Evolution of catabolic pathways: Genomic insights into microbial s-triazine metabolism.

In recent years, studies on the catabolism of organonitrogen compounds have accelerated due to the recognition that these compounds are widespread and significant environmentally. Nitrogen is the second most abundant macronutrient in cellular organisms, where it is found in major macromolecules (proteins and nucleic acids), primary metabolites (ATP and NADH), and secondary metabolites, such as antibiotics. Well over 50,000 organonitrogen compounds are biosynthesized by plants and microbes (27). Many of these compounds are Nheterocycles, ring structures containing one or more nitrogen atoms in the rings. A significant fraction of anthropogenic compounds, commodity chemicals and pharmaceuticals, are N-heterocycles. One class of industrial N-heterocycles, also known as s-triazines, contain the 1,3,5-triazine ring. Humans introduced s-triazine herbicides, such as atrazine (Fig. 1), into the environment one-half century ago. Commercial s-triazines characteristically contain ring carbon atoms that contain substituents other than hydrogen (Fig. 1, upper left). This fundamental ring structure resembles the 1,3-diazenes, or pyrimidines, and as such, their metabolic transformation by microbes should be reasonably facile. However, s-triazine compounds were initially found to be poorly biodegradable. In the decades following its introduction, measured environmental half-lives of atrazine were variable and relatively long, typically 60 to 400 days (28, 35, 41, 46, 67, 69). Soil metabolite and biochemical studies provided evidence for nonspecific oxidation reactions leading to partial metabolism. More recently, environmental half-lives have decreased dramatically; they are now typically measured at 1 to 50 days (4, 32, 48, 80). Additionally, metabolite profiles have changed. In the period between 1960 and 1990, many studies reported bacterial metabolism of atrazine to occur via dealkylation of the N-alkyl substituents on the s-triazine ring (20, 21, 34), a pathway that does not typically lead to s-triazine ring cleavage (44, 62). Since 1995, most reports of metabolic pathways for atrazine degradation have described metabolism via hydroxyatrazine and not involving dealkylation (18, 49, 53, 56, 70, 72, 73, 75, 76). Earlier reports expressed the view that isolating bacteria able to grow on atrazine as a sole nitrogen or carbon source was difficult (13, 20). Most recently, pure cultures of bacteria capable of growing on atrazine could be obtained from most soils (39). These observations are consistent with the idea that a new metabolic pathway for atrazine catabolism may have evolved and spread in recent evolutionary times. These observations of metabolism in soil have been complemented by the discovery that a set of nearly identical s-triazine-catabolic genes has been found worldwide in diverse bacterial genera (17, 19, 75, 76). The genes atzABCDEF or trzN-atzBCDEF encode the pathway shown in Fig. 1. Almost invariably, the s-triazine-catabolic genes have been identified as residing on plasmids, packaged via flanking insertion sequence elements (1, 53, 76). A deeper understanding of how the atrazine-catabolic genes move and become fixed in bacterial populations requires greater insight into the complete gene complement of atrazine-degrading organisms.