Degradation Of Uracil Research Articles

The Allosteric Regulation of Β-Ureidopropionase Depends on Fine-Tuned Stability of Active-Site Loops and Subunit Interfaces.

The activity of β-ureidopropionase, which catalyses the last step in the degradation of uracil, thymine, and analogous antimetabolites, is cooperatively regulated by the substrate and product of the reaction. This involves shifts in the equilibrium of the oligomeric states of the enzyme, but how these are achieved and result in changes in enzyme catalytic competence has yet to be determined. Here, the regulation of human β-ureidopropionase was further explored via site-directed mutagenesis, inhibition studies, and cryo-electron microscopy. The active-site residue E207, as well as H173 and H307 located at the dimer-dimer interface, are shown to play crucial roles in enzyme activation. Dimer association to larger assemblies requires closure of active-site loops, which positions the catalytically crucial E207 stably in the active site. H173 and H307 likely respond to ligand-induced changes in their environment with changes in their protonation states, which fine-tunes the active-site loop stability and the strength of dimer-dimer interfaces and explains the previously observed pH influence on the oligomer equilibrium. The correlation between substrate analogue structure and effect on enzyme assembly suggests that the ability to favourably interact with F205 may distinguish activators from inhibitors. The cryo-EM structure of human β-ureidopropionase assembly obtained at low pH provides first insights into the architecture of its activated state. and validates our current model of the allosteric regulation mechanism. Closed entrance loop conformations and dimer-dimer interfaces are highly conserved between human and fruit fly enzymes.

Effects of UV and Calcium Perchlorates on Uracil Deposited on Strontium Fluoride Substrates at Mars Pressure and Temperature.

Organic matter is actively searched on Mars with current and future space missions as it is a key to detecting potential biosignatures. Given the current harsh environmental conditions at the surface of Mars, many organic compounds might not be preserved over a long period as they are exposed to energetic radiation such as ultraviolet light, which is not filtered above 190 nm by the martian atmosphere. Moreover, the presence of strong oxidizing species in the regolith, such as perchlorate salts, might enhance the photodegradation of organic compounds of astrobiological interest. Because current space instruments analyze samples collected in the upper surface layer, it is necessary to investigate the stability of organic matter at the surface of Mars. Previous experimental studies have shown that uracil, a molecule relevant to astrobiology, is quickly photolyzed when exposed to UV radiation under the temperature and pressure conditions of the martian surface with an experimental quantum efficiency of photodecomposition (φexp) of 0.30 ± 0.26 molecule·photon-1. Moreover, the photolysis of uracil leads to the formation of more stable photoproducts that were identified as uracil dimers. The present work aims to characterize the additional effect of calcium perchlorate detected on Mars on the degradation of uracil. Results show that the presence of calcium perchlorate enhances the photodecomposition of uracil with φexp = 12.3 ± 8.3 molecule·photon-1. Although some of the photoproducts formed during these experiments are common to those formed from pure uracil only, the Fourier transformation infrared (FTIR) detection of previously unseen chemical functions such as alkyne C ≡ C or nitrile C ≡ N has shown that additional chemical species are formed in the presence of calcium perchlorate in the irradiated sample. This implies that the effect of calcium perchlorate on the photolysis of uracil is not only kinetic but also related to the nature of the photoproducts formed.

Design of Uracil-Modified DNA Nanotubes for Targeted Drug Release via DNA-Modifying Enzyme Reactions.

DNA nanostructure-based responsive drug delivery has become an increasingly potent method in cancer therapy. However, a variety of important cancer biomarkers have not been explored in searching of new and efficient targeted delivery systems. Uracil degradation glycosylase and human apurinic/apyrimidinic endonuclease are significantly more active in cancer cells. Here, we developed uracil-modified DNA nanotubes that can deliver drugs to tumor cells through an enzyme-induced disassembly process. Although the reaction of these enzymes on their natural DNA substrates has been established, their reactivity on self-assembled nanostructures of nucleic acids is not well understood. We leveraged molecular dynamic simulation based on coarse-grained model to forecast the enzyme reactivity on different DNA designs. The experimental data are highly consistent with the simulation results. It is the first example of molecule simulation being used to guide the design of enzyme-responsive DNA nano-delivery systems. Importantly, we found that the efficiency of drug release from the nanotubes can be regulated by tuning the positions of uracil modification. The DNA nanotubes equipped with cancer-specific aptamer AS1411 are used to deliver doxorubicin to tumor-bearing mice not only effectively inhibiting tumor growth but also protecting major organs from drug-caused damage. We believe that this work provides new knowledge on and insights into future design of enzyme-responsive DNA-based nanocarriers for drug delivery.

Individual and combined degradation of N-heterocyclic compounds under sulfate radical-based advanced oxidation processes

Although the inhibitory effect of purines and phenols on the degradation of N-heterocyclic compounds under UV/peroxymonosulfate (PMS) has been reported, the understanding of contaminants' underlying mechanisms and kinetics is still very limited. In this study, five omnipresent nitrogenous bases (adenine, guanine, cytosine, thymine, and uracil) in the aquatic environment were used to study the inhibitory effect of N-heterocyclic compounds under UV/PMS by quantum chemical calculations. We found that HO• and SO4•− initiate base degradation with second-order rate constants of (0.11 – 15.6) × 109 M−1 s−1 and (7.25 – 13.5) × 109 M−1 s−1, respectively, and the primary products contain hydroxyl derivatives (HO-P), intermediate radicals (P(-H)•) and cationic radicals (P•+, only for purines). Because of the lower oxidation potentials of HO-P than their parent compounds (P), we first proposed a self-inhibition pathway in which HO-P can revert P(-H)• and P•+ back to P through H atom abstraction and single electron transfer reactions, respectively. A more significant self-inhibition was found in the degradation of uracil than that of adenine under UV/PMS because the former has a higher yield of hydroxylated derivatives. The main hydroxylated product (6-HO-U) of uracil repairs the uracil radical (U(-4H)•) at the reaction rate constants of 1.01 × 109 M−1 s−1. The combined degradation of bases showed that the reduction rate constants of purine cationic radicals have a linear relationship with the oxidation potentials of reductants. In the adenine-uracil mixture system, adenine inhibits uracil degradation by repairing U(-4H)• (2.33 × 105 M−1 s−1). This work revealed the mechanisms and kinetics of self-inhibition and joint-degradation of N-heterocyclic compounds, which is of great significance for understanding the collective removal of contaminants in the real water environment.

Reconstruction and analysis of genome-scale metabolic model of weak Crabtree positive yeast Lachancea kluyveri

Lachancea kluyveri, a weak Crabtree positive yeast, has been extensively studied for its unique URC pyrimidine catabolism pathway. It produces more biomass than Saccharomyces cerevisiae due to the underlying weak Crabtree effect and resorts to fermentation only in oxygen limiting conditions that renders it as a suitable industrial host. The yeast also produces ethyl acetate as a major overflow metabolite in aerobic conditions. Here, we report the first genome-scale metabolic model, iPN730, of L. kluyveri comprising of 1235 reactions, 1179 metabolites, and 730 genes distributed in 8 compartments. The in silico viability in different media conditions and the growth characteristics in various carbon sources show good agreement with experimental data. Dynamic flux balance analysis describes the growth dynamics, substrate utilization and product formation kinetics in various oxygen-limited conditions. We have also demonstrated the effect of switching carbon sources on the production of ethyl acetate under varying oxygen uptake rates. A phenotypic phase plane analysis described the energetic cost penalty of ethyl acetate and ethanol production on the specific growth rate of L. kluyveri. We generated the context specific models of L. kluyveri growing on uracil or ammonium salts as the sole nitrogen source. Differential flux calculated using flux variability analysis helped us in highlighting pathways like purine, histidine, riboflavin and pyrimidine metabolism associated with uracil degradation. The genome-scale metabolic construction of L. kluyveri will provide a better understanding of metabolism behind ethyl acetate production as well as uracil catabolism (pyrimidine degradation) pathway. iPN730 is an addition to genome-scale metabolic models of non-conventional yeasts that will facilitate system-wide omics analysis to understand fungal metabolic diversity.

A Pathway for Degradation of Uracil to Acetyl Coenzyme A in Bacillus megaterium.

Bacteria utilize diverse biochemical pathways for the degradation of the pyrimidine ring. The function of the pathways studied to date has been the release of nitrogen for assimilation. The most widespread of these pathways is the reductive pyrimidine catabolic pathway, which converts uracil into ammonia, carbon dioxide, and β-alanine. Here, we report the characterization of a β-alanine:pyruvate aminotransferase (PydD2) and an NAD+-dependent malonic semialdehyde dehydrogenase (MSDH) from a reductive pyrimidine catabolism gene cluster in Bacillus megaterium Together, these enzymes convert β-alanine into acetyl coenzyme A (acetyl-CoA), a key intermediate in carbon and energy metabolism. We demonstrate the growth of B. megaterium in defined medium with uracil as its sole carbon and energy source. Homologs of PydD2 and MSDH are found in association with reductive pyrimidine pathway genes in many Gram-positive bacteria in the order Bacillales Our study provides a basis for further investigations of the utilization of pyrimidines as a carbon and energy source by bacteria.IMPORTANCE Pyrimidine has wide occurrence in natural environments, where bacteria use it as a nitrogen and carbon source for growth. Detailed biochemical pathways have been investigated with focus mainly on nitrogen assimilation in the past decades. Here, we report the discovery and characterization of two important enzymes, PydD2 and MSDH, which constitute an extension for the reductive pyrimidine catabolic pathway. These two enzymes, prevalent in Bacillales based on our bioinformatics studies, allow stepwise conversion of β-alanine, a previous "end product" of the reductive pyrimidine degradation pathway, to acetyl-CoA as carbon and energy source.

Outside Front Cover: Biotechnology Journal 3/2020

A label-free and enzyme-free uracil DNA glycosylase (UDG) activity assay is described. In the upper left bubble, detection duplex probe serving as substrate for UDG releases a catalyst strand (blue strand) due to the UDG-catalyzed degradation of uracil, which subsequently promotes the toehold-mediated strand displacement (TMSD) reaction in the upper right bubble. As a result, active split G-quadruplexes are produced leading to the colorimetric response in the bottom bubble. This is reported by Youna Kim, Yeonkyung Park, Chang Yeol Lee, Hyun Gyu Park in article 1900420.

A novel way to synthesize pantothenate in bacteria involves β-alanine synthase present in uracil degradation pathway.

Pantothenate is an indispensable vitamin precursor of the synthesis of coenzyme A (CoA), a key metabolite required in over 100 metabolic reactions. β‐Alanine (β‐ala) is an indispensable component of pantothenate. Due to the metabolic relevance of this pathway, we assumed that orthologous genes for ß‐alanine synthesis would be present in the genomes of bacteria, archaea, and eukaryotes. However, comparative genomic studies revealed that orthologous gene replacement and loss of synteny occur at high frequency in panD genes. We have previously reported the atypical plasmid‐encoded location of the pantothenate pathway genes panC and panB (two copies) in R. etli CFN42. This study also revealed the unexpected absence of a panD gene encoding the aspartate decarboxylase enzyme (ADC), required for the synthesis of β‐ala. The aim of this study was to identify the source of β‐alanine in Rhizobium etli CFN42. In this study, we present a bioinformatic analysis and an experimental validation demonstrating that the source of β‐ala in this R. etli comes from β‐alanine synthase, the last enzyme of the uracil degradation pathway.

The Arabidopsis thaliana gene annotated by the locus tag At3g08860 encodes alanine aminotransferase.

The aminotransferase gene family in the model plant Arabidopsis thaliana consists of 44 genes, eight of which are suggested to be alanine aminotransferases. One of the putative alanine aminotransferases genes, At3g08860, was attributed the function of alanine:glyoxylate aminotransferase/β‐alanine:pyruvate aminotransferase based on the analysis of gene expression networks and homology to other β‐alanine aminotransferases in plants. It was earlier demonstrated that At3g08860 is specifically upregulated in response to osmotic stress, but not other stresses (β‐alanine is an osmoprotectant in plants). Furthermore, it was shown that the expression of At3g08860 is highly coordinated with the genes of the uracil degradation pathway leading to the non‐proteinogenic amino acid β‐alanine. These evidence were suggestive of the involvement of At3g08860 in β‐alanine metabolism. However, direct experimental evidence for the function of At3g08860 was lacking, and therefore, the goal of this study was to elucidate the function of the uncharacterized aminotransferase annotated by the locus tag At3g08860. The cDNA of At3g08860 was demonstrated to functionally complement two E. coli mutants auxotrophic for the amino acids, L‐alanine (proteinogenic) and β‐alanine (non‐proteinogenic). Enzyme activity using purified recombinant At3g08860 further demonstrated that the enzyme is endowed with L‐alanine:glyoxylate aminotransferase activity.

Characterization of the Pyrimidine Catabolic Pathway of Oryza sativa

ObjectiveTo characterize plant pyrimidine catabolic enzymes and to identify potential candidate for additional enzymes participating in the pathwayRice is a primary global food source and is an important crop in Colombia. Its production is affected by abiotic stress, caused by climate change and other factors. Recently, genes of the pyrimidine catabolic pathway have emerged as potential participants in the abiotic stress response of plants.In mammals, three enzymes are involved in the degradation of uracil or thymine. The first is dihydropyrimidine dehydrogenase (DHPD), the second is dihydropyrimidinase (DHP) and the last is β‐ureidopropionase (β‐UP). Liu and coworkers (2009) found that overexpression of DHPD in rice plants (OsDHPD) results in tolerance to salt and drought stress, however, in that study OsDHPD was misidentified as a type I dihydroorotate dehydrogenase. DHP appears to be involved in cold stress‐response in grass (Xuan et al., 2013). In addition, the overexpression of β‐UP in transgenic tomatoes plants made them resistant to heat during anthesis (Shen et al., 2014). The role of pyrimidine catabolism in stress tolerance could be related to this pathway's production of precursors for proline biosynthesis. In plants, a complete characterization of the pathway is lacking. Comparison of plant and mammalian DHPD sequences showed that the plant protein lacks a domain needed for binding NADH(P), FAD, and Fe/S clusters, suggesting that another, unidentified, partner protein should be interacting with OsDHPD.ResultsWe cloned and expressed three enzymes of the pathway, OsDHPD, OsDHP and Osβ‐UP. The third enzyme, Osβ‐UP, was soluble, and preliminary kinetics revealed a Km 0.85 ± 0.11 mM for 3‐ureidopropionic acid, and a specific activity apparently 10‐fold faster (Vmax 384.3 ± 12.0 nmol/min/mg) than the Arabidopsis thaliana recombinant enzyme (30 nmol/min/mg) (Walsh et al., 2001). Truncations lacking chloroplast localization signals were required to produce soluble recombinant proteins of the first two enzymes. Truncated OsDHPD, was soluble, but inactive, presumably because it requires a partner protein for catalysis. By screening the rice database for proteins with the appropriate combination of cofactors we identified two potential candidates that may act as partners of OsDHPD; the first was a salt‐induced chloroplast ferredoxin, and the second was a rice chloroplast “fruit protein”. Both were cloned and expressed, and testing of interactions with OsDHPD on native gels are in progress. In addition, we produced polyclonal antibodies to OsDHPD to permit pull‐down assays of chloroplast extracts.ConclusionsThree rice pyrimidine catabolic enzymes were cloned, expressed and purified. Potential candidates for the missing protein in the pathway were identified using bioinformatics tools, and antibodies to OsDHPD were generated. Together these approaches may allow identification of the missing participant in pyrimidine catabolism in plants.Support or Funding InformationThe research was supported by funding from Colciencias project 120471250531, and from the Facultad de Ciencias and the Vicerrectoria de Investigaciones (Universidad de los Andes, Colombia).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Identifying novel genes and biological processes relevant to the development of cancer therapy-induced mucositis: An informative gene network analysis.

Mucositis is a complex, dose-limiting toxicity of chemotherapy or radiotherapy that leads to painful mouth ulcers, difficulty eating or swallowing, gastrointestinal distress, and reduced quality of life for patients with cancer. Mucositis is most common for those undergoing high-dose chemotherapy and hematopoietic stem cell transplantation and for those being treated for malignancies of the head and neck. Treatment and management of mucositis remain challenging. It is expected that multiple genes are involved in the formation, severity, and persistence of mucositis. We used Ingenuity Pathway Analysis (IPA), a novel network-based approach that integrates complex intracellular and intercellular interactions involved in diseases, to systematically explore the molecular complexity of mucositis. As a first step, we searched the literature to identify genes that harbor or are close to the genetic variants significantly associated with mucositis. Our literature review identified 27 candidate genes, of which ERCC1, XRCC1, and MTHFR were the most frequently studied for mucositis. On the basis of this 27-gene list, we used IPA to generate gene networks for mucositis. The most biologically significant novel molecules identified through IPA analyses included TP53, CTNNB1, MYC, RB1, P38 MAPK, and EP300. Additionally, uracil degradation II (reductive) and thymine degradation pathways (p = 1.06−08) were most significant. Finally, utilizing 66 SNPs within the 8 most connected IPA-derived candidate molecules, we conducted a genetic association study for oral mucositis in the head and neck cancer patients who were treated using chemotherapy and/or radiation therapy (186 head and neck cancer patients with oral mucositis vs. 699 head and neck cancer patients without oral mucositis). The top ranked gene identified through this association analysis was RB1 (rs2227311, p-value = 0.034, odds ratio = 0.67). In conclusion, gene network analysis identified novel molecules and biological processes, including pathways related to inflammation and oxidative stress, that are relevant to mucositis development, thus providing the basis for future studies to improve the management and treatment of mucositis in patients with cancer.

Structure of Escherichia coli RutC, a member of the YjgF family and putative aminoacrylate peracid reductase of the rut operon.

RutC is the third enzyme in the Escherichia coli rut pathway of uracil degradation. RutC belongs to the highly conserved YjgF family of proteins. The structure of the RutC protein was determined and refined to 1.95 Å resolution. The crystal belonged to space group P2(1)2(1)2 and contained six molecules in the asymmetric unit. The structure was solved by SAD phasing and was refined to an Rwork of 19.3% (Rfree=21.7%). The final model revealed that this protein has a Bacillus chorismate mutase-like fold and forms a homotrimer with a hydrophobic cavity in the center of the structure and ligand-binding clefts between two subunits. A likely function for RutC is the reduction of peroxy-aminoacrylate to aminoacrylate as a part of a detoxification process.

Role of Glutamate Decarboxylase-like Protein 1 (GADL1) in Taurine Biosynthesis

This manuscript concerns the tissue-specific transcription of mouse and cattle glutamate decarboxylase-like protein 1 (GADL1) and the biochemical activities of human GADL1 recombinant protein. Bioinformatic analysis suggested that GADL1 appears late in evolution, only being found in reptiles, birds, and mammals. RT-PCR determined that GADL1 mRNA is transcribed at high levels in mouse and cattle skeletal muscles and also in mouse kidneys. Substrate screening determined that GADL1, unlike its name implies, has no detectable GAD activity, but it is able to efficiently catalyze decarboxylation of aspartate, cysteine sulfinic acid, and cysteic acid to β-alanine, hypotaurine, and taurine, respectively. Western blot analysis verified the presence of GADL1 in mouse muscles, kidneys, C2C12 myoblasts, and C2C12 myotubes. Incubation of the supernatant of fresh muscle or kidney extracts with cysteine sulfinic acid resulted in the detection of hypotaurine or taurine in the reaction mixtures, suggesting the possible involvement of GADL1 in taurine biosynthesis. However, when the tissue samples were incubated with aspartate, no β-alanine production was observed. We proposed several possibilities that might explain the inactivation of ADC activity of GADL1 in tissue protein extracts. Although β-alanine-producing activity was not detected in the supernatant of tissue protein extracts, its potential role in β-alanine synthesis cannot be excluded. There are several inhibitors of the ADC activity of GADL1 identified. The discovery of GADL1 biochemical activities, in conjunction with its expression and activities in muscles and kidneys, provides some tangible insight toward establishing its physiological function(s).

A multi‐faceted analysis of RutD reveals a novel family of α/β hydrolases

AbstractThe rut pathway of pyrimidine catabolism is a novel pathway that allows pyrimidine bases to serve as the sole nitrogen source in suboptimal temperatures. The rut operon in E. coli evaded detection until 2006, yet consists of seven proteins named RutA, RutB, etc. through RutG. The operon is comprised of a pyrimidine transporter and six enzymes that cleave and further process the uracil ring. Herein, we report the structure of RutD, a member of the α/β hydrolase superfamily, which is proposed to enhance the rate of hydrolysis of aminoacrylate, a toxic side product of uracil degradation, to malonic semialdehyde. Although this reaction will occur spontaneously in water, the toxicity of aminoacrylate necessitates catalysis by RutD for efficient growth with uracil as a nitrogen source. RutD has a novel and conserved arrangement of residues corresponding to the α/β hydrolase active site, where the nucleophile's spatial position occupied by Ser, Cys, or Asp of the canonical catalytic triad is replaced by histidine. We have used a combination of crystallographic structure determination, modeling and bioinformatics, to propose a novel mechanism for this enzyme. This approach also revealed that RutD represents a previously undescribed family within the α/β hydrolases. We compare and contrast RutD with PcaD, which is the closest structural homolog to RutD. PcaD is a 3‐oxoadipate‐enol‐lactonase with a classic arrangement of residues in the active site. We have modeled a substrate in the PcaD active site and proposed a reaction mechanism. Proteins 2012;. © 2012 Wiley Periodicals, Inc.

Simultaneous Changes In Muscle Carnosine and Taurine During and Following Supplementation with b-alanine

Carnosine in muscle (M-Carn) contributes significantly to pH control through physio-chemical buffering of H+. Its synthesis in muscle is limited by the availability of b-Alanine (b-Ala). b-Ala is synthesised in the liver from the degradation of uracil and is available also from carnosine, anserine and balanine with ingestion of red meat, fish and poultry. Direct supplementation of the diet with b-Ala for up to 10 weeks has been shown to increase the muscle carnosine content by 80% and this is paralleled by an increase in anaerobic exercise capacity. The transport of b-Ala into muscle is mediated by the same transporter involved with Taurine (Tau) transport into muscle. Previous studies have pointed to a reciprocal relationship between muscle Tau (M-Tau) and M-Carn. PURPOSE: To test if the reciprocal relationship between M-Tau and M-Carn is maintained when b-Ala supplementation results in an increase in M-Carn. METHOD: Seven males received 2x800mg b-Ala controlled release tablets, twice daily for 4w. The study was explained to each of the subjects before their prior informed consent was obtained. Controlled release tablets (CarnoSyn®) were supplied by Collegiate Sport Nutrition, USA. A muscle biopsy from the vastus lateralis was taken at 0 and 4w, and, 3 and 6w post supplementation and analysed by HPLC. No control group was included as previous studies have demonstrated no change in M-Carn or M-Tau in the absence of b-Ala supplementation. RESULTS: Pre and post supplementation M-Carn was 25.9 ± 4.3 and 41.3 ± 5.5 mmol.kg-1dry muscle and M-Tau 28.1 ± 7.1 and 22.6 ± 7.0 mmol.kg-1dry muscle. Despite the 20% fall in M-Tau, values of M-Tau remained within the normal physiological range. Before supplementation M-Tau was negatively correlated with M-Carn, evidenced by subjects with the highest M-Carn having the lowest M-Tau, expressing a similar relationship to that reported earlier. The same negative relationship was preserved after b-Ala supplementation and during the 6 weeks recovery from supplementation (overall data: [M-Tau] = -0.634 · [M-Carn] + 46.6; r = 0.72; p<0.001; n = 28). CONCLUSION: The decrease in M-Tau, occurring with M-Carn increase, are consistent with a role of M-Tau in osmoregulation in which M-Tau compensates for changes in M-Carn. Financial support was provided by UK Sport, London, UK and NAI, San Marcos, Ca, USA.

Alterations in urine, serum and brain metabolomic profiles exhibit sexual dimorphism during malaria disease progression

BackgroundMetabolic changes in the host in response to Plasmodium infection play a crucial role in the pathogenesis of malaria. Alterations in metabolism of male and female mice infected with Plasmodium berghei ANKA are reported here.Methods1H NMR spectra of urine, sera and brain extracts of these mice were analysed over disease progression using Principle Component Analysis and Orthogonal Partial Least Square Discriminant Analysis.ResultsAnalyses of overall changes in urinary profiles during disease progression demonstrate that females show a significant early post-infection shift in metabolism as compared to males. In contrast, serum profiles of female mice remain unaltered in the early infection stages; whereas that of the male mice changed. Brain metabolite profiles do not show global changes in the early stages of infection in either sex. By the late stages urine, serum and brain profiles of both sexes are severely affected. Analyses of individual metabolites show significant increase in lactate, alanine and lysine, kynurenic acid and quinolinic acid in sera of both males and females at this stage. Early changes in female urine are marked by an increase of ureidopropionate, lowering of carnitine and transient enhancement of asparagine and dimethylglycine. Several metabolites when analysed individually in sera and brain reveal significant changes in their levels in the early phase of infection mainly in female mice. Asparagine and dimethylglycine levels decrease and quinolinic acid increases early in sera of infected females. In brain extracts of females, an early rise in levels is also observed for lactate, alanine and glycerol, kynurenic acid, ureidopropionate and 2-hydroxy-2-methylbutyrate.ConclusionsThese results suggest that P. berghei infection leads to impairment of glycolysis, lipid metabolism, metabolism of tryptophan and degradation of uracil. Characterization of early changes along these pathways may be crucial for prognosis and better disease management. Additionally, the distinct sexual dimorphism exhibited in these responses has a bearing on the understanding of the pathophysiology of malaria.

A functional analysis of the pyrimidine catabolic pathway in Arabidopsis.

Reductive catabolism of pyrimidine nucleotides occurs via a three-step pathway in which uracil is degraded to β-alanine, CO2 and NH3 through sequential activities of dihydropyrimidine dehydrogenase (EC 1.3.1.2, PYD1), dihydropyrimidinase (EC 3.5.2.2, PYD2) and β-ureidopropionase (EC 3.5.1.6, PYD3).A proposed function of this pathway, in addition to the maintenance of pyrimidine homeostasis, is the recycling of pyrimidine nitrogen to general nitrogen metabolism. PYD expression and catabolism of [2-14C]-uracil are markedly elevated in response to nitrogen limitation in plants, which can utilize uracil as a nitrogen source.PYD1, PYD2 and PYD3 knockout mutants were used for functional analysis of this pathway in Arabidopsis. pyd mutants exhibited no obvious phenotype under optimal growing conditions. pyd2 and pyd3 mutants were unable to catabolize [2-14C]-uracil or to grow on uracil as the sole nitrogen source. By contrast, catabolism of uracil was reduced by only 40% in pyd1 mutants, and pyd1 seedlings grew nearly as well as wild-type seedlings with a uracil nitrogen source. These results confirm PYD1 function and suggest the possible existence of another, as yet unknown, activity for uracil degradation to dihydrouracil in this plant.The localization of PYD-green fluorescent protein fusions in the plastid (PYD1), secretory system (PYD2) and cytosol (PYD3) suggests potentially complex metabolic regulation.

Degradation of Pyrimidines in Saccharomyces Kluyveri: Transamination of β-Alanine

Beta-alanine is an intermediate in the reductive degradation of uracil. Recently we have identified and characterized the Saccharomyces kluyveri PYD4 gene and the corresponding enzyme β -alanine aminotransferase ( Sk Pyd4p), highly homologous to eukaryotic γ-aminobutyrate aminotransferase (GABA-AT). S. kluyveri has two aminotransferases, GABA aminotransferase ( Sk Uga1p) with 80% and Sk Pyd4p with 55% identity to S. cerevisiae GABA-AT. Sk Pyd4p is a typical pyridoxal phosphate-dependent aminotransferase, specific for α -ketoglutarate (α KG), β -alanine (BAL) and γ -aminobutyrate (GABA), showing a ping-pong kinetic mechanism involving two half-reactions and substrate inhibition. Sk Uga1p accepts only α KG and GABA but not BAL, thus only Sk Pydy4p belongs to the uracil degradative pathway.

A Second Pathway to Degrade Pyrimidine Nucleic Acid Precursors in Eukaryotes

Pyrimidine bases are the central precursors for RNA and DNA, and their intracellular pools are determined by de novo, salvage and catabolic pathways. In eukaryotes, degradation of uracil has been believed to proceed only via the reduction to dihydrouracil. Using a yeast model, Saccharomyces kluyveri, we show that during degradation, uracil is not reduced to dihydrouracil. Six loci, named URC1–6 (for uracil catabolism), are involved in the novel catabolic pathway. Four of them, URC3,5, URC6, and URC2 encode urea amidolyase, uracil phosphoribosyltransferase, and a putative transcription factor, respectively. The gene products of URC1 and URC4 are highly conserved proteins with so far unknown functions and they are present in a variety of prokaryotes and fungi. In bacteria and in some fungi, URC1 and URC4 are linked on the genome together with the gene for uracil phosphoribosyltransferase ( URC6). Urc1p and Urc4p are therefore likely the core components of this novel biochemical pathway. A combination of genetic and analytical chemistry methods demonstrates that uridine monophosphate and urea are intermediates, and 3-hydroxypropionic acid, ammonia and carbon dioxide the final products of degradation. The URC pathway does not require the presence of an active respiratory chain and is therefore different from the oxidative and rut pathways described in prokaryotes, although the latter also gives 3-hydroxypropionic acid as the end product. The genes of the URC pathway are not homologous to any of the eukaryotic or prokaryotic genes involved in pyrimidine degradation described to date.

Heterogeneous photocatalyzed degradation of uracil and 5-bromouracil in aqueous suspensions of titanium dioxide

Photocatalyzed degradation of uracil ( 1) and 5-bromouracil ( 2) has been investigated in aqueous suspensions of titanium dioxide under a variety of conditions. The degradation was studied by monitoring the change in substrate concentration employing UV spectroscopic analysis technique and depletion in total organic carbon (TOC) content as a function of irradiation time. The degradation of the compounds under investigation was studied using various parameters such as, different types of TiO 2 powders, pH, catalyst concentration, substrate concentrations, and in the presence of electron acceptors like hydrogen peroxide (H 2O 2) and potassium bromate (KBrO 3) besides molecular oxygen. Photocatalyst Degussa P25 was found to be more efficient for the degradation of both compounds as compared with other TiO 2 powders such as UV100, PC500 and TTP.