A Genetic Circuit System Based on Quorum Sensing Signaling for Directed Evolution of Quorum‐Quenching Enzymes

Quorum sensing is a cell–cell communication mechanism that is involved in the regulation of biological functions such as luminescence, virulence, and biofilm formation. Quorum‐quenching enzymes, which interrupt quorum‐sensing signaling through degradation of quorum‐sensing molecules, have emerged as a new approach to controlling and preventing bacterial virulence and pathogenesis. In an effort to develop quorum‐quenching enzymes with improved catalytic activities, a genetic circuit system based on acylhomoserine‐lactone (AHL)‐mediated quorum‐sensing signaling was constructed. The genetic circuit system was composed of lux‐R, lux‐I promoter, β‐lactamase, and β‐lactamase inhibitor, and designed to confer antibiotic resistance on host cells expressing an AHL‐degrading enzyme, thereby enabling rapid screening of quorum‐quenching enzymes. To demonstrate the utility of the genetic circuit system, we attempted the directed evolution of the AHL hydrolase from Bacillus sp. The genetic circuit system was shown to be effective in screening of quorum‐quenching enzymes with high catalytic efficiency. From these results it is expected that the genetic circuit system can be widely used for the isolation and directed evolution of quorum‐quenching enzymes with greater potential.     

Altering the Substrate Specificity of RhlI by Directed Evolution

Reducing virulence : RhlI catalyzes the synthesis of N‐butanoyl homoserine lactone (BHL), with a minor product N‐hexanoyl homoserine lactone (HHL). By using directed evolution and a genetic screen, RhlI has been engineered for enhanced production of both BHL and HHL at a similar level.

     

Improvement of an Acid Phosphatase/DHAP‐Dependent Aldolase Cascade Reaction by Using Directed Evolution

To enhance the phosphorylating activity of the bacterial nonspecific acid phosphatase from Salmonella enterica ser. typhimurium LT2 towards dihydroxyacetone (DHA), a mutant library was generated from the native enzyme. Three different variants that showed enhanced activity were identified after one round of epPCR. The single mutant V78L was the most active and showed an increase in the maximal DHAP concentration to 25 % higher than that of the wild‐type enzyme at pH 6.0. This variant is 17 times more active than the wild‐type acid phosphatase from Salmonella enterica ser. typhimurium LT2 in the acid phosphatase/aldolase cascade reaction at pH 6.0 and is also six times more active than the phosphatase from Shigella flexneri that we previously used.     

A high-throughput screen for porphyrin metal chelatases: application to the directed evolution of ferrochelatases for metalloporphyrin biosynthesis

Porphyrins are of particular interest in a variety of applications ranging from biocatalysis and chemical synthesis to biosensor and electronic technologies as well as cancer treatment. Recently, we have developed a versatile system for the high-level production of porphyrins in engineered E. coli cells with the aim of diversifying substitution patterns and accessing porphyrin systems not readily available through chemical synthesis. However, this approach failed to produce significant amounts of the metalloporphyrin in vivo from overproduced protoporphyrin due to insufficient metal insertion. Therefore, we systematically assessed the activity of the B. subtilis ferrochelatase in vivo and in vitro. A true high-throughput-screening approach based on catalytic in vivo ferrochelatase activity was developed by using fluorescence-activated cell sorting (FACS). This assay was used to screen a library of 2.4 x 10(6) ferrochelatase mutants expressed in protoporphyrin-overproducing recombinant E. coli cells. Several selected protein variants were purified, and their improved catalytic activity was confirmed in vitro. In addition to ferrochelatase activity, metal transport into E. coli was identified as another limitation for in vivo heme overproduction. Overexpression of the metal transporter zupT as part of the assembled pathway increased the overall metalloporphyrin production twofold. This report represents the most exhaustive in vitro evolution study of a ferrochelatase and demonstrates the effectiveness of our novel high-throughput-screening system for directed evolution of ferrochelatases based on their catalytic activity.     

High‐Throughput Miniaturized Screening of Nanoparticle Formation via Inkjet Printing

The self‐assembly of specific polymers into well‐defined nanoparticles (NPs) is of great interest to the pharmaceutical industry as the resultant materials can act as drug delivery vehicles. In this work, a high‐throughput method to screen the ability of polymers to self‐assemble into NPs using a picoliter inkjet printer is presented. By dispensing polymer solutions in dimethyl sulfoxide (DMSO) from the printer into the wells of a 96‐well plate, containing water as an antisolvent, 50 suspensions are screened for nanoparticle formation rapidly using only nanoliters to microliters. A variety of polymer classes are used and in situ characterization of the submicroliter nanosuspensions shows that the particle size distributions match those of nanoparticles made from bulk suspensions. Dispensing organic polymer solutions into well plates via the printer is thus shown to be a reproducible and fast method for screening nanoparticle formation which uses two to three orders of magnitude less material than conventional techniques. Finally, a pilot study for a high‐throughput pipeline of nanoparticle production, physical property characterization, and cytocompatibility demonstrates the feasibility of the printing approach for screening of nanodrug delivery formulations. Nanoparticles are produced in the well plates, characterized for size and evaluated for effects on metabolic activity of lung cancer cells.     

A Practical NMR‐Based High‐Throughput Assay for Screening Enantioselective Catalysts and Biocatalysts

Two NMR‐based approaches for high‐throughput screening of enantioselective catalysts and biocatalysts are described. One version makes use of pseudo‐enantiomers or pseudo‐meso‐compounds based on ¹³C‐labeling. A throughput of at least 1400 ee determinations per day is possible by using an appropriate flow‐through cell and an autosampler. The other approach is based on traditional diastereomer formation using a chiral reagent or complexing agent. The ee values are accurate to within ±2% and ±5% of the true values.     

Synthesis of a Fluorogenic Analogue of Sphingosine‐1‐Phosphate and Its Use to Determine Sphingosine‐1‐Phosphate Lyase Activity

Illuminating an ER enzyme : We report on the design and synthesis of a fluorogenic chemical sensor ( 1 ) to measure sphingosine‐1‐phosphate lyase activity in high‐throughput screening formats, as well as its validation using lyase knockout (Sgpl1?/?) cells.

     

A Novel Reporter System for Molecular Imaging and High‐Throughput Screening of Anticancer Drugs

Apoptosis is irreversible programmed cell death, characterized by a cellular cascade activation of caspase 3, which subsequently degrades proteins and other components of cells with a motif sequence. Here we report a novel reporter system to detect apoptosis, growth arrest, and cell death based on controlled and self‐amplified protein degradation. The key element of the reporter system is an apoptotic sensor chimerical protein which consists of three components: procaspase 3, ubiquitin (Ub), and a strong consensus sequence of N‐degron. Between each of these units is a DEVD (Asp‐Glu‐Val‐Asp) sequence, which acts as the cleavage target of caspase 3. This non‐conventional signal loss approach is much more sensitive than other native methods that are based on signal gain. The superior sensitivity is demonstrated by its effective application in 386‐well high‐throughput screening (HTS) with low drug concentrations and a short incubation time. The HTS selection process using this reporter system is very simple and economic. The simplicity eliminates potential errors introduced by multiple steps; there is no need for any substrate. Furthermore, the cells in the assay need not be disrupted, and the morphology of the cells can provide additional information on mechanisms. After HTS, the intact cells can also be used for other analytic analysis. This system thus has a potentially important role in the discovery and development of new anticancer drugs. It also appears to be very versatile, can be used both in vitro and in vivo with different linked reporter genes, and can be used for a variety of imaging applications.     

Screening for Cytochrome P450 Reactivity by Harnessing Catalase as Reporter Enzyme

The big screen : We have devised a high‐throughput screening method for organic peroxide‐dependent P450 reactivity by taking advantage of a previously undescribed activity of catalase, which was used as reporter enzyme. This two‐step assay, followed by liquid chromatography/mass spectrometry analyses, allowed the facile identification of several new substrates for bacterial P450 enzymes.

     

High‐Throughput Screening Technology for Automotive Applications

The development of advanced emission control systems to meet the strict regulations requires efficient and flexible material screening capabilities. Here, a high throughput test unit is described. Two case studies demonstrate the rapid screening of relevant parameter spaces and material functionalities which can be used in product development. One involves steady‐state testing of hydrocarbon oxidation in Diesel aftertreatment systems, while the other shows the evaluation of oxygen storage capacity in the optimization of three‐way catalysts for gasoline engines.     

High‐Throughput Virtual Screening Using Quantum Mechanical Probes: Discovery of Selective Kinase Inhibitors

A procedure based on semi‐empirical quantum mechanical (QM) calculations of interaction energy is proposed for the rapid screening of compound poses generated by high‐throughput docking. Small molecules (consisting of 2–10 atoms and termed “probes”) are overlapped with polar groups in the binding site of the protein target. The interaction energy values between each compound pose and the probes, calculated by a semi‐empirical Hamiltonian, are used as filters. The QM probe method does not require fixed partial charges and takes into account polarization and charge‐transfer effects which are not captured by conventional force fields. The procedure is applied to screen ～100 million poses (of 2.7 million commercially available compounds) obtained by high‐throughput docking in the ATP binding site of the tyrosine kinase erythropoietin‐producing human hepatocellular carcinoma receptor B4 (EphB4). Three QM probes on the hinge region and one at the entrance pocket are employed to select for binding affinity, while a QM probe on the side chain of the so‐called gatekeeper residue (a hypervariable residue in the kinome) is used to enforce selectivity. The poses with favorable interactions with the five QM probes are filtered further for hydrophobic matching and low ligand strain. In this way, a single‐digit micromolar inhibitor of EphB4 with a relatively good selectivity profile is identified in a multimillion‐compound library upon experimental tests of only 23 molecules.     

Screening Collagenase Activity in Bacterial Lysate for Directed Enzyme Applications

Collagenases are essential enzymes capable of digesting triple-helical collagen under physiological conditions. These enzymes play a key role in diverse physiological and pathophysiological processes. Collagenases are used for diverse biotechnological applications, and it is thus of major interest to identify new enzyme variants with improved characteristics such as expression yield, stability, or activity. The engineering of new enzyme variants often relies on either rational protein design or directed enzyme evolution. The latter includes screening of a large randomized or semirational genetic library, both of which require an assay that enables the identification of improved variants. Moreover, the assay should be tailored for microplates to allow the screening of hundreds or thousands of clones. Herein, we repurposed the previously reported fluorogenic assay using 3,4-dihydroxyphenylacetic acid for the quantitation of collagen, and applied it in the detection of bacterial collagenase activity in bacterial lysates. This enabled the screening of hundreds of E. coli colonies expressing an error-prone library of collagenase G from C. histolyticum, in 96-well deep-well plates, by measuring activity directly in lysates with collagen. As a proof-of-concept, a single variant exhibiting higher activity than the starting-point enzyme was expressed, purified, and characterized biochemically and computationally. This showed the feasibility of this method to support medium-high throughput screening based on direct evaluation of collagenase activity.     

A High-Throughput Screening Method for the Directed Evolution of Hydroxynitrile Lyase towards Cyanohydrin Synthesis

Chiral cyanohydrins are useful intermediates in the pharmaceutical and agricultural industries. In nature, hydroxynitrile lyases (HNLs) are a kind of elegant tool for enantioselective hydrocyanation of carbonyl compounds. However, currently available methods for demonstrating hydrocyanation are still stalled at precise, but low-throughput, GC or HPLC analyses. Herein, we report a chromogenic high-throughput screening (HTS) method that is feasible for the cyanohydrin synthesis reaction. This method was highly anti-interference and sensitive, and could be used to directly profile the substrate scope of HNLs either in cell-free extract or fermentation clear broth. This HTS method was also validated by generating new variants of PcHNL5 that presented higher catalytic efficiency and stronger acidic tolerance in variant libraries.     

A High‐Throughput Screening Approach for the Determination of Additive Effects in Organozinc Addition Reactions to Aldehydes

The effects of additives in phenylzinc addition reactions to an aldehyde have been studied using an automated high‐throughput screening approach. With 2‐bromobenzaldehyde as test substrate and N,N‐dibutylnorephedrine (dbne) as chiral ligand, an improvement of 20% ee over the catalyzed reaction in the absence of the additive was observed. The described results enable a novel access towards chiral diarylmethanols using commercially available substrates, reagents and ligands as well as fast, automated techniques.     

A pH‐Based High‐Throughput Assay for Transketolase: Fingerprinting of Substrate Tolerance and Quantitative Kinetics

A pH‐based high‐throughput assay method has been developed for the rapid and reliable measurement of transketolase (TK) activity. The method is based on the decarboxylation of lithium hydroxypyruvate (HPA) as a hydroxyacetyl donor with an aldehyde acceptor, using phenol red as the pH indicator. Upon release of carbon dioxide from HPA, the pH increase in the reaction mixture can be determined photometrically by the color change of the pH indicator. At low buffer concentration (2 mM triethanolamine, pH 7.5), the method is highly sensitive and allows continuous monitoring, for quantitative determination of the kinetic parameters. By using this method, the substrate specificities of the TK enzymes from Escherichia coli and Saccharomyces cerevisiae, as well as two active‐site‐modified variants of the E. coli TK (D469E, H26Y) were evaluated against a panel of substrate analogues; specific activities and kinetic constants could be rapidly determined. Substrate quality indicated by assay determination was substantiated with novel TK applications by using achiral 3‐hydroxypropanal and 4‐hydroxybutanal for preparative synthesis of chiral deoxyketose‐type products. Determination of ee for the latter could be performed by chiral GC analysis, with an unambiguous correlation of the absolute configuration from rotation data. This pH‐based assay method is broadly applicable and allows rapid, sensitive, and reliable screening of the substrate tolerance of known TK enzymes and variants obtained from directed evolution.     

Directed Evolution of an Enantioselective Enoate‐Reductase: Testing the Utility of Iterative Saturation Mutagenesis

Directed evolution utilizing iterative saturation mutagenesis (ISM) has been applied to the old yellow enzyme homologue YqjM in the quest to broaden its substrate scope, while controlling the enantioselectivity in the bioreduction of a set of substituted cyclopentenone and cyclohexenone derivatives. Guided by the known crystal structure of YqjM, 20 residues were selected as sites for saturation mutagenesis, a pooling strategy based on the method of Phizicky [M. R. Martzen, S. M. McCraith, S. L. Spinelli, F. M. Torres, S. Fields, E. J. Grayhack, E. M. Phizicky, Science 1999 , 286, 1153–1155] being used in the GC screening process. The genes of some of the hits were subsequently employed as templates for randomization experiments at the other putative hot spots. Both (R)‐ and (S)‐selective variants were evolved using 3‐methylcyclohexenone as the model substrate in the asymmetric bioreduction of the olefinic functionality, only small mutant libraries and thus minimal screening effort being necessary. Some of the best mutants also proved to be excellent catalysts when testing other prochiral substrates without resorting to additional mutagenesis/screening experiments. Thus, the results constitute an important step forward in generalizing the utility of ISM as an efficient method in laboratory evolution of enzymes as catalysts in organic chemistry.     

Cover Picture: Screening for Cytochrome P450 Reactivity by Harnessing Catalase as Reporter Enzyme (ChemBioChem 4/2009)

The cover picture shows a bacterial cytochrome P450 enzyme (CYP152A1, blue protein) screening for new substrates, such as nifidepine (highlighted green). The identification of novel reactivities of P450 enzymes is of major importance for applications in biocatalysis, biosensing and metabolic engineering. In their contribution on p. 751 ff, Niemeyer et al. report a novel assay for the rapid and facile screening of substrate libraries for organic hydroperoxide‐mediated P450 reactivity. Peroxide depletion is monitored in a fluorescence microplate assay, by harnessing a previously undescribed reactivity of the enzyme catalase (orange protein structure). The assay thus connects the occurrence of P450 reactivity with a universal read‐out, thereby circumventing the need for substrate‐specific detection schemes.

     

Corrosion‐Resistant Parallel Fixed‐Bed Reactors for High‐Throughput Screening of New Deacon Reaction Catalysts

Two ten‐channel fixed‐bed reactor systems were developed for high‐throughput screening of new Deacon catalysts. The sequential ten‐channel reactor allows the determination of the activity of up to ten catalysts per day. With a ten‐channel ageing reactor the long‐time stability of catalytic activity can be tested in parallel. Both systems are robust, quite resistant against corrosion, and use the identical reaction tubes which enable the direct transfer of a catalyst from one to the other system. A mass‐spectrometric pulse method has been developed and applied successfully for the analysis of the corrosive product gas mixture of the Deacon reaction.