Modeling non-inherited antibiotic resistance

A mathematical model is presented for the increase and decrease of non-inherited antibiotic resistance levels in bacteria. The model is applied to experimental data on E. coli exposed to amoxicillin or tetracyclin in different concentrations. The parameters of the model are estimated using a Monte Carlo Markov Chain method. The model accurately describes build-up and decline of antibiotic resistance caused by physiological adaptations as long as no genetic changes have occurred. The main conclusion of the analysis is that short time periods are sufficient to re-obtain low MIC-values after long-lasting exposure to these antibiotics.

Transcriptome meets metabolome: hierarchical and metabolic regulation of the glycolytic pathway

The fact that information flows from DNA to RNA to protein to function suggests that regulation is 'hierarchical', i.e. dominated by regulation of gene expression. In the case of dominant regulation at the metabolic level, however, there is no quantitative relationship between mRNA levels and function. We here develop a method to quantitate the relative contributions of metabolic and hierarchical regulation. Applying this method to the glycolytic flux in three species of parasitic protists, we conclude that it is rarely regulated by gene expression alone. This casts strong doubts on whether transcriptome and proteome analysis suffices to assess biological function.

The length of the combined 3' untranslated region and poly(A) tail does not control rates of glyceraldehyde-3-phosphate dehydrogenase mRNA translation in three species of parasitic protists

Experimental observations suggested that the length of the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA 3' end has a role in regulating rates of translation in the parasitic protists Trypanosoma brucei, Leishmania donovani, and Trichomonas vaginalis. Using a PCR assay for poly(A) tail length, we measured the size of the RNA 3' end under different growth conditions in all three species. Our results showed that the combined 3' untranslated region and poly(A) tail of GAPDH mRNA do not vary with different rates of translation.

Contribution of glucose transport to the control of the glycolytic flux in Trypanosoma brucei

The rate of glucose transport across the plasma membrane of the bloodstream form of Trypanosoma brucei was modulated by titration of the hexose transporter with the inhibitor phloretin, and the effect on the glycolytic flux was measured. A rapid glucose uptake assay was developed to measure the transport activity independently of the glycolytic flux. Phloretin proved a competitive inhibitor. When the effect of the intracellular glucose concentration on the inhibition was taken into account, the flux control coefficient of the glucose transporter was between 0.3 and 0.5 at 5 mM glucose. Because the flux control coefficients of all steps in a metabolic pathway sum to 1, this result proves that glucose transport is not the rate-limiting step of trypanosome glycolysis. Under physiological conditions, transport shares the control with other steps. At glucose concentrations much lower than physiological, the glucose carrier assumed all control, in close agreement with model predictions.

Regulation and adaptation of glucose metabolism of the parasitic protist Leishmania donovani at the enzyme and mRNA levels

Adaptation of the glucose metabolism of Leishmania donovani promastigotes (insect stage) was investigated by simultaneously measuring metabolic rates, enzyme activities, message levels, and cellular parameters under various conditions. Chemostats were used to adapt cells to different growth rates with growth rate-limiting or excess glucose concentrations. L. donovani catabolized glucose to CO(2), succinate, acetate, and pyruvate in ratios that depended on growth rate and glucose availability. Rates of glucose consumption were a linear function of growth rate and were twice as high in excess glucose-grown cells as in glucose-limited organisms. The major end product was CO(2), but organic end products were also formed in ratios that varied strongly with growth conditions. The specific activities of the 14 metabolic enzymes measured varied by factors of 3 to 17. Two groups of enzymes adapted specific activities in parallel, but there was no correlation between the groups. The activities of only one group correlated with specific rates of glucose metabolism. Total RNA content per cellular protein varied by a factor of 6 and showed a linear relationship with the rate of glucose consumption. There was no correlation between steady-state message levels and activities of the corresponding enzymes, suggesting regulation at the posttranscriptional level. A comparison of the adaptation of energy metabolism in L. donovani and other species suggests that the energy metabolism of L. donovani is inefficient but is well suited to the environmental challenges that it encounters during residence in the sandfly, its insect vector.

Adaptation of metabolic enzyme activities of Trypanosoma brucei promastigotes to growth rate and carbon regimen

The insect stage of Trypanosoma brucei adapted the activities of 16 metabolic enzymes to growth rate and carbon source. Cells were grown in chemostats with glucose, rate limiting or in excess, or high concentrations of proline as carbon and energy sources. At each steady state, samples were collected for measurements of substrate and end product concentrations, cellular parameters, and enzyme activities. Correlation coefficients were calculated for all parameters and used to analyze the data set. Rates of substrate consumption and end product formation increased with increasing growth rate. Acetate and succinate were the major nonvolatile end products, but measurable quantities of alanine were also produced. More acetate than succinate was formed during growth on glucose, but growth on proline yielded an equimolar ratio. Growth rate barely affected the relative amounts of end products formed. The end products accounted for the glucose consumed during glucose-limited growth and growth at high rates on excess glucose. A discrepancy, indicating production of CO2, occurred during slow growth on excess glucose and, even more pronounced, in cells growing on proline. The activities of the metabolic enzymes varied by factors of 2 to 40. There was no single enzyme that correlated with consumption of substrate and/or end product formation in all cases. A group of enzymes whose activities rigorously covaried could also not be identified. These findings indicate that T. brucei adapted the activities of each of the metabolic enzymes studied separately. The results of this complex manner of adaptation were more or less constant ratios of the end products and a very efficient energy metabolism.

Metabolic adaptation of Trichomonas vaginalis to growth rate and glucose availability

The parasitic protist Trichomonas vaginalis adapted the specific activities of twelve of the enzymes involved in glucose metabolism to the growth rate an glucose availability. These changes in enzyme activities were induced by culturing T. vaginalis in chemostats with glucose, present in rate-limiting or excess concentrations, as carbon and energy source. The specific activities were measured in pelleted cells at each steady state, while metabolic end products were determined in filtered culture fluid. The specific activities were lower in cells grown on growth-rate-limiting concentrations of glucose and higher in organisms cultured in the presence of excess glucose. In both cases enzyme activities were higher at increasing growth rates. For most enzymes the difference between the highest and lowest activities was an order of magnitude. The specific activities of eleven of the enzymes were strongly correlated to each other (correlation coefficients 0.83-0.99), the exception being lactate dehydrogenase. The rates of production of the three major end products, lactate, acetate and glycerol, increased with increasing growth rates. Alanine was not formed in measurable quantities. The ratio of the end products formed was strongly influenced by the growth rates and glucose availability. The rates of formation of acetate and glycerol correlated best with the specific activities of the enzymes catalysing the final reactions of their respective pathways. This suggests that the production of acetate and glycerol is rate-limited by these final steps. In contrast, the formation of lactate did not correlate with the specific activity of lactate dehydrogenase but was determined by the rate of glucose consumption.

Maltose utilization by extracellular hydrolysis followed by glucose transport in Trichomonas vaginalis

The amitochondriate parasitic protist Trichomonas vaginalis can utilize either glucose or maltose as carbon and energy source. The mechanisms of maltose utilization were explored with uptake experiments using radio-isotope labelled maltose in combination with the silicone-oil centrifugation technique and enzymatic assays measuring maltose hydrolysis. The uptake of maltose label became saturated after 2-3 h. The uptake of maltose as a function of the external maltose concentration was linear at low concentrations with no further increase at higher levels, kinetics characteristic of reactions obeying Michaelis-Menten kinetics preceded by a diffusion-limited step. Increased viscosity of the medium resulted in decreased maltose uptake, indicating an extracellular location of the diffusion-limited step. Most of the cellular alpha-glucosidase activity of T. vaginalis was detected on the cell surface, suggesting that maltose is hydrolysed to glucose outside the cell. Glucose interfered more with maltose uptake, and maltose less with glucose uptake, than would be expected if 1 mol of maltose were the equivalent of 2 mol of glucose. This pattern of interaction indicated that the interference occurs before the common metabolic pathway and even before the transport step, supporting the idea of extracellular maltose hydrolysis. We conclude that maltose is hydrolysed to glucose in the boundary layer of the cell, a process akin to membrane digestion in vertebrate enterocytes and on the teguments of helminths. The glucose formed is then transported by the glucose carrier of the organism.

Adaptation of the carbon metabolism of Trichomonas vaginalis to the nature and availability of the carbon source

The anaerobic parasitic protist Trichomonas vaginalis was adapted in chemostats to eight different conditions defined by different growth rates and carbon regimens. Glucose or maltose was used as carbon and energy source. Cells cultured under well-defined steady states were tested in short-term experiments. The kinetics of glucose and maltose uptake were determined and their glucokinase and alpha-glucosidase activities were measured. Uptake in 20 min was measured with radiolabelled glucose and maltose, rather than analogues, using the silicone oil centrifugation technique. Hence, the accumulated label represents both transport and metabolic activity. The total uptake of glucose was highest in organisms that had been starved for glucose during growth. The kinetics of glucose uptake can be understood by assuming rate-limitation by transport across the plasma membrane at low external concentrations and by the subsequent metabolism at concentrations exceeding a cross-over value. The specific glucokinase activity correlated in only four out of eight cases with the saturation uptake. The kinetics of maltose uptake indicated rate-limitation at low maltose concentrations by a diffusion-limited step and at higher levels by metabolic steps. The uptake of maltose was primarily affected by the growth rate during culture, the highest growth rates resulting in most uptake. Maltose uptake was determined only partially by the cellular alpha-glucosidase activity. The activities of both transport and metabolic enzymes changed due to the culture conditions suggesting that the control over glucose and maltose metabolism is shared by several steps in the pathway.

Carbohydrate metabolism and physiology of the parasitic protist Trichomonas vaginalis studied in chemostats

The parasitic protist Trichomonas vaginalis was cultured in chemostats with glucose or maltose as carbon and energy source. The maximum growth rate was about six divisions per day independent of the substrate, and the apparent Km for glucose was 0.375 mM. While growing on maltose, the growth rate depended linearly on the maltose concentration, indicating that in contrast to glucose metabolism a diffusion step is rate-limiting to maltose metabolism. Cultures were examined over a wide range of growth rates under four conditions: utilizing glucose or maltose as carbon and energy source, with the carbon source rate-limiting or present in excess. Cell density, cellular protein and carbohydrate content as well as residual substrate concentration in the culture fluid were measured at each steady state. The protein content was constant at 100 pg protein per cell except when T. vaginalis was cultured under glucose limitation; in the latter case, slow-growing cells had less protein than cells grown at high rates. When growing under glucose limitation T. vaginalis metabolism changed to become more energy efficient at growth rates exceeding about half the maximum rate. The maintenance energy at the low growth rates accounted for approximately half of the total carbon consumption, which is high in comparison to other micro-organisms. At low growth rates the yield on maltose exceeded that on glucose, when expressed in terms of carbon equivalents. The yields on maltose and glucose were equal, but much lower, when the carbon source was not rate-limiting.(ABSTRACT TRUNCATED AT 250 WORDS)

The kinetics of facilitated diffusion followed by enzymatic conversion of the substrate

The uptake of a substrate that is transported into the cell by facilitated diffusion and subsequently converted in a series of enzymatic reactions, measured as a function of the external concentration, does not usually show the rectangular hyperbolic function characteristic of Michaelis-Menten kinetics. Instead, a seemingly biphasic curve is observed, consisting of Michaelis-Menten kinetics at low concentrations and no further uptake at higher levels. By combining the equations for facilitated diffusion and an enzymatic reaction, we have derived an equation that describes the overall rate of uptake and metabolism of a substrate that is transported across the plasma membrane by facilitated diffusion. Modelling based on this equation simulated the kinetics found experimentally, as long as the kinetic parameters of the carrier were chosen to render it asymmetric. The overall rate was influenced by the kinetics of both reactions over a wide range of concentrations, confirming the principles of the 'Control Analysis' theory in an independent manner.

Membrane-related processes and overall energy metabolism in Trypanosoma brucei and other kinetoplastid species

An electrochemical proton gradient exists across the plasma membrane and the mitochondrial membrane of the bloodstream form of Trypanosoma brucei. The membrane potential across the plasma membrane and the regulation of the internal pH depend on the temperature. Leishmania donovani regulates its internal pH and maintains a constant electrochemical proton gradient across its plasma membrane under all conditions examined. The mitochondrion of the T. brucei bloodstream form is energized, even though the reactions taking place in it do not result in net ATP synthesis and the Kreb's cycle and the respiratory chain are absent. Glucose is transported across the plasma membrane of T. brucei by a facilitated diffusion carrier, that can transport a wider range of substrates than its mammalian counterparts. Pyruvate exits the cell via a facilitated diffusion transporter as well. Conflicting evidence exists for the mechanism of glucose transport in L. donovani; biochemical evidence suggests proton/glucose symport, while facilitated diffusion is indicated by physiological data.

Interaction between facilitated diffusion of glucose across the plasma membrane and its metabolism in Trichomonas vaginalis

The parasitic protist Trichomonas vaginalis transports glucose across the plasma membrane by facilitated diffusion. The Km of the transporter for glucose was 1.6 mM. The uptake of labelled glucose in a minimal medium not allowing growth reached saturation only after 2.5 h, indicating the turnover of storage carbohydrate. Organisms grown on glucose showed higher activities both of the transporter and of the subsequent metabolic pathway than organisms grown on maltose. At low external glucose concentrations the transport step was rate limiting, at higher levels a subsequent enzymatic step. The uptake mechanism for glucose of T. vaginalis resembled that of parasitic kinetoplastid protists and Entamoeba histolytica.

Comparative physiology of two protozoan parasites, Leishmania donovani and Trypanosoma brucei, grown in chemostats

Cultures of the insect stage of the protozoan parasites Leishmania donovani and Trypanosoma brucei were grown in chemostats with glucose as the growth rate-limiting substrate. L. donovani has a maximum specific growth rate (mu max) of 1.96 day-1 and a Ks for glucose of 0.1 mM; the mu max of T. brucei is 1.06 day-1 and the Ks is 0.06 mM. At each steady state (specific growth rate, mu, equals D, the dilution rate), the following parameters were measured: external glucose concentration (Glcout), cell density, dry weight, protein, internal glucose concentration (Glcin), cellular ATP level, and hexokinase activity. L. donovani shows a relationship between mu and yield that allows an estimation of the maintenance requirement (ms) and the yield per mole of ATP (YATP). Both the ms and the YATP are on the higher margin of the range found for prokaryotes grown on glucose in a complex medium. L. donovani maintains the Glcin at a constant level of about 50 mM as long as it is not energy depleted. T. brucei has a decreasing yield with increasing mu, suggesting that it oxidizes its substrate to a lesser extent at higher growth rates. Glucose is not concentrated internally but is taken up by facilitated diffusion, while phosphorylation by hexokinase is probably the rate-limiting step for glucose metabolism. The Ks is constant as long as glucose is the rate-limiting substrate. The results of this study demonstrate that L. donovani and T. brucei have widely different metabolic strategies for dealing with varying external conditions, which reflect the conditions they are likely to encounter in their respective insect hosts.

Mutual adjustment of glucose uptake and metabolism in Trypanosoma brucei grown in a chemostat

The mutual adjustment of glucose uptake and metabolism in the insect stage of the protozoan parasite Trypanosoma brucei was studied. T. brucei was preadapted in the chemostat to conditions in which either glucose or proline served as the major carbon and energy source. Cells were grown and adapted to either energy or non-energy limitation at a low dilution rate (0.5 day-1) or a high dilution rate (1 day-1). The cells were then used in short- to medium-term uptake experiments with D-[14C]glucose as a tracer. In time course experiments a steady state was reached after 15 min regardless of the preadaptation conditions. This steady-state level increased with increasing glucose availability during preadaptation. The rate of glucose uptake and the hexokinase activity were linearly correlated. In short-term 5- to 90-s) uptake experiments a high transport rate was measured with cultures grown in excess glucose, an intermediate rate was measured with proline-grown cultures, and a low rate was measured in organisms grown under glucose limitation. Glucose metabolism and proline metabolism did not affect each other during the 15-min incubations. Glucose uptake, as a function of the external glucose concentration, did not obey simple Michaelis-Menten kinetics but could be described by a two-step mechanism: (i) transport of glucose by facilitated diffusion and (ii) subsequent metabolism of glucose. The respective rates of the two steps were adjusted to each other. It is concluded that T. brucei is capable of adjusting the different metabolic processes in a way that gives maximum energy efficiency at the cost of short-term flexibility.