Assay and properties of diaminopimelate epimerase from Bacillus megaterium

A new method for evaluation and dietary therapy of congenital: deficiencies of amino acid metabolic enzymes. Linear system analysis and optimization of feedback inputs for the metabolic pathways of lysine, methionine and isoleucine

We intended to elucidate an integrated mathematical model of amino acid metabolism and we propose a system for optimization treatment of disturbed metabolic states caused by congenital enzyme deficiencies. Our analysis focused on the metabolic pathway starting at asparaginic acid proceeding to isoleucine, methionine and lysine. The rate of change in the concentration of the biochemical species was expressed as 21 linear rate equations. We obtained the rate constants and the magnitude of feedback from reported experimental data. Linear systems analysis revealed that the metabolic system under study was stable but uncontrollable. These properties were insensitive to changes in the magnitude of feedback. To show the effect of optimizing the feedback so that it minimizes the square of the concentration of the species and the control input, we analyzed the impulse response of the species, transient response and the singular value of the system for four cases; (1) at the physiological state without optimizing the feedback, (2) at the physiological state attained after optimizing the feedback, (3) at the pathophysiological state attained with enzyme deficiency states for lysine and methionine metabolism without optimizing the feedback, and (4) at the pathophysiological state attained after optimizing the feedback for enzyme deficiencies. In the enzyme deficient model, the impulse response oscillated and lasted longer than that in the physiological state. These changes appeared even in the species on other branched pathways. The singular value was elevated in the enzyme deficient state. By optimizing the feedback, all the impulse responses in the enzyme deficient state recovered to nearly those in the normal physiological state. Similarly, the transient response and the singular value in the enzyme deficient state recovered to nearly the normal physiological values. We elucidated the numerical value of the feedback gain for this optimization. The present analysis is useful for the evaluation of the integrated properties of amino acid metabolism and the optimization technique is potentially of use for determining a treatment course for congenital metabolic enzyme deficiencies.

Expression of recombinant diaminopimelate epimerase in Escherichia coli. Isolation and inhibition with an irreversible inhibitor

Recombinant diaminopimelate epimerase is overproduced to give 1% of soluble protein when grown under the appropriate conditions in Escherichia coli. This compares with 0.02% of the constitutive level of wild-type enzyme. A new purification procedure now yields milligram quantities of homogeneous enzyme of high specific activity (192 U/mg). This has enabled sufficient amounts of enzyme both to compare with wild-type enzyme and to enable active site modification studies to be performed. Incubation of the enzyme with 2-(4-amino-4-carboxybutyl)-2-aziridine-carboxylic acid (AZIDAP), results in time-dependent irreversible inhibition. Tryptic digestion of the inactivated enzyme and peptide-mapping show that AZIDAP is specifically and covalently bound to the enzyme at a unique peptide. Determination of the amino acid sequence of this peptide and comparison with the sequence deduced from the DNA sequence of the dapF gene shows that Cys73 is labelled. Finally based on limited sequence similarities around this cysteine and active-site cysteines of proline racemase and 1-hydroxyproline 2-epimerase, together with mechanistic considerations, we propose that all three non-pyridoxal-phosphate-containing racemases/epimerases derive from a common evolutionary origin.

A high-performance liquid chromatography method for the simultaneous assay of diaminopimelate epimerase and decarboxylase

A sensitive and comparatively simple method for the assay of diaminopimelate (DAP) decarboxylase, which simultaneously monitors DAP epimerase activity, in the reverse of the biosynthetic direction, is described. The substrate, meso-DAP and products LL-DAP and L-lysine are derivatized with o-phthaldialdehyde and resolved by reversed-phase high-performance liquid chromatography. Separation is achieved on a Spherisorb C18 column using a gradient elution system. This technique offers a high degree of sensitivity as the detection method described can measure picomole quantities of substrate and products.

Enzymic assays for isomers of 2,6-diaminopimelic acid in walls of Bacillus cereus and Bacillus megaterium

An enzymic assay for individual isomers (meso-, LL- and DD-) of 2,6-diaminopimelate was developed. The enzyme 2,6-diaminopimelate decarboxylase specifically attacked meso-diaminopimelate and was used to measure this isomer manometrically. The meso- and LL-isomers were measured together manometrically in a coupled assay with diaminopimelate decarboxylase and diaminopimelate epimerase (which converts LL-diaminopimelate into meso-diaminopimelate). The DD-isomer was not attacked by either enzyme and was measured, as residual diaminopimelate after the coupled assay, by a colorimetric method, which was also used to measure total diaminopimelate before enzymic treatments. The coupled enzymes were also used to prepare pure DD-isomer from chemically synthesized diaminopimelate. A mixture of diaminopimelate isomers was present in walls of four strains of Bacillus megaterium [in each about 75% (w/w) meso-, 18% LL- and 7% DD-] and in walls of two strains of Bacillus cereus (about 85% meso-, 8% LL- and 7% DD-). One strain of B. cereus contained at least 95% meso-diaminopimelate, with only traces of LL- and DD-isomers. Peptidoglycan from Escherichia coli was assayed as containing at least 95% meso-isomer. The proportion of isomers in the wall of a strain of B. megaterium remained constant after growth in a variety of different media.

Lipoic acid content of Escherichia coli and other microorganisms

A mutant strain of Escherichia coli K-12 requiring lipoic acid. W1485lip 2 (ATCC 25645), was used to develop a turbidimetric assay for lipoic acid and a polarographic assay based on the oxidation of pyruvate by suspensions of lipoic acid-deficient organisms. The turbidmetric assay was more sensitive with a working range equivalent to 0.2-2.0 ng of DL-alpha-lipoic acid compared with 5-50 ng for the polarographic method. The mutant responded equally to racemic mixtures of alpha-lipoic acid, beta-lipoic acid and dihydrolipoic acid but gave little response to lipoamide, and other derivatives without prior hydrolysis; 8-methyllipoic acid was a competitive inhibitor of the response to lipoic acid. A high specificity of the mutant for the natural steroisomer was indicated by the fact that (+)-alpha-lipoic acid had twice the activity of the racemic mixture. Escherichia coli K12 contained less than 0.05 ng of free (+)-alpha-lipoic acid per mg dry weight but, depending on the growth substrate, the equivalent of between 13 and 47 ng of (+)-alpha-lipoic acid per mg dry weight after acid extraction. There was a strong correlation between the lipoic acid content and the sum of the specific activities for the pyruvate and alpha-ketoglutarate dehydrogenase complexes. Experiments with washed suspensions of Escherichia coli showed only small increases in lipoic acid content (18%) when incubated with pyruvate, cysteine and methionine. When supplied with exogenous lipoic acid the mutant, W1485lip2, accumulated very little more than was demanded by its metabolism. The lipoic acid contents of several organisms were measured and correlated with their metabolism.