Purification and characterization of urease from schizosaccharomyces pombe

Biochemical and thermodynamic properties of de novo synthesized urease from Vicia sativa seeds with enhanced industrial applications

Urease is one of the most significant enzymes in the industry. The objective of this research was to isolate and partially purify urease from Vicia sativa seeds with urease characterization. With a 6.4 % yield, the purification fold was 9.0. By using chromatography, it was determined that the isolated urease had a molecular weight of 55 kDa. The maximum urease activity was found following a 60-s incubation period at 40 °C and pH 8. The activity of urease was significantly boosted by a mean of calcium, barium, DL-dithiothreitol, Na2EDTA, and citrate (16.9, 26.6, 18.6, 13.6, and 31 %), respectively. But nickel and mercury caused inhibitory effects and completely inhibited urease activity, indicating the presence of a thiol (-SH) group in the enzyme active site. The Arrhenius plot was used to analyze the thermodynamic constants of activation, Ea, ΔH*, ΔG*, and ΔS*. The results showed that the values were 30 kJ/mol, 93.14 kJ/mol, 107.17 kJ/mol/K, and -40.80 J/mol/K, respectively. The significance of urease extraction from various sources may contribute to our understanding of the metabolism of urea in plants. The current report has novelty as it explained for the first time the kinetics and thermodynamics of hydrolysis of urea and inactivation of urease from V. sativa seeds.

Investigating purification and activity analysis of urease enzyme extracted from jack bean source: A green chemistry approach

Urease is an enzyme of historical importance in the field of biochemistry, generally microbial and plant urease is the primary sources of urease. The significant applications of urease enzyme are found to be foremost in food industry, medical equipment's and biosensors. In this work, urease has been extracted from Jack bean meal using ammonium sulphate and acetone precipitation. A significant amount of urease was precipitated and concentrated at 60% saturated solution of ammonium sulphate. The obtained precipitates were dissolved in 50 mM phosphate buffer (pH 8) after centrifugation, and subjected to sodium dodecyl-sulphate polyacrylamide gel electrophoresis (SDS-PAGE) to determine the molecular weight of urease. Results obtained from the SDS-PAGE were validated using Zymography. Anion exchange chromatography was used to separate the desired protein at different pH (7.0, 7.5 and 8.0). The eluted fractions were assessed for urease activity using phenol-nitroprusside dependent ammonia release assay. Under these assay conditions, one unit of urease activity was calibrated as the amount of enzyme liberating 1 μM of NH3 from urea per unit time. The eluted fraction and Zymography analysis show the purified urease observed at 90 kDa and activity of purified urease, respectively. The obtained results for specific activity (173.67Units mg) and % purification (99.71%) for urease has been compared with the available literature, which are found to be in close relation with existing results. The proposed method is a novel approach which has recorded highest % purification and specific activity. Furthermore, it can be suitable for extracting urease from jack bean source for various industrial applications.

Wine yeast selection in the Iberian Peninsula: Saccharomyces and non-Saccharomyces as drivers of innovation in Spanish and Portuguese wine industries

Yeast selection for the wine industry in Spain started in 1950 for the understanding of the microbial ecology, and for the selection of optimal strains to improve the performance of alcoholic fermentation and the overall wine quality. This process has been strongly developed over the last 30 years, firstly on Saccharomyces cerevisiae, and, lately, with intense activity on non-Saccharomyces. Several thousand yeast strains have been isolated, identified and tested to select those with better performance and/or specific technological properties. The present review proposes a global survey of this massive ex-situ preservation of eukaryotic microorganisms, a reservoir of biotechnological solutions for the wine sector, overviewing relevant screenings that led to the selection of strains from 12 genera and 22 species of oenological significance. In the first part, the attention goes to the selection programmes related to relevant wine-producing areas (i.e. Douro, Extremadura, Galicia, La Mancha and Uclés, Ribera del Duero, Rioja, Sherry area, and Valencia). In the second part, the focus shifted on specific non-Saccharomyces genera/species selected from different Spanish and Portuguese regions, exploited to enhance particular attributes of the wines. A fil rouge of the dissertation is the design of tailored biotechnological solutions for wines typical of given geographic areas.

Rational Development of Bacterial Ureases Inhibitors

Urease, an enzyme that catalyzes the hydrolysis of urea, is a virulence factor of various pathogenic bacteria. In particular, Helicobacter pylori, that colonizes the digestive tract and Proteus spp., that can infect the urinary tract, are related to urease activity. Therefore, urease inhibitors are considered as potential therapeutics against these infections. This review describes current knowledge of the structures, activity, and biological importance of bacterial ureases. Moreover, the structure-based design of several classes of bacterial urease inhibitors is presented and discussed. Phosphinic and phosphonic acids were applied as transition-state analogues, while Michael acceptors and ebselen derivatives were applied as covalent binders of cysteine residue. This review incorporates bacterial urease inhibitors from literature published between 2008 and 2021.

Advances in Wine Fermentation

Fermentation is a well-known natural process that has been used by humanity for thousands of years, with the fundamental purpose of making alcoholic beverages such as wine, and also other non-alcoholic products. From a strictly biochemical point of view, fermentation is a process of central metabolism in which an organism converts a carbohydrate, such as starch or sugar, into an alcohol or an acid. The fermentation process turns grape juice (must) into wine. This is a complex chemical reaction whereby the yeast interacts with the sugars (glucose and fructose) in the must to create ethanol and carbon dioxide. Fermentation processes to produce wines are traditionally carried out with Saccharomyces cerevisiae strains, the most common and commercially available yeast, and some lactic acid bacteria. They are well-known for their fermentative behavior and technological characteristics, which allow obtaining products of uniform and standard quality. However, fermentation is influenced by other factors as well. The initial sugar content of the must and the fermentation temperature are also crucial to preserve volatile aromatics in the wine and retain fruity characters. Finally, once fermentation is completed, and most of the yeast dies, wine evolution continues until the production of the final product.

Marine urease with higher thermostability, pH and salinity tolerance from marine sponge-derived Penicillium steckii S4-4

Urease has a broad range of applications, however, the current studies on urease mainly focus on terrestrial plants or microbes. Thus, it is quite necessary to determine if marine-derived ureases have different characteristics from terrestrial origins since the finding of ureases with superior performance is of industrial interest. In this study, the marine urease produced by Penicillium steckii S4-4 derived from marine sponge Siphonochalina sp. was investigated. This marine urease exhibited a maximum specific activity of 1542.2 U mg protein^-1. The molecular weight of the enzyme was 183 kDa and a single subunit of 47 kDa was detected, indicating that it was a tetramer. The N-terminal amino acid sequence of the urease was arranged as GPVLKKTKAAAV with greatest similarity to that from marine algae Ectocarpus siliculosus. This urease exhibited a K _m of 7.3 mmol L^-1 and a V _max of 1.8 mmol urea min^-1 mg protein^-1. The optimum temperature, pH and salinity are 55 ℃, 8.5 and 10%, respectively. This urease was stable and more than 80% of its maximum specific activity was detected after incubating at 25-60 ℃ for 30 min, pH 5.5-10.0 or 0-25% salinity for 6 h. Compared with the terrestrial urease from Jack bean, this marine urease shows higher thermostability, alkaline preference and salinity tolerance, which extends the potential application fields of urease to a great extent.

Non-Saccharomyces in Winemaking: Source of Mannoproteins, Nitrogen, Enzymes, and Antimicrobial Compounds

Traditionally, non-Saccharomyces yeasts have been considered contaminants because of their high production of metabolites with negative connotations in wine. This aspect has been changing in recent years due to an increased interest in the use of these yeasts in the winemaking process. The majority of these yeasts have a low fermentation power, being used in mixed fermentations with Saccharomyces cerevisiae due to their ability to produce metabolites of enological interest, such as glycerol, fatty acids, organic acids, esters, higher alcohols, stable pigments, among others. Additionally, existing literature reports various compounds derived from the cellular structure of non-Saccharomyces yeasts with benefits in the winemaking process, such as polysaccharides, proteins, enzymes, peptides, amino acids, or antimicrobial compounds, some of which, besides contributing to improving the quality of the wine, can be used as a source of nitrogen for the fermentation yeasts. These compounds can be produced exogenously, and later incorporated into the winemaking process, or be uptake directly by S. cerevisiae from the fermentation medium after their release via lysis of non-Saccharomyces yeasts in sequential fermentations.

Lead Molecules for Targeted Urease Inhibition: An Updated Review from 2010 -2018

The field of enzyme inhibition is a tremendous and quickly growing territory of research. Urease a nickel containing metalloenzyme found in bacteria, algae, fungi, and plants brings hydrolysis of urea and plays important role in environmental nitrogen cycle. Apart from this it was found to be responsible for many pathological conditions due to its presence in many microorganisms such as H. Pylori, a ureolytic bacteria having urease which elevates pH of gastric medium by hydrolyzing urea present in alimentary canal and help the bacteria to colonize and spread infection. Due to the infections caused by the various bacterial ureases such as Bacillus pasteurii, Brucella abortus, H. pylori, H. mustelae, Klebsiella aerogenes, Klebsiella tuberculosis, Mycobacterium tuberculosis, Pseudomonas putida, Sporosarcina pasteurii and Yersinia enterocolitica, it has been the current topic of today's research. About a wide range of compounds from the exhaustive literature survey has been discussed in this review which is enveloped into two expansive classes, as Inhibitors from synthetic origin and Inhibitors from natural origin. Moreover active site details of enzyme, mechanism of catalysis of substrate by enzyme, uses of plant urease and its pathogenic behavior has been included in the current review. So, overall, this review article diagrams the current landscape of the developments in the improvements in the thriving field of urease inhibitory movement in medicinal chemistry from year 2010 to 2018, with an emphasis on mechanism of action of inhibitors that may be used for more development of recent and strong urease inhibitors and open up new doors for assist examinations in a standout amongst the most lively and promising regions of research.

Urease immobilization on magnetic micro/nano-cellulose dialdehydes: Urease inhibitory of Biginelli product in Hantzsch reaction by urea

Micro/nano celluloses (MC)/NC) were magnetized by nanoγ-Fe₂O₃ into the nanoγ-Fe₂O₃@MC (NMMC) and nanoγ-Fe₂O₃@NC (NMMC) which oxidized to NMMCD and NMNCD dialdehydes for Schiff-base immobilization of urease as NMMCD/urease and NMMCD/urease. The relative enzyme-activity of the immobilized ureases were comparable with the free-urease, although 75%-80% of the enzyme activity preserved for NMMCD/urease and NMNCD/urease after six cycles. The compared catalytic activities of the NMMCD/urease and NMMCD/urease in Biginelli/Hantzsch reactions in water at 60 °C surprised us by 100% selectivity for the Biginelli product 3,4-dihydropyrimidin-2(1H)-one (DHPM₁). With the superiority of NMNCD/urease, this high selectivity using immobilized ureases is owing to the admirable urease inhibitory of the formed Biginelli product DHPM₁ by urea condensation instead of urea hydrolysis. The robust enzyme inhibitory of the DHPM₁ for free urease was also confirmed by phenol red test to show the deactivation of enzyme for enzymatic hydrolysis of urea and ammonia production in water.

Ureases: Historical aspects, catalytic, and non-catalytic properties - A review

Urease (urea amidohydrolase, EC 3.5.1.5) is a nickel-containing enzyme produced by plants, fungi, and bacteria that catalyzes the hydrolysis of urea into ammonia and carbamate. Urease is of historical importance in Biochemistry as it was the first enzyme ever to be crystallized (1926). Finding nickel in urease's active site (1975) was the first indication of a biological role for this metal. In this review, historical and structural features, kinetics aspects, activation of the metallocenter and inhibitors of the urea hydrolyzing activity of ureases are discussed. The review also deals with the non-enzymatic biological properties, whose discovery 40 years ago started a new chapter in the study of ureases. Well recognized as virulence factors due to the production of ammonia and alkalinization in diseases by urease-positive microorganisms, ureases have pro-inflammatory, endocytosis-inducing and neurotoxic activities that do not require ureolysis. Particularly relevant in plants, ureases exert insecticidal and fungitoxic effects. Data on the jack bean urease and on jaburetox, a recombinant urease-derived peptide, have indicated that interactions with cell membrane lipids may be the basis of the non-enzymatic biological properties of ureases. Altogether, with this review we wanted to invite the readers to take a second look at ureases, very versatile proteins that happen also to catalyze the breakdown of urea into ammonia and carbamate.

Schizosaccharomyces pombe: A Promising Biotechnology for Modulating Wine Composition

There are numerous yeast species related to wine making, particularly non-Saccharomyces, that deserve special attention due to the great potential they have when it comes to making certain changes in the composition of the wine. Among them, Schizosaccharomyces pombe stands out for its particular metabolism that gives it certain abilities such as regulating the acidity of wine through maloalcoholic fermentation. In addition, this species is characterized by favouring the formation of stable pigments in wine and releasing large quantities of polysaccharides during ageing on lees. Moreover, its urease activity and its competition for malic acid with lactic acid bacteria make it a safety tool by limiting the formation of ethyl carbamate and biogenic amines in wine. However, it also has certain disadvantages such as its low fermentation speed or the development of undesirable flavours and aromas. In this chapter, the main oenological uses of Schizosaccharomyces pombe that have been proposed in recent years will be reviewed and discussed.

Lachancea thermotolerans, the Non-Saccharomyces Yeast that Reduces the Volatile Acidity of Wines

To improve the quality of fermented drinks, or more specifically, wine, some strains of yeast have been isolated, tested and studied, such as Saccharomyces and non-Saccharomyces. Some non-conventional yeasts present good fermentative capacities and are able to ferment in quite undesirable conditions, such as the case of must, or wines that have a high concentration of acetic acid. One of those yeasts is Lachancea thermotolerants (L. thermotolerans), which has been studied for its use in wine due to its ability to decrease pH through L-lactic acid production, giving the wines a pleasant acidity. This review focuses on the recent discovery of an interesting feature of L. thermotolerans—namely, its ability to decrease wines’ volatile acidity.

First report of urease activity in the novel systemic fungal pathogen Emergomyces africanus: a comparison with the neurotrope Cryptococcus neoformans

Cryptococcus neoformans is an opportunistic pathogen responsible for the AIDS-defining illness, cryptococcal meningitis. During the disease process, entry of cryptococcal cells into the brain is facilitated by virulence factors that include urease enzyme activity. A novel species of an Emmonsia-like fungus, recently named Emergomyces africanus, was identified as a cause of disseminated mycosis in HIV-infected persons in South Africa. However, in contrast to C. neoformans, the enzymes produced by this fungus, some of which may be involved in pathogenesis, have not been described. Using a clinical isolate of C. neoformans as a reference, the study aim was to confirm, characterise and quantify urease activity in E. africanus clinical isolates. Urease activity was tested using Christensen's urea agar, after which the presence of a urease gene in the genome of E. africanus was confirmed using gene sequence analysis. Subsequent evaluation of colorimetric enzyme assay data, using Michaelis-Menten enzyme kinetics, revealed similarities between the substrate affinity of the urease enzyme produced by E. africanus (Km ca. 26.0 mM) and that of C. neoformans (Km ca. 20.6 mM). However, the addition of 2.5 g/l urea to the culture medium stimulated urease activity of E. africanus, whereas nutrient limitation notably increased cryptococcal urease activity.

Accumulation of Biogenic Amines in Wine: Role of Alcoholic and Malolactic Fermentation

Biogenic amines (BAs) are detrimental to health and originate in foods mainly from decarboxylation of the corresponding amino acid by the activity of exogenous enzymes released by various microorganisms. BAs can be generated at different stages of the wine production. Some of them are formed in the vineyard and are normal constituents of grapes with amounts varying with variety, soil type and composition, fertilization and climatic conditions during growth and degree of maturation. BAs can be also formed by the yeasts during the alcoholic fermentation (AF), as well as by the action of bacteria involved in the malolactic fermentation (MLF). As aminogenesis is a complex and multifactorial phenomenon, the studies carried out to identify the main vinification stage of BAs production yielded contradictory results. In particular, there is not a general consensus yet on which fermentation supports mostly the accumulation of BAs in wine. In this context, the aim of the present paper deals with the most recent results related with the influence of alcoholic and malolactic fermentation parameters on BAs-producer microorganism in wine.

Schizosaccharomyces pombe Biotechnological Applications in Winemaking

The traditional way of producing wine is through the use of Saccharomyces cerevisiae in order to convert glucose and fructose into alcohol. In the case of red wines, after this alcoholic fermentation lactic bacteria Oenococus oeni is used to stabilize wine from a microbiological point of view by converting malic acid into lactic acid that it is not a microbiological substract. The yeast species Schizosaccharomyces pombe was traditionally considered spoilage yeast. Nevertheless, during the last decade it started to be used due to its unique malic acid deacidification ability to reduce the harsh acidity of wines from northern Europe, by converting malic acid to ethanol and CO₂ without producing lactic acid as lactic bacteria does. Additionally, during the last years, S. pombe has started to be used to solve the problems of modern winemaking industry such as increasing food quality or food safety. Some of those new uses, different from its traditional malic acid deacidification, are: high autolytic polysaccharides release, gluconic acid reduction, urease activity that make impossible ethyl carbamate (toxic compound) formation, high pyruvic acid production, that is related to color improvement, and removing lactic bacteria subtracts while avoiding biogenic amines (toxic compounds such as histamine) formation.

The Combined Use of Schizosaccharomyces pombe and Lachancea thermotolerans-Effect on the Anthocyanin Wine Composition

The most popular methodology to make red wine is through the combined use of Saccharomyces cerevisiae yeast and lactic acid bacteria, for alcoholic fermentation and malolactic fermentation respectively. This classic winemaking practice produces stable red wines from a microbiological point of view. This study aims to investigate a recent red winemaking biotechnology, which through the combined use of Lachancea thermotolerans and Schizosaccharomyces pombe is used as an alternative to the classic malolactic fermentation. In this new methodology, Schizosaccharomycespombe totally consumes malic acid, while Lachancea thermotolerans produces lactic acid, avoiding excessive deacidification of musts with low acidity in warm viticulture areas such as Spain. This new methodology has been reported to be a positive alternative to malolactic fermentation in low acidity wines, since it has the advantage to produce wines with a more fruity flavor, less acetic acid, less ethyl carbamate originators and less biogenic amines than the traditional wines produced via conventional fermentation techniques. The study focuses on unexplored facts related to this novel biotechnology such as color and anthocyanin profile.

Urea enhances cell lysis of Schizosaccharomyces pombe ura4 mutants

Cell lysis is induced in Schizosaccharomyces pombe ∆ura4 cells grown in YPD medium, which contains yeast extract, polypeptone, and glucose. To identify the medium components that induce cell lysis, we first tested various kinds of yeast extracts from different suppliers. Cell lysis of ∆ura4 cells on YE medium was observed when yeast extracts from OXOID, BD, Oriental, and Difco were used, but not when using yeast extract from Kyokuto. To determine which compounds induced cell lysis, we subjected yeast extract and polypeptone to GC-MS analysis. Ten kinds of compounds were detected in OXOID and BD yeast extracts, but not in Kyokuto yeast extract. Among them was urea, which was also present in polypeptone, and it clearly induced cell lysis. Deletion of the ure2 gene, which is responsible for utilizing urea, abolished the lytic effect of urea. The effect of urea was suppressed by deletion of pub1, and a similar phenotype was observed in the presence of polypeptone. Thus, urea is an inducer of cell lysis in S. pombe ∆ura4 cells.

Combined Use of S. pombe and L. thermotolerans in Winemaking. Beneficial Effects Determined Through the Study of Wines' Analytical Characteristics

The most common way to produce red wine is through the use of Saccharomyces cerevisiae strains for alcoholic fermentation and lactic acid bacteria for malolactic fermentation. This traditional winemaking methodology produces microbiologically stable red wines. However, under specific conditions off-flavours can occur, wine quality can suffer and human health problems are possible, especially after the second fermentation by the lactic acid bacteria. In warm countries, problems during the malolactic fermentation arise because of the high pH of the must, which makes it very difficult to properly control the process. Under such conditions, wines with high acetic acid and histamine concentrations are commonly produced. This study investigates a recent red wine-making technology that uses a combination of Lachancea thermotolerans and Schizosaccharomyces pombe as an alternative to the conventional malolactic fermentation. This work studies new parameters such as aroma compounds, amino acids, ethanol index and sensory evaluation. Schizosaccharomyces pombe totally consumes malic acid while Lachancea thermotolerans produces lactic acid, avoiding excessive deacidification of musts with low acidity in warm viticulture areas. This methodology also reduces the malolactic fermentation hazards in wines with low acidity. The main products are wines that contain less acetic acid, less biogenic amines and precursors and less ethyl carbamate precursors than the traditional wines produced via conventional fermentation techniques.

Selected Schizosaccharomyces pombe Strains Have Characteristics That Are Beneficial for Winemaking

At present, wine is generally produced using Saccharomyces yeast followed by Oenococus bacteria to complete malolactic fermentation. This method has some unsolved problems, such as the management of highly acidic musts and the production of potentially toxic products including biogenic amines and ethyl carbamate. Here we explore the potential of the fission yeast Schizosaccharomyces pombe to solve these problems. We characterise an extensive worldwide collection of S. pombe strains according to classic biochemical parameters of oenological interest. We identify three genetically different S. pombe strains that appear suitable for winemaking. These strains compare favourably to standard Saccharomyces cerevisiae winemaking strains, in that they perform effective malic acid deacidification and significantly reduce levels of biogenic amines and ethyl carbamate precursors without the need for any secondary bacterial malolactic fermentation. These findings indicate that the use of certain S. pombe strains could be advantageous for winemaking in regions where malic acid is problematic, and these strains also show superior performance with respect to food safety.

Combine Use of Selected Schizosaccharomyces pombe and Lachancea thermotolerans Yeast Strains as an Alternative to the Traditional Malolactic Fermentation in Red Wine Production

Most red wines commercialized in the market use the malolactic fermentation process in order to ensure stability from a microbiological point of view. In this second fermentation, malic acid is converted into l-lactic acid under controlled setups. However this process is not free from possible collateral effects that on some occasions produce off-flavors, wine quality loss and human health problems. In warm viticulture regions such as the south of Spain, the risk of suffering a deviation during the malolactic fermentation process increases due to the high must pH. This contributes to produce wines with high volatile acidity and biogenic amine values. This manuscript develops a new red winemaking methodology that consists of combining the use of two non-Saccharomyces yeast strains as an alternative to the traditional malolactic fermentation. In this method, malic acid is totally consumed by Schizosaccharomyces pombe, thus achieving the microbiological stabilization objective, while Lachancea thermotolerans produces lactic acid in order not to reduce and even increase the acidity of wines produced from low acidity musts. This technique reduces the risks inherent to the malolactic fermentation process when performed in warm regions. The result is more fruity wines that contain less acetic acid and biogenic amines than the traditional controls that have undergone the classical malolactic fermentation.

Nic1 inactivation enables stable isotope labeling with 13C615N4-arginine in Schizosaccharomyces pombe

Stable Isotope Labeling by Amino Acids (SILAC) is a commonly used method in quantitative proteomics. Because of compatibility with trypsin digestion, arginine and lysine are the most widely used amino acids for SILAC labeling. We observed that Schizosaccharomyces pombe (fission yeast) cannot be labeled with a specific form of arginine, (13)C(6) (15)N(4)-arginine (Arg-10), which limits the exploitation of SILAC technology in this model organism. We hypothesized that in the fission yeast the guanidinium group of (13)C(6) (15)N(4)-arginine is catabolized by arginase and urease activity to (15)N1-labeled ammonia that is used as a precursor for general amino acid biosynthesis. We show that disruption of Ni(2+)-dependent urease activity, through deletion of the sole Ni(2+) transporter Nic1, blocks this recycling in ammonium-supplemented EMMG medium to enable (13)C(6) (15)N(4)-arginine labeling for SILAC strategies in S. pombe. Finally, we employed Arg-10 in a triple-SILAC experiment to perform quantitative comparison of G1 + S, M, and G2 cell cycle phases in S. pombe.

Extraction, purification, kinetic and thermodynamic properties of urease from germinating Pisum Sativum L. seeds

BACKGROUND

Urease, one of the highly efficient known enzymes, catalyzes the hydrolysis of urea into ammonia and carbon dioxide. The present study aimed to extract urease from pea seeds (Pisum Sativum L). The enzyme was then purified in three consequence steps: acetone precipitation, DEAE-cellulose ion-exchange chromatography, and gel filtration chromatography (Sephacryl S-200 column).

RESULTS

The purification fold was 12.85 with a yield of 40%. The molecular weight of the isolated urease was estimated by chromatography to be 269,000 Daltons. Maximum urease activity (190 U/g) was achieved at the optimum conditions of 40°C and pH of 7.5 after 5 min of incubation. The kinetic parameters, Km and Vmax, were estimated by Lineweaver-Burk fits and found to be 500 mM and 333.3 U/g, respectively. The thermodynamic constants of activation, ΔH, Ea, and ΔS, were determined using Arrhenius plot and found to be 21.20 kJ/mol, 23.7 kJ/mol, and 1.18 kJ/mol/K, respectively.

CONCLUSIONS

Urease was purified from germinating Pisum Sativum L. seeds. The purification fold, yield, and molecular weight were determined. The effects of pH, concentration of enzyme, temperature, concentration of substrate, and storage period on urease activity were examined. This may provide an insight on the various aspects of the property of the enzyme. The significance of extracting urease from different sources could play a good role in understanding the metabolism of urea in plants.

Structural insight into the binding interactions of modeled structure of Arabidopsis thaliana urease with urea: an in silico study

Urease (EC 3.5.1.5., urea amidohydrolase) catalyzes the hydrolysis of urea to ammonia and carbon dioxide. Urease is present to a greater abundance in plants and plays significant role related to nitrogen recycling from urea. But little is known about the structure and function of the urease derived from the Arabidopsis thaliana, the model system of choice for research in plant biology. In this study, a three-dimensional structural model of A. thaliana urease was constructed using computer-aided molecular modeling technique. The characteristic structural features of the modeled structure were then studied using atomistic molecular dynamics simulation. It was observed that the modeled structure was stable and regions between residues index (50-80, 500-700) to be significantly flexible. From the docking studies, we detected the possible binding interactions of modeled urease with urea. Ala399, Ile675, Thr398, and Thr679 residues of A. thaliana urease were observed to be significantly involved in binding with the substrate urea. We also compared the docking studies of ureases from other sources such as Canavalia ensiformis, Helicobacter pylori, and Bacillus pasteurii. In addition, we carried out mutation analysis to find the highly mutable amino acid residues of modeled A. thaliana urease. In this particular study, we observed Met485, Tyr510, Ser786, Val426, and Lys765 to be highly mutable amino acids. These results are significant for the mutagenesis analysis. As a whole, this study expounds the salient structural features as well the binding interactions of the modeled structure of A. thaliana urease.

Interplay of metal ions and urease

Urease, the first enzyme to be crystallized, contains a dinuclear nickel metallocenter that catalyzes the decomposition of urea to produce ammonia, a reaction of great agricultural and medical importance. Several mechanisms of urease catalysis have been proposed on the basis of enzyme crystal structures, model complexes, and computational efforts, but the precise steps in catalysis and the requirement of nickel versus other metals remain unclear. Purified bacterial urease is partially activated via incubation with carbon dioxide plus nickel ions; however, in vitro activation also has been achieved with manganese and cobalt. In vivo activation of most ureases requires accessory proteins that function as nickel metallochaperones and GTP-dependent molecular chaperones or play other roles in the maturation process. In addition, some microorganisms control their levels of urease by metal ion-dependent regulatory mechanisms.

Jack bean (Canavalia ensiformis) urease. Probing acid-base groups of the active site by pH variation

A pH-variation study of jack bean (Canavalia ensiformis) urease steady-state kinetic parameters and of the inhibition constant of boric acid, a urease competitive inhibitor, was performed using both noninhibitory organic (MES, HEPES and CHES) and inhibitory inorganic (phosphate) buffers, in an effort to elucidate the functions exercised in the catalysis by the ionizable groups of the enzyme active site. The results obtained are consistent with the requirement for three groups utilized by urease with pK(a)s equal to 5.3+/-0.2, 6.6+/-0.2 and 9.1+/-0.4. Based on the appearance of the ionization step with pK(a)=5.3 in v(max)-pH, K(M)-pH and K(i)-pH profiles, we assigned this group as participating both in the substrate binding and catalytic reaction. As shown by its presence in v(max)-pH and K(M)-pH curves, the obvious role of the group with pK(a)=9.1 is the participation in the catalytic reaction. One function of the group featuring pK(a)=6.6, which was derived from a two-maxima v(max)-pH profile obtained upon increasing phosphate buffer concentration, an effect the first time observed for urease-phosphate systems, is the substrate binding, another possible function being modulation of the active site structure controlled by the ionic strength. It is also possible that the pK(a)=6.6 is a merger of two pK(a)s close in value. The study establishes that regular bell-shaped activity-pH profiles, commonly reported for urease, entail more complex pH-dependent behavior of the urease active site ionizable groups, which could be experimentally derived using species interacting with the enzyme, in addition to changing solution pH and ionic strength.

Purification and characterization of urease isolated from the pathogenic fungus Coccidioides immitis

Coccidioides immitis, the causative agent of San Joaquin Valley fever (coccidioidomycosis), produces a urease which has been suggested to contribute to the virulence of this fungal pathogen. Urease catalyzes the hydrolysis of urea and has been proposed to at least partly account for alkalinity of the microenvironment in which C. immitis grows due to the release of ammonia and ammonium ions. The C. immitis urease was purified to homogeneity (1048-fold) from the mycelial cytosol by chromatographic fractionation. The sequence of 12 N-terminal amino-acid residues of the purified, native polypeptide was identical to that predicted by the translated urease gene sequence which has been reported. The isolated enzyme exhibited a specific activity in the presence of urea of 1750 micromol min(-1) mg(-1) protein, has a native molecular mass of 450 kDa, revealed a Km for urea of 4.1 mM, had a pH optimum of 8.0 and is heat stable. Hydroxyurea, acetohydroxamic acid (AHA) and boric acid each inhibited activity of the purified enzyme. Urease activity was enhanced by the presence of 5-10 mM concentrations of Mg2+ or Mn2+, but inhibited by Li+, Ni2+, Cu2+ or Zn2+. The reversible urease inhibitor, AHA, blocked enzyme activity in the crude mycelial cytosolic fraction when added at a concentration of 10 mM. On the other hand, 10 mM AHA added to 4-day-old mycelial cultures only partially decreased the amount of ammonium detected in the culture medium. It is evident, therefore, that C. immitis urease activity does not account for the total amount of ammonia secreted during in vitro growth of the pathogen. Other metabolic sources of ammonia, which may also contribute to the virulence of C. immitis, are under investigation.

In-gel detection of urease with nitroblue tetrazolium and quantification of the enzyme from different crop plants using the indophenol reaction

Two methods for measurement of urease activity are described and demonstrated on extracts from several crop plants. With an in-gel staining method based on the principle of Fishbein's noninhibitory stain for urease as little as 25 microU of jackbean urease can be detected within 2 h following electrophoresis. A comparison with published in-gel staining methods shows that the sensitivity is improved by at least two orders of magnitude. The second method allows quantification of urease activity from small amounts of plant material without the need for special laboratory equipment. It employs the detection of ammonium by the indophenol reaction. To eliminate reducing agents which are often necessary to maintain urease activity during extraction, but which interfere with ammonium detection, a simple spin-column procedure is used. The quantification of less than 5 mU/ml extract is possible.

Kinetic and structural characterization of urease active site variants

Klebsiella aerogenes urease uses a dinuclear nickel active site to catalyze urea hydrolysis at >10(14)-fold the spontaneous rate. To better define the enzyme mechanism, we examined the kinetics and structures for a suite of site-directed variants involving four residues at the active site: His320, His219, Asp221, and Arg336. Compared to wild-type urease, the H320A, H320N, and H320Q variants exhibit similar approximately 10(-)(5)-fold deficiencies in rates, modest K(m) changes, and disorders in the peptide flap covering their active sites. The pH profiles for these mutant enzymes are anomalous with optima near 6 and shoulders that extend to pH 9. H219A urease exhibits 10(3)-fold increased K(m) over that of native enzyme, whereas the increase is less marked ( approximately 10(2)-fold) in the H219N and H219Q variants that retain hydrogen bonding capability. Structures for these variants show clearly resolved active site water molecules covered by well-ordered peptide flaps. Whereas the D221N variant is only moderately affected compared to wild-type enzyme, D221A urease possesses low activity ( approximately 10(-)(3) that of native enzyme), a small increase in K(m), and a pH 5 optimum. The crystal structure for D221A urease is reminiscent of the His320 variants. The R336Q enzyme has a approximately 10(-)(4)-fold decreased catalytic rate with near-normal pH dependence and an unaffected K(m). Phenylglyoxal inactivates the R336Q variant at over half the rate observed for native enzyme, demonstrating that modification of non-active-site arginines can eliminate activity, perhaps by affecting the peptide flap. Our data favor a mechanism in which His219 helps to polarize the substrate carbonyl group, a metal-bound terminal hydroxide or bridging oxo-dianion attacks urea to form a tetrahedral intermediate, and protonation occurs via the general acid His320 with Asp221 and Arg336 orienting and influencing the acidity of this residue. Furthermore, we conclude that the simple bell-shaped pH dependence of k(cat) and k(cat)/K(m) for the native enzyme masks a more complex underlying pH dependence involving at least four pK(a)s.

Nic1p, a relative of bacterial transition metal permeases in Schizosaccharomyces pombe, provides nickel ion for urease biosynthesis

The Schizosaccharomyces pombe genome sequencing project identified an open reading frame (O74869 and O74912, named Nic1p in the present study) with significant similarity to members of a family of bacterial transition metal permeases. These uptake systems transport Ni(2+) ion with extremely high affinity across the bacterial cytoplasmic membrane, but they differ in selectivity toward divalent transition metal cations. An S. pombe mutant harboring an interrupted nic1 allele (nic1-1) was strongly impaired in (63)Ni(2+) uptake in the presence of a high molar ratio of Mg(2+) relative to Ni(2+), conditions that reflect the natural situation. Under these conditions, the nic1-1 mutant contained only background activities of the nickel-dependent cytoplasmic enzyme urease and could not catabolize urea. Among a series of divalent transition metal cations tested (Cd(2+), Co(2+), Cu(2+), Mn(2+), and Zn(2+)), only Co(2+) caused considerable inhibition of Nic1p-mediated Ni(2+) uptake. On the other hand, experiments with (57)Co(2+) (at nm concentrations) did not show significant differences in Co(2+) uptake between the nic1-1 mutant and the parental strain. Our data suggest that Nic1p acts as a plasma-membrane nickel transporter in fission yeast, a finding that invites searches for isologous counterparts in higher eukaryotes.

Purification and properties of urease from the leaf of mulberry, Morus alba

Urease was purified from leaves of mulberry (Morus alba, L.) by ammonium sulfate fractionation, acetone fractionation and sequential column chromatography including Q-Sepharose HP, Phenyl-Sepharose HP, Superdex 200 HR and Mono Q. The enzyme was purified 5700-fold to apparent homogeneity with a recovery of 3.6%. The molecular mass of the enzyme was determined to be 90.5 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis and 175 kDa by gel filtration, indicating that the enzyme was a homodimer. In the western blot analysis, 90.5 kDa subunit of the mulberry leaf urease cross-reacted with antiserum raised against jack bean seed urease. The N-terminal sequence of the first 20 residues of the enzyme revealed that it has a high similarity (80-90%) to ureases from other plant sources, suggesting that the mulberry leaf urease is closely related to other plant ureases. However, the mulberry leaf enzyme showed an optimum pH for activity of 9.0, while the optimum pH of most ureases isolated from plants and bacterial is neutral. In addition, the K(m) value for urea was 0.16 mM, which is lower than those of ureases from other sources. It is also proposed that urease activity ingested by browsing silkworm releases ammonia that is subsequently used in silkworm protein synthesis.

Mapping of ure1, ure2 and ure3 markers in fission yeast

The following urease genes of the fission yeast Schizosaccharomyces pombe have been mapped by induced haploidization and tetrad analysis--ure1: chromosome are III-L; ure2 and ure3: chromosome are I-R. The previously determined tps19-rad1 interval (11-12 cM) has been increased to 18 cM. A convenient medium for rapidly scoring the ure gene markers of fission yeast was developed.