The unique Phe–His dyad of 2-ketopropyl coenzyme M oxidoreductase/carboxylase selectively promotes carboxylation and S–C bond cleavage

The 2-ketopropyl-coenzyme M oxidoreductase/carboxylase (2-KPCC) enzyme is the only member of the disulfide oxidoreductase (DSOR) family of enzymes, which are important for reductively cleaving S–S bonds, to have carboxylation activity. 2-KPCC catalyzes the conversion of 2-ketopropyl-coenzyme M to acetoacetate, which is used as a carbon source, in a controlled reaction to exclude protons. A conserved His–Glu motif present in DSORs is key in the protonation step; however, in 2-KPCC, the dyad is substituted by Phe–His. Here, we propose that this difference is important for coupling carboxylation with C–S bond cleavage. We substituted the Phe–His dyad in 2-KPCC to be more DSOR like, replacing the phenylalanine with histidine (F501H) and the histidine with glutamate (H506E), and solved crystal structures of F501H and the double variant F501H_H506E. We found that F501 protects the enolacetone intermediate from protons and that the F501H variant strongly promotes protonation. We also provided evidence for the involvement of the H506 residue in stabilizing the developing charge during the formation of acetoacetate, which acts as a product inhibitor in the WT but not the H506E variant enzymes. Finally, we determined that the F501H substitution promotes a DSOR-like charge transfer interaction with flavin adenine dinucleotide, eliminating the need for cysteine as an internal base. Taken together, these results indicate that the 2-KPCC dyad is responsible for selectively promoting carboxylation and inhibiting protonation in the formation of acetoacetate.     

Structural basis for CO2 fixation by a novel member of the disulfide oxidoreductase family of enzymes, 2-ketopropyl-coenzyme M oxidoreductase/carboxylase

The NADPH:2-ketopropyl-coenzyme M oxidoreductase/carboxylase (2-KPCC) is the terminal enzyme in a metabolic pathway that results in the conversion of propylene to the central metabolite acetoacetate in Xanthobacter autotrophicus Py2. This enzyme is an FAD-containing enzyme that is a member of the NADPH:disulfide oxidoreductase (DSOR) family of enzymes that include glutathione reductase, dihydrolipoamide dehydrogenase, trypanothione reductase, thioredoxin reductase, and mercuric reductase. In contrast to the prototypical reactions catalyzed by members of the DSOR family, the NADPH:2-ketopropyl-coenzyme M oxidoreductase/carboxylase catalyzes the reductive cleavage of the thioether linkage of 2-ketopropyl-coenzyme M, and the subsequent carboxylation of the ketopropyl cleavage product, yielding the products acetoacetate and free coenzyme M. The structure of 2-KPCC reveals a unique active site in comparison to those of other members of the DSOR family of enzymes and demonstrates how the enzyme architecture has been adapted for the more sophisticated biochemical reaction. In addition, comparison of the structures in the native state and in the presence of bound substrate indicates the binding of the substrate 2-ketopropyl-coenzyme M induces a conformational change resulting in the collapse of the substrate access channel. The encapsulation of the substrate in this manner is reminiscent of the conformational changes observed in the well-characterized CO2-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxidase (Rubisco).     

A catalytic dyad modulates conformational change in the CO2-fixing flavoenzyme 2-ketopropyl coenzyme M oxidoreductase/carboxylase

2-Ketopropyl-coenzyme M oxidoreductase/carboxylase (2-KPCC) is a member of the flavin and cysteine disulfide containing oxidoreductase family (DSOR) that catalyzes the unique reaction between atmospheric CO₂ and a ketone/enolate nucleophile to generate acetoacetate. However, the mechanism of this reaction is not well understood. Here, we present evidence that 2-KPCC, in contrast to the well-characterized DSOR enzyme glutathione reductase, undergoes conformational changes during catalysis. Using a suite of biophysical techniques including limited proteolysis, differential scanning fluorimetry, and native mass spectrometry in the presence of substrates and inhibitors, we observed conformational differences between different ligand-bound 2-KPCC species within the catalytic cycle. Analysis of site-specific amino acid variants indicated that 2-KPCC-defining residues, Phe501-His506, within the active site are important for transducing these ligand induced conformational changes. We propose that these conformational changes promote substrate discrimination between H⁺ and CO₂ to favor the metabolically preferred carboxylation product, acetoacetate.     

Prebiotic syntheses of vitamin coenzymes: I. Cysteamine and 2-mercaptoethanesulfonic acid (coenzyme M)

Summary The reaction of NH₃ and SO _sup2– ^inf3 with ethylene sulfide is shown to be a prebiotic synthesis of cysteamine and 2-mercaptoethanesulfonic acid (coenzyme M). A similar reaction with ethylene imine would give cysteamine and taurine. Ethylene oxide would react with NH3 and N(CH₃)₃ to give the phospholipid components ethanolamine and choline. The prebiotic sources of ethylene sulfide, ethylene imine and ethylene oxide are discussed. Cysteamine itself is not a suitable thioester for metabolic processes because of acyl transfer to the amino group, but this can be prevented by using an amide of cysteamine. The use of cysteamine in coenzyme A may have been due to its prebiotic abundance. The facile prebiotic synthesis of both cysteamine and coenzyme M suggests that they were involved in very early metabolic pathways. Offprint requests to: S.L. Miller     

Structural basis for the alteration of coenzyme specificity in a malate dehydrogenase mutant

To elucidate the structural basis for the alteration of coenzyme specificity from NADH toward NADPH in a malate dehydrogenase mutant EX7 from Thermus flavus, we determined the crystal structures at 2.0 A resolution of EX7 complexed with NADPH and NADH, respectively. In the EX7-NADPH complex, Ser42 and Ser45 form hydrogen bonds with the 2'-phosphate group of the adenine ribose of NADPH, although the adenine moiety is not seen in the electron density map. In contrast, although Ser42 and Ser45 occupy a similar position in the EX7-NADH complex structure, both the adenine and adenine ribose moieties of NADH are missing in the map. These results and kinetic analysis of site-directed mutant enzymes indicate (1) that the preference of EX7 for NADPH over NADH is ascribed to the recognition of the 2'-phosphate group by two Ser and Arg44, and (2) that the adenine moiety of NADPH is not recognized in this mutant.     

Stimulation of the methyltetrahydromethanopterin: coenzyme M methyltransferase reaction in cell-free extracts of Methanobacterium thermoautotrophicum by the heterodisulfide of coenzyme M and 7-mercaptoheptanoylthreonine phosphate

The conversion of formaldehyde to methylcoenzyme M in cell-free extracts of Methanobacterium thermoautotrophicum was stimulated up to 10-fold by catalytic amounts of the heterodisulfide (CoM-S-S-HTP) of coenzyme M and 7-mercaptoheptanoylthreonine phosphate. The stimulation required the additional presence of ATP, also in catalytic concentrations. ATP and CoM-S-S-HTP were mutually stimulatory on the methylcoenzyme M formation and it was concluded that the compounds were both involved in the reductive activation of the methyltetrahydromethanopterin: coenzyme M methyltransferase. Micromolar concentrations of benzyl viologen or cyanocobalamin inhibited the formaldehyde conversion; these compounds, however, strongly stimulated the reduction of CoM-S-S-HTP. The results described here closely resemble observations made on the activation and reduction of CO₂ to formylmethanofuran indicating that this step and the reductive activation of the methyltransferase are controlled by some common mechanism.Abbreviations HS-CoM Coenzyme M, 2-mercaptoethanesulfonate - CH₃S-CoM methylcoenzyme M, 2-(methylthio)ethanesulfonate - H₄MPT 5,6,7,8-tetrahydromethanopterin - MFR methanofuran - HS-HTP 7-mercaptoheptanoylthreonine phosphate - CoM-S-S-HTP the heterodisulfide of HS-CoM and HS-HTP - BES 2-bromoethanesulfonate - TES N-tris(hydroxymethyl)methyl-2-aminoethanesulfonate - CN-Cbl cyanocobalamin - HO-Cbl hydroxycobalamin - HBI 5-hydroxybenzimidazole - DMBI 5,6-dimethylbenzimidazole     

Control of the circadian rhythm of carbon dioxide assimilation in Bryophyllum leaves by exposure to darkness and high carbon dioxide concentrations

The circadian rhythm of CO₂ assimilation in detached leaves of Bryophyllum fedtschenkoi at 15° C in normal air and continuous illumination is inhibited both by exposure to darkness, and to an atmosphere enriched with 5% CO₂. During such exposures substantial fixation of CO₂ takes place, and the malate concentration in the cell sap increases from about 20 mM to a constant value of 40–50 mM after 16 h. On transferring the darkened leaves to light, and those exposed to 5% CO₂ to normal air, a circadian rhythm of CO₂ assimilation begins again. The phase of this rhythm is determined by the time the transfer is made since the first peak occurs about 24 h afterwards. This finding indicates that the circadian oscillator is driven to, and held at, an identical, fixed phase point in its cycle after 16 h exposure to darkness or to 5% CO₂, and it is from this phase point that oscillation begins after the inhibiting condition is removed. This fixed phase point is characterised by the leaves having acquired a high malate content. The rhythm therefore begins with a period of malate decarboxylation which lasts for about 8 h, during which time the malate content of the leaf cells must be reduced to a value that allows phosphoenolpyruvate carboxylase to become active. Inhibition of the rhythm in darkness, and on exposure to 5% CO₂ in continuous illumination, appears to be due to the presence of a high concentration of CO₂ within the leaf inhibiting malic enzyme which leads to the accumulation of high concentrations of malate in the leaf cells. The malate then allosterically inhibits phosphoenolpyruvate carboxylase upon which the rhythm depends. The results give support to the view that malate synthesis and breakdown form an integral part of the circadian oscillator in this tissue.Abbreviations B. Bryophyllum - PEPCase phosphoenolpyruvate carboxylase     

Studies on the anesthetic mechanism of carbon dioxide by using Bombyx mori larvae.

The study of heartbeat variations of Bombyx mori larvae submitted to CO2 narcosis has provided new information on carbon dioxide anesthesia. Purely anoxiant action must be dismissed. Action at a nerve level is possible since CO2 produces the same effect as ether, which is a classical anesthetic.     

Biomass production and carbon dioxide fixation by Aphanothece microscopica Nägeli in a bubble column photobioreactor

The objective of the present study was to evaluate the growth kinetics of Aphanothece microscopica Nägeli under different conditions of temperature, light intensity and CO₂ concentration. The growth kinetics of the microorganism and carbon biofixation were evaluated using a central composite design, considering five different temperature levels (21.5, 25, 30, 35 and 38.5 °C), light intensities (0.96, 3, 6, 9 and 11 klux) and carbon dioxide concentrations (3, 15, 25, 50 and 62%). The results obtained showed the effects of temperature, light intensity and CO₂ concentration (p < 0.05) on the photosynthetic metabolism of the microorganism. Response surface methodology was adequate for process optimisation, providing a carbon fixation rate to the order of 109.2 mg L⁻¹ h⁻¹ under conditions of 11 klux, 35 °C and 15% carbon dioxide, representing an increase of 58.1% as compared to the conditions tested initially.     

Immobilization of D-ribulose-1,5-bisphosphate carboxylase/oxygenase: a step toward carbon dioxide fixation bioprocess

Immobilization of D-ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from spinach leaves is described. This enzyme enables the fixation of carbon dioxide on a five-carbon sugar D-ribulose-1,5-bisphosphate (RuBP). Two different immobilization methods were employed: dicyclohexylcarbodiimide coupling on nylon membrane matrix and dimethylpimelimidate immobilization on protein A agarose. The reusability of immobilized enzymes, coupling efficiency, and temperature-activity relationship of soluble and immobilized Rubisco are presented. The immobilization imparted greater thermal and storage stability. The thermal deactivation rates of the immobilized enzymes were considerably lower than those of the soluble enzyme.     

Fluxes of dissolved carbon dioxide and inorganic carbon from an upland peat catchment: implications for soil respiration

This study uses long-term water chemistry records for a circum-neutral peat stream to reconstruct a 7-year record of dissolved CO₂ and DIC flux from the catchment. Combining catchment flux with a knowledge of in-stream metabolism and gas evasion from the stream surface enables an estimate of the dissolved CO₂ content of water emerging from the peat profile to be made; furthermore, these can be used to estimate soil CO₂ respiration. In this way multi-annual records of CO₂ production can be reconstructed, and therefore inter-annual controls on production examined. The results suggest that:(i) Stream evasion of CO₂ within the catchment varied between 80 and 220 g C/m of stream/yr, while in-stream metabolism produces between 1.0 and 2.9 g C/m of stream/yr;Export of dissolved CO₂ emerging from the soil profile, above that expected at equilibrium with the atmosphere, varies between 9.6 and 25.6 tonnes,C/km²/yr; andThe export of dissolved CO₂ implies a soil respiration rate of between 64.2 and 94.9 tonnes C/km²/yr.The inter-annual variation in both dissolved CO₂ flux and soil CO₂ respiration suggests that severe drought has no long-term effect on CO₂ production and that temperature-based models of soil CO₂ respiration will be adequate in all but the severest of summer droughts. The inter-annual variation in CO₂ flux shows that CO₂ production is decoupled from dissolved organic carbon (DOC) production. The decoupling of DOC and dissolved CO₂ production shows that enzymatic-latch production of DOC is an anaerobic process and will not increase soil CO₂ respiration.     

An automated technique for monitoring carbon dioxide respired by insects*

ABSTRACT. A non-dispersive infrared gas analyser equipped with a Luft-type sonic detector and flow-through reference cell was automated to monitor the total volume of carbon dioxide (CO₂) respired by single insects or groups of insects. The infrared analyser was interfaced with an integrator for quantification, a microprocessor to control intermittent air flow through the insect respiration chambers, and a microcomputer for data storage and reduction. This technique has been used to monitor the CO₂ Output of diapausing and non-diapausing mature fifth instar larvae and of developing pupae of the codling moth, Cydia pomonella (L.) (Lepidoptera: Tortricidae). The resulting data were accurate, quantitative and reproducible.     

Elevated carbon dioxide concentrations indirectly affect plant fitness by altering plant tolerance to herbivory

Global environmental changes, such as rising atmospheric CO₂ concentrations, have a wide range of direct effects on plant physiology, growth, and fecundity. These environmental changes also can affect plants indirectly by altering interactions with other species. Therefore, the effects of global changes on a particular species may depend on the presence and abundance of other community members. We experimentally manipulated atmospheric CO₂ concentration and amounts of herbivore damage (natural insect folivory and clipping to simulate browsing) to examine: (1) how herbivores mediate the effects of elevated CO₂ (eCO₂) on the growth and fitness of Arabidopsis thaliana; and (2) how predicted changes in CO₂ concentration affect plant resistance to herbivores, which influences the amount of damage plants receive, and plant tolerance of herbivory, or the fitness consequences of damage. We found no evidence that CO₂ altered resistance, but plants grown in eCO₂ were less tolerant of herbivory—clipping reduced aboveground biomass and fruit production by 13 and 22%, respectively, when plants were reared under eCO₂, but plants fully compensated for clipping in ambient CO₂ (aCO₂) environments. Costs of tolerance in the form of reduced fitness of undamaged plants were detected in eCO₂ but not aCO₂ environments. Increased costs could reduce selection on tolerance in eCO₂ environments, potentially resulting in even larger fitness effects of clipping in predicted future eCO₂ conditions. Thus, environmental perturbations can indirectly affect both the ecology and evolution of plant populations by altering both the intensity of species interactions as well as the fitness consequences of those interactions.     

Control of photosynthetic carbon dioxide fixation by the boundary layer, stomata and ribulose 1,5-biphosphate carboxylase/oxygenase

Abstract Coefficients describing the sensitivity of the rate of photosynthetic carbon dioxide fixation to small changes in the stomatal conductance and boundary layer conductance are derived. These sensitivity or ‘control’ coefficients, together with those for the carboxylase and oxygenase activities of ribulose 1,5-bisphosphate carboxylase/oxygenase, are calculated from standard gas exchange data and apply under conditions where leaf temperature and water vapour concentration at the leaf surface remain largely constant. It is shown that the magnitude of the control coefficients depends on conditions such as photon flux density, ambient CO₂ concentration and relative humidity at the leaf surface. The extension of this analysis to encompass the sensitivity of the photosynthetic fluxes to changes in enzyme concentrations and kinetic properties is also discussed.     

Inhibition by coenzyme Q of ethanol- and carbon tetrachloride-stimulated lipid peroxidation in vivo and catalyzed by microsomal and mitochondrial systems

The ability of coenzyme Q to inhibit lipid peroxidation in intact animals as well as in mitochondrial, submitochondrial, and microsomal systems has been tested. Rats fed coenzyme Q prior to being treated with carbon tetrachloride or while being treated with ethanol excrete less thiobarbituric acid-reacting material in the urine than such rats not fed coenzyme Q. Liver homogenates, mitochondria, and microsomes isolated from rats treated with carbon tetrachloride and ethanol catalyze lipid peroxidation at rates which exceed those from animals also fed coenzyme Q. The rate of lipid peroxidation catalyzed by submitochondrial particles isolated from hearts of young, old, and endurance trained elderly rats was inversely proportional to the coenzyme Q content of the submitochondrial preparation in assays in which succinate was employed to reduce the endogenous coenzyme Q. Reduced, but not oxidized, coenzyme Q inhibited lipid peroxidation catalyzed by rat liver microsomal preparations. These results provide additional evidence in support of an antioxidant role for coenzyme Q.     

Importance of carbon dioxide for the cultivation of Thermoactinomyces vulgaris from spores

Thermoactinomyces vulgaris has been used for the production of the serine protease Thermitase [EC 3.4.21.14] by fermentation. Spore germination of this strain is influenced by the gas composition of the medium. Since the outgrowth of the germ tubes occurs only in the presence of a raised CO₂ concentration, the cultivation in aerated stirred fermenters is not reproducible. However, if cultivation takes place in a closed fermentation system, initially unaerated, in which the CO₂ formed by spore respiration accumulates, reproducible germination can be obtained. From an O₂-balance, indirect conclusions can be drawn with regard to the effect of CO₂, and the process of germination can be described. The cultivation method described permits almost complete germination of all inoculated spores and reproducible rates of biomass and enzyme production in the subsequent fermentation. Thus, stabilization of the procedure with increased enzyme yields is ensured.     

Calculation of diffusion coefficient for supercritical carbon dioxide and carbon dioxide+naphthalene system by molecular dynamics simulation using EPM2 model

NVT ensemble molecular dynamics (MD) simulation has been applied to calculate the self-diffusion coefficients of carbon dioxide and the tracer diffusion coefficients of naphthalene in supercritical carbon dioxide. The simulation was carried out in the pressure range from 8 to 40 MPa. The elementary physical model proposed by Harris and Yung was adopted for carbon dioxide and some approximation models were used for naphthalene. The systems of MD simulation for carbon dioxide consist of 256 particles. One naphthalene molecule was added for carbon dioxide+naphthalene system. The system can be assumed to be an infinite dilution condition for carbon dioxide+naphthalene system and the mutual diffusion coefficients are equal to the tracer diffusion coefficients of naphthalene. The self-diffusion coefficients of carbon dioxide and the tracer diffusion coefficients of naphthalene in supercritical carbon dioxide can be calculated by mean square displacement. The calculated results of diffusion coefficients showed good agreement with the experimental data without adjustable parameters.