The ever-expanding limits of enzyme catalysis and biodegradation: polyaromatic, polychlorinated, polyfluorinated, and polymeric compounds

Abstract

Biodegradation is simply the metabolism of anthropogenic, or otherwise unwanted, chemicals in our environment, typically by microorganisms. The metabolism of compounds commonly found in living things is limited to several thousand metabolites whereas ∼100 million chemical substances have been devised by chemical synthesis, and ∼100 000 are used commercially. Since most of those compounds are not natively found in living things, and some are toxic or carcinogenic, the question arises as to whether there is some organism somewhere with the enzymes that can biodegrade them. Repeatedly, anthropogenic chemicals have been denoted ‘non-biodegradable,’ only to find they are reactive with one or more enzyme(s). Enzyme reactivity has been organized into categories of functional group transformations. The discovery of new functional group transformations has continually expanded our knowledge of enzymes and biodegradation. This expansion of new-chemical biodegradation is driven by the evolution and spread of newly evolved enzymes. This review describes the biodegradation of widespread commercial chemicals with a focus on four classes: polyaromatic, polychlorinated, polyfluorinated, and polymeric compounds. Polyaromatic hydrocarbons include some of the most carcinogenic compounds known. Polychlorinated compounds include polychlorinated biphenyls (PCBs) and many pesticides of the twentieth century. Polyfluorinated compounds are a major focus of bioremediation efforts today. Polymers are clogging landfills, killing aquatic species in the oceans and increasingly found in our bodies. All of these classes of compounds, each thought at one time to be non-biodegradable, have been shown to react with natural enzymes. The known limits of enzyme catalysis, and hence biodegradation, are continuing to expand.

Filling in the Gaps in Metformin Biodegradation: a New Enzyme and a Metabolic Pathway for Guanylurea

“…A similar observation has been made with anthropogenic s -triazine compounds, such as the herbicide atrazine, in which atrazine chlorohydrolases arose independently from divergent members of the amidohydrolase protein superfamily ( 51 , 52 ). Moreover, the fate of anthropogenic chemicals and their metabolites in the environment has been observed to change in recent times as the result of microbial enzyme evolution ( 53 ). Given that GuuH enzymes can readily arise from a biuret hydrolase via simple mutation(s), and the increasing environmental prevalence of compounds giving rise to guanylurea, we expect that guanylurea will increasingly lose its designation as a “dead-end” metabolite.…”

Per- and Polyfluoroalkyl Substances (PFAS) in Integrated Crop–Livestock Systems: Environmental Exposure and Human Health Risks

“…In fact, PFAS were added to the Persistent Organic Pollutant (POPs) list under the Stockholm Convention in 2009 for their persistence and subsequent negative environmental and health impacts [ 32 ]. There is evidence of biological degradation of perfluorinated chains by breaking bonds one carbon at a time starting at the carboxyl end, with carbon dioxide and fluoride as end products [ 33 ]. There is research underway explaining the biological and enzymatic degradation of the “forever chemicals”.…”

Comparative biochemistry of four polyester (PET) hydrolases

“…4, suggest that molar η is at least 10 6 M −1 s −1 for IsP on PET. High specificity constants for the degradation of soluble, synthetic compounds have been observed before (see (47) for a review), but it is noteworthy that this parameter increased for insoluble substrates. While the exact meaning of molarη remains to be elucidated, one possible explanation is that the enzyme adsorbs nonspecifically on the hydrophobic surface of the substrate particles.…”

“…The overall efficacy of enzymes (natural or engineered) that act on anthropogenic substrates is typically gauged by the specificity constant (47). For insoluble substrates this parameter is readily calculated according to eq.…”