Biotransformations using prokaryotic P450 monooxygenases

Sequence-based screening for self-sufficient P450 monooxygenase from a metagenome library

AIMS

Cytochrome P450 monooxygenases (CYPs) are useful catalysts for oxidation reactions. Self-sufficient CYPs harbour a reductive domain covalently connected to a P450 domain and are known for their robust catalytic activity with great potential as biocatalysts. In an effort to expand genetic sources of self-sufficient CYPs, we devised a sequence-based screening system to identify them in a soil metagenome.

METHODS AND RESULTS

We constructed a soil metagenome library and performed sequence-based screening for self-sufficient CYP genes. A new CYP gene, syk181, was identified from the metagenome library. Phylogenetic analysis revealed that SYK181 formed a distinct phylogenic line with 46% amino-acid-sequence identity to CYP102A1 which has been extensively studied as a fatty acid hydroxylase. The heterologously expressed SYK181 showed significant hydroxylase activity towards naphthalene and phenanthrene as well as towards fatty acids.

CONCLUSIONS

Sequence-based screening of metagenome libraries is expected to be a useful approach for searching self-sufficient CYP genes. The translated product of syk181 shows self-sufficient hydroxylase activity towards fatty acids and aromatic compounds.

SIGNIFICANCE AND IMPACT OF THE STUDY

SYK181 is the first self-sufficient CYP obtained directly from a metagenome library. The genetic and biochemical information on SYK181 are expected to be helpful for engineering self-sufficient CYPs with broader catalytic activities towards various substrates, which would be useful for bioconversion of natural products and biodegradation of organic chemicals.

Hydroxylation of the Triterpenoid Nigranoic Acid by the FungusGliocladium roseum YMF1.00133

The ability of the fungus Gliocladium roseum YMF1.00133 to transform the bioactive nigranoic acid (=(24Z)-9,19-cyclo-3,4-secolanosta-4(28),24-diene-3,26-dioic acid) was investigated. Three new products from the co-cultures of nigranoic acid and G. roseum YMF1.00133 were obtained by employing a combination of Sephadex LH-20 and silica-gel column chromatography. The major metabolite was identified as 15beta-hydroxynigranoic acid, and the minor metabolites as 6alpha,15beta-dihydroxynigranoic acid and 7beta,15beta-dihydroxynigranoic acid by mass spectrometry and NMR spectroscopy. This is the first report of the biotransformation of the A-ring-secocycloartene triterpenoid, nigranoic acid.

Identification of Critical Residues in Novel Drug Metabolizing Mutants of Cytochrome P450 BM3 Using Random Mutagenesis

Previously, we've described a site-directed triple mutant of cytochrome P450 BM3 (BM3) that is able to convert various drugs (van Vugt-Lussenburg, B. M. A., et al. Biochem. Biophys. Res. Commun. 2006, 346, 810-818). In the present study, random mutagenesis was used to improve the activity of this mutant. With three generations of error-prone PCR, mutants were obtained with 200-fold increased turnover toward drug substrates dextromethorphan and 3,4-methylenedioxymethylamphetamine. The initial activities of these mutants were up to 90-fold higher than that of human P450 2D6. These highly active drug metabolizing enzymes have great potential for biotechnology. Using sequencing analysis, the mutations responsible for the increase in activity were determined. The mutations that had the greatest effects on the activity were F81I, E267V, and particularly L86I, which is not located in the active site. Computer modeling studies were used to rationalize the effects of the mutations. This study shows that random mutagenesis can be used to identify novel critical residues, and to increase our insight into P450s.

Monoterpenes as novel substrates for oxidation and halo-hydroxylation with chloroperoxidase from Caldariomyces fumago

Chloroperoxidase (CPO) from Caldariomyces fumago was analysed for its ability to oxidize ten different monoterpenes with hydrogen peroxide as oxidant. In the absence of halide ions geraniol and, to a lesser extent, citronellol and nerol were converted into the corresponding aldehydes, whereas terpene hydrocarbons did not serve as substrates under these conditions. In the presence of chloride, bromide and iodide ions, every terpene tested was converted into one or more products. (1S)-(+)-3-carene was chosen as a model substrate for the CPO-catalysed conversion of terpenes in the presence of sodium halides. With chloride, bromide and iodide, the reaction products were the respective (1S,3R,4R,6R)-4-halo-3,7,7-trimethyl-bicyclo[4.1.0]-heptane-3-ols, as identified by 1H and 13C nuclear magnetic resonance. These product formations turned out to be strictly regio- and stereoselective and proceeded very rapidly and almost quantitatively. Initial specific activities of halohydrin formation increased from 4.22 U mg-1 with chloride to 12.22 U mg-1 with bromide and 37.11 U mg-1 with iodide as the respective halide ion. These results represent the first examples of the application of CPO as a highly efficient biocatalyst for monoterpene functionalization. This is a promising strategy for 'green' terpene chemistry overcoming drawbacks usually associated with cofactor-dependent oxygenases, whole-cell biocatalysts and conventional chemical methods used for terpene conversions.

Evaluation of alkoxyresorufins as fluorescent substrates for cytochrome P450 BM3 and site-directed mutants

In this study, the first fluorescent assay for bacterial cytochrome P450 BM3 (BM3) and mutants is described. BM3 mutants are potentially very versatile biocatalysts for the production of fine chemicals. A fluorescent assay would be very useful for the identification of nonnatural ligands in high-throughput inhibition assays. Because of the ease and sensitivity of alkoxyresorufin O-dealkylation assays, four different alkoxyresorufins were evaluated as substrates. Wild-type BM3 showed extremely low activity toward all four alkoxyresorufins tested. Five different BM3 mutants were constructed, carrying different combinations of mutations R47L, F87V, and L188Q, which were previously shown to increase activity toward nonnatural substrates. For all mutants, a high benzyloxyresorufin O-dealkylation (BROD) activity was found. The triple mutant of BM3, R47L/F87V/L188Q, showed the highest activity, increasing 900-fold compared to wild-type BM3. The BROD assay could also be applied in whole Escherichia coli cells; permeabilization by lipopolysaccharide deficiency strongly increased activity. To demonstrate the applicability of the BROD assay to screening for novel ligands of BM3 R47L/F87V/L188Q, a library of 45 drug-like compounds was tested for inhibition. Of these compounds, 8 showed strong inhibition of the BROD activity, demonstrating for the first time that drug-like molecules also can bind with high affinity to BM3 mutants.

Electrochemistry of heme–thiolate proteins

Heme-thiolate proteins (HTPs) play critical biological roles by catalyzing challenging chemical reactions. The ability of HTPs to selectively oxidize inert substrates under mild conditions has led to much research aimed at the development of useful in vitro oxidation technology. Very complex electron transfer machinery is required to support HTP chemistry, and electrochemical methods provide many of the needed components. The challenge is to find a system that has good electrode-enzyme electronic coupling that, in turn, would drive catalytic turnover at relatively high rates. Several systems reviewed herein have shown promise in experimental work on components that could be part of a molecular machine for the selective oxidation of organic substrates.

Laboratory-directed protein evolution

Systematic approaches to directed evolution of proteins have been documented since the 1970s. The ability to recruit new protein functions arises from the considerable substrate ambiguity of many proteins. The substrate ambiguity of a protein can be interpreted as the evolutionary potential that allows a protein to acquire new specificities through mutation or to regain function via mutations that differ from the original protein sequence. All organisms have evolutionarily exploited this substrate ambiguity. When exploited in a laboratory under controlled mutagenesis and selection, it enables a protein to "evolve" in desired directions. One of the most effective strategies in directed protein evolution is to gradually accumulate mutations, either sequentially or by recombination, while applying selective pressure. This is typically achieved by the generation of libraries of mutants followed by efficient screening of these libraries for targeted functions and subsequent repetition of the process using improved mutants from the previous screening. Here we review some of the successful strategies in creating protein diversity and the more recent progress in directed protein evolution in a wide range of scientific disciplines and its impacts in chemical, pharmaceutical, and agricultural sciences.

Direct electrochemical regeneration of monooxygenase subunits for biocatalytic asymmetric epoxidation

We report the first example of direct electrochemical regeneration of a flavin-dependent monooxygenase for asymmetric epoxidation catalysis. It is shown that electrochemical regeneration of the oxygenase subunit of the multicomponent styrene monooxygenase is sufficient to perform enantiospecific S-epoxidation of various styrene derivatives. Kinetic bottlenecks of the novel electroenzymatic reaction are identified. This work opens up new alternatives for asymmetric oxyfunctionalization catalysis.

Substrate specificity for the 12β-hydroxylation of bufadienolides by Alternaria alternata

Hydroxylation is an important route to synthesize more hydrophilic compounds of pharmaceutical significance. Microbial hydroxylation offers advantages over chemical means for its high specificity. In this study, a fungal strain Alternaria alternata AS 3.4578 was found to be able to catalyze the specific 12beta-hydroxylation of a variety of cytotoxic bufadienolides. Cinobufagin and resibufogenin could be completely metabolized by A. alternata to generate their 12beta-hydroxylated products in high yields (>90%) within 8 h of incubation. A. alternata could also convert 3-epi-desacetylcinobufagin into 3-epi-12beta-hydroxyl desacetylcinobufagin as the major product (70% yield). C-3 dehydrogenated products were detected in these reactions in fair yields, while their accumulation was relatively slow. The 12beta-hydroxylation of bufadienolides could be significantly inhibited by the substitution of 1beta-, 5-, or 16alpha-hydroxyl groups, and the 14beta,15beta-epoxy ring appeared to be a necessary structural requirement for the specificity. For the biotransformation of bufalin, a 14beta-OH bufadienolide, this reaction was not specific, and accompanied by 7beta-hydroxylation as a parallel and competing metabolic route. The biotransformation products were identified by comparison with authentic samples or tentatively characterized by high-performance liquid chromatography-diode array detection-atmospheric pressure chemical ionization-mass spectrometry analyses.

Enantioselective epoxidation of linolenic acid catalysed by cytochrome P450BM3 from Bacillus megaterium

Cytochrome P450(BM3), from Bacillus megaterium, catalyses the epoxidation of linolenic acid yielding 15,16-epoxyoctadeca-9,12-dienoic acid with complete regio- and moderate enantio-selectivity (60% ee). The absolute configuration of the product is tentatively assigned as 15(R),16(S)-. The Michaelis-Menten parameters kcat and Km for the reaction were determined to be 3126 +/- 226 min(-1) and 24 +/- 6 microM respectively.

Process implementation aspects for biocatalytic hydrocarbon oxyfunctionalization

Oxidoreductases catalyze a large variety of regio-, stereo-, and chemoselective hydrocarbon oxyfunctionalizations, reactions, which are important in industrial organic synthesis but difficult to achieve by chemical means. This review summarizes process implementation aspects for the in vivo application of the especially versatile enzyme class of oxygenases, capable of specifically introducing oxygen from molecular oxygen into a large range of organic molecules. Critical issues such as reaching high enzyme activity and specificity, product degradation, cofactor recycling, reactant toxicity, and substrate and oxygen mass transfer can be overcome by biochemical process engineering and biocatalyst engineering. Both strategies provide a growing toolset to facilitate process implementation, optimization, and scale-up. Major advances were achieved via heterologous overexpression of oxygenase genes, directed evolution, metabolic engineering, and in situ product removal. Process examples from industry and academia show that the combined use of different concepts enables efficient oxygenase-based whole-cell catalysis of various commercially interesting reactions such as the biosynthesis of chiral compounds, the specific oxyfunctionalization of complex molecules, and also the synthesis of medium-priced chemicals. Better understanding of the cell metabolism and future developments in both biocatalyst and bioprocess engineering are expected to promote the implementation of many and various industrial biooxidation processes.

Novel cytotoxic bufadienolides derived from bufalin by microbial hydroxylation and their structure-activity relationships

Microbial transformation was used to prepare novel cytotoxic bufadienolides. Twelve products (3-14) were obtained from bufalin (1) by the fungus Mucor spinosus. Their structures were elucidated by high-resolution mass spectroscopy (HR-MS) and extensive NMR techniques, including 1H NMR, 13C NMR, DEPT, 1H-1H correlation spectroscopy (COSY), two dimensional nuclear Overhauser effect correlation spectroscopy (NOESY), heteronuclear multiple quantum coherence (HMQC), and heteronuclear multiple bond coherence (HMBC). Compounds 3, 4, 9 and 11-14 are new mono- or dihydroxylated derivatives of bufalin with novel oxyfunctionalities at C-1beta, C-7beta, C-11beta, C-12beta and C-16alpha positions. The in vitro cytotoxic activities against human cancer cell lines of 3-14, together with 16 biotransformed products derived from cinobufagin (15-30) were determined by the MTT method, and their structure-activity relationships (SAR) were discussed.

Specific 12 beta-hydroxylation of cinobufagin by filamentous fungi

Biotransformation of natural products has great potential for producing new drugs and could provide in vitro models of mammalian metabolism. Microbial transformation of the cytotoxic steroid cinobufagin was investigated. Cinobufagin could be specifically hydroxylated at the 12 beta-position by the fungus Alternaria alternata. Six products from a scaled-up fermentation were obtained by silica gel column chromatography and reversed-phase liquid chromatography and were identified as 12 beta-hydroxyl cinobufagin, 12 beta-hydroxyl desacetylcinobufagin, 3-oxo-12 beta-hydroxyl cinobufagin, 3-oxo-12 beta-hydroxyl desacetylcinobufagin, 12-oxo-cinobufagin, and 3-oxo-12 alpha-hydroxyl cinobufagin. The last five products are new compounds. 12 beta-Hydroxylation of cinobufagin by A. alternata is a fast catalytic reaction and was complete within 8 h of growth with the substrate. This reaction was followed by dehydrogenation of the 3-hydroxyl group and then deacetylation at C-16. Hydroxylation at C-12 beta also was the first step in the metabolism of cinobufagin by a variety of fungal strains. In vitro cytotoxicity assays suggest that 12 beta-hydroxyl cinobufagin and 3-oxo-12 alpha-hydroxyl cinobufagin exhibit somewhat decreased but still significant cytotoxic activities. The 12 beta-hydroxylated bufadienolides produced by microbial transformation are difficult to obtain by chemical synthesis.

Regio- and enantioselective alkane hydroxylation with engineered cytochromes P450 BM-3

Cytochrome P450 BM-3 from Bacillus megaterium was engineered using a combination of directed evolution and site-directed mutagenesis to hydroxylate linear alkanes regio- and enantioselectively using atmospheric dioxygen as an oxidant. BM-3 variant 9-10A-A328V hydroxylates octane at the 2-position to form S-2-octanol (40% ee). Another variant, 1-12G, also hydroxylates alkanes larger than hexane primarily at the 2-position but forms R-2-alcohols (40-55% ee). These biocatalysts are highly active (rates up to 400 min(-1)) and support thousands of product turnovers. The regio- and enantioselectivities are retained in whole-cell biotransformations with Escherichia coli, where the engineered P450s can be expressed at high levels and the cofactor is supplied endogenously.

Biotransformation of ent-13-epi-manoyl oxides difunctionalized at C-3 and C-12 by filamentous fungi

Biotransformation of ent-3beta,12alpha-dihydroxy-13-epi-manoyl oxide with Fusarium moniliforme gave the regioselective oxidation of the hydroxyl group at C-3 and the ent-7beta-hydroxylation. The action of Gliocladium roseum in the 3,12-diketoderivative originated monohydroxylations at C-1 and C-7, both by the ent-beta face, while Rhizopus nigricans produced hydroxylation at C-7 or C-18, epoxidation of the double bond, reduction of the keto group at C-3, and combined actions as biohydroxylation at C-2/epoxidation of the double bond and hydroxylation at C-7/reduction of the keto group at C-3. In the ent-3-hydroxy-12-keto epimers, G. roseum originated monohydroxylations at C-1 and C-7 and R. nigricans originated the oxidation at C-3 as a major transformation, epoxidation of double bond and hydroxylation at C-2. Finally, in the ent-3beta-hydroxy epimer R. nigricans also originated minor hydroxylations at C-1, C-6, C-7 and C-20 and F. moniliforme produced an hydroxylation at C-7 and a dihydroxylation at C-7/C-11.

Protein engineering in bioelectrocatalysis

Electrochemistry of redox proteins is a broadly applicable technology with important applications in biosensors, biofuel cells and chemical syntheses. Escalating attention in this area is driven by remarkable progress in designing efficient interfaces for transferring electrons between electrode surfaces and redox proteins. Research in interface design is slowly shifting from modifying electrode surfaces towards the engineering of redox proteins. Protein engineering, which encompasses rational design, directed evolution and combined methods, offers many powerful methods and strategies for improving the electron transfer properties of redox proteins.