Toward the development of a molecular toolkit for the microbial remediation of per-and polyfluoroalkyl substances

Abstract

Per- and polyfluoroalkyl substances (PFAS) are highly fluorinated synthetic organic compounds that have been used extensively in various industries owing to their unique properties. The PFAS family encompasses diverse classes, with only a fraction being commercially relevant. These substances are found in the environment, including in water sources, soil, and wildlife, leading to human exposure and fueling concerns about potential human health impacts. Although PFAS degradation is challenging, biodegradation offers a promising, eco-friendly solution. Biodegradation has been effective for a variety of organic contaminants but is yet to be successful for PFAS due to a paucity of identified microbial species capable of transforming these compounds. Recent studies have investigated PFAS biotransformation and fluoride release; however, the number of specific microorganisms and enzymes with demonstrable activity with PFAS remains limited. This review discusses enzymes that could be used in PFAS metabolism, including haloacid dehalogenases, reductive dehalogenases, cytochromes P450, alkane and butane monooxygenases, peroxidases, laccases, desulfonases, and the mechanisms of microbial resistance to intracellular fluoride. Finally, we emphasize the potential of enzyme and microbial engineering to advance PFAS degradation strategies and provide insights for future research in this field.

Keywords: PFAS; defluorinase; defluorination; dehalogenase; microbial remediation.

Fig 1

Classification of PFAS compounds. Abbreviations and structures of PFAS subclasses are mentioned in this review. This figure was created with BioRender.com.

Fig 2

Hydrolytic defluorinases. Cartoon representation of the dimeric structures of the fluoroacetate dehalogenase (A) and defluorinating haloacid dehalogenase (B) from Rhodopseudomonas palustris (PDB 3R3W) (67) and Polaromonas sp. JS666 (PDB 3UM9) (PDB DOI: https://doi.org/10.2210/pdb3um9/pdb), respectively. The homodimers are shown with the two identical chains shown in green and cyan. A more detailed view of the active sites is shown (C and D) with the nucleophilic aspartate residue shown (Asp*, this is an Asn residue in the Asp110Asn variant of fluoroacetate dehalogenase shown). The substrate is bound in fluoroacetate dehalogenase (FA, orange), and the residues that stabilize the charge developed on the fluoride (halide pocket, purple) are also shown. The reaction mechanism is shown (E; an S_N² nucleophilic attack, followed by the formation of a tetrahedral intermediate and regeneration of the nucleophile via attack by water). This figure was created with BioRender.com.

Fig 3

Reductive dehalogenase. Cartoon representation of the structure of the reductive dehalogenase, PCE, from Sulfurospirillum multivorans (PDB 5MA1) (92). The dimer is shown on the left, with the two identical chains shown in green and blue. A more detailed view of the active site is given on the right, showing the iron and sulfur of the two [4Fe-4S] clusters as red and yellow spheres, respectively. Cobalamin is shown as green sticks, and the substrate (2,4,6-tribromophenol) is shown in pink. This figure was created with BioRender.com.

Fig 4

Overview of the cytochrome P450-mediated defluorination of 4-fluorophenol. 4-Fluorophenol binds to complex I, which displaces fluoride via attack of the oxygen of complex I on the fluorinated carbon to form a semiquinone, which is then reduced to form 4-hydroxyphenol.

Fig 5

Schematic regarding uptake and desulfonation of alkanesulfonates and taurine by (A) TauABCD and (B) SsuEADCB systems, based on data from van der Ploeg et al. (153). This figure was created with BioRender.com.

Fig 6

Bacterial response to fluoride toxicity. Hydrogen fluoride and fluoride (F⁻) are present in pH-dependent equilibrium, and only HF can cross biological membranes without the aid of efflux channels. At low environmental pH, this drives the accumulation of intracellular F⁻. F⁻ -responsive riboswitches bind F⁻, allowing the translation of F⁻-specific efflux proteins, including Fluc F⁻ channel (PDB: 6B2A) (177) and the H⁺/F⁻ CLC^F antiporter (PDB: 36D0J) (178). This figure was created with BioRender.com.