Lactate oxygenase of Mycobacterium phlei

Combining chemoinformatics with bioinformatics: in silico prediction of bacterial flavor-forming pathways by a chemical systems biology approach "reverse pathway engineering"

The incompleteness of genome-scale metabolic models is a major bottleneck for systems biology approaches, which are based on large numbers of metabolites as identified and quantified by metabolomics. Many of the revealed secondary metabolites and/or their derivatives, such as flavor compounds, are non-essential in metabolism, and many of their synthesis pathways are unknown. In this study, we describe a novel approach, Reverse Pathway Engineering (RPE), which combines chemoinformatics and bioinformatics analyses, to predict the “missing links” between compounds of interest and their possible metabolic precursors by providing plausible chemical and/or enzymatic reactions. We demonstrate the added-value of the approach by using flavor-forming pathways in lactic acid bacteria (LAB) as an example. Established metabolic routes leading to the formation of flavor compounds from leucine were successfully replicated. Novel reactions involved in flavor formation, i.e. the conversion of alpha-hydroxy-isocaproate to 3-methylbutanoic acid and the synthesis of dimethyl sulfide, as well as the involved enzymes were successfully predicted. These new insights into the flavor-formation mechanisms in LAB can have a significant impact on improving the control of aroma formation in fermented food products. Since the input reaction databases and compounds are highly flexible, the RPE approach can be easily extended to a broad spectrum of applications, amongst others health/disease biomarker discovery as well as synthetic biology.

Cyanide toxicity in hepatocytes under aerobic and anaerobic conditions

The effect of cyanide on cell viability and mitochondrial function was studied in hepatocytes exposed to air or argon. Cells were more susceptible to cyanide toxicity under air than under argon. Analysis of the disposition of cyanide showed that the difference in susceptibility to KCN was not due to O2-dependent differences in cyanide metabolism or elimination. Studies of mitochondrial function revealed that cyanide under aerobic conditions resulted in substantial swelling of the mitochondria, which corresponded to a matrix loading of phosphate. In addition, cyanide caused a loss of the mitochondrial protonmotive force. This was in contrast to the results for cells exposed to 30 min of anoxia alone in which there was no loss of mitochondrial delta pH, no detectable change in mitochondrial volume, and little matrix loading of phosphate. These results show that at least some of the protective mechanisms elicited by anoxia (B. S. Andersson, T. Y. Aw, and D. P. Jones. Am. J. Physiol. 252 (Cell Physiol. 21): C349-C355, 1987) are not elicited by cyanide alone. Thus cyanide under aerobic conditions does not provide a completely valid model for simple anoxia. Moreover, the results suggest that the molecular sensor necessary to signal suppression of metabolic and transport functions during neahypoxia is dependent on O2 and is neither stimulated nor antagonized by KCN.

Meso and racemic organisms and the transition to asymmetry

In this paper we analyse extensive but previously unappreciated and scattered data on anomalous enzyme modulation by metabolite enantiomers for enzymes in the principle metabolic cycles and develop a coherent theory for their derivation from reciprocally coupled antipodal metabolisms in antecedent meso and racemic organisms. Structures for such chirally symmetric organisms are outlined, as is the gradual decoupling of their integrated antipodal metabolisms upon an evolutionary progression from meso organism to racemic organism to racemate of organisms. The driving forces and the dynamics for a transition to asymmetry are developed.

Inactivation of L-lactate monooxygenase with 2,3-butanedione and phenylglyoxal

L-Lactate monooxygenase from Mycobacterium phlei is inactivated by reaction either with 2,3-butanedione in borate or in 2,6-lutidine buffer or with phenyglyoxal in 2,6-lutidine buffer. The activation with 2.3 butanedione in borate buffer is irreversible in the presence of excess borate, but essentially complete recovery of activity occurs on exchange of phosphate for borate buffer. In 50 mM borate, inactivation with 2,3-butanedione exhibits saturation kinetics with respect to increasing concentrations of 2,3-butanedione, whereas second-order kinetics for inactivation are seen in 200 mM borate. In 2.6-lutidine buffer, the inactivation is rapid, irreversible on change of buffer, and second order overall. Complete inactivation of the enzyme by phenylglyoxal in 2,6-lutidine buffer occurs on incorporation of 2 equiv of phenylglyoxal per subunit, but only one arginyl residue per subunit is modified. The inactivation is irreversible and second order in phenyglyoxal. There is substantial protection from inactivation in the presence of D-lactate, a competitive inhibitor of the enzyme. It is suggested that an arginyl residue in the active site in L-lactate monooxygenase is involved in the binding of the carboxyl group of substrates to the enzyme. An explanation for the unusual kinetics of inactivation with 2,3-butanedione in borate and with phenylglyoxal in 2,6-lutidine is offered.