Bacterial Cyanuric Acid Hydrolase for Water Treatment

A Model for Mechanical Stress Limited Bacterial Growth and Resporulation in Confinement

In this study, we propose a self-limiting growth model forBacillus subtilisspores confined within porous polyacrylamide (PA) hydrogels. We observed thatB. subtilisspores germinate into vegetative cells within the hydrogel matrix, forming spherical colonies. These colonies expand until the mechanical stress they exert on their environment surpasses the yield stress of the hydrogel, leading to formation of a nonpermeable layer that halts nutrient diffusion and forces the bacteria to resporulate. These novel observations suggest a model to explain why bacterial growth in confined environments and material interfaces may be limited, providing insight for natural phenomena and biotechnological applications involving bacterial encapsulation.

A Procedure for Removal of Cyanuric Acid in Swimming Pools Using a Cell-Free Thermostable Cyanuric Acid Hydrolase

Cyanuric acid (CYA) is used commercially for maintaining active chlorine to inactivate microbial and viral pathogens in swimming pools and hot tubs. Repeated CYA addition can cause a lack of available chlorine and adequate disinfection. Acceptable CYA levels can potentially be restored via cyanuric acid hydrolases (CAH), enzymes that hydrolyze CYA to biuret under mild conditions. Here we describe a previously unknown CAH enzyme from Pseudolabrys sp. Root1462 (CAH-PR), mined from public databases by bioinformatic analysis of potential CAH genes, which we show to be suitable in a cell-free form for industrial applications based upon favorable enzymatic and physical properties, combined with high-yield expression in aerobic cell culture. The kinetic parameters and modeled structure were similar to known CAH enzymes, but the new enzyme displayed a surprising thermal and storage stability. The new CAH enzyme was applied, following addition of inexpensive sodium sulfite, to hydrolyze CYA to biuret. At the desired endpoint, hypochlorite addition inactivated remaining enzyme and oxidized biuret to primarily dinitrogen and carbon dioxide gases. The mechanism of biuret oxidation with hypochlorite under conditions relevant to recreational pools is described.

Robustness of anaerobes exposed to cyanuric acid contaminated wastewater and achieving efficient removal via optimized co-digestion scheme

The impact of various industrial pollutants on anaerobes and the biodegradation potentials need much emphasis. This study aims to investigate the response of anaerobic microbial systems to cyanuric acid (CA) exposure; CA is toxic and possible carcinogen. First, the long-term exposure of mixed culture bacteria (i.e., municipal sludge) to low-strength wastewater containing 20 mg/L CA was conducted in an up-flow anaerobic staged reactor. Stable performance and sludge granulation were observed, and the microbial community structure showed the progression of genus Acinetobacter known as CA degrader. Second, batch-mode experiment was performed to examine the CA biodegradability at higher doses (up to 250 mg/L of CA) in the absence and presence of glucose as a co-substrate; response surface-based optimization was used to design this experiment and to estimate the optimum CA-glucose combination. CA removal of 77-98% was achieved when CA was co-digested with glucose (250-1,000 mg/L), after 7 days-incubation at temperature of 37 °C, compared to 34% when CA was solely digested. Further, the obtained methane yield dropped when CA exceeded over 125 mg/L, though the deterioration was mitigated by addition of higher concentration of glucose. Overall, we conclude that CA is efficiently degraded under anaerobic conditions when being co-digested with readily assimilable substrate.

Bacterial catabolism of s-triazine herbicides: biochemistry, evolution and application

The synthetic s-triazines are abundant, nitrogen-rich, heteroaromatic compounds used in a multitude of applications including, herbicides, plastics and polymers, and explosives. Their presence in the environment has led to the evolution of bacterial catabolic pathways in bacteria that allow use of these anthropogenic chemicals as a nitrogen source that supports growth. Herbicidal s-triazines have been used since the mid-twentieth century and are among the most heavily used herbicides in the world, despite being withdrawn from use in some areas due to concern about their safety and environmental impact. Bacterial catabolism of the herbicidal s-triazines has been studied extensively. Pseudomonas sp. strain ADP, which was isolated more than thirty years after the introduction of the s-triazine herbicides, has been the model system for most of these studies; however, several alternative catabolic pathways have also been identified. Over the last five years, considerable detail about the molecular mode of action of the s-triazine catabolic enzymes has been uncovered through acquisition of their atomic structures. These structural studies have also revealed insights into the evolutionary origins of this newly acquired metabolic capability. In addition, s-triazine-catabolizing bacteria and enzymes have been used in a range of applications, including bioremediation of herbicides and cyanuric acid, introducing metabolic resistance to plants, and as a novel selectable marker in fermentation organisms. In this review, we cover the discovery and characterization of bacterial strains, metabolic pathways and enzymes that catabolize the s-triazines. We also consider the evolution of these new enzymes and pathways and discuss the practical applications that have been considered for these bacteria and enzymes. One Sentence Summary: A detailed understanding of bacterial herbicide catabolic enzymes and pathways offer new evolutionary insights and novel applied tools.

Fate of atrazine and its relationship with environmental factors in distinctly different lake sediments associated with hydrophytes

Atrazine contamination is of great concern due to its widespread occurrence in shallow lakes. Here, the distribution and degradation of atrazine in acidic and alkaline lake systems were investigated. Meanwhile, the bacterial communities in different sediments and the effects of environmental factors on atrazine-degrading bacteria were evaluated. In the lake systems without plants, atrazine levels in sediment interstitial water reached peak concentrations on the 4th d. More than 90% of atrazine was then degraded in all sediment interstitial water by day 30. Meanwhile, the degradation rate of atrazine in alkaline sediments was faster than that in acidic sediments. Values of hydroxylated metabolites in the acidic lake sediments tended to be greater. Moreover, the amounts of Proteobacteria, Actinobacteria, Firmicute, Nitrospinae, Aminicenantes, Ignavibacteriae and Saccharibacteria in acidic Tangxunhu Lake sediments were significantly different from alkaline Honghu Lake sediments, while the amounts of Cyanobacteria and Saccharibacteria in sediments treated with atrazine were significantly greater than those in sediments without atrazine (P < 0.05). Notably, pH was the most relevant environmental factor in the quantitative variation of atrazine-degrading bacteria, including in Clostridium-sensu-stricto, Pseudomonas, Comamonas and Rhodobacter. The Mantel test results indicated that the degradation of atrazine in different sediments was mainly affected by the sediment physicochemical properties rather than by the addition of atrazine and the cultivation of hydrophytes.

Crystal structures of Moorella thermoacetica cyanuric acid hydrolase reveal conformational flexibility and asymmetry important for catalysis

An ancient enzyme family responsible for the catabolism of the prebiotic chemical cyanuric acid (1,3,5-triazine-2,4,6-triol) was recently discovered and is undergoing proliferation in the modern world due to industrial synthesis and dissemination of 1,3,5-triazine compounds. Cyanuric acid has a highly stabilized ring system such that bacteria require a unique enzyme with a novel fold and subtle active site construction to open the ring. Each cyanuric acid hydrolase monomer consists of three isostructural domains that coordinate and activate the three-fold symmetric substrate cyanuric acid for ring opening. We have now solved a series of X-ray structures of an engineered, thermostable cyanuric acid ring-opening enzyme at 1.51 ~ 2.25 Å resolution, including various complexes with the substrate, a tight-binding inhibitor, or an analog of the reaction intermediate. These structures reveal asymmetric interactions between the enzyme and bound ligands, a metal ion binding coupled to conformational changes and substrate binding important for enzyme stability, and distinct roles of the isostructural domains of the enzyme. The multiple conformations of the enzyme observed across a series of structures and corroborating biochemical data suggest importance of the structural dynamics in facilitating the substrate entry and the ring-opening reaction, catalyzed by a conserved Ser-Lys dyad.

Structural and biochemical characterization of the biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841

Biuret deamination is an essential step in cyanuric acid mineralization. In the well-studied atrazine degrading bacterium Pseudomonas sp. strain ADP, the amidase AtzE catalyzes this step. However, Rhizobium leguminosarum bv. viciae 3841 uses an unrelated cysteine hydrolase, BiuH, instead. Herein, structures of BiuH, BiuH with bound inhibitor and variants of BiuH are reported. The substrate is bound in the active site by a hydrogen bonding network that imparts high substrate specificity. The structure of the inactive Cys175Ser BiuH variant with substrate bound in the active site revealed that an active site cysteine (Cys175), aspartic acid (Asp36) and lysine (Lys142) form a catalytic triad, which is consistent with biochemical studies of BiuH variants. Finally, molecular dynamics simulations highlighted the presence of three channels from the active site to the enzyme surface: a persistent tunnel gated by residues Val218 and Gln215 forming a potential substrate channel and two smaller channels formed by Val28 and a mobile loop (including residues Phe41, Tyr47 and Met51) that may serve as channels for co-product (ammonia) or co-substrate (water).

The fate of cyanuric acid in biological wastewater treatment system and its impact on biological nutrient removal

Cyanuric acid (CA) is widely used in living and production. It is a kind of environmental priority pollutants which exists chronically in soil and water, but is difficult to be chemically hydrolyzed or oxidized. The behavior of CA at different levels of 0, 0.01, 0.10 and 1.00 mg L^-1 in biological wastewater treatment process was investigated in this paper. Experimental results showed that CA (0.01 and 0.10 mg L^-1) was removed in biological wastewater treatment process, which was mainly achieved by biodegradation of particular species (Acidovorax and Pseudomonas) in the anaerobic condition. However, 1.00 mg L^-1 CA was reluctant to be degraded in biological wastewater treatment system. With the CA level increase from 0 to 1.00 mg L^-1, total nitrogen removal efficiency decreased from 97.23 to 74.72%. The presence of CA promoted both the synthesis and decomposition metabolisms of poly-hydroxyalkanoates and glycogen, thereby providing the advantage for phosphorus removal. CA could inhibit nitrification process because of inhibition to nitrite oxidizing bacteria (NOB). Moreover, the microbial community of activated sludge was changed by the exposure of CA. Polyphosphate accumulating organisms, such as Bacteroidetes, Chloroflexi and Saccharibacteria increased, but the abundance of Nitrospirae was decreased.

Integrated preservation and sample clean up procedures for studying water ingestion by recreational swimmers via urinary biomarker determination

The use of cyanuric acid as a biomarker for ingestion of swimming pool water may lead to quantitative knowledge of the volume of water ingested during swimming, contributing to a better understanding of disease resulting from ingestion of environmental contaminants. When swimming pool water containing chlorinated cyanurates is inadvertently ingested, cyanuric acid is excreted quantitatively within 24 h as a urinary biomarker of ingestion. Because the volume of water ingested can be quantitatively estimated by calculation from the concentration of cyanuric acid in 24 h urine samples, a procedure for preservation, cleanup, and analysis of cyanuric acid was developed to meet the logistical demands of large scale studies. From a practical stand point, urine collected from swimmers cannot be analyzed immediately, given requirements of sample collection, shipping, handling, etc. Thus, to maintain quality control to allow confidence in the results, it is necessary to preserve the samples in a manner that ensures as quantitative analysis as possible. The preservation and clean-up of cyanuric acid in urine is complicated because typical approaches often are incompatible with the keto-enol tautomerization of cyanuric acid, interfering with cyanuric acid sample preparation, chromatography, and detection. Therefore, this paper presents a novel integration of sample preservation, clean-up, chromatography, and detection to determine cyanuric acid in 24 h urine samples. Fortification of urine with cyanuric acid (0.3-3.0 mg/L) demonstrated accuracy (86-93% recovery) and high reproducibility (RSD < 7%). Holding time studies in unpreserved urine suggested sufficient cyanuric acid stability for sample collection procedures, while longer holding times suggested instability of the unpreserved urine. Preserved urine exhibited a loss of around 0.5% after 22 days at refrigerated storage conditions of 4 °C.

Structure of the Cyanuric Acid Hydrolase TrzD Reveals Product Exit Channel

Cyanuric acid hydrolases are of industrial importance because of their use in aquatic recreational facilities to remove cyanuric acid, a stabilizer for the chlorine. Degradation of excess cyanuric acid is necessary to maintain chlorine disinfection in the waters. Cyanuric acid hydrolase opens the cyanuric acid ring hydrolytically and subsequent decarboxylation produces carbon dioxide and biuret. In the present study, we report the X-ray structure of TrzD, a cyanuric acid hydrolase from Acidovorax citrulli. The crystal structure at 2.19 Å resolution shows a large displacement of the catalytic lysine (Lys163) in domain 2 away from the active site core, whereas the two other active site lysines from the two other domains are not able to move. The lysine displacement is proposed here to open up a channel for product release. Consistent with that, the structure also showed two molecules of the co-product, carbon dioxide, one in the active site and another trapped in the proposed exit channel. Previous data indicated that the domain 2 lysine residue plays a role in activating an adjacent serine residue carrying out nucleophilic attack, opening the cyanuric acid ring, and the mobile lysine guides products through the exit channel.

Immobilized Biocatalyst for Detection and Destruction of the Insensitive Explosive, 2,4-Dinitroanisole (DNAN)

Accurate and convenient detection of explosive components is vital for a wide spectrum of applications ranging from national security and demilitarization to environmental monitoring and restoration. With the increasing use of DNAN as a replacement for 2,4,6-trinitrotoluene (TNT) in insensitive explosive formulations, there has been a growing interest in strategies to minimize its release and to understand and predict its behavior in the environment. Consequently, a convenient tool for its detection and destruction could enable development of more effective decontamination and demilitarization strategies. Biosensors and biocatalysts have limited applicability to the more traditional explosives because of the inherent limitations of the relevant enzymes. Here, we report a highly specific, convenient and robust biocatalyst based on a novel ether hydrolase enzyme, DNAN demethylase (that requires no cofactors), from a Nocardioides strain that can mineralize DNAN. Biogenic silica encapsulation was used to stabilize the enzyme and enable it to be packed into a model microcolumn for application as a biosensor or as a bioreactor for continuous destruction of DNAN. The immobilized enzyme was stable and not inhibited by other insensitive munitions constituents. An alternative method for DNAN detection involved coating the encapsulated enzyme on cellulose filter paper. The hydrolase based biocatalyst could provide the basis for a wide spectrum of applications including detection, identification, destruction or inertion of explosives containing DNAN (demilitarization operations), and for environmental restorations.

Toward Bioremediation of Methylmercury Using Silica Encapsulated Escherichia coli Harboring the mer Operon

Mercury is a highly toxic heavy metal and the ability of the neurotoxin methylmercury to biomagnify in the food chain is a serious concern for both public and environmental health globally. Because thousands of tons of mercury are released into the environment each year, remediation strategies are urgently needed and prompted this study. To facilitate remediation of both organic and inorganic forms of mercury, Escherichia coli was engineered to harbor a subset of genes (merRTPAB) from the mercury resistance operon. Protein products of the mer operon enable transport of mercury into the cell, cleavage of organic C-Hg bonds, and subsequent reduction of ionic mercury to the less toxic elemental form, Hg(0). E. coli containing merRTPAB was then encapsulated in silica beads resulting in a biological-based filtration material. Performing encapsulation in aerated mineral oil yielded silica beads that were smooth, spherical, and similar in diameter. Following encapsulation, E. coli containing merRTPAB retained the ability to degrade methylmercury and performed similarly to non-encapsulated cells. Due to the versatility of both the engineered mercury resistant strain and silica bead technology, this study provides a strong foundation for use of the resulting biological-based filtration material for methylmercury remediation.

Ancient Evolution and Recent Evolution Converge for the Biodegradation of Cyanuric Acid and Related Triazines

Cyanuric acid was likely present on prebiotic Earth, may have been a component of early genetic materials, and is synthesized industrially today on a scale of more than one hundred million pounds per year in the United States. In light of this, it is not surprising that some bacteria and fungi have a metabolic pathway that sequentially hydrolyzes cyanuric acid and its metabolites to release the nitrogen atoms as ammonia to support growth. The initial reaction that opens the s-triazine ring is catalyzed by the unusual enzyme cyanuric acid hydrolase. This enzyme is in a rare protein family that consists of only cyanuric acid hydrolase (CAH) and barbiturase, with barbiturase participating in pyrimidine catabolism by some actinobacterial species. The X-ray structures of two cyanuric acid hydrolase proteins show that this family has a unique protein fold. Phylogenetic, bioinformatic, enzymological, and genetic studies are consistent with the idea that CAH has an ancient protein fold that was rare in microbial populations but is currently becoming more widespread in microbial populations in the wake of anthropogenic synthesis of cyanuric acid and other s-triazine compounds that are metabolized via a cyanuric acid intermediate. The need for the removal of cyanuric acid from swimming pools and spas, where it is used as a disinfectant stabilizer, can potentially be met using an enzyme filtration system. A stable thermophilic cyanuric acid hydrolase from Moorella thermoacetica is being tested for this purpose.

Silica Gel for Enhanced Activity and Hypochlorite Protection of Cyanuric Acid Hydrolase in Recombinant Escherichia coli

Chlorinated isocyanuric acids are widely used water disinfectants that generate hypochlorite, but with repeated application, they build up cyanuric acid (CYA) that must be removed to maintain disinfection. 3-Aminopropyltriethoxysilane (APTES)-treated Escherichia coli cells expressing cyanuric acid hydrolase (CAH) from Moorella thermoacetica exhibited significantly high CYA degradation rates and provided protection against enzyme inactivation by hypochlorite (chlorine). APTES coating or encapsulation of cells had two benefits: (i) overcoming diffusion limitations imposed by the cell wall and (ii) protecting against hypochlorite inactivation of CAH activity. Cells encapsulated in APTES gels degraded CYA three times faster than nonfunctionalized tetraethoxysilane (TEOS) gels, and cells coated with APTES degraded CYA at a rate of 29 µmol/min per mg of CAH protein, similar to the rate with purified enzyme. UV spectroscopy, fluorescence spectroscopy, and scanning electron microscopy showed that the higher rates were due to APTES increasing membrane permeability and enhancing cyanuric acid diffusion into the cytoplasm to reach the CAH enzyme. Purified CAH enzyme was shown to be rapidly inactivated by hypochlorite. APTES aggregates surrounding cells protected via the amine groups reacting with hypochlorite as shown by pH changes, zeta potential measurements, and infrared spectroscopy. APTES-encapsulated E. coli cells expressing CAH degraded cyanuric acid at high rates in the presence of 1 to 10 ppm hypochlorite, showing effectiveness under swimming pool conditions. In contrast, CAH activity in TEOS gels or free cells was completely inactivated by hypochlorite. These studies show that commercially available silica materials can selectively enhance, protect, and immobilize whole-cell biocatalysts for specialized applications.

Hypochlorite is used in vast quantities for water disinfection, killing bacteria on surfaces, and washing and whitening. In pools, spas, and other waters, hypochlorite is frequently delivered as chlorinated isocyanuric acids that release hypochlorite and cyanuric acid. Over time, cyanuric acid accumulates and impairs disinfection and must be removed. The microbial enzyme cyanuric acid hydrolase can potentially remove cyanuric acid to restore disinfection and protect swimmers. Whole bacterial cells expressing cyanuric acid hydrolase were encapsulated in an inert silica matrix containing an amine group. The amine group serves to permeabilize the cell membrane and accelerate cyanuric acid degradation, and it also reacts with hypochlorite to protect against inactivation of cyanuric acid hydrolase. Methods for promoting whole-cell biocatalysis are important in biotechnology, and the present work illustrates approaches to enhance rates and protect against an inhibitory substance.