Neil C. Bruce

'New uses for an old enzyme': the Old Yellow Enzyme family of flavoenzymes

As the first flavin-dependent enzyme identified, and by virtue of its simplicity, the yeast Old Yellow Enzyme (OYE) has been characterized in detail by the whole gamut of physical techniques. Despite this scrutiny, the true physiological role of the enzyme remains a mystery. After 60 years in isolation, OYE has become the archetype of a growing family of flavoenzymes that have been discovered through studies of bacterial metabolism and genome sequencing projects.

Biodegradation of explosives by transgenic plants expressing pentaerythritol tetranitrate reductase

Plants offer many advantages over bacteria as agents for bioremediation; however, they typically lack the degradative capabilities of specially selected bacterial strains. Transgenic plants expressing microbial degradative enzymes could combine the advantages of both systems. To investigate this possibility in the context of bioremediation of explosive residues, we generated transgenic tobacco plants expressing pentaerythritol tetranitrate reductase, an enzyme derived from an explosive-degrading bacterium that enables degradation of nitrate ester and nitroaromatic explosives. Seeds from transgenic plants were able to germinate and grow in the presence of 1 mM glycerol trinitrate (GTN) or 0.05 mM trinitrotoluene, at concentrations that inhibited germination and growth of wild-type seeds. Transgenic seedlings grown in liquid medium with 1 mM GTN showed more rapid and complete denitration of GTN than wild-type seedlings. This example suggests that transgenic plants expressing microbial degradative genes may provide a generally applicable strategy for bioremediation of organic pollutants in soil.

Phytodetoxification of TNT by transgenic plants expressing a bacterial nitroreductase

There is major international concern over the wide-scale contamination of soil and associated ground water by persistent explosives residues. 2,4,6-Trinitrotoluene (TNT) is one of the most recalcitrant and toxic of all the military explosives. The lack of affordable and effective cleanup technologies for explosives contamination requires the development of better processes. Significant effort has recently been directed toward the use of plants to extract and detoxify TNT. To explore the possibility of overcoming the high phytotoxic effects of TNT, we expressed bacterial nitroreductase in tobacco plants. Nitroreductase catalyzes the reduction of TNT to hydroxyaminodinitrotoluene (HADNT), which is subsequently reduced to aminodinitrotoluene derivatives (ADNTs). Transgenic plants expressing nitroreductase show a striking increase in ability to tolerate, take up, and detoxify TNT. Our work suggests that expression of nitroreductase (NR) in plants suitable for phytoremediation could facilitate the effective cleanup of sites contaminated with high levels of explosives.

Biotransformation of Explosives by the Old Yellow Enzyme Family of Flavoproteins

ABSTRACT Several independent studies of bacterial degradation of nitrate ester explosives have demonstrated the involvement of flavin-dependent oxidoreductases related to the old yellow enzyme (OYE) of yeast. Some of these enzymes also transform the nitroaromatic explosive 2,4,6-trinitrotoluene (TNT). In this work, catalytic capabilities of five members of the OYE family were compared, with a view to correlating structure and function. The activity profiles of the five enzymes differed substantially; no one compound proved to be a good substrate for all five enzymes. TNT is reduced, albeit slowly, by all five enzymes. The nature of the transformation products differed, with three of the five enzymes yielding products indicative of reduction of the aromatic ring. Our findings suggest two distinct pathways of TNT transformation, with the initial reduction of TNT being the key point of difference between the enzymes. Characterization of an active site mutant of one of the enzymes suggests a structural basis for this difference.

Cloning, sequencing, and characterization of the hexahydro-1,3,5-trinitro-1,3,5-triazine degradation gene cluster from Rhodococcus rhodochrous

ABSTRACT Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) is a high explosive which presents an environmental hazard as a major land and groundwater contaminant. Rhodococcus rhodochrous strain 11Y was isolated from explosive contaminated land and is capable of degrading RDX when provided as the sole source of nitrogen for growth. Products of RDX degradation in resting-cell incubations were analyzed and found to include nitrite, formaldehyde, and formate. No ammonium was excreted into the medium, and no dead-end metabolites were observed. The gene responsible for the degradation of RDX in strain 11Y is a constitutively expressed cytochrome P450-like gene, xplA, which is found in a gene cluster with an adrenodoxin reductase homologue, xplB. The cytochrome P450 also has a flavodoxin domain at the N terminus. This study is the first to present a gene which has been identified as being responsible for RDX biodegradation. The mechanism of action of XplA on RDX is thought to involve initial denitration followed by spontaneous ring cleavage and mineralization.

An explosive-degrading cytochrome P450 activity and its targeted application for the phytoremediation of RDX

The widespread presence in the environment of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), one of the most widely used military explosives, has raised concern owing to its toxicity and recalcitrance to degradation. To investigate the potential of plants to remove RDX from contaminated soil and water, we engineered Arabidopsis thaliana to express a bacterial gene xplA encoding an RDX-degrading cytochrome P450 (ref. 1). We demonstrate that the P450 domain of XplA is fused to a flavodoxin redox partner and catalyzes the degradation of RDX in the absence of oxygen. Transgenic A. thaliana expressing xplA removed and detoxified RDX from liquid media. As a model system for RDX phytoremediation, A. thaliana expressing xplA was grown in RDX-contaminated soil and found to be resistant to RDX phytotoxicity, producing shoot and root biomasses greater than those of wild-type plants. Our work suggests that expression of xplA in landscape plants may provide a suitable remediation strategy for sites contaminated by this class of explosives.

Biodegradation, Biotransformation, and Biocatalysis (B3)

When one adult meets another at a party, they often get to know each other by asking the question, “What do you do?” Translated, this question asks how you earn a living. When a microbiologist meets a newly isolated bacterium for the first time, the initial question is similar: What does it do?

Plants disarm soil: engineering plants for the phytoremediation of explosives.

Explosives are toxic, recalcitrant to degradation and contaminate large areas of land and ground water. Remediation of these synthetic compounds is difficult and an enormous logistical task. Phytoremediation is a technique that offers an environmentally friendly, low-cost alternative to current remediation techniques; however, this approach is hindered by the low inherent metabolic abilities of plants towards these xenobiotic compounds and the phytotoxicity of these compounds. As a result of recent advances in our knowledge of the biochemistry underlying endogenous plant detoxification systems and the use of genetic engineering to combine bacterial explosives-detoxifying genes with the phytoremediatory benefits of plants, this technology is now poised for testing in the field and in a wider range of plants, such as poplar and perennial grasses.

Phytoremediation of explosives

Referee: Dr. C. Neal Stewart, Jr., Department of Plant Science and Landscape Systems, The University of Tennessee, 2431 Center Drive, Knoxville, TN 37996-4561 There is major international concern over the widescale contamination of soil and associated groundwater by persistant explosives residues. The development of methods to remediate these contaminants has been a significant research interest for several decades. In the last 10 years, phytoremediation has emerged as a focus for explosives remediation because of its low cost, low energy requirements, and promising research observing explosives removal from contaminated groundwater and soil. More recent work has focused on the modes of transformation and metabolism of energetic compounds by plants. These biochemical studies and the experimental conditions enabling the degradation and uptake of explosives by different plant species are discussed.

Crystal structure of a bacterial cocaine esterase

Here we report the first structure of a cocaine-degrading enzyme. The bacterial esterase, cocE, hydrolyzes pharmacologically active (−)-cocaine to a nonpsychoactive metabolite with a rate faster than any other reported cocaine esterase (kcat = 7.8 s−1 and KM = 640 nM). Because of the high catalytic proficiency of cocE, it is an attractive candidate for novel protein-based therapies for cocaine overdose. The crystal structure of cocE, solved by multiple anomalous dispersion (MAD) methods, reveals that cocE is a serine esterase composed of three domains: (i) a canonical α/β hydrolase fold (ii) an α-helical domain that caps the active site and (iii) a jelly-roll-like β-domain that interacts extensively with the other two domains. The active site was identified within the interface of all three domains by analysis of the crystal structures of transition state analog adduct and product complexes, which were refined at 1.58 Å and 1.63 Å resolution, respectively. These structural studies suggest that substrate recognition arises partly from interactions between the benzoyl moiety of cocaine and a highly evolved specificity pocket.