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

Assessing the impact of soil microbial fuel cells on atrazine removal in soil

Widespread pesticide use in agriculture is a major source of soil pollution, driving biodiversity loss and posing serious threads to human health. The recalcitrant nature of most of these pesticides demands for effective remediation strategies. In this study, we assess the ability of soil microbial fuel cell (SMFC) technology to bioremediate soil polluted by the model pesticide atrazine. To elucidate the degradation mechanism and consequently define effective implementation strategies, we provide the first comprehensive investigation of the SMFC performance, in which the monitoring of the electrochemical performance of the system is combined with Quadrupole Time-of-Flight (QTOF) mass spectrometry and microbial analyses. Our results show that, while both SMFC and natural attenuation lead to a reduction on atrazine levels, the SMFC modulates the activity of different microbial pathways. As a result, atrazine degradation by natural attenuation leads to high levels of deisoproylatrazine (DIPA), a very toxic degradation metabolite, while DIPA levels in soil treated by SMFC remain comparatively low. The beta diversity and differential abundance analyses revealed how the microbial community evolves over time in the SMFCs degrading atrazine, demonstrating the enrichment of electroactive taxa on the anode, and the enrichment of a mixture of electroactive and atrazine-degrading taxa at the cathode. The detection and taxonomic classification of peripheral atrazine degrading genes, atzA, atzB and atzC, was carried out in combination with the differential abundance analysis. Results revealed that these genes are likely harboured by members of the order Rhizobiales enriched at the cathode, thus promoting atrazine degradation via the conversion of hydroxyatrazine (HA) into N-isopropylammelide (NIPA), as confirmed by mass spectrometry data. Overall, the comprehensive approach adopted in this work, provides fundamental insights into the degradation pathways of atrazine in soil by SMFC technology, which is critical for practical applications, thus suggesting an effective approach to advance research in the field.

Study on the health risk of cyanuric acid in swimming pool water and its prevention and control measures

Cyanuric acid is a widely used fine chemical intermediate that acts as a free chlorine buffer in swimming pool water, wherein it is often used as a stabilizer to maintain the germicidal efficacy of chlorinated disinfectants. However, it has also been associated with health risks. Herein, we introduced the sources and functions of cyanuric acid in swimming pool water, focusing on potential health risks associated with excessive concentration of the component and the current control standards worldwide. Also, the prevention and control measures were summarized in terms of physical chemistry, biodegradation, and ultraviolet radiation to provide a basis for the development of public health policies for swimming pool management.

Retracing the Rapid Evolution of an Herbicide-Degrading Enzyme by Protein Engineering

The mechanisms underlying the rapid evolution of novel enzymatic activities from promiscuous side activities are poorly understood. Recently emerged enzymes catalyzing the catabolic degradation of xenobiotic substances that have been spread out into the environment during the last decades provide an exquisite opportunity to study these mechanisms. A prominent example is the herbicide atrazine (2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine), which is degraded through a number of enzymatic reactions constituting the Atz pathway. Here, we analyzed the evolution of the hydroxyatrazine ethylaminohydrolase AtzB, a Zn(II)-dependent metalloenzyme that adopts the amidohydrolase fold and catalyzes the second step of the Atz pathway. We searched for promiscuous side activities of AtzB, which might point to the identity of its progenitor. These investigations revealed that AtzB has low promiscuous guanine deaminase activity. Furthermore, we found that the two closest AtzB homologues, which have not been functionally annotated up to now, are guanine deaminases with modest promiscuous hydroxyatrazine hydrolase activity. Based on sequence comparisons with the closest AtzB homologues, the guanine deaminase activity of AtzB could be increased by three orders of magnitude through the introduction of only four active site mutations. Interestingly, introducing the inverse four mutations into the AtzB homologues significantly enhanced their hydroxyatrazine hydrolase activity, and in one case is even equivalent to that of wild-type AtzB. Molecular dynamics simulations elucidated the structural and molecular basis for the mutation-induced activity changes. The example of AtzB highlights how novel enzymes with high catalytic proficiency can evolve from low promiscuous side activities by only few mutational events within a short period of time.

Investigation of the Persistence, Toxicological Effects, and Ecological Issues of S-Triazine Herbicides and Their Biodegradation Using Emerging Technologies: A Review

S-triazines are a group of herbicides that are extensively applied to control broadleaf weeds and grasses in agricultural production. They are mainly taken up through plant roots and are transformed by xylem tissues throughout the plant system. They are highly persistent and have a long half-life in the environment. Due to imprudent use, their toxic residues have enormously increased in the last few years and are frequently detected in food commodities, which causes chronic diseases in humans and mammals. However, for the safety of the environment and the diversity of living organisms, the removal of s-triazine herbicides has received widespread attention. In this review, the degradation of s-triazine herbicides and their intermediates by indigenous microbial species, genes, enzymes, plants, and nanoparticles are systematically investigated. The hydrolytic degradation of substituents on the s-triazine ring is catalyzed by enzymes from the amidohydrolase superfamily and yields cyanuric acid as an intermediate. Cyanuric acid is further metabolized into ammonia and carbon dioxide. Microbial-free cells efficiently degrade s-triazine herbicides in laboratory as well as field trials. Additionally, the combinatorial approach of nanomaterials with indigenous microbes has vast potential and considered sustainable for removing toxic residues in the agroecosystem. Due to their smaller size and unique properties, they are equally distributed in sediments, soil, water bodies, and even small crevices. Finally, this paper highlights the implementation of bioinformatics and molecular tools, which provide a myriad of new methods to monitor the biodegradation of s-triazine herbicides and help to identify the diverse number of microbial communities that actively participate in the biodegradation process.

Atrazine uptake, translocation, bioaccumulation and biodegradation in cattail (Typha latifolia) as a function of exposure time

The extensive use and environmental persistence of atrazine has resulted in its ubiquitous occurrence in water resources. Some reports have described atrazine bioaccumulation and biodegradation pathways in terrestrial plants, but few have done so in aquatic macrophytes. Thus, in this study, we aimed to analyze morphological changes, uptake, translocation and bioaccumulation patterns in tissues of the aquatic macrophyte Typha latifolia (cattail) after long-term atrazine exposure and to determine the presence of atrazine biodegradation metabolites, desethylatrazine (DEA) and desisopropylatrazine (DIA), in tissues. Plants were hydroponically exposed to 20 μg/L atrazine (18 exposed and 18 non-exposed) for 7, 14, 21, 28, 35 and 42 days. Plants were separated into root, rhizome, stem, and lower, middle and upper leaf sections. Atrazine was analyzed by LC-MS/MS and DIA and DEA by LC-DAD. Plants showed reductions in weight (after 21 days) and transpiration (after 28 days), both symptoms of chronic phytotoxicity. The distribution of atrazine within tissues, expressed as concentration levels (μg/kg dry weight), was as follows: middle leaf (406.10 ± 71.77) = upper leaf (339.15 ± 47.60) = lower leaf (262.43 ± 7.66) = sprout (274.53 ± 58.1) > stem (38.63 ± 7.55) = root (36.00 ± 3.49) = rhizome (26.15 ± 3.96). In submerged tissues, DEA and DIA were detected at similar concentrations. In leaves, DIA was the main metabolite identified. Results indicated that atrazine was taken up from roots to shoots and induced phytotoxicity effects that reduced the translocation to shoots. Typha likely is able to biodegrade atrazine via different metabolic pathways.

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.

Cyanuric Acid Biodegradation via Biuret: Physiology, Taxonomy, and Geospatial Distribution

Cyanuric acid is an industrial chemical produced during the biodegradation of s-triazine pesticides. The biodegradation of cyanuric acid has been elucidated using a single model system, Pseudomonas sp. strain ADP, in which cyanuric acid hydrolase (AtzD) opens the s-triazine ring and AtzEG deaminates the ring-opened product. A significant question remains as to whether the metabolic pathway found in Pseudomonas sp. ADP is the exception or the rule in bacterial genomes globally. Here, we show that most bacteria utilize a different pathway, metabolizing cyanuric acid via biuret. The new pathway was determined by reconstituting the pathway in vitro with purified enzymes and by mining more than 250,000 genomes and metagenomes. We isolated soil bacteria that grow on cyanuric acid as a sole nitrogen source and showed that the genome from a Herbaspirillum strain had a canonical cyanuric acid hydrolase gene but different flanking genes. The flanking gene trtB encoded an enzyme that we show catalyzed the decarboxylation of the cyanuric acid hydrolase product, carboxybiuret. The reaction generated biuret, a pathway intermediate further transformed by biuret hydrolase (BiuH). The prevalence of the newly defined pathway was determined by cooccurrence analysis of cyanuric acid hydrolase genes and flanking genes. Here, we show the biuret pathway was more than 1 order of magnitude more prevalent than the original Pseudomonas sp. ADP pathway. Mining a database of over 40,000 bacterial isolates with precise geospatial metadata showed that bacteria with concurrent cyanuric acid and biuret hydrolase genes were distributed throughout the United States.IMPORTANCE Cyanuric acid is produced naturally as a contaminant in urea fertilizer, and it is used as a chlorine stabilizer in swimming pools. Cyanuric acid-degrading bacteria are used commercially in removing cyanuric acid from pool water when it exceeds desired levels. The total volume of cyanuric acid produced annually exceeds 200 million kilograms, most of which enters the natural environment. In this context, it is important to have a global understanding of cyanuric acid biodegradation by microbial communities in natural and engineered systems. Current knowledge of cyanuric acid metabolism largely derives from studies on the enzymes from a single model organism, Pseudomonas sp. ADP. In this study, we obtained and studied new microbes and discovered a previously unknown cyanuric acid degradation pathway. The new pathway identified here was found to be much more prevalent than the pathway previously established for Pseudomonas sp. ADP. In addition, the types of environment, taxonomic prevalences, and geospatial distributions of the different cyanuric acid degradation pathways are described here.

Assembly of an atrazine catabolic operon and its introduction to Gram-negative hosts for robust and stable degradation of triazine herbicides

In 1995, Pseudomonas sp. ADP, capable of metabolizing atrazine, was isolated from contaminated soil. Genes responsible for atrazine mineralization were found scattered in the 108.8 kb pADP-1 plasmid carried by this strain, some of them flanked by insertion sequences rendering them unstable. The goal of this work was to construct a transcriptional unit containing the atz operon in an easy to transfer manner, to be introduced and inherited stably by Gram-negative bacteria. atz genes were PCR amplified, joined into an operon and inserted onto the mobilizable plasmid pBAMD1–2. Primers were designed to add efficient transcription and translation signals. Plasmid bearing the atz operon was transferred to different Gram-negative strains by conjugation, which resulted in Tn5 transposase-mediated chromosomal insertion of the atz operon. To test the operon activity, atrazine degradation by transposants was assessed both colorimetrically and by high-performance liquid chromatography (HPLC). Transposants mineralized atrazine more efficiently than wild-type Pseudomonas sp. ADP and did not accumulate cyanuric acid. Atrazine degradation was not repressed by simple nitrogen sources. Genes conferring atrazine-mineralizing capacities were stable and had little or null effect on the fitness of different transposants. Introduction of catabolic operons in a stable fashion could be used to develop bacteria with better degrading capabilities useful in bioremediation.

Triazine Probes Target Ascorbate Peroxidases in Plants

Though they are rare in nature, anthropogenic 1,3,5-triazines have been used in herbicides as chemically stable scaffolds. Here, we show that small 1,3,5-triazines selectively target ascorbate peroxidases (APXs) in Arabidopsis (Arabidopsis thaliana), tomato (Solanum lycopersicum), rice (Oryza sativa), maize (Zea mays), liverwort (Marchantia polymorpha), and other plant species. The alkyne-tagged 2-chloro-4-methyl-1,3,5-triazine probe KSC-3 selectively binds APX enzymes, both in crude extracts and in living cells. KSC-3 blocks APX activity, thereby reducing photosynthetic activity under moderate light stress, even in apx1 mutant plants. This suggests that APX enzymes in addition to APX1 protect the photosystem against reactive oxygen species. Profiling APX1 with KCS-3 revealed that the catabolic products of atrazine (a 1,3,5-triazine herbicide), which are common soil pollutants, also target APX1. Thus, KSC-3 is a powerful chemical probe to study APX enzymes in the plant kingdom.

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.

Comparative genome analysis reveals the evolution of chloroacetanilide herbicide mineralization in Sphingomonas wittichii DC-6

The environmental fate of the extensively used chloroacetanilide herbicides (CH) has been a cause of increasing concern in the past decade because of their carcinogenic properties. Although microbes play important roles in CH degradation, Sphingomonas wittichii DC-6 was the first reported CH-mineralizing bacterium. In this study, the complete genome of strain DC-6 was sequenced and comparative genomic analysis was performed using strain DC-6 and other three partial CH-degrading bacteria, Sphingobium quisquiliarum DC-2, Sphingobium baderi DE-13, and Sphingobium sp. MEA3-1. 16S rDNA phylogenetic analysis indicated that strain DC-2, MEA3-1, and DE-13 are closely related and DC-6 has relatively distant genetic relationship with the other three strains. The identified CH degradation genes responsible for the upstream and downstream pathway, including cndA, cmeH, meaXY, and meaAB, were all located in conserved DNA fragments (or genetic islands) in the vicinity of mobile element proteins. Protein BLAST in the NCBI database showed that cndA and cmeH were present in the genomes of other sequenced strains isolated from various habitats; however, the gene compositions in these host strains were completely different from those of other sphingomonads, and codon usage of genes for upstream pathway were also different from that of downstream pathway. These results showed that the upstream and downstream pathways of CH degradation in strain DC-6 have evolved by horizontal gene transfer and gene combination. In addition, the genes of the ring-cleavage pathway were not conserved and may have evolved directly from bacterial degradation of hydroxyquinol. The present study provides insights into the evolutionary strategy and microbial catabolic pathway of CH mineralization.

The Metabolic Redox Regime of Pseudomonas putida Tunes Its Evolvability toward Novel Xenobiotic Substrates

During evolution of biodegradation pathways for xenobiotic compounds involving Rieske nonheme iron oxygenases, the transition toward novel substrates is frequently associated with faulty reactions. Such events release reactive oxygen species (ROS), which are endowed with high mutagenic potential. In this study, we evaluated how the operation of the background metabolic network by an environmental bacterium may either foster or curtail the still-evolving pathway for 2,4-dinitrotoluene (2,4-DNT) catabolism. To this end, the genetically tractable strain Pseudomonas putida EM173 was implanted with the whole genetic complement necessary for the complete biodegradation of 2,4-DNT (recruited from the environmental isolate Burkholderia sp. R34). By using reporter technology and direct measurements of ROS formation, we observed that the engineered P. putida strain experienced oxidative stress when catabolizing the nitroaromatic substrate. However, the formation of ROS was neither translated into significant activation of the SOS response to DNA damage nor did it result in a mutagenic regime (unlike what has been observed in Burkholderia sp. R34, the original host of the pathway). To inspect whether the tolerance of P. putida to oxidative challenges could be traced to its characteristic reductive redox regime, we artificially altered the NAD(P)H pool by means of a water-forming, NADH-specific oxidase. Under the resulting low-NAD(P)H status, catabolism of 2,4-DNT triggered a conspicuous mutagenic and genomic diversification scenario. These results indicate that the background biochemical network of environmental bacteria ultimately determines the evolvability of metabolic pathways. Moreover, the data explain the efficacy of some bacteria (e.g., pseudomonads) to host and evolve with new catabolic routes.IMPORTANCE Some environmental bacteria evolve with new capacities for the aerobic biodegradation of chemical pollutants by adapting preexisting redox reactions to novel compounds. The process typically starts by cooption of enzymes from an available route to act on the chemical structure of the substrate-to-be. The critical bottleneck is generally the first biochemical step, and most of the selective pressure operates on reshaping the initial reaction. The interim uncoupling of the novel substrate to preexisting Rieske nonheme iron oxygenases usually results in formation of highly mutagenic ROS. In this work, we demonstrate that the background metabolic regime of the bacterium that hosts an evolving catabolic pathway (e.g., biodegradation of the xenobiotic 2,4-DNT) determines whether the cells either adopt a genetic diversification regime or a robust ROS-tolerant status. Furthermore, our results offer new perspectives to the rational design of efficient whole-cell biocatalysts, which are pursued in contemporary metabolic engineering.

Microbial biodegradation of biuret: defining biuret hydrolases within the isochorismatase superfamily

Biuret is a minor component of urea fertilizer and an intermediate in s-triazine herbicide biodegradation. The microbial metabolism of biuret has never been comprehensively studied. Here, we enriched and isolated bacteria from a potato field that grew on biuret as a sole nitrogen source. We sequenced the genome of the fastest-growing isolate, Herbaspirillum sp. BH-1 and identified genes encoding putative biuret hydrolases (BHs). We purified and characterized a functional BH enzyme from Herbaspirillum sp. BH-1 and two other bacteria from divergent phyla. The BH enzymes reacted exclusively with biuret in the range of 2-11 µmol min^-1 mg^-1 protein. We then constructed a global protein superfamily network to map structure-function relationships in the BH subfamily and used this to mine > 7000 genomes. High-confidence BH sequences were detected in Actinobacteria, Alpha- and Beta-proteobacteria, and some fungi, archaea and green algae, but not animals or land plants. Unexpectedly, no cyanuric acid hydrolase homologs were detected in > 90% of genomes with BH homologs, suggesting BHs may have arisen independently of s-triazine ring metabolism. This work links genotype to phenotype by enabling accurate genome-mining to predict microbial utilization of biuret. Importantly, it advances understanding of the microbial capacity for biuret biodegradation in agricultural systems.

CATALOGIC 301C model - validation and improvement

In Europe, REACH legislation encourages the use of alternative in silico methods such as (Q)SAR models. According to the recent progress of Chemical Substances Control Law (CSCL) in Japan, (Q)SAR predictions are also utilized as supporting evidence for the assessment of bioaccumulation potential of chemicals along with read across. Currently, the effective use of read across and QSARs is examined for other hazards, including biodegradability. This paper describes the results of external validation and improvement of CATALOGIC 301C model based on more than 1000 tested new chemical substances of the publication schedule under CSCL. CATALOGIC 301C model meets all REACH requirements to be used for biodegradability assessment. The model formalism built on scientific understanding for the microbial degradation of chemicals has a well-defined and transparent applicability domain. The model predictions are adequate for the evaluation of the ready degradability of chemicals.

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.