Driving evolution of the biodegradative machinery
Microorganisms are instrumental to the biochemical cycle of many natural and synthetic compounds; the process involved in their breakdown is known as biodegradation. Usually, the substances that are broken down are utilised as sources of energy, carbon and nitrogen or other nutrients. However, xenobiotics — compounds that are foreign to the biosphere — may resist biodegradation or transformation, accumulate in the environment and prove harmful. The EU-funded 'Programmed acceleration of evolution of the biodegradative gene inventory' (PROACTIVE) project proposed to address the persistence of xenobiotics by harnessing the natural mechanism of generation of diversity and selection. The ultimate goal was to accelerate the evolution of biodegradative pathways for these compounds. As a first step, scientists performed bioinformatics analysis in order to identify and plylogenetically reconstruct enzyme families involved in biodegradation. In particular, they were interested in aromatic oxygenases that could be utilised for the biodegradation of aromatic xenobiotics. These predicted sequences represented for the first time the application of ancestral reconstruction to biodegradative enzymes and were subsequently incorporated by mutagenesis in various catabolic pathways (toluene pathway, 2,4-dichlorophenoxyacetate pathway, 2,4-dinitrotoluene pathway). During the project, it became evident that fine tuning of metabolic pathways was required to avoid oxidative stress. By focusing on the evolution of the DNT genes implicated in the 2,4-dinitrotoluene pathway, scientists uncovered an association between the endogenous production of reactive oxygen species (ROS) and DNA repair mechanisms. This suggested that evolution of xenobiotic compound biodegradation could be elicited by the mutagenic stress caused by faulty performance of pre-existing enzymes on suboptimal substrates. Taken together, PROACTIVE results paint a picture for the evolution of xenobiotic-degrading microorganisms and the catabolic pathways for aromatic xenobiotics. This information could be applied in evolutionary engineering in order to address the biodegradation of xenobiotic compounds.
