Self-sufficient reductive dehalogenases for bioremediation

Halogenated organic compounds have found widespread use in the chemical and pharmaceutical industries, in agriculture, and as solvents and materials, with production on the multi-ton scale per annum. Their persistent nature and (un)controlled release has led to worldwide accumulation of such compounds in the environment. Furthermore, bioaccumulation and toxicity has led to many organohalides presenting significant challenges to human and environmental health. Indeed, the majority of persistent organic pollutants (POPs) contain halogens, with many of them now falling under the 2004 Stockholm convention that serves to eliminate their use. While regulation has reduced some levels of contamination, remaining reservoirs in sediments and waste remain of concern. Furthermore, few alternatives are available for the use of organohalides, and society is balancing human benefit with environmental detriment when regulating organohalide production and use. However, significant knowledge gaps remain in understanding the (long-term) effects of human/environmental exposure. Counter to popular perception, organohalides are not exclusively of anthropogenic origin, with an ever-increasing amount of natural compounds identified, the majority of biological origin. Indeed, the last decades have seen identification and characterisation of a range of halogenase and dehalogenase enzymes that feature in organohalide biochemistry. While dehalogenases can serve in bioremediation or biosensing of POPs, the inherent properties of these enzymes do not match the human-made xenobiotic repertoire. We seek to study a particular type of dehalogenases, the reductive dehalogenases (Rdh) or organohalide reductases, which present unique opportunities in terms of substrate scope, bioremediation and biosensing. In recent years, our own group and that of others have provided detailed insights into these enigmatic proteins that depend on vitamin B12 for activity. However, the exact mode of operation remains somewhat enigmatic, while protein engineering efforts aimed at generating robust biocatalyst based on the Rdh-template have yet to meet with success. We seek to use specific reductive dehalogenases selected and studied in our lab to provide a complete fundamental insight into the mechanism of action. We seek this information to guide directed evolution experiments aimed at generating a toolbox of dehalogenases that can act on POPs and related compounds of interest.

The reductive dehalogenases (Rdhs) are key enzymes in organohalide respiration. The Rdhs are cobalamin-dependent and able to selectively cleave carbon-halogen bonds through reduction. As a result, Rdh-containing organisms have been targeted as a potential bioremediation tool. The Rdhs can be split into three classes: i) the canonical respiratory reductive dehalogenases (rRdh), which use a halogenated compound as a final electron acceptor during organohalide respiration, ii) the catabolic reductive dehalogenases (cRdh) that occur in the catabolic pathways of non-organohalide respiring bacteria and iii) the self-sufficient reductive dehalogenases (ssRdh), that combine the properties of the cRdh with the ability to oxidise NADPH and couple this to substrate reduction. Both cRdh and ssRdh enzymes tend to be oxygen-tolerant and of a soluble nature, and are thus desirable targets for future mechanistic studies and bioremediation applications. However, substrate specificity is remarkably narrow when compared to the broad repertoire of the rRdh enzymes. We seek to determine the structure and mechanism of ssRdh, and translate that knowledge into guiding targeting laboratory evolution of ssRdh to repurpose and expand the substrate scope. Our efforts are aimed at generating a toolbox of enzymes for in vivo/in vitro bioremediation/biosensing of environmentally relevant organohalides. Our biophysical studies will take full advantage of the rich spectral signals associated with the various ssRdh cofactors, while our laboratory evolution studies will benefit from robust screening methods that mimic the natural bacterial evolution on contaminated sites.