Ureolytic Activity Research Articles

Comparison of rates of ureolysis between Sporosarcina pasteurii and an indigenous groundwater community under conditions required to precipitate large volumes of calcite

Ureolysis-driven calcite precipitation has potential to seal porosity and fracture networks in rocks thus preventing groundwater flow and contaminant transport. In this study urea hydrolysis and calcite precipitation rates for the model bacterium Sporosarcina pasteurii were compared with those of indigenous groundwater communities under conditions required to precipitate large volumes of calcite (up to 50 g L −1). We conducted microcosm experiments in oxic artificial and anoxic natural groundwaters (collected from the Permo-Triassic sandstone aquifer at Birmingham, UK) that were inoculated with aerobically grown S. pasteurii. The rate constants for urea hydrolysis, k urea, ranged between 0.06 and 3.29 d −1 and were only affected by inoculum density. Higher Ca 2+ concentration (50–500 mM Ca 2+) as well as differences in fO 2 did not inhibit the ureolytic activity of S. pasteurii and did not significantly impact k urea. These results demonstrate that S. pasteurii has potential to improve calcite precipitation in both oxic and anoxic groundwaters, especially if indigenous communities lack ureolytic activity. Urea hydrolysis by indigenous groundwater communities was investigated in anoxic, natural groundwaters amended with urea and CaCl 2. A notable increase in ureolysis rates was measured only when these communities were stimulated with dilute nutrients (with best results from blackstrap molasses). Furthermore, there was a considerable lag time (12–20 days) before ureolysis and calcite precipitation began. Calculated ureolysis rate constants, k urea, ranged between 0.03 and 0.05 d −1 and were similar to k urea values produced by S. pasteurii at low inoculum densities. Overall, this comparative study revealed that the growth of ureolytic microorganisms present within groundwaters can easily be stimulated to enhance rates of urea hydrolysis in the subsurface, and thus can be used to induce calcite precipitation in these environments. The time required for urea hydrolysis to begin is almost instantaneous if an inoculum of S. pasteurii is included, while it may take several weeks for ureolytic groundwater communities to grow and become ureolytically active.

Analysis of cultivable aerobic bacteria isolated from bottom sediments in the Wijdefjorden region, Spitsbergen

Analysis of cultivable aerobic bacteria isolated from bottom sediments in the Wijdefjorden region, SpitsbergenThe paper presents the first physicochemical and microbiological studies conducted in the northern area of Svalbard (Spitsbergen). Ten sediment samples were collected from the bottom of the longest fjord in the region, Wijdefjorden. Bottom sediments from ten lakes lo- cated along the shores of Wijdefjorden and Woodfjorden were also sampled. Organic matter content (LOI), water content, temperature, pH, and salinity of the sediments were determined. The quantity of aerobic bacteria cultured on various growth media at 4°C, 14°C, and 37°C ranged from 102to 106cfu/g of wet sediment mass, depending on the type of sampling station (fjord or lake). The number of bacteria did not correlate with organic matter content. Out of the 37 bacterial strains isolated from Wijdefjorden, 48% and 70% revealed ureolytic and proteolytic activity, respectively. The proportion of freshwater strains with ureolytic and proteolytic activitywas 32% and 55%, respectively. Antibiotic resistance testing indicated that bacterial strains from the bottom sediments of the lakes were resistant to 8 antibiotics (out of the 18 investigated). Possible sources of this resistance are discussed. Using 16S DNA analysis, bacterial isolates from the lakes were identified asPseudomonassp., whereas frequently occurring strains in bottom sediment of the fjord werePseudoalteromonassp.

Evaluating the Potential of Native Ureolytic Microbes To Remediate a 90Sr Contaminated Environment

This study was a preliminary evaluation of ureolytically driven calcite precipitation and strontium coprecipitation for remediating (90)Sr contamination at the Hanford 100-N Area in Washington; in particular the approach is suitable for treating sorbed (90)Sr that could otherwise be a long-term source for groundwater contamination. Geochemical conditions at the site are compatible with long-term calcite stability, and therefore groundwater and sediment samples were examined to assess the ureolytic capabilities of the native microbiota. Quantitative assays detected up to 2 × 10(4) putative ureC gene copies mL(-1) in water and up to 9 × 10(5) copies g(-1) in sediment. The ureC assays and laboratory-based estimates of ureolytic activity indicated that the distribution of in situ ureolytic potential was very heterogeneous with depth and also that the ureolytic activity was predominantly associated with attached organisms. A mixed kinetic-equilibrium model was developed for the 100-N site to simulate urea treatment and predict strontium removal. Together, the microbial characterization data and modeling suggest that the site has the requisite biogeochemical characteristics for application of the calcite precipitation remediation approach for (90)Sr.

Cloning and expression of Streptococcus salivarius urease gene in Escherichia coli

To clone Streptococcus salivarius (Ss) 57. I urease gene, which can express ureolytic activity in Escherichia coli (Ec) without adding extra nickel ions. Urease gene was cloned by polymerase chain reaction in three separate parts. The three separate plasmids were digested by specific restriction enzymes and ligated together. The expression of the complete urease gene in Ec was detected by phenol red assay and pH analysis. Urease gene of Ss 57.I was eventually cloned and proved correct. Urease activity of the obtained clone was positive in Ec. Without adding extra NiCl(2), the recombinant Ec could hydrolyze urea to produce ammonia, resulting in the increase of pH value. The clone of Ss urease gene obtained in this study could express ureolytic activity in Ec without adding extra nickel ions. The current clone can be used to construct ureolytic effector strain used in replacement therapy in caries prevention.

Helicobacter pylori urease activates blood platelets through a lipoxygenase‐mediated pathway

The bacterium Helicobacter pylori causes peptic ulcers and gastric cancer in human beings by mechanisms yet not fully understood. H. pylori produces urease which neutralizes the acidic medium permitting its survival in the stomach. We have previously shown that ureases from jackbean, soybean or Bacillus pasteurii induce blood platelet aggregation independently of their enzyme activity by a pathway requiring platelet secretion, activation of calcium channels and lipoxygenase-derived eicosanoids. We investigated whether H. pylori urease displays platelet-activating properties and defined biochemical pathways involved in this phenomenon. For that the effects of purified recombinant H. pylori urease (HPU) added to rabbit platelets were assessed turbidimetrically. ATP secretion and production of lipoxygenase metabolites by activated platelets were measured. Fluorescein-labelled HPU bound to platelets but not to erythrocytes. HPU induced aggregation of rabbit platelets (ED50 0.28 μM) accompanied by ATP secretion. No correlation was found between platelet activation and ureolytic activity of HPU. Platelet aggregation was blocked by esculetin (12-lipoxygenase inhibitor) and enhanced ∼3-fold by indomethacin (cyclooxygenase inhibitor). A metabolite of 12-lipoxygenase was produced by platelets exposed to HPU. Platelet responses to HPU did not involve platelet-activating factor, but required activation of verapamil-inhibitable calcium channels. Our data show that purified H. pylori urease activates blood platelets at submicromolar concentrations. This property seems to be common to ureases regardless of their source (plant or bacteria) or quaternary structure (single, di- or tri-chain proteins). These properties of HPU could play an important role in pathogenesis of gastrointestinal and associated cardiovascular diseases caused by H. pylori.

Crystal Structure of the First Plant Urease from Jack Bean: 83 Years of Journey from Its First Crystal to Molecular Structure

Urease, a nickel-dependent metalloenzyme, is synthesized by plants, some bacteria, and fungi. It catalyzes the hydrolysis of urea into ammonia and carbon dioxide. Although the amino acid sequences of plant and bacterial ureases are closely related, some biological activities differ significantly. Plant ureases but not bacterial ureases possess insecticidal properties independent of its ureolytic activity. To date, the structural information is available only for bacterial ureases although the jack bean urease ( Canavalia ensiformis; JBU), the best-studied plant urease, was the first enzyme to be crystallized in 1926. To better understand the biological properties of plant ureases including the mechanism of insecticidal activity, we initiated the structural studies on some of them. Here, we report the crystal structure of JBU, the first plant urease structure, at 2.05 Å resolution. The active-site architecture of JBU is similar to that of bacterial ureases containing a bi-nickel center. JBU has a bound phosphate and covalently modified residue (Cys592) by β-mercaptoethanol at its active site, and the concomitant binding of multiple inhibitors (phosphate and β-mercaptoethanol) is not observed so far in bacterial ureases. By correlating the structural information of JBU with the available biophysical and biochemical data on insecticidal properties of plant ureases, we hypothesize that the amphipathic β-hairpin located in the entomotoxic peptide region of plant ureases might form a membrane insertion β-barrel as found in β-pore-forming toxins.

Toxic Properties of Urease

Plant ureases have long been known for their ureolytic activities, dependent on a Ni metallocenter active site. We report here on more recently discovered novel toxic properties of ureases—properties independent of enzyme activity. Plant ureases have potent toxicity against insects that are not affected by Bt toxins. Entomotoxicity relies on an internal peptide released by insect digestive enzymes. Plant ureases are fungitoxic—in the absence of ureolytic activity—a property shared with some microbial ureases. We have found that both plant and microbial ureases also induce secretion in animal cells (and thus might be defense and pathogen factors, respectively). We suggest that in the soil, bacterial urease‐induced secretion by plant roots may play a role in rhizosphere relationships. While ureases of plant, fungi, and bacteria align with greater than 50% amino acid identity, toxicity and signaling may be due to more divergent domains, such as that for the insecticidal sub‐peptide. These domains are potential targets for manipulation to improve plant defense against herbivores and pathogens.

Urease from Cotton (Gossypium hirsutum) Seeds: Isolation, Physicochemical Characterization, and Antifungal Properties of the Protein

Ureases (EC 3.5.1.5) are metalloenzymes that hydrolyze urea to produce ammonia and carbon dioxide These enzymes, which are found in fungi, bacteria, and plants, show very similar structures. Despite an abundance of urease in vegetal tissues, the physiological role of this enzyme in plants is still poorly understood. It has been previously described that ureases from the legumes jackbean ( Canavalia ensiformis) and soybean ( Glycine max) have insecticidal activity and antifungal properties. This work presents the physicochemical purification and characterization of a urease from cotton ( Gossypium hirsutum) seeds, the first description of this enzyme in Malvaceae. The urease content varied among different cotton cultivars. Cotton seed urease (98.3 kDa) displayed low ureolytic activity but exhibited potent antifungal properties at sub-micromolar concentrations against different phytopathogenic fungi. As described for other ureases, the antifungal effect of cotton urease persisted after treatment with an irreversible inhibitor of its enzyme activity. The data suggest an important role of these proteins in plant defense.

Antifungal activity of plant and bacterial ureases

Ureases (EC 3.5.1.5) are nickel-dependent metalloenzymes that catalyze the hydrolysis of urea to ammonia and carbon dioxide. Produced by plants, fungi and bacteria, but not by animals, ureases share significant homology and similar mechanisms of catalysis, although differing in quaternary structures. While fungal and plant ureases are homo-oligomeric proteins of 90 kDa subunits, bacterial ureases are multimers of two (e.g. Helicobacter pylori) or three subunit complexes. It has been proposed that in plants these enzymes are involved in nitrogen bioavailability and in protection against pathogens. Previous studies by our group have shown that plant ureases, but not a bacterial ( Bacillus pasteurii) urease, display insecticidal activity. Herein we demonstrate that ( Glycine max) embryo-specific soybean urease, jackbean ( Canavalia ensiformis) major urease and a recombinant H. pylori urease impair growth of selected phytopathogenic fungi at sub-micromolar concentrations. This antifungal property of ureases is not affected by treatment of the proteins with an irreversible inhibitor of the ureolytic activity. Scanning electron microscopy of urease-treated fungi suggests plasmolysis and cell wall injuries. Altogether, our data indicate that ureases probably contribute to the plant arsenal of defense compounds against predators and phytopathogens and that the urease defense mechanism is independent of ammonia release from urea.

In‐gel detection of urease activity by nitroprusside–thiol reaction

A new staining method for urease activity in non-denaturing polyacrylamide gels is described. The increase in local pH of the gel, resulting from ureolytic activity of urease, causes a purple red coloured band after incubation of the polyacrylamide gel with urea. Staining of urease activity using this method is very specific for catalytically active urease even in crude preparations. Detection of urease activity by this method is rapid, simple and economical. The described method is also more sensitive than existing methods of urease staining. A minimum of 0.25 mU of urease activity can be detected after 5 min of incubation with the substrate. The method has been used to demonstrate the presence of different charge isoforms of urease in a member of the plant family Cucurbitaceae.

Enzimas hidrolíticas extracelulares de isolados de rizóbia nativos da Amazônia Central, Amazonas, Brasil

A associação rizóbia x leguminosa contribui para enriquecer o solo com nitrogênio por meio da fixação biológica. Entretanto, pouco se conhece a respeito do perfil enzimático desses microrganismos. Nesse contexto, a presente investigação propõe avaliar a produção de enzimas hidrolíticas extracelulares por isolados de rizóbia nativos da Amazônia Central. Essa triagem constitui o primeiro passo na seleção de microrganismos nativos que são potencialmente exploráveis como produtores de enzimas. Foram testados 67 isolados nativos de rizóbia para as atividades amilolítica, celulolítica, lactolítica, lipolítica, pectinolítica e proteolítica, em meio YMA modificado. A atividade ureolítica foi detectada em meio ágar-uréia. As bactérias isoladas dos nódulos de feijão caupi mostraram maior capacidade em produzir enzimas do que os isolados bacterianos de soja. De todas as enzimas hidrolíticas avaliadas, apenas a pectinase não foi detectada neste estudo. Amilase (32,8%), protease (28,4%), urease (20,9%) e carboximetilcelulase (9,0%) foram as enzimas mais freqüentes produzidas pelos isolados. Neste trabalho, apenas as enzimas amilase e protease variaram significativamente entre os isolados de rizóbia. Os isolados INPA R-926 e INPA R-915 exibiram os maiores índices amilolíticos (IE = 3,1) e proteolíticos (IE = 6,6), respectivamente. Este estudo revelou alguns isolados de rizóbia nativos da Amazônia Central como fontes promissoras de enzimas de importância industrial para uso biotecnológico.

Ureases display biological effects independent of enzymatic activity: Is there a connection to diseases caused by urease-producing bacteria?

Ureases are enzymes from plants, fungi and bacteria that catalyze the hydrolysis of urea to form ammonia and carbon dioxide. While fungal and plant ureases are homo-oligomers of 90-kDa subunits, bacterial ureases are multimers of two or three subunit complexes. We showed that some isoforms of jack bean urease, canatoxin and the classical urease, bind to glycoconjugates and induce platelet aggregation. Canatoxin also promotes release of histamine from mast cells, insulin from pancreatic cells and neurotransmitters from brain synaptosomes. In vivo it induces rat paw edema and neutrophil chemotaxis. These effects are independent of ureolytic activity and require activation of eicosanoid metabolism and calcium channels. Helicobacter pylori, a Gram-negative bacterium that colonizes the human stomach mucosa, causes gastric ulcers and cancer by a mechanism that is not understood. H. pylori produces factors that damage gastric epithelial cells, such as the vacuolating cytotoxin VacA, the cytotoxin-associated protein CagA, and a urease (up to 10% of bacterial protein) that neutralizes the acidic medium permitting its survival in the stomach. H. pylori whole cells or extracts of its water-soluble proteins promote inflammation, activate neutrophils and induce the release of cytokines. In this paper we review data from the literature suggesting that H. pylori urease displays many of the biological activities observed for jack bean ureases and show that bacterial ureases have a secretagogue effect modulated by eicosanoid metabolites through lipoxygenase pathways. These findings could be relevant to the elucidation of the role of urease in the pathogenesis of the gastrointestinal disease caused by H. pylori.

Bacillus pasteurii urease shares with plant ureases the ability to induce aggregation of blood platelets

Ureases (EC 3.5.1.5) are highly homologous enzymes found in plants, bacteria and fungi. Canatoxin, an isoform Canavalia ensiformis urease, has several biological properties unrelated to its ureolytic activity, like platelet-aggregating and pro-inflammatory effects. Here, we describe that Bacillus pasteurii urease (BPU) also induces aggregation of rabbit platelets, similar to the canatoxin-induced effect (ED 50 0.4 and 0.015 mg/mL, respectively). BPU induced-aggregation was blocked in platelets pretreated with dexamethasone and esculetin, a phospholipase A 2 and a lipoxygenase inhibitor, respectively, while platelets treated with indomethacin, a cyclooxygenase inhibitor, showed increased response to BPU. Methoxyverapamil (Ca 2+ channel blocker) and AMP (ADP antagonist) abrogated urease-induced aggregation, whereas the PAF-acether antagonist Web2170 had no effect. We concluded that platelet aggregation induced by BPU is mediated by lipoxygenase-derived eicosanoids and secretion of ADP from the platelets through a calcium-dependent mechanism. Potential relevance of these findings for bacterium–plant interactions and pathogenesis of bacterial infections are discussed.

Characterization of the Actinomyces naeslundii ureolysis and its role in bacterial aciduricity and capacity to modulate pH homeostasis

Ammonia production from urea by ureolytic oral bacteria is believed to have a significant impact on oral health and ecological balance of oral microbial populations. Actinomyces naeslundii is an important ureolytic organism in the oral cavity. In this study, we aimed to investigate the substrate affinity and pH optimum for ureolysis of A. naeslundii (ATCC12104), and expression of urease under different environmental factors. In addition, in vitro acid killing and pH drop experiments were used to detect the role of ureolysis in bacterial aciduricity and capacity to modulate pH homeostasis. We observed the K(s) value of the ureolytic activity was 7.5mM and a pH optimum near 6.5. Urease expression by A. naeslundii (ATCC12104) was affected by multiple factors, including environmental pH, glucose and nitrogen availability. The cells could be protected against acid killing through hydrolysis of physiologically relevant concentrations of urea. A. naeslundii (ATCC12104) demonstrated a significant capacity to temper glycolytic acidification in vitro at urea concentrations normally found in the oral cavity.

Mechanisms of inhibition by fluoride of urease activities of cell suspensions and biofilms of Staphylococcus epidermidis, Streptococcus salivarius, Actinomyces naeslundii and of dental plaque

Fluoride is known to be a potent inhibitor of bacterial ureases and can also act in the form of hydrofluoric acid as a transmembrane proton conductor to acidify the cytoplasm of intact cells with possible indirect, acid inhibition of urease. Our research objectives were to assess the inhibitory potencies of fluoride for three urease-positive bacteria commonly found in the mouth and to determine the relative importance of direct and indirect inhibition of ureases for overall inhibition of intact cells or biofilms. The experimental design involved intact bacteria in suspensions, mono-organism biofilms, cell extracts, and dental plaque. Standard enzymatic assays for ammonia production from urea were used. We found that ureolysis by cells in suspensions or mono-organism biofilms of Staphylococcus epidermidis, Streptococcus salivarius or Actinomyces naeslundii was inhibited by fluoride at plaque levels of 0.1-0.5 mm in a pH-dependent manner. The results of experiments with the organic weak acids indomethacin and capric acid, which do not directly inhibit urease enzyme, indicated that weak-acid effects leading to cytoplasmic acidification are also involved in fluoride inhibition. However, direct fluoride inhibition of urease appeared to be the major mechanism for reduction in ureolytic activity in acid environments. Results of experiments with freshly harvested supragingival dental plaque indicated responses to fluoride similar to those of S. salivarius with pH-dependent fluoride inhibition and both direct and indirect inhibition of urease. Fluoride can act to diminish alkali production from urea by oral bacteria through direct and indirect mechanisms.

Effect of chemical modification of histidines on the copper-induced oligomerization of jack bean urease (EC 3.5.1.5)

Aggregation of jack bean urease (JBU) is associated with alterations of its biological properties, notably the ureolytic and entomotoxic activities. We investigated the influence of metals on protein oligomerization and biological properties. Besides protein aggregation, Cu 2+ induces inhibition of both ureolytic and insecticidal activities of JBU. Chemical modification of histidine residues in JBU with diethylpyrocarbonate (DEPC) decreases its affinity for Cu 2+ and inhibits oligomerization induced by this metal. Furthermore, this modification protects the insecticidal properties of JBU from being inactivated by Cu 2+. Although DEPC-treated JBU displayed lower ureolytic activity, the modified protein is less susceptible to inhibition by Cu 2+ when compared to native enzyme. Our findings show that Cu 2+ promotes JBU aggregation and differently of other heavy metals studied here, it apparently inhibits the ureolytic activity by inducing protein polymerization along with blockage of sulfhydryl groups.

Environmental pH as an important factor for the distribution of urease positive ammonia-oxidizing bacteria

The effect of pH on ureolytic activity of a number of chemolithotrophic ammonia-oxidizing bacteria (AOB) has been studied in context with distribution patterns of these species. The pH-optima for urea-based nitrification were found to differ clearly among the examined species. Pronounced optima ranged between pH 5.0 and 8.0. Urease is an intracytoplasmic enzyme and should therefore be independent of the external pH. Our first results indicated the presence of a pH-dependent uptake system for urea. Simultaneous oxidation of free ammonia, possible only at high pH values, led to a strong intensification of ureolysis. The lag-phase of growth on urea as the sole energy source was clearly prolonged compared to free ammonia. Our results point on the existence of an active, most likely energy-linked urea-uptake system in addition to a possible passive diffusion of urea. The different pH-optima of urea-uptake agree with known distribution patterns of distinct AOB. It might be a reason for the shift of dominant Nitrosospira populations along pH gradients in acid soils as observed by others in molecular analyses of natural AOB populations.

Jack bean urease (EC 3.5.1.5) aggregation monitored by dynamic and static light scattering

Aggregation of jack bean urease (JBU) is involved in many alterations of its biological properties, notably the ureolytic and entomotoxic activities. In order to investigate this phenomenon, protein aggregates were characterized by dynamic (DLS) and static light scattering (SLS) spectroscopies through determination of apparent hydrodynamic radii, the average molecular masses, radii of gyration and second virial coefficients. No effect of disulfide reducing agents on protein association was observed contrasting with previous reports implicating their function in the prevention of JBU aggregation. The influence of freeze–thawing cycles on protein aggregation was also investigated. Our results showed that after freeze–thawing cycles the native form of JBU with apparent hydrodynamic radius of 7 nm and radius of gyration of 12 nm is replaced by high-order oligomers and this aggregation is not reverted neither by dithiothreitol (DTT) treatment nor by high concentration of salts. Altogether the data help to understand the complex behavior of JBU in solution and may correlate with the diversity of biological properties of this enzyme.

Separation of jack bean (Canavalia ensiformis) urease isoforms by immobilized metal affinity chromatography and characterization of insecticidal properties unrelated to ureolytic activity

In this work we described the separation of two isoforms of urease from jack bean seeds, the “classical” jack bean urease (JBU) and canatoxin (CNTX), using immobilized metal affinity chromatography (IMAC). Jack bean urease isoforms presented differential behavior on a cobalt-loaded iminodiacetic acid (IDA)–Sepharose column and IMAC is proposed as an efficient method to isolate the isoenzymes. The metal content of the urease isoforms was determined by particle induced X-ray emission (PIXE). CNTX displays ca. 1 eq. of nickel per monomer, contrasting with 2 eq. of nickel found per monomer for JBU. Beside nickel, CNTX contains 1 eq. of zinc per monomer, while no zinc is found in JBU. The insecticidal property of these ureases was investigated in feeding trials with the cotton sucker bug, Dysdercus peruvianus (Hemiptera) as an insect model. Both ureases were lethal to the insects, being CNTX more potent than JBU. This property was not affected by treatment with p-hydroxymercurybenzoate (pHMB), an irreversible inhibitor of ureolytic activity. Altogether the data show that IMAC is a suitable method for separating jack bean urease isoforms and that the isoenzymes display entomotoxic effects, independent of their ureolytic activity, suggestive of a role in plant defense against insect predators.

Jack bean urease (EC 3.5.1.5) aggregation monitored by dynamic and static light scattering

Aggregation of jack bean urease (JBU) is involved in many alterations of its biological properties, notably the ureolytic and entomotoxic activities. In order to investigate this phenomenon, protein aggregates were characterized by dynamic (DLS) and static light scattering (SLS) spectroscopies through determination of apparent hydrodynamic radii, the average molecular masses, radii of gyration and second virial coefficients. No effect of disulfide reducing agents on protein association was observed contrasting with previous reports implicating their function in the prevention of JBU aggregation. The influence of freeze–thawing cycles on protein aggregation was also investigated. Our results showed that after freeze–thawing cycles the native form of JBU with apparent hydrodynamic radius of 7 nm and radius of gyration of 12 nm is replaced by high-order oligomers and this aggregation is not reverted neither by dithiothreitol (DTT) treatment nor by high concentration of salts. Altogether the data help to understand the complex behavior of JBU in solution and may correlate with the diversity of biological properties of this enzyme.