Molecular mechanics evaluation of the proposed mechanisms for the degradation of urea by urease

Illuminating the Cryptococcus neoformans species complex: unveiling intracellular structures with fluorescent-protein-based markers

Cryptococcus neoformans is a fungal pathogen of the top critical priority recognized by the World Health Organization. This clinically important fungus also serves as a eukaryotic model organism. A variety of resources have been generated to facilitate investigation of the C. neoformans species complex, including congenic pairs, well-annotated genomes, genetic editing tools, and gene deletion sets. Here, we generated a set of strains with all major organelles fluorescently marked. We tested short organelle-specific targeting sequences and successfully labeled the following organelles by fusing the targeting sequences with a fluorescence protein: the plasma membrane, the nucleus, the peroxisome, and the mitochondrion. We used native cryptococcal Golgi and late endosomal proteins fused with a fluorescent protein to label these two organelles. These fluorescence markers were verified via colocalization using organelle-specific dyes. All the constructs for the fluorescent protein tags were integrated in an intergenic safe haven region. These organelle-marked strains were examined for growth and various phenotypes. We demonstrated that these tagged strains could be employed to track cryptococcal interaction with the host in phagocytosis assays. These strains also allowed us to discover remarkable differences in the dynamics of proteins targeted to different organelles during sexual reproduction. Additionally, we revealed that "dormant" spores transcribed and synthesized their own proteins and trafficked the proteins to the appropriate subcellular compartments, demonstrating that spores are metabolically active. We anticipate that these newly generated fluorescent markers will greatly facilitate further investigation of cryptococcal biology and pathogenesis.

A Review of Enzyme-Induced Calcium Carbonate Precipitation Applicability in the Oil and Gas Industry

Enzyme-induced calcium carbonate precipitation (EICP) techniques are used in several disciplines and for a wide range of applications. In the oil and gas industry, EICP is a relatively new technique and is actively used for enhanced oil recovery applications, removal of undesired chemicals and generating desired chemicals in situ, and plugging of fractures, lost circulation, and sand consolidation. Many oil- and gas-bearing formations encounter the problem of the flow of sand grains into the wellbore along with the reservoir fluids. This study offers a detailed review of sand consolidation using EICP to solve and prevent sand production issues in oil and gas wells. Interest in bio-cementation techniques has gained a sharp increase recently due to their sustainable and environmentally friendly nature. An overview of the factors affecting the EICP technique is discussed with an emphasis on the in situ reactions, leading to sand consolidation. Furthermore, this study provides a guideline to assess sand consolidation performance and the applicability of EICP to mitigate sand production issues in oil and gas wells.

Antiureolytic activity of new water-soluble thiadiazole derivatives: Spectroscopic, DFT, and molecular docking studies

Two new water-soluble thiadiazole compounds are prepared and characterized with various techniques. These compounds, 5-amino-1,3,4-thiadiazole hydrochloride (1) and 5-amino-3-(N-propane-2-imine)-1,3,4-thiadiazole chloride salt (2) were synthesized via Mannich reaction, and characterized by microelemental analysis, and some spectroscopic means (FTIR, UV-Vis, ¹H NMR, ¹³C NMR and mass), in addition to single-crystal X-ray diffraction for compound 2. DFT calculations were conducted to study their geometry optimization, vibrational spectra, MEP maps, and NBO analysis. In addition, TD-DFT calculations were performed to study their absorption spectra. The prepared compounds were tested against Jack beans urease enzyme (in vitro) to indicate their antiureolytic activity potency. The activity of the enzyme was measured under optimal conditions, before and after mixing with the prepared organic compounds. The results showed that both compounds have potentially inhibited the enzyme activity with respect to their IC₅₀ values: 13.76 µM ± 0.15 for 1, and 18.81 µM ± 0.18 for 2. These values are even lower than that of thiourea (21.40 ± 0.21 µM) as a standard inhibitor. The inhibition activity of urease enzyme was confirmed by a Lineweaver-Burk plot. According to the kinetic parameters obtained from the Lineweaver-Burk plot, the inhibition of urease enzyme by compounds 1 and 2 seems to be non-competitive. Molecular docking studies of the prepared compounds 1 and 2 were performed in order to interpret the obtained biological results and to investigate their interactions with the urease enzyme active site. These studies reveal that compounds 1 and 2 are good candidates as inhibitors for urease enzyme. Moreover, compound 1 exhibits a higher promising inhibition activity.

Breast milk urea as a nitrogen source for urease positive Bifidobacterium infantis

Human milk stimulates a health-promoting gut microbiome in infants. However, it is unclear how the microbiota salvages and processes its required nitrogen from breast milk. Human milk nitrogen sources such as urea could contribute to the composition of this early life microbiome. Urea is abundant in human milk, representing a large part of the non-protein nitrogen (NPN). We found that B. longum subsp. infantis (ATCC17930) can use urea as a main source of nitrogen for growth in synthetic medium and enzyme activity was induced by the presence of urea in the medium. We furthermore confirmed the expression of both urease protein subunits and accessory proteins of B. longum subsp. infantis through proteomics. To the same end, metagenome data were mined for urease-related genes. It was found that the breastfed infant's microbiome possessed more urease-related genes than formula fed infants (51.4:22.1; 2.3-fold increase). Bifidobacteria provided a total of 106 of urease subunit alpha alignments, found only in breastfed infants. These experiments show how an important gut commensal that colonizes the infant intestine can metabolize urea. The results presented herein further indicate how dietary nitrogen can determine bacterial metabolism in the neonate gut and shape the overall microbiome.

Theoretical Studies of Nickel-Dependent Enzymes

The advancements of quantum chemical methods and computer power allow detailed mechanistic investigations of metalloenzymes. In particular, both quantum chemical cluster and combined QM/MM approaches have been used, which have been proven to successfully complement experimental studies. This review starts with a brief introduction of nickel-dependent enzymes and then summarizes theoretical studies on the reaction mechanisms of these enzymes, including NiFe hydrogenase, methyl-coenzyme M reductase, nickel CO dehydrogenase, acetyl CoA synthase, acireductone dioxygenase, quercetin 2,4-dioxygenase, urease, lactate racemase, and superoxide dismutase.

Urea Is Both a Carbon and Nitrogen Source for Microcystis aeruginosa: Tracking 13C Incorporation at Bloom pH Conditions

The use of urea as a nitrogenous fertilizer has increased over the past two decades, with urea itself being readily detected at high concentrations in many lakes. Urea has been linked to cyanobacterial blooms as it is a readily assimilated nitrogen (N) - source for cyanobacteria that possess the enzyme urease. We tested the hypothesis that urea may also act as a carbon (C) source to supplemental growth requirements during the alkaline conditions created by dense cyanobacterial blooms, when concentrations of dissolved CO2 are vanishingly low. High rates of photosynthesis markedly reduce dissolved CO2 concentrations and drive up pH. This was observed in Lake Erie during the largest bloom on record (2015) over long periods (months) and short periods (days) of time, suggesting blooms experience periods of CO2-limitation on a seasonal and daily basis. We used 13C-urea to demonstrate that axenic cultures of the model toxic cyanobacterium, Microcystis aeruginosa NIES843, assimilated C at varying environmentally relevant pH conditions directly into a spectrum of metabolic pools during urea hydrolysis. Primarily, 13C from urea was assimilated into central C metabolism and amino acid biosynthesis pathways, including those important for the production of the hepatotoxin, microcystin, and incorporation into these pathways was at a higher percentage during growth at higher pH. This corresponded to increased growth rates on urea as the sole N source with increasing pH. We propose this ability to incorporate C from urea represents yet another competitive advantage for this cyanobacterium during dense algal blooms.

Increasing atmospheric deposition nitrogen and ammonium reduced microbial activity and changed the bacterial community composition of red paddy soil

Atmospheric deposition nitrogen (ADN) increases the N content in soil and subsequently impacts microbial activity of soil. However, the effects of ADN on paddy soil microbial activity have not been well characterized. In this study, we studied how red paddy soil microbial activity responses to different contents of ADN through a 10-months ADN simulation on well managed pot experiments. Results showed that all tested contents of ADN fluxes (27, 55, and 82kgNha^-1 when its ratio of NH₄⁺/NO₃^--N (R_N) was 2:1) enhanced the soil enzyme activity and microbial biomass carbon and nitrogen and 27kgNha^-1 ADN had maximum effects while comparing with the fertilizer treatment. Generally, increasing of both ADN flux and R_N (1:2, 1:1 and 2:1 with the ADN flux of 55kgNha^-1) had similar reduced effects on microbial activity. Furthermore, both ADN flux and R_N significantly reduced soil bacterial alpha diversity (p<0.05) and altered bacterial community structure (e.g., the relative abundances of genera Dyella and Rhodoblastus affiliated to Proteobacteria increased). Redundancy analysis demonstrated that ADN flux and R_N were the main drivers in shaping paddy soil bacteria community. Overall, the results have indicated that increasing ADN flux and ammonium reduced soil microbial activity and changed the soil bacterial community. The finding highlights how paddy soil microbial community response to ADN and provides information for N management in paddy soil.

Cryptococcus neoformans urease affects the outcome of intracellular pathogenesis by modulating phagolysosomal pH

Cryptococcus neoformans is a facultative intracellular pathogen and its interaction with macrophages is a key event determining the outcome of infection. Urease is a major virulence factor in C. neoformans but its role during macrophage interaction has not been characterized. Consequently, we analyzed the effect of urease on fungal-macrophage interaction using wild-type, urease-deficient and urease-complemented strains of C. neoformans. The frequency of non-lytic exocytosis events was reduced in the absence of urease. Urease-positive C. neoformans manifested reduced and delayed intracellular replication with fewer macrophages displaying phagolysosomal membrane permeabilization. The production of urease was associated with increased phagolysosomal pH, which in turn reduced growth of urease-positive C. neoformans inside macrophages. Interestingly, the ure1 mutant strain grew slower in fungal growth medium which was buffered to neutral pH (pH 7.4). Mice inoculated with macrophages carrying urease-deficient C. neoformans had lower fungal burden in the brain than mice infected with macrophages carrying wild-type strain. In contrast, the absence of urease did not affect survival of yeast when interacting with amoebae. Because of the inability of the urease deletion mutant to grow on urea as a sole nitrogen source, we hypothesize urease plays a nutritional role involved in nitrogen acquisition in the environment. Taken together, our data demonstrate that urease affects fitness within the mammalian phagosome, promoting non-lytic exocytosis while delaying intracellular replication and thus reducing phagolysosomal membrane damage, events that could facilitate cryptococcal dissemination when transported inside macrophages. This system provides an example where an enzyme involved in nutrient acquisition modulates virulence during mammalian infection.

Skin squames contribute to ammonia and volatile fatty acid production from bacteria colonizing in air-cooling units with odor complaints

One of the most notable Indoor Air Quality problems is odor emission. This study investigated the potential contribution of skin squames to the production of ammonia (NH₃ ) and volatile organic acids (VFAs) by 7 bacteria isolated from air-cooling (AC) units with complaints of urine and body odors. Our previous study showed that keratinolytic activity is higher in AC units with odor complaints than those without. In the offices where these units are located, the most likely source of keratins is from human skin squames. Most bacteria can produce NH₃ and VFAs in the skin squame culture. Some correlations between the levels of NH₃ , NH4+, VFAs, and keratinolytic activity were found. The odor production pathway with skin squames was proposed. Staphylococcus haemolyticus was abundant in the AC units with odor problems and had a high level of keratinolytic activity in addition to odor production. For long-term odor control, it is important to reduce the level of skin squames entering the AC units.

Recognition of AMP, ADP and ATP through Cooperative Binding by Cu(II) and Zn(II) Complexes Containing Urea and/or Phenylboronic-Acid Moieties

We report a series of Cu(II) and Zn(II) complexes with different ligands containing a dipicolyl unit functionalized with urea groups that may contain or not a phenylboronic acid function. These complexes were designed for the recognition of phosphorylated anions through coordination to the metal ion reinforced by hydrogen bonds involving the anion and NH groups of urea. The complexes were isolated and several adducts with pyrophosphate were characterized using X-ray diffraction measurements. Coordination of one of the urea nitrogen atoms to the metal ion promoted the hydrolysis of the ligands containing 1,3-diphenylurea units, while ligands bearing 1-ethyl-3-phenylurea groups did not hydrolyze significantly at room temperature. Spectrophotometric titrations, combined with ¹H and ³¹P NMR studies, were used in investigating the binding of phosphate, pyrophosphate (PPi), and nucleoside 5′-polyphosphates (AMP, ADP, ATP, CMP, and UMP). The association constants determined in aqueous solution (pH 7.0, 0.1 M MOPS) point to a stronger association with PPi, ADP, and ATP as compared with the anions containing a single phosphate unit. The [CuL⁴]²⁺ complex shows important selectivity for pyrophosphate (PPi) over ADP and ATP.

Effect of different ammonia sources on aceticlastic and hydrogenotrophic methanogens

Ammonium chloride (NH₄Cl) was usually used as a model ammonia source to simulate ammonia inhibition during anaerobic digestion (AD) of nitrogen-rich feedstocks. However, ammonia in AD originates mainly from degradation of proteins, urea and nucleic acids, which is distinct from NH₄Cl. Thus, in this study, the inhibitory effect of a "natural" ammonia source (urea) and NH₄Cl, on four pure methanogenic strains (aceticlastic: Methanosarcina thermophila, Methanosarcina barkeri; hydrogenotrophic: Methanoculleus bourgensis, Methanoculleus thermophilus), was assessed under mesophilic (37 °C) and thermophilic (55 °C) conditions. The results showed that urea hydrolysis increased pH significantly to unsuitable levels for methanogenic growth, while NH₄Cl had a negligible effect on pH. After adjusting initial pH to 7 and 8, urea was significantly stronger inhibitor with longer lag phases to methanogenesis compared to NH₄Cl. Overall, urea seems to be more toxic on both aceticlastic and hydrogenotrophic methanogens compared to NH₄Cl under the same total and free ammonia levels.

Lactic Acid Fermentation, Urea and Lime Addition: Promising Faecal Sludge Sanitizing Methods for Emergency Sanitation

In this research, three faecal sludge sanitizing methods—lactic acid fermentation, urea treatment and lime treatment—were studied for application in emergency situations. These methods were investigated by undertaking small scale field trials with pit latrine sludge in Blantyre, Malawi. Hydrated lime was able to reduce the E. coli count in the sludge to below the detectable limit within 1 h applying a pH > 11 (using a dosage from 7% to 17% w/w, depending faecal sludge alkalinity), urea treatment required about 4 days using 2.5% wet weight urea addition, and lactic acid fermentation needed approximately 1 week after being dosed with 10% wet weight molasses (2 g (glucose/fructose)/kg) and 10% wet weight pre-culture (99.8% pasteurised whole milk and 0.02% fermented milk drink containing Lactobacillus casei Shirota). Based on Malawian prices, the cost of sanitizing 1 m³ of faecal sludge was estimated to be €32 for lactic acid fermentation, €20 for urea treatment and €12 for hydrated lime treatment.

Enzymatic and toxigenic ability of opportunistic fungi contaminating intensive care units and operation rooms at Assiut University Hospitals, Egypt

Total of 110 isolates belonging to 8 fungal species collected from intensive care units (ICUs) and operation rooms (ORs) at Assiut University hospitals were examined for their ability to produce some extracellular enzymes and mycotoxins which are considered as important factors involved in for fungal pathogenicity. The results revealed that 73, 92 and 78 out of the 110 tested isolates produced protease, lipase and urease respectively; meanwhile, 77 of the tested isolates exhibited some hemolytic activities. Chromatographic analysis (TLC) of the crude extract of the fungal isolates tested revealed that 79 isolates of them had the ability to produce at least one of these mycotoxic compounds (aflatoxins B₁, B₂, G₁, gliotoxin, fumigillin, T-2, zearalenone, roridin A & E, verrucarin A & J, trichoveroids, satratoxin H & E). These results demonstrate that the opportunistic fungal species isolated from (ICUs) and (ORs) and tested exhibited some enzymatic and mycotoxic ability which are the most effective virulence factors contributing to fungal pathogenicity indicating that the management of infection control unit at Assiut University hospitals must be aware of not only bacterial but also fungal contamination.

Computational modeling of the mechanism of urease

In order to elucidate aspects of the mechanism of the hydrolytic enzyme urease, theoretical calculations were undertaken on a model of the active site, using density functional theory. The bridging oxygen donor that has been found in the crystal structures was determined to be a hydroxide ion. The initial coordination of urea at the active site occurs most likely through the urea oxygen to the nickel ion with the lowest coordination number. This coordination can be made without much gain in energy. The calculations also showed that weak coordination of one of the urea amine nitrogen atoms to the second nickel atom is energetically feasible. Furthermore, a proposed mechanism including a tetrahedral intermediate generated by hydrolytic attack on the urea carbon by the bridging hydroxide was modeled, and the tetrahedral intermediate was found to be energetically unfavorable relative to terminal coordination of the substrate (urea).

Quantum mechanical and molecular dynamics simulations of ureases and Zn beta-lactamases

Herein we briefly review theoretical contributions that have increased our understanding of the structure and function of metallo-beta-lactamases and ureases. Both are bimetallic metalloenzymes, with the former containing two zinc ions and the latter containing two nickel ions. We describe the use of several different methodologies, including quantum chemical calculations, molecular dynamic simulations, as well as mixed QM/MM approaches and how they have impacted our understanding of the structure and function of metallo-beta-lactamases and ureases.

Urea decomposition facilitated by a urease model complex: a theoretical investigation

Density functional theory calculations were used to examine the role of the urease model complex [Ni2(bdptz)(micro-OH)(micro-H2O)(H2O)2](OTs)3(bdptz=1,4-bis(2,2'-dipyridylmethyl)-phthalazine; OTs=tosylate) in the degradation of urea. An elimination mechanism that converts urea to ammonium cyanate was investigated in detail. The lowest energy pathway involves urea coordination through the oxygen atom to a Ni center followed by protonation of a urea NH2 group by the bridging water ligand. Subsequent rotation of the protonated urea, followed by deprotonation of the NH2 by a bridging OH ligand generates the bound, disproportionated urea substrate, HNCONH3, from which ammonium cyanate was produced.

Enzymatic Catalysis of Urea Decomposition: Elimination or Hydrolysis?

We present a high-level quantum chemical study of possible reaction mechanisms associated with the catalytic decomposition of urea by a bioinorganic mimetic of the dinickel active site of urease. We chose the phthalazine-dinickel complexes of Lippard and co-workers, because these mimetics have been shown to hydrolytically degrade urea. High-level quantum chemical methodologies were utilized to identify stable intermediates and transition-state structures along several possible reaction pathways. The computed results were then used to further analyze what may occur in the active site of urease. Valuable information on the latter has been extracted from experimental data, computational approaches, and unpublished molecular dynamics simulations. On the basis of these comparative studies, we propose that both the elimination and hydrolytic pathways may compete for urea decomposition in the active site of urease.

Ureases: Quantum Chemical Calculations on Cluster Models

Herein, we present results from a computational study of dinickel complexes that are relevant to the catalytic hydrolysis of urea exerted by the urease enzymes. The B3LYP density functional is used to characterize the equilibrium geometry, electronic and magnetic properties, and energies for a series of realistic complexes modeling the active site of ureases. The analysis of the theoretical results gives new insight into the structure, substrate binding, and catalytic mechanism. The water bridge between the two Ni(II) ions observed in the crystallographic structures of the ureases was assigned to a hydroxide bridge in agreement with the observed small antiferromagnetic coupling. Both monodentate and bidentate urea-bound complexes, in which urea had favorable orientations for catalysis, were characterized. Finally, two reaction mechanisms were investigated starting from the monodentate and bidentate urea-bound complexes, respectively. Both a Ni1...Ni2 bridging hydroxide and a Ni2-bound water molecule play crucial roles in the two mechanisms.

Decomposition of alkyl-substituted urea molecules at a hydroxide-bridged dinickel center

The interactions between N-methylurea, N,N'-dimethylurea, N,N-dimethylurea, tetramethylurea, and thiourea and the hydroxide-bridged dinickel complex [Ni(2)(mu-OH)(mu-H2O)(bdptz)(H2O2](OTs)(3) were investigated. Structural characterization of [Ni(2)(mu-OH)(mu-H2O)(bdptz)(Me-urea)(CH3CN)](ClO4)(3) (1) and [Ni(2)(mu-OH)(mu-H2O)(bdptz)(thiourea)(CH3CN)](ClO4)(3) (2) provided insight into the interactions of the substrates with the dinickel center. In 1, the methylurea molecule coordinates to the dinickel complex through its carbonyl oxygen atom. Complex 2 has a similar geometry, with the thiourea molecule bound to a nickel ion through its sulfur atom. When the urea substrates are heated in the presence of the hydroxide-bridged dinickel complex, N-methylurea and N,N-dimethylurea react to form methylammonium cyanate and dimethylammonium cyanate, respectively. After long reaction times, thiourea reacts similarly, producing ammonium thiocyanate. The other substrates are unreactive. These results indicate that the dinickel complex promotes the elimination of alkylamines from urea substrates to form cyanate but cannot effect the direct hydrolysis of such substrates.