Switching mechanism of a cyclic enzyme system: role as a "chemical diode"

We previously showed with computer simulations that cyclic enzyme systems play a role in metabolic switching events. In the present study, the detailed switching mechanism was investigated by clarifying the relationship between the switching mode and the phase-difference of two sinusoidal inputs to the cyclic enzyme system. The switching time could be predicted theoretically. Half-wave and full-wave rectifications were observed when the phase-difference of two sinusoidal inputs is equal to pi. This result indicates the possibility that this cyclic enzyme system is available for use as a switching circuit (biochip) in a bio-computer.     

Biochemical switching device: monocyclic enzyme system

The switching characteristics of a monocyclic enzyme system, in which two enzymes share substrates or co-factors in a cyclic manner, such as, --> X(1) + B + E(1) right arrow over left arrow A + E(1) + X(2) -->, --> X(3) + A + E(2) right arrow over left arrow B + E(2) + X(4) --> (E(1), E(2) are enzymes, X(1), X(3) are substrates, X(2), X(4) are products, A, B are cofactors), were demonstrated using computer simulations. The detailed mathematical models of biochemically possible cyclic enzyme systems were built up and the effects of rate constants and the effects of initial concentrations of enzymes and cofactors on switching characteristics were discussed. The cyclic enzyme system could function as a switching circuit when the initial concentrations of enzymes or cofactors are over a certain threshold value. Based on the present results, we further discuss the dynamic characteristics of a biochemical reactor system (bioreactor) involving this cyclic enzyme system as a switching controller.     

Biochemical switching device: biomimetic approach and application to neural network study.

There are many examples of enzymes that share substrates or cofactors in a cyclic manner. Techniques have been developed that use cyclic enzyme systems to assay quantitatively small amounts of biochemical substances (cofactor, substrate), however, only a few studies of the control of these systems have been published. The author previously showed with computer simulations that cyclic enzyme systems have the reliability of ON-OFF types of operation (McCulloch-Pitts' neuronic equation) capable of storing short-memory, and the applicability for a switching circuit in a biocomputer. This paper introduces a unique switching mechanism of cyclic enzyme system (basic switching element), and next, building the integrated biochemical switching system being composed of the basic switching element, shows the physiological phenomenon termed 'selective elimination of synapses' generally produced as a result of low-frequency train of electrical stimuli to the synapses (Kuroda, Y. 1989) Neurochem. Int. 14, 309-319).     

Biochemical switching device realizing McCulloch-Pitts type equation

We analyzed cyclic enzyme systems, one of the best candidates for biochemical switching devices, especially focusing on their control mode against external perturbations. Since these systems have the reliability of ON-OFF types of operation (McCulloch-Pitts' neuronic equation), we shall present here the mechanical difference between these systems and electronic switching circuit, especially on the mnemonic mechanism of biochemical switching devices.     

Information flow in heterogeneously interacting systems

Motivated by studies on the dynamics of heterogeneously interacting systems in neocortical neural networks, we studied heterogeneously-coupled chaotic systems. We used information-theoretic measures to investigate directions of information flow in heterogeneously coupled Rössler systems, which we selected as a typical chaotic system. In bi-directionally coupled systems, spontaneous and irregular switchings of the phase difference between two chaotic oscillators were observed. The direction of information transmission spontaneously switched in an intermittent manner, depending on the phase difference between the two systems. When two further oscillatory inputs are added to the coupled systems, this system dynamically selects one of the two inputs by synchronizing, selection depending on the internal phase differences between the two systems. These results indicate that the effective direction of information transmission dynamically changes, induced by a switching of phase differences between the two systems.     

Photothermal Switching of SOI Waveguide-Based Mach-Zehnder Interferometer with Integrated Plasmonic Nanoheater

We theoretically and numerically investigated the photothermal switching of a Mach-Zehnder interferometer (MZI) based on two Si waveguides integrated with plasmonic nanoheaters. The nanoheater is a composite nanowire with Au/Al₂O₃/Au three-layer structure, which is designed to have a highly efficient optical absorption peak at wavelength of 1,064 nm. Based on this finding, we further analyze a MZI built with two 40-μm-long symmetric waveguide branches, each integrated with a 20-μm-long nanoheater. The optical switching power of the MZI device is 190 mW (280 mW) for the capped (buried) channel waveguide, when pumped by a circular Gaussian beam with a waist of 10 μm. Alternatively, the switching power can be reduced to 38 mW (56 mW) by using an astigmatic Gaussian beam, with a semi-major axis of 10 μm and an aspect ratio of 5. The switching response time of the MZI is 0.7 μs (1.0 μs) for capped (buried) channel waveguide design. Our design opens a new route for optically driven non-contact optical on-off switching with sub-microsecond time response.     

Rapid restriction map constructions using a modified pWE15 cosmid vector and a robotic workstation

This paper describes a number of techniques for rapid restriction mapping of cosmid clones. First, we have replaced the cloning site of cosmid vector pWE15 with a polylinker containing 15 infrequently cleaved restriction enzyme sites that are placed asymmetrically on each side of the BamHI cloning site. DNA cloned into this vector can be fully recovered by using several pairs of restriction enzymes. Second, we have designed a simple electrical circuit device that allows the performance of asymmetric voltage gradient field inversion gel electrophoresis (AFIGE) to improve the resolution of DNA molecules in the range of 20-50 kbp. AFIGE can be obtained by simply placing the device in between a commercially available switching unit and the gel box in a standard field inversion system. Finally, the restriction digestion procedure has been automated by using a Beckman Biomek 1000 robotic workstation. Using this automated system, 96 restriction reactions, including gel loading, can be performed in less than two hours. In summary, these methods represent at least a tenfold improvement in the speed and/or mapping data that can be obtained in a single gel.     

Multi-bit biomemory consisting of recombinant protein variants, azurin

In this study a protein-based multi-bit biomemory device consisting of recombinant azurin with its cysteine residue modified by site-directed mutagenesis method has been developed. The recombinant azurin was directly immobilized on four different gold (Au) electrodes patterned on a single silicon substrate. Using cyclic voltammetry (CV), chronoamperometry (CA) and open circuit potential amperometry (OCPA) methods the memory function of the fabricated biodevice was validated. The charge transfer occurs between protein molecules and Au electrode enables a bi-stable electrical conductivity allowing the system to be used as a digital memory device. Data storage is achieved by applying redox potentials which are within the range of 200mV. Oxidation and open circuit potentials with current sensing were used for writing and reading operations respectively. Applying oxidation potentials in different combinations to each Au electrodes, multi-bit information was stored in to the azurin molecules. Finally, the switching robustness and reliability of the proposed device has been examined. The results suggest that the proposed device has a function of memory and can be used for the construction of nano-scale multi-bit information storage device.     

Robustness in Escherichia coli Glutamate and Glutamine Synthesis Studied by a Kinetic Model

Metabolic control of glutamine and glutamate synthesis from ammonia and oxoglutarate in Escherichia coli is tight and complex. In this work, the role of glutamine synthetase (GS) and glutamate dehydrogenase (GDH) regulation in this control was studied. Both enzymes form a linear pathway, which can also have a cyclic topology if glutamate–oxoglutarate amino transferase (GOGAT) activity is included. We modelled the metabolic pathways in the linear or cyclic topologies using a coupled nonlinear differential equations system. To simulate GS regulation by covalent modification, we introduced a relationship that took into account the levels of oxoglutarate and glutamine as signal inputs, as well as the ultrasensitive response of enzyme adenylylation. Thus, by including this relationship or not, we were able to model the system with or without GS regulation. In addition, GS and GDH activities were changed manually. The response of the model in different stationary states, or under the influence of N-input exhaustion or oscillation, was analyzed in both pathway topologies. Our results indicate a metabolic control coefficient for GDH ranging from 0.94 in the linear pathway with GS regulation to 0.24 in the cyclic pathway without regulation, employing a default GDH concentration of 8 μM. Thus, in these conditions, GDH seemed to have a high degree of control in the linear pathway while having limited influence in the cyclic one. When GS was regulated, system responses to N-input perturbations were more sensitive, especially in the cyclic pathway. Furthermore, we found that effects of regulation against perturbations depended on the relative values of the glutamine and glutamate output first-order kinetic constants, which we named k ₆ and k ₇, respectively. Effects of regulation grew exponentially with a factor around 2, with linear increases of (k ₇???k ₆). These trends were sustained but with lower differences at higher GS concentration. Hence, GS regulation seemed important for metabolic stability in a changing environment, depending on the cell’s metabolic status.     

Adenylate cyclase is required for chemotaxis to phosphotransferase system sugars by Escherichia coli.

We report that in Escherichia coli, chemotaxis to sugars transported by the phosphotransferase system is mediated by adenylate cyclase, the nucleotide cyclase linked to the phosphotransferase system. We conclude that adenylate cyclase is required in this chemotaxis pathway because mutations in the cyclase gene (cya) eliminate or impair the response to phosphotransferase system sugars, even though other components of the phosphotransferase system known to be required for the detection of these sugars are relatively unaffected by such mutations. Moreover, merely supplying the mutant bacteria with the products of this enzyme, cyclic AMP and cyclic GMP, does not restore the chemotactic response. Because a residual chemotactic response is observed in certain strains with residual cyclic GMP synthesis but no cyclic AMP synthesis, it appears that the guanylate cyclase activity rather than the adenylate cyclase activity of the enzyme may be required for chemotaxis to sugars transported by the phosphotransferase system. Mutations in the cyclic nucleotide phosphodiesterase gene, which increase the level of both cyclic AMP and cyclic GMP, also reduce chemotaxis to these sugars. Therefore, it appears that control of the level of a cyclic nucleotide is critical for the chemotactic response to phosphotransferase system sugars.     

Coexistence of species in a defensive switching model

We consider a simple mathematical model of two-predators and one-prey system which has the defensive switching property of predation-avoidance. We assume that the prey remains vigilant against relatively abundant predator species and guards against it by switching to another (relatively rare) predator species. We analyze how the intensity of defensive switching affects the stability of the model system. It is seen that the system generally has a stable three species coexisting equilibrium state. In the special case that the intensity of defensive switching equals one and the two predators have the same mortality rates, it is shown that the system asymptotically settles to a Volterra's oscillation in three-dimensional space. It is observed that a sufficiently small or sufficiently large value of intensity of defensive switching can make the system unstable. Finally, it is shown that the handling time may have a stabilizing effect on predator-prey systems with defensive switching.     

Flow-injection-type biosensor system for salivary amylase activity

The authors aim to establish a method that can quantitatively evaluate vital reactions to stress. We have been examining the correlation between stress and salivary amylase activity in order to verify its validity as a stress index. In order to quantify human stress, which changes over time, the relationship between stress and salivary amylase activity must be verified by fast and repeated analysis of salivary amylase activity. Standard biosensors are designed such that the enzyme immobilized on an electrode (enzyme electrode) and the substrate-dependent activity is measured. The reverse approach of measuring the alpha-amylase-dependent activity was adopted. We fabricated an amylase activity analytical system. Maltopentaose was selected as a substrate for alpha-amylase and a flow-injection-type device was used to supply maltopentaose continuously. alpha-Glucosidase, having relatively low enzyme activity, was immobilized on a pre-activated membrane so that it could be enclosed in a pre-column, Glucose oxidase, having higher enzyme activity, was immobilized on a working electrode so that it could function as an amperometric biosensor. A saliva-collecting device was fabricated to make saliva pretreatment unnecessary. As a result, an amylase activity analytical system was fabricated that enabled us to measure salivary amylase activity from 0 to 30 kU/l, with an R(2) value of 0.97. The time-course changes in the salivary amylase activities for 1 week were 5.1%, and the initial sensitivity remained nearly constant. Through this study, we were able to verify the possible development of the amylase activity analytical system.     

Effect of catabolite repression on the mer operon

The plasmid-determined mer operon, which provides resistance to inorganic mercury compounds, was subject to a 2.5-fold decrease in expression when glucose was administered at the same time as the inducer HgCl2. This glucose-mediated transient repression of the operon was overcome by the addition of cyclic AMP. Permanent catabolite repression of the operon was observed in the 1.6- to 1.9-fold decrease in expression in mutants lacking either adenyl cyclase (cya) or the catabolite activator protein (crp). The effect of the cya mutation on mer expression could be overcome by the addition of cyclic AMP at the time of induction, In addition to these effects on the whole cells of a wild-type strains, we examined the effect of catabolite repression on the expression of the mercuric ion [Hg(II)] reductase enzyme, assayable in cell extracts, and on the Hg(II) uptake system, assayable in a mutant strain which lacked reductase activity. There was a two- to threefold effect of repression on the Hg(II) reductase enzyme assayable in vitro after induction under catabolite repressing conditions (either with glucose or in the crp and cya mutants). We did not find a similar repressing effect on the induction of the Hg(II) uptake system, which is also determined by the mer operon.     

A biosensor for the determination of amylase activity

A new biosensing flow injection method for the determination of alpha-amylase activity has been introduced. The method is based on the analysis of maltose produced during the hydrolysis of starch in the presence of alpha-amylase. Maltose determination in the flow system was allowed by the application of peroxide electrode equipped with an enzyme membrane. The membrane was obtained by immobilisation of glucose oxidase, alpha-glucosidase and optionally mutarotase on a cellophane, co-crosslinked by gelatin-glutaraldehyde together with bovine serum albumine. alpha-Glucosidase hydrolyses maltose to alpha-D-glucose, which is converted to beta-D-glucose by mutarotase. beta-D-Glucose is then determined via glucose oxidase. The new biosensor has the limit of detection of 50 nmol l(-1) maltose, which means 2 nkat ml(-1) in alpha-amylase activity units, when the reaction time of amylase was 5 min (determined with respect to a signal-to-noise ratio 3:1). When the reaction time of alpha-amylase was 30 min, the limit of detection was 0.5 nkat ml(-1). A linear range of current response was 0.1-3 mmol l(-1) maltose, with a response time of 35s. The biosensor was stable at least two months and retained 70% of its original activity (with mutarotase the stability is decreased to 3 weeks). When the enzyme membrane was stored in a dry state at 4 degrees C in a refrigerator, the lifetime was approximately 6 months (with mutarotase only 3 months).     

Ca2+-independent cyclic GMP phosphodiesterases from rat liver and HTC hepatoma cells.

We have separated and characterized a Ca2+- and calmodulin-insensitive cyclic nucleotide phosphodiesterase from rat liver supernatant as well as an analogous enzyme from HTC hepatoma cells. Chromatography of rat liver supernatant on DEAE-cellulose in the presence and subsequently in the absence of 0.1 mM-CaCl2 resulted in the separation of two distinct phosphodiesterase activities, both of which preferentially hydrolysed cyclic GMP rather than cyclic AMP. One enzyme, E-Ib, was activated in the presence of Ca2+ and calmodulin, and the other, E-Ia, was not. The E-Ia enzyme, which did not bind to calmodulin-Sepharose, had Mr 325 000 and displayed anomalous kinetic behaviour [Km (cyclic GMP) 1.2 microM; Km (cyclic AMP) 15.4 microM]. The E-Ib enzyme, which bound to calmodulin-Sepharose in the presence of Ca2+, had Mr 150 000 and exhibited Michaelis-Menten kinetics for hydrolysis of cyclic GMP [Km (basal) 6.5 microM; Km (activated) 12.0 microM]. E-Ia activity was diminished by incubation with alpha-chymotrypsin and was unaffected by the action of a rat kidney lysosomal proteinase. Partial hydrolysis of E-Ib enzyme by alpha-chymotrypsin or the kidney proteinase resulted in irreversible activation of the enzyme. The E-I enzyme isolated from HTC hepatoma cells was similar to the rat liver E-Ia enzyme in many respects. Its apparent Mr was 325 000. Its activity was unaffected by calmodulin in the presence of Ca2+ or by incubation with the kidney proteinase, and was decreased by digestion with alpha-chymotrypsin. Unlike the liver E-Ia enzyme, however, the hepatoma enzyme exhibited normal kinetic behaviour, with Km (cyclic GMP) 3.2 microM. Although HTC cells contain two other phosphodiesterases analogous to those in rat liver and a calmodulin-like activator of phosphodiesterase, no calmodulin-sensitive phosphodiesterase was detected.     

Cyclic guanosine 3',5'-monophosphate and phosphodiesterase activity in mitogen-stimulated human lymphocytes.

The cyclic adenosine 3′,5′-monophosphate (cyclic AMP) phosphodiesterase from human leukemic lymphocytes differes from the normal cell enzyme in having a much higher activity and a loss of inhibition by cyclic guanosine 3′,5′-monophosphate (cyclic GMP). In an effort to determine the mechanism of these alterations, we have studied this enzyme in a model system, lectin-stimulated normal human lymphocytes. Following stimulation of cells with concanavalin A (con A) the enzyme activity gradually becomes altered, until it fully resembles the phosphodiesterase found in leukemic lymphocytes. The changes in the enzyme parallel cell proliferation as measured by increases in thymidine incorporation into DNA. The addition of a guanylate cyclase inhibitor preparation from the bitter melon prevents both the changes in the phosphodiesterase and the thymidine incorporation into DNA. This blockage can be partially reversed by addition of 8-bromo cyclic guanosine 3′,5′-monophosphate (8-bromo cyclic GMP) to the con A-stimulated normal lymphocytes. These results indicate a possible role of cyclic GMP in a growth related alteration of cyclic AMP phosphodiesterase.     

Organic matter inputs shift soil enzyme activity and allocation patterns in a wet tropical forest

Soil extracellular enzymes mediate organic matter turnover and nutrient cycling yet remain little studied in one of Earth’s most rapidly changing, productive biomes: tropical forests. Using a long-term leaf litter and throughfall manipulation, we explored relationships between organic matter (OM) inputs, soil chemical properties and enzyme activities in a lowland tropical forest. We assayed six hydrolytic soil enzymes responsible for liberating carbon (C), nitrogen (N) and phosphorus (P), calculated enzyme activities and ratios in control plots versus treatments, and related these to soil biogeochemical variables. While leaf litter addition and removal tended to increase and decrease enzyme activities per gram soil, respectively, shifts in enzyme allocation patterns implied changes in relative nutrient constraints with altered OM inputs. Enzyme activity ratios in control plots suggested strong belowground P constraints; this was exacerbated when litter inputs were curtailed. Conversely, with double litter inputs, increased enzymatic investment in N acquisition indicated elevated N demand. Across all treatments, total soil C correlated more strongly with enzyme activities than soluble C fluxes, and enzyme ratios were sensitive to resource stoichiometry (soil C:N) and N availability (net N mineralization). Despite high annual precipitation in this site (MAP ~5 m), soil moisture positively correlated with five of six enzymes. Our results suggest resource availability regulates tropical soil enzyme activities, soil moisture plays an additional role even in very wet forests, and relative investment in C, N and P degrading enzymes in tropical soils will often be distinct from higher latitude ecosystems yet is sensitive to OM inputs.     

Regulation of transglutaminase activity in Chinese hamster ovary cells

We have investigated the regulation of transglutaminase activity (epsilon-(gamma-glutamyl)lysine crosslinking enzyme) in Chinese hamster ovary cells in culture. We report that transglutaminase activity increases several-fold in CHO cells at maximum density in suspension culture. This increase cannot be explained by the presence of soluble regulators of the enzyme activity or the appearance of a new enzyme activity with a different affinity for substrate, but appears to be due to an increase in total enzyme activity. Treatment of CHO cells at low cell density with 8-bromo cyclic AMP results in a small increase (20--70%) in transglutaminase activity. By studying CHO mutants which have altered or absent cyclic-AMP-dependent protein kinases, we have demonstrated that the effect of cyclic AMP on transglutaminase activity at low cell density is mediated by cyclic-AMP-dependent protein kinase. However, the protein kinase mutants show normal increases in transglutaminase activity at high cell density, indicating that cyclic AMP-dependent protein kinase does not mediate density-dependent changes in transglutaminase activity.