The diversity of naturally produced organohalogens

Tryptophan 7-halogenase (PrnA) structure suggests a mechanism for regioselective chlorination

Chlorinated natural products include vancomycin and cryptophycin A. Their biosynthesis involves regioselective chlorination by flavin-dependent halogenases. We report the structural characterization of tryptophan 7-halogenase (PrnA), which regioselectively chlorinates tryptophan. Tryptophan and flavin adenine dinucleotide (FAD) are separated by a 10 angstrom-long tunnel and bound by distinct enzyme modules. The FAD module is conserved in halogenases and is related to flavin-dependent monooxygenases. On the basis of biochemical studies, crystal structures, and by analogy with monooxygenases, we predict that FADH2 reacts with O2 to make peroxyflavin, which is decomposed by Cl-. The resulting HOCl is guided through the tunnel to tryptophan, where it is activated to participate in electrophilic aromatic substitution.

Halogenated natural products in five species of Antarctic sponges: compounds with POP-like properties?

Purified extracts of five species of Antarctic sponges (Demospongiae: Kirkpatrickia variolosa, Artemisina apollinis, Phorbas glaberrima, and Halichondria sp. and Calcarea: Leucetta antarctica) from King George Island were analyzed by GC/MS for the presence of persistent and lipophilic halogenated compounds to identify bioaccumulative halogenated natural products. Sample extracts were prepared using methods identical for the determination of POPs, namely, microwave-assisted extraction with organic solvents, gel permeation chromatography, and column chromatography on deactivated silica. In addition, samples were treated with sulfuric acid to remove acid-destructible compounds. PCBs were not detectable and only traces of lindane, p,p'-DDE, and alpha-HCH were detected in these samples in decreasing order of abundance, underscoring their uncontaminated state. In contrast, 146 brominated compounds were identified by correct isotopic ratios m/z 79 and 81, 50% of which eluted prior to lindane including the most abundant peaks. Each sponge sample contained > or = 35 brominated compounds of natural origin, 14 of which were detected in all species. Estimated concentrations ranged from the high ng/kg to mg/kg (air-dried weights) and relative distributions of the same compounds in different sponges were highly variable. The high abundance of these compounds relative to known anthropogenic pollutants strongly suggests a natural origin. Multiple mode (EI-, ECNI-, and PCI-) GC/MS enabled identification of an aliphatic ketone tentatively identified as 1,1,2-tribromo-oct-1-en-3-one, present in all species but highest in Phorbas glaberrima. Several halogenated phenols including 2,4,6-tribromophenol were also abundant in Phorbas glaberrima as were halogenated anisoles in lower relative abundances. The halogenated phenols were analyzed without derivatization. The sample of Halichondria sp. contained the dibromotrichloro monoterpene MHC-1, a recently described environmental contaminant in fish and seals. Retrospective analysis of other marine samples confirmed that 2,4,6-tribromophenol was present in seal blubber from both the Arctic and the Antarctic. The presence of naturally occurring organohalogens such as 2,4,6-tribromophenol and MHC-1 in Antarctic marine invertebrates thus provides a link to their occurrence in marine mammals.

Enantiomer fractions of organic chlorinated pesticides in arctic marine ice fauna, zooplankton, and benthos

Stereoisomers of chiral chlorinated pesticides (alpha-HCH (HCH = hexachlorocyclohexane), trans- and cis-chlordane, MC5, o,p'-DDT) were quantified in arctic marine invertebrates (ice-associated amphipods Gammarus wilkitzkii, pelagic copepods Calanus hyperboreus, krill Thysanoessa inermis, and amphipods Themisto libellula, and benthic amphipods Paramphithoe hystrix). Enantiomer fractions (EFs) were calculated to investigate the influence of habitat, geographic area, and diet on selective bioaccumulation of the (-)- or (+)-enantiomer. Depletion of the (+)-alpha-HCH enantionmer increased from ice fauna to zooplankton to benthos, corresponding to previous reports of EF variations with depth. Chlordanes and o,p'-DDT also showed the strongest enantioselective bioaccumulation in benthic amphipods and less so in zooplankton and ice fauna, which had closer to racemic EFs. Neither diet nor geographic area explained EF differences among samples. Nonracemic EFs in benthos may be related to stereoselective biotransformation, but is most likely reflecting vertical distribution of EFs in the water column and sediments, as demonstrated earlier for alpha-HCH in the Canadian and European Arctic.

Isolation and structure elucidation of the new fungal metabolite (-)-xylariamide A

Chemical investigations of the terrestrial microfungus Xylaria sp. have afforded the new natural product (-)-xylariamide A (1). The gross structure of 1 was determined by interpretation of 1D and 2D NMR, UV, IR, and MS data. Confirmation of the structure and the absolute stereochemistry of 1 were determined by the total synthesis of (+)-xylariamide A (2). Synthetic 2 was produced by N,O-bis(trimethylsilyl)acetamide-induced coupling of 3-chloro-L-tyrosine (3) with (E)-but-2-enedioic acid 2,5-dioxo-pyrrolidin-1-yl ester methyl ester (4). Optical rotation comparison of 1 with 2 indicated that the natural product (1) contained 3-chloro-D-tyrosine. Both enantiomers of xylariamide A were tested in a brine shrimp lethality assay, and only the natural product (1) showed toxicity.

3,4,5,3′,5′-Pentabromo-2-(2′-hydroxybenzoyl)pyrrole: a potential lead compound as anti-Gram-positive and anti-biofilm agent

The activity against Gram-positive bacteria of 3,4,5,3',5'-pentabromo-2-(2'-hydroxybenzoyl)pyrrole I, a synthetic anti-bacterial compound related to pyrrolomycins, was tested in vitro using seven reference bacterial strains and Staphylococcus epidermidis and Staphylococcus aureus preformed biofilms. Compound I was active against all strains tested, with minimum inhibitory concentration (MIC) values ranging from 0.002 to 0.097 mg/l and minimum bactericidal concentrations (MBCs) from 0.37 to 12.5 mg/l. Compound I was also active at low concentrations against preformed S. epidermidis and S. aureus biofilms.

2-Haloacrylate reductase, a novel enzyme of the medium chain dehydrogenase/reductase superfamily that catalyzes the reduction of a carbon-carbon double bond of unsaturated organohalogen compounds

A soil bacterium, Burkholderia sp. WS, grows on 2-chloroacrylate as the sole carbon source. To identify the enzymes metabolizing 2-chloroacrylate, we carried out comparative two-dimensional gel electrophoresis of the proteins from 2-chloroacrylate- and lactate-grown bacterial cells. As a result, we found that a protein named CAA43 was inducibly synthesized when the cells were grown on 2-chloroacrylate. The CAA43 gene was cloned and shown to encode a protein of 333 amino acid residues (M(r) 35,788) that shared a significant sequence similarity with NADPH-dependent quinone oxidoreductase from Escherichia coli (38.2% identity). CAA43 was overproduced in E. coli and purified to homogeneity. The purified protein catalyzed the NADPH-dependent reduction of the carbon-carbon double bond of 2-chloroacrylate to produce (S)-2-chloropropionate, which is probably further metabolized to (R)-lactate by (S)-2-haloacid dehalogenase in Burkholderia sp. WS. NADH did not serve as a reductant. Despite the sequence similarity to quinone oxidoreductases, CAA43 did not act on 1,4-benzoquinone and 1,4-naphthoquinone. 2-Chloroacrylate analogs, such as acrylate and methacrylate, were also inert as the substrates. In contrast, 2-bromoacrylate served as the substrate. Thus, we named this novel enzyme 2-haloacrylate reductase. This study revealed a new pathway for the degradation of unsaturated organohalogen compounds. It is also notable that the enzyme is useful for the production of (S)-2-chloropropionate, which is used for the industrial production of aryloxyphenoxypropionic acid herbicides.

Robust in vitro activity of RebF and RebH, a two-component reductase/halogenase, generating 7-chlorotryptophan during rebeccamycin biosynthesis

The indolocarbazole antitumor agent rebeccamycin is modified by chlorine atoms on each of two indole moieties of the aglycone scaffold. These halogens are incorporated during the initial step of its biosynthesis from conversion of L-Trp to 7-chlorotryptophan. Two genes in the biosynthetic cluster, rebF and rebH, are predicted to encode the flavin reductase and halogenase components of an FADH2-dependent halogenase, a class of enzymes involved in the biosynthesis of numerous halogenated natural products. Here, we report that, in the presence of O2, chloride ion, and L-Trp as cosubstrates, purified RebH displays robust regiospecific halogenating activity to generate 7-chlorotryptophan over at least 50 catalytic cycles. Halogenation by RebH required the addition of RebF, which catalyzes the NADH-dependent reduction of FAD to provide FADH2 for the halogenase. Maximal rates were achieved at a RebF/RebH ratio of 3:1. In air-saturated solutions, a k(cat) of 1.4 min(-1) was observed for the RebF/RebH system but increased at least 10-fold in low-pO2 conditions. RebH was also able to use bromide ions to generate monobrominated Trp. The demonstration of robust chlorinating activity by RebF/RebH sets up this system for the probing of mechanistic questions regarding this intriguing class of enzymes.

Vanadium-dependent iodoperoxidases in Laminaria digitata, a novel biochemical function diverging from brown algal bromoperoxidases

The brown alga Laminaria digitata features a distinct vanadium-dependent iodoperoxidase (vIPO) activity, which has been purified to electrophoretic homogeneity. Steady-state analyses at pH 6.2 are reported for vIPO (K (m) (I-) = 2.5 mM; k (cat) (I-) = 462 s(-1)) and for the previously characterised vanadium-dependent bromoperoxidase in L. digitata (K (m) (I-) =18.1 mM; k (cat) (I-) = 38 s(-1)). Although the vIPO enzyme specifically oxidises iodide, competition experiments with halides indicate that bromide is a competitive inhibitor with respect to the fixation of iodide. A full-length complementary ANA (cDNA) was cloned and shown to be actively transcribed in L. digitata and to encode the vIPO enzyme. Mass spectrometry analyses of tryptic digests of vIPO indicated the presence of at least two very similar proteins, in agreement with Southern analyses showing that vIPOs are encoded by a multigenic family in L. digitata. Phylogenetic analyses indicated that vIPO shares a close common ancestor with brown algal vanadium-dependent bromoperoxidases. Based on a three-dimensional structure model of the vIPO active site and on comparisons with those of other vanadium-dependent haloperoxidases, we propose a hypothesis to explain the evolution of strict specificity for iodide in L. digitata vIPO.

Biological activity and physicochemical parameters of marine halogenated natural products 2,3,3',4,4',5,5'-heptachloro-1'-methyl-1,2'-bipyrrole and 2,4,6-tribromoanisole

Physicochemical parameters (vapor pressure, water solubility, Henry's law constant) and biological activities of two halogenated natural products frequently detected in marine samples and food were determined. Synthetic 2,3,3',4,4',5,5'-heptachloro-1'-methyl-1,2'-bipyrrole (Q1) and 2,4,6-tribromoanisole (TBA) were available in pure form. The physicochemical parameters were in the range of anthropogenic chlorinated compounds of concern. The aqueous solubilities at 25 degrees C (S(w,25)) of Q1 and TBA were 4.6 microg/L and 12,200 microg/L, respectively, whereas subcooled liquid vapor pressures were 0.00168 Pa (Q1) and 0.06562 Pa (TBA) as measured by the gas chromatographic-retention time technique. Q1 was negative by established test systems for the determination of ethoxyresorufin-O-deethylase (EROD) induction and by sulforhodamine B assay. EROD induction potency was at least 10(-7) times lower than that of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). At a relatively high concentration (20 microM), Q1 inhibited specific binding of 2 nM [(3)H]TCDD to the in vitro-expressed human aryl hydrocarbon receptor (AHR) by 18%; lower concentrations showed no effect. Molecular modeling showed that Q1 is nonplanar, consistent with its relatively modest affinity as an AHR ligand. When tested for cell-growth inhibitory/cytocidal activity in human tumor cells, Q1 was only marginally, if at all, active with an IC(50) value >50 microM compared with five to ten times lower IC(50) values for potent cytotoxins tested in the test system used. Furthermore, standard pesticide tests on insecticidal, herbicidal, and fungicidal activity did not provide any significant activity at highest concentrations. For TBA, the results in all tests were comparable with Q1. The SRB assay was also applied to the halogenated natural product 4,6-dibromo-2-(2',4'-dibromo)phenoxyanisole, but no toxic response was found. Although it was apparent that Q1 and TBA had been proven to have relatively low biological activity in all tests performed, further research is necessary to clarify whether metabolites of the compounds eventually may possess a risk to humans or other living organisms. Nevertheless, the role of Q1 in nature remains uncertain.

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"

Neocarzilins (NCZs) are antitumor chlorinated polyenones produced by "Streptomyces carzinostaticus" var. F-41. The gene cluster responsible for the biosynthesis of NCZs was cloned and characterized. DNA sequence analysis of a 33-kb region revealed a cluster of 14 open reading frames (ORFs), three of which (ORF4, ORF5, and ORF6) encode type I polyketide synthase (PKS), which consists of four modules. Unusual features of the modular organization is the lack of an obvious acyltransferase domain on modules 2 and 4 and the presence of longer interdomain regions more than 200 amino acids in length on each module. Involvement of the PKS genes in NCZ biosynthesis was demonstrated by heterologous expression of the cluster in Streptomyces coelicolor CH999, which produced the apparent NCZ biosynthetic intermediates dechloroneocarzillin A and dechloroneocarzilin B. Disruption of ORF5 resulted in a failure of NCZ production, providing further evidence that the cluster is essential for NCZ biosynthesis. Mechanistic consideration of NCZ formation indicates the iterative use of at least one module of the PKS, which subsequently releases its product by decarboxylation to generate an NCZ skeleton, possibly catalyzed by a type II thioesterase encoded by ORF7. This is a novel type I PKS system of bacterial origin for the biosynthesis of a reduced polyketide chain. Additionally, the protein encoded by ORF3, located upstream of the PKS genes, closely resembles the FADH(2)-dependent halogenases involved in the formation of halometabolites. The ORF3 protein could be responsible for the halogenation of NCZs, presenting a unique example of a halogenase involved in the biosynthesis of an aliphatic halometabolite.

Root nodule Bradyrhizobium spp. harbor tfdAalpha and cadA, homologous with genes encoding 2,4-dichlorophenoxyacetic acid-degrading proteins

The distribution of tfdAalpha and cadA, genes encoding 2,4-dichlorophenoxyacetate (2,4-D)-degrading proteins which are characteristic of the 2,4-D-degrading Bradyrhizobium sp. isolated from pristine environments, was examined by PCR and Southern hybridization in several Bradyrhizobium strains including type strains of Bradyrhizobium japonicum USDA110 and Bradyrhizobium elkanii USDA94, in phylogenetically closely related Agromonas oligotrophica and Rhodopseudomonas palustris, and in 2,4-D-degrading Sphingomonas strains. All strains showed positive signals for tfdAalpha, and its phylogenetic tree was congruent with that of 16S rRNA genes in alpha-Proteobacteria, indicating evolution of tfdAalpha without horizontal gene transfer. The nucleotide sequence identities between tfdAalpha and canonical tfdA in beta- and gamma-Proteobacteria were 46 to 57%, and the deduced amino acid sequence of TfdAalpha revealed conserved residues characteristic of the active site of alpha-ketoglutarate-dependent dioxygenases. On the other hand, cadA showed limited distribution in 2,4-D-degrading Bradyrhizobium sp. and Sphingomonas sp. and some strains of non-2,4-D-degrading B. elkanii. The cadA genes were phylogenetically separated between 2,4-D-degrading and nondegrading strains, and the cadA genes of 2,4-D degrading strains were further separated between Bradyrhizobium sp. and Sphingomonas sp., indicating the incongruency of cadA with 16S rRNA genes. The nucleotide sequence identities between cadA and tftA of 2,4,5-trichlorophenoxyacetate-degrading Burkholderia cepacia AC1100 were 46 to 53%. Although all root nodule Bradyrhizobium strains were unable to degrade 2,4-D, three strains carrying cadA homologs degraded 4-chlorophenoxyacetate with the accumulation of 4-chlorophenol as an intermediate, suggesting the involvement of cadA homologs in the cleavage of the aryl ether linkage. Based on codon usage patterns and GC content, it was suggested that the cadA genes of 2,4-D-degrading and nondegrading Bradyrhizobium spp. have different origins and that the genes would be obtained in the former through horizontal gene transfer.

Chemical investigation of predator-deterred macroalgae from the Antarctic peninsula

Chemical investigation of five Antarctic macroalgae whose tissues and crude extracts displayed ecologically relevant feeding deterrence in field bioassays was performed. Eleven compounds were characterized from the three red algae studied, of which four (1-3 and 9) were previously unreported, and four compounds were found from two brown algae, two (12 and 14) of which are new natural products. Several of these pure compounds have been individually investigated in ecological and/or pharmacological bioassays.

Probing the activity differences of simple and complex brominated aryl compounds against 15-soybean, 15-human, and 12-human lipoxygenase

Lipoxygenases (LO) have been implicated in asthma, immune disorders, and various cancers. As a consequence of these broad biological implications, there is great interest in understanding the effects of naturally occurring and environmental contaminants against its activity. On the basis of our earlier studies indicating that polybrominated diphenol ethers are potent inhibitors to mammalian 15-LO, we expanded our structure-activity study to include marine-derived brominated phenol ethers (including a newly discovered tribrominated diphenyl ether), dioxins, and bastadins, as well as the synthetic brominated fire retardants, brominated bisphenol A (BBPA), and polybrominated diphenyl ethers (PBDEs). We report herein the effects of 21 simple and complex organobromine compounds against human platelet 12-LO, human reticulocyte 15-LO, and soybean 15-LO-1.

Halometabolites and cellular dehalogenase systems: an evolutionary perspective

We review the role of iodothyronine deiodinases (IDs) in the evolution of vertebrate thyroidal systems within the larger context of biological metabolism of halogens. Since the beginning of life, the ubiquity of organohalogens in the biosphere has provided a major selective pressure for the evolution and conservation of cellular mechanisms specialized in halogen metabolism. Among naturally available halogens, iodine emerged as a critical component of unique developmental and metabolic messengers. Metabolism of iodinated compounds occurs in the three major domains of life, and invertebrate deuterostomes possess several biochemical traits and molecular homologs of vertebrate thyroidal systems, including ancestral homologs of IDs identified in urochordates. The finely tuned cellular regulation of iodometabolite uptake and disposal is a remarkable event in evolution and might have been decisive for the explosive diversification of ontogenetic strategies in vertebrates.

Halogen retention, organohalogens, and the role of organic matter decomposition on halogen enrichment in two Chilean peat bogs

Natural formation of organohalogen compounds can be shown to occur in all natural environments. Peat bogs, which are built up exclusively of organic matter and cover approximately 3% of the total continental world area, are potentially significant reservoirs for organohalogen formation. Up to now, fluxes and retention rates of halogens and organohalogen formation in peat bogs were mostly unquantified. In our study, we investigated the retention of atmospheric derived halogens and the natural formation of organohalogens by differential halogen analysis in two peat bogs in southernmost Chile. Atmospheric wet deposition rates of chlorine, bromine, and iodine range between 600 and 36000, 6 and 160, and 1 and 3 mg m(-2) yr(-1), respectively. Mean annual net accumulation rates of these halogens in peat are calculated to be 12-72 mg of Cl m(-2), 1.7-12 mg of Br m(-2), and 0.4-1.2 mg of l m(-2). Retention rates are similarly high for iodine (36-46%) and bromine (7.5-50%), and substantially lower for chlorine (0.2-2%). To evaluate influences of peat decomposition processes on halogen enrichment, halogen concentrations were compared to carbon/nitrogen ratios (C/N). Our results indicate that up to 95% of chlorine, 91% of bromine, and 81% of iodine in peat exist in an organically bound form. The results also indicate that the concentrations of halogens, especially of bromine and iodine, in peat are largely determined by peat decomposition processes and that halogens are not conservative in bogs.

Long-chain (C19-C29) 1-chloro-n-alkanes in leaf waxes of halophytes of the Chenopodiaceae

The hydrocarbon fraction of leaf waxes of three halophytes of the Chenopodiaceae common to Mediterranean salt marshes (Suaeda vera, Sarcocornia fruticosa and Halimione portulacoides) revealed the presence of a minor series of odd and even chains 1-chloro-n-alkanes ranging from C(19) to C(29). The identification of these new chlorinated plant constituents was based on a combination of mass spectrometry data with selective chlorine detection (CPG-AED) and was confirmed by comparison with authentic standards. The qualitative and quantitative distributions of these 1-chloro-n-alkanes varied inter-specifically. Homologues with an odd carbon-chain were predominant in all species but maximised at C(25) and C(27) in S. vera and S. fruticosa, and at C(27) and C(29) in H. portulacoides. Remarkably, 1-chloro-nonacosane was an abundant homologue only in this latter species. Leaves of S. vera contained 4 to 7 times more of total chloroalkanes than leaves of the other two species. These compounds accounted for 10, 4 and 1% of the hydrocarbon fraction of leaf waxes of S. vera, S. fruticosa and H. portulacoides, respectively. Attempts to link the occurrence of these chloroalkanes with other classes of leaf waxes (n-alkenes, n-aldehydes and n-alcohols) did not allowed a clear precursor-product relationship to be established. The biological functions as well as the mode of synthesis of alkylchlorides in (halophyte) plants remain unknown but undoubtedly deserve further attention.

Peatlands: a major sink of naturally formed organic chlorine

It is a little known fact that many chlorinated organic compounds occur naturally and that some are also indispensable to life on earth. Here, we show that chlorination of organic compounds during humification processes in peat is widespread in nature. Globally this process has led to the accumulation of approximately 280-1000 million tons of organically bound chlorine in peatlands during the postglacial period.