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

Wackett, Lawrence P., Robinson, Serina L.·2020·Biochemical Journal
DOI 10.1042/bcj20190720PMC PMC7428800
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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.

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Figure 1. Timeline of past, present, and possible future discoveries of microbes and enzymes capable of breaking down natural and anthropogenic compounds including benzo[a]pyrene (I), perchloro-1,1′-biphenyl (a PCB) (II), and polyethylene terephthalate (III). One major challenge currently facing our society are the ‘forever chemicals' such as perfluorooctanoic acid (IV) poised at the current ‘limit' of biodegradation. As the field advances, our understanding will also expand to the biodegradation of recalcitrant polymers such as polystyrene (V), polyvinyl chloride (VI), polypropylene (VII) and yet-to-be-synthesized chemicals.
Figure 1. Timeline of past, present, and possible future discoveries of microbes and enzymes capable of breaking down natural and anthropogenic compounds including benzo[a]pyrene (I), perchloro-1,1′-biphenyl (a PCB) (II), and polyethylene terephthalate (III). One major challenge currently facing our society are the ‘forever chemicals' such as perfluorooctanoic acid (IV) poised at the current ‘limit' of biodegradation. As the field advances, our understanding will also expand to the biodegradation of recalcitrant polymers such as polystyrene (V), polyvinyl chloride (VI), polypropylene (VII) and yet-to-be-synthesized chemicals.CC BY-NC-ND · PubMed Central
Figure 2. Evolution of biodegradation prediction tools from reaction-rule based software (Eawag-BBD) towards the integration of relative reasoning and meta-rules to limit the combinatorial explosion of possibilities [15]. The latest software (e.g. enviPath) incorporates probabilistic machine learning models to further prune the search space and predict additional likely pathways for biodegradation [18]. Possible degradation pathways for benzo[a]pyrene are collated from the Eawag-BBD, PPS, and enviPath. At the top (Rule prioritization), rule bt0340 in the Eawag-BBD is the prioritized rule for dihydroxylation of polyaromatics overriding rule bt0064 for formation of hydroxybenzenoid derivatives.
Figure 2. Evolution of biodegradation prediction tools from reaction-rule based software (Eawag-BBD) towards the integration of relative reasoning and meta-rules to limit the combinatorial explosion of possibilities [15]. The latest software (e.g. enviPath) incorporates probabilistic machine learning models to further prune the search space and predict additional likely pathways for biodegradation [18]. Possible degradation pathways for benzo[a]pyrene are collated from the Eawag-BBD, PPS, and enviPath. At the top (Rule prioritization), rule bt0340 in the Eawag-BBD is the prioritized rule for dihydroxylation of polyaromatics overriding rule bt0064 for formation of hydroxybenzenoid derivatives.CC BY-NC-ND · PubMed Central
Figure 3. Distribution of kcat/KM enzyme values, comparing all enzymes in the BRENDA database to enzymes for which there is evidence of their recent evolution to specifically react with new anthropogenic chemicals. The pink curve represents the nearly Gaussian distribution of kcat/KM values for 4451 enzymes as analyzed by Davidi et al. [32]. The symbols each represent an enzyme isolated specifically for its activity against an anthropogenic chemical and derived from a microorganism evolved to biodegrade the chemical. Details of each enzyme, its source, and steady-state kinetic parameters can be found in Supplementary Table S1.
Figure 3. Distribution of kcat/KM enzyme values, comparing all enzymes in the BRENDA database to enzymes for which there is evidence of their recent evolution to specifically react with new anthropogenic chemicals. The pink curve represents the nearly Gaussian distribution of kcat/KM values for 4451 enzymes as analyzed by Davidi et al. [32]. The symbols each represent an enzyme isolated specifically for its activity against an anthropogenic chemical and derived from a microorganism evolved to biodegrade the chemical. Details of each enzyme, its source, and steady-state kinetic parameters can be found in Supplementary Table S1.CC BY-NC-ND · PubMed Central
Figure 4. Differential activation of a representative polycyclic aromatic hydrocarbon (PAH) under aerobic (A & B) and anaerobic conditions (C) showing the key ring activation mechanism by each of the three major types of metabolic pathways. (A) shows ring activation by a cytochrome P450 monooxygenase that breaks the aromaticity of the central ring to make an epoxide intermediate shown at the top in the dotted box. Further reactions serve to make the molecule more water soluble for excretion and so this pathway is common in eukaryotes, including humans [66]. (B) shows ring activation by a dioxygenase enzyme to produce a dihydrodiol intermediate in the middle of the dotted box [67]. Further oxidations lead to cleavage of the aromatic ring and ultimate assimilation of the carbon by biodegrading bacteria. (C) shows initial ring activation by a carboxylase enzyme to make a carboxylated PAH at the bottom in the dotted box. The carboxyl group is further functionalized with coenzyme A and then reductases reduce the aromatic ring to allow hydrolases, dehydrogenases, and ring cleavage enzymes to degrade the structure and allow carbon assimilation [60].
Figure 4. Differential activation of a representative polycyclic aromatic hydrocarbon (PAH) under aerobic (A & B) and anaerobic conditions (C) showing the key ring activation mechanism by each of the three major types of metabolic pathways. (A) shows ring activation by a cytochrome P450 monooxygenase that breaks the aromaticity of the central ring to make an epoxide intermediate shown at the top in the dotted box. Further reactions serve to make the molecule more water soluble for excretion and so this pathway is common in eukaryotes, including humans [66]. (B) shows ring activation by a dioxygenase enzyme to produce a dihydrodiol intermediate in the middle of the dotted box [67]. Further oxidations lead to cleavage of the aromatic ring and ultimate assimilation of the carbon by biodegrading bacteria. (C) shows initial ring activation by a carboxylase enzyme to make a carboxylated PAH at the bottom in the dotted box. The carboxyl group is further functionalized with coenzyme A and then reductases reduce the aromatic ring to allow hydrolases, dehydrogenases, and ring cleavage enzymes to degrade the structure and allow carbon assimilation [60].CC BY-NC-ND · PubMed Central
Figure 5. Chlorinated compounds are biodegraded by different mechanisms and complete biodegradation of highly chlorinated compounds may require multiple mechanisms. (A) Four mechanisms of dehalogenation are illustrated by four different enzymatic examples. The examples (left to right, top to bottom) are haloalkane dehalogenase (DhaA), lindane dehalogenase (LinA), perchloroethylene reductive dehalogenase (PceA), and soluble methane monooxygenase (sMMO). (B) Biodegradation of pentachloroethane by a recombinant bacterium combines reductive and eliminative dechlorination at low oxygen tension and oxygenative biodegradation at ambient oxygen tension [70]. This mimics an ideal situation in the environment in which highly chlorinated compounds can be biodegraded by reductive dehalogenation and subsequent oxygenative dehalogenation either by different or the same microorganism(s), as some anaerobes are known to express oxygenases.
Figure 5. Chlorinated compounds are biodegraded by different mechanisms and complete biodegradation of highly chlorinated compounds may require multiple mechanisms. (A) Four mechanisms of dehalogenation are illustrated by four different enzymatic examples. The examples (left to right, top to bottom) are haloalkane dehalogenase (DhaA), lindane dehalogenase (LinA), perchloroethylene reductive dehalogenase (PceA), and soluble methane monooxygenase (sMMO). (B) Biodegradation of pentachloroethane by a recombinant bacterium combines reductive and eliminative dechlorination at low oxygen tension and oxygenative biodegradation at ambient oxygen tension [70]. This mimics an ideal situation in the environment in which highly chlorinated compounds can be biodegraded by reductive dehalogenation and subsequent oxygenative dehalogenation either by different or the same microorganism(s), as some anaerobes are known to express oxygenases.CC BY-NC-ND · PubMed Central
Figure 6. Perfluorinated compound biodegradation is currently under intense investigation. Specific biodegradative enzymes are yet to be identified and the proposed mechanism for defluorination is based on chemical studies. (A) shows important commercial perfluorinated compounds. (B) shows a proposed mechanism by which a representative perfluorocarboxylate (PFOA) could be completely degraded by one or more enzymes via consecutive one-carbon chain shortening cycles. Although enzyme(s) responsible for catalyzing PFOA degradation have not yet been characterized, this proposal is consistent with studies on Acidimicrobium sp. strain A6 [97] and abiotic chemical degradation reactions. The key intermediate is a carbon-centered radical that could be generated via a reductive or oxidative enzymatic process. Recombination of the radical with a yet unknown oxygen species (hydroxyl radical only represents the proper electron balance) could generate a difluorohydroxy species that could undergo spontaneous displacement of two fluorine atoms. That would generate a new fluorocarboxylate that is one carbon shorter, and then the cycle can repeat, leading to complete degradation. R = one or more CFx groups.
Figure 6. Perfluorinated compound biodegradation is currently under intense investigation. Specific biodegradative enzymes are yet to be identified and the proposed mechanism for defluorination is based on chemical studies. (A) shows important commercial perfluorinated compounds. (B) shows a proposed mechanism by which a representative perfluorocarboxylate (PFOA) could be completely degraded by one or more enzymes via consecutive one-carbon chain shortening cycles. Although enzyme(s) responsible for catalyzing PFOA degradation have not yet been characterized, this proposal is consistent with studies on Acidimicrobium sp. strain A6 [97] and abiotic chemical degradation reactions. The key intermediate is a carbon-centered radical that could be generated via a reductive or oxidative enzymatic process. Recombination of the radical with a yet unknown oxygen species (hydroxyl radical only represents the proper electron balance) could generate a difluorohydroxy species that could undergo spontaneous displacement of two fluorine atoms. That would generate a new fluorocarboxylate that is one carbon shorter, and then the cycle can repeat, leading to complete degradation. R = one or more CFx groups.CC BY-NC-ND · PubMed Central

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Metadata

Authors
Wackett, L. P., & Robinson, S. L.
Affiliations
  • Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Twin Cities, Minneapolis, MN 55108, U.S.A.
  • Biotechnology Institute, University of Minnesota, Twin Cities, Minneapolis, MN 55108, U.S.A.
ORCID
Wackett, Lawrence P.
Venue
Biochemical Journal
Publisher
Portland Press Ltd.
Published
2020-08-14
Volume
477
Issue
15
Pages
2875-2891
ISSN
  • 0264-6021
  • 1470-8728
DOI
10.1042/bcj20190720
PMC
PMC7428800
Cited by
71
References
9
Language
en
Licence
creativecommons.org/licenses/by-nc-nd/4.0/ (vor)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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