Elucidation of molecular mechanisms underlying degradation of nicosulfuron and its derivative by Klebsiella jilinsis 2N3 using multiomic analysis

Nicosulfuron is a herbicide used in agricultural production. Its prolonged application causes significant ecological risks to soil and water environment. In this study, the molecular mechanisms underlying degradation of nicosulfuron and its derivative by Klebsiella jilinsis 2N3 was determined. Strain 2N3 degraded nicosulfuron primarily via cleavage of the sulfonylurea bridge and deamination and demethoxylation of its derivative, 2-amino-4,6-dimethoxypyrimidine (ADMP). Multiomic analysis indicated significant alterations in genes and proteins predominantly associated with glycolysis, tricarboxylic acid cycle, quorum sensing, signal transduction, energy metabolism, and nucleotide synthesis. Heterologous expression and gene knockout confirmed that degradation of the sulfonylurea bridge in nicosulfuron by strain 2N3 was accompanied by a hydrolysis process, in which arginine hydrolase Kj-CY657_RS10725 participated in nicosulfuron degradation Deletion of its gene decreased the biodegradation rate of nicosulfuron by 11.04 % in 24 h. Moreover, our study demonstrated that nicosulfuron derivative ADMP can effectively dock within the active site of the Kj-CY657_RS01600 protein, forming hydrogen bonds that enhanced the catalytic activity. Kj-CY657_RS01600 could degrade 10 mg mL −1 ADMP by 43.08 % within 30 min, resulting in the formation of 4,6-dimethoxypyrimidine as a byproduct. Additionally, after Kj - CY657_RS01600 knockout, the ability of strain 2N3 to biodegrade ADMP decreased by 52.48 %. This study provided molecular mechanism for comprehensive understanding the biodegradation of nicosulfuron and its derivative ADMP by strain 2N3.