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J M Rohwer

Publications and source records attributed to J M Rohwer.

13 recordsLinked to original sources
PubMed2002

How to distinguish between the vacuum cleaner and flippase mechanisms of the lmrA multi-drug transporter in Lactococcus lactis.

A numerical model of the LmrA multi-drug transport system of Lactococcus lactis is used to explore the possibility of distinguishing experimentally between two putative transport mechanisms, i.e., the vacuum-cleaner and the flippase mechanisms. This comparative model also serves as an example of numerical simulation with the scripting language Python and its scientific add-on Scipy.

Bacterial Proteins↗
PubMed2002

Experimental supply-demand analysis of anaerobic yeast energy metabolism.

Experimental supply-demand analysis of yeast fermentative energy metabolism shows that control of the glycolytic flux is shared between supply and demand. In glucose limited chemostat cultures the supply block was modulated in a dilution rate change and demand block via a benzoic acid titration. Under these conditions the supply block had a flux control of 0.90 and the demand block a flux control of 0.10.

Adenosine Diphosphate↗
PubMed2001

Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data.

Sucrose accumulation in developing sugar cane (Saccharum officinarum) is accompanied by a continuous synthesis and cleavage of sucrose in the storage tissues. Despite numerous studies, the factors affecting sucrose accumulation are still poorly understood, and no consistent pattern has emerged which pinpoints certain enzyme activities as important controlling steps. Here, we develop an approach based on pathway analysis and kinetic modelling to assess the biochemical control of sucrose accumulation and futile cycling in sugar cane. By using the concept of elementary flux modes, all possible routes of futile cycling of sucrose were enumerated in the metabolic system. The available kinetic data for the pathway enzymes were then collected and assembled in a kinetic model of sucrose accumulation in sugar cane culm tissue. Although no data were fitted, the model agreed well with independent experimental results: in no case was the difference between calculated and measured fluxes and concentrations greater than 2-fold. The model thus validated was then used to assess different enhancement strategies for increasing sucrose accumulation. First, the control coefficient of each enzyme in the system on futile cycling of sucrose was calculated. Secondly, the activities of those enzymes with the numerically largest control coefficients were varied over a 5-fold range to determine the effect on the degree of futile cycling, the conversion efficiency from hexoses into sucrose, and the net sucrose accumulation rate. In view of the modelling results, overexpression of the fructose or glucose transporter or the vacuolar sucrose import protein, as well as reduction of cytosolic neutral invertase levels, appear to be the most promising targets for genetic manipulation. This offers a more directed improvement strategy than cumbersome gene-by-gene manipulation. The kinetic model can be viewed and interrogated on the World Wide Web at http://jjj.biochem.sun.ac.za.

Agriculture↗
PubMed2000

Understanding glucose transport by the bacterial phosphoenolpyruvate:glycose phosphotransferase system on the basis of kinetic measurements in vitro.

The kinetic parameters in vitro of the components of the phosphoenolpyruvate:glycose phosphotransferase system (PTS) in enteric bacteria were collected. To address the issue of whether the behavior in vivo of the PTS can be understood in terms of these enzyme kinetics, a detailed kinetic model was constructed. Each overall phosphotransfer reaction was separated into two elementary reactions, the first entailing association of the phosphoryl donor and acceptor into a complex and the second entailing dissociation of the complex into dephosphorylated donor and phosphorylated acceptor. Literature data on the K(m) values and association constants of PTS proteins for their substrates, as well as equilibrium and rate constants for the overall phosphotransfer reactions, were related to the rate constants of the elementary steps in a set of equations; the rate constants could be calculated by solving these equations simultaneously. No kinetic parameters were fitted. As calculated by the model, the kinetic parameter values in vitro could describe experimental results in vivo when varying each of the PTS protein concentrations individually while keeping the other protein concentrations constant. Using the same kinetic constants, but adjusting the protein concentrations in the model to those present in cell-free extracts, the model could reproduce experiments in vitro analyzing the dependence of the flux on the total PTS protein concentration. For modeling conditions in vivo it was crucial that the PTS protein concentrations be implemented at their high in vivo values. The model suggests a new interpretation of results hitherto not understood; in vivo, the major fraction of the PTS proteins may exist as complexes with other PTS proteins or boundary metabolites, whereas in vitro, the fraction of complexed proteins is much smaller.

Biological Transport↗
PubMed1998

Implications of macromolecular crowding for signal transduction and metabolite channeling.

The effect of different total enzyme concentrations on the flux through the bacterial phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) in vitro was determined by measuring PTS-mediated carbohydrate phosphorylation at different dilutions of cell-free extract of Escherichia coli. The dependence of the flux on the protein concentration was more than linear but less than quadratic. The combined flux-response coefficient of the four enzymes constituting the glucose PTS decreased slightly from values of approximately 1.8 with increasing protein concentrations in the assay. Addition of the macromolecular crowding agents polyethylene glycol (PEG) 6000 and PEG 35000 led to a sharper decrease in the combined flux-response coefficient, in one case to values of approximately 1. PEG 6000 stimulated the PTS flux at lower protein concentrations and inhibited the flux at higher protein concentrations, with the transition depending on the PEG 6000 concentration. This suggests that macromolecular crowding decreases the dissociation rate constants of enzyme complexes. High concentrations of the microsolute glycerol did not affect the combined flux-response coefficient. The data could be explained with a kinetic model of macromolecular crowding in a two-enzyme group-transfer pathway. Our results suggest that, because of the crowded environment in the cell, the different PTS enzymes form complexes that live long on the time-scale of their turnover. The implications for the metabolic behavior and control properties of the PTS, and for the effect of macromolecular crowding on nonequilibrium processes, are discussed.

Cell-Free System↗
PubMed1998

Limits to inducer exclusion: inhibition of the bacterial phosphotransferase system by glycerol kinase.

The uptake of methyl alpha-D-glucopyranoside by the phosphoenolpyruvate-dependent phosphotransferase system of Salmonella typhimurium could be inhibited by prior incubation of the cells with glycerol. Inhibition was only observed for glycerol preincubation times longer than 45 s and required the preinduction of both the glucose and the glycerol-catabolizing systems. Larger extents of inhibition by glycerol correlated with higher intracellular levels of glycerol kinase when the glp regulon had been induced to different extents. Preincubation with lactate did not inhibit methyl alpha-D-glucopyranoside uptake significantly, although both lactate and glycerol were oxidized by the cells. The cellular free-energy state of the cells (intracellular [ATP]/[ADP] ratio) was virtually identical for lactate and glycerol preincubation, suggesting that the inhibition of phosphotransferase-mediated uptake was not a metabolic effect. In vitro, phosphotransferase activity was inhibited to a maximal extent of 32% upon titrating cell-free extracts with high concentrations of commercial glycerol kinase. The results show that uptake systems that have hitherto been regarded merely as targets of the phosphotransferase system component IIA(Glc) also have the capacity themselves to retroinhibit the phosphotransferase system flux, presumably by sequestration of the available IIA(Glc), provided that these systems are induced to appropriate levels.

Adenosine Diphosphate↗
PubMed1998

Subtleties in control by metabolic channelling and enzyme organization.

Because of its importance to cell function, the free-energy metabolism of the living cell is subtly and homeostatically controlled. Metabolic control analysis enables a quantitative determination of what controls the relevant fluxes. However, the original metabolic control analysis was developed for idealized metabolic systems, which were assumed to lack enzyme-enzyme association and direct metabolite transfer between enzymes (channelling). We here review the recently developed molecular control analysis, which makes it possible to study non-ideal (channelled, organized) systems quantitatively in terms of what controls the fluxes, concentrations, and transit times. We show that in real, non-ideal pathways, the central control laws, such as the summation theorem for flux control, are richer than in ideal systems: the sum of the control of the enzymes participating in a non-ideal pathway may well exceed one (the number expected in the ideal pathways), but may also drop to values below one. Precise expressions indicate how total control is determined by non-ideal phenomena such as ternary complex formation (two enzymes, one metabolite), and enzyme sequestration. The bacterial phosphotransferase system (PTS), which catalyses the uptake and concomitant phosphorylation of glucose (and also regulates catabolite repression) is analyzed as an experimental example of a non-ideal pathway. Here, the phosphoryl group is channelled between enzymes, which could increase the sum of the enzyme control coefficients to two, whereas the formation of ternary complexes could decrease the sum of the enzyme control coefficients to below one. Experimental studies have recently confirmed this identification, as well as theoretically predicted values for the total control. Macromolecular crowding was shown to be a major candidate for the factor that modulates the non-ideal behaviour of the PTS pathway and the sum of the enzyme control coefficients.

Energy Metabolism↗
PubMed1996

How to recognize monofunctional units in a metabolic system.

In intracellular metabolic networks, it is often useful to discern subsystems (modules) of which the metabolites are only produced or consumed by reactions within that subsystem or by a limited number of fluxes crossing the borders of the subsystem. In many cases such subsystems function as units with respect to their effect on the remainder of the system. In this paper we show that the co-response of two metabolic variables outside that subsystem to a perturbation of a subsystem reaction does not depend on which subsystem reaction is perturbed if three conditions are fulfilled: (1) the reactions outside the subsystem are not affected directly by metabolites belonging to the subsystem; (2) there are no conservation relations linking the subsystem to the rest; and (3) the subsystem is linked to the remainder of the system only via one degree of freedom in fluxes. We propose the name "monofunctional units" for subsystems fulfilling these three criteria. Identification of such units greatly simplifies metabolic control analysis. Only one reaction per unit needs to be perturbed to analyse control in the system. Difficulties, such as the inaccessibility of some reactions to experimental perturbation, may be circumvented by perturbing another reaction within the unit that leads to the same co-response coefficients. The analysis can also serve to identify unsuspected regulatory interactions in the metabolic network. The differences in the behaviour between metabolic units and other types of subsystems are illustrated by numerical examples.

Animals↗
PubMed1996

Changes in the cellular energy state affect the activity of the bacterial phosphotransferase system.

The effect of different cellular free-energy states on the uptake of methyl alpha-D-glucopyranoside, an analogue of glucose, by the Escherichia coli phosphoenolpyruvate:carbohydrate phosphotransferase system was investigated. The intracellular [ATP]/[ADP] ratio was varied by changing the expression of the atp operon, which codes for the H+-ATPase, or by adding an uncoupler of oxidative phosphorylation or an inhibitor of respiration. Corresponding initial phosphotransferase uptake rates were determined using an improved uptake assay that works with growing cells in steady state. The results show that the initial uptake rate was decreased under conditions of lowered intracellular [ATP]/[ADP] ratios, irrespective of which method was used to change the cellular energy state. When either the expression of the atp operon was changed or 2,4-dinitrophenol was added to wild-type cells, the relationship between initial phosphotransferase uptake rate and the logarithm of the [ATP]/[ADP] ratio was approximately linear. These results suggest that the cellular free-energy state, as reflected in the intracellular [ATPI]/[ADP] ratio, plays an important role in regulating the activity of the phosphotransferase system.

2,4-Dinitrophenol↗
PubMed1995

Composite control of cell function: metabolic pathways behaving as single control units.

This paper shows that under some conditions the control exerted by a part of a metabolic network (a pathway) on a flux or concentration in any other part can be described through a single (overall) control coefficient. This has the following implications: (i) the relative contributions of a pathway enzyme to the regulation of the pathway (output) flux and of any flux or concentration outside are identical; therefore, the control analysis of the pathway 'in isolation' allows one to determine the control exerted by any pathway enzyme on the rest of the cell by estimation of the control efficient of just one, arbitrarily chosen enzyme; (ii) the relative control of any two metabolic variables outside the pathway (measured as the ratio of the control coefficients over these two variables outside) is the same for all pathway enzymes. These properties allow one to substitute effectively a pathway by a single (super)reaction and make it possible to consider such a pathway as a metabolic unit within the cellular enzyme network.

Cells↗
PubMed1993

Taking enzyme kinetics out of control; putting control into regulation.

The matrix formulation of metabolic control analysis, which states that multiplying the elasticity matrix for any system by the corresponding control matrix yields an identity matrix, can be transformed into a statement that multiplying a matrix expressing internal regulatory properties by a matrix expressing external regulatory properties also yields an identity matrix. This transformation supplies the formal basis for metabolic regulation analysis, and provides the key to determining the control structure of a system without the need to know the exact changes in enzyme activities that are made to measure control coefficients.

Enzymes↗