Screening for Novel Enzymes

Novel enzymatic route to the synthesis of C-8 hydroxyflavonoids including flavonols and isoflavones

Flavin-dependent monooxygenases (FMOs) are a valuable group of biocatalysts that can regioselectively introduce a hydroxy group for the targeted modification of biologically active compounds. Here, we present the fdeE, the FMO from Herbaspirillum seropedicae SmR1 that is a part of the naringenin degradation pathway and is active towards a wide range of flavonoids-flavanones, flavones, isoflavones, and flavonols. Bioinformatics and biochemical analysis revealed a high similarity between the analyzed enzyme and other F8H FMOs what might indicate convergent evolutionary mechanism of flavonoid degradation pathway emergence by microorganism. A simple approach with the manipulation of the reaction environment allowed the stable formation of hydroxylation products, which showed very high reactivity in both in vivo and in vitro assays. This approach resulted in an 8-hydroxyquercetin-gossypetin titer of 0.16 g/L and additionally it is a first report of production of this compound.

A High-Throughput Amenable Colorimetric Assay for Enantioselective Screening of Nitrilase-Producing Microorganisms Using pH Sensitive Indicators

Based on the color change of an indicator due to the release of hydrogen ion from a nitrilase-catalyzed reaction, a rapid colorimetric method was established for the enantioselective screening of nitrilase-producing microorganisms. The formation of acids due to the nitrilase-mediated hydrolysis of nitriles causes a drop in the pH, which in turn results in a change of color of the solution (containing indicator) that can be observed visually. The buffer (0.01 M phosphate, pH 7.2) and indicator (Bromothymol blue, 0.01%) were selected in such a way that both have the same affinity for the released protons. The enantioselectivity of nitrilases was estimated by comparing the hydrolysis of ( R)-mandelonitrile with that of racemate under the same conditions. The method was used to screen a library of nitrilase-producing microorganisms, isolated in the authors' laboratory for their ability to enantioselectively hydrolyze mandelonitrile to mandelic acid, an important chiral building block. ( Journal of Biomolecular Screening 2003:559-565).

Rapid electrochemical screening of NAD-dependent dehydrogenases in a 96-well format

The electrochemical detection of dehydrogenase activity in crude cell lysates is performed simultaneously using 96 carbon electrodes modified with electrografted phenazines. The method is applied to the screening of a library of formate dehydrogenase mutants obtained by directed evolution.

Identification of novel enzymes with different hydrolytic activities by metagenome expression cloning

Metagenome cloning has become a powerful tool to exploit the biocatalytic potential of microbial communities for the discovery of novel biocatalysts. In a novel variant of direct expression cloning, metagenomic DNA was isolated from compost by a modified direct lysis method, purified by size exclusion chromatography and cloned into an expression vector allowing bidirectional transcription. Transformation of Escherichia coli DH5alpha resulted in a metagenomic expression library with an average insert size of 3.2 kb. To estimate the functional diversity of the constructed library, it was screened by different approaches based on functional heterologous expression. A large number of active clones were identified, including lipolytic enzymes, amylases, phosphatases and dioxygenases. Molecular analysis of one important class of industrial biocatalysts, the lipolytic enzymes, confirmed the novelty and dissimilarity of all recovered genes, which exhibited only limited similarity to known enzymes. Equally, the novelty of another three genes encoding phosphatase or dioxygenase activity, respectively, was shown. These results demonstrate the suitability of this direct cloning approach, which comprised a dual-orientation expression vector and a simple one-step DNA purification method, for the efficient discovery of numerous active novel clones. By this means it provides an efficient way for the rapid generation of large libraries of hitherto unknown enzyme candidates which could be screened for different specific target reactions.

Reduction of activated carbonyl groups by alkyl phosphines: formation of α-hydroxy esters and ketones

Reduction of activated carbonyl groups such as alpha-keto esters, benzils, 1,2-cyclohexanedione, and alpha-ketophosphonates by alkyl phosphines afforded the corresponding alpha-hydroxy esters or ketones in good to excellent yields in THF at room temperature. The mechanism of the proton transfer and intramolecular hydrolysis has been studied on the basis of deuterium and 18O labeling experiments.

High-throughput assays for lipases and esterases

In the past few years a considerable number of high-throughput screening (HTS) systems have been developed, especially for lipases and esterases. In this review, a range of HTS methods for the directed evolution of these hydrolases are covered. This includes spectrophotometric and fluorimetric formats as well as other approaches to allow for fast, efficient and reliable identification of desired enzyme variants within large mutant libraries. In addition, methods for library creation and application of lipases and esterases are briefly covered.

Understanding and improving NADPH-dependent reactions by nongrowing Escherichia coli cells

We have shown that whole Escherichia coli cells overexpressing NADPH-dependent cyclohexanone monooxygenase carry out a model Baeyer-Villiger oxidation with high volumetric productivity (0.79 g epsilon-caprolactone/L.h ) under nongrowing conditions (Walton, A. Z.; Stewart, J. D. Biotechnol. Prog. 2002, 18, 262-268). This is approximately 20-fold higher than the space-time yield for reactions that used growing cells of the same strain. Here, we show that the intracellular stability of cyclohexanone monooxygenase and the rate of substrate transport across the cell membrane were the key limitations on the overall reaction duration and rate, respectively. Directly measuring the levels of intracellular nicotinamide cofactors under bioprocess conditions suggested that E. coli cells could support even more efficient NADPH-dependent bioconversions if a more suitable enzyme-substrate pair were identified. This was demonstrated by reducing ethyl acetoacetate with whole cells of an E. coli strain that overexpressed an NADPH-dependent, short-chain dehydrogenase from baker's yeast (Saccharomyces cerevisiae). Under glucose-fed, nongrowing conditions, this reduction proceeded with a space-time yield of 2.0 g/L.h and a final product titer of 15.8 g/L using a biocatalyst:substrate ratio (g/g) of only 0.37. These values are significantly higher than those obtained previously. Moreover, the stoichiometry linking ketone reduction and glucose consumption (2.3 +/- 0.1) suggested that the citric acid cycle supplied the bulk of the intracellular NADPH under our process conditions. This information can be used to improve the efficiency of glucose utilization even further by metabolic engineering strategies that increase carbon flux through the pentose phosphate pathway.

Developments and trends in enzyme catalysis in nonconventional media

The conventional notion that enzymes are only active in aqueous media has long been discarded, thanks to the numerous studies documenting enzyme activities in nonaqueous media, including pure organic solvents and supercritical fluids. Enzymatic reactions in nonaqueous solvents offer new possibilities for producing useful chemicals (emulsifiers, surfactants, wax esters, chiral drug molecules, biopolymers, peptides and proteins, modified fats and oils, structured lipids and flavor esters). The use of enzymes in both macro- and microaqueous systems has been investigated especially intensively in the last two decades. Although enzymes exhibit considerable activity in nonaqueous media, the activity is low compared to that in water. This observation has led to numerous studies to modify enzymes for specific purposes by various means including protein engineering. This review covers the historical developments, major technological advances and recent trends of enzyme catalysis in nonconventional media. A brief description of different classes of enzymes and their use in industry is provided with representative examples. Recent trends including use of novel solvent systems, role of water activity, stability issues, medium and biocatalyst engineering aspects have been discussed with examples. Special attention is given to protein engineering and directed evolution.

Immunologically driven chemical engineering of antibodies for catalytic activity

We describe a new strategy for the preparation of catalytic antibodies based on a two-step procedure. Firstly, monoclonal antibodies are selected only if displaying the following binding features: binding both the substrate and a reactive group in such a way that the two groups are in a reactive position towards each other. Secondly, the selected monoclonal antibodies (mAbs) are chemically engineered by covalently binding the reactive group into the binding pocket of the antibody. Using previously isolated monoclonal antibodies, we have focused our studies on the control of this second step.

Investigating and Engineering Enzymes by Genetic Selection

Natural enzymes have arisen over millions of years by the gradual process of Darwinian evolution. The fundamental steps of evolution-mutation, selection, and amplification-can also be exploited in the laboratory to create and characterize protein catalysts on a human timescale. In vivo genetic selection strategies enable the exhaustive analysis of protein libraries with 10(10) different members, and even larger ensembles can be studied with in vitro methods. Evolutionary approaches can consequently yield statistically meaningful insight into the complex and often subtle interactions that influence protein folding, structure, and catalytic mechanism. Such methods are also being used increasingly as an adjunct to design, thus providing access to novel proteins with tailored catalytic activities and selectivities.

Novel methods for biocatalyst screening

There have been a number of recent advances in catalysis assays applicable for screening biocatalyst libraries in high-throughput format. These include instrumental assays such as high-performance liquid chromatography, mass spectrometry, capillary electrophoresis and IR-thermography, reagent-based assays producing spectroscopic signals (UV/VIS or fluorescence) in response to reaction progress, and assays based on fluorogenic or chromogenic substrates. These fluorogenic substrates enable the assaying of a variety of enzymes in enantioselective and stereoselective manner, including alcohol dehydrogenases, aldolases, lipases, amidases, epoxide hydrolases and phosphatases.

Industrial biocatalysis

The number of industrial processes for the synthesis of fine and commodity chemicals, pharmaceutical and agrochemical intermediates and drug substances utilizing biological catalysts continues to grow. The combination of new molecular biology techniques, such as directed evolution and pathway engineering, with new and efficient high-throughput screening methods is poised to bolster this field and further advance the contribution of biocatalysis to the chemical and the pharmaceutical industries.

Enzymes from extremophiles

The industrial application of enzymes that can withstand harsh conditions has greatly increased over the past decade. This is mainly a result of the discovery of novel enzymes from extremophilic microorganisms. Recent advances in the study of extremozymes point to the acceleration of this trend. In particular, enzymes from thermophilic organisms have found the most practical commercial use to date because of their overall inherent stability. This has also led to a greater understanding of stability factors involved in adaptation of these enzymes to their unusual environments.

Fluorogenic polypropionate fragments for detecting stereoselective aldolases

A series of fluorogenic polypropionate fragments has been prepared. These undergo retroaldolization to an intermediate aldehyde that liberates the fluorescent product umbelliferone by a secondary beta-elimination reaction. leading to a >20-fold increase in fluorescence (lambda(em) = 460 +/- 20 nm, lambdaex = 360 +/- 20 nm). By applying the principle of microscopic reversibility to the reversible aldol reaction, we can use these substrates to detect stereoselective aldolases. Test substrates are available to probe the classical cases of syn- and anti-selective aldolization (11a-d), Cram/ anti-Cram-selective aldolization (10a-d), and double stereoselective aldolization (3a-h). The selectivity of aldolase antibody 38C2 for these substrates is demonstrated as an example. The assay is suitable for high-throughput screening for catalysis in microtiter plates, and therefore provides a convenient tool for the isolation of new stereoselective aldolases from catalyst libraries.

Directed evolution of enantioselective enzymes for organic chemistry

The production of enantiopure compounds is of steadily increasing importance to the chemical and biotechnological industries. In principal, the application of directed evolution in combination with newly developed screening methods enables the generation of enzymes with improved enantioselectivity. The first and most advanced example relates to a bacterial lipase from Pseudomonas aeruginosa. This enzyme was evolved towards a model substrate to yield in a lipase mutant showing > 90% enantiomeric excess as compared to 2% for the wild-type lipase. The creation of enantioselective enzymes by directed evolution will become an important technology in the near future.

Visualization of enzyme-catalyzed reactions using pH indicators: rapid screening of hydrolase libraries and estimation of the enantioselectivity

The use of pH indicators to monitor hydrolase-catalyzed reactions is described. The formation of acid following an enzyme-mediated hydrolysis causes a drop in the pH that can be visualized by a change in the color of the indicator-containing solution. The best indicators are those showing a color transition within the operational pH range of the hydrolases, like bromothymol blue and phenol red. The enantioselectivity of lipases and esterases can be estimated using single isomers under the same conditions and comparing the color turnover for each one. The method has been tested to quickly evaluate the enantioselectivity of a lipase towards a set of ester substrates and applied to the hierarchical screening of a library of thermophilic esterases.