BioTechnology Institute, College of Biological Sciences, University of Minnesota, - Twin Cities, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA.
Environ Microbiol. 2018 Jun;20(6):2099-2111. doi: 10.1111/1462-2920.14094. Epub 2018 Mar 26.
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 mg 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.
缩二脲是尿素肥料的一个次要成分，也是三嗪类除草剂生物降解的一个中间产物。微生物对缩二脲的代谢从未被全面研究过。在这里，我们从以缩二脲为唯一氮源的马铃薯田中富集和分离了细菌。我们对生长最快的分离菌 Herbaspirillum sp. BH-1 的基因组进行了测序，并鉴定了编码潜在的缩二脲水解酶 (BHs)的基因。我们从 Herbaspirillum sp. BH-1 和另外两种来自不同门的细菌中纯化和表征了一种功能性 BH 酶。BH 酶在 2-11 µmol min mg protein 的范围内仅与缩二脲反应。然后，我们构建了一个全球蛋白质超级家族网络，以映射 BH 亚家族的结构-功能关系，并利用该网络挖掘了 >7000 个基因组。在放线菌、α-和β-变形菌以及一些真菌、古菌和绿藻中检测到高可信度的 BH 序列，但在动物或陆地植物中没有检测到。出乎意料的是，在 >90%的具有 BH 同源物的基因组中没有检测到氰尿酸水解酶同源物，这表明 BHs 可能是独立于三嗪环代谢而产生的。这项工作通过使准确的基于基因组挖掘预测微生物对缩二脲的利用成为可能，将基因型与表型联系起来。重要的是，它推进了对农业系统中微生物降解缩二脲能力的理解。
