BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA.
Department of Biochemistry, Hamline University, St. Paul, Minnesota, USA.
Appl Environ Microbiol. 2020 Jan 7;86(2). doi: 10.1128/AEM.01964-19.
Cyanuric acid is an industrial chemical produced during the biodegradation of -triazine pesticides. The biodegradation of cyanuric acid has been elucidated using a single model system, sp. strain ADP, in which cyanuric acid hydrolase (AtzD) opens the -triazine ring and AtzEG deaminates the ring-opened product. A significant question remains as to whether the metabolic pathway found in 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 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 strain had a canonical cyanuric acid hydrolase gene but different flanking genes. The flanking gene 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 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. 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, 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 sp. ADP. In addition, the types of environment, taxonomic prevalences, and geospatial distributions of the different cyanuric acid degradation pathways are described here.
三聚氰胺酸是一种工业化学品，在三嗪类农药的生物降解过程中产生。三聚氰胺酸的生物降解已经通过单个模型系统得到了阐明，即 sp. 菌株 ADP，其中三聚氰胺酸水解酶（AtzD）打开三嗪环，AtzEG 脱氨基化环开产物。一个重要的问题仍然是，ADP 菌株中发现的代谢途径是细菌基因组中普遍存在的例外还是规则。在这里，我们表明，大多数细菌利用不同的途径，通过缩二脲代谢三聚氰胺酸。新途径是通过用纯化的酶重新构建途径以及挖掘超过 250,000 个基因组和宏基因组来确定的。我们分离出以三聚氰胺酸为唯一氮源生长的土壤细菌，并表明来自 菌株的基因组具有典型的三聚氰胺酸水解酶基因，但侧翼基因不同。侧翼基因编码一种我们证明催化三聚氰胺酸水解酶产物脱羧的酶，即羧基缩二脲。反应生成缩二脲，该途径中间体进一步由缩二脲水解酶（BiuH）转化。通过三聚氰胺酸水解酶基因和侧翼基因的共现分析确定了新定义途径的普遍性。在这里，我们表明，与原始的 sp. ADP 途径相比，新定义的途径的流行度超过 1 个数量级。对具有精确地理位置元数据的超过 40,000 个细菌分离株的数据库进行挖掘表明，同时具有三聚氰胺酸和缩二脲水解酶基因的细菌分布在美国各地。三聚氰胺酸自然产生作为尿素肥料的污染物，并且在游泳池中用作氯稳定剂。当游泳池水中的三聚氰胺酸含量超过所需水平时，商业上使用三聚氰胺酸降解细菌从池水中去除三聚氰胺酸。每年生产的三聚氰胺酸总量超过 2000 万吨，其中大部分进入自然环境。在这种情况下，了解微生物群落在自然和工程系统中对三聚氰胺酸的生物降解具有重要的全球意义。目前对三聚氰胺酸代谢的了解主要来自于对单个模式生物 sp. ADP 酶的研究。在这项研究中，我们获得并研究了新的微生物，并发现了一种以前未知的三聚氰胺酸降解途径。这里确定的新途径比以前为 sp. ADP 建立的途径更为普遍。此外，还描述了这里不同三聚氰胺酸降解途径的环境类型、分类流行率和地理空间分布。
