Iron-Dependent Enzyme Catalyzes the Initial Step in Biodegradation of N -Nitroglycine by Variovorax sp. Strain JS1663

Abstract

Nitramines are key constituents of most of the explosives currently in use and consequently contaminate soil and groundwater at many military facilities around the world. Toxicity from nitramine contamination poses a health risk to plants and animals. Thus, understanding how nitramines are biodegraded is critical to environmental remediation. The biodegradation of synthetic nitramine compounds such as hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) has been studied for decades, but little is known about the catabolism of naturally produced nitramine compounds. In this study, we report the isolation of a soil bacterium, Variovorax sp. strain JS1663, that degrades N-nitroglycine (NNG), a naturally produced nitramine, and the key enzyme involved in its catabolism. Variovorax sp. JS1663 is a Gram-negative, non-sporeforming motile bacterium isolated from activated sludge based on its ability to use NNG as a sole growth substrate under aerobic conditions. A single gene (nnlA) encodes an iron-dependent enzyme that releases nitrite from NNG through a proposed ␤-elimination reaction. Bioinformatics analysis of the amino acid sequence of NNG lyase identified a PAS (Per-Arnt-Sim) domain. PAS domains can be associated with heme cofactors and function as signal sensors in signaling proteins. This is the first instance of a PAS domain present in a denitration enzyme. The NNG biodegradation pathway should provide the basis for the identification of other enzymes that cleave the NON bond and facilitate the development of enzymes to cleave similar bonds in RDX, nitroguanidine, and other nitramine explosives. IMPORTANCEThe production of antibiotics and other allelopathic chemicals is a major aspect of chemical ecology. The biodegradation of such chemicals can play an important ecological role in mitigating or eliminating the effects of such compounds. N-Nitroglycine (NNG) is produced by the Gram-positive filamentous soil bacterium Streptomyces noursei. This study reports the isolation of a Gram-negative soil bacterium, Variovorax sp. strain JS1663, that is able to use NNG as a sole growth substrate. The proposed degradation pathway occurs via a ␤-elimination reaction that releases nitrite from NNG. The novel NNG lyase requires iron(II) for activity. The identification of a novel enzyme and catabolic pathway provides evidence of a substantial and underappreciated flux of the antibiotic in natural ecosystems. Understanding the NNG biodegradation pathway will help identify other enzymes that cleave the NON bond and facilitate the development of enzymes to cleave similar bonds in synthetic nitramine explosives.

Identification and Characterization of a Novel pic Gene Cluster Responsible for Picolinic Acid Degradation in Alcaligenes faecalis JQ135

“…Interestingly, some of these strains are toxic-compound degraders (e.g., Achromobacter xylosoxidans A8 and Variovorax sp. strain JS1663 (40,41), human pathogens (e.g., Bordetella pertussis Tohama I and Bordetella bronchiseptica RB50) (42), and nematicidal bacteria (e.g., A. faecalis ZD02) (43), whereas other strains represent typical soil bacteria (e.g., Pseudomonas), plant rhizosphere-associated bacteria (e.g., Bradyrhizobium), arctic bacteria (Octadecabacter arcticus 238) (44), and Antarctic bacteria (Hoeflea sp. strain IMCC20628) (45).)…”

Altered Gut Microbiota Composition in Subjects Infected With Clonorchis sinensis

“…In C. sinensis -infected individuals, the higher relative abundance of Enterococcus might not be conducive to recovery from clonorchiasis. Variovorax , an important environmental taxa ( Thomas et al, 2017 ; Woo et al, 2017 ), has been reported to produce nitramine ( Mahan et al, 2017 ), which is harmful to humans and animals. This taxa was only detected in the C. sinensis infected groups, however, it was not correlated with EPG.…”

Identification and characterization of a novelpicgene cluster responsible for picolinic acid degradation inAlcaligenes faecalisJQ135

“…Interestingly, some of these strains are toxic compound degraders (e.g., Achromobacter xylosoxidans A8 and Variovorax sp. JS1663) (36, 37), human pathogens (e.g., Bordetella pertussis Tohama I and Bordetella bronchiseptica RB50) (38), and nematicidal bacteria (e.g., A. faecalis ZD02) (39), whereas other strains represent typical soil bacteria (e.g., Pseudomonas ), plant rhizosphere-associated bacteria (e.g., Bradyrhizobium ), arctic bacterium ( Octadecabacter arcticus 238) (40), and antarctic bacterium ( Hoeflea sp. IMCC20628) (41).…”