrolases.

A colorimetric method for detection and quantification of chlorinating activity of hemeperoxidases

A method of detecting and assaying the halogenating activity of hemeperoxidases using the colored substrate, thionin, is reported here. In the presence of suitable amounts of peroxide and chloride, chloroperoxidase chlorinates thionin and bleaches the intense color of this substrate. The kinetics was quite similar to that of the established monochlorodimedone assay. Therefore, the thionin assay can be taken as an index of chlorinating activity. This reaction affords an escape from background problems and allows easy processing of large volumes of samples.

Cloning, recombinant expression and biochemical characterisation of novel esterases from Bacillus sp. associated with the marine sponge Aplysina aerophoba

Two novel esterases (EstB1 and EstB2) were isolated from a genomic library of Bacillus sp. associated with the marine sponge Aplysina aerophoba. EstB1 shows low identity (26-44%) with the published hydrolases of the genus Bacillus, whereas EstB2 shows high identity (73-74%) with the carboxylesterases from B. cereus and B. anthracis. Both esterases were efficiently expressed in Escherichia coli under the control of T7 promoter using the vector pET-22b(+). Recombinant EstB1 was purified in a single step to electrophoretic homogeneity by IMAC. A method for the refolding of inclusion bodies formed by the recombinant EstB2 was established to obtain active enzyme. Substrate specificity of the two enzymes towards p-nitrophenyl and methyl esters and the respective kinetic parameters K(m) and V(max) were determined. The temperature optima of EstB1 and EstB2 were determined to be in the range of 30-50 degrees C and 20-35 degrees C, respectively. The pH optima were found to be in the range of 6.5-7.5 and 6.5-8.0, respectively. Both enzymes showed the highest stability in up to 50% (v/v) DMSO followed by methanol, ethanol and 2-propanol. The influence of high NaCl and KCl concentrations was tested. The inhibition effect of 10-50 mM Zn(2+) and 50 mM Mg(2+) and Ca(2+) ions was observed for both esterases. One to five millimolar PMSF deactivated the enzymes, whereas beta-mercaptoethanol, DTT and EDTA had no effect on the enzymes activity.

Biochemical characterization of StyAB from Pseudomonas sp. strain VLB120 as a two-component flavin-diffusible monooxygenase

Pseudomonas sp. VLB120 uses styrene as a sole source of carbon and energy. The first step in this metabolic pathway is catalyzed by an oxygenase (StyA) and a NADH-flavin oxidoreductase (StyB). Both components have been isolated from wild-type Pseudomonas strain VLB120 as well as from recombinant Escherichia coli. StyA from both sources is a dimer, with a subunit size of 47 kDa, and catalyzes the enantioselective epoxidation of CC double bonds. Styrene is exclusively converted to S-styrene oxide with a specific activity of 2.1 U mg(-1) (k(cat) = 1.6 s(-1)) and K(m) values for styrene of 0.45 +/- 0.05 mM (wild type) and 0.38 +/- 0.09 mM (recombinant). The epoxidation reaction depends on the presence of a NADH-flavin adenine dinucleotide (NADH-FAD) oxidoreductase for the supply of reduced FAD. StyB is a dimer with a molecular mass of 18 kDa and a NADH oxidation activity of 200 U mg(-1) (k(cat) [NADH] = 60 s(-1)). Steady-state kinetics determined for StyB indicate a mechanism of sequential binding of NADH and flavin to StyB. This enzyme reduces FAD as well as flavin mononucleotide and riboflavin. The NADH oxidation activity does not depend on the presence of StyA. During the epoxidation reaction, no formation of a complex of StyA and StyB has been observed, suggesting that electron transport between reductase and oxygenase occurs via a diffusing flavin.

Biotransformation of alkaloids

Biotransformations of alkaloids over the last decade have continued to encompass a wide variety of substrates and enzymes. The elucidation of novel alkaloid biosynthetic and catabolic pathways will continue to furnish new biocatalysts for the synthetic organic chemist. Furthermore, an improved understanding of the genetic and biochemical basis of metabolic pathways will also permit the engineering of pathways in plants and other heterologous hosts for the production of therapeutically important alkaloids. The combination of increasing commercial interest and advances in molecular biology will facilitate the availability of robust biocatalysts which are a prerequsite to achieve economically feasible processes for the production of alkaloid-based therapeutics.

Role of Acinetobacter calcoaceticus 3,4-dihydrocoumarin hydrolase in oxidative stress defence against peroxoacids

The physiological role of a bifunctional enzyme, 3,4-dihydrocoumarin hydrolase (DCH), which is capable of both hydrolysis of ester bonds and organic acid-assisted bromination of organic compounds, was investigated. Purified DCH from Acinetobacter calcoaceticus F46 catalysed dose- and time-dependent degradation of peracetic acid. The gene (dch) was cloned from the chromosomal DNA of the bacterium. The dch ORF was 831 bp long, corresponding to a protein of 272 amino acid residues, and the deduced amino acid sequence showed high similarity to those of bacterial serine esterases and perhydrolases. The dch gene was disrupted by homologous recombination on the A. calcoaceticus genome. The dch disruptant strain was more sensitive to growth inhibition by peracetic acid than the parent strain. On the other hand, the recombinant Escherichia coli cells expressing dch were more resistant to peracetic acid. A putative catalase gene was found immediately downstream of dch, and Northern blot hybridization analysis revealed that they are transcribed as part of a polycistronic mRNA. These results suggested that in vivo DCH detoxifies peroxoacids in conjunction with the catalase, i.e. peroxoacids are first hydrolysed to the corresponding acids and hydrogen peroxide by DCH, and then the resulting hydrogen peroxide is degraded by the catalase.

Natural halogenated fatty acids: their analogues and derivatives

A comprehensive survey has been made of all fatty acids containing halogen atoms covalently bonded to carbon and which are deemed as naturally occurring. Generally thought to be minor components produced by many different organisms, these interesting compounds now number more than 300. Recent research, especially in the marine area, indicates this number will increase in the future. Sources of halogenated fatty acids include microorganisms, algae, marine invertebrates, and higher plants and some animals. Their possible biological significance has also been discussed

Evaluation of peracid formation as the basis for resistance to infection in plants transformed with haloperoxidase

Nonheme haloperoxidase (HPO-P) isolated from Pseudomonas pyrrocinia catalyzed the peroxidation of alkyl acids to peracids. Among acids tested as substrates, acetic acid was most readily peroxidized. The reaction product peracetate possessed potent antifungal activity: 50% death (LD(50)) of Aspergillus flavus occurred at 25 microM peracetate. Viability of A. flavus was inhibited by up to 80% by leaf extracts of tobacco plants transformed with the HPO-P gene from P. pyrrocinia compared to viability of fungi exposed to extracts from controls. To elucidate if peracid formation by HPO-P was the basis for antifungal activity in transgenic leaf tissues, lethalities of hydrogen peroxide-acetate-HPO-P combinations against A. flavus were examined in vitro. LD(50) of A. flavus exposed to the combinations occurred at 30 mM acetate when concentrations of hydrogen peroxide and HPO-P were held constant. This value was identical to the LD(50) produced by 30 mM acetate in the absence of hydrogen peroxide-HPO-P and therefore did not account for enhanced antifungal activity in transgenic plants. For clarification, kinetics of the enzymic reaction were examined. According to the concentration of acetate needed for enzyme saturation (K(m) = 250 mM), acetate was lethal prior to its oxidation to peracetate. Results indicate that peracid generation by HPO-P was not the basis for enhanced antifungal activity in transgenic plants expressing the HPO-P gene.

Biotransformation of alkaloids

Biotransformations of alkaloids over the last decade have continued to encompass a wide variety of substrates and enzymes. The elucidation of novel alkaloid biosynthetic and catabolic pathways will continue to furnish new biocatalysts for the synthetic organic chemist. Furthermore, an improved understanding of the genetic and biochemical basis of metabolic pathways will also permit the engineering of pathways in plants and other heterologous hosts for the production of therapeutically important alkaloids. The combination of increasing commercial interest and advances in molecular biology will facilitate the availability of robust biocatalysts which are a prerequsite to achieve economically feasible processes for the production of alkaloid-based therapeutics.

Physiological function of bromoperoxidase in the red marine alga, Corallina pilulifera: production of bromoform as an allelochemical and the simultaneous elimination of hydrogen peroxide

The physiological function of vanadium-bromoperoxidase (BPO) in the marine red alga, Corallina pilulifera, has been characterized from the viewpoint of allelochemical formation. The algae emit bromoform (CHBr3) depending on the enzyme activity level in vivo (Itoh, N., Shinya, M., 1994. Seasonal evolution of bromomethanes from coralline algae and its effect on atmospheric ozone. Marine Chemistry 45, 95-103). We demonstrated that bromoform produced by C. pilulifera played an important role in eliminating epiphytic organisms, especially microalgae on the surface. Such data suggest a strong relationship between the coralline algae and the coralline flat (deforested area in the marine environment: called isoyake in Japanese). Lithophyllum yessoense, the main inhabitant of coralline flats in Japan, produced a lower level of CHBr3 than C. pilulifera, and showed BPO activity. On the other hand, the seasonal change of BPO activity in C. pilulifera in vivo was in proportion to superoxide dismutase (SOD) activity and in inverse proportion to catalase activity. The phenomenon implies that BPO could be a potential substitute for catalase, because the enzyme catalyzes an efficient Br(-)-dependent catalase reaction.

Antifungal and peroxidative activities of nonheme chloroperoxidase in relation to transgenic plant protection

Nonheme chloroperoxidase (CPO-P) of Pseudomonas pyrrocinia catalyzes the oxidation of alkyl acids to peracids by hydrogen peroxide. Alkyl peracids possess potent antifungal activity as found with peracetate: 50% killing (LD(50)) of Aspergillus flavus occurred at 25 microM compared to 3.0 mM for the hydrogen peroxide substrate. To evaluate whether CPO-P could protect plants from fungal infection, tobacco was transformed with a gene for CPO-P from P. pyrrocinia and assayed for antifungal activity. Leaf extracts from transformed plants inhibited growth of A. flavus by up to 100%, and levels of inhibition were quantitatively correlated to the amounts of CPO-P activity expressed in leaves. To clarify if the peroxidative activity of CPO-P could be the basis for the increased resistance, the antifungal activity of the purified enzyme was investigated. The LD(50) of hydrogen peroxide combined with CPO-P occurred at 2.0 mM against A. flavus. Because this value was too small to account for the enhanced antifungal activity of transgenic plants, the kinetics of the enzyme reaction was examined and it was found that the concentration of hydrogen peroxide needed for enzyme saturation (K(m) = 5.9 mM) was already lethal. Thus, the peroxidative activity of CPO-P is not the basis for antifungal activity or enhanced resistance in transgenic plants expressing the gene.

Enzymatic halogenation catalyzed via a catalytic triad and by oxidoreductases

During the search for haloperoxidases in bacteria we detected a type of enzymes that catalyzed the peroxide-dependent halogenation of organic substrates. However, in contrast to already known haloperoxidases, these enzymes do not contain a prosthetic group or metal ions nor any other cofactor. Biochemical and molecular genetic studies revealed that they contain a catalytic triad consisting of a serine, a histidine, and an aspartate. The reaction they catalyze is actually the perhydrolysis of an acetic acid serine ester leading to the formation of peracetic acid. As a strong oxidizing agent the enzymatically formed peracetic acid can oxidize halide ions, resulting in the formation of hypohalous acid which then acts as the actual halogenating agent. Since hypohalous acid is also formed by the heme- and vanadium-containing haloperoxidases, enzymatic halogenation catalyzed by haloperoxidases and perhydrolases in general lacks substrate specificity and regioselectivity. However, detailed studies on the biosynthesis of several halometabolites led to the detection of a novel type of halogenases. These enzymes consist of a two-component system and require NADH and FAD for activity. Whereas the gene for one of the components is part of the biosynthetic cluster of the halometabolite, the second component is an enzyme which is also present in bacteria from which no halometabolites have ever been isolated, like Escherichia coli. In contrast to haloperoxidases and perhydrolases the newly detected NADH/FAD-dependent halogenases are substrate-specific and regioselective and might provide ideal tools for specific halogenation reactions.

Haloperoxidases and their role in biotransformation reactions

The past year has seen further structural characterisation of both nonmetal and vanadium haloperoxidase enzymes to add to that already known for the haem- and vanadium-containing enzymes. Exploitation of these enzymes for halogenation, sulfoxidation, epoxidation, oxidation of indoles and other biotransformations has increased as more information on their catalytic mechanism has been obtained.

Isolation and characterization of vanadium bromoperoxidase from a marine macroalga, Ecklonia stolonifera

The bromoperoxidase has been isolated from the marine brown alga, Ecklonia stolonifera (83 kDa) and has been characterized. Bromoperoxidase requires vanadium for enzyme activity as has been evidenced by EPR spectroscopy. The enzyme activity increased ca. 250% with the action of V5+ on the isolated enzyme, since more than 2/3 of the protein molecules were in the apo form. The increase in the enzyme activity was specific to V5+, while Fe2+, Fe3+, and Cu2+ inhibited the enzyme activity. This effect of V5+ addition was inhibited in phosphate buffer, probably because phosphate and vanadate compete for the active site. The bromoperoxidase exhibited a high thermostability (Tm = 68 degrees C) and a high stability in organic solvents (completely intact even in the presence of 50% methanol, ethanol and 1-propanol).

Structural investigation of the cofactor-free chloroperoxidases

The structures of cofactor-free haloperoxidases from Streptomyces aureofaciens, Streptomyces lividans, and Pseudomonas fluorescens have been determined at resolutions between 1.9 A and 1.5 A. The structures of two enzymes complexed with benzoate or propionate identify the binding site for the organic acids which are required for the haloperoxidase activity. Based on these complexes and on the structure of an inactive variant, a reaction mechanism is proposed for the halogenation reaction with peroxoacid and hypohalous acid as reaction intermediates. Comparison of the structures suggests that a specific halide binding site is absent in the enzymes but that hydrophobic organic compounds may fit into the active site pocket for halogenation at preferential sites.

Synthesis of enantiopure epoxides through biocatalytic approaches

Enantiopure epoxides, as well as their corresponding vicinal diols, are valuable intermediates in fine organic synthesis, in particular for the preparation of biologically active compounds. The necessity of preparing such target molecules in an optically pure form has triggered much research, leading to the emergence of various new methods based on either conventional chemistry or enzymatically catalyzed reactions. In this review, we focus on the biocatalytic approaches, which include direct epoxidation of olefinic double bonds as well as indirect biocatalytic methods, and which allow for the synthesis of these important chiral building blocks in enantiomerically enriched or even enantiopure form.

Thiocarbamate herbicide-inducible nonheme haloperoxidase of Rhodococcus erythropolis NI86/21

During biodegradation of thiocarbamate herbicides by Rhodococcus erythropolis NI86/21, a protein with an M(r) of 30,000 is induced (I. Nagy, G. Schoofs, F. Compernolle, P. Proost, J. Vanderleyden, and R.De Mot, J. Bacteriol. 177:676-687, 1995). Based on N-terminal sequence data for the protein purified by two-dimensional electrophoresis, the corresponding structural gene, thcF, was cloned and sequenced. The deduced protein sequence of ThcF is homologous to those of nonheme haloperoxidases. A particularly high level of sequence identity (72.6%) was observed for the chloroperoxidase from Pseudomonas pyrrocinia. A polyclonal antibody against the latter enzyme cross-reacted with ThcF either produced by the original Rhodococcus cells or overexpressed heterologously in Escherichia coli. In both thiocarbamate-grown Rhodococcus cells and E. coli cells expressing thcF, the haloperoxidase activity of ThcF was demonstrated. The thiocarbamate-inducible R. erythropolis ThcF protein represents the first (nonheme) haloperoxidase to be identified in a nocardioform actinomycete.

From phosphatases to vanadium peroxidases: a similar architecture of the active site

We show here that the amino acid residues contributing to the active sites of the vanadate containing haloperoxidases are conserved within three families of acid phosphatases; this suggests that the active sites of these enzymes are very similar. This is confirmed by activity measurements showing that apochloroperoxidase exhibits phosphatase activity. These observations not only reveal interesting evolutionary relationships between these groups of enzymes but may also have important implications for the research on acid phosphatases, especially glucose-6-phosphatase-the enzyme affected in von Gierke disease-of which the predicted membrane topology may have to be reconsidered.

Biosynthesis of halogenated metabolites by bacteria

Halogenated metabolites, originally thought to be infrequent in nature, are actually nothing unusual at all, and are produced by many different organisms, including bacteria. Whereas marine bacteria usually produce brominated compounds, terrestrial bacteria preferentially synthesize chlorometabolites, but fluoro- and iodometabolites can also be found. Haloperoxidases, enzymes capable of catalyzing the formation of carbon halogen bonds in the presence of hydrogen peroxide and halide ions (Cl-, Br- and I-) have been isolated and characterized from different bacteria. These enzymes turned out to be very unspecific and are obviously not the type of halogenating enzymes responsible for the formation of halometabolites in bacteria. A yet-unknown type of halogenating enzyme having both substrate and regio-specificity must be involved in the biosynthesis of halogenated compounds.

A catalytic triad is required by the non-heme haloperoxidases to perform halogenation

The bacterial non-heme haloperoxidases are highly related to an esterase from Pseudomonas fluorescens, at structural and functional levels. Both types of enzymes displayed brominating activity and esterase activity. The presence of the serine-hydrolase motif Gly-X-Ser-X-Gly, in the esterase as well as in all aligned haloperoxidase sequences, strongly suggested that they belong to the serine-hydrolase family. Sequence alignment with several serine-hydrolases and secondary structure superimposition revealed the striking conservation of structural features characterising the alpha/beta-hydrolase fold structure in all haloperoxidases. These structural predictions allowed us to identify a potential catalytic triad in haloperoxidases, perfectly matching the triad of all aligned serine-hydrolases. The structurally equivalent triad in the chloroperoxidase CPO-P comprised the amino acids Serine 97, Aspartic acid 229 and Histidine 258. The involvement of this catalytic triad in halogenation was further assessed by inhibition studies and site-directed mutagenesis. Inactivation of CPO-P by PMSF and DEPC strongly suggested that the serine residue from the serine-hydrolase motif and an histidine residue are essential for halogenation, similar to that demonstrated for typical serine-hydrolases. By site-directed mutagenesis of CPO-P, Ser-97 was exchanged against alanine or cysteine, Asp-229 against alanine and His-258 against glutamine. Western blot analysis indicated that each mutant gene was efficiently expressed. Whereas the mutant S97C conserved a very low residual activity, each other mutant S97A, D229A or H258Q was totally inactive. This study gives the direct demonstration of the requirement of a catalytic triad in the halogenation mechanism.

Purification and properties of a non-haem chloroperoxidase from Serratia marcescens

A non-haem chloroperoxidase was isolated from the enteric bacterium Serratia marcescens. The enzyme was purified to homogeneity by heat treatment, ammonium sulfate precipitation, ion exchange chromatography, gel filtration and dye-ligand affinity chromatography. Native chloroperoxidase has a molecular mass of 58 kDa and consists of two identical subunits of 29 kDa. Whereas chloroperoxidase catalyses only the bromination of monochlorodimedone, indole is chlorinated by this enzyme. Chloroperoxidase also catalyses the oxidation of amino to nitro groups. The enzyme is thermostable and does not lose any activity when incubated at 65 degrees C for 2 h. Comparison of the first 15 amino-terminal amino acids showed a sequence identity of 80% to the chloroperoxidases from Streptomyces lividans and Pseudomonas pyrrocinia. However, no precipitation band was obtained in the Ouchterlony agar diffusion assay with antibodies raised against the chloroperoxidases from Pseudomonas pyrrocinia and Streptomyces aureofaciens Tü24.

Purification and characterization of a novel metal-containing nonheme bromoperoxidase from Pseudomonas putida

A novel bromoperoxidase was purified to homogeneity from the bacterium Pseudomonas putida IF-3 strain, which produces the antibiotic pyrrolnitrin. The enzyme had a molecular mass of 68,000 and was composed of two identical subunits (33,000). It was specific for I- and Br- and inactive toward Cl- and F- in the monochlorodimedone assay system. The optimum pH of the enzyme was around 4.2 and it rapidly lost its activity below 3.5, but it was stable over of range pH of 4 to 11. The purified enzyme was activated several fold by incubation with only cobalt ions, and did not contain an organic prosthetic group such as heme, flavin and cobalamin. Analyses of prosthetic metal compounds in the enzyme using plasma atomic emission spectroscopy (ICP-AES) combined with mass-spectroscopy (MS) and trace metal determination by high performance liquid chromatography (HPLC)-spectrometry, revealed that the enzyme contained 0.35 +/- 0.1 mol of cobalt ions, 1.0 +/- 0.2 mol of nickel ions, 0.8 +/- 0.2 mol of zinc ions and 2.0 +/- 0.2 mol of ferric iron per mol of enzyme, assuming the molecular weight of 68,000. There was no trace of vanadium in the enzyme, unlike in some nonheme haloperoxidases. Thus the bromoperoxidase of P. putida is a novel nonheme metal-containing bromoperoxidase.

The metal-ion-free oxidoreductase from Streptomyces aureofaciens has an alpha/beta hydrolase fold

The crystal structure of the bromoperoxidase A2 from Streptomyces aureofaciens (ATCC 10762) has been determined by isomorphous replacement and refined to 2.05 A resolution with an R-value of 18.4%. The enzyme catalyzes the bromination of organic compounds in the presence of bromide and peroxide. The structure confirms the absence of cofactors such as metal ions or haem groups and shows the general topology of the alpha/beta hydrolase fold. The active centre is at the end of a deep pocket and includes a catalytic triad of Ser 98, Asp 228 and His 257. The active centre is connected by a narrow tunnel to a second pocket on the enzyme surface.

Chloroperoxidase from Streptomyces lividans: isolation and characterization of the enzyme and the corresponding gene

For the first time, a halogenating enzyme which is not known to produce halogenated metabolites has been isolated from a bacterial strain. The gene encoding the nonheme chloroperoxidase (CPO-L) from Streptomyces lividans TK64 was cloned, and its gene product was characterized. S. lividans TK64 produced only very small amounts of the enzyme. After cloning of the gene into Streptomyces aureofaciens Tü24-88, the enzyme was overexpressed up to 3,000-fold. Based on the overexpression, a simple purification procedure using acid precipitation and hydrophobic interaction chromatography was developed. Thus, 54 mg of homogeneous CPO-L could be obtained from 27 g (wet weight) of mycelium. The native enzyme has a molecular weight of 64,000 and consists of two identical subunits. The enzyme does not exhibit an absorption peak in the Soret region of the optical spectrum. X-ray fluorescence spectroscopy revealed that the enzyme does not contain any metal ions in equimolar amounts. CPO-L showed cross-reaction with antibodies raised against the nonheme chloroperoxidase from Pseudomonas pyrrocinia but not with antibodies raised against CPO-T from S. aureofaciens Tü24. CPO-L exhibits substrate specificity only for chlorination, not for bromination. Therefore, monochlorodimedone is only brominated by CPO-L, whereas indole is brominated and chlorinated. The functional chloroperoxidase gene was located on a 1.9-kb SalI DNA fragment. DNA sequence analysis revealed an open reading frame encoding a predicted polypeptide of 276 amino acids. The overall identity of the amino acid sequence to that of chloroperoxidase from P. pyrrocinia was 71%, whereas that to bromoperoxidase BPO-A2 from S. aureofaciens ATCC 10762 was only 42%.