Regulation Of Enzyme Levels Research Articles

Biochemical investigation of the tryptophan biosynthetic enzyme anthranilate phosphoribosyltransferase in plants

While mammals require the essential amino acid tryptophan (Trp) in their diet, plants and microorganisms synthesize Trp de novo. The five-step Trp pathway starts with the shikimate pathway product, chorismate. Chorismate is converted to the aromatic compound anthranilate, which is then conjugated to a phosphoribosyl sugar in the second step by anthranilate phosphoribosyltransferase (PAT1). As a single-copy gene in plants, all fixed carbon flux to indole and Trp for protein synthesis, specialized metabolism, and auxin hormone biosynthesis proceeds through PAT1. While bacterial PAT1s have been studied extensively, plant PAT1s have escaped biochemical characterization. Using a structure model, we identified putative active site residues that were variable across plants and kinetically characterized six PAT1s (Arabidopsis thaliana (thale cress), Citrus sinensis (sweet orange), Pistacia vera (pistachio), Juglans regia (English walnut), Selaginella moellendorffii (spike moss), and Physcomitrium patens (spreading earth-moss)). We probed the catalytic efficiency, substrate promiscuity, and regulation of these six enzymes and found that the C. sinensis PAT1 is highly specific for its cognate substrate, anthranilate. Investigations of site-directed mutants of the A. thaliana PAT1 uncovered an active site residue that contributes to promiscuity. While Trp inhibits bacterial PAT1 enzymes, the six plant PAT1s that we tested were not modulated by Trp. Instead, the P. patens PAT1 was inhibited by tyrosine, and the S. moellendorffii PAT1 was inhibited by phenylalanine. This structure-informed biochemical examination identified variations in activity, efficiency, specificity, and enzyme-level regulation across PAT1s from evolutionarily diverse plants.

Allosteric Feedback Inhibition Enables Robust Amino Acid Biosynthesis in E.coli by Enforcing Enzyme Overabundance.

SummaryMicrobes must ensure robust amino acid metabolism in the face of external and internal perturbations. This robustness is thought to emerge from regulatory interactions in metabolic and genetic networks. Here, we explored the consequences of removing allosteric feedback inhibition in seven amino acid biosynthesis pathways in Escherichia coli (arginine, histidine, tryptophan, leucine, isoleucine, threonine, and proline). Proteome data revealed that enzyme levels decreased in five of the seven dysregulated pathways. Despite that, flux through the dysregulated pathways was not limited, indicating that enzyme levels are higher than absolutely needed in wild-type cells. We showed that such enzyme overabundance renders the arginine, histidine, and tryptophan pathways robust against perturbations of gene expression, using a metabolic model and CRISPR interference experiments. The results suggested a sensitive interaction between allosteric feedback inhibition and enzyme-level regulation that ensures robust yet efficient biosynthesis of histidine, arginine, and tryptophan in E. coli.

Regulation Systems of Bacteria such as Escherichia coli in Response to Nutrient Limitation and Environmental Stresses.

An overview was made to understand the regulation system of a bacterial cell such as Escherichia coli in response to nutrient limitation such as carbon, nitrogen, phosphate, sulfur, ion sources, and environmental stresses such as oxidative stress, acid shock, heat shock, and solvent stresses. It is quite important to understand how the cell detects environmental signals, integrate such information, and how the cell system is regulated. As for catabolite regulation, F1,6B P (FDP), PEP, and PYR play important roles in enzyme level regulation together with transcriptional regulation by such transcription factors as Cra, Fis, CsrA, and cAMP-Crp. αKG plays an important role in the coordinated control between carbon (C)- and nitrogen (N)-limitations, where αKG inhibits enzyme I (EI) of phosphotransferase system (PTS), thus regulating the glucose uptake rate in accordance with N level. As such, multiple regulation systems are co-ordinated for the cell synthesis and energy generation against nutrient limitations and environmental stresses. As for oxidative stress, the TCA cycle both generates and scavenges the reactive oxygen species (ROSs), where NADPH produced at ICDH and the oxidative pentose phosphate pathways play an important role in coping with oxidative stress. Solvent resistant mechanism was also considered for the stresses caused by biofuels and biochemicals production in the cell.

Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.

BackgroundIt is quite important to simulate the metabolic changes of a cell in response to the change in culture environment and/or specific gene knockouts particularly for the purpose of application in industry. If this could be done, the cell design can be made without conducting exhaustive experiments, and one can screen out the promising candidates, proceeded by experimental verification of a select few of particular interest. Although several models have so far been proposed, most of them focus on the specific metabolic pathways. It is preferred to model the whole of the main metabolic pathways in Escherichia coli, allowing for the estimation of energy generation and cell synthesis, based on intracellular fluxes and that may be used to characterize phenotypic growth.ResultsIn the present study, we considered the simulation of the main metabolic pathways such as glycolysis, TCA cycle, pentose phosphate (PP) pathway, and the anapleorotic pathways using enzymatic reaction models of E. coli. Once intracellular fluxes were computed by this model, the specific ATP production rate, the specific CO2 production rate, and the specific NADPH production rate could be estimated. The specific ATP production rate thus computed was used for the estimation of the specific growth rate. The CO2 production rate could be used to estimate cell yield, and the specific NADPH production rate could be used to determine the flux of the oxidative PP pathway. The batch and continuous cultivations were simulated where the changing patterns of extracellular and intra-cellular metabolite concentrations were compared with experimental data. Moreover, the effects of the knockout of such pathways as Ppc, Pck and Pyk on the metabolism were simulated. It was shown to be difficult for the cell to grow in Ppc mutant due to low concentration of OAA, while Pck mutant does not necessarily show this phenomenon. The slower growth rate of the Ppc mutant was properly estimated by taking into account the lower specific ATP production rate. In the case of Pyk mutant, the enzyme level regulation was made clear such that Pyk knockout caused PEP concentration to be up-regulated and activated Ppc, which caused the increase in MAL concentration and backed up reduced PYR through Mez, resulting in the phenotypic growth characteristics similar to the wild type.ConclusionsIt was shown to be useful to simulate the main metabolism of E. coli for understanding metabolic changes inside the cell in response to specific pathway gene knockouts, considering the whole main metabolic pathways. The comparison of the simulation result with the experimental data indicates that the present model could simulate the effect of the specific gene knockouts to the changes in the metabolisms to some extent.

Effects of arcA and arcB genes knockout on the metabolism in Escherichia coli under aerobic condition

The effects of arcA and arcB genes knockout on the metabolism in Escherichia coli were investigated for the aerobic batch and continuous cultivations based on gene expressions, enzyme activities, and the metabolic flux distributions obtained by 13C-labeling experiment. The integration of the different levels of information indicates that arcB gene knockout activated TCA cycle by gene and enzyme levels regulation as compared with the wild type BW25113 under aerobic condition. The TCA cycle was further activated for arcA gene knockout mutant as compared with arcB mutant. Since the TCA cycle is the source of energy for the cell, its activation together with up-regulation of cyoA gene expression is attractive for the improvement of the cell growth and useful metabolite production, etc. The present research shows the reduction of acetate production in arcA/B mutants, which is the common obstacle for useful metabolite production using E. coli. The activation of TCA cycle together with limited respiratory capacity caused NADH accumulation, which in turn repress the TCA cycle activity by enzyme level regulation. This could be released by adding nicotinic acid.

Heparan Sulfate Proteoglycans as Extracellular Docking Molecules for Matrilysin (Matrix Metalloproteinase 7)

Many matrix metalloproteinases (MMPs) are tightly bound to tissues; matrilysin (MMP-7), although the smallest of the MMPs, is one of the most tightly bound. The most likely docking molecules for MMP-7 are heparan sulfate proteoglycans on or around epithelial cells and in the underlying basement membrane. This is established by extraction experiments and confocal microscopy. The enzyme is extracted from homogenates of postpartum rat uterus by heparin/heparan sulfate and by heparinase III treatment. The enzyme is colocalized with heparan sulfate in the apical region of uterine glandular epithelial cells and can be released by heparinase digestion. Heparan sulfate and MMP-7 are expressed at similar stages of the rat estrous cycle. The strength of heparin binding by recombinant rat proMMP-7 was examined by affinity chromatography, affinity coelectrophoresis, and homogeneous enzyme-based binding assay; the K(D) is 5-10 nM. Zymographic measurement of MMP-7 activity is greatly enhanced by heparin. Two putative heparin-binding peptides have been identified near the C- and N-terminal regions of proMMP-7; however, molecular modeling suggests a more extensive binding track or cradle crossing multiple peptide strands. Evidence is also found for the binding of MMP-2, -9, and -13. Binding of MMP-7 and other MMPs to heparan sulfate in the extracellular space could prevent loss of secreted enzyme, provide a reservoir of latent enzyme, and facilitate cellular sensing and regulation of enzyme levels. Binding to the cell surface could position the enzyme for directed proteolytic attack, for activation of or by other MMPs and for regulation of other cell surface proteins. Dislodging MMPs by treatment with compounds such as heparin might be beneficial in attenuating excessive tissue breakdown such as occurs in cancer metastasis, arthritis, and angiogenesis.

Response of aromatic‐pathway enzymes to changing physiological states of growth in suspension cultures of Nicotiana silvestris

The activity levels of enzymes of aromatic amino acid biosynthesis respond to changing physiological states of growth, as illustrated by results obtained from suspension‐cultured cells of Nicotiana silvestris Speg. et Comes line ANS 1 (2N=24). The experimental system provides a foundation for interpretations about overall regulation of enzyme levels in relationship to growth physiology. Levels of activity for shikimate dehydrogenase (EC 1.1.1.25), prephenate aminotransferase and arogenate dehydrogenase were followed throughout a growth cycle obtained by a conventional subculture protocol. Enzyme date were also obtained from cell cultures maintained in continuous exponential growth for greater than 10 generations (EE cells). Both shikimate dehydrogenase and prephenate aminotransferase exhibited elevated stationary‐phase levels of enzyme, much of which was carried over into a subsequent subculture. At least 4 generations of exponential growth were required before diminution of the latter two enzymes to the levels characteristic of truly exponential‐phase growth (EE cells) occurred. This is reminiscent of the overall behavior of 3‐deoxy‐D‐arabino‐heptulosonate 7‐phosphate (DAHP) synthase (EC 4.1.2.15), specifically attributed to the properties of the cytosolic isozyme species (DAHP synthase‐Co). Elevation of arogenate dehydrogenase also occurred in stationary‐phase cells, but diminished rapidly during lag phase to reach the level characteristic of EE cells.

Cytochromes P-450

1. 1. The cytochromes P-450 are of interest in fields as diverse as biochemistry, pharmacology, mechanistic and synthetic chemistry, carcinogenesis, toxicology, endocrinology, and nutrition. 2. 2. Cytochrome P-450 enzymes are coded by a multi-gene family. 3. 3. The many forms have some elements of similarity in their primary sequences and catalyze chemically equivalent reactions, either mixed-function oxidations or reductions. 4. 4. The catalytic specificity of the individual forms of the enzyme is related to three-dimensional interactions between individual substrates and their binding sites, and the reactions are related in their chemistry. 5. 5. Regulation of enzyme levels appears to involve transcriptional and post-transcriptional aspects.

Regulation of enzyme levels by proteolysis: The role of pest regions

Enzymes can be regulated in a variety of ways. Readily reversible mechanisms, such as phosphorylation, are frequently used by cells to control metabolic pathways. Less often, enzyme levels are regulated by changing the rate at which the protein is destroyed. Although these changes, too, are reversible through protein synthesis, large variations in enzyme concentration can be produced in very short periods of time by combinations of transcriptional control, translational control and rapid degradation. We recently examined the primary sequences of proteins whose intracellular half-lives are less than two hours. With a single exception, each short-lived protein contains one or more regions rich in proline (P), glutamic acid (E), serine (S) and threonine (T). These PEST regions range in length from 12 to 60 residues, and they are often flanked by possibly charged amino acids. Similar inspection of 35 more stable, structurally characterized proteins revealed only three weak PEST regions. All PEST proteins appear to be important regulatory molecules, and their fast turnover surely reflects a metabolic requirement for rapid changes in their concentrations. Known PEST proteins include oncogene products, key enzymes and components of signal pathways. In addition, there are a number of PEST-containing proteins that are suspected of being rapidly degraded. These proteins include Drosophila homeotic proteins (e.g., notch, snake, caudal, ftz and even-skipped) and a host of yeast cdc mutants. PEST regions, which target the molecules containing them for destruction, thus appear to be widely distributed among metabolically unstable proteins.

Studies onAspergillus niger glutamine synthetase: Regulation of enzyme levels by nitrogen sources and identification of active site residues

The specific activity of glutamine synthetase (L-glutamate: ammonia ligase, EC 6.3.1.2) in surface grown Aspergillus niger was increased 3-5 fold when grown on L-glutamate or potassium nitrate, compared to the activity obtained on ammonium chloride. The levels of glutamine synthetase was regulated by the availability of nitrogen source like NH4 + , and further, the enzyme is repressed by increasing concentrations of NH4 +. In contrast to other micro-organisms, the Aspergillus niger enzyme was neither specifically inactivated by NH4+ or L-glutamine nor regulated by covalent modification.Glutamine synthetase from Aspergillus niger was purified to homogenity. The native enzyme is octameric with a molecular weight of 385,000±25,000. The enzyme also catalyses Mn2+ or Mg2+-dependent synthetase and Mn2+-dependent transferase activity.Aspergillus niger glutamine synthetase was completely inactivated by two mol of phenylglyoxal and one mol of N-ethylmaleimide with second order rate constants of 3·8 M–1 min–1 and 760 M–1 min–1 respectively. Ligands like Mg. ATP, Mg. ADP, Mg. AMP, L-glutamate NH4+, Mn2+ protected the enzyme against inactivation. The pattern of inactivation and protection afforded by different ligands against N-ethylamaleimide and phenylglyoxal was remarkably similar. These results suggest that metal ATP complex acts as a substrate and interacts with an arginine ressidue at the active site. Further, the metal ion and the free nucleotide probably interact at other sites on the enzyme affecting the catalytic activity.

IMP dehydrogenase mutants: cell culture model for hyperuricemia.

These studies with wild-type and mutant cells defective in IMP dehydrogenase and the previous data with the adenylosuccinate synthetase-deficient cell line suggest that among the clinical population with dominantly inherited hyperuricemia, patients with partial deficiencies in these enzymes exist. It is hoped that these pharmacogenetic cell culture models for overproduction hyperuricemia will lead to the initiation of a search for hyperuricemia patients with either of these deficiencies. If such patients are found it may be possible to design chemotherapeutic regimens by which effectors (inhibitors) of purine synthesis might ameliorate the overproduction of purines by the de novo pathway.

Modulation of L-phenylalanine ammonia-lyase by pathway intermediates in cell suspension cultures of dwarf French bean (Phaseolus vulgaris L.)

The increase in extractable phenylalanine ammonia-lyase (PAL;EC 4.3.1.5.) activity induced in French bean cell suspension cultures in response to treatment with autoclaved ribonuclease A was inhibited by addition of the phenylpropanoid pathway intermediates cinnamic acid, 4-coumaric acid or ferulic acid. The effectiveness of inhibition was in the order cinnamic acid>4-coumaric acid>ferulic acid. Cinnamic acid also inhibited the PAL activity increase induced by dilution of the suspensions into an excess of fresh culture medium. Addition of low concentrations (<10(-5)M) of the pathway intermediates to cultures at the time of application of ribonuclease gave variable responses ranging from inhibition to 30-40% stimulation of the PAL activity measured at 8 h. Following addition of pathway intermediates to cultures 4-5 h after ribonuclease treatment, rapid increases followed by equally rapid declines in PAL activity were observed. The cinnamic acid-stimulated increase in enzyme activity was unaffected by treatment with cycloheximide at a concentration which gave complete inhibition of the ribonuclease-induced response. However, cycloheximide completely abolished the subsequent decline in enzyme activity. Treatment of induced cultures with α-aminooxy-β-phenylpropionic acid (AOPPA) resulted in increased but delayed rates of enzyme appearance when compared to controls not treated with the phenylalanine analogue. The results are discussed in relation to current views on the regulation of enzyme levels in higher plants.

Regulation of gene expression in primary cultures of adult rat hepatocytes on collagen gels.

The studies described in this paper demonstrate rather conclusively the efficacy of the study of the regulation of gene expression in primary cultures of adult rat hepatocytes. The utilization of these cells in completely defined medium allows one to determine the exact environmental conditions for the regulation of the expression of specific genes. In the studies described in this work, we have demonstrated that the regulation of glucokinase involved three hormones, insulin, corticosteroids, and T3. In contrast, the regulation of an enzyme involved primarily in fatty acid metabolism, ATP-citrate lyase, required only insulin and T3 for its full expression. Cyclic GMP appeared to be involved in the regulation of glucokinase, but not ATP-citrate lyase, a fact that would be extremely difficult to demonstrate clearly in vivo. The regulation of the gluconeogenic enzyme, ornithine aminotransferase, in vitro involved only a single hormone, glucagon, the inhibition of induction by corticoid steroids demonstrable in vivo being absent in cell culture. However, the repressive effect of glucose on the induction of this enzyme was quite comparable to that seen in vivo and was not mediated through cyclic AMP or insulin, based on findings in cell culture. Thus, the requirements for and the mechanisms involved in enzyme induction and repression by hormones and glucose may be much more easily studied in primary cultures of rat hepatocytes than in vivo, or even in hepatoma cell lines, where relatively few genes are expressed as compared with adult liver. In addition to the regulation of enzyme levels, the characteristics of protein secretion may be investigated in primary cultures of rat hepatocytes and compared with the biochemical and physiological parameters in the whole organism. This was exemplified by the study of the synthesis and secretion of alpha 2u-globulin that was secreted into the culture medium in both glycosylated and nonglycosylated forms but was maintained in the circulation in vivo, principally as the glycosylated form. Furthermore, the function of glycosylation in this particular instance may be deduced from a combination of the in vivo and in vitro approaches. The advantages of the use of primary hepatocyte cultures for the study of the regulation of gene expression in mammalian tissue has only recently been explored. Future investigations of the regulation of a variety of enzymes in these cultures as well as a study of the regulation of the synthesis of their messenger RNA are now possible and should provide an exciting system in which to understand at a molecular level the regulation of the expression of a number of genes.

Measurement of the rates of synthesis and degradation of hypoxanthine-guanine phosphoribosyltransferase in human lymphoblasts.

The steady state amount of cellular proteins is determined by the net sum of both their rates of synthesis and degradation. Individual proteins in mammalian cells each have a characteristic rate of degradation as well as synthesis. In recent years, protein catabolism has gained increased recognition as a fundamental intracellular process: 1) during nutritional starvation, 2) in the regulation of enzyme levels, and 3) in the elimination of abnormal proteins.1,2,3

Human mutations affecting aging — a review

A review of human genetic mutations that affect aging and their potential contribution to help understand normal aging proceses is presented. The lifespans of most animal species, including man, have a genetically determined maximum. The lifespan of man appears to have evolved exceedingly rapidly, which suggests that relatively few genes may determine longevity. Analysis of biochemical evolution suggests that the regulation of enzyme levels may underlie most evolutionary changes. There is a wide spectrum of human genetic mutations. Some, such as progeria and Werner's syndrome, produce a phenotype resembling premature aging and may involve genes related to the aging process. Certain human chromosomal abnormalities, such as Down's syndrome, produce an appearance of premature aging and may be due to abnormal gene regulatory mechanisms. Progress in understanding the genetic mechanisms underlying aging is likely to come from elucidation of the molecular defects that result in the premature aging syndromes and from insights gained regarding the regulatory mechanisms governing eukaryotic genetic expression.

Regulation of enzyme levels in phenylpropanoid biosynthesis: Characterization of the modulation by light and pathway intermediates

The accumulation of chlorogenic acid in disks of potato ( Solanum tuberosum cv King Edward) tuber tissue is controlled by rapid, interrelated changes in the activity levels of the biosynthetic enzymes phenylalanine ammonia-lyase (EC 4.3.1.5), cinnamic acid 4-hydroxylase (EC 1.14.13.11), and hydroxycinnamoyl-CoA:quinic acid hydroxycinnamoyl transferase (EC 2.3.1.-). The modulation of enzyme levels by light and by the pathway intermediates cinnamic acid and p-coumaric acid has been characterized by (a) effectiveness at various stages during the development of enzyme activity, (b) the kinetics of the regulatory responses, and (c) application of the inhibitors cordycepin, cycloheximide, and actinomycin-D. Using these criteria, clear mechanistic differences between modulation of enzyme levels by light and modulation by pathway intermediates have been observed. Photomodulation of enzyme levels occurs by a relatively slow, actinomycin-D-sensitive mechanism. In contrast, modulation by pathway intermediates occurs by a rapid, post-transcriptional mechanism acting at the rate-limiting step in the development of enzyme activity. This mechanism is consistent with the hypothesis that the coordination of enzyme levels is maintained by modulation by pathway intermediates.

Regulation of enzyme levels by phytochrome in mustard cotyledons: Multiple mechanisms?

Phytochrome controls the appearance of many enzymes in the mustard (Sinapis alba L.) cotyledons. The problem has been whether the effect of phytochrome on the appearance of enzymes in this organ is due to a common initial action of Pfr, e.g. due to the liberation of a "second messenger". We have compared the modulation by light (phytochrome) of the appearance of phenylalanine ammonia lyase (PAL)(+) and ribulosebisphosphate carboxylase (Carboxylase)(+). PAL becomes detectable in the mustard cotyledons at 27 h after sowing while Carboxylase starts to appear only at 42 h after sowing (starting points, 25° C). The starting points cannot be shifted by light. As a major result, in the case of PAL the inductive effect of continuous red light (given from the time of sowing) remains fully reversible by 756 nm-light up to the starting point (27 h after sowing) while with Carboxylase full reversibility in continuous red light is lost at approximately 15 h after sowing. While the induction of Carboxylase is already saturated at a very low level of Pfr (e.g. continuous 756 nm-light saturates the response) and does not depend on irradiance (e.g. continuous 675 mW m(-2) red light and 67.5 mW m(-2) red light lead to the same time course), PAL induction is a graded response over a wide range of Pfr doses and depends strongly on the fluence rate (high irradiance response, HIR). It is concluded that PAL induction and Carboxylase induction are not only separated in time but differ in every regard except that both responses are mediated by phytochrome.The present data support the previous conclusion that the specification of the temporal and spatial pattern of development is independent of phytochrome even though the realization of the pattern of development can only occur in the presence of phytochrome (Pfr). It seems that there is no feedback from pattern realization to pattern specification.

Regulation of enzyme levels in the rat epididymis by androgens

Regulation of enzyme levels in the rat epididymis by androgens

Comparison of mucosal metabolism in the small intestine of specific pathogen-free and conventional rats.

The fresh weight of jejunal mucosa was significantly lower in specific pathogen-free (SPF) than in conventional rats. An almost two-fold higher activity of mucosal alkaline phosphatase, ATPase, and maltase was observed in the duodenum and jejunum of the SPF rats. The SPF rats also had a significantly higher glucuronide synthesizing activity in tissue slices from the duodenum, where UDP glucuronyltransferase activity was also slightly higher than in conventional controls. The results suggest that the microflora is of importance in the regulation of enzyme levels in the small intestinal mucosa of the rat.

Lactate dehydrogenase ontogeny, paternal gene activation, and tetramer assembly in embryos of brook trout, lake trout, and their hybrids.

Measurement of lactate dehydrogenase in reciprocal hybrids of trout during development revealed that a maternal effect was involved in the regulation of enzyme levels until resorption of the yolk sac was completed. Malate dehydrogenase specific activities were the same in these embryos and larvae. The more negatively charged B subunits of LDH predominated during early stages of embryogenesis in lake trout and brook trout with an increase in synthesis of A subunits evident as development progressed. Activation of the paternal A gene in reciprocal hybrids occurred at a relatively late stage with the LDH subunit specific to the retina appearing after hatching. Analysis of brook trout progeny from a cross of parental types with a variant and wild-type B subunit suggested nonrandom LDH tetramer assembly which may be genetically controlled.