Cysteine and iron accelerate the formation of ribose-5-phosphate, providing insights into the evolutionary origins of the metabolic network structure

The structure of the metabolic network is highly conserved, but we know little about its evolutionary origins. Key for explaining the early evolution of metabolism is solving a chicken–egg dilemma, which describes that enzymes are made from the very same molecules they produce. The recent discovery of several nonenzymatic reaction sequences that topologically resemble central metabolism has provided experimental support for a “metabolism first” theory, in which at least part of the extant metabolic network emerged on the basis of nonenzymatic reactions. But how could evolution kick-start on the basis of a metal catalyzed reaction sequence, and how could the structure of nonenzymatic reaction sequences be imprinted on the metabolic network to remain conserved for billions of years? We performed an in vitro screening where we add the simplest components of metabolic enzymes, proteinogenic amino acids, to a nonenzymatic, iron-driven reaction network that resembles glycolysis and the pentose phosphate pathway (PPP). We observe that the presence of the amino acids enhanced several of the nonenzymatic reactions. Particular attention was triggered by a reaction that resembles a rate-limiting step in the oxidative PPP. A prebiotically available, proteinogenic amino acid cysteine accelerated the formation of RNA nucleoside precursor ribose-5-phosphate from 6-phosphogluconate. We report that iron and cysteine interact and have additive effects on the reaction rate so that ribose-5-phosphate forms at high specificity under mild, metabolism typical temperature and environmental conditions. We speculate that accelerating effects of amino acids on rate-limiting nonenzymatic reactions could have facilitated a stepwise enzymatization of nonenzymatic reaction sequences, imprinting their structure on the evolving metabolic network.

Asymmetric sulfoxidation of thioether catalyzed by soybean pod peroxidase ：kinetic model

The asymmetric sulfoxidation catalyzed by soybean pod peroxidase (SPP) in water-in-oil microemulsions were carried out with the yield of 91.56% and e.e of 96.08% at the activity of SPP of 3200 U ml-1 and 50℃ for 5 h. The mechanism with a two-electron reduction of SPP-I is accompanied with a single-electron transfer to SPP-I and nonenzymatic reactions, indicating that three concomitant sub-mechanisms contribute to the asymmetric oxidation involving five enzymatic and two nonenzymatic reactions, which can represent the asymmetric sulfoxidation of organic sulfides to form enantiopure sulfoxides. With 5.44% of the average relative deviation, a kinetic model fitting experimental data was developed. The enzymatic reactions may follow ping-pong mechanism with substrate inhibition of H2O2 and product inhibition of esomeprazole, while nonenzymatic reactions, a power law. Those results indicate that SPP with a lower cost and higher thermal stability may be used as an effective substitute for Horseradish Peroxidase.

Asymmetric sulfoxidation of thioether catalyzed by soybean pod peroxidase to form enantiopure sulfoxide in water-in-oil microemulsions: kinetic model

The asymmetric sulfoxidation catalyzed by soybean pod peroxidase (SPP) in water-in-oil microemulsions were carried out with the yield of 91.56% and e.e of 96.08% at the activity of SPP of 3200 U ml-1 and 50℃ for 5 h. The mechanism with a two-electron reduction of SPP-I is accompanied with a single-electron transfer to SPP-I and nonenzymatic reactions, indicating that three concomitant sub-mechanisms contribute to the asymmetric oxidation involving five enzymatic and two nonenzymatic reactions, which can represent the asymmetric sulfoxidation of organic sulfides to form enantiopure sulfoxides. With 5.44% of the average relative deviation, a kinetic model fitting experimental data very well was developed. The enzymatic reactions may follow ping-pong mechanism with substrate inhibition of H2O2 and product inhibition of esomeprazole, while nonenzymatic reactions, a power law. Those results indicate that SPP with a lower cost and higher thermal stability may be used as an effective substitute for Horseradish Peroxidase.

Enhanced Biotransformation of Carbon Tetrachloride by Acetobacterium woodii upon Addition of Hydroxocobalamin and Fructose

ABSTRACT The objective of this study was to evaluate the effect of hydroxocobalamin (OH-Cbl) on transformation of high concentrations of carbon tetrachloride (CT) by Acetobacterium woodii (ATCC 29683). Complete transformation of 470 μM (72 mg/liter [aqueous]) CT was achieved by A. woodii within 2.5 days, when 10 μM OH-Cbl was added along with 25.2 mM fructose. This was approximately 30 times faster than A. woodii cultures (live or autoclaved) and medium that did not receive OH-Cbl and 5 times faster than those controls that did receive OH-Cbl, but either live A. woodiior fructose was missing. CT transformation in treatments with only OH-Cbl was indicative of the important contribution of nonenzymatic reactions. Besides increasing the rate of CT transformation, addition of fructose and OH-Cbl to live cultures increased the percentage of [14C]CT transformed to 14CO2 (up to 31%) and 14C-labeled soluble materials (principallyl-lactate and acetate), while decreasing the percentage of CT reduced to chloroform and abiotically transformed to carbon disulfide. 14CS2 represented more than 35% of the [14C]CT in the presence of reduced medium and OH-Cbl. Conversion of CT to CO was a predominant pathway in formation of CO2 in the presence of live cells and added fructose and OH-Cbl. These results indicate that the rate and distribution of products during cometabolic transformation of CT by A. woodii can be improved by the addition of fructose and OH-Cbl.