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The link between ancient microbial fluoride resistance mechanisms and bioengineering organofluorine degradation or synthesis
Open accessAbstract
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.
Overview
AI snapshot
Written from the paper’s full text.
TL;DR
This Perspective argues that fluoride toxicity, not only C–F bond strength, is a central bottleneck for microbial organofluorine degradation and biosynthesis. It synthesizes ancient microbial fluoride-resistance mechanisms and proposes bioengineering, adaptive evolution, and growth-condition strategies to improve PFAS bioremediation and fluorinated-compound synthesis.
Key findings
- Fluoride strongly inhibits central metabolism: enzyme \(K_i\) values are typically ~100 μM, enolase is inhibited at ~80 μM, wild-type bacteria respond at intracellular fluoride around 60 μM and extracellular concentrations as low as 200 μM, and engineered *Pseudomonas putida* growing on fluorinated substrates accumulated fluoride in medium above 50 mM.
- Fluoride exporters are ancient and widespread: >85% of surveyed GEBA representative prokaryotic genomes possess a fluoride exporter, CLCF and Fluc exporters are usually mutually exclusive with only ~3% of strains possessing both, Fluc channels efflux at ~10^6 ions/s with >10,000-fold fluoride selectivity, and CLCFs are >80-fold selective for fluoride over chloride.
- Fluoride stress also constrains biosynthesis: the well-studied *Streptomyces cattleya* fluorinase has \(k_{cat}\) up to 0.4 min⁻¹ and a fluoride \(K_m\) of 2 mM, requiring cells to tolerate intracellular fluoride levels far above those that trigger stress responses.
- The paper recommends using naturally fluoride-resistant hosts, adaptive evolution/acclimation, engineering fluoride exporters or fluoride-sensitive enzymes, optimizing pH/phosphate/divalent-cation/antioxidant conditions, and integrating fluorobiosynthesis with fluoride tolerance.
Methods
- Design: a Perspective/review that synthesizes emerging ideas on microbial defluorination/fluorination and fluoride resistance; no new primary experimental data are reported.
- Data/sample: cited literature plus a comparative genomic survey of the Joint Genome Institute GEBA representative prokaryotic genomes, and a compiled table of fluoride resistance phenotypes and transport rates.
- Analysis: narrative synthesis of microbial physiology, enzymology, and bioengineering proposals, with comparative genomics used to describe fluoride exporter distribution.
Limitations
- Stated: the authors note that they are “not aware of any systematic investigation of fluoride acclimation in bacteria,” that molecular mechanisms of fluoride sequestration are “not as well understood,” and that in some reported PFAS-degradation studies “no enzymes were directly identified.”
- Evident: as a Perspective, it does not perform a systematic review or new experiments, and several recommendations are explicitly theoretical or proposed rather than demonstrated.
Model-written summary. Check it against the paper before relying on it.
Integrity signals
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Cites
Statistics
Verification
Claims the paper makes
0 of 178 cited sources checked · 0 supported · 0 flagged
- Findingown data
The authors have measured enzymatic C-F bond cleavage in one instance to be as fast as 10 bonds cleaved per second per enzyme.
“We have measured enzymatic C–F bond cleavage in one instance to be as fast as 10 bonds cleaved per second per enzyme (and there are thousands of enzymes per cell).”
Quote in the paperSubstantial claim- Rests on an assumption: There are thousands of enzymes per cell.
- Premisecitation
The ionic form of fluoride becomes trapped in the cell, accumulating to levels dictated by the pH gradient across the membrane.
“The ionic form becomes trapped in the cell, accumulating to levels dictated by the pH gradient across the membrane71.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [71] Ji, C., Stockbridge, R. B. & Miller, C. Bacterial fluoride resistance, Fluc channels, and the weak acid accumulation effect. J. Gen. Physiol. 144, 257–261 (2014). This study quantitatively showed the interplay between pH, intracellular fluoride, and fitness in bacterial populations. source
- Premisecitation
Fluorinase catalyzes the reaction of fluoride anion and S-adenosyl-L-methionine (SAM) to make 5′-fluoro-5′deoxyadenosine (5′-FDA) and L-methionine.
“Nature offers the enzyme fluorinase, which catalyzes the reaction of fluoride anion and S-adenosyl-L-methionine (SAM) to make 5′-fluoro-5′deoxyadenosine (5′-FDA) and L-methionine53.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [53] Dong, C. et al. Crystal structure and mechanism of a bacterial fluorinating enzyme. Nature 427, 561–565 (2004). source
- Premisecitation
WT bacteria mount a gene expression response at intracellular fluoride concentrations around 60 μM.
“Congruent with this, WT bacteria mount a gene expression response at intracellular fluoride concentrations around 60 μM67, and extracellular concentrations as low as 200 μM68.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [67] Baker, J. L. et al. Widespread genetic switches and toxicity resistance proteins for fluoride. Science 335, 233–235 (2012). This is the first study to establish a molecular basis for the fluoride stress response. source
- Interpretationreasoning
The mM Km values of fluorinase for fluoride require that cells tolerate intracellular fluoride levels 100-fold greater than those that begin to elicit fluoride stress responses.
“The mM Km values of fluorinase for fluoride require that cells tolerate intracellular fluoride levels 100-fold greater than those that begin to elicit fluoride stress responses.”
Quote in the paperSubstantial claim
- Interpretationcitation
Enzymatic synthesis of fluorinated organic molecules has the potential to make tailored structures that are difficult to make via conventional synthesis.
“Enzymatic synthesis of fluorinated organic molecules has the potential to make tailored structures that are difficult to make via conventional synthesis20.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [20] Chan, K. K. & O’Hagan, D. The rare fluorinated natural products and biotechnological prospects for fluorine enzymology. Methods Enzymol. 516, 219–235 (2012). source
- Premisecitation
The intracellular volume of a typical bacterial cell is on the order of a femtoliter.
“The intracellular volume of a typical bacterial cell is on the order of a femtoliter69 – in other words, if one femtomole of PFAS enters a cell and undergoes one C–F bond cleavage, the fluoride concentration will approach 1 M.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [69] Wang, L., Zhou, Y. J., Ji, D. & Zhao, Z. K. An accurate method for estimation of the intracellular aqueous volume of Escherichia coli cells. J. Microbiol. Methods 93, 73–76 (2013). source
- Premisecitation
Plants of several varieties in Australia, Africa, and South America produce fluoroacetate to deter feeding by animals.
“Plants of several varieties in Australia, Africa, and South America produce fluoroacetate to deter feeding by animals, since the compound becomes highly toxic to central metabolism after metabolic conversion to fluorocitrate24,25.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [24] Walsh, C. Fluorinated substrate analogs: routes of metabolism and selective toxicity. Adv. Enzymol. Relat. Areas Mol. Biol. 55, 197–289 (1983).
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- cites [25] Marais, J. S. C. The isolation of the toxic principle “potassium cymonate” from “Gifblaar” Dichapetalum cymosum. Onderstepoort J. Vet. Sci. Anim. Ind. 18, 203–206 (1943).
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Premisecitation
Fluoride is highly toxic to the bacteria carrying out biosynthetic or biodegradation reactions.
“Though NaF is much safer for humans than HF and fluorine gas, fluoride is highly toxic to the bacteria carrying out biosynthetic or biodegradation reactions21,22.”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [21] Calero, P., Gurdo, N. & Nikel, P. I. Role of the CrcB transporter of Pseudomonas putida in the multi-level stress response elicited by mineral fluoride. Environ. Microbiol. 24, 5082–5104 (2022). source
- cites [22] Calero, P. et al. A fluoride-responsive genetic circuit enables in vivo biofluorination in engineered Pseudomonas putida. Nat. Commun. 11, 5045 (2020). This study is among the first to leverage fluoride stress response mechanisms for bioengineering applications. source
- Premisecitation
Fluoroacetate dehalogenases prefer fluorine over other halogen substituents.
“These fluoroacetate dehalogenases prefer fluorine over other halogen substituents, suggesting that they were selected for fluoroacetate detoxification or assimilation of fluoroacetate as a carbon source30,33.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [30] Goldman, P. The enzymatic cleavage of the carbon-fluorine bond in fluoroacetate. J. Biol. Chem. 240, 3434–3438 (1965). source
- cites [33] Heffernan, B., Murphy, C. D. & Casey, E. Comparison of planktonic and biofilm cultures of Pseudomonas fluorescens DSM 8341 cells grown on fluoroacetate. Appl. Environ. Microbiol 75, 2899–2907 (2009). source
- Premisecitation
WT bacteria mount a gene expression response at extracellular fluoride concentrations as low as 200 μM.
“Congruent with this, WT bacteria mount a gene expression response at intracellular fluoride concentrations around 60 μM67, and extracellular concentrations as low as 200 μM68.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [68] Banerjee, A. et al. Fluoride export is required for competitive fitness of pathogenic microorganisms in dental biofilm models. mBio 15, e00184–24 (2024). source
- Premisecitation
A survey of the elemental composition of several dozen prokaryotes did not identify fluorine amongst the 33 elements found.
“Fluorine is more common in the earth’s crust than phosphorus, nitrogen, and sulfur and yet a survey of the elemental composition of several dozen prokaryotes did not identify fluorine amongst the 33 elements found, making it less prevalent than non-biological metals like cadmium, tin, and silver23.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [23] Novoselov, A. A. et al. From cytoplasm to environment: the inorganic ingredients for the origin of life. Astrobiology 13, 294–302 (2013). source
- Premisecitation
Organisms that have evolved natural fluorination capabilities, like S. cattleya, separate growth and energy metabolism from organofluorine biosynthesis, only expressing fluorinases in stationary phase.
“Organisms that have evolved natural fluorination capabilities, like S. cattleya, separate growth and energy metabolism from organofluorine biosynthesis, only expressing fluorinases in stationary phase72,73.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [72] Walker, M. C., Wen, M., Weeks, A. M. & Chang, M. C. Y. Temporal and fluoride control of secondary metabolism regulates cellular organofluorine biosynthesis. ACS Chem. Biol. 7, 1576–1585 (2012). source
- cites [73] Reid, K. A., Bowden, R. D., Dasaradhi, L., Amin, M. R. & Harper, D. B. Biosynthesis of fluorinated secondary metabolites by Streptomyces cattleya. Microbiology 141, 1385–1393 (1995). source
- Premisecitation
Environmental fluoride enters cells largely as HF.
“Environmental fluoride enters cells largely as HF71.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [71] Ji, C., Stockbridge, R. B. & Miller, C. Bacterial fluoride resistance, Fluc channels, and the weak acid accumulation effect. J. Gen. Physiol. 144, 257–261 (2014). This study quantitatively showed the interplay between pH, intracellular fluoride, and fitness in bacterial populations. source
- Interpretationreasoning
Microbial PFAS and organofluorine degradation and biosynthesis of less-fluorinated replacement chemicals are undermined by the substantial toxicity of fluoride.
“Both efforts are undermined by the substantial toxicity of fluoride, an anion that powerfully inhibits metabolism.”
Quote in the paperNot a substantial claim - Premisecitation
Fluorinase has high Km values for fluoride (2 mM for the well-studied S. cattleya enzyme).
“However, fluorinase also has limitations for biosynthesis, including low kcat values (up to 0.4 min−1)55 and high Km values for fluoride (2 mM for the well-studied S. cattleya enzyme)20.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [20] Chan, K. K. & O’Hagan, D. The rare fluorinated natural products and biotechnological prospects for fluorine enzymology. Methods Enzymol. 516, 219–235 (2012). source
- Premisecitation
Fluoroacetate synthesis in P. putida KT2440 was achieved by harnessing natural fluoride response elements to deliver fluoride to the cells in a controlled manner.
“Likewise, fluoroacetate synthesis in P. putida KT2440 was achieved by harnessing natural fluoride response elements to deliver fluoride to the cells in a controlled manner55.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [55] Pardo, I. et al. A nonconventional archaeal fluorinase identified by in silico mining for enhanced fluorine biocatalysis. ACS Catal. 12, 6570–6577 (2022). source
- Interpretationreasoning
Biosynthetic reactions require circumventing bacteria's fluoride defenses to deliver fluoride in a controlled manner.
“Biosynthetic reactions require circumventing bacteria’s fluoride defenses to deliver fluoride in a controlled manner.”
Quote in the paperSubstantial claim - Premisecitation
Fluorinase has been successfully leveraged in biosynthetic pathways to produce a variety of simple organofluorines used as PET tracers and medical imaging agents.
“Nonetheless, fluorinase has been successfully leveraged in biosynthetic pathways to produce a variety of simple organofluorines used as PET tracers and medical imaging agents58–60.”
Quote in the paperNot a substantial claim0 of 3 sources checked- cites [58] Fraley, A. E. & Sherman, D. H. Halogenase engineering and its utility in medicinal chemistry. Bioorg. Med Chem. Lett. 28, 1992–1999 (2018). source
- cites [59] Lowe, P. T. et al. A new class of fluorinated A2A adenosine receptor agonist with application to last-step enzymatic [18 F] fluorination for PET imaging. Chembiochem 18, 2156–2164 (2017). source
- cites [60] Dall’Angelo, S. et al. Tumour imaging by positron emission tomography using fluorinase generated 5-[18F]fluoro-5-deoxyribose as a novel tracer. Nucl. Med. Biol. 40, 464–470 (2013). source
- Premisecitation
Fluoride produced intracellularly and released, or produced in the periplasm, readily re-enters and accumulates in cells via weak acid accumulation.
“Moreover, fluoride produced intracellularly and released, or produced in the periplasm, readily re-enters and accumulates in cells via a process called weak acid accumulation65,71, especially as the medium pH acidifies, which is typical with dense bacterial cultures.”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [65] McIlwain, B. C., Ruprecht, M. T. & Stockbridge, R. B. Membrane exporters of fluoride ion. Annu. Rev. Biochem. 90, 559–579 (2021). This work reviews biochemical mechanisms of fluoride toxicity, along with the structures and mechanisms of microbial fluoride exporters that maintain cytoplasmic fluoride at sub-inhibitory concentrations. source
- cites [71] Ji, C., Stockbridge, R. B. & Miller, C. Bacterial fluoride resistance, Fluc channels, and the weak acid accumulation effect. J. Gen. Physiol. 144, 257–261 (2014). This study quantitatively showed the interplay between pH, intracellular fluoride, and fitness in bacterial populations. source
- Rests on an assumption: The medium pH acidifies in dense bacterial cultures.
- Interpretationreasoning
Biological systems have been exposed to toxic levels of fluoride over evolutionary time.
“Thus, biological systems have been exposed to toxic levels of the anion over evolutionary time.”
Quote in the paperSubstantial claim - Premisecitation
Naturally evolved defluorinase enzymes are inherently rare given the scarcity of fluorinated natural products.
“Naturally evolved defluorinase enzymes are inherently rare given the scarcity of fluorinated natural products, such as fluoroacetate described above29.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [29] Seong, H. J., Kwon, S. W., Seo, D. C., Kim, J. H. & Jang, Y. S. Enzymatic defluorination of fluorinated compounds. Appl. Biol. Chem. 62, 62 (2019). source
- Premisecitation
Fluoride is a poor nucleophile in water due to the high free energy of hydration of the anion.
“Fluoride is a poor nucleophile in water due to the high free energy of hydration of the anion56, which must be overcome by the enzyme to catalyze a nucleophilic displacement reaction with SAM.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [56] Zhan, C. G. & Dixon, D. A. Hydration of the fluoride anion: structures and absolute hydration free energy from first-principles electronic structure calculations. J. Phys. Chem. A 108, 2020–2029 (2004). source
- Premisecitation
For Acetobacterium spp. that catalyze reductive defluorination of perfluorinated unsaturated carboxylic acids, strains that lacked a functional fluoride export protein failed to perform defluorination.
“Similarly, for Acetobacterium spp. that catalyze reductive defluorination of perfluorinated unsaturated carboxylic acids, strains that lacked a functional fluoride export protein failed to perform defluorination, linking fluoride detoxification and enzymatic defluorination51.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [51] Wackett, L. P. Evolutionary obstacles and not C–F bond strength make PFAS persistent. Microb. Biotechnol. 17, e14463 (2024). source
- Premisecitation
Fluoride inhibitory constants (Ki values) for enzymes like enolase, pyrophosphatase, and various kinases are typically in the range of 100 μM.
“The fluoride inhibitory constants (Ki values) for enzymes like enolase (which catalyzes the penultimate step in glycolysis), pyrophosphatase, and various kinases are typically in the range of 100 μM66.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [66] Adamek, E., Pawlowska-Goral, K. & Bober, K. In vitro and in vivo effects of fluoride ions on enzyme activity. Ann. Acad. Med. Stetin. 51, 69–85 (2005).
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Premisecitation
Biological systems that degrade perfluorinated compounds have been reported recently.
“Biological systems that degrade perfluorinated compounds have also been reported recently44,45, including reports of the defluorination of perfluorinated acids in consortia46–48 and by a single bacterium49.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [44] Weber, E. J., Tebes-Stevens, C., Washington, J. W. & Gladstone, R. Development of a PFAS reaction library: identifying plausible transformation pathways in environmental and biological systems. Environ. Sci. Process Impacts 24, 689–753 (2022). source
- cites [45] Zhang, Z., Sarkar, D., Biswas, J. K. & Datta, R. Biodegradation of per- and polyfluoroalkyl substances (PFAS): a review. Bioresour. Technol. 344, 126223 (2022). source
- Premisecitation
In an engineered strain of Pseudomonas putida expressing a defluorinase enzyme and grown on α-fluorocarboxylic acids, fluoride stress limits the growth rate.
“In an engineered strain of Pseudomonas putida expressing a defluorinase enzyme and grown on α-fluorocarboxylic acids, fluoride stress limits the growth rate63.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [63] Dodge, A. G., Thoma, C. J., O’Connor, M. R. & Wackett, L. P. Recombinant Pseudomonas growing on non-natural fluorinated substrates shows stress but overall tolerance to cytoplasmically released fluoride anion. mBio 15, e0278523 (2023). This article directly demonstrates fluoride toxicity due to intracellular enzymatic defluorination, with multiple signs of cellular stress. source
- Interpretationreasoning
Fluoride toxicity becomes particularly acute in the context of organofluorine bioremediation and biosynthesis.
“Fluoride toxicity becomes particularly acute in the context of organofluorine bioremediation and biosynthesis.”
Quote in the paperSubstantial claim - Interpretationreasoning
For bacteria metabolizing polyfluorinated compounds, PFAS or organofluorine degradation will rapidly release enough fluoride to impact cellular physiology.
“Thus, for bacteria metabolizing such polyfluorinated compounds, PFAS or organofluorine degradation will rapidly release enough fluoride to impact cellular physiology.”
Quote in the paperSubstantial claim - Premisenone given
Canonical fluoroacetate dehalogenases exhibit little to no activity with α,α-difluoro carboxylic acids characteristic of many PFAS chemicals of interest to remediate.
“In most cases, canonical fluoroacetate dehalogenases exhibit little to no activity with α,α-difluoro carboxylic acids characteristic of many PFAS chemicals of interest to remediate.”
Quote in the paperNot a substantial claim - Premisereasoning
With a pKa value of 3.4, appreciable HF is formed in niches with a pH below ~7.
“With a pKa value of 3.4, appreciable HF is formed in niches with a pH below ~7.”
Quote in the paperSubstantial claim - Premisecitation
Mutagenesis strategies have not significantly lowered the Km for fluoride.
“Likewise, mutagenesis strategies have not significantly lowered the Km for fluoride57.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [57] Sun, H. et al. Directed evolution of a fluorinase for improved fluorination efficiency with a non-native substrate. Angew. Chem. Int Ed. Engl. 55, 14277–14280 (2016). source
- Interpretationreasoning
In a hypothetical scenario of environmental PFAS degradation, a cell will approach toxic levels of intracellular fluoride (>100 μM) upon uptake and defluorination of perfluorooctanoic acid from just 10 pL of medium contaminated with 1 ppb of this substance.
“In a hypothetical scenario of environmental PFAS degradation, a cell will approach toxic levels of intracellular fluoride (>100 μM) upon uptake and defluorination of perfluorooctanoic acid from just 10 pL of medium contaminated with 1 ppb of this substance, a value that is observed in PFAS-polluted environmental samples70.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [70] Ackerman Grunfeld, D. et al. Underestimated burden of per- and polyfluoroalkyl substances in global surface waters and groundwaters. Nat. Geosci. 17, 340–346 (2024). source
- Premisenone given
Organofluorine degradation yields fluoride ions.
“In particular, organofluorine degradation yields fluoride ions, and biological syntheses use NaF.”
Quote in the paperSubstantial claim - Premisereasoning
C-F bond cleavage by any mechanism releases fluorine as a fluoride anion.
“Some commercial PFAS molecules contain 15 or more fluorines, and due to this atom’s electronegativity, C–F bond cleavage by any mechanism releases fluorine as a fluoride anion.”
Quote in the paperSubstantial claim- Rests on an assumption: C–F bond cleavage by any mechanism releases fluorine as a fluoride anion.
- Interpretationcitation
Fluoride detoxification and enzymatic defluorination are linked.
“Similarly, for Acetobacterium spp. that catalyze reductive defluorination of perfluorinated unsaturated carboxylic acids, strains that lacked a functional fluoride export protein failed to perform defluorination, linking fluoride detoxification and enzymatic defluorination51.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [51] Wackett, L. P. Evolutionary obstacles and not C–F bond strength make PFAS persistent. Microb. Biotechnol. 17, e14463 (2024). source
- Interpretationreasoning
If C-F bond cleavage occurs in the cytoplasm, fluoride will accumulate intracellularly.
“Because fluoride cannot passively diffuse across the membrane, if this reaction occurs in the cytoplasm, fluoride will accumulate intracellularly.”
Quote in the paperSubstantial claim - Premisecitation
A range of other fluorinase enzymes have been tested but so far none show markedly different steady-state kinetic parameters.
“A range of other fluorinase enzymes have been tested but so far, none show markedly different steady-state kinetic parameters55.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [55] Pardo, I. et al. A nonconventional archaeal fluorinase identified by in silico mining for enhanced fluorine biocatalysis. ACS Catal. 12, 6570–6577 (2022). source
- Premisecitation
Members of the haloacid dehalogenase-like hydrolase (HAD) superfamily catalyze the defluorination of fluoroacetate to yield glycolic acid and HF.
“More recently, members of the haloacid dehalogenase-like hydrolase (HAD) superfamily have also been shown to catalyze the defluorination of fluoroacetate to yield glycolic acid and HF32.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [32] Chan, P. W. Y. et al. Defluorination capability of L-2-haloacid dehalogenases in the HAD-like hydrolase superfamily correlates with active site compactness. Chembiochem 23, e202100414 (2022). source
- Premisecitation
Fluoride inhibits essential enzymes in central metabolism, often by forming tight complexes with metallo-cofactors like calcium or magnesium within the enzyme's active site.
“Unlike other monovalent anions like chloride, fluoride inhibits essential enzymes in central metabolism, often by forming tight complexes with metallo-cofactors like calcium or magnesium within the enzyme’s active site65.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [65] McIlwain, B. C., Ruprecht, M. T. & Stockbridge, R. B. Membrane exporters of fluoride ion. Annu. Rev. Biochem. 90, 559–579 (2021). This work reviews biochemical mechanisms of fluoride toxicity, along with the structures and mechanisms of microbial fluoride exporters that maintain cytoplasmic fluoride at sub-inhibitory concentrations. source
- Premisecitation
1 ppb of perfluorooctanoic acid is observed in PFAS-polluted environmental samples.
“In a hypothetical scenario of environmental PFAS degradation, a cell will approach toxic levels of intracellular fluoride (>100 μM) upon uptake and defluorination of perfluorooctanoic acid from just 10 pL of medium contaminated with 1 ppb of this substance, a value that is observed in PFAS-polluted environmental samples70.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [70] Ackerman Grunfeld, D. et al. Underestimated burden of per- and polyfluoroalkyl substances in global surface waters and groundwaters. Nat. Geosci. 17, 340–346 (2024). source
- Interpretationreasoning
The synthesis of PFAS alternatives by bacteria involves substantial fluoride stress.
“Similarly, the synthesis of PFAS alternatives by bacteria involves substantial fluoride stress, since the microbe must take up fluoride in a controlled manner as a substrate for synthesis.”
Quote in the paperSubstantial claim - Premisecitation
The enzyme products of difluoroacetic acid defluorination are two fluoride anions and an α-keto acid.
“The enzyme products of difluoroacetic acid defluorination are two fluoride anions and an α-keto acid.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [35] Khusnutdinova, A. N. et al. Structural insights into hydrolytic defluorination of difluoroacetate by microbial fluoroacetate dehalogenases. FEBS J. 290, 4966–4983 (2023). In this work, a well-studied class of enzymes was shown to be reactive in the defluorination of difluoromethylene carbon centers. source
- Premisecitation
For cultures of P. putida engineered to grow on fluorinated substrates, fluoride accumulates in the medium to concentrations exceeding 50 mM.
“For cultures of P. putida engineered to grow on fluorinated substrates, fluoride accumulates in the medium to concentrations exceeding 50 mM63.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [63] Dodge, A. G., Thoma, C. J., O’Connor, M. R. & Wackett, L. P. Recombinant Pseudomonas growing on non-natural fluorinated substrates shows stress but overall tolerance to cytoplasmically released fluoride anion. mBio 15, e0278523 (2023). This article directly demonstrates fluoride toxicity due to intracellular enzymatic defluorination, with multiple signs of cellular stress. source
- Premisereasoning
Trifluoroacetic acid is highly recalcitrant to further degradation.
“Since α-keto acid decarboxylases are known, a plausible degradative pathway for perfluorocarboxylic acids would use consecutive paired reactions of α,α-defluorination and decarboxylation, releasing fluoride ions at each step and culminating in trifluoroacetic acid, an end product that is highly recalcitrant to further degradation.”
Quote in the paperSubstantial claim - Premisecitation
Fluorinase has low kcat values up to 0.4 min−1.
“However, fluorinase also has limitations for biosynthesis, including low kcat values (up to 0.4 min−1)55 and high Km values for fluoride (2 mM for the well-studied S. cattleya enzyme)20.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [55] Pardo, I. et al. A nonconventional archaeal fluorinase identified by in silico mining for enhanced fluorine biocatalysis. ACS Catal. 12, 6570–6577 (2022). source
- Premisecitation
Fluoride powerfully inhibits metabolism.
“Both efforts are undermined by the substantial toxicity of fluoride, an anion that powerfully inhibits metabolism.”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [21] Calero, P., Gurdo, N. & Nikel, P. I. Role of the CrcB transporter of Pseudomonas putida in the multi-level stress response elicited by mineral fluoride. Environ. Microbiol. 24, 5082–5104 (2022). source
A check is scheduled.
- cites [22] Calero, P. et al. A fluoride-responsive genetic circuit enables in vivo biofluorination in engineered Pseudomonas putida. Nat. Commun. 11, 5045 (2020). This study is among the first to leverage fluoride stress response mechanisms for bioengineering applications. source
A check is scheduled.
- Interpretationreasoning
If one femtomole of PFAS enters a cell and undergoes one C-F bond cleavage, the fluoride concentration will approach 1 M.
“The intracellular volume of a typical bacterial cell is on the order of a femtoliter69 – in other words, if one femtomole of PFAS enters a cell and undergoes one C–F bond cleavage, the fluoride concentration will approach 1 M.”
Quote in the paperSubstantial claim - Premisecitation
Earlier studies strongly indicate that fluoride anion toxicity is a major impediment to progress in both organofluorine synthesis and degradation.
“Earlier studies on biological organofluorine synthesis and degradation strongly indicate that fluoride anion toxicity is a major impediment to progress in both fields of study21,55,63,64.”
Quote in the paperSubstantial claim0 of 4 sources checked- cites [21] Calero, P., Gurdo, N. & Nikel, P. I. Role of the CrcB transporter of Pseudomonas putida in the multi-level stress response elicited by mineral fluoride. Environ. Microbiol. 24, 5082–5104 (2022). source
- cites [55] Pardo, I. et al. A nonconventional archaeal fluorinase identified by in silico mining for enhanced fluorine biocatalysis. ACS Catal. 12, 6570–6577 (2022). source
- cites [63] Dodge, A. G., Thoma, C. J., O’Connor, M. R. & Wackett, L. P. Recombinant Pseudomonas growing on non-natural fluorinated substrates shows stress but overall tolerance to cytoplasmically released fluoride anion. mBio 15, e0278523 (2023). This article directly demonstrates fluoride toxicity due to intracellular enzymatic defluorination, with multiple signs of cellular stress. source
- cites [64] Markakis, K. et al. An engineered E. coli strain for direct in vivo fluorination. Chembiochem 21, 1856–1860 (2020). source
- Premisecitation
Microorganisms have evolved a suite of fluoride detoxification mechanisms.
“Microorganisms have contended with environmental mineral fluoride over evolutionary time, evolving a suite of detoxification mechanisms.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [65] McIlwain, B. C., Ruprecht, M. T. & Stockbridge, R. B. Membrane exporters of fluoride ion. Annu. Rev. Biochem. 90, 559–579 (2021). This work reviews biochemical mechanisms of fluoride toxicity, along with the structures and mechanisms of microbial fluoride exporters that maintain cytoplasmic fluoride at sub-inhibitory concentrations. source
A check is scheduled.
- Premisecitation
In E. coli, high concentrations of fluoride stall cell division and growth, which is only resumed after fluoride is removed.
“In E. coli, high concentrations of fluoride stall cell division and growth, which is only resumed after fluoride is removed71.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [71] Ji, C., Stockbridge, R. B. & Miller, C. Bacterial fluoride resistance, Fluc channels, and the weak acid accumulation effect. J. Gen. Physiol. 144, 257–261 (2014). This study quantitatively showed the interplay between pH, intracellular fluoride, and fitness in bacterial populations. source
- Premisecitation
Several defluorinases that act on difluoroacetic acid have been discovered recently.
“However, several defluorinases that act on difluoroacetic acid have been discovered recently, holding open the possibility that naturally evolved enzymes might be able to degrade longer chain α,α-difluoro acids35.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [35] Khusnutdinova, A. N. et al. Structural insights into hydrolytic defluorination of difluoroacetate by microbial fluoroacetate dehalogenases. FEBS J. 290, 4966–4983 (2023). In this work, a well-studied class of enzymes was shown to be reactive in the defluorination of difluoromethylene carbon centers. source
- Premisecitation
The electron bifurcating caffeoyl-CoA reductase system of Acetobacterium spp. was implicated in the reductive defluorination of perfluorinated unsaturated carboxylic acids.
“Most recently, the electron bifurcating caffeoyl-CoA reductase system of Acetobacterium spp. was implicated in the reductive defluorination of perfluorinated unsaturated carboxylic acids51.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [51] Wackett, L. P. Evolutionary obstacles and not C–F bond strength make PFAS persistent. Microb. Biotechnol. 17, e14463 (2024). source
- Premisecitation
Microorganisms have contended with environmental mineral fluoride over evolutionary time.
“Microorganisms have contended with environmental mineral fluoride over evolutionary time, evolving a suite of detoxification mechanisms.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [65] McIlwain, B. C., Ruprecht, M. T. & Stockbridge, R. B. Membrane exporters of fluoride ion. Annu. Rev. Biochem. 90, 559–579 (2021). This work reviews biochemical mechanisms of fluoride toxicity, along with the structures and mechanisms of microbial fluoride exporters that maintain cytoplasmic fluoride at sub-inhibitory concentrations. source
A check is scheduled.
- Premisecitation
Extreme fluoride tolerant strains have been identified in the context of organofluorine biosynthesis, biodegradation, and fluoride sequestration.
“Such strains have been identified in the context of organofluorine biosynthesis21, biodegradation63 and fluoride sequestration113.”
Quote in the paperSubstantial claim0 of 3 sources checked- cites [21] Calero, P., Gurdo, N. & Nikel, P. I. Role of the CrcB transporter of Pseudomonas putida in the multi-level stress response elicited by mineral fluoride. Environ. Microbiol. 24, 5082–5104 (2022). source
- cites [63] Dodge, A. G., Thoma, C. J., O’Connor, M. R. & Wackett, L. P. Recombinant Pseudomonas growing on non-natural fluorinated substrates shows stress but overall tolerance to cytoplasmically released fluoride anion. mBio 15, e0278523 (2023). This article directly demonstrates fluoride toxicity due to intracellular enzymatic defluorination, with multiple signs of cellular stress. source
- cites [113] Let, M., Majhi, K. & Bandopadhyay, R. Defluoridation efficiency of a novel fluoride-resistant Exiguobacterium indicum MLN15. Natl. Acad. Sci. Lett. 46, 511–515 (2023). source
- Premisecitation
Stress-response pathways, especially oxidative stress responses, are activated in a broad cross-section of bacterial species upon fluoride challenge.
“Stress-response pathways, especially oxidative stress responses, are activated in a broad cross-section of bacterial species upon fluoride challenge21,88,95,97,101.”
Quote in the paperNot a substantial claim0 of 5 sources checked- cites [21] Calero, P., Gurdo, N. & Nikel, P. I. Role of the CrcB transporter of Pseudomonas putida in the multi-level stress response elicited by mineral fluoride. Environ. Microbiol. 24, 5082–5104 (2022). source
A check is scheduled.
- cites [88] Strobel, S. A., Johnston, N. R. & Cline, G. Cells adapt to resist fluoride through metabolic deactivation and intracellular acidification. Chem. Res. Toxicol. 35, 2085–2096 (2022). By acclimating yeast to high fluoride over several generations, this study uncovered several novel fluoride stress mitigation mechanisms in microbes. source
A check is scheduled.
- cites [95] Liu, X. et al. Identification of an operon involved in fluoride resistance in Enterobacter cloacae FRM. Sci. Rep. 7, 6786 (2017). source
A check is scheduled.
- cites [97] Johnston, N. R. & Strobel, S. A. Nitrate and phosphate transporters rescue fluoride toxicity in yeast. Chem. Res. Toxicol. 32, 2305–2319 (2019). source
A check is scheduled.
- cites [101] Dame-Teixeira, N., Deng, D. & Do, T. Streptococcus mutans transcriptome in the presence of sodium fluoride and sucrose. Arch. Oral. Biol. 102, 186–192 (2019). source
- Interpretationreasoning
Even low levels of environmental fluoride can breach the cell and evoke a cellular stress response.
“Via this process, even low levels of environmental fluoride can breach the cell and evoke a cellular stress response.”
Quote in the paperSubstantial claim - Premisecitation
The importance of fluoride exporters to fluoride resistance has been demonstrated in diverse organisms.
“The importance of these exporters to fluoride resistance has been demonstrated in diverse organisms (Table 1).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Table 1
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- Premisecitation
Fluoride mineralization has been engineered into some bacteria.
“Based on these principles, fluoride mineralization has been engineered into some bacteria119,120.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [119] Yang, W. S. et al. Microbial induced calcium precipitation based anaerobic immobilized biofilm reactor for fluoride, calcium, and nitrate removal from groundwater. Chemosphere 295, 133955 (2022). source
- cites [120] Let, M. et al. Exploration of urease-mediated biomineralization for defluoridation by Proteus columbae MLN9 with an emphasis on its genomic characterization. J. Environ. Chem. Eng. 11, 109791 (2023). source
- Premisecitation
The majority of enzymes with the haloacid dehalogenase fold are in fact phosphoesterases.
“These were initially assumed to be related to fluorine metabolism, but it has since been shown that the majority of enzymes with the haloacid dehalogenase fold are in fact phosphoesterases31,98.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [31] Chan, W. Y. et al. Sequence- and activity-based screening of microbial genomes for novel dehalogenases. Micro. Biotechnol. 3, 107–120 (2010). source
- cites [98] Burroughs, A. M., Allen, K. N., Dunaway-Mariano, D. & Aravind, L. Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes. J. Mol. Biol. 361, 1003–1034 (2006). source
- Premisecitation
Using fluorinated compounds as the sole carbon source generates dual and opposite selective pressures for sufficient carbon metabolism to provide cellular metabolites and ATP, counterbalanced by toxicity from excessive intracellular fluoride flux.
“Recent studies show that using fluorinated compounds as the sole carbon source generates dual and opposite selective pressures for sufficient carbon metabolism to provide cellular metabolites and ATP, counterbalanced by toxicity from excessive intracellular fluoride flux35,63.”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [35] Khusnutdinova, A. N. et al. Structural insights into hydrolytic defluorination of difluoroacetate by microbial fluoroacetate dehalogenases. FEBS J. 290, 4966–4983 (2023). In this work, a well-studied class of enzymes was shown to be reactive in the defluorination of difluoromethylene carbon centers. source
- cites [63] Dodge, A. G., Thoma, C. J., O’Connor, M. R. & Wackett, L. P. Recombinant Pseudomonas growing on non-natural fluorinated substrates shows stress but overall tolerance to cytoplasmically released fluoride anion. mBio 15, e0278523 (2023). This article directly demonstrates fluoride toxicity due to intracellular enzymatic defluorination, with multiple signs of cellular stress. source
- Premisecitation
Fluoride-stressed P. putida has elevated levels of methionine and tyrosine.
“For example, fluoride-stressed P. putida has elevated levels of methionine and tyrosine21.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [21] Calero, P., Gurdo, N. & Nikel, P. I. Role of the CrcB transporter of Pseudomonas putida in the multi-level stress response elicited by mineral fluoride. Environ. Microbiol. 24, 5082–5104 (2022). source
- Premisecitation
In fluoride-acclimated S. cerevisiae, one of the most frequent physiological adjustments was tolerance to lower homeostatic pH.
“In fluoride-acclimated S. cerevisiae, one of the most frequent physiological adjustments was tolerance to lower homeostatic pH88.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [88] Strobel, S. A., Johnston, N. R. & Cline, G. Cells adapt to resist fluoride through metabolic deactivation and intracellular acidification. Chem. Res. Toxicol. 35, 2085–2096 (2022). By acclimating yeast to high fluoride over several generations, this study uncovered several novel fluoride stress mitigation mechanisms in microbes. source
- Premisecitation
CLCFs are fluoride/proton antiporters that harness the proton gradient to expel fluoride from the cytoplasm.
“The CLCFs are fluoride/proton antiporters that harness the proton gradient to expel fluoride from the cytoplasm77.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [77] Stockbridge, R. B. et al. Fluoride resistance and transport by riboswitch-controlled CLC antiporters. Proc. Natl Acad. Sci. USA 109, 15289–15294 (2012). source
- Premisenone given
Species that lack fluoride exporters tend to be obligate intracellular symbionts with reduced genomes, for example members of the genera Tenericutes, Spirochetes, and Fusobacteria.
“Species that lack fluoride exporters tend to be obligate intracellular symbionts with reduced genomes, for example members of the genera Tenericutes, Spirochetes, and Fusobacteria.”
Quote in the paperNot a substantial claim - Premisecitation
Bacillus subtilis, Neisseria subflava, and Streptococcus species exhibit varying degrees of autolysis in response to fluoride stress.
“Other bacteria, like Bacillus subtilis, Neisseria subflava, and Streptococcus species exhibit varying degrees of autolysis in response to fluoride stress106.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [106] Lesher, R. J., Bender, G. R. & Marquis, R. E. Bacteriolytic action of fluoride ions. Antimicrob. Agents Chemother. 12, 339–345 (1977). source
- Premisecitation
Additional CLC homologs for chloride transport are not capable of transporting fluoride.
“Many bacteria also possess additional CLC homologs for chloride transport; these are not capable of transporting fluoride80.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [80] Lim, H. H., Stockbridge, R. B. & Miller, C. Fluoride-dependent interruption of the transport cycle of a CLC Cl-/H+ antiporter. Nat. Chem. Biol. 9, 721–725 (2013). source
- Premisecitation
Some species, including Exiguobacterium indicum MLN15 and Bacillus licheniformis, absorb fluoride in electron-dense granules on the surface and in the cytoplasm, respectively.
“It has been shown that some species, including the extremely fluoride-resistant Exiguobacterium indicum MLN15 and Bacillus licheniformis absorb fluoride in electron-dense granules on the surface and in the cytoplasm, respectively, although the molecular identity of these is unknown112,113.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [112] Thesai, A. S., Nagarajan, G., Rajakumar, S., Pugazhendhi, A. & Ayyasamy, P. M. Bioaccumulation of fluoride from aqueous system and genotoxicity study on Allium cepa using Bacillus licheniformis. J. Hazard Mater. 407, 124367 (2021). source
- cites [113] Let, M., Majhi, K. & Bandopadhyay, R. Defluoridation efficiency of a novel fluoride-resistant Exiguobacterium indicum MLN15. Natl. Acad. Sci. Lett. 46, 511–515 (2023). source
- Premisecitation
In Streptococcus mutans, which do not possess a fluoride riboswitch, CLCF expression is induced by fluoride addition to the medium.
“For instance, in Streptococcus mutans, which do not possess a fluoride riboswitch, CLCF expression is induced by fluoride addition to the medium68.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [68] Banerjee, A. et al. Fluoride export is required for competitive fitness of pathogenic microorganisms in dental biofilm models. mBio 15, e00184–24 (2024). source
- Premisecitation
Yeast, fungi, plants, and some ocean-dwelling animals possess fluoride exporters of the FEX family.
“Yeast, fungi, plants, and some ocean-dwelling animals like corals and sponges also possess fluoride exporters that belong to a third molecular family known as FEX85,86.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [85] Li, S. et al. Eukaryotic resistance to fluoride toxicity mediated by a widespread family of fluoride export proteins. Proc. Natl Acad. Sci. USA 110, 19018–19023 (2013). source
- cites [86] Berbasova, T. et al. Fluoride export (FEX) proteins from fungi, plants and animals are ‘single barreled’ channels containing one functional and one vestigial ion pore. PLoS ONE 12, e0177096 (2017). source
- Premisecitation
Genes annotated as haloacid dehalogenases are often associated with fluoride riboswitches.
“In addition, genes annotated as haloacid dehalogenases are often associated with riboswitches67.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [67] Baker, J. L. et al. Widespread genetic switches and toxicity resistance proteins for fluoride. Science 335, 233–235 (2012). This is the first study to establish a molecular basis for the fluoride stress response. source
- Interpretationreasoning
Fluoride stress is a major constraint on sustained organofluorine biodegradation in engineered, and perhaps highly contaminated, natural systems.
“The high degree of fluorination coupled with the lack of known metabolic energy provided by PFAS metabolism suggests that fluoride stress is a major constraint on sustained organofluorine biodegradation in engineered, and perhaps highly contaminated, natural systems.”
Quote in the paperSubstantial claim - Premisecitation
During PFAS biodegradation, the release of fluoride anion intracellularly can cause cessation of energy metabolism before a fluoride stress response is mounted.
“During PFAS biodegradation, the release of fluoride anion intracellularly can cause cessation of energy metabolism before a fluoride stress response is mounted63.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [63] Dodge, A. G., Thoma, C. J., O’Connor, M. R. & Wackett, L. P. Recombinant Pseudomonas growing on non-natural fluorinated substrates shows stress but overall tolerance to cytoplasmically released fluoride anion. mBio 15, e0278523 (2023). This article directly demonstrates fluoride toxicity due to intracellular enzymatic defluorination, with multiple signs of cellular stress. source
- Premisecitation
In both prokaryotic and eukaryotic microorganisms, fluoride potentiates the effect of drugs that inhibit cell wall biosynthesis.
“In both prokaryotic and eukaryotic microorganisms, fluoride potentiates the effect of drugs that inhibit cell wall biosynthesis109–111.”
Quote in the paperNot a substantial claim0 of 3 sources checked- cites [109] Li, S. & Breaker, R. R. Fluoride enhances the activity of fungicides that destabilize cell membranes. Bioorg. Med. Chem. Lett. 22, 3317–3322 (2012). source
- cites [110] Nelson, J. W., Plummer, M. S., Blount, K. F., Ames, T. D. & Breaker, R. R. Small molecule fluoride toxicity agonists. Chem. Biol. 22, 527–534 (2015). source
- cites [111] Binder, J., Held, J. & Krappmann, S. Impairing fluoride export of Aspergillus fumigatus mitigates its voriconazole resistance. Int J. Antimicrob. Agents 53, 689–693 (2019). source
- Interpretationreasoning
Adaptive evolution or fluoride acclimation has the potential to rapidly generate strains with better fluoride tolerance.
“Because so many fluoride resistance mechanisms involve rewiring metabolic pathways to circumvent inhibition of glycolysis, cytoplasmic acidification, or oxidative stress, adaptive evolution or fluoride acclimation has the potential to rapidly generate strains with better fluoride tolerance.”
Quote in the paperSubstantial claim - Premisecitation
FEX proteins export fluoride via a channel mechanism driven by the membrane potential.
“Like the Flucs, these proteins export fluoride via a channel mechanism driven by the membrane potential87.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [87] Smith, K. D. et al. Yeast Fex1p is a constitutively expressed fluoride channel with functional asymmetry of its two homologous domains. J. Biol. Chem. 290, 19874–19887 (2015). source
- Interpretationown data
The widespread distribution of fluoride export genes among microbes emphasizes the pervasive impact of environmental fluoride over evolutionary time.
“The widespread distribution of these fluoride export genes among microbes emphasizes the pervasive impact of environmental fluoride over evolutionary time.”
Quote in the paperNot a substantial claim - Premisecitation
Flucs function as passive fluoride channels that exploit the positive-outside membrane potential to drive expulsion of fluoride.
“In contrast to the CLCFs, the Flucs (Fluoride channel) function as passive fluoride channels81 that exploit the positive-outside membrane potential (the electrical component of the proton-motive force) to drive the expulsion of this anionic species71.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [81] Stockbridge, R. B., Robertson, J. L., Kolmakova-Partensky, L. & Miller, C. A family of fluoride-specific ion channels with dual-topology architecture. eLife 2, e01084 (2013). source
- cites [71] Ji, C., Stockbridge, R. B. & Miller, C. Bacterial fluoride resistance, Fluc channels, and the weak acid accumulation effect. J. Gen. Physiol. 144, 257–261 (2014). This study quantitatively showed the interplay between pH, intracellular fluoride, and fitness in bacterial populations. source
- Premisecitation
In E. coli, fluoride accumulation is bacteriostatic, halting metabolism while fluoride is present.
“For some bacteria, like E. coli, fluoride accumulation is bacteriostatic, halting metabolism while fluoride is present71.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [71] Ji, C., Stockbridge, R. B. & Miller, C. Bacterial fluoride resistance, Fluc channels, and the weak acid accumulation effect. J. Gen. Physiol. 144, 257–261 (2014). This study quantitatively showed the interplay between pH, intracellular fluoride, and fitness in bacterial populations. source
- Premisecitation
Genes encoding other ion transporters are overrepresented in fluoride-related operons and gene expression analyses.
“In addition to phosphate importers and Na+/H+ antiporters, genes encoding other ion transporters are also overrepresented in fluoride-related operons and gene expression analyses95.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [95] Liu, X. et al. Identification of an operon involved in fluoride resistance in Enterobacter cloacae FRM. Sci. Rep. 7, 6786 (2017). source
- Premisecitation
Fluoride-specific CLCFs can be identified by three signature sequences: GNNLI/GMGLI in the N-terminal domain, GREGT/V at the transport machinery, and GEVTP in the C-terminal domain.
“Fluoride-specific CLCFs can be identified based on three signature sequences: the GNNLI/GMGLI in the N-terminal domain that defines ion selectivity, GREGT/V at the heart of the transport machinery, and the GEVTP sequence in the C-terminal domain that contributes fluoride-binding residues77–79.”
Quote in the paperNot a substantial claim0 of 3 sources checked- cites [77] Stockbridge, R. B. et al. Fluoride resistance and transport by riboswitch-controlled CLC antiporters. Proc. Natl Acad. Sci. USA 109, 15289–15294 (2012). source
- cites [78] Brammer, A. E., Stockbridge, R. B. & Miller, C. F-/Cl- selectivity in CLCF-type F-/H+ antiporters. J. Gen. Physiol. 144, 129–136 (2014). source
- cites [79] Last, N. B. et al. A CLC-type F(-)/H(+) antiporter in ion-swapped conformations. Nat. Struct. Mol. Biol. 25, 601–606 (2018). source
- Premisecitation
Bacteria are known to biomineralize calcium in crystal lattices that can incorporate fluoride, including francolite, aragonite, dolomite, and apatite.
“Bacteria are known to biomineralize calcium in crystal lattices that can incorporate fluoride, including francolite, aragonite, dolomite, and apatite114–118.”
Quote in the paperSubstantial claim0 of 5 sources checked- cites [114] Paramasivan, M., Kumar, T. S. S., Kanniyappan, H., Muthuvijayan, V. & Chandra, T. S. Microbial biomineralization of hydroxyapatite nanocrystals using Bacillus tequilensis. Ceram. Int. 49, 5621–5629 (2023). source
- cites [115] Boyan, B. D., Landis, W. J., Knight, J., Dereszewski, G. & Zeagler, J. Microbial hydroxyapatite formation as a model of proteolipid-dependent membrane-mediated calcification. Scan. Electron Microsc. 4, 1793−1800 (1984).
- cites [116] García, M., Márquez, M. A. & Moreno, C. X. Characterization of bacterial diversity associated with calcareous deposits and drip-waters, and isolation of calcifying bacteria from two Colombian mines. Microbiol. Res. 182, 21–30 (2016). source
- cites [117] Dhami, N. K., Mukherjee, A. & Watkin, E. L. J. Microbial diversity and mineralogical-mechanical properties of calcitic cave speleothems in natural and in vitro biomineralization conditions. Front. Microbiol. 9, 40 (2018). source
- cites [118] Tribovillard, N., Récourt, P. & Trentesaux, A. Bacterial calcification as a possible trigger for francolite precipitation under sulfidic conditions. Comptes Rendus Geosci. 342, 27–35 (2010). source
- Premisecitation
Enolase is inhibited by fluoride with a Ki value of ~80 μM.
“Enolase (which converts 2-phosphoglycerate to phosphoenolpyruvate, or PEP) is inhibited by fluoride with a Ki value of ~80 μM100.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [100] Qin, J., Chai, G., Brewer, J. M., Lovelace, L. L. & Lebioda, L. Fluoride inhibition of enolase: crystal structure and thermodynamics. Biochemistry 45, 793–800 (2006). source
- Interpretationreasoning
Fluoride-stressed microorganisms enact substantial, but sometimes dissimilar, changes to metabolism.
“Fluoride-stressed microorganisms enact substantial, but sometimes dissimilar, changes to metabolism.”
Quote in the paperNot a substantial claim - Premisecitation
Fluoride-acclimated strains of Saccharomyces cerevisiae exhibited a 700-fold gain in fluoride resistance, independent of fluoride export.
“In one illustration of the potential contribution of these additional fluoride resistance mechanisms, fluoride-acclimated strains of Saccharomyces cerevisiae exhibited a 700-fold gain in fluoride resistance, independent of fluoride export88.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [88] Strobel, S. A., Johnston, N. R. & Cline, G. Cells adapt to resist fluoride through metabolic deactivation and intracellular acidification. Chem. Res. Toxicol. 35, 2085–2096 (2022). By acclimating yeast to high fluoride over several generations, this study uncovered several novel fluoride stress mitigation mechanisms in microbes. source
- Interpretationreasoning
By exploiting fundamental microbial physiologies - in particular fluoride stress responses - we can unlock better strategies for biodegradation or biosynthesis of organofluorine molecules such as PFAS.
“We argue that by exploiting fundamental microbial physiologies — in particular fluoride stress responses — we can unlock better strategies for biodegradation or biosynthesis of organofluorine molecules such as PFAS.”
Quote in the paperNot a substantial claim - Premisecitation
Across the tree of life, the first lines of defense against fluoride toxicity are membrane exporters that maintain this anion at low cytoplasmic concentrations.
“Across the tree of life, the first lines of defense against fluoride toxicity are membrane exporters that maintain this anion at low cytoplasmic concentrations65.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [65] McIlwain, B. C., Ruprecht, M. T. & Stockbridge, R. B. Membrane exporters of fluoride ion. Annu. Rev. Biochem. 90, 559–579 (2021). This work reviews biochemical mechanisms of fluoride toxicity, along with the structures and mechanisms of microbial fluoride exporters that maintain cytoplasmic fluoride at sub-inhibitory concentrations. source
- Premisecitation
Constitutive expression of fluoride exporters is one naturally evolved response that improves bacterial fluoride tolerance.
“Constitutive expression of fluoride exporters is one naturally evolved response that improves bacterial fluoride tolerance91.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [91] Liao, Y. et al. Identification and functional analysis of genome mutations in a fluoride-resistant Streptococcus mutans strain. PLoS ONE 10, e0122630 (2015). source
- Premisecitation
Among bacteria, two fundamentally different fluoride export proteins have been identified, the CLCFs and the Flucs.
“Among bacteria, two fundamentally different fluoride export proteins have been identified, the CLCFs (gene name may be annotated sycA, eriC, clcA, clcB) and the Flucs (gene name may be annotated crcB or fluC)65.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [65] McIlwain, B. C., Ruprecht, M. T. & Stockbridge, R. B. Membrane exporters of fluoride ion. Annu. Rev. Biochem. 90, 559–579 (2021). This work reviews biochemical mechanisms of fluoride toxicity, along with the structures and mechanisms of microbial fluoride exporters that maintain cytoplasmic fluoride at sub-inhibitory concentrations. source
- Premisecitation
S. mutans shows evidence of a shift away from oxidative metabolism under fluoride.
“For other bacteria, like S. mutans, there is evidence of a shift away from oxidative metabolism101.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [101] Dame-Teixeira, N., Deng, D. & Do, T. Streptococcus mutans transcriptome in the presence of sodium fluoride and sucrose. Arch. Oral. Biol. 102, 186–192 (2019). source
- Premisecitation
Increased cytoplasmic phosphate is protective against fluoride toxicity.
“But there is also evidence that increased cytoplasmic phosphate is protective against fluoride toxicity88,97, perhaps partly due to phosphate’s buffering capacity at neutral pH.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [88] Strobel, S. A., Johnston, N. R. & Cline, G. Cells adapt to resist fluoride through metabolic deactivation and intracellular acidification. Chem. Res. Toxicol. 35, 2085–2096 (2022). By acclimating yeast to high fluoride over several generations, this study uncovered several novel fluoride stress mitigation mechanisms in microbes. source
- cites [97] Johnston, N. R. & Strobel, S. A. Nitrate and phosphate transporters rescue fluoride toxicity in yeast. Chem. Res. Toxicol. 32, 2305–2319 (2019). source
- Premisecitation
Flucs assemble as unusual antiparallel dimers, with one protomer facing out and the other facing in.
“The Flucs assemble as unusual antiparallel dimers, where one protomer is inserted into the membrane facing out, and the other is inserted into the membrane facing in81,83.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [81] Stockbridge, R. B., Robertson, J. L., Kolmakova-Partensky, L. & Miller, C. A family of fluoride-specific ion channels with dual-topology architecture. eLife 2, e01084 (2013). source
- cites [83] Stockbridge, R. B. et al. Crystal structures of a double-barrelled fluoride ion channel. Nature 525, 548–551 (2015). source
- Premisecitation
Extreme fluoride challenges can cause complete lysis of the population.
“Extreme fluoride challenges can cause complete lysis of the population68.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [68] Banerjee, A. et al. Fluoride export is required for competitive fitness of pathogenic microorganisms in dental biofilm models. mBio 15, e00184–24 (2024). source
- Premisecitation
Only ~3% of strains surveyed possess both CLCF and Fluc proteins.
“The CLCF and Fluc proteins are usually mutually exclusive in bacterial genomes; only ~3% of strains surveyed possess both.”
Quote in the paperNot a substantial claim - Premisecitation
A survey of bacterial genomes from the Joint Genome Institute's GEBA set of representative prokaryotic genomes shows that >85% of strains in the collection possess a fluoride exporter.
“A survey of bacterial genomes from the Joint Genome Institute’s GEBA set of representative prokaryotic genomes76 shows that >85% of strains in the collection possess a fluoride exporter (Fig. 3).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [76] Mukherjee, S. et al. 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. Nat. Biotechnol. 35, 676–683 (2017). source
- Premisecitation
Extensive riboswitch-based regulation is used by S. cattleya and Methylobacterium DM4, microbes capable of synthesizing and degrading fluorinated compounds, respectively.
“Indeed, extensive riboswitch-based regulation is used by S. cattleya and Methylobacterium DM4, microbes capable of synthesizing and degrading fluorinated compounds, respectively72,90.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [72] Walker, M. C., Wen, M., Weeks, A. M. & Chang, M. C. Y. Temporal and fluoride control of secondary metabolism regulates cellular organofluorine biosynthesis. ACS Chem. Biol. 7, 1576–1585 (2012). source
- cites [90] Blocki, F. A., Logan, M. S. P., Baoli, C. & Wackett, L. P. Reaction of rat-liver glutathione S-transferases and bacterial dichloromethane dehalogenase with dihalomethanes. J. Biol. Chem. 269, 8826–8830 (1994). source
- Premisecitation
Genes associated with adhesion, biofilm formation, cell membrane structure and integrity, and polysaccharide export are upregulated in response to fluoride by diverse bacteria, including P. putida, S. mutans, S. sobrinus, and A. ferrooxidans.
“Genes associated with adhesion, biofilm formation, cell membrane structure and integrity, and polysaccharide export are upregulated in response to fluoride by diverse bacteria, including P. putida, S. mutans, S. sobrinus, and A. ferrooxidans21,96,101.”
Quote in the paperNot a substantial claim0 of 3 sources checked- cites [21] Calero, P., Gurdo, N. & Nikel, P. I. Role of the CrcB transporter of Pseudomonas putida in the multi-level stress response elicited by mineral fluoride. Environ. Microbiol. 24, 5082–5104 (2022). source
- cites [96] Ma, L. Y. et al. Insights into the fluoride-resistant regulation mechanism of Acidithiobacillus ferrooxidans ATCC 23270 based on whole genome microarrays. J. Ind. Microbiol. Biotechnol. 43, 1441–1453 (2016). source
- cites [101] Dame-Teixeira, N., Deng, D. & Do, T. Streptococcus mutans transcriptome in the presence of sodium fluoride and sucrose. Arch. Oral. Biol. 102, 186–192 (2019). source
- Interpretationnone given
Sequestration of fluoride in an insoluble form is a mechanism of fluoride resistance that averts inhibition of metabolic enzymes.
“Another mechanism of fluoride resistance is sequestration of the anion in an insoluble form, to avert its inhibition of metabolic enzymes.”
Quote in the paperNot a substantial claim - Premisecitation
In P. putida, fluoride causes accumulation of metabolites in upper glycolysis and depletion of PEP and other downstream products, including TCA cycle intermediates.
“In P. putida, this is reflected by the accumulation of metabolites in upper glycolysis, and the depletion of PEP and other downstream products, including TCA cycle intermediates21.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [21] Calero, P., Gurdo, N. & Nikel, P. I. Role of the CrcB transporter of Pseudomonas putida in the multi-level stress response elicited by mineral fluoride. Environ. Microbiol. 24, 5082–5104 (2022). source
- Interpretationnone given
Some bacteria exhibit extreme fluoride tolerance, managing growth and metabolism even at high environmental fluoride concentrations.
“In contrast, some bacteria exhibit extreme fluoride tolerance, managing growth and metabolism even at high environmental fluoride concentrations.”
Quote in the paperSubstantial claim - Premisenone given
Reductive defluorination coupled to ATP generation has not been demonstrated.
“The carbon atoms in perfluorinated compounds are highly oxidized already and reductive defluorination coupled to ATP generation has not, to our knowledge, been demonstrated.”
Quote in the paperNot a substantial claim - Premisecitation
CLCFs are >80-fold selective for fluoride over chloride.
“Biochemical experiments have demonstrated that CLCFs are >80-fold selective for fluoride over chloride, the halide that is closest in size and the main biological anion77,78.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [77] Stockbridge, R. B. et al. Fluoride resistance and transport by riboswitch-controlled CLC antiporters. Proc. Natl Acad. Sci. USA 109, 15289–15294 (2012). source
- cites [78] Brammer, A. E., Stockbridge, R. B. & Miller, C. F-/Cl- selectivity in CLCF-type F-/H+ antiporters. J. Gen. Physiol. 144, 129–136 (2014). source
- Premisecitation
In fluoride-resistant S. mutans, pyruvate kinase is heavily mutated.
“In this same fluoride-resistant S. mutans strain, pyruvate kinase, the enzyme that directs PEP towards pyruvate oxidation and the TCA cycle, is heavily mutated91, suggesting that other PEP-consuming biosynthetic pathways, such as aromatic amino acid production, might be favored under fluoride stress.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [91] Liao, Y. et al. Identification and functional analysis of genome mutations in a fluoride-resistant Streptococcus mutans strain. PLoS ONE 10, e0122630 (2015). source
- Premisecitation
A Pseudomonas strain was adapted to metabolize high levels of cytotoxic hydroxycinnamic acids from lignin breakdown.
“In a comparable case, a Pseudomonas strain was adapted to metabolize high levels of cytotoxic hydroxycinnamic acids from lignin breakdown122.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [122] Mohamed, E. T. et al. Adaptive laboratory evolution of Pseudomonas putida KT2440 improves p-coumaric and ferulic acid catabolism and tolerance. Metab. Eng. Commun. 11, e00143 (2020). source
- Premisecitation
Homologs to a newly discovered reductive defluorinating enzyme system were recently identified in metagenomes found on six continents.
“For example, homologs to a newly discovered reductive defluorinating enzyme system were recently identified in metagenomes found on six continents, greatly expanding the range of enzymes of this type to be studied51.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [51] Wackett, L. P. Evolutionary obstacles and not C–F bond strength make PFAS persistent. Microb. Biotechnol. 17, e14463 (2024). source
- Premisecitation
Enzymes that break the C-F bond are more diverse than previously thought.
“Progress along this front is promising: although such enzymes are rare, recent studies show that they are more diverse than previously thought51, and advancements in metagenomic sequencing and protein engineering will support future discovery and optimization of organisms, genes, and pathways that support organofluorine synthesis and degradation.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [51] Wackett, L. P. Evolutionary obstacles and not C–F bond strength make PFAS persistent. Microb. Biotechnol. 17, e14463 (2024). source
- Probably not a substantial claim. 27
- It may state two separate claims as one. 38
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
InterpretationreasoningFluoroacetate production is thought to be an ancient function given the geographic and taxonomic distribution of the fluoroacetate producers.
“Fluoroacetate production is thought to be an ancient function given the geographic and taxonomic distribution of the fluoroacetate producers.”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
PremisecitationFluorinated organic chemicals such as PFAS and fluorinated pesticides are broadly useful and unusually long-lived.
“Fluorinated organic chemicals, such as per- and polyfluorinated alkyl substances (PFAS) and fluorinated pesticides, are both broadly useful and unusually long-lived.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [3] Evich, M. G. et al. Per- and polyfluoroalkyl substances in the environment. Science 375, 512 (2022). This comprehensive current review conveys the scale of PFAS environmental contamination and exposure, and the burden of remediation. source
It may state two separate claims as one.
PremisereasoningHF is membrane permeant but dissociates to H+ and F− at the physiological cytoplasmic pH.
“HF is membrane permeant but dissociates to H+ and F− at the physiological cytoplasmic pH.”
Quote in the paperSubstantial claimProbably not a substantial claim. It may be too vague to check against evidence. The paper’s conclusions may not depend on it. The paper may give no reason why it holds.
Interpretationnone givenBiologically-generated replacement chemicals could be designed to have less toxicity and greater biodegradability.
“Likewise, biologically-generated replacement chemicals could be designed to have less toxicity and greater biodegradability.”
Quote in the paperNot a substantial claim- Rests on an assumption: Biologically-generated replacement chemicals could be designed to have less toxicity and greater biodegradability.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationGlobally, almost the entire human population has detectable blood serum levels of PFAS.
“Globally, almost the entire human population has detectable blood serum levels of PFAS8, in major part due to environmental exposure from water or food sources12.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [8] Fenton, S. E. et al. Per- and polyfluoroalkyl substance toxicity and human health review: current state of knowledge and strategies for informing future research. Environ. Toxicol. Chem. 40, 606–630 (2021). source
Probably not a substantial claim. The paper may give no reason why it holds.
Premisenone givenFluoride cannot passively diffuse across the membrane.
“Because fluoride cannot passively diffuse across the membrane, if this reaction occurs in the cytoplasm, fluoride will accumulate intracellularly.”
Quote in the paperNot a substantial claim- Rests on an assumption: Fluoride cannot passively diffuse across the membrane.
It may state two separate claims as one.
InterpretationcitationFluoroacetate dehalogenases were selected for fluoroacetate detoxification or assimilation of fluoroacetate as a carbon source.
“These fluoroacetate dehalogenases prefer fluorine over other halogen substituents, suggesting that they were selected for fluoroacetate detoxification or assimilation of fluoroacetate as a carbon source30,33.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [30] Goldman, P. The enzymatic cleavage of the carbon-fluorine bond in fluoroacetate. J. Biol. Chem. 240, 3434–3438 (1965). source
- cites [33] Heffernan, B., Murphy, C. D. & Casey, E. Comparison of planktonic and biofilm cultures of Pseudomonas fluorescens DSM 8341 cells grown on fluoroacetate. Appl. Environ. Microbiol 75, 2899–2907 (2009). source
It may state two separate claims as one.
PremisecitationDefluorination of perfluorinated acids has been reported in consortia and by a single bacterium.
“Biological systems that degrade perfluorinated compounds have also been reported recently44,45, including reports of the defluorination of perfluorinated acids in consortia46–48 and by a single bacterium49.”
Quote in the paperNot a substantial claim0 of 4 sources checked- cites [46] Yu, Y. C. et al. Microbial cleavage of C-F bonds in two C6 per- and polyfluorinated compounds via reductive defluorination. Environ. Sci. Technol. 54, 14393–14402 (2020). This study establishes the reductive defluorination of perfluorinated compounds by microbial consortia. source
- cites [47] Jin, B. S. et al. Aerobic biotransformation and defluorination of fluoroalkylether substances (ether PFAS): substrate specificity, pathways, and applications. Environ. Sci. Technol. Lett. 10, 755–761 (2023). source
- cites [48] Wang, N., Buck, R. C., Szostek, B., Sulecki, L. M. & Wolstenholme, B. W. 5:3 Polyfluorinated acid aerobic biotransformation in activated sludge via novel “one-carbon removal pathways”. Chemosphere 87, 527–534 (2012). source
- cites [49] Huang, S. & Jaffe, P. R. Defluorination of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) by Acidimicrobium sp. strain A6. Environ. Sci. Technol. 53, 11410–11419 (2019). source
It may state two separate claims as one.
PremisecitationBiosynthesis of fluoroacetate in E. coli requires not only the biosynthetic genes from S. cattleya, but also chromosomal knockouts of the crcB gene, which encodes a fluoride channel.
“For example, biosynthesis of fluoroacetate in E. coli requires not only the biosynthetic genes from S. cattleya, but also chromosomal knockouts of the crcB gene, which encodes a fluoride channel64.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [64] Markakis, K. et al. An engineered E. coli strain for direct in vivo fluorination. Chembiochem 21, 1856–1860 (2020). source
It may state two separate claims as one.
InterpretationreasoningAlthough perfluorinated organic compounds are an anthropogenic stressor, fluoride resistance mechanisms are ancient and diverse.
“Although perfluorinated organic compounds are an anthropogenic stressor, fluoride resistance mechanisms are ancient and diverse (Fig. 2).”
Quote in the paperSubstantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationOver the last 22 years, more than 50% of newly registered pesticides are organofluorine compounds.
“For example, over the last 22 years, more than 50% of newly registered pesticides are organofluorine compounds6.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [6] Ogawa, Y., Tokunaga, E., Kobayashi, O., Hirai, K. & Shibata, N. Current contributions of organofluorine compounds to the agrochemical industry. Iscience 23, 101467 (2020). source
Probably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationFluorine is more common in the earth's crust than phosphorus, nitrogen, and sulfur.
“Fluorine is more common in the earth’s crust than phosphorus, nitrogen, and sulfur and yet a survey of the elemental composition of several dozen prokaryotes did not identify fluorine amongst the 33 elements found, making it less prevalent than non-biological metals like cadmium, tin, and silver23.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [23] Novoselov, A. A. et al. From cytoplasm to environment: the inorganic ingredients for the origin of life. Astrobiology 13, 294–302 (2013). source
Probably not a substantial claim. The paper’s conclusions may not depend on it.
InterpretationreasoningA plausible degradative pathway for perfluorocarboxylic acids would use consecutive paired reactions of α,α-defluorination and decarboxylation, releasing fluoride ions at each step and culminating in trifluoroacetic acid.
“Since α-keto acid decarboxylases are known, a plausible degradative pathway for perfluorocarboxylic acids would use consecutive paired reactions of α,α-defluorination and decarboxylation, releasing fluoride ions at each step and culminating in trifluoroacetic acid, an end product that is highly recalcitrant to further degradation.”
Quote in the paperNot a substantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationFluorine in the earth's crust is largely found as fluoride bound in mineral form, for example fluorite, fluorapatite, topaz, cryolite, sellaite, and villiaumite.
“Fluorine in the earth’s crust is largely found as fluoride bound in mineral form, for example: fluorite, fluorapatite, topaz, cryolite, sellaite, and villiaumite74.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [74] Fuge, R. Fluorine in the environment, a review of its sources and geochemistry. Appl. Geochem. 100, 393–406 (2019). source
Probably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationFluoroacetate becomes highly toxic to central metabolism after metabolic conversion to fluorocitrate.
“Plants of several varieties in Australia, Africa, and South America produce fluoroacetate to deter feeding by animals, since the compound becomes highly toxic to central metabolism after metabolic conversion to fluorocitrate24,25.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [24] Walsh, C. Fluorinated substrate analogs: routes of metabolism and selective toxicity. Adv. Enzymol. Relat. Areas Mol. Biol. 55, 197–289 (1983).
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
- cites [25] Marais, J. S. C. The isolation of the toxic principle “potassium cymonate” from “Gifblaar” Dichapetalum cymosum. Onderstepoort J. Vet. Sci. Anim. Ind. 18, 203–206 (1943).
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationPFAS blood serum levels are in major part due to environmental exposure from water or food sources.
“Globally, almost the entire human population has detectable blood serum levels of PFAS8, in major part due to environmental exposure from water or food sources12.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [12] Sunderland, E. M. et al. A review of the pathways of human exposure to poly- and perfluoroalkyl substances (PFASs) and present understanding of health effects. J. Expo. Sci. Environ. Epidemiol. 29, 131–147 (2019). source
Probably not a substantial claim. The paper may give no reason why it holds.
Premisenone givenBiological syntheses use NaF.
“In particular, organofluorine degradation yields fluoride ions, and biological syntheses use NaF.”
Quote in the paperNot a substantial claimProbably not a substantial claim. It may be too vague to check against evidence.
InterpretationreasoningApplying fundamental physiological considerations to bioengineer solutions to PFAS and organofluorine persistence can help circumvent some common roadblocks.
“We argue that applying fundamental physiological considerations to bioengineer solutions to PFAS and organofluorine persistence can help circumvent some of the common roadblocks that have emerged in these fields of study.”
Quote in the paperNot a substantial claimProbably not a substantial claim. The paper may give no reason why it holds.
Interpretationnone givenBioremediation would be cheaper and more effective than physico-chemical remediation in some circumstances if suitable biological systems can be identified or engineered.
“Bioremediation would be cheaper and more effective than physico-chemical remediation in some circumstances if suitable biological systems can be identified or engineered.”
Quote in the paperNot a substantial claim- Rests on an assumption: Bioremediation would be cheaper and more effective than physico-chemical remediation in some circumstances if suitable biological systems can be identified or engineered.
It may state two separate claims as one.
PremisecitationEnolase is often observed in operons controlled by fluoride riboswitches, and in fluoride-resistant E. cloacae FRM, enolase transcripts are upregulated 176-fold in response to fluoride.
“Enolase is often observed in operons controlled by fluoride riboswitches67, and in fluoride-resistant E. cloacae FRM, enolase transcripts are upregulated 176-fold in response to fluoride95.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [67] Baker, J. L. et al. Widespread genetic switches and toxicity resistance proteins for fluoride. Science 335, 233–235 (2012). This is the first study to establish a molecular basis for the fluoride stress response. source
- cites [95] Liu, X. et al. Identification of an operon involved in fluoride resistance in Enterobacter cloacae FRM. Sci. Rep. 7, 6786 (2017). source
It may state two separate claims as one.
PremisecitationNo systematic investigation of fluoride acclimation in bacteria has been conducted, but fluoride acclimation over multiple generations yielded S. cerevisiae strains with ~700-fold better fluoride resistance, independent of fluoride exporter expression.
“We are not aware of any systematic investigation of fluoride acclimation in bacteria, but the example of S. cerevisiae is encouraging, as fluoride acclimation over multiple generations yielded strains with ~700-fold better fluoride resistance, independent of fluoride exporter expression88.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [88] Strobel, S. A., Johnston, N. R. & Cline, G. Cells adapt to resist fluoride through metabolic deactivation and intracellular acidification. Chem. Res. Toxicol. 35, 2085–2096 (2022). By acclimating yeast to high fluoride over several generations, this study uncovered several novel fluoride stress mitigation mechanisms in microbes. source
Probably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationFormate hydrogen lyase is another of the most common fluoride riboswitch-associated enzymes.
“Formate hydrogen lyase, which oxidizes formic acid to produce ATP during anaerobic sugar fermentation, is another of the most common fluoride riboswitch-associated enzymes67.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [67] Baker, J. L. et al. Widespread genetic switches and toxicity resistance proteins for fluoride. Science 335, 233–235 (2012). This is the first study to establish a molecular basis for the fluoride stress response. source
It may state two separate claims as one.
PremisecitationFluoride stress causes changes to cell morphology, including cell shortening or lack of separation following septation, and increased extracellular carbohydrate content.
“Similarly, changes to cell morphology, including cell shortening or lack of separation following septation, and increased extracellular carbohydrate content, are also caused by fluoride stress63,107,108.”
Quote in the paperNot a substantial claim0 of 3 sources checked- cites [63] Dodge, A. G., Thoma, C. J., O’Connor, M. R. & Wackett, L. P. Recombinant Pseudomonas growing on non-natural fluorinated substrates shows stress but overall tolerance to cytoplasmically released fluoride anion. mBio 15, e0278523 (2023). This article directly demonstrates fluoride toxicity due to intracellular enzymatic defluorination, with multiple signs of cellular stress. source
- cites [107] Evans, K., Stone, V., Chen, L., Ge, X. C. & Xu, P. Systematic study of genes influencing cellular chain length in Streptococcus sanguinis. Microbiology 160, 307–315 (2014). source
- cites [108] Mukherjee, S., Sahu, P. & Halder, G. Microbial remediation of fluoride-contaminated water via a novel bacterium Providencia vermicola (KX926492). J. Environ. Manag. 204, 413–423 (2017). source
Probably not a substantial claim. The paper may give no reason why it holds. It may state two separate claims as one.
InterpretationreasoningFluoride tolerance is required for the synthesis of organofluorine chemicals, since fluoride ions must be supplied to bacteria for fluorination reactions.
“Likewise, fluoride tolerance is required for the synthesis of organofluorine chemicals, since fluoride ions must be supplied to bacteria for fluorination reactions.”
Quote in the paperNot a substantial claimProbably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
PremisecitationFluc proteins can be encoded by single genes forming antiparallel homodimers, or by paired genes forming heterodimers of obligate inward- and outward-facing subunits.
“Fluc proteins can be encoded by single genes, in which case a single protomer is inserted into the membrane in both inward and outward-facing conformations, assembling as an antiparallel homodimer, or they can be encoded by paired genes that express to form heterodimers of obligate inward- and outward-facing subunits84.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [84] Macdonald, C. B. & Stockbridge, R. B. A topologically diverse family of fluoride channels. Curr. Opin. Struct. Biol. 45, 142–149 (2017). source
It may state two separate claims as one.
PremisecitationThe gene encoding pyrophosphatase is among the genes most frequently associated with fluoride riboswitches, and in various organisms, expression of pyrophosphatase, polyphosphatase, and phosphate importers has been functionally linked to fluoride resistance.
“The gene encoding pyrophosphatase is among the genes most frequently associated with fluoride riboswitches67, and in various organisms, including Enterobacter cloacae FRM95, Acidithiophilus ferredoxins96, and S. cerevisiae97, the expression of pyrophosphatase, polyphosphatase, and phosphate importers has been functionally linked to fluoride resistance.”
Quote in the paperNot a substantial claim0 of 3 sources checked- cites [67] Baker, J. L. et al. Widespread genetic switches and toxicity resistance proteins for fluoride. Science 335, 233–235 (2012). This is the first study to establish a molecular basis for the fluoride stress response. source
- cites [95] Liu, X. et al. Identification of an operon involved in fluoride resistance in Enterobacter cloacae FRM. Sci. Rep. 7, 6786 (2017). source
- cites [96] Ma, L. Y. et al. Insights into the fluoride-resistant regulation mechanism of Acidithiobacillus ferrooxidans ATCC 23270 based on whole genome microarrays. J. Ind. Microbiol. Biotechnol. 43, 1441–1453 (2016). source
Probably not a substantial claim. The paper may give no reason why it holds.
InterpretationreasoningAlthough this review focuses on bacteria, fluoride stress responses are ancient and conserved, at least in part, among microorganisms.
“Although this review focuses on bacteria, fluoride stress responses are ancient and conserved, at least in part, among microorganisms.”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
PremisecitationAfter fluoride exporters, the next-most common class of riboswitch-associated genes is Na+/H+ antiporters, which contribute to pH homeostasis in bacteria.
“Indeed, after fluoride exporters, the next-most common class of riboswitch-associated genes is Na+/H+ antiporters67, which contribute to pH homeostasis in bacteria94.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [67] Baker, J. L. et al. Widespread genetic switches and toxicity resistance proteins for fluoride. Science 335, 233–235 (2012). This is the first study to establish a molecular basis for the fluoride stress response. source
- cites [94] Zilberstein, D., Agmon, V., Schuldiner, S. & Padan, E. The sodium proton antiporter is part of the pH homeostasis mechanism in Escherichia coli. J. Biol. Chem. 257, 3687–3691 (1982). source
It may state two separate claims as one.
InterpretationreasoningMaintaining pH homeostasis is important for fluoride resistance in microorganisms, and acid stress-response pathways are commonly upregulated in response to fluoride.
“As a result, maintaining pH homeostasis is important for fluoride resistance in microorganisms, and acid stress-response pathways are commonly upregulated in response to fluoride88,93.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [88] Strobel, S. A., Johnston, N. R. & Cline, G. Cells adapt to resist fluoride through metabolic deactivation and intracellular acidification. Chem. Res. Toxicol. 35, 2085–2096 (2022). By acclimating yeast to high fluoride over several generations, this study uncovered several novel fluoride stress mitigation mechanisms in microbes. source
- cites [93] Johnston, N. R., Nallur, S., Gordon, P. B., Smith, K. D. & Strobel, S. A. Genome-wide identification of genes involved in general acid stress and fluoride toxicity in Saccharomyces cerevisiae. Front. Microbiol. 11, 1410 (2020). source
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
PremisecitationTypically, genes for heterodimeric Flucs are adjacent in genomes, and both genes are required for fluoride efflux activity.
“Typically, the genes for the heterodimeric Flucs are adjacent to each other in genomes, and both genes are required for fluoride efflux activity84.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [84] Macdonald, C. B. & Stockbridge, R. B. A topologically diverse family of fluoride channels. Curr. Opin. Struct. Biol. 45, 142–149 (2017). source
It may state two separate claims as one.
InterpretationreasoningFluoride export is dependent on the proton-motive force, either as an explicit chemical driving force for CLCFs or as a component of the electrical gradient for Flucs.
“In addition, fluoride export is dependent on the proton-motive force – either as an explicit chemical driving force for the CLCFs, or as a component of the electrical gradient, as for the Flucs.”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
PremisecitationFluoride-acclimated S. cerevisiae exhibited increased clumping and mutations to genes associated with flocculation, pseudohyphal growth, cell surface properties, and adhesion.
“Fluoride-acclimated S. cerevisiae exhibited increased clumping and mutations to genes associated with flocculation, pseudohyphal growth, cell surface properties, and adhesion88.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [88] Strobel, S. A., Johnston, N. R. & Cline, G. Cells adapt to resist fluoride through metabolic deactivation and intracellular acidification. Chem. Res. Toxicol. 35, 2085–2096 (2022). By acclimating yeast to high fluoride over several generations, this study uncovered several novel fluoride stress mitigation mechanisms in microbes. source
It may state two separate claims as one.
InterpretationreasoningSequestration can be used as a fluoride mitigation strategy by biology and could be stimulated by divalent metal and phosphate uptake.
“Thus, sequestration can be used as a fluoride mitigation strategy by biology, and, in principle, could be stimulated by the divalent metal and phosphate uptake described above.”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
PremisecitationFEX proteins are structurally related to Flucs but possess a more complex two-domain fold.
“FEX proteins are related structurally to the Flucs but possess a more complex two-domain fold83,87.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [83] Stockbridge, R. B. et al. Crystal structures of a double-barrelled fluoride ion channel. Nature 525, 548–551 (2015). source
- cites [87] Smith, K. D. et al. Yeast Fex1p is a constitutively expressed fluoride channel with functional asymmetry of its two homologous domains. J. Biol. Chem. 290, 19874–19887 (2015). source
It may state two separate claims as one.
PremisecitationIn yeast, fluoride resistance is imparted by the export of compounds like nitrates that contribute to oxidative stress, and the import of antioxidant metabolites like sulfite.
“In yeast, fluoride resistance is imparted by the export of compounds like nitrates that contribute to oxidative stress, and the import of antioxidant metabolites like sulfite97.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [97] Johnston, N. R. & Strobel, S. A. Nitrate and phosphate transporters rescue fluoride toxicity in yeast. Chem. Res. Toxicol. 32, 2305–2319 (2019). source
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. It may state two separate claims as one.
Interpretationnone givenOne natural mechanism of fluoride resistance is metabolic deactivation, which may be at odds with the end goal of improving fluoride resistance in order to metabolize fluorinated substrates.
“However, it should be noted that one natural mechanism of fluoride resistance is metabolic deactivation, which may be at odds with the end goal of improving fluoride resistance in order to metabolize fluorinated substrates.”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
PremisecitationAmong oral streptococci, fluoride inhibits lectins that shape biofilm architecture and increases turnover of cell wall peptidoglycans, contributing to cellular lysis.
“Among the oral streptococci, fluoride has been shown to inhibit lectins that shape biofilm architecture105, and increase turnover of cell wall peptidoglycans, contributing to cellular lysis106.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [105] Cox, S. D., Lassiter, M. O., Taylor, K. G. & Doyle, R. J. Fluoride inhibits the glucan-binding lectin of Streptococcus sobrinus. FEMS Microbiol. Lett. 123, 331–334 (1994). source
- cites [106] Lesher, R. J., Bender, G. R. & Marquis, R. E. Bacteriolytic action of fluoride ions. Antimicrob. Agents Chemother. 12, 339–345 (1977). source
It may state two separate claims as one.
PremisecitationFluoride-adapted S. cerevisiae exhibit metabolic shifts to anaerobic fermentation pathways and are depleted in TCA cycle intermediates.
“Fluoride-adapted S. cerevisiae also exhibit metabolic shifts to anaerobic fermentation pathways, and like P. putida, are depleted in TCA cycle intermediates88.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [88] Strobel, S. A., Johnston, N. R. & Cline, G. Cells adapt to resist fluoride through metabolic deactivation and intracellular acidification. Chem. Res. Toxicol. 35, 2085–2096 (2022). By acclimating yeast to high fluoride over several generations, this study uncovered several novel fluoride stress mitigation mechanisms in microbes. source
Probably not a substantial claim. The paper’s conclusions may not depend on it. It may state two separate claims as one.
PremisecitationFlucs are the most selective ion channel yet described, and no role besides fluoride export has been ascribed to any protein in this family.
“The Flucs are the most selective ion channel yet described, and no role besides fluoride export has been ascribed to any protein in this family65.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [65] McIlwain, B. C., Ruprecht, M. T. & Stockbridge, R. B. Membrane exporters of fluoride ion. Annu. Rev. Biochem. 90, 559–579 (2021). This work reviews biochemical mechanisms of fluoride toxicity, along with the structures and mechanisms of microbial fluoride exporters that maintain cytoplasmic fluoride at sub-inhibitory concentrations. source
Probably not a substantial claim. The paper’s conclusions may not depend on it.
Premiseown dataThe CLCF and Fluc proteins are usually mutually exclusive in bacterial genomes.
“The CLCF and Fluc proteins are usually mutually exclusive in bacterial genomes; only ~3% of strains surveyed possess both.”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
PremisecitationE. coli appears to shut down metabolism entirely under fluoride, only resuming growth once the fluoride insult is removed.
“Other bacteria, like E. coli, appear to shut down metabolism entirely, only resuming growth once the fluoride insult is removed71.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [71] Ji, C., Stockbridge, R. B. & Miller, C. Bacterial fluoride resistance, Fluc channels, and the weak acid accumulation effect. J. Gen. Physiol. 144, 257–261 (2014). This study quantitatively showed the interplay between pH, intracellular fluoride, and fitness in bacterial populations. source
Probably not a substantial claim. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. It may state two separate claims as one.
Interpretationnone givenFluoride chelation impacts ion homeostasis, especially for divalent cations, and these perturbations can contribute to oxidative stress.
“Fluoride chelation impacts ion homeostasis, especially for divalent cations, and these perturbations can contribute to oxidative stress.”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
PremisecitationThe most common proteins found in operons with fluoride riboswitches are fluoride exporters, although only ~15% of Flucs and ~30% of CLCFs are regulated by riboswitches.
“The most common proteins found in operons with these riboswitches are the fluoride exporters67, although only ~15% of Flucs and ~30% of CLCFs are regulated by riboswitches.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [67] Baker, J. L. et al. Widespread genetic switches and toxicity resistance proteins for fluoride. Science 335, 233–235 (2012). This is the first study to establish a molecular basis for the fluoride stress response. source
It may state two separate claims as one.
InterpretationreasoningAlthough fluoride exporters contribute most to fluoride resistance, different organisms exhibit substantial variability in tolerated fluoride concentrations, suggesting additional physiological determinants of fluoride resistance.
“Although the fluoride exporters contribute most to fluoride resistance, different organisms still exhibit substantial variability in the fluoride concentrations that they tolerate (Table 1), suggesting that there are additional physiological determinants of fluoride resistance.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Table 1
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
It may state two separate claims as one.
PremisecitationA fluoride-resistant strain of S. mutans exhibits constitutive expression of CLCF genes, and a single nucleotide polymorphism in the intergenic region 5′ to the operon was linked to this mechanism.
“A fluoride-resistant strain of S. mutans exhibits a constitutive expression of the CLCF genes, and a single nucleotide polymorphism in the intergenic region 5′ to the operon was linked to this mechanism91.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [91] Liao, Y. et al. Identification and functional analysis of genome mutations in a fluoride-resistant Streptococcus mutans strain. PLoS ONE 10, e0122630 (2015). source
It may state two separate claims as one.
PremisecitationThe best-studied regulatory element is the fluoride riboswitch, which binds fluoride as a fluoride-magnesium complex and upregulates transcription of downstream genes.
“The best-studied regulatory element is the fluoride riboswitch, which binds fluoride as a fluoride-magnesium complex and upregulates the transcription of downstream genes67,89.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [67] Baker, J. L. et al. Widespread genetic switches and toxicity resistance proteins for fluoride. Science 335, 233–235 (2012). This is the first study to establish a molecular basis for the fluoride stress response. source
- cites [89] Ren, A., Rajashankar, K. R. & Patel, D. J. Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch. Nature 486, 85–89 (2012). source
It may state two separate claims as one.
PremisecitationSome plants accumulate fluoride as insoluble calcium or magnesium complexes in the vacuole, and fluoride-acclimated yeast exhibited far lower soluble calcium compared to total calcium, suggesting calcium's presence in an insoluble form.
“For example, some plants accumulate fluoride as insoluble calcium or magnesium complexes in the vacuole121, and fluoride-acclimated yeast exhibited far lower soluble calcium compared to total calcium, suggesting calcium’s presence in an insoluble form88.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [121] Baunthiyal, M. & Ranghar, S. Accumulation of fluoride by plants: potential for phytoremediation. Clean.-Soil Air Water 43, 127–132 (2015). source
- cites [88] Strobel, S. A., Johnston, N. R. & Cline, G. Cells adapt to resist fluoride through metabolic deactivation and intracellular acidification. Chem. Res. Toxicol. 35, 2085–2096 (2022). By acclimating yeast to high fluoride over several generations, this study uncovered several novel fluoride stress mitigation mechanisms in microbes. source
It may state two separate claims as one.
PremisecitationMembrane permeation of the weak acid HF is the major route to fluoride accumulation in the cytosol, and fluoride exposure is correlated with cytoplasmic acidification.
“Since membrane permeation of the weak acid HF is the major route to fluoride accumulation in the cytosol92, fluoride exposure is correlated with cytoplasmic acidification21.”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [92] Marquis, R. E., Clock, S. A. & Mota-Meira, M. Fluoride and organic weak acids as modulators of microbial physiology. FEMS Microbiol. Rev. 26, 493–510 (2003). source
- cites [21] Calero, P., Gurdo, N. & Nikel, P. I. Role of the CrcB transporter of Pseudomonas putida in the multi-level stress response elicited by mineral fluoride. Environ. Microbiol. 24, 5082–5104 (2022). source
It may state two separate claims as one.
PremisecitationFlucs have a rapid rate of F− efflux (10^6 ions/s) and extremely high selectivity for fluoride over other anions, exceeding 10,000-fold.
“The Flucs are notable for their rapid rate of F− efflux (106 ions/s) and extremely high selectivity for fluoride over other anions, which exceeds 10,000-fold81,82.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [81] Stockbridge, R. B., Robertson, J. L., Kolmakova-Partensky, L. & Miller, C. A family of fluoride-specific ion channels with dual-topology architecture. eLife 2, e01084 (2013). source
- cites [82] McIlwain, B. C., Gundepudi, R., Koff, B. B. & Stockbridge, R. B. The fluoride permeation pathway and anion recognition in Fluc family fluoride channels. eLife 10, e69482 (2021). source
It may state two separate claims as one.
PremisecitationThe gene encoding chorismate mutase is one of the most common genes in fluoride exporter gene neighborhoods, and its expression is upregulated in fluoride-resistant S. mutans together with the fluoride exporters in the same operon.
“The gene encoding chorismate mutase, a key enzyme in the biosynthesis of aromatic amino acids, is one of the most common genes in fluoride exporter gene neighborhoods67, and its expression is upregulated in fluoride-resistant S. mutans together with the fluoride exporters in the same operon91.”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [67] Baker, J. L. et al. Widespread genetic switches and toxicity resistance proteins for fluoride. Science 335, 233–235 (2012). This is the first study to establish a molecular basis for the fluoride stress response. source
- cites [91] Liao, Y. et al. Identification and functional analysis of genome mutations in a fluoride-resistant Streptococcus mutans strain. PLoS ONE 10, e0122630 (2015). source
Probably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationA SAM regenerating system has been developed for the purpose of supporting in vitro cobalamin biosynthesis.
“A SAM regenerating system has been developed for the purpose of supporting in vitro cobalamin biosynthesis and this could be useful in fluorinase biochemistry, too131.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [131] Xiao, K. X. et al. Optimization of hydrogenobyrinic acid synthesis in a cell-free multienzyme reaction by novel S-adenosyl-methionine regeneration. ACS Synth. Biol. 12, 1339–1348 (2023). source
It may state two separate claims as one.
Premiseown dataFluc channels are more widely distributed among diverse bacteria than CLCF transporters, and Flucs are found more commonly in strains that resist high fluoride or that use fluoride for synthesis.
“Fluc channels are more widely distributed among diverse bacteria than CLCF transporters (Fig. 3), and Flucs are found more commonly in strains that resist high fluoride or that use fluoride for synthesis.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Fig. 3
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
PremisecitationA variety of fluoride-binding materials have been developed for treating potable waters that naturally contain high levels of fluoride.
“A variety of fluoride-binding materials have been developed for treating potable waters that naturally contain high levels of fluoride128.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [128] Tolkou, A. K., Manousi, N., Zachariadis, G. A., Katsoyiannis, I. A. & Deliyanni, E. A. Recently developed adsorbing materials for fluoride removal from water and fluoride analytical determination techniques: a review. Sustainability 13, 7061 (2021). source
It may state two separate claims as one.
InterpretationreasoningThe F−/H+ antiport mechanism couples fluoride export to the proton gradient, sustaining a lower intracellular fluoride concentration at equilibrium, whereas fluoride channels have the advantage of more rapid fluoride removal that does not depend on a proton gradient.
“The F−/H+ antiport mechanism couples fluoride export to the proton gradient, sustaining a lower intracellular fluoride concentration at equilibrium, whereas fluoride channels have the advantage of more rapid fluoride removal that does not depend on a proton gradient.”
Quote in the paperSubstantial claimProbably not a substantial claim. It may be too vague to check against evidence.
InterpretationreasoningDefluorination chemistry is only a part of the challenge in this field.
“Furthermore, we argue here that defluorination chemistry is only a part of the challenge in this field.”
Quote in the paperNot a substantial claimProbably not a substantial claim. It may be too vague to check against evidence.
InterpretationreasoningAcquiring a deep understanding of fundamental microbial physiologies, in particular fluoride stress responses, can help better harness ancient fluoride resistance mechanisms to address organofluorine biodegradation or biosynthesis.
“By acquiring a deep understanding of the fundamental microbial physiologies — in particular the fluoride stress responses — that support biodegradation or biosynthesis of organofluorine molecules, we can better harness ancient fluoride resistance mechanisms to address this very contemporary biochemical problem.”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
PremisecitationPseudomonas sp. HXF1 calcium carbonate precipitate can sequester fluoride in the form of CaF2 and Ca5(PO4)3F and diminish fluoride in groundwater.
“One recent study showed that calcium carbonate precipitate generated by Pseudomonas sp. HXF1 could sequester fluoride in the form of CaF2 and Ca5(PO4)3F and diminish fluoride in groundwater127.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [127] Wang, Z., Su, J. F., Hu, X. F., Ali, A. & Wu, Z. Z. Isolation of biosynthetic crystals by microbially induced calcium carbonate precipitation and their utilization for fluoride removal from groundwater. J. Hazard. Mater. 406, 124748 (2021). source
Probably not a substantial claim. The paper may give no reason why it holds.
Premisenone givenThere is a measurable background rate of non-enzymatic fluorophosphate hydrolysis.
“However, there is a measurable background rate of non-enzymatic fluorophosphate hydrolysis and so more stable, but inexpensive, fluoride salts like BF4− could be efficacious in this regard.”
Quote in the paperNot a substantial claimIt may state two separate claims as one.
PremisecitationSynthetic proteins that inhibit fluoride channels have been developed but have not been tested in biological systems, and no such natural regulatory mechanism has been identified.
“Although synthetic proteins that inhibit fluoride channels have been developed123–125, they have not been tested in biological systems, and no such natural regulatory mechanism has been identified.”
Quote in the paperNot a substantial claim0 of 3 sources checked- cites [123] Stockbridge, R. B., Koide, A., Miller, C. & Koide, S. Proof of dual-topology architecture of Fluc F- channels with monobody blockers. Nat. Commun. 5, 5120 (2014). source
- cites [124] Turman, D. L. & Stockbridge, R. B. Mechanism of single- and double-sided inhibition of dual topology fluoride channels by synthetic monobodies. J. Gen. Physiol. 149, 511–522 (2017). source
- cites [125] McIlwain, B. C., Newstead, S. & Stockbridge, R. B. Cork-in-bottle occlusion of fluoride ion channels by crystallization chaperones. Structure 26, 635–639 e1 (2018). source
The paper relies on this without support.
Microbial processes are more easily applied in scenarios with dilute PFAS that preclude technologies relying on PFAS capture and concentration.
“since microbial processes are more easily applied in scenarios with dilute PFAS that preclude technologies that rely on PFAS capture and concentration.”
The paper relies on this without support.
Bioremediation would be cheaper and more effective than physico-chemical remediation in some circumstances if suitable biological systems can be identified or engineered.
“Bioremediation would be cheaper and more effective than physico-chemical remediation in some circumstances if suitable biological systems can be identified or engineered.”
The paper relies on this without support.
Biologically-generated replacement chemicals could be designed to have less toxicity and greater biodegradability.
“Likewise, biologically-generated replacement chemicals could be designed to have less toxicity and greater biodegradability.”
The paper relies on this without support.
PFAS utilization will continue for the foreseeable future.
“PFAS utilization will continue for the foreseeable future.”
The paper relies on this without support.
Fluoride cannot passively diffuse across the membrane.
“Because fluoride cannot passively diffuse across the membrane, if this reaction occurs in the cytoplasm, fluoride will accumulate intracellularly.”
The paper relies on this without support.
C–F bond cleavage by any mechanism releases fluorine as a fluoride anion.
“Some commercial PFAS molecules contain 15 or more fluorines, and due to this atom’s electronegativity, C–F bond cleavage by any mechanism releases fluorine as a fluoride anion.”
The paper relies on this without support.
The medium pH acidifies in dense bacterial cultures.
“especially as the medium pH acidifies, which is typical with dense bacterial cultures.”
The paper relies on this without support.
There are thousands of enzymes per cell.
“We have measured enzymatic C–F bond cleavage in one instance to be as fast as 10 bonds cleaved per second per enzyme (and there are thousands of enzymes per cell).”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
CrcB functions as a passive ion channel and is considered a primary defense against fluoride toxicity in many bacteria, including Escherichia coli, Bacillus subtilis, and Pseudomonas species.
“CrcB functions as a passive ion channel and is considered a primary defense mechanism against fluoride toxicity in many bacteria, including Escherichia coli, Bacillus subtilis, and Pseudomonas species (5–7).”
From Adaptive evolution of Pseudomonas putida in the presence of fluoride exposes novel functions of a benzoate transporter (2026) · cites this paper as [5]
There are two distinct classes of fluoride export proteins: ClCF and CrcB (Fluc) channels.
“There are two distinct classes of fluoride export proteins: ClCF and CrcB (Fluc) channels (5, 6, 22).”
From Adaptive evolution of Pseudomonas putida in the presence of fluoride exposes novel functions of a benzoate transporter (2026) · cites this paper as [5]
At sublethal concentrations, fluoride disrupts microbial metabolic processes by inhibiting key enzymes such as enolase and pyrophosphatases, often by forming complexes with essential metal cofactors.
“At sublethal concentrations, fluoride disrupts metabolic processes by inhibiting key enzymes, such as enolase and pyrophosphatases, often by forming complexes with essential metal cofactors (4, 5).”
From Adaptive evolution of Pseudomonas putida in the presence of fluoride exposes novel functions of a benzoate transporter (2026) · cites this paper as [5]
CrcB export proteins function as passive fluoride-specific ion channels that require Na+ ions for transport activity.
“In contrast, CrcB export proteins function as passive fluoride-specific ion channels that require Na+ ions for transport activity (4, 5, 23–26).”
From Adaptive evolution of Pseudomonas putida in the presence of fluoride exposes novel functions of a benzoate transporter (2026) · cites this paper as [5]
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Metadata
- Authors
- Stockbridge, R. B., & Wackett, L. P.
- Affiliations
- University of Michigan (US)
- University of Minnesota (US)
- Corresponding author
- Stockbridge, Randy B.
- Wackett, Lawrence P.
- Venue
- Nature Communications
- Published
- 2024-05-30
- Volume
- 15
- Issue
- 1
- Pages
- 4593-4593
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC11139923
- OpenAlex
- W4399181105
- Semantic Scholar
- 201950658930be11daff73885148ad8e6cfeb3e1
- Cited by
- 80
- References
- 131
- Citations by year
- 2026: 42 · 2025: 30 · 2024: 8
- FWCI
- 2.34
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- U.S. Department of Health & Human Services | National Institutes of Health (R35 GM128768)
- MnDRIVE Industry and the Environment Program
- Topics
- Physical Sciences › Environmental Science › Environmental Chemistry › Per- and polyfluoroalkyl substances research
- Physical Sciences › Chemistry › Organic Chemistry › Fluorine in Organic Chemistry
- Physical Sciences › Environmental Science › Water Science and Technology › Fluoride Effects and Removal
- Keywords
- fluoride resistance, per- and polyfluoroalkyl substances, fluorinated pesticides, bioengineering
- MeSH terms
- Bacteria, Biodegradation, Environmental, Fluorides, Hydrocarbons, Fluorinated, Halogenation, Bioengineering
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