Semi-rational engineering of an amino acid racemase that is stabilized in aqueous/organic solvent mixtures.

Enzymes are industrially applied under increasingly diverse environmental conditions that are dictated by the efforts to optimize overall process efficiency. Engineering the operational stability of biocatalysts to enhance their half-lives under the desired process conditions is a widely applied strategy to reduce costs. Here, we present a simple method to enhance enzyme stability in the presence of monophasic aqueous/organic solvent mixtures based on the concept of strengthening the enzyme's surface hydrogen-bond network by exchanging surface-located amino acid residues for arginine. Suitable residues are identified from sequence comparisons with homologous enzymes from thermophilic organisms and combined using a shuffling approach to obtain an enzyme variant with increased stability in monophasic aqueous/organic solvent mixtures. With this approach, we increase the stability of the broad-spectrum amino acid racemase of Pseudomonas putida DSM 3263 eightfold in mixtures with 40% methanol and sixfold in mixtures with 30% acetonitrile.

In vivo directed enzyme evolution in nanoliter reactors with antimetabolite selection.

Scoring changes in enzyme or pathway performance by their effect on growth behavior is a widely applied strategy for identifying improved biocatalysts. While in directed evolution this strategy is powerful in removing non-functional catalysts in selections, measuring subtle differences in growth behavior remains difficult at high throughput, as it is difficult to focus metabolic control on only one or a few enzymatic steps over the entire process of growth-based discrimination. Here, we demonstrate successful miniaturization of a growth-based directed enzyme evolution process. For cultivation of library clones we employed optically clear gel-like microcarriers of nanoliter volume (NLRs) as reaction vessels and used fluorescence-assisted particle sorting to estimate the growth behavior of each of the gel-embedded clones in a highly parallelized fashion. We demonstrate that the growth behavior correlates with the desired improvements in enzyme performance and that we can fine-tune selection stringency by including an antimetabolite in the assay. As a model enzyme reaction, we improve the racemization of ornithine, a possible starting block for the large-scale synthesis of sulphostin, by a broad-spectrum amino acid racemase and confirm the discriminatory power by showing that even moderately improved enzyme variants can be readily identified.

Exploiting racemases.

Chiral resolutions of racemic mixtures are limited to a theoretical yield of 50 %. This yield can be doubled by integration of a step-wise or continuous racemization of the non-desired enantiomer. Many of the different routes along which the racemization step can be conducted require harsh treatments and are therefore often incompatible with the highly functionalized state of many compounds relevant for the life science industries. Employing enzymatic catalysis for racemization can therefore be highly beneficial. Racemases allow racemization in one reaction step. Most representatives from this group are found in the domain of amino acid or amino acid derivative racemization, with few other examples, notably the racemization of mandelic acid. Corresponding to the importance of enantiospecific conversion of amino acid precursor racemates for the production of enantiopure amino acids, the most important biotechnological use for racemases is the racemization of such precursors. However, alternative uses, in particular for mandelate and amino acid racemases, are emerging. Here, we summarize the natural roles of racemases and their occurrence, the applications, and the biochemistry and engineering of this promising class of biocatalysts.

Highly efficient production of rare sugars D-psicose and L-tagatose by two engineered D-tagatose epimerases.

Rare sugars are monosaccharides that do not occur in nature in large amounts. However, many of them demonstrate high potential as low-calorie sweetener, chiral building blocks or active pharmaceutical ingredients. Their production by enzymatic means from broadly abundant epimers is an attractive alternative to synthesis by traditional organic chemical means, but often suffers from low space-time yields and high enzyme costs due to rapid enzyme degradation. Here we describe the detailed characterization of two variants of d-tagatose epimerase under operational conditions that were engineered for high stability and high catalytic activity towards the epimerization of d-fructose to d-psicose and l-sorbose to l-tagatose, respectively. A variant optimized for the production of d-psicose showed a very high total turnover number (TTN) of up to 10(8) catalytic events over a catalyst's lifetime, determined under operational conditions at high temperatures in an enzyme-membrane reactor (EMR). Maximum space-time yields as high as 10.6 kg L(-1) d(-1) were obtained with a small laboratory-scale EMR, indicating excellent performance. A variant optimized for the production of l-tagatose performed less stable in the same setting, but still showed a very good TTN of 5.8 × 10(5) and space-time yields of up to 478 g L(-1) d(-1) . Together, these results confirm that large-scale enzymatic access to rare sugars is feasible.

A separation-integrated cascade reaction to overcome thermodynamic limitations in rare-sugar synthesis.

Enzyme cascades combining epimerization and isomerization steps offer an attractive route for the generic production of rare sugars starting from accessible bulk sugars but suffer from the unfavorable position of the thermodynamic equilibrium, thus reducing the yield and requiring complex work-up procedures to separate pure product from the reaction mixture. Presented herein is the integration of a multienzyme cascade reaction with continuous chromatography, realized as simulated moving bed chromatography, to overcome the intrinsic yield limitation. Efficient production of D-psicose from sucrose in a three-step cascade reaction using invertase, D-xylose isomerase, and D-tagatose epimerase, via the intermediates D-glucose and D-fructose, is described. This set-up allowed the production of pure psicose (99.9%) with very high yields (89%) and high enzyme efficiency (300 g of D-psicose per g of enzyme).

Directed divergent evolution of a thermostable D-tagatose epimerase towards improved activity for two hexose substrates.

Functional promiscuity of enzymes can often be harnessed as the starting point for the directed evolution of novel biocatalysts. Here we describe the divergent morphing of an engineered thermostable variant (Var8) of a promiscuous D-tagatose epimerase (DTE) into two efficient catalysts for the C3 epimerization of D-fructose to D-psicose and of L-sorbose to L-tagatose. Iterative single-site randomization and screening of 48 residues in the first and second shells around the substrate-binding site of Var8 yielded the eight-site mutant IDF8 (ninefold improved kcat for the epimerization of D-fructose) and the six-site mutant ILS6 (14-fold improved epimerization of L-sorbose), compared to Var8. Structure analysis of IDF8 revealed a charged patch at the entrance of its active site; this presumably facilitates entry of the polar substrate. The improvement in catalytic activity of variant ILS6 is thought to relate to subtle changes in the hydration of the bound substrate. The structures can now be used to select additional sites for further directed evolution of the ketohexose epimerase.

Model-based identification of optimal operating conditions for amino acid simulated moving bed enantioseparation using a macrocyclic glycopeptide stationary phase.

Teicoplanin aglycone columns allow efficient separation of amino acid enantiomers in aqueous mobile phases and enable robust and predictable simulated moving bed (SMB) separation of racemic methionine despite a dependency of the adsorption behavior on the column history (memory effect). In this work we systematically investigated the influence of the mobile phase (methanol content) and temperature on SMB performance using a model-based optimization approach that accounts for methionine solubility, adsorption behavior and back pressure. Adsorption isotherms became more favorable with increasing methanol content but methionine solubility was decreased and back pressure increased. Numerical optimization suggested a moderate methanol content (25-35%) for most efficient operation. Higher temperature had a positive effect on specific productivity and desorbent requirement due to higher methionine solubility, lower back pressure and virtually invariant selectivity at high loadings of racemic methionine. However, process robustness (defined as a difference in flow rate ratios) decreased strongly with increasing temperature to the extent that any significant increase in temperature over 32°C will likely result in operating points that cannot be realized technically even with the lab-scale piston pump SMB system employed in this study.

Simulated moving bed enantioseparation of amino acids employing memory effect-constrained chromatography columns.

Teicoplanin aglycone-based chromatography columns (Chirobiotic TAG) enable amino acid enantioseparation with aqueous mobile phases, which perfectly accommodates the distinct hydrophilicity of most amino acids. Therefore, this stationary phase constitutes a promising option in particular for preparative-scale separations that require high feed concentrations for economic operation. However, detailed studies revealed a solute-related memory effect when this column is subjected to high loadings of amino acids, conditions that prevail in SMB operation. High loadings yield an activation of the column as indicated by increased retention times when comparing finite injection chromatograms obtained before and after the column had been subjected to a concentrated amino acid feed. This effect can be slowly reversed by flushing the column with solvent devoid of amino acid. Obviously, the activation of the stationary phase needs to be accounted for in the determination of adsorption isotherms that are used for SMB design. In this work we introduce a perturbation method adapted specifically to capture the stationary phase behaviour at SMB-like conditions. The adsorption isotherms obtained from this method indeed allowed for accurate SMB design of a methionine enantioseparation as judged by the very good agreement of experimentally obtained and model-predicted purities. Furthermore, SMB operation over 3 days with constant purities (besides deviations originating from a dip in temperature) was accomplished indicating that the adsorption behaviour in the activated state is indeed time invariant and stable long-term SMB operation with these columns is principally feasible.

Novel method for high-throughput colony PCR screening in nanoliter-reactors.

We introduce a technology for the rapid identification and sequencing of conserved DNA elements employing a novel suspension array based on nanoliter (nl)-reactors made from alginate. The reactors have a volume of 35 nl and serve as reaction compartments during monoseptic growth of microbial library clones, colony lysis, thermocycling and screening for sequence motifs via semi-quantitative fluorescence analyses. nl-Reactors were kept in suspension during all high-throughput steps which allowed performing the protocol in a highly space-effective fashion and at negligible expenses of consumables and reagents. As a first application, 11 high-quality microsatellites for polymorphism studies in cassava were isolated and sequenced out of a library of 20,000 clones in 2 days. The technology is widely scalable and we envision that throughputs for nl-reactor based screenings can be increased up to 100,000 and more samples per day thereby efficiently complementing protocols based on established deep-sequencing technologies.

Towards preparative asymmetric synthesis of beta-hydroxy-alpha-amino acids: L-allo-threonine formation from glycine and acetaldehyde using recombinant GlyA.

The diastereospecific formation of L-allo-threonine, catalyzed by the serine hydroxymethyltransferase GlyA form Escherichia coli, was studied with regard to the application in continuous processes. Process design will rely on a suitable description of enzyme stability and kinetics under relevant process conditions. Therefore, the effects of addition of organic co-solvents--methanol and acetonitrile--to the reaction mixtures on activity, stability, and diastereoselectivity were investigated. A series of progress curves from batch reactions at 35 degrees C in 50mM sodium phosphate buffer pH 6.6 and 50mM sodium phosphate buffer pH 6.6 in 20% methanol was used to estimate the respective kinetic parameters for an appropriate kinetic model. The experimental data agreed well with a kinetic model for an ordered reaction mechanism of the type bi-uni including the formation of a ternary complex and a pseudo-equilibrium assumption. The model was then applied in order to simulate the performance of the enzyme in an enzyme membrane reactor (EMR) and gave an excellent agreement with the corresponding experimental data. A space time yield of 227g L(-1)d(-1) was achieved in a continuous running EMR without significant loss of enzyme activity over 120 h of operation.

Adsorption behavior of a teicoplanin aglycone bonded stationary phase under harsh overload conditions.

Silica-bonded teicoplanin aglycone allows enantioseparation of amino acids by reversed-phase liquid chromatography with a low organic solvent content. However, a reversible change in the adsorption behavior leading to a retention time shift (RTS) was observed when a preparative scale column was treated with harsh preparative chromatography-like conditions between finite-injection HPLC runs conducted under exactly the same conditions. This behavior was observed for all five investigated aliphatic and aromatic amino acids. In all cases, the retention times were prolonged after the overload conditions and the RTS was more pronounced for the later eluting d-enantiomer. We defined a standardized method for measuring the RTS and performed a systematic investigation on the influence of experimental conditions (type and concentration of pH modifier and organic modifier, temperature, pH) on the RTS. In this way a solvent composition--90/10 50 mM NH4Ac pH 5.8/MeOH--was identified that yielded no observable shift in retention time after overload conditions for both enantiomers. In order to treat the observed phenomenon on a mechanistic level, we applied band profile analysis based on the stochastic theory of chromatography and identified two different enantioselective sites. When the band profile analysis was performed on elution profiles obtained from runs with prolonged retention time after harsh overload conditions, the retention time shift could be attributed to both differentiable types of adsorption sites. One site was found to make both, enantioselective and non-selective contributions.

Integrated operation of continuous chromatography and biotransformations for the generic high yield production of fine chemicals.

The rapid progress in biocatalysis in the identification and development of enzymes over the last decade has enormously enlarged the chemical reaction space that can be addressed not only in research applications, but also on industrial scale. This enables us to consider even those groups of reactions that are very promising from a synthetic point of view, but suffer from drawbacks on process level, such as an unfavourable position of the reaction equilibrium. Prominent examples stem from the aldolase-catalyzed enantioselective carbon-carbon bond forming reactions, reactions catalyzed by isomerising enzymes, and reactions that are kinetically controlled. On the other hand, continuous chromatography concepts such as the simulating moving bed technology have matured and are increasingly realized on industrial scale for the efficient separation of difficult compound mixtures - including enantiomers - with unprecedented efficiency. We propose that coupling of enzyme reactor and continuous chromatography is a very suitable and potentially generic process concept to address the thermodynamic limitations of a host of promising biotransformations. This way, it should be possible to establish novel in situ product recovery processes of unprecedented efficiency and selectivity that represent a feasible way to recruit novel biocatalysts to the industrial portfolio.

Suitability of teicoplanin-aglycone bonded stationary phase for simulated moving bed enantioseparation of racemic amino acids employing composition-constrained eluents.

The suitability of a teicoplanin-aglycone based chiral stationary phase for the simulated moving bed (SMB) enantioseparation of amino acids under enzyme-compatible conditions was shown following a procedure that is based solely on model-based simulations and HPLC experiments. A set of eight amino acids could be separated employing aqueous solvent containing only 10% (v/v) methanol, five of them with baseline resolution. The impact of type and concentration of organic modifier and pH modifier and pH on the separation characteristics of racemic methionine was investigated. Invariant elution profiles of repetitive adsorption/desorption of large amounts of methionine representing SMB-like conditions suggest stable adsorption behavior. Competitive loading capacity (20 mg of methionine per g of chiral stationary phase (CSP)) and SMB productivity (1 g of D-methionine per g of CSP per day) were predicted. The applied transport-dispersive model based on a competitive Bi-Langmuir isotherm was validated and its parameter estimated by model-based experimental analysis.