Genome mining approach for the discovery of novel cytochrome P450 biocatalysts

Bacterial cytochrome P450 enzymes: Semi-rational design and screening of mutant libraries in recombinant Escherichia coli cells

Bacterial cytochromes P450 (P450s) have been recognized as attractive targets for biocatalysis and protein engineering. They are soluble cytosolic enzymes that demonstrate higher stability and activity than their membrane-associated eukaryotic counterparts. Many bacterial P450s possess broad substrate spectra and can be produced in well-known expression hosts like Escherichia coli at high levels, which enables quick and convenient mutant libraries construction. However, the majority of bacterial P450s interacts with two auxiliary redox partner proteins, which significantly increase screening efforts. We have established recombinant E. coli cells for screening of P450 variants that rely on two separate redox partners. In this chapter, a case study on construction of a selective P450 to synthesize a precursor of several chemotherapeutics, (-)-podophyllotoxin, is described. The procedure includes co-expression of P450 and redox partner genes in E. coli with subsequent whole-cell conversion of the substrate (-)-deoxypodophyllotoxin in 96-deep-well plates. By omitting the chromatographic separation while measuring mass-to-charge ratios specific for the substrate and product via MS in so-called multiple injections in a single experimental run (MISER) LC/MS, the analysis time could be drastically reduced to roughly 1 min per sample. Screening results were verified by using isolated P450 variants and purified redox partners.

Discovery of diphenyl ether-degrading Streptomyces strains by direct screening based on ether bond-cleaving activity

Diphenyl ethers (DEs), which are widely used in the agricultural and chemical industries, have become hazardous contaminants in the environment. Although several DE-degrading bacteria have been reported, discovering new types of such microorganisms could enhance understanding of the degradation mechanism in the environment. In this study, we used a direct screening method based on detection of ether bond-cleaving activity to screen for microorganisms that degrade 4,4'-dihydroxydiphenyl ether (DHDE) as a model DE. Microorganisms isolated from soil samples were incubated with DHDE, and strains producing hydroquinone via ether bond cleavage were selected using hydroquinone-sensitive Rhodanine reagent. This screening procedure resulted in the isolation of 3 bacteria and 2 fungi that transform DHDE. Interestingly, all of the isolated bacteria belonged to one genus, Streptomyces. To our knowledge, these are the first microorganisms of the genus Streptomyces shown to degrade a DE. Streptomyces sp. TUS-ST3 exhibited high and stable DHDE-degrading activity. HPLC, LC-MS, and GC-MS analyses revealed that strain TUS-ST3 converts DHDE to its hydroxylated analogue and generates hydroquinone as an ether bond-cleavage product. Strain TUS-ST3 also transformed DEs other than DHDE. In addition, glucose-grown TUS-ST3 cells began to transform DHDE after incubation with this compound for 12 h, and produced 75 μM hydroquinone in 72 h. These activities of streptomycetes may play an important role in DE degradation in the environment. We also report the whole genome sequence of strain TUS-ST3.

Use of engineered cytochromes P450 for accelerating drug discovery and development

Numerous steps in drug development, including the generation of authentic metabolites and late-stage functionalization of candidates, necessitate the modification of often complex molecules, such as natural products. While it can be challenging to make the required regio- and stereoselective alterations to a molecule using purely chemical catalysis, enzymes can introduce changes to complex molecules with a high degree of stereo- and regioselectivity. Cytochrome P450 enzymes are biocatalysts of unequalled versatility, capable of regio- and stereoselective functionalization of unactivated CH bonds by monooxygenation. Collectively they catalyze over 60 different biotransformations on structurally and functionally diverse organic molecules, including natural products, drugs, steroids, organic acids and other lipophilic molecules. This catalytic versatility and substrate range makes them likely candidates for application as potential biocatalysts for industrial chemistry. However, several aspects of the P450 catalytic cycle and other characteristics have limited their implementation to date in industry, including: their lability at elevated temperature, in the presence of solvents, and over lengthy incubation times; the typically low efficiency with which they metabolize non-natural substrates; and their lack of specificity for a single metabolic pathway. Protein engineering by rational design or directed evolution provides a way to engineer P450s for industrial use. Here we review the progress made to date toward engineering the properties of P450s, especially eukaryotic forms, for industrial application, and including the recent expansion of their catalytic repertoire to include non-natural reactions.

Sustainable Approach for Peroxygenase-Catalyzed Oxidation Reactions Using Hydrogen Peroxide Generated from Spent Coffee Grounds and Tea Leaf Residues

Peroxygenases are promising catalysts for use in the oxidation of chemicals as they catalyze the direct oxidation of a variety of compounds under ambient conditions using hydrogen peroxide (H₂O₂) as an oxidant. Although the use of peroxygenases provides a simple method for oxidation of chemicals, the anthraquinone process currently used to produce H₂O₂ requires significant energy input and generates considerable waste, which negatively affects process sustainability and production costs. Thus, generating H₂O₂ for peroxygenases on site using an environmentally benign method would be advantageous. Here, we utilized spent coffee grounds (SCGs) and tea leaf residues (TLRs) for the production of H₂O₂. These waste biomass products reacted with molecular oxygen and effectively generated H₂O₂ in sodium phosphate buffer. The resulting H₂O₂ was utilized by the bacterial P450 peroxygenase, CYP152A1. Both SCG-derived and TLR-derived H₂O₂ promoted the CYP152A1-catalyzed oxidation of 4-methoxy-1-naphthol to Russig's blue as a model reaction. In addition, when CYP152A1 was incubated with styrene, the SCG and TLR solutions enabled the synthesis of styrene oxide and phenylacetaldehyde. This new approach using waste biomass provides a simple, cost-effective, and sustainable oxidation method that should be readily applicable to other peroxygenases for the synthesis of a variety of valuable chemicals.

Toward the Heterologous Biosynthesis of Plant Natural Products: Gene Discovery and Characterization

Plant natural products (PNPs) represent a vast and diverse group of natural products, which have wide applications such as emulsifiers in cosmetics, sweeteners in foods, and active ingredients in medicines. Large-scale production of certain PNPs (e.g., artemisinin, taxol) has been implemented by reconstruction of biosynthetic pathways in heterologous hosts. However, unknown biosynthetic pathways greatly restrict wide applications of heterologous production of PNPs of interest. With the rapid development of sequencing and multiomics analysis technologies, huge amounts of omics data, i.e., genomics, transcriptomics, and proteomics, have been deposited in public databases, which is a precious resource for identification of the unknown biosynthetic pathway of PNPs. Herein, we have enumerated the approaches which have been widely used to screen candidate genes involved in the biosynthesis of PNPs of interest. We also discuss recent developments in the characterization of putative genes and elucidation of the complete biosynthetic pathway in heterologous hosts.

Whole-cell biocatalysis using cytochrome P450 monooxygenases for biotransformation of sustainable bioresources (fatty acids, fatty alkanes, and aromatic amino acids)

Cytochrome P450s (CYPs) are heme-thiolated enzymes that catalyze the oxidation of CH bonds in a regio and stereoselective manner. Activation of the non-activated carbon atom can be further enhanced by multistep chemo-enzymatic reactions; moreover, several useful chemicals can be synthesized to provide alternative organic synthesis routes. Given their versatile functionality, CYPs show promise in a number of biotechnological fields. Recently, various CYPs, along with their sequences and functionalities, have been identified owing to rapid developments in sequencing technology and molecular biotechnology. In addition to these discoveries, attempts have been made to utilize CYPs to industrially produce biochemicals from available and sustainable bioresources such as oil, amino acids, carbohydrates, and lignin. Here, these accomplishments, particularly those involving the use of CYP enzymes as whole-cell biocatalysts for bioresource biotransformation, will be reviewed. Further, recently developed biotransformation pathways that result in gram-scale yields of fatty acids and fatty alkanes as well as aromatic amino acids, which depend on the hosts used for CYP expression, and the nature of the multistep reactions will be discussed. These pathways are similar regardless of whether the hosts are CYP-producing or non-CYP-producing; the limitations of these methods and the ways to overcome them are reviewed here.

Selective biocatalytic hydroxylation of unactivated methylene C-H bonds in cyclic alkyl substrates

The cytochrome P450 monooxygenase CYP101B1 from Novosphingobium aromaticivorans selectively hydroxylated methylene C-H bonds in cycloalkyl rings. Cycloketones and cycloalkyl esters containing C6, C8, C10 and C12 rings were oxidised with high selectively on the opposite side of the ring to the carbonyl substituent. Cyclodecanone was oxidised to oxabicycloundecanol derivatives in equilibrium with the hydroxycyclodecanones.

Computational Design of Protein Function

The computational design of enzymes is a tremendous challenge for both chemistry and biochemistry. The ability to design stable and functional biocatalysts that could operate under different conditions to perform chemical reactions without precedent in nature, allowing the large-scale production of chemicals à la carte, would revolutionise both synthetic, pharmacologic and materials chemistry. Despite the great advances achieved, this highly multidisciplinary area of research is still in its infancy. This chapter describes the ‘inside-out’ protocol for computational enzyme design and both the achievements and limitations of the current technology are highlighted. Furthermore, molecular dynamics simulations have proved to be invaluable in the enzyme design process, constituting an important tool for discovering elusive catalytically relevant conformations of the engineered or designed enzyme. As a complement to the ‘inside-out’ design protocol, different examples where hybrid QM/MM approaches have been directly applied to discover beneficial mutations in rational computational enzyme design are described.

Draft Genome Sequences of Three Actinobacteria Strains Presenting New Candidate Organisms with High Potentials for Specific P450 Cytochromes

The three Actinobacteria strains Streptomyces platensis DSM 40041, Pseudonocardia autotrophica DSM 535, and Streptomyces fradiae DSM 40063 were described to selectively oxyfunctionalize several drugs. Here, we present their draft genomes to unravel their gene sets encoding promising cytochrome P450 monooxygenases associated with the generation of drug metabolites.

Selective C-H bond functionalization using repurposed or artificial metalloenzymes

Catalytic CH bond functionalization has become an important tool for organic synthesis. Metalloenzymes offer a solution to one of the foremost challenges in this field, site-selective CH functionalization, but they are only capable of catalyzing a subset of the CH functionalization reactions known to small molecule catalysts. To overcome this limitation, metalloenzymes have been repurposed by exploiting the reactivity of their native cofactors toward substrates not found in nature. Additionally, new reactivity has been accessed by incorporating synthetic metal cofactors into protein scaffolds to form artificial metalloenzymes. The selectivity and activity of these catalysts has been tuned using directed evolution. This review covers the recent progress in developing and optimizing both repurposed and artificial metalloenzymes as catalysts for selective CH bond functionalization.

The selective oxidation of substituted aromatic hydrocarbons and the observation of uncoupling via redox cycling during naphthalene oxidation by the CYP101B1 system

Oxidation of polyaromatic hydrocarbons by P450s can be lowered by redox cycling but CYP101B1 regioselectively hydroxylated substituted naphthalenes and biphenyls.

A substrate-binding-state mimic of H2O2-dependent cytochrome P450 produced by one-point mutagenesis and peroxygenation of non-native substrates

H₂O₂-dependent cytochrome P450s that can catalyze monooxygenation of nonnative substrates were constructed by one-point mutagenesis.

The efficient and selective biocatalytic oxidation of norisoprenoid and aromatic substrates by CYP101B1 from Novosphingobium aromaticivorans DSM12444

CYP101B1 fromNovosphingobium aromaticivoransoxidises ionone derivatives and phenylcyclohexane with high activity and regioselectivity.

Computational enzyme design

Recent developments in computational chemistry and biology have come together in the "inside-out" approach to enzyme engineering. Proteins have been designed to catalyze reactions not previously accelerated in nature. Some of these proteins fold and act as catalysts, but the success rate is still low. The achievements and limitations of the current technology are highlighted and contrasted to other protein engineering techniques. On its own, computational "inside-out" design can lead to the production of catalytically active and selective proteins, but their kinetic performances fall short of natural enzymes. When combined with directed evolution, molecular dynamics simulations, and crowd-sourced structure-prediction approaches, however, computational designs can be significantly improved in terms of binding, turnover, and thermal stability.

Biotechnological production of caffeic acid by bacterial cytochrome P450 CYP199A2

Caffeic acid is a biologically active molecule that has various beneficial properties, including antioxidant, anticancer, and anti-inflammatory activities. In this study, we explored the catalytic potential of a bacterial cytochrome P450, CYP199A2, for the biotechnological production of caffeic acid. When the CYP199A2 enzyme was reacted with p-coumaric acid, it stoichiometrically produced caffeic acid. The crystal structure of CYP199A2 shows that Phe at position 185 is situated directly above, and only 6.35 Å from, the heme iron. This F185 residue was replaced with hydrophobic or hydroxylated amino acids using site-directed mutagenesis to create mutants with novel and improved catalytic properties. In whole-cell assays with the known substrate of CYP199A2, 2-naphthoic acid, only the wild-type enzyme hydroxylated 2-naphthoic acid at the C-7 and C-8 positions, whereas all of the active F185 mutants exhibited a preference for C-5 hydroxylation. Interestingly, several F185 mutants (F185V, F185L, F185I, F185G, and F185A mutants) also acquired the ability to hydroxylate cinnamic acid, which was not hydroxylated by the wild-type enzyme. These results demonstrate that F185 is an important residue that controls the regioselectivity and the substrate specificity of CYP199A2. Furthermore, Escherichia coli cells expressing the F185L mutant exhibited 5.5 times higher hydroxylation activity for p-coumaric acid than those expressing the wild-type enzyme. By using the F185L whole-cell catalyst, the production of caffeic acid reached 15 mM (2.8 g/liter), which is the highest level so far attained in biotechnological production of this compound.

Cytochromes P450: exploiting diversity and enabling application as biocatalysts

The remarkable chemical reactivity and substrate range displayed by cytochromes P450 (P450s) renders them attractive as potential catalysts for a host of challenging chemical reactions in industry. The opportunities afforded by these biocatalysts are increased by the availability of greater diversity provided by the genomic resource and the variant libraries of well-known P450s produced by rational and random engineering techniques. The exploitation of this enormous diversity will require novel tools in screening, to identify enzyme reactions of interest, and also in the enabling of these valuable activities through protein engineering and bioprocess optimisation.