Modeling of growth kinetics for Pseudomonas spp. during benzene degradation

A modeling study was conducted on growth kinetics of three different strains of Pseudomonas spp. (Pseudomonas aeruginosa, Pseudomonas fluorescens, Pseudomonas putida) during benzene degradation to determine optimum substrate concentrations for most efficient biodegradation. Batch tests were performed for eight different initial substrate concentrations to observe cell growth and associated substrate degradation using benzene-adapted cells. Kinetic parameters of both inhibitory (Haldane–Andrews, Aiba–Edwards) and noninhibitory (Monod) models were fitted to the relationship between specific growth rate and substrate concentration obtained from the growth curves. Results showed that half-saturation constant of P. fluorescens was the highest among the three strains, indicating that this strain could grow well at high concentration, while P. putida could grow best at low concentration. The inhibition constant of P. aeruginosa was the highest, implying that it could tolerate high benzene concentration and therefore could grow at a wider concentration range. Estimated specific growth rate of P. putida was lower, but half-saturation constant was higher than those from literature study due to high substrate concentration range used in this study. These two kinetic parameters resulted in substantial difference between Monod- and Haldane-type models, indicating that distinction should be made in applying those models.     

The inhibition kinetics and thermodynamic changes of tyrosinase via the zinc ion

We found that Zn(2+) conspicuously inactivated tyrosinase in a mixed-type inhibition manner: the final level of residual activity was abolished at the equilibrium state with concentration of 0.25 mM Zn(2+). Changes of both K(m) and V(max) by various concentrations of Zn(2+) in Lineweaver-Burk plot were observed. To see whether Zn(2+) also induced conformational change of tyrosinase and how thermodynamical changes by ligand binding were occurred, the intrinsic fluorescence studies as well as calorimetric measurements were conducted. The results showed that the Zn(2+) binding to tyrosinase directly induced conformational change of tyrosinase, and the changes of thermodynamic parameters such as enthalpy (DeltaH), Gibbs free-energy (DeltaG), and entropy (DeltaS) were obtained as 60+/-7.0 kJ/mol, -14.54 kJ/mol and 248.53 J/(K mol), respectively. The inactivating effect of Zn(2+) on tyrosinase was completely prevented by incubation with bovine serum albumin, which has a Zn(2+) binding motif in its structure. We suggested that Zn(2+) ligand-binding affected the substrate's accessibility due to the conformational changes and thus, the complex type of inhibition has occurred with the calorimetric changes.     

Factors affecting the activation of pulps with laccase

Activation of fibres by radical formation is the first step when aiming at oxidative coupling of new functional groups on the fibre bound lignin. In this work, factors affecting the amount of phenoxy radicals created to unbleached TMP, CTMP, softwood kraft and hardwood kraft pulp fibres in the laccase catalysed oxidation were determined by EPR. Laccase was able to catalyse the oxidation of all the pulps studied. The reactivity of the pulp was found to be affected by both the physical accessibility of lignin in the fibres and the chemistry of the surface lignin accessible to laccase. Laccase dosage, use of extra oxygen in the laccase catalysed radicalization reaction, treatment time and also the amount and type of low-molecular weight compounds (LMWC) present in the pulp were all found to contribute to the radical content of pulp fibres measured after the enzymatic reaction. It could not been excluded that two types of reactions take place during the radical formation in fibres. Within the fibre matrix there may be both fibre material bound and soluble lignin fragments differing with respect to accessibility, molecular weight or chemical structure which can be radicalized at various rates, and the formed radicals may also undergo cross-coupling reactions reducing the amount of the total radicals.     

Improved methodology for intracellular enzyme reaction and inhibition kinetics by flow cytometry

Flow cytoenzymology is the determination of enzyme activities or concentrations in single intact cells. Using the flow cytometer built and designed in our laboratory and recent modifications to hardware and software, we have developed an improved dynamic flow cytoenzymological procedure for the assay of cellular enzyme kinetics. The reaction mixture is sampled continuously, and the computer clock incorporates time as a parameter for kinetic determinations. Conditions for cellular esterase analysis were optimized and the rates of hydrolysis of two fluorogenic substrates, fluorescein diacetate (FDA) and 4-methylumbelliferone acetate (MUA), by esterases in EMT6 mouse mammary tumor cells were studied. Reaction kinetics were characterized, and Km values of 19 and 72 microM were obtained for the hydrolysis of FDA and MUA respectively. The kinetics of the cellular efflux of fluorescein were investigated, and a half-life of 7.5 min obtained. Enzyme inhibition kinetics were investigated using the competitive substrates p-nitrophenyl acetate and phenyl acetate, and the carbamoylating agents physostigmine and n-butyl isocyanate. The latter was particularly potent with an I50 of 4.8 X 10(-5) M for FDA hydrolysis compared with 6.5 X 10(-3) M for physostigmine. The I50 of 8.8 X 10(-5) M for n-butyl isocyanate inhibition of MUA hydrolysis was similar to that obtained with FDA as substrate. By monitoring FDA and MUA reactions separately and simultaneously, we showed them to act as competitive substrates. A comparison of flow cytoenzymological and conventional spectrofluorimetric analysis was also made, and differences identified in some cases.     

Factors affecting xylanase functionality in the degradation of arabinoxylans

Endo-beta-1,4-xylanases are key enzymes in the degradation of arabinoxylans, the main non-starch polysaccharides from grain cell walls. Due to the heterogeneity of arabinoxylans, xylanases with different characteristics are required in industrial applications but the choice of the enzyme is still largely empirical. Although the classification into glycoside hydrolase families greatly helped to derive mechanistic information on the catalytic and substrate specificity of xylanases, other factors e.g. their sensitivity to endogenous inhibitors, the presence of carbohydrate-binding module(s) and their degree of selectivity towards soluble versus insoluble substrate may play a role in determining the functionality of these enzymes in the degradation of arabinoxylans.     

Factors affecting the microbial degradation of phenanthrene in soil

Summary Because phenanthrene was mineralized more slowly in soils than in liquid media, a study was conducted to determine the environmental factors that may account for the slow biodegradation in soil. Mineralization was enhanced by additions of phosphate but not potassium, and it was reduced by additions of nitrate. Aeration or amending the soil with glucose affected the rate of mineralization, although not markedly. Phenanthrene was sorbed to soil constituents, the extent of sorption being directly related to the percentage of organic matter in the soil. Soluble phenanthrene was not detected after addition of the compound to a muck soil. The rate of mineralization was slow in the organic soil and higher in mineral soils with lower percentages of organic matter. We suggest that sorption by soil organic matter slows the biodegradation of polycyclic aromatic hydrocarbons that are otherwise readily metabolized. Offprint requests to: M. Alexander     

Mechanistic and kinetic studies of inhibition of enzymes

A graphical method for analyzing enzyme data to obtain kinetic parameters, and to identify the types of inhibition and the enzyme mechanisms, is described. The method consists of plotting experimental data as nu/(V0 - nu) vs 1/(I) at different substrate concentrations. I is the inhibitor concentration; V0 and nu are the rates of enzyme reaction attained by the system in the presence of a fixed amount of substrate, and in the absence and presence of inhibitor, respectively. Complete inhibition gives straight lines that go through the origin; partial inhibition gives straight lines that converge on the 1-I axis, at a point away from the origin. For competitive inhibition, the slopes of the lines increase with increasing-substrate concentration; with noncompetitive inhibition, the slopes are independent of substrate concentration; with uncompetitive inhibition, the slopes of the lines decrease with increasing substrate concentrations. The kinetic parameters, Km, Ki, Ki', and beta (degree of partiality) can best be determined from respective secondary plots of slope and intercept vs substrate concentration, for competitive and noncompetitive inhibition mechanism or slope and intercept vs reciprocal substrate concentration for uncompetitive inhibition mechanism. Functional consequencs of these analyses are represented in terms of specific enzyme-inhibitor systems.     

Factors affecting the thermodynamic stability of small asymmetric internal loops in RNA

Optical melting experiments were used to determine the thermodynamic parameters for oligoribonucleotides containing small asymmetric internal loops. The results show a broad range of thermodynamic stabilities, which depend on loop size, asymmetry, sequence, closing base pairs, and length of helix stems. Imino proton NMR experiments provide evidence for possible hydrogen bonding in GA and UU mismatches in some asymmetric loops. The stabilizing effects of GA, GG, and UU mismatches on the thermodynamic stability of internal loops vary depending on the size and asymmetry of the loop. The dependence of loop stability on Watson-Crick closing base pairs may be explained by an account of hydrogen bonds. Models are presented for approximating the free energy increments of 2 x 3 and 1 x 3 internal loops.     

The kinetics of the degradation of chloroform and benzene in anaerobic sediment from the River Rhine

In anaerobic methanogenic sediment microcosms¹⁴C labelled chloroform was degraded mainly to carbon dioxide. At a concentration of 4 g.l^–1 the mineralization followed first order kinetics with a half life of 12 days at 10°C and 2.6 days at 20°C. At a concentration of 400 g.l^–1 the mineralization rate increased with time and followed logarithmic kinetics with a _max of 0.02.d^–1 at 10°C. The logarithmic kinetics can be explained by growth of the bacteria on the higher concentration of chloroform with a generation time of 35 days. Shaking and oxygenation did not inhibit the mineralization of chloroform, probably because of bacterial consumption of the dissolved oxygen. ¹⁴C labelled benzene was mineralized only for a small percentage to¹⁴C labelled carbon dioxide while other, not acid extractable, degradation products were formed. Under anaerobic conditions after one day when 5% of the benzene was degraded to carbon dioxide, the mineralization ceased, while the disappearance of benzene proceeded. With air in the headspace of the incubation bottles 25% of the benzene was mineralized to carbon dioxide. The anaerobic degradation of benzene at a concentration of 100 .l^–1 showed similar kinetics as the degradation at 1 g.l^–1. Hence no adaptation of the microflora in the sediment occurred during the 63 days of the experiment at 100 g.l^–1.     

Factors affecting the activation of rabbit muscle phosphofructokinase by actin

The consistent application of phosphatase inhibitors and a novel final purification step using a connected series of DE-51, DE-52, and DE-53 anion-exchange chromatography columns facilitate the preparation of electrophoretically homogeneous subpopulations of rabbit muscle phosphofructokinase which differ in their catalytic properties and endogenous covalent phosphate content. A band of "high"-phosphate enzyme (fraction II) flanked by regions of "low"-phosphate enzyme (fractions I and III) is an unusual feature of the final purification profile. Fractions I (containing in this case 0.42 mol of P/82 000 g of enzyme) and II (containing 1.26 mol of P/82 000 g of enzyme) exhibit the most pronounced functional differences of the fractions. Following our original report [Liou, R.-S., & Anderson, S. R. (1980) Biochemistry 19, 2684], both are activated by the addition of rabbit skeletal muscle F-actin. Under the assay conditions, half-maximal stimulation of phosphofructokinase activity occurs at 15.4 nM actin (in terms of monomer) for fraction I and 9.7 nM for fraction II. The low-phosphate enzyme is synergistically activated in the presence of 0.12 microM actin plus 3.0 microM fructose 2,6-bisphosphate, with a marked increase in Vmax, while the high-phosphate enzyme is not. Neither fraction is activated appreciably by the addition of G-actin or the chymotrypsin-resistant actin "core". The covalently cross-linked trimer of actin stimulates the activity of both the low- and high-phosphate enzyme fractions. However, the previously mentioned synergistic activation characteristic of fraction I fails to occur in solutions containing the trimer plus fructose 2,6-bisphosphate. Phosphorylation of fraction I in an in vitro reaction catalyzed by the cAMP-dependent protein kinase causes its properties to become more like those of fraction II. The total amount of covalent phosphate present after in vitro phosphorylation approaches 2 mol of P/82 000 g of enzyme for both fractions.     

Simplified velocity equations for characterizing the partial inhibition or nonessential activation of bireactant enzymes

The steady state velocity equation for a bireactant enzyme in the presence of a partial inhibitor or nonessential activator, M, contains squared substrate concentration and higher-ordered M concentration terms. The equation is too complex to be useful in kinetic analyses. Simplification by the method of Cha (J. Biol. Chem. 243, 820 825 (1968)) eliminates squared substrate concentration terms, but retains higher-ordered terms in [M]. It is shown that if strict equilibrium is assumed between free E, M, and EM and for all but one other M-binding reaction, a velocity equation is obtained for an ordered bireactant enzyme that is first degree in all ligands in the absence of products. The equation is an approximation (because it was derived assuming only one M-binding reaction in the steady state), but it contains five inhibition (or activation) constants associated with M, all of which can be obtained by diagnostic replots and/or curve-fitting procedures. The equation also provides a framework for obtaining limiting constants (V'max, K'ia, K'mA, K'mB) that characterize the enzyme at saturating M. The same approach is applicable to an enzyme that catalyzes a steady state ping pong reaction.     

Factors affecting the inhibition of yeast plasma membrane ATPase by vanadate

Inhibition of yeast plasma membrane ATPase by vanadate occurs only if either Mg2+ or MgATP2- is bound to the enzyme. The dissociation constant of the complex of vanadate and inhibitory sites is 0.14-0.20 microM in the presence of optimal concentrations of Mg2+ and of the order of 1 microM if the enzyme is saturated with MgATP2-. The dissociation constants of Mg2+ and MgATP2- for the sites involved are 0.4 and 0.62-0.73 mM, respectively, at pH 7. KCl does not increase the affinity of vanadate to the inhibitory sites as was found with (Na+ + K+)-ATPase. On the other hand, the effect of Mg2+ upon vanadate binding is similar to that upon (Na+ + K+)-ATPase, and the corresponding affinity constants of Mg2+ and vanadate for the two enzymes are of the same order of magnitude.