Oliver Vielhauer

Simplified absolute metabolite quantification by gas chromatography–isotope dilution mass spectrometry on the basis of commercially available source material

In the field of metabolomics, GC-MS has rather established itself as a tool for semi-quantitative strategies like metabolic fingerprinting or metabolic profiling. Absolute quantification of intra- or extracellular metabolites is nowadays mostly accomplished by application of diverse LC-MS techniques. Only few groups have so far adopted GC-MS technology for this exceptionally challenging task. Besides numerous and deeply investigated problems related to sample generation, the pronounced matrix effects in biological samples have led to the almost mandatory application of isotope dilution mass spectrometry (IDMS) for the accurate determination of absolute metabolite concentrations. Nevertheless, access to stable isotope labeled internal standards (ILIS), which are in many cases commercially unavailable, is quite laborious and very expensive. Here we present an improved and simplified gas chromatography-isotope dilution mass spectrometry (GC-IDMS) protocol for the absolute determination of intra- and extracellular metabolite levels. Commercially available (13)C-labeled algal cells were used as a convenient source for the preparation of internal standards. Advantages as well as limitations of the described method are discussed.

On the kinetics of the enzyme-catalyzed hydrolysis of axial chiral alkyl allenecarboxylates: preparation of optically active R-(−)-2-ethyl-4-phenyl-2,3-hexadiene-carboxylic acid and its optically pure S-(+)-methylester

Abstract Pig liver esterase (PLE) was used for the preparation of optically active alkyl allenecarboxylates with axial chirality. Free and immobilized enzymes were used as biocatalysts for the kinetic resolution of racemic ester substrates. Whereas the biotransformations using the free biocatalyst resulted in moderately to high enantiomeric ratios, the immobilization significantly decreased the E -value. The reaction conditions were optimized with respect to the enantiomeric ratio and scaled up. The enantiomeric ratio ( E -value) was thereby enhanced by a factor of four to E =60. Under optimized conditions (free enzyme, addition of acetone as a cosolvent and Triton X-100 as an emulgator) in a preparative scale biotransformation, 282 mg of optically pure S -(+)-2-ethyl-4-phenyl-2,3-hexadiene-carboxylic acid methylester (96% ee, 82% yield) and 257 mg of R -(−)-2-ethyl-4-phenyl-2,3-hexadiene-carboxylic acid (83% ee, 80% yield) could be synthesized from the racemic substrate.

Kinetic analysis and modeling of the liquid–liquid conversion of emulsified di‐rhamnolipids by Naringinase from Penicillium decumbens

The enzymatic conversion of an aggregate‐forming substrate was kinetically analyzed and a model was applied for the prediction of reaction‐time courses. An L‐rhamnose molecule from a di‐rhamnolipid is cleaved by Naringinase from Penicillium decumbens leading to a mono‐rhamnolipid. Optimal reaction rates were found when both, substrate and product build large co‐aggregates in a slightly acidic aqueous phase. On the other hand, reaction rates were independent of initial di‐rhamnolipid concentration and this was interpreted by assuming that the reaction occurs in the aqueous phase according to Michaelis–Menten kinetics in combination with competitive L‐rhamnose inhibition. Rhamnolipids were therefore assumed to be highly concentrated in aggregates, a second liquid phase, whereas diffusive rhamnolipid transport from and to the aqueous phase occurs due to the enzymatic reaction. Furthermore, ideal surfactant mixing between di‐ and mono‐rhamnolipid was assumed for interpretation of the negative effect of the last on the reaction rate. A model was created that describes the system accordingly. The comparison of the experimental data, were in excellent agreement with the predicted values. The findings of this study may beneficially be adapted for any bioconversion involving aggregate‐forming substrate and/or product being catalyzed by hydrophilic enzymes. Biotechnol. Bioeng. 2009;102: 9–19.

Dynamics of benzoate metabolism in Pseudomonas putida KT2440

Soil microorganisms mineralize lignin-derived aromatic carbon sources using oxidative catabolic pathways, such as the β-ketoadipate pathway. Although this aromatic pathway is one of the best-studied pathways in biochemistry, the complete pathway, including its regulation by aromatic carbon sources, has not been integrated into the metabolic network. In particular, information about the in vivo operation (e.g., kinetics and flux capacity) of the pathway is lacking. In this contribution, we use kinetic modeling and thermodynamic analysis to evaluate the in vivo operation of this key aromatic multi-step pathway. The resulting ab initio deterministic model of benzoate degradation via the β-ketoadipate (ortho-cleavage) pathway in Pseudomonas putida KT2440 is presented. The kinetic model includes mechanistic rate expressions for the enzymes and transport processes. The design and experimental validation of the model are driven by data generated from short-term perturbation experiments in a benzoate-limited continuous culture. The results of rigorous modeling of the in vivo dynamics provide strong support for flux regulation by the benzoate transporter and the enzymes forming and cleaving catechol. Revisiting the β-ketoadipate pathway might be valuable for applications in different fields, such as biochemistry and metabolic engineering, that use lignin monomers as a carbon source.