Mathematical modelling of the urea cycle. A numerical investigation into substrate channelling.

Metabolite channelling, the process in which consecutive enzymes have confined substrate transfer in metabolic pathways, has been proposed as a biochemical mechanism that has evolved because it enhances catalytic rates and protects unstable intermediates. Results from experiments on the synthesis of radioactive urea [Cheung, C., Cohen, N.S. & Raijman, L (1989) J. Biol. Chem.264, 4038-4044] have been interpreted as implying channelling of arginine between argininosuccinate lyase and arginase in permeabilized hepatocytes. To investigate this interpretation further, a mathematical model of the urea cycle was written, using Mathematica it simulates time courses of the reactions. The model includes all relevant intermediates, peripheral metabolites, and subcellular compartmentalization. Analysis of the output from the simulations supports the argument for a high degree of, but not absolute, channelling and offers insights for future experiments that could shed more light on the quantitative aspects of this phenomenon in the urea cycle and other pathways.     

Biophysical Characterization of the Dimer and Tetramer Interface Interactions of the Human Cytosolic Malic Enzyme

The cytosolic NADP⁺-dependent malic enzyme (c-NADP-ME) has a dimer-dimer quaternary structure in which the dimer interface associates more tightly than the tetramer interface. In this study, the urea-induced unfolding process of the c-NADP-ME interface mutants was monitored using fluorescence and circular dichroism spectroscopy, analytical ultracentrifugation and enzyme activities. Here, we demonstrate the differential protein stability between dimer and tetramer interface interactions of human c-NADP-ME. Our data clearly demonstrate that the protein stability of c-NADP-ME is affected predominantly by disruptions at the dimer interface rather than at the tetramer interface. First, during thermal stability experiments, the melting temperatures of the wild-type and tetramer interface mutants are 8–10°C higher than those of the dimer interface mutants. Second, during urea denaturation experiments, the thermodynamic parameters of the wild-type and tetramer interface mutants are almost identical. However, for the dimer interface mutants, the first transition of the urea unfolding curves shift towards a lower urea concentration, and the unfolding intermediate exist at a lower urea concentration. Third, for tetrameric WT c-NADP-ME, the enzyme is first dissociated from a tetramer to dimers before the 2 M urea treatment, and the dimers then dissociated into monomers before the 2.5 M urea treatment. With a dimeric tetramer interface mutant (H142A/D568A), the dimer completely dissociated into monomers after a 2.5 M urea treatment, while for a dimeric dimer interface mutant (H51A/D90A), the dimer completely dissociated into monomers after a 1.5 M urea treatment, indicating that the interactions of c-NADP-ME at the dimer interface are truly stronger than at the tetramer interface. Thus, this study provides a reasonable explanation for why malic enzymes need to assemble as a dimer of dimers.     

Acid denaturation of recombinant porcine growth hormone: formation and self-association of folding intermediates

We have investigated the conformational changes incurred during the acid-induced unfolding and self-association of recombinant porcine growth hormone (pGH). Acidification (pH 8 to pH 2) of pGH resulted in intrinsic fluorescence, UV absorbance, and near-UV CD transitions centered at pH 4.10. At pH 2.0, a red shift in the fluorescence emission maximum of approximately 3 nm and a 15% loss of the far-UV CD signal at 222 nm imply that the protein did not become extensively unfolded. Acidification in the presence of 4 M urea resulted in similar pH-dependent transitions. However, these occurred at a higher pH (approximately 5.2). At pH 2.0 + 4 M urea, an 8 nm red shift in the fluorescence emission maximum suggests that unfolding was greater than in the absence of urea. The presence of a prominent peak centered at 298 nm in the near-UV CD spectrum, which is absent without urea, signifies further differences in the intermediates generated at pH 2. Sedimentation equilibrium experiments in the analytical ultracentrifuge showed that native pGH and the partially unfolded intermediates reversibly self-associate. Self-association was strongly promoted at pH 2 while urea reduced self-association at both pH 8 and pH 2. These results demonstrate that acidification of pGH in the absence or presence of 4 M urea induced the formation of molten globule-like states with measurable differences in conformation. Similarities and differences in these structural conformations with respect to other growth hormones are discussed.     

Signaling and gene regulation by urea in cells of the mammalian kidney medulla

Signaling by urea, although incompletely understood, is relevant both to cells of the mammalian kidney inner medulla and to all cells of the organism in the setting of advanced renal failure with its attendant accumulation of urea in the systemic circulation. The molecular events initiated by urea stress are distinct from those occurring in response to hypertonic stress; urea activates a characteristic subset of signaling events, which are in large part specific to cultured renal tubular epithelial cells. Interestingly, urea is protective of hypertonic NaCl-inducible apoptosis in this model. Details of this phenomenon are reviewed. The effect of urea has been likened to that of either hypertonicity or of a peptide mitogen. In preliminary expression array analyses, the profile of genes activated by urea stress in renal medullary cells, however, was found to be unique.     

The nature of urea transport across the luminal membrane of Bufo bufo urinary bladder

By using the washing-out technique, counterflow acceleration for urea was demonstrated on the luminal membrane of Bufo bufo urinary bladder, in the absence of ADH. This phenomenon completely disappears in the presence of phloretin 10-4 M on the luminal side and is consistent with the presence of a mobile carrier mechanism for urea transport across the luminal membrane, in basal conditions. In the presence of ADH, counterflow acceleration is completely absent. This result is in agreement with the presence of urea selective channels, induced by ADH, as proposed by Levine & Worthington (1976).     

Characterization of the near native conformational states of the SAM domain of Ste11 protein by NMR spectroscopy

The sterile alpha motif or SAM domain is one of the most frequently present protein interaction modules with diverse functional attributions. SAM domain of the Ste11 protein of budding yeast plays important roles in mitogen‐activated protein kinase cascades. In the current study, urea‐induced, at subdenaturing concentrations, structural, and dynamical changes in the Ste11 SAM domain have been investigated by nuclear magnetic resonance spectroscopy. Our study revealed that a number of residues from Helix 1 and Helix 5 of the Ste11 SAM domain display plausible alternate conformational states and largest chemical shift perturbations at low urea concentrations. Amide proton (H/D) exchange experiments indicated that Helix 1, loop, and Helix 5 become more susceptible to solvent exchange with increased concentrations of urea. Notably, Helix 1 and Helix 5 are directly involved in binding interactions of the Ste11 SAM domain. Our data further demonstrate that the existence of alternate conformational states around the regions involved in dimeric interactions in native or near native conditions. Proteins 2014; 82:2957–2969. © 2014 Wiley Periodicals, Inc.     

Rate of hydrolysis of urea as influenced by thiourea and pellet size

Summary Two incubation experiments and a number of field experiments were conducted to determine the effect of soil moisture tension, pellet size and addition of thiourea to urea on the rate of urea hydrolysis. In the incubation experiments at 20°C, the rate of hydrolysis of urea increased from 15 bar to 1/3 bar soil moisture tension, with the largest change (doubling) occurring from 15 bar to 7 bar moisture tension. Increasing pellet size reduced the rate of urea hydrolysis by about 12% with urea pellets weighing 0.21 g as compared to 0.01 g urea pellets after 114h. When thiourea (a metabolic inhibitor) was pelleted with urea in a ratio of two parts urea and one part thiourea, the rate of hydrolysis was halved.In a field experiment, the addition of thiourea to urea and increasing pellet size suppressed the rate of urea hydrolysis considerably for 8 days. The amount of urea hydrolyzed with urea+thiourea (21) pellets weighing 2.51 g was one-fourth of the amount of urea hydrolyzed with 0.01 g pellets of urea alone. In the other six field experiments which were set out in October, only 22% to 39% of urea +thiourea (21) was hydrolyzed at two weeks after application, while almost all of the urea was hydrolyzed when it was mixed into the soil without an inhibitor.Unter our field conditions, we would estimate that the hydrolysis of urea can be inhibited for at least one week. The inhibition of urea hydrolysis appears to be great enough that the problems encountered from the rapid hydrolysis of urea, wherever these occur, may be reduced by combined use of thiourea and either increased pellet size or band placement.     

Photoreactivation of thymine dimers in UV-irradiated human cells: Unique dependence on culture conditions

UV-irradiated human fibroblasts in tissue culture were exposed to photoreactivating light in an attempt to demonstrate a light-dependent loss of thymine dimers from the acid-insoluble fraction of the DNA. The only experimental conditions in which this phenomenon was observed was if the cells were grown for at least 10 days in Dulbecco's modified Eagle's minimum essential medium. Such cells lost a maximum of between 10–30% of the thymine dimers from their DNA during illumination for 1 h. When cells were grown in a variety of other media the phenomenon was not observed. The present experiments do not discriminate between true enzymatic photoreactivation and a medium-dependent photosensitization phenomenon that is not enzymatic in nature.     

Effect of perfusate hematocrit on urea permeability-surface area in isolated dog lung

Seven dog lower left lung lobes were statically inflated and perfused at a constant rate for each lobe with a perfusate in which the hematocrit was altered over a wide range. The permeability-surface area of urea was calculated from multiple indicator dilution curves using two separate injectates for each hematocrit level. One injectate contained only 125I-albumin as the vascular reference tracer and the other contained both 51Cr-erythrocytes and 125I-albumin as the vascular reference tracers; both contained [14C]urea as the permeating tracer. The results strongly indicate that the phenomenon of "erythrocyte trapping" of urea does not affect the calculation of urea permeability-surface area product provided the appropriate albumin-erythrocyte composite reference tracer is utilized in its calculation.     

The nuclear receptor FXR regulates hepatic transport and metabolism of glutamine and glutamate

Hepatic transport and metabolism of glutamate and glutamine are regulated by intervention of several proteins. Glutamine is taken up by periportal hepatocytes and is the major source of ammonia for urea synthesis and glutamate for N-acetylglutamate (NAG) synthesis, which is catalyzed by the N-acetylglutamate synthase (NAGS). Glutamate is taken up by perivenous hepatocytes and is the main source for the synthesis of glutamine, catalyzed by glutamine synthase (GS). Accumulation of glutamate and ammonia is a common feature of chronic liver failure, but mechanism that leads to failure of the urea cycle in this setting is unknown. The Farnesoid X Receptor (FXR) is a bile acid sensor in hepatocytes. Here, we have investigated its role in the regulation of the metabolism of both glutamine and glutamate. In vitro studies in primary cultures of hepatocytes from wild type and FXR(-/-) mice and HepG2 cells, and in vivo studies, in FXR(-/-) mice as well as in a rodent model of hepatic liver failure induced by carbon tetrachloride (CCl(4)), demonstrate a role for FXR in regulating this metabolism. Further on, promoter analysis studies demonstrate that both human and mouse NAGS promoters contain a putative FXRE, an ER8 sequence. EMSA, ChIP and luciferase experiments carried out to investigate the functionality of this sequence demonstrate that FXR is essential to induce the expression of NAGS. In conclusion, FXR activation regulates glutamine and glutamate metabolism and FXR ligands might have utility in the treatment of hyperammonemia states.     

Stabilization of molten globule state of papain by urea

Papain exists in molten globule (MG) state at pH 2.0 and in this state protein tends to aggregate in the presence of lower concentrations of guanidine hydrochloride (GuHC1). Such aggregation is prevented if a low concentration of urea is also present in the buffer; in addition, stabilization of the protein is also induced. Intrinsic fluorescence properties of papain as well as ANS binding suggest significant changes in the structure of papain, in the presence of urea with the absence of major changes in the secondary structure of the protein. The GuHCl- and temperature-induced unfolding of papain, in the presence of urea, indicates stabilization of the protein as seen from the higher transition midpoints, when monitored by fluorescence and circular dichroism (CD). However, a similar phenomenon is not seen under neutral conditions in the presence of urea either at low or high concentrations. The utility of prevention of aggregation by urea is also discussed.     

Induction of the allantoin degradative enzymes by allophanic acid, the last intermediate of the pathway

$\text{Saccharomyces cerevisiae}$ can utilize allantoin as a sole nitrogen source by degrading it in five steps to ammonia, “CO₂”, and glyoxylate. We have previously shown that allophanic acid is the inducer of the urea carboxylase: allophanate hydrolase multienzyme complex. Since these enzymes catalyse the last two steps of allantoin degradation, experiments were performed to determine if allophanate was also the inducer of any other enzymes in the pathway. Our data demonstrate that allophanate induces synthesis of at least five of the seven purine degradative enzymes.     

Various effects of prostaglandin E2 on reabsorption of water and urea in the amphibia osmosis-regulating epithelium

Principal similarities between molecular pathways providing the enhancement of water and urea reabsorption under the action of argininvasotocin (AVT) in amphibian urinary bladder suggest that prostaglandin E2 (PGE2) could be a negative regulator of urea transport. To analyse this hypothesis, the role of PGE2 in regulation of urea transport was studied in isolated frog (Rana temporaria L.) urinary bladder. The urea permeability (Pu) was determined from the rate of efflux of (14) Curea from mucosal to serosal solution in isoosmotic conditions. The water permeability was measured in separate experiments in presence of an osmotic gradient. In contrast to water permeability, we were unable to demonstrate any inhibitory effect of 10-1000 nM PGE2 on AVT-stimulated urea transport using a variety of protocols. It was found that basolateral PGE2 exposure (10 nM-1 microM) caused an increase in Pu with no effect on osmotic water flow. The PGE2 effect was markedly inhibited by phloretin, a specific inhibitor of urea transporter. Sulprostone, an EP1/EP3 prostaglandin E2 receptor agonist, had no effect on Pu suggesting the contribution of EP2/EP4 receptor subtypes. In presence of osmotic water flow, the AVT-induced urea transport was significantly higher. This water flow-dependent urea permeability was inhibited by PGE2 although the inhibitory effect was less pronounced in comparison to the action of PGE2 on osmotic water flow. On the basis of these results we can make a conclusion that PGE2 has different role in regulation of water and urea transport in the frog urinary bladder. PGE2 could be considered as a stimulator of urea transport and an inhibitor of osmotic water flow activated by the AVT. The ability of PGE2 to regulate various types of cAMP-dependent transport by different mechanisms seems to be based on the presence of multiple basolateral PGE2 receptor subtypes in amphibian osmosis-regulatory epithelium.     

Effect of 5-azacytidine on the frequency of polycentric chromosomes in cells with micronuclei during exposure to 5-bromodeoxyuridine

Telomeric fusion of metaphase chromosomes was studied in conditions of DNA hypomethylation induced with 5-azacytidine. It was shown that the increased number of dicentric chromosomes was statistically significant in experiments when 5-azacytidine was used together with colcemid and 5-bromodeoxyuridine. These data demonstrate that DNA hypomethylation plays an important role in the manifestation of this phenomenon.     

Inhibiting nitrification and increasing yield of barley by band placement of thiourea with fall-applied urea

Incubation and field experiments were conducted on the influence of thiourea in inhibiting nitrification of urea N, and subsequently on reducing over-winter losses of fallapplied N. Under incubation, most of the added urea placed in bands was nitritified within five or six weeks. However, thiourea when pelleted with urea (21 urea to thiourea by weight) reduced the amount of nitrification to less than one-half during the same period.In two uncropped field experiments in an early dry fall, the application of pelleted urea+thiourea (21) in bands resulted in almost complete inhibition of nitrification of urea for four weeks. In two other uncropped field experiments begun in June with the same fertilizer in bands, half or less of applied N appeared as nitrate after eight weeks. In 10 cropped field experiments with 56 kg N ha^–1, urea+thiourea placed in bands depressed nitrification of fall-applied urea over the winter. By early May, the urea mixed into the soil in the previous fall was nearly all nitrified, while only one-half of the banded urea+thiourea was nitrified. The loss of mineral N by early May was 38% with urea mixed into the soil, but only 18% with bands of urea+thiourea.The 10 sites were cropped to spring barley. The increase in yield of grain or the increase in %N uptake from fertilier N was approximately only one-half as much with fall-applied urea mixed into the soil as compared to spring-applied urea added in the same way. Specifically, fall-applied mixed urea produced 930 kg ha^–1 less grain yield and 32% less N uptake from fertilizer N than did mixed urea in spring. On fall-application there was some benefit from banding of urea or with mixing urea+thiourea pellets into the soil, but the banding of urea+thiourea pellets gave more benefit. Among the fall applications, banded urea+thiourea pellets produced 670 kg ha^–1 more grain yield and 26% more N uptake in grain from fertilizer N than did urea mixed into the soil.     

Evidence for a lymphokine enhancing arginase activity during allograft rejection

The production of urea and ornithine is increased greatly in spleen cell cultures of an allograft recipient in the presence of donor cells (secondary MLC) in comparison to that of primary MLC (without previous allograft). This phenomenon appears after 24 hr of culture and reaches its maximum at 48 hr. The greatest increase in urea production is observed when the recipient spleen cells are collected at the time of allograft rejection. To obtain this extra production of urea, the stimulating cells in MLC should specifically be of the donor type or at least bear one homology with donor cells at the K or D locus. The increased production of urea and ornithine during MLC results from the action of a lymphokine released by recipient cells in the presence of donor cells. This factor acts upon cells present in bone marrow, spleen, and elicited peritoneal cells but is absent or is present in smaller quantities in thymus and lymph node cells. Target cells of this factor possess numerous macrophage features and could be immature cells of the macrophage line. The lymphokine responsible for this phenomenon is heat-stable, destroyed by trypsin, chymotrypsin, and neuraminidase, and has a m.w. around 32,000. It acts upon its target cells by increasing arginase activity, which results in the production of a large amount of ornithine, an important precursor of polyamine biosynthesis.     

CHARACTERIZATION OF NITROGEN UPTAKE BY NATURAL POPULATIONS OF AUREOCOCCUS ANOPHAGEFFERENS (CHRYSOPHYCEAE) AS A FUNCTION OF INCUBATION DURATION,SUBSTRATE CONCENTRATION,LIGHT, AND TEMPERATURE1

Nitrogen uptake studies were conducted during an aestival “brown tide” bloom in Shinnecock Bay, Long Island, New York. The same station was sampled in late July and mid-August 1995 when Aureococcus anophagefferens composed >90% and 30–40% of the total cell density, respectively. Experiments were designed to examine the effect of incubation duration on the uptake kinetics, and the effect of light and temperature dependencies of NH₄⁺, urea, and NO₃^? uptake. Maximum specific uptake rates (V'_max) decreased in the order NH₄⁺, urea, NO₃^? and were nonlinear with time for NH₄⁺ and urea, both of which exhibited an exponential decline between 1 and 10 min and then did nut significantly change for 60 min. Nitrogen uptake kinetic experiments exhibited a typical hyperbolic response for urea and NO₃^?. Half-saturation constants. (K_s) were calculated to he 0.03 and 0.12 μmol · L^?1 for urea and NO₃^?; respectively, but could not be calculated for NH₄⁺ under these experimental conditions. Nutrient uptake rate versus, irradiance (NI) experiments showed that maximum uptake rates occurred at ≤% of incident irradiance on both sampling dates and that values of V′_max-cell (NH₄⁺) were on average 30% greater than V′_max-cell (urea). A7°–9°C temperature decrease in incubation temperature between the two NI experiments in August resulted in a 30% decrease in V′_max-cell(NH₄⁺), no change in V′_max-cell(urea), and a 3–4-fold decrease in calculated K_lt values for both NH₄⁺ and urea. The results from these experiments demonstrate that A. anophagefferens has a higher affinity for NH₄⁺ and urea than for NO₃^? and that this particular species is adapted to use these substrates at low irradiances and concentrations. The data presented in this study are also consistent with the hypothesis that A. anophagefferens may be an oceanic clone that was displaced by an anomalous oceanographic event.     

Urea Production and Putrescine Biosynthesis by Escherichia coli

Cultures of Escherichia coli B and K-12 produce urea during growth in minimal medium. Results of isotopic labeling experiments were consistent with the sole source of urea being from the conversion of arginine to putrescine. Since E. coli itself has no demonstrable urease activity, the rate of urea production is a measure of the flux through the arginine to putrescine pathway.     

Thermodynamic and Kinetic Characterization of a Germ Line Human λ6 Light-Chain Protein: The Relation between Unfolding and Fibrillogenesis

Proteins encoded by the gene segment 6a of the λ variable light-chain repertoire are strongly associated with amyloid deposition. 6aJL2 is a model protein constructed with the predicted sequences encoded by the 6a and JL2 germ line genes. In this work, we characterized the urea- and temperature-induced unfolding of 6aJL2. In the short time scale, spectroscopic, hydrodynamic and calorimetric experiments were compatible with a two-state transition. Furthermore, ΔG, m and the midpoint urea concentration obtained from equilibrium experiments were compatible with those obtained from kinetic experiments. Since fibril formation is a slow process, samples were also incubated for longer times. After incubation for several hours at 37 °C, spectroscopic, hydrodynamic and calorimetric experiments revealed the presence of a partially unfolded off-pathway intermediate around the midpoint urea concentration (1.5-3.0 M urea). In vitro fibrillogenesis assays show that the maximum growth rate for fibril formation and the minimum lag time were obtained at urea concentrations where the partially unfolded state was populated (2.5 M urea at 37 °C). This indicates that this partially unfolded state is critical for in vitro fibril formation. Concentration-dependent kinetics and hydrodynamic properties of the intermediate were consistent with a soluble oligomeric state. The intermediate is formed around the midpoint urea concentration, where the native and unfolded states are equally populated and their rate of interconversion is the slowest. This situation may promote the slow accumulation of an intermediate state that is prone to aggregate.