Computer simulation of purine metabolism

A computer model of purine metabolism, including catabolism, salvage pathways and interconversion among nucleotides, is given. Steady-state rate equations corresponding to metabolic enzymes are written based on information from the literature about their kinetic behaviour. Numerical integration of this set of equations is performed employing selected parameters taken from the literature. After stabilization of purine compound concentrations is reached, simulation of enzyme deficit and enzyme overproduction is carried out. The latter is calculated by varying specified maximum velocities in the numerical integration. A pattern of intermediate metabolite concentrations is found. These results form a basis for the comparison of normal patterns or patterns reflecting the effects of inborn errors of metabolism. The aim of this paper is to demonstrate the usefulness of this computer simulation method in complex metabolism pathways.     

The purine metabolism of human erythrocytes

This review summarizes currently available information about a crucial part of erythrocyte metabolism, that is, purine nucleotide conversions and their relationships with other conversion pathways. We describe the cellular resynthesis, interconversion, and degradation of purine compounds, and also the regulatory mechanisms in the conversion pathways. We also mention purine metabolism disorders and their clinical consequences. The literature is fragmentary because studies have concentrated only on selected aspects of purine metabolism; hence the need for a synthetic approach. Published in Russian in Biokhimiya, 2006, Vol. 71, No. 5, pp. 581–591.     

Regulation of purine metabolism in lymphocytes

Three general questions regarding nucleosides and lymphocytes are discussed: (a) Why are so many measurements being made of adenosine deaminase activity, what do the results mean, and why is there still disagreement about some of the conclusions; (b) what do we understand about nucleosides and lymphocyte death; and (c) to what extent do we really understand nucleoside and nucleotide metabolism in lymphocytes? Experimental studies show that treatment of mice with deoxycoformycin, to produce accumulation of deoxyadenosine, leads to rapid thymus involution, elevated dATP concentrations in thymus and liver, and inhibition of adenosylhomocysteine hydrolase in these tissues. Deoxyguanosine inhibits the growth of mouse lymphoma L5178Y cells, and this toxicity is prevented by deoxycytidine plus adenine. In cells treated with deoxyguanosine, concentrations of both GTP and dGTP are elevated, and this is not affected by deoxycytidine. Adenine, however, reduces GTP concentrations to normal, and prevents most of the elevation in dGTP concentrations. Contrary to previous belief, it has been demonstrated that lymphocytes and nucleated bone marrow cells will synthesize purine nucleotides de novo if incubated in an appropriate medium; carbon dioxide is particularly important for this process.     

Enzymes of the purine metabolism in rat brain microsomes

Rat brain microsomes, when they are suspended in moderate ionic strength medium, released enzyme activities of lactate dehydrogenase (LDH, E.C.1.1.1.27), malate dehydrogenase (MDH, E.C.1.1.1.37), adenosine deaminase (ADA, E.C.3.5.4.4), guanine deaminase (GAH, E.C.3.5.4.3), and purine nucleoside phosphorylase (PNP, E.C.2.1.2.4). The activities released decreased when the saline concentration of the medium was increased and the opposite occurred when 50 mM, pH 7.4 sodium phosphate medium was used. Rat brain microsomes that had been extracted previously by moderate ionic strength solutions still had activities of all the enzymes tested, and released these activities upon sonication or deoxycholate (DOC) treatment. The proportion of the activity released was similar for all the enzymes. DOC treatment released higher enzymic activities and a smaller amount of protein than sonication did. The proportion of activities released was similar to that found in the 105,000 g supernatant. The suspension of microsomes still retained activities of the above-mentioned enzymes after consecutive extractions with increasing concentrations of detergent solutions (DOC and Triton X-100). The amount of enzymic activities released from the microsomes by sonication or DOC treatment did not depend on the protein composition of the homogenization medium. Thus, on increasing the enzyme concentration in the homogenization medium, the activities released did not increase in parallel. The set of results obtained showed that the microsomal fraction is as useful as the cytosolic one for studying purine catabolism in rat brain. Furthermore, the conditions in which purine enzymes are attached to the microsomal fraction are probably closer to "in vivo" conditions than those in which these enzymes are found in the soluble fraction.     

Mathematical modelling of the purine metabolism of the rat liver

The regulation of the purine metabolism of the rat liver is studied on the basis of a mathematical model which comprises rate laws and kinetic constants of all physiologically relevant reactions. The computed stationary and time-dependent concentrations are in good accordance with experimental data obtained in the ischaemic rat liver and in isolated hepatocytes. In particular, model-based simulations of the adenine nucleotide metabolism have been performed for situations where ATP-deficient states of the cell (hypoxia, anoxia or ischaemia) of various length are followed by onset of ATP production (reoxygenation). These simulations confirm the experimentally observed incomplete recovery of ATP and of the total pool of adenine nucleotides within a few hours of reoxygenation after long-term ATP depletion. Therefore, it can be concluded that this phenomenon is an intrinsic regulatory property of the purine metabolism and not necessarily due to some irreversible changes in the activity of the enzymes involved.     

Inborn errors of purine and pyrimidyne metabolism

Inborn errors of purine and pyrimidine metabolism (P/P) manifest themselves by a variety of clinical picture. They may be recognized at any age and may affect any system--immunological, hematological, neurological, musculoskeletal, and because of the relative insolubility of purine bases, renal as well. At present, a total of 30 defects have been described. Fifteen of them can have serious clinical consequences. Analysis of prevalence estimated by comparing the number of detected P/P patients in Poland and the number of newborns as well as delay of diagnosis, point at insufficient degree of detectability of these defects in our country. It is necessary to improve the education among physicians as well as to popularize screening methods for these defects.     

Altered purine and pyrimidine metabolism in erythrocytes with purine nucleoside phosphorylase deficiency

Purine and pyrimidine metabolism was compared in erythrocytes from three patients from two families with purine nucleoside phosphorylase deficiency and T-cell immunodeficiency, one heterozygote subject for this enzyme deficiency, one patient with a complete deficiency of hypoxanthine-guanine phosphoribosyltransferase, and two normal subjects. The erythrocytes from the heterozygote subject were indistinguishable from the normal erythrocytes. The purine nucleoside phosphorylase deficient erythrocytes had a block in the conversion of inosine to hypoxanthine. The erythrocytes with 0.07% of normal purine nucleoside phosphorylase activity resembled erythrocytes with hypoxanthine-guanine phosphoribosyltransferase deficiency by having an elevated intracellular concentration of PP-ribose-P, increased synthesis of PP-ribose-P, and an elevated rate of carbon dioxide release from orotic acid during its conversion to UMP. Two hypotheses to account for the associated immunodeficiency—that the enzyme deficiency leads to a block of PP-ribose-P synthesis or inhibition of pyrimidine synthesis—could not be supported by observations in erythrocytes from both enzyme-deficient families.This work was supported by U.S. Public Health Service Grant AM 19674 and 5 M01 RR 42 and by a Grant-In-Aid from American Heart Association (77-849) and with funds contributed in part by the Michigan Heart Association. N.L.E. is a Rheumatology Fellow from the Rackman Arthritis Research Unit supported by Training Grant USPHS AM 07080.     

Mitochondrial purine and pyrimidine metabolism and beyond

ABSTRACT

Carefully balanced deoxynucleoside triphosphate (dNTP) pools are essential for both nuclear and mitochondrial genome replication and repair. Two synthetic pathways operate in cells to produce dNTPs, e.g., the de novo and the salvage pathways. The key regulatory enzymes for de novo synthesis are ribonucleotide reductase (RNR) and thymidylate synthase (TS), and this process is considered to be cytosolic. The salvage pathway operates both in the cytosol (TK1 and dCK) and the mitochondria (TK2 and dGK). Mitochondrial dNTP pools are separated from the cytosolic ones owing to the double membrane structure of the mitochondria, and are formed by the salvage enzymes TK2 and dGK together with NMPKs and NDPK in postmitotic tissues, while in proliferating cells the mitochondrial dNTPs are mainly imported from the cytosol produced by the cytosolic pathways. Imbalanced mitochondrial dNTP pools lead to mtDNA depletion and/or deletions resulting in serious mitochondrial diseases. The mtDNA depletion syndrome is caused by deficiencies not only in enzymes in dNTP synthesis (TK2, dGK, p53R2, and TP) and mtDNA replication (mtDNA polymerase and twinkle helicase), but also in enzymes in other metabolic pathways such as SUCLA2 and SUCLG1, ABAT and MPV17. Basic questions are why defects in these enzymes affect dNTP synthesis and how important is mitochondrial nucleotide synthesis in the whole cell/organism perspective? This review will focus on recent studies on purine and pyrimidine metabolism, which have revealed several important links that connect mitochondrial nucleotide metabolism with amino acids, glucose, and fatty acid metabolism.     

The effect of fructose on purine metabolism in the lung

Oral administration of fructose to rats resulted in a transient depression of pulmonary adenosine triphosphate and a marked increase in serum uric acid and allantoin. Accompanying this increase were elavations in activity of 5′ nucleotidase, adenylate deaminase and adenosine deaminase in the lung. Increased enzyme activity resulted from enhanced protein synthesis as demonstrated by an increased incorporation of (4-5-³H) leucine and a partial inhibition by inhibitors of protein synthesis. These data confirm the presence of an active purine nucleotide cycle in lung and that the enzymes involved in purine catabolism can be stimulated in a manner similar to those in the liver.     

Modulation of macrophage superoxide release by purine metabolism

Metabolic flux through the purine salvage pathway appears to modulate superoxide secretion by elicited macrophages. Exogenous adenosine, the first substrate of this pathway, stimulates superoxide secretion, and Allopurinol, a specific inhibitor of xanthine oxidase, inhibits superoxide secretion. The effects of these agents are additive since it was possible for each to neutralize the effects of the other when given in combination. In these experiments, the purine salvage pathway was responsible for over ten times the superoxide production attributable to the NADPH oxidase system.     

The purine and pyrimidine metabolism of Tetrahymena pyriformis

The metabolism of purines and pyrimidines by the ciliated protozoan Tetrahymena was investigated with the use of enzymatic assays and radioactive tracers. A survey of enzymes involved in purine metabolism revealed that the activities of inosine and guanosine phosphorylase (purine nucleoside: orthophosphate ribosyltransferase, E.C. 2.4.2.1) were high, but adenosine phosphorylase activity could not be demonstrated. The apparent K_m for guanosine in the system catalyzing its phosphorolysis was 4.1 ± 0.6 × 10^?3 M. Pyrophosphorylase activities for IMP and GMP (GMP: pyrophosphate phosphoribosyltransferase, E.C. 2.4.2.8), AMP (AMP: pyrophosphate phosphoribosyltransferase, E.C. 2.4.2.7), and 6-mercaptopurine ribonucleotide were also found in this organism; but a number of purine and pyrimidine analogs did not function as substrates for these enzymes. The metabolism of labeled guanine and hypoxanthine by intact cells was consistent with the presence of the phosphorylases and pyrophosphorylases of purine metabolism found by enzymatic studies. Assays for adenosine kinase (ATP: adenosine 5'-phosphotransferase, E.C. 2.7.1.20) inosine kinase, guanosine kinase, xanthine oxidase (xanthine: O₂ oxidoreductase, E.C. 1.2.3.2), and GMP reductase (reduced-NADP: GMP oxidoreductase [deaminating], E.C. 1.6.6.8) were all negative. In pyrimidine metabolism, cytidine-deoxycytidine deaminase (cytidine aminohydrolase, E.C. 3.5.4.5), thymidine phosphorylase (thymidine: orthophosphate ribosyltransferase, E.C. 2.4.2.4), and uridine-deoxyuridine phosphorylase (uridine: orthophosphate ribosyltransferase, E.C. 2.4.2.3) were active; but cytidine kinase, uridine kinase (ATP: uridine 5'-phosphotransferase, E.C. 2.7.1.48), and CMP pyrophosphorylase could not be demonstrated.     

Short term metabolism of urea and purine cytokinins

Approximately 20 to 25% of the cytokinin benzyladenine (BA) taken up by soybean tissues in culture is converted to a stable, long-lived derivative which contains BA as part of its structure. This derivative may be metabolically related to 6-benzylamino-9-β-d-ribofuranosylpurine 5′-monophosphate (BAMP). In in vivo incubations of 2 hours or less, we recover only BA, benzyladenosine, and BAMP. Benzyladenosine never accounts for more than 10% of the total radioactivity while BAMP builds up to about 20% of the total within 2 to 4 hours. After this period it begins to disappear, and a new, unidentified substance arises at a rate which roughly parallels the loss of BAMP. After about 48 hours this substance, which has good cytokinin activity, accounts for some 20 to 25% of the total radioactivity and persists at this level for at least 60 days. In the meantime the remainder of the BA, as well as benzyladenosine and BAMP, disappear completely. In addition, evidence is presented which suggests that the urea cytokinins are not active as such but first are metabolically transformed into other substances.     

Effects of benzimidazole on the purine and pyrimidine metabolism of yeast

Yeast cells inhibited by benzimidazole accumulate hypoxanthine with an associated efflux of xanthine. Unlike control cells, inhibited cells contain no detectable free UMP and CMP. Benzimidazole decreases uptake of [8-¹⁴C]-hypoxanthine into the intracellular pool of hypoxanthine and xanthine but causes radioactive xanthine to accumulate in the medium. In inhibited cultures there is a threefold increase in incorporation of [8-¹⁴C]hypoxanthine into the total (intracellular plus extracellular) xanthine. Uptake of [8-¹⁴C]hypoxanthine into free nucleotides and into bound adenine and guanine was inhibited by 70%. Uptake of [U-¹⁴C]glycine into IMP, AMP, GMP, DNA and RNA was also substantially decreased. Incorporation of [2-¹⁴C]uracil into the intracellular uracil pool was inhibited by 30% and into free uridine and cytidine by over 90%. Benzimidazole inhibited incorporation of [8-³H]IMP into AMP and GMP, and decreased substantially the activity of glutamine-amidophosphoribosyltransferase (EC 2.4.2.14). Yeast cultures were shown to N-ribotylate benzimidazole. Results are consistent with benzimidazole inhibiting yeast growth by competing for P-rib-PP and so depriving other ribotylation processes such as the ‘salvage’ pathways and de novo synthesis of purines and pyrimidines.     

Mapping two genes in the purine metabolism pathway of soybean.

Mapping genes in biochemical pathways allow study of the genomic organization of pathways and geneic relationships within these pathways. Additionally, molecular markers located within the boundaries of a specific gene sequence represent important marker assisted selection resources. We report map locations of two geneic markers from the purine synthesis pathway in soybean (Glycine max (L. merr.)), utilizing a 90 plant F(2) population created from the cross of "DT97-4290" x "DS97-84-1". Primers were designed based on sequences from annotated soybean complimentary DNA. A polymorphic, co-dominant, sequence-characterized amplified region marker was created for hypoxanthine phosphoribosyl transferase (EC 2.4.2.8). Linkage analysis placed this gene on linkage group (LG) O. In addition, a single-nucleotide polymorphism (SNP) marker was developed for a urate oxidase gene (EC 1.7.3.3). Linkage analysis of the SNP placed the urate oxidase gene on LG I. For both genes, amplicon sequence data confirmed the identification of the respective gene. Mapping these genes represents the first step in understanding the genomic organization of the purine biochemical pathway in soybean.