Bacterial degradation of xenobiotic compounds: evolution and distribution of novel enzyme activities

Abstract

SummaryBacterial dehalogenases catalyse the cleavage of carbon-halogen bonds, which is a key step in aerobic mineralization pathways of many halogenated compounds that occur as environmental pollutants. There is a broad range of dehalogenases, which can be classified in different protein superfamilies and have fundamentally different catalytic mechanisms. Identical dehalogenases have repeatedly been detected in organisms that were isolated at different geographical locations, indicating that only a restricted number of sequences are used for a certain dehalogenation reaction in organohalogen-utilizing organisms. At the same time, massive random sequencing of environmental DNA, and microbial genome sequencing projects have shown that there is a large diversity of dehalogenase sequences that is not employed by known catabolic pathways. The corresponding proteins may have novel functions and selectivities that could be valuable for biotransformations in the future. Apparently, traditional enrichment and metagenome approaches explore different segments of sequence space. This is also observed with alkane hydroxylases, a category of proteins that can be detected on basis of conserved sequence motifs and for which a large number of sequences has been found in isolated bacterial cultures and genomic databases. It is likely that ongoing genetic adaptation, with the recruitment of silent sequences into functional catabolic routes and evolution of substrate range by mutations in structural genes, will further enhance the catabolic potential of bacteria toward synthetic organohalogens and ultimately contribute to cleansing the environment of these toxic and recalcitrant chemicals.

Animals in a bacterial world, a new imperative for the life sciences

“…On a broader scale, the evolution of animals provided novel physical environments for bacterial colonization, such as aerated deep sediments resulting from animal burrowing. Finally, human activities, which make a range of molecules not previously found in nature, such as halogenated hydrocarbons, have driven selection on bacterial catabolic pathways (19), leaving a signature of our presence in microbial metabolism.…”

Degradation of fuel oxygenates and their main intermediates by Aquincola tertiaricarbonis L108

“…The former statement refers to the observation that the conversion of a pollutant is often catalysed by defined enzymes in an unspecific manner, resulting in low rates due to the xenobiotic structure of the compounds (Janssen et al, 2005). Although the oxygenate degradation pathway(s) have not been elucidated completely, three important steps have already been identified in strain L108.…”

A Mechanistic Analysis of Enzymatic Degradation of Organohalogen Compounds

“…A variety of enzymes that act on organohalogen compounds have been discovered. [2][3][4][5] Some of them, called dehalogenases, catalyze the removal of a halogen atom from the substrates. Enzymes that catalyze the conversion of organohalogen compounds to other organohalogen compounds are also known.…”