Arsenate, arsenite and dimethyl arsinic acid (DMA) uptake and tolerance in maize (Zea mays L.)

The influx of arsenate, arsenite and dimethyl arsinic acid (DMA) were studied in 7-day-old excised maize roots (Zea mays L.), and then related to arsenate, arsenite and DMA toxicity. Arsenate, arsenite and DMA influx was all found concentration dependent with significant genotypic differences for arsenite and DMA. Arsenate influx in phosphate starved plants best fitted the four-parameter Michaelis–Menten model corresponding to an additive high and low affinity uptake system, while the uptake of phosphate replete plants followed the two parameter model of Michaelis–Menten kinetics. Arsenite influx was well described by the two parameter model of ‘Michaelis–Menten’ kinetics. DMA influx was comprised of linear phase and a hyperbolic phase. DMA influx was much lower than that for arsenite and arsenate. Arsenate and DMA influx decreased when phosphate was given as a pre-treatment as opposed to phosphate starved plants. The +P treatment tended to decrease influx by 50% for arsenate while this figure was 90% for DMA. Arsenite influx increasing slightly at higher arsenite concentrations in P starved plants but at lower arsenite concentrations, there was little or no difference in arsenite uptake. Low toxicity was found for DMA on maize compared with arsenate and arsenite and the relative toxicity of arsenic species was As(V) > As(III) >> DMA.     

Organic acids enhance the uptake of lead by wheat roots

The uptake and bioavailability of lead (Pb) in soil–plant systems remain poorly understood. This study indicates that acetic and malic acids enhance the uptake of Pb by wheat (Triticum aestivum L.) roots under hydroponic conditions. The net concentration-dependent uptake influx of Pb in the presence and absence of organic acids was characterized by Michaelis–Menten type nonsaturating kinetic curves that could be resolved into linear and saturable components. Fitted maximum uptake rates (V _max) of the Michaelis–Menton saturable component in the presence of acetic and malic acids were, respectively, 2.45 and 1.63 times those of the control, while the Michaelis–Menten K _m values of 5.5, 3.7 and 2.2 μM, respectively, remained unchanged. Enhanced Pb uptake by organic acids was partially mediated by Ca²⁺ and K⁺ channels, and also depended upon the physiological function of the plasma membrane P-type ATPase. Uptake may have been further enhanced by an effectively thinner unstirred layer of Pb adjacent to the roots, leading to more rapid diffusion towards roots. X-ray absorption spectroscopic studies provided evidence that the coordination environment of Pb in wheat roots was similar to that of Pb(CH₃COO)₂·3H₂O in that one Pb atom was coordinated to four oxygen atoms via the carboxylate group.     

A method to describe enzyme-catalyzed reactions by combining steady state and time course enzyme kinetic parameters

Background

Complete analysis of single substrate enzyme-catalyzed reactions has required a separate use of two distinct approaches. Steady state approximations are employed to obtain substrate affinity and initial velocity information. Alternatively, first order exponential decay models permit simulation of the time course data for the reactions. Attempts to use integrals of steady state equations to describe reaction time courses have so far met with little success.

Methods

Here we use equations based on steady state approximations to directly model time course plots.

Results

Testing these expressions with the enzyme β-galactosidase, which adheres to classical Michaelis–Menten kinetics, produced a good fit between observed and calculated values.

General significance

This study indicates that, in addition to providing information on initial kinetic parameters, steady state approximations can be employed to directly model time course kinetics.Integrated forms of the Michaelis–Menten equation have previously been reported in the literature. Here we describe a method to directly apply steady state approximations to time course analysis for predicting product formation and simultaneously obtain multiple kinetic parameters.     

A hydrogen peroxide biosensor based on the direct electrochemistry of hemoglobin modified with quantum dots

Direct electron transfer of hemoglobin modified with quantum dots (QDs) (CdS) has been performed at a normal graphite electrode. The response current is linearly dependent on the scan rate, indicating the direct electrochemistry of hemoglobin in that case is a surface-controlled electrode process. UV–vis spectra suggest that the conformation of hemoglobin modified with CdS is little different from that of hemoglobin alone, and the conformation changes reversibly in the pH range 3.0–10.0. The hemoglobin in a QD film can retain its bioactivity and the modified electrode can work as a hydrogen peroxide biosensor because of its peroxidase-like activity. This biosensor shows an excellent response to the reduction of H₂O₂ without the aid of an electron mediator. The catalytic current shows a linear dependence on the concentration of H₂O₂ in the range 5 × 10⁻⁷–3 × 10⁻⁴ M with a detection limit of 6 × 10⁻⁸ M. The response shows Michaelis–Menten behavior at higher H₂O₂ concentrations and the apparent Michaelis–Menten constant is estimated to be 112 μM.     

Catecholase activity of a μ-hydroxodicopper(II) macrocyclic complex: structures, intermediates and reaction mechanism

The monohydroxo-bridged dicopper(II) complex (1), its reduced dicopper(I) analogue (2) and the trans-μ-1,2-peroxo-dicopper(II) adduct (3) with the macrocyclic N-donor ligand [22]py4pz (9,22-bis(pyridin-2′-ylmethyl)-1,4,9,14,17,22,27,28,29,30- decaazapentacyclo -[22.2.1^14,7.1^11,14.1^17,20]triacontane-5,7(28),11(29),12,18,20(30), 24(27),25-octaene), have been prepared and characterized, including a 3D structure of 1 and 2. These compounds represent models of the three states of the catechol oxidase active site: met, deoxy (reduced) and oxy. The dicopper(II) complex 1 catalyzes the oxidation of catechol model substrates in aerobic conditions, while in the absence of dioxygen a stoichiometric oxidation takes place, leading to the formation of quinone and the respective dicopper(I) complex. The catalytic reaction follows a Michaelis–Menten behavior. The dicopper(I) complex binds molecular dioxygen at low temperature, forming a trans-μ-1,2-peroxo-dicopper adduct, which was characterized by UV–Vis and resonance Raman spectroscopy and electrochemically. This peroxo complex stoichiometrically oxidizes a second molecule of catechol in the absence of dioxygen. A catalytic mechanism of catechol oxidation by 1 has been proposed, and its relevance to the mechanisms earlier proposed for the natural enzyme and other copper complexes is discussed. Electronic Supplementary Material Supplementary material is available for this article at     

Observed quasi-steady kinetics of yeast cell growth and ethanol formation under very high gravity fermentation condition

Using a generalSaccharomyces cerevisiae as a model strain, continuous ethanol fermentation was carried out in a stirred tank bioreactor with a working volume of 1,500 mL. Three different gravity media containing glucose of 120, 200 and 280 g/L, respectively, supplemented with 5 g/L yeast extract and 3 g/L peptone, were fed into the fermentor at different dilution rates. Although complete steady states developed for low gravity medium containing 120 g/L glucose, quasi-steady states and oscillations of the fermented parameters, including residual glucose, ethanol and biomass were observed when high gravity medium containing 200 g/L glucose and very high gravity medium containing 280 g/L glucose were fed at the designated dilution rate of 0.027 h⁻¹. The observed quasi-steady states that incorporated these steady states, quasi-steady states and oscillations were proposed as these oscillations were of relatively short periods of time and their averages fluctuated up and down almost symmetrically. The continuous kinetic models that combined both the substrate and product inhibitions were developed and correlated for these observed quasi-steady states.     

Spectrophotometric assay for detection of aromatic hydroxylation catalyzed by fungal haloperoxidase–peroxygenase

Agrocybe aegerita peroxidase (AaP) is a versatile heme-thiolate protein that can act as a peroxygenase and catalyzes, among other reactions, the hydroxylation of aromatic rings. This paper reports a rapid and selective spectrophotometric method for directly detecting aromatic hydroxylation by AaP. The weakly activated aromatic compound naphthalene served as the substrate that was regioselectively converted into 1-naphthol in the presence of the co-substrate hydrogen peroxide. Formation of 1-naphthol was followed at 303 nm (ɛ ₃₀₃ = 2,010 M⁻¹ cm⁻¹), and the apparent Michaelis–Menten (K _m) and catalytic (k _cat) constants for the reaction were estimated to be 320 μM and 166 s⁻¹, respectively. This method will be useful in screening of fungi and other microorganisms for extracellular peroxygenase activities and in comparing and assessing different catalytic activities of haloperoxidase–peroxygenases.     

Active Silicon Uptake by Wheat

The absorption of Si by wheat, Triticum aestivum L. ‘Yecora Rojo,’ followed Michaelis–Menten kinetics over a concentration range of 0.004–1.0 mM. K_m and V_max were determined using linear transformations and the calculated curve fitted the data closely. The absorption resulted in accumulation ratios of 200/1 or more. In keeping with that finding, this study also demonstrated that Si uptake by wheat is under metabolic control, being severely restricted by dinitrophenol (DNP) and potassium cyanide (KCN). Silicon uptake by wheat was not significantly affected by phosphate ions, but the chemical analog Ge exerted a direct competitive effect on Si uptake, and vice versa.     

Esterification of phenolic acids catalyzed by lipases immobilized in organogels

Lipases from Rhizomucor miehei and Candida antarctica B were immobilized in hydroxypropylmethyl cellulose organogels based on surfactant-free microemulsions consisting of n-hexane, 1-propanol and water. Both lipases kept their catalytic activity, catalyzing the esterification reactions of various phenolic acids including cinnamic acid derivatives. High reaction rates and yields (up to 94%) were obtained when lipase from C. antarctica was used. Kinetic studies have been performed and apparent kinetic constants were determined showing that ester synthesis catalyzed by immobilized lipases occurs via the Michaelis–Menten mechanism.     

Influence of synthetic packing materials on the gas dispersion and biodegradation kinetics in fungal air biofilters

The biodegradation of toluene was studied in two lab-scale air biofilters operated in parallel, packed respectively with perlite granules (PEG) and polyurethane foam cubes (PUC) and inoculated with the same toluene-degrading fungus. Differences on the material pore size, from micrometres in PEG to millimetres in PUC, were responsible for distinct biomass growth patterns. A compact biofilm was formed around PEG, being the interstitial spaces progressively filled with biomass. Microbial growth concentrated at the core of PUC and the excess of biomass was washed-off, remaining the gas pressure drop comparatively low. Air dispersion in the bed was characterised by tracer studies and modelled as a series of completely stirred tanks (CSTR). The obtained number of CSTR (n) in the PEG packing increased from 33 to 86 along with the applied gas flow (equivalent to empty bed retention times from 48 to 12 s) and with operation time (up to 6 months). In the PUC bed, n varied between 9 and 13, indicating that a stronger and steadier gas dispersion was achieved. Michaelis–Menten half saturation constant (k _m) estimates ranged 71–113 mg m⁻³, depending on the experimental conditions, but such differences were not significant at a 95% confidence interval. The maximum volumetric elimination rate (r _m) varied from 23 to 50 g m⁻³ h⁻¹. Comparison between volumetric and biomass specific biodegradation activities indicated that toluene mass transfer was slower with PEG than with PUC as a consequence of a smaller biofilm surface and to the presence of larger zones of stagnant air.     

Logical identification of all steady states: The concept of feedback loop characteristic states

Biological regulatory systems can be described in terms of non-linear differential equations or in logical terms (using an “infinitely non-linear” approximation). Until recently, only part of the steady states of a system could be identified on logical grounds. The reason was that steady states frequently have one or more variable located on a threshold (see below); those steady states were not detected because so far no logical status was assigned to threshold values. This is why we introduced logical scales with values 0,¹θ, 1²θ, 2, ..., in which¹θ,²θ, ... are the logical values assigned to the successive thresholds of the scale. We thus have, in addition to the regular logical states,singular states in which one or more variables is located on a threshold. This permits identifyingall the steady states on logical grounds. It was noticed that each feedback loop (or reunion of disjointed loops) can be characterized by a logical state located at the thresholds at which the variables of the loop operate. This led to the concept ofloop-characteristic state, which, as we will see, enormously simplifies the analysis.The core of this paper is a formal demonstration that among the singular states of a system, only loop-characteristic states can be steady. Reciprocally, given a loop-characteristic state, there are parameter values for which this state is steady; in this case, the loop is effective (i.e. it generates multistationarity if it is a positive loop, homeostasis if it is a negative loop). This not only results in the above-mentioned radical simplification of the identification of the steady states, but in an entirely new view of the relation between feedback loops and steady states.     

Predicting radiocaesium root uptake based on potassium uptake parameters. A mechanistic approach

This paper describes the application of a mechanistic model in the study of radionuclide soil–plant transfer and the obtainment of predictive estimates of radionuclide plant contamination. Soil–plant K and ¹³⁴Cs transfer rates were measured and compared with those predicted by the Barber–Cushman model. The experiment was performed on pea plants grown in pots and in two different types of soil (Calcic Luvisol and Fluvisol). For K, model predictions proved valid for all development stages sampled; for ¹³⁴Cs, the quality of the prediction depended on the plant stage. In both, parameter estimates varied depending on plant age and soil type. The model was also run for ¹³⁴Cs using the Michaelis–Menten parameters obtained for K. In this case, the predicted values were significantly correlated with those measured, but about three times higher. Thus, a positive plant discrimination of K versus ¹³⁴Cs in plant absorption is observed for the types of soil studied. As regression proved to be significant, K absorption rates may be used to estimate ¹³⁴Cs absorption in determining radiocaesium plant uptake. This revised version was published online in June 2006 with corrections to the Cover Date.     

Bacterial Decolorization of Azo Dyes by Rhodopseudomonas palustris

Summary The ability of Rhodopseudomonas palustris AS1.2352 possessing azoreductase activity to decolorize azo dyes was investigated. It was demonstrated that anaerobic conditions were necessary for bacterial decolorization, and the optimal pH and temperature were pH 8 and 30–35 °C, respectively. Decolorization of dyes with different molecular structures was performed to compare their degradability. The strain could decolorize azo dye up to 1250 mg l⁻¹, and the correlation between the specific decolorization rate and dye concentration could be described by Michaelis–Menten kinetics. Long-term repeated operations showed that the strain was stable and efficient during five runs. Cell extracts from the strain demonstrated oxygen-insensitive azoreductase activity in vitro.     

Decolorization of sulfonated azo dyes with two photosynthetic bacterial strains and a genetically engineered Escherichia coli strain

Sulfonated azo dyes were decolorized by two wild type photosynthetic bacterial (PSB) strains (Rhodobacter sphaeroides AS1.1737 and Rhodopseudomonas palustris AS1.2352) and a recombinant strain (Escherichia coli YB). The effects of environmental factors (dissolved oxygen, pH and temperature) on decolorization were investigated. All the strains could decolorize azo dye up to 900 mg l⁻¹, and the correlations between the specific decolorization rate and dye concentration could be described by Michaelis–Menten kinetics. Repeated batch operations were performed to study the persistence and stability of bacterial decolorization. Mixed azo dyes were also decolorized by the two PSB strains. Azoreductase was overexpressed in E. coli YB; however, the two PSB strains were better decolorizers for sulfonated azo dyes.     

Production and properties of a dextransucrase from Leuconostoc mesenteroides IBT-PQ isolated from ‘pulque’, a traditional Aztec alcoholic beverage

Dextransucrase was produced from a Leuconostoc mesenteroides isolated from pulque, a traditional Aztec alcoholic beverage produced from agave juice containing sucrose as the main carbon source. Almost all the dextransucrase activity (87%) was associated with the cells, and was unusually high (1.04 U mg⁻¹ of cells). The culture medium composition was optimized through a Box-Behnken method resulting in a process yielding 2.2 U ml⁻¹ of insoluble glucosyltransferase activity. The enzyme had a molecular weight of 166 kDa. Optimal temperature was 35°C with a half-life of 137 min at the same temperature. As with dextransucrase from the industrial strain L. mesenteroides NRRL B-512F, the enzyme showed Michaelis–Menten kinetic behavior with excess substrate inhibition (K _m and K _i values of 0.026 M and 1.23 M respectively); produced soluble linear dextran with glucose molecules linked mainly in α(1–6) with branching in α(1–3) in a proportion of 4:1 as shown by NMR studies; and produced a high yield of isomalto-oligosaccharides in the presence of maltose. Received 4 February 1998/ Accepted in revised form 25 July 1998     

Identification and cloning of a gene encoding dichloromethane dehalogenase from a methylotrophic bacterium, <Emphasis Type="Italic">Bacillus circulans</Emphasis> WZ-12 CCTCC M 207006

The gene dehalA encoding a novel dichloromethane dehalogenases (DehalA), has been cloned from Bacillus circulans WZ-12 CCTCC M 207006. The open reading frame of dehalA, spanning 864 bp, encoded a 288-amino acid protein that showed 85.76% identity to the dichloromethane dehalogenases of Hyphomicrobium sp. GJ21 with several commonly conserved sequences. These sequences could not be found in putative dichloromethane (DCM) dehalogenases reported from other bacteria and fungi. DehalA was expressed in Escherichia coli BL21 (DE3) from a pET28b(+) expression system and purified. The subunit molecular mass of the recombinant DehalA as estimated by sodium dodecyl sulfate–polyacrylamide gel electrophoresis was approximately 33 kDa. Subsequent enzymatic characterization revealed that DehalA was most active in a acidic pH range at 30°, which was quite different from that observed from a facultative bacterium dichloromethane dehalogenases of Methylophilus sp. strain DM11. The Michaelis–Menten constant of DCM dehalogenase was markedly lower than that of standard DCM dehalogenases.     

Tolbutamide hydroxylation by hepatic microsomes from Atlantic salmon (<Emphasis Type="Italic">Salmo salar</Emphasis> L.)

Metabolic transformations of two substrates for human cytochrome P450 (CYP450) 2C9, tolbutamide and diclofenac, were investigated in hepatic microsomes from Atlantic salmon (Salmo salar L.). Tolbutamide hydroxylation followed Michaelis–Menten kinetics. Mean apparent Michaelis–Menten constant (K_m) and maximum reaction velocity (V_max) values for 4-hydroxytolbutamide (TBOH) formation were 0.09 ± 0.031 mM and 49.5 ± 6.03 pmol/min/mg, respectively. Addition of sulfaphenazole, an inhibitor for mammalian CYP2C9, in a range from 1 to 200 μM decreased formation of TBOH in a concentration-dependent manner, but not to 50%. Neither fluconazole, an inhibitor of human CYP2C9, nor ketoconazole, inhibitor of CYP1A and CYP3A in fish, affected TBOH formation. In contrast ellipticine, an inhibitor of CYP1A in fish inhibited TBOH formation with the IC₅₀ value of 12.1 μM. The rate of TBOH formation was competitively inhibited by 100 μM of sesamin in the incubations, but the degree of inhibition did not increase with increased sesamin concentration. Ethoxyresorufin hydroxylase (EROD) activity was inhibited by tolbutamide in a non-competitive manner (inhibition constant K_i = 218 μM). Our data suggest that tolbutamide is metabolized by salmon microsomes with formation of TBOH. CYP1A might be involved in this reaction as suggested by decreased TBOH formation in the presence of ellipticine and decreased EROD activity in the presence of tolbutamide. Incubation of diclofenac with the microsomes yielded no metabolite formation, suggesting that salmon does not possess diclofenac-metabolizing activity.     

Screening of tree leaves as annual renewable green biomass for phenol oxidase production and biochemical characterization of mulberry (Morus alba) leaf phenol oxidases

Fruit tree leaf tissues were screened in a search for determination of an alternative source(s) for commercial phenol oxidase (PO) production considering the importance of utilization of green biomass for production of value-added products. Mulberry, pear, sour cherry and apricot leaves were identified as promising PO production sources, due to their comparable enzyme activities with respect to mushroom (Agaricus bisporus), a well-known PO source. Within the scope of this research, further biochemical characterization was only performed for mulberry (Morus alba) leaf tissue due to its high PO activity (ca. 19 EU g⁻¹ tissue) and also its known non-toxic and edible nature which are important properties of an enzyme source to be used without detailed purification. In mulberry leaves, presence of three different PO activities, laccase, peroxidase and catechol oxidase of 62–64 kDa molecular weights, were identified. Since simple extraction/concentration steps without fractionation/purification was aimed as PO production process, operational parameters such as optimal temperature, pH and kinetic studies of overall PO activity were investigated using concentrated crude extract. The highest PO activity against 4-methyl catechol was observed at 45°C and pH 7. Michaelis–Menten kinetic parameters, K _m and V _max, of PO activity were determined as 6 mM 4-methyl catechol and 2.2 μmol quinone produced min⁻¹ ml⁻¹, respectively. PO activity of mulberry leaves increased up to late November. Consequently, mulberry leaves seem as a suitable PO source for industrial applications in which a wide range of substrate utilization is necessary.     

Continuous spectrofluorometric and spectrophotometric assays for NADPH-cytochrome P450 reductase activity using 5-cyano-2,3-ditolyl tetrazolium chloride

Mammalian NADPH-cytochrome P450 reductase (CPR) transfers electrons from NADPH to cytochrome P450 enzymes and other several microsomal enzymes. It also catalyzes the one-electron reduction of many chemicals and drugs. Reduction of 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) by CPR was assessed as a method for monitoring CPR activity. The electrons released from NADPH by CPR were transferred to CTC in the reaction medium, and CTC reduction activity could be assessed spectrophotometrically and spectrofluorometrically. The reduction kinetics of CTC follows classical Michaelis–Menten kinetics (K _m = 50 μM, k _cat = 2,520 min⁻¹). This method offers a continuous assay of the enzymatic activity of CPR. D. H. Kim and S. K. Yim are contributed equally to this work.     

Characteristics of amino acid uptake in barley

Plants have the ability to take up organic nitrogen (N) but this has not been thoroughly studied in agricultural plants. A critical question is whether agricultural plants can acquire amino acids in a soil ecosystem. The aim of this study was to characterize amino acid uptake capacity in barley (Hordeum vulgare L.) from a mixture of amino acids at concentrations relevant to field conditions. Amino acids in soil solution under barley were collected in microlysimeters. The recorded amino acid composition, 0–8.2 μM of l-Serine, l-Glutamic acid, Glycine, l-Arginine and l-Alanine, was then used as a template for uptake studies in hydroponically grown barley plants. Amino acid uptake during 2 h was studied at initial concentrations of 2–25 μM amino acids and recorded as amino acid disappearance from the incubation solution, analysed with HPLC. The uptake was verified in control experiments using several other techniques. Uptake of all five amino acids occurred at 2 μM and below. The concentration dependency of the uptake rate could be described by Michaelis–Menten kinetics. The affinity constant (K _m) was in the range 19.6–33.2 μM. These K _m values are comparable to reported values for soil micro-organisms.