Membrane Exporters of Fluoride Ion

PII-like signaling proteins: a new paradigm in orchestrating cellular homeostasis

Members of the PII superfamily are versatile, multitasking signaling proteins ubiquitously found in all domains of life. They adeptly monitor and synchronize the cell's carbon, nitrogen, energy, redox, and diurnal states, primarily by binding interdependently to adenyl-nucleotides, including charged nucleotides (ATP, ADP, and AMP) and second messengers such as cyclic adenosine monophosphate (cAMP), cyclic di-adenosine monophosphate (c-di-AMP), and S-adenosylmethionine-AMP (SAM-AMP). These proteins also undergo a variety of posttranslational modifications, such as phosphorylation, adenylation, uridylation, carboxylation, and disulfide bond formation, which further provide cues on the metabolic state of the cell. Serving as precise metabolic sensors, PII superfamily proteins transmit this information to diverse cellular targets, establishing dynamic regulatory assemblies that fine-tune cellular homeostasis. Recently discovered, PII-like proteins are emerging families of signaling proteins that, while related to canonical PII proteins, have evolved to fulfill a diverse range of cellular functions, many of which remain elusive. In this review, we focus on the evolution of PII-like proteins and summarize the molecular mechanisms governing the assembly dynamics of PII complexes, with a special emphasis on the PII-like protein SbtB.

The link between ancient microbial fluoride resistance mechanisms and bioengineering organofluorine degradation or synthesis

Fluorinated organic chemicals, such as per- and polyfluorinated alkyl substances (PFAS) and fluorinated pesticides, are both broadly useful and unusually long-lived. To combat problems related to the accumulation of these compounds, microbial PFAS and organofluorine degradation and biosynthesis of less-fluorinated replacement chemicals are under intense study. Both efforts are undermined by the substantial toxicity of fluoride, an anion that powerfully inhibits metabolism. Microorganisms have contended with environmental mineral fluoride over evolutionary time, evolving a suite of detoxification mechanisms. In this perspective, we synthesize emerging ideas on microbial defluorination/fluorination and fluoride resistance mechanisms and identify best approaches for bioengineering new approaches for degrading and making organofluorine compounds.

Fluoride export is required for the competitive fitness of pathogenic microorganisms in dental biofilm models

Microorganisms resist fluoride toxicity using fluoride export proteins from one of several different molecular families. Cariogenic species Streptococcus mutans and Candida albicans extrude intracellular fluoride using a CLCF F-/H+ antiporter and FEX fluoride channel, respectively, whereas oral commensal eubacteria, such as Streptococcus gordonii, export fluoride using a Fluc fluoride channel. In this work, we examine how genetic knockout of fluoride export impacts pathogen fitness in single-species and three-species dental biofilm models. For biofilms generated using S. mutans with the genetic knockout of the CLCF transporter, exposure to low fluoride concentrations decreased S. mutans counts, synergistically reduced the populations of C. albicans, increased the relative proportion of oral commensal S. gordonii, and reduced properties associated with biofilm pathogenicity, including acid production and hydroxyapatite dissolution. Biofilms prepared with C. albicans with genetic knockout of the FEX channel also exhibited reduced fitness in the presence of fluoride but to a lesser degree. Imaging studies indicate that S. mutans is highly sensitive to fluoride, with the knockout strain undergoing complete lysis when exposed to low fluoride for a moderate amount of time. Biochemical purification of the S. mutans CLCF transporter and functional reconstitution establishes that the functional protein is a dimer encoded by a single gene. Together, these findings suggest that fluoride export by oral pathogens can be targeted by specific inhibitors to restore biofilm symbiosis in dental biofilms and that S. mutans is especially susceptible to fluoride toxicity.

IMPORTANCE

Dental caries is a globally prevalent condition that occurs when pathogenic species, including Streptococcus mutans and Candida albicans, outcompete beneficial species, such as Streptococcus gordonii, in the dental biofilm. Fluoride is routinely used in oral hygiene to prevent dental caries. Fluoride also has antimicrobial properties, although most microbes possess fluoride exporters to resist its toxicity. This work shows that sensitization of cariogenic species S. mutans and C. albicans to fluoride by genetic knockout of fluoride exporters alters the microbial composition and pathogenic properties of dental biofilms. These results suggest that the development of drugs that inhibit fluoride exporters could potentiate the anticaries effect of fluoride in over-the-counter products like toothpaste and mouth rinses. This is a novel strategy to treat dental caries.

Evolutionary obstacles and not C-F bond strength make PFAS persistent

The fate of organic matter in the environment, including anthropogenic chemicals, is largely predicated on the enzymatic capabilities of microorganisms. Microbes readily degrade, and thus recycle, most of the ~100,000 commercial chemicals used in modern society. Per- and polyfluorinated compounds (PFAS) are different. Many research papers posit that the general resistance of PFAS to microbial degradation is based in chemistry and that argument relates to the strength of the C-F bond. Here, I advance the opinion that the low biodegradability of PFAS is best formulated as a biological optimization problem, hence evolution. The framing of the problem is important. If it is framed around C-F bond strength, the major effort should focus on finding and engineering new C-F cleaving enzymes. The alternative, and preferred approach suggested here, is to focus on the directed evolution of biological systems containing known C-F cleaving systems. There are now reports of bacteria degrading and/or growing on multiply fluorinated arenes, alkenoic and alkanoic acids. The impediment to more efficient and widespread biodegradation in these systems is biological, not chemical. The rationale for this argument is made in the five sections below that follow the Introduction.

Transport of metformin metabolites by guanidinium exporters of the small multidrug resistance family

Proteins from the small multidrug resistance (SMR) family are frequently associated with horizontally transferred multidrug resistance gene arrays found in bacteria from wastewater and the human-adjacent biosphere. Recent studies suggest that a subset of SMR transporters might participate in the metabolism of the common pharmaceutical metformin by bacterial consortia. Here, we show that both genomic and plasmid-associated transporters of the SMRGdx functional subtype export byproducts of microbial metformin metabolism, with particularly high export efficiency for guanylurea. We use solid-supported membrane electrophysiology to evaluate the transport kinetics for guanylurea and native substrate guanidinium by four representative SMRGdx homologs. Using an internal reference to normalize independent electrophysiology experiments, we show that transport rates are comparable for genomic and plasmid-associated SMRGdx homologs, and using a proteoliposome-based transport assay, we show that 2 proton:1 substrate transport stoichiometry is maintained. Additional characterization of guanidinium and guanylurea export properties focuses on the structurally characterized homolog, Gdx-Clo, for which we examined the pH dependence and thermodynamics of substrate binding and solved an x-ray crystal structure with guanylurea bound. Together, these experiments contribute in two main ways. By providing the first detailed kinetic examination of the structurally characterized SMRGdx homolog Gdx-Clo, they provide a functional framework that will inform future mechanistic studies of this model transport protein. Second, this study casts light on a potential role for SMRGdx transporters in microbial handling of metformin and its microbial metabolic byproducts, providing insight into how native transport physiologies are co-opted to contend with new selective pressures.

Lanthanum-fluoride electrode-based methods to monitor fluoride transport in cells and reconstituted lipid vesicles

Fluoride (F-) export proteins, including F- channels and F- transporters, are widespread in biology. They contribute to cellular resistance against fluoride ion, which has relevance as an ancient xenobiotic, and in more modern contexts like organofluorine biosynthesis and degradation or dental medicine. This chapter summarizes quantitative methods to measure fluoride transport across membranes using fluoride-specific lanthanum-fluoride electrodes. Electrode-based measurements can be used to measure unitary fluoride transport rates by membrane proteins that have been purified and reconstituted into lipid vesicles, or to monitor fluoride efflux into living microbial cells. Thus, fluoride electrode-based measurements yield quantitative mechanistic insight into one of the major determinants of fluoride resistance in microorganisms, fungi, yeasts, and plants.

Measurement and analysis of microbial fluoride resistance in dental biofilm models

The interactions between communities of microorganisms inhabiting the dental biofilm is a major determinant of oral health. These biofilms are periodically exposed to high concentrations of fluoride, which is present in almost all oral healthcare products. The microbes resist fluoride through the action of membrane export proteins. This chapter describes the culture, growth and harvest conditions of model three-species dental biofilm comprised of cariogenic pathogens Streptococcus mutans and Candida albicans and the commensal bacterium Streptococcus gordonii. In order to examine the role of fluoride export by S. mutans in model biofilms, procedures for generating a strain of S. mutans with a genetic knockout of the fluoride exporter are described. We present a case study examining the effects of this mutant strain on the biofilm mass, acid production and mineral dissolution under exposure to low levels of fluoride. These general approaches can be applied to study the effects of any gene of interest in physiologically realistic multispecies oral biofilms.

Fluoride export is required for competitive fitness of pathogenic microorganisms in dental biofilm models

Microorganisms resist fluoride toxicity using fluoride export proteins from one of several different molecular families. Cariogenic species Streptococcus mutans and Candida albicans extrude intracellular fluoride using a CLCF F-/H+ antiporter and FEX fluoride channel, respectively, whereas commensal eubacteria, such as Streptococcus gordonii, export fluoride using a Fluc fluoride channel. In this work, we examine how genetic knockout of fluoride export impacts pathogen fitness in single-species and three-species dental biofilm models. For biofilms generated using S. mutans with genetic knockout of the CLCF transporter, exposure to low fluoride concentrations decreased S. mutans counts, synergistically reduced the populations of C. albicans, increased the relative proportion of commensal S. gordonii, and reduced properties associated with biofilm pathogenicity, including acid production and hydroxyapatite dissolution. Biofilms prepared with C. albicans with genetic knockout of the FEX channel also exhibited reduced fitness in the presence of fluoride, but to a lesser degree. Imaging studies indicate that S. mutans is highly sensitive to fluoride, with the knockout strain undergoing complete lysis when exposed to low fluoride for a moderate amount of time, and biochemical purification the S. mutans CLCF transporter and functional reconstitution establishes that the functional protein is a dimer encoded by a single gene. Together, these findings suggest that fluoride export by oral pathogens can be targeted by specific inhibitors to restore biofilm symbiosis in dental biofilms, and that S. mutans is especially susceptible to fluoride toxicity.

Direct fluoride monitoring using a fluorogenic RNA-based biosensor

Fluorinated compounds, whether naturally occurring or from anthropogenic origin, have been extensively exploited in the last century. Degradation of these compounds by physical or biochemical processes is expected to result in the release of fluoride. Several fluoride detection mechanisms have been previously described. However, most of these methods are not compatible with high- and ultrahigh-throughput screening technologies, lack the ability to real-time monitor the increase of fluoride concentration in solution, or rely on costly reagents (such as cell-free expression systems). Our group recently developed "FluorMango" as the first completely RNA-based and direct fluoride-specific fluorogenic biosensor. To do so, we merged and engineered the Mango-III light-up RNA aptamer and the fluoride-specific aptamer derived from a riboswitch, crcB. In this chapter, we explain how this RNA-based biosensor can be produced in large scale before providing examples of how it can be used to quantitatively detect (end-point measurement) or monitor in real-time fluoride release in complex biological systems by translating it into measurable fluorescent signal.

Microwell fluoride assay screening for enzymatic defluorination

There is intense interest in removing fluorinated compounds from the environment, environments are most efficiently remediated by microbial enzymes, and defluorinating enzymes are readily monitored by fluoride determination. Fluorine is the most electronegative element. Consequently, all mechanisms of enzymatic C-F bond cleavage produce fluoride anion, F-. Therefore, methods for the determination of fluoride are critical for C-F enzymology and apply to any fluorinated organic compounds, including PFAS, or per- and polyfluorinated alkyl substances. The biodegradation of most PFAS chemicals is rare or unknown. Accordingly, identifying new enzymes, or re-engineering the known defluorinases, will require rapid and sensitive methods for measuring fluoride in aqueous media. Most studies currently use ion chromatography or fluoride specific electrodes which are relatively sensitive but low throughput. The methods here describe refashioning a drinking water test to efficiently determine fluoride in enzyme and cell culture reaction mixtures. The method is based on lanthanum alizarin complexone binding of fluoride. Reworking the method to a microtiter well plate format allows detection of as little as 4 nmol of fluoride in 200 μL of assay buffer. The method is amenable to color imaging, spectrophotometric plate reading and automated liquid handling to expedite assays with thousands of enzymes and/or substrates for discovering and improving enzymatic defluorination.

Fluoride Transport and Inhibition Across CLC Transporters

The Chloride Channel (CLC) family includes proton-coupled chloride and fluoride transporters. Despite their similar protein architecture, the former exchange two chloride ions for each proton and are inhibited by fluoride, whereas the latter efficiently transport one fluoride in exchange for one proton. The combination of structural, mutagenesis, and functional experiments with molecular simulations has pinpointed several amino acid changes in the permeation pathway that capitalize on the different chemical properties of chloride and fluoride to fine-tune protein function. Here we summarize recent findings on fluoride inhibition and transport in the two prototypical members of the CLC family, the chloride/proton transporter from Escherichia coli (CLC-ec1) and the fluoride/proton transporter from Enterococcus casseliflavus (CLCF-eca).

Electron-bifurcation and fluoride efflux systems in Acetobacterium spp. drive defluorination of perfluorinated unsaturated carboxylic acids

Enzymatic cleavage of C-F bonds in per- and polyfluoroalkyl substances (PFAS) is largely unknown but avidly sought to promote systems biology for PFAS bioremediation. Here, we report the reductive defluorination of α, β-unsaturated per- and polyfluorocarboxylic acids by Acetobacterium spp. Two critical molecular features in Acetobacterium species enabling reductive defluorination are (i) a functional fluoride efflux transporter (CrcB) and (ii) an electron-bifurcating caffeate reduction pathway (CarABCDE). The fluoride transporter was required for detoxification of released fluoride. Car enzymes were implicated in defluorination by the following evidence: (i) only Acetobacterium spp. with car genes catalyzed defluorination; (ii) caffeate and PFAS competed in vivo ; (iii) models from the X-ray structure of the electron-bifurcating reductase (CarC) positioned the PFAS substrate optimally for reductive defluorination; (iv) products identified by 19 F-NMR and high-resolution mass spectrometry were consistent with the model. Defluorination biomarkers identified here were found in wastewater treatment plant metagenomes on six continents.

Biodegradation Potential of C7-C10 Perfluorocarboxylic Acids and Data from the Genome of a New Strain of Pseudomonas mosselii 5(3)

The use of bacteria of the genus Pseudomonas-destructors of persistent pollutants for biotechnologies of environmental purification-is an interesting area of research. The aim of this work was to study the potential of Pseudomonas mosselii strain 5(3) isolated from pesticide-contaminated soil as a degrader of C7-C10 perfluorocarboxylic acids (PFCAs) and analyze its complete genome. The genome of the strain has been fully sequenced. It consists of a chromosome with a length of 5,676,241 b.p. and containing a total of 5134 genes, in particular, haloalkane dehalogenase gene (dhaA), haloacetate dehalogenase H-1 gene (dehH1), fluoride ion transporter gene (crcB) and alkanesulfonate monooxygenase gene (ssuE), responsible for the degradation of fluorinated compounds. The strain P. mosselii 5(3) for was cultivated for 7 days in a liquid medium with various C7-C10 PFCAs as the sole source of carbon and energy, and completely disposed of them. The results of LC-MS analysis showed that the transformation takes place due to perfluorohexanoic acid with the release of various levels of stoichiometry (depending on PFCA) of fluorine ion mineralization indicators determined by ion chromatography. Thus, Pseudomonas mosselii strain 5(3) demonstrates a genetically confirmed high potential for the decomposition of C7-C10 PFCA.

The role of plant growth promoting rhizobacteria in strengthening plant resistance to fluoride toxicity: a review

A wide variety of bacteria are present in soil but in rhizospheric area, the majority of microbes helps plant in defending diseases and facilitate nutrient uptake. These microorganisms are supported by plants and they are known as plant growth-promoting rhizobacteria (PGPR). The PGPRs have the potential to replace chemical fertilizers in a way that is more advantageous for the environment. Fluoride (F) is one of the highly escalating, naturally present contaminants that can be hazardous for PGPRs because of its antibacterial capacity. The interactions of F with different bacterial species in groundwater systems are still not well understood. However, the interaction of PGPR with plants in the rhizosphere region reduces the detrimental effects of pollutants and increases plants' ability to endure abiotic stress. Many studies reveal that PGPRs have developed F defense mechanisms, which include efflux pumps, Intracellular sequestration, enzyme modifications, enhanced DNA repair mechanism, detoxification enzymes, ion transporter/antiporters, F riboswitches, and genetic mutations. These resistance characteristics are frequently discovered by isolating PGPRs from high F-contaminated areas or by exposing cells to fluoride in laboratory conditions. Numerous studies have identified F-resistant microorganisms that possess additional F transporters and duplicates of the well-known targets of F. Plants are prone to F accumulation despite the soil's low F content, which may negatively affect their growth and development. PGPRs can be used as efficient F bioremediators for the soil environment. Environmental biotechnology focuses on creating genetically modified rhizobacteria that can degrade F contaminants over time. The present review focuses on a thorough systemic analysis of contemporary biotechnological techniques, such as gene editing and manipulation methods, for improving plant-microbe interactions for F remediation and suggests the importance of PGPRs in improving soil health and reducing the detrimental effects of F toxicity. The most recent developments in the realm of microbial assistance in the treatment of F-contaminated environments are also highlighted.

Fluoride permeation mechanism of the Fluc channel in liposomes revealed by solid-state NMR

Solid-state nuclear magnetic resonance (ssNMR) methods can probe the motions of membrane proteins in liposomes at the atomic level and propel the understanding of biomolecular processes for which static structures cannot provide a satisfactory description. In this work, we report our study on the fluoride channel Fluc-Ec1 in phospholipid bilayers based on ssNMR and molecular dynamics simulations. Previously unidentified fluoride binding sites in the aqueous vestibules were experimentally verified by 19F-detected ssNMR. One of the two fluoride binding sites in the polar track was identified as a water molecule by 1H-detected ssNMR. Meanwhile, a dynamic hotspot at loop 1 was observed by comparing the spectra of wild-type Fluc-Ec1 in variant buffer conditions or with its mutants. Therefore, we propose that fluoride conduction in the Fluc channel occurs via a "water-mediated knock-on" permeation mechanism and that loop 1 is a key molecular determinant for channel gating.

Transport of metformin metabolites by guanidinium exporters of the Small Multidrug Resistance family

Proteins from the Small Multidrug Resistance (SMR) family are frequently associated with horizontally transferred multidrug resistance gene arrays found in bacteria from wastewater and the human-adjacent biosphere. Recent studies suggest that a subset of SMR transporters might participate in metabolism of the common pharmaceutical metformin by bacterial consortia. Here, we show that both genomic and plasmid-associated transporters of the SMRGdx functional subtype export byproducts of microbial metformin metabolism, with particularly high export efficiency for guanylurea. We use solid supported membrane electrophysiology to evaluate the transport kinetics for guanylurea and native substrate guanidinium by four representative SMRGdx homologues. Using an internal reference to normalize independent electrophysiology experiments, we show that transport rates are comparable for genomic and plasmid-associated SMRGdx homologues, and using a proteoliposome-based transport assay, we show that 2 proton:1 substrate transport stoichiometry is maintained. Additional characterization of guanidinium and guanylurea export properties focuses on the structurally characterized homologue, Gdx-Clo, for which we examined the pH dependence and thermodynamics of substrate binding and solved an x-ray crystal structure with guanylurea bound. Together, these experiments contribute in two main ways. By providing the first detailed kinetic examination of the structurally characterized SMRGdx homologue Gdx-Clo, they provide a functional framework that will inform future mechanistic studies of this model transport protein. Second, this study casts light on a potential role for SMRGdx transporters in microbial handling of metformin and its microbial metabolic byproducts, providing insight into how native transport physiologies are co-opted to contend with new selective pressures.

The inhibitory effect and mechanism of theaflavins on fluoride transport and uptake in HIEC-6 cell model

Fluoride (F^-) is widely present in nature, while long-term excessive F^- intake can lead to fluorosis. Theaflavins are an important bioactive ingredient of black and dark tea, and black and dark tea water extracts showed a significantly lower F^- bioavailability than NaF solutions in previous studies. In this study, the effect and mechanism of four theaflavins (theaflavin, theaflavin-3-gallate, theaflavin-3'-gallate, theaflavin-3,3'-digallate) on F^- bioavailability were investigated using normal human small intestinal epithelial cells (HIEC-6) as a model. The results showed that theaflavins could inhibit the absorptive (apical - basolateral) transport of F^- while promote its secretory (basolateral - apical) transport in HIEC-6 cell monolayers in a time- and concentration-dependent (5-100 μg/mL) manner, and significantly reduce the cellular F^- uptake. Moreover, the HIEC-6 cells treated with theaflavins showed a reduction in cell membrane fluidity and cell surface microvilli. Transcriptome, qRT-PCR and Western blot analysis revealed that theaflavin-3-gallate (TF3G) addition could significantly enhance the mRNA and protein expression levels of tight junction-related genes in HIEC-6 cells, such as claudin-1, occludin and zonula occludens-1 (ZO-1). Overall, theaflavins may reduce F^- absorptive transport by regulating tight junction-related proteins, and decreasing intracellular F^- accumulation by affecting the cell membrane structure and properties in HIEC-6 cells.

Influence of PFDA on the nutrient removal from wastewater by hydrogels containing microalgae-bacteria

PFAS have demonstrated to affect some aerobic microorganisms applied for wastewater treatment. This study evaluated the nutrient removal of three types of hydrogels containing a consortium of microalgae-bacteria (HB), activated carbon (HC), or both (HBC) in presence of perfluorodecanoic acid (PFDA). The nutrients evaluated were ammonium nitrogen (NH₄-N), nitrate nitrogen (NO₃-N), phosphate (PO₄), and chemical oxygen demand (COD). Fluorine (F^-) concentration and the integrity of HB exposed to PFDA were also determined at the end of experiments to understand the potential sorption and effects of PFDA on hydrogel. The results indicated that the presence of PFDA did affect the nitrification process, 13% and 36% to HB and HBC, respectively. Mass balance confirmed negative impact of PFDA on nitrogen consumption in HB (-31.37%). However, NH₄-N was removed by all types of hydrogels in a range of 61-79%, while PO₄ was mainly removed by hydrogels containing activated carbon (AC), 37.5% and 29.2% for HC and HBC, respectively. The removal of both NH₄ and PO₄, was mainly attributed to sorption processes in hydrogels, which was enhanced by the presence of AC. PFDA was also adsorbed in hydrogels, decreasing its concentration between 18% and 28% from wastewater, and up to 39% using HC. Regarding COD concentration, this increased overtime but was not related to hydrogel structure, since Transmission Electron Microscopy imaging revealed that their structure was preserved in presence of PFDA. COD increasement could be attributed to soluble algal products as well as to PVA leaching from hydrogels. In general, the presence of AC in hydrogels can contribute to mitigate the toxic effect of PFDA over microorganisms involved in biological nutrient removal, and hydrogels can be a technique to partially remove this contaminant from aqueous matrices.

Uncovering the Mechanism of the Proton-Coupled Fluoride Transport in the CLCF Antiporter

Fluoride is a natural antibiotic abundantly present in the environment and, in micromolar concentrations, is able to inhibit enzymes necessary for bacteria to survive. However, as is the case with many antibiotics, bacteria have evolved resistance methods, including through the use of recently discovered membrane proteins. One such protein is the CLC^F F^-/H⁺ antiporter protein, a member of the CLC superfamily of anion-transport proteins. Though previous studies have examined this F^- transporter, many questions are still left unanswered. To reveal details of the transport mechanism used by CLC^F, we have employed molecular dynamics simulations and umbrella sampling calculations. Our results have led to several discoveries, including the mechanism of proton import and how it is able to aid in the fluoride export. Additionally, we have determined the role of the previously identified residues Glu118, Glu318, Met79, and Tyr396. This work is among the first studies of the CLC^F F^-/H⁺ antiporter and is the first computational investigation to model the full transport process, proposing a mechanism which couples the F^- export with the H⁺ import.

The role of conformational change and key glutamic acid residues in the ClC-ec1 antiporter

The triple glutamine (Q) mutant (QQQ) structure of a Cl-/H+ antiporter from Escherichia coli (ClC-ec1) displaying a novel backbone arrangement has been used to challenge the long-held notion that Cl-/H+ antiporters do not operate through large conformational motions. The QQQ mutant substitutes the glutamine residue for an external glutamate E148, an internal glutamate E203, and a third glutamate E113 that hydrogen-bonds with E203. However, it is unknown if QQQ represents a physiologically relevant state, as well as how the protonation of the wild-type glutamates relates to the global dynamics. We herein apply continuous constant-pH molecular dynamics to investigate the H+-coupled dynamics of ClC-ec1. Although any large-scale conformational rearrangement upon acidification would be due to the accumulation of excess charge within the protein, protonation of the glutamates significantly impacts mainly the local structure and dynamics. Despite the fact that the extracellular pore enlarges at acidic pHs, an occluded ClC-ec1 within the active pH range of 3.5-7.5 requires a protonated E148 to facilitate extracellular Cl- release. E203 is also involved in the intracellular H+ transfer as an H+ acceptor. The water wire connection of E148 with the intracellular solution is regulated by the charge states of the E113/E203 dyad with coupled proton titration. However, the dynamics extracted from our simulations are not QQQ-like, indicating that the QQQ mutant does not represent the behavior of the wild-type ClC-ec1. These findings reinforce the necessity of having a protonatable residue at the E203 position in ClC-ec1 and suggest that a higher level of complexity exists for the intracellular H+ transfer in Cl-/H+ antiporters.

A review of microbial degradation of per- and polyfluoroalkyl substances (PFAS): Biotransformation routes and enzymes

Since the 1950s, copious amounts of per- and polyfluoroalkyl substances (PFAS) (dubbed "forever chemicals") have been dumped into the environment, causing heavy contamination of soil, surface water, and groundwater sources. Humans, animals, and the environment are frequently exposed to PFAS through food, water, consumer products, as well as waste streams from PFAS-manufacturing industries. PFAS are a large group of synthetic organic fluorinated compounds with widely diverse chemical structures that are extremely resistant to microbial degradation. Their persistence, toxicity to life on earth, bioaccumulation tendencies, and adverse health and ecological effects have earned them a "top priority pollutant" designation by regulatory bodies. Despite that a number of physicochemical methods exist for PFAS treatment, they suffer from major drawbacks regarding high costs, use of high energy and incomplete mineralization (destruction of the CF bond). Consequently, microbial degradation and enzymatic treatment of PFAS are highly sought after as they offer a complete, cheaper, sustainable, and environmentally friendly alternative. In this critical review, we provide an overview of the classification, properties, and interaction of PFAS within the environment relevant to microbial degradation. We discuss latest developments in the biodegradation of PFAS by microbes, transformation routes, transformation products and degradative enzymes. Finally, we highlight the existing challenges, limitations, and prospects of bioremediation approaches in treating PFAS and proffer possible solutions and future research directions.

Role of the CrcB transporter of Pseudomonas putida in the multi-level stress response elicited by mineral fluoride

The presence of mineral fluoride (F^- ) in the environment has both a geogenic and anthropogenic origin, and the halide has been described to be toxic in virtually all living organisms. While the evidence gathered in different microbial species supports this notion, a systematic exploration of the effects of F^- salts on the metabolism and physiology of environmental bacteria remained underexplored thus far. In this work, we studied and characterized tolerance mechanisms deployed by the model soil bacterium Pseudomonas putida KT2440 against NaF. By adopting systems-level omic approaches, including functional genomics and metabolomics, we gauged the impact of this anion at different regulatory levels under conditions that impair bacterial growth. Several genes involved in halide tolerance were isolated in a genome-wide Tn-Seq screening-among which crcB, encoding an F^- -specific exporter, was shown to play the predominant role in detoxification. High-resolution metabolomics, combined with the assessment of intracellular and extracellular pH values and quantitative physiology experiments, underscored the key nodes in central carbon metabolism affected by the presence of F^- . Taken together, our results indicate that P. putida undergoes a general, multi-level stress response when challenged with NaF that significantly differs from that caused by other saline stressors. While microbial stress responses to saline and oxidative challenges have been extensively studied and described in the literature, very little is known about the impact of fluoride (F^- ) on bacterial physiology and metabolism. This state of affairs contrasts with the fact that F^- is more abundant than other halides in the Earth crust (e.g. in some soils, the F^- concentration can reach up to 1 mg g_soil ^-1 ). Understanding the global effects of NaF treatment on bacterial physiology is not only relevant to unveil distinct mechanisms of detoxification but it could also guide microbial engineering approaches for the target incorporation of fluorine into value-added organofluorine molecules. In this regard, the soil bacterium P. putida constitutes an ideal model to explore such scenarios, since this species is particularly known for its high level of stress resistance against a variety of physicochemical perturbations.

Synthetic Cell as a Platform for Understanding Membrane-Membrane Interactions

In the pursuit of understanding life, model membranes made of phospholipids were envisaged decades ago as a platform for the bottom-up study of biological processes. Micron-sized lipid vesicles have gained great acceptance as their bilayer membrane resembles the natural cell membrane. Important biological events involving membranes, such as membrane protein insertion, membrane fusion, and intercellular communication, will be highlighted in this review with recent research updates. We will first review different lipid bilayer platforms used for incorporation of integral membrane proteins and challenges associated with their functional reconstitution. We next discuss different methods for reconstitution of membrane fusion and compare their fusion efficiency. Lastly, we will highlight the importance and challenges of intercellular communication between synthetic cells and synthetic cells-to-natural cells. We will summarize the review by highlighting the challenges and opportunities associated with studying membrane-membrane interactions and possible future research directions.

The fluoride permeation pathway and anion recognition in Fluc family fluoride channels

Fluc family fluoride channels protect microbes against ambient environmental fluoride by undermining the cytoplasmic accumulation of this toxic halide. These proteins are structurally idiosyncratic, and thus the permeation pathway and mechanism have no analogy in other known ion channels. Although fluoride-binding sites were identified in previous structural studies, it was not evident how these ions access aqueous solution, and the molecular determinants of anion recognition and selectivity have not been elucidated. Using x-ray crystallography, planar bilayer electrophysiology, and liposome-based assays, we identified additional binding sites along the permeation pathway. We used this information to develop an oriented system for planar lipid bilayer electrophysiology and observed anion block at one of these sites, revealing insights into the mechanism of anion recognition. We propose a permeation mechanism involving alternating occupancy of anion-binding sites that are fully assembled only as the substrate approaches.

Introduction to the Theme on Membrane Channels

This volume of the Annual Review of Biochemistry contains three reviews on membrane channel proteins: the first by Szczot et al., titled The Form and Function of PIEZO2; the second by Ruprecht & Kunji, titled Structural Mechanism of Transport of Mitochondrial Carriers; and the third by McIlwain et al., titled Membrane Exporters of Fluoride Ion. These reviews provide nice illustrations of just how far evolution has been able to play with the basic helix-bundle architecture of integral membrane proteins to produce membrane channels and transporters of widely different functions.

Mechanisms Underlying Proton Release in CLC-type F-/H+ Antiporters

The CLC family of anion channels and transporters includes Cl^-/H⁺ exchangers (blocked by F^-) and F^-/H⁺ exchangers (or CLC^Fs). CLC^Fs contain a glutamate (E318) in the central anion-binding site that is absent in CLC Cl^-/H⁺ exchangers. The X-ray structure of the protein from Enterococcus casseliflavus (CLC^F-eca) shows that E318 tightly binds to F^- when the gating glutamate (E118; highly conserved in the CLC family) faces the extracellular medium. Here, we use classical and DFT-based QM/MM metadynamics simulations to investigate proton transfer and release by CLC^F-eca. After up to down movement of protonated E118, both glutamates combine with F^- to form a triad, from which protons and F^- anions are released as HF. Our results illustrate how glutamate insertion into the central anion-binding site of CLC^F-eca permits the release of H⁺ to the cytosol as HF, thus enabling a net 1:1 F^-/H⁺ stoichiometry.