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

Molecular Insights into Fluoride Ion Uptake and Selectivity in the CLCF Fluoride/Proton Antiporter

In this study, we investigated the effect of the protonation state of glutamate E118 (Gluex) and glutamate E318 (Gluin) on fluoride ion uptake and selectivity in the CLCF F-/H+ antiporter using molecular dynamics simulations. Analyses of pore size and the potential of mean force (PMF) revealed that fluoride uptake is facilitated under the deprotonated E118 and protonated E318 state, consistent with the fluoride uptake state proposed in the original windmill mechanism. In this state, an increased pore size reduces the energy barrier, promoting fluoride transport from the intracellular solution to the intracellular binding site (Scen). Interestingly, we also observed a helix-to-coil transition (residues 74-87) in the presence of chloride at Scen, which enhances chloride dehydration and stabilizes its interaction with the coil structure. This conformational change likely impedes chloride transport, contributing to fluoride ion selectivity. Our findings confirm that fluoride ion selectivity is enhanced in the E118_E318p state, reinforcing its role in the original windmill mechanism. Additionally, we propose that refining the fluoride uptake process in the modified windmill mechanism could lead to a comparable selectivity mechanism, ultimately converging on a unified fluoride-selective uptake mechanism that integrates key aspects of both pathways.

Molecules Targeting EriCF1 Increase Streptococcus mutans Fluoride Sensitivity

Dental caries, as one of the prevalent oral infectious diseases worldwide, constitutes a considerable disease burden. Fluoride has been widely used to prevent dental caries for decades. However, fluoride alone may not always be sufficient. The major cariogenic bacterial species, Streptococcus mutans, has not been effectively controlled by daily fluoride exposure, possibly because it has a detoxification mechanism. Studies have shown that most microorganisms have fluoride exporters dedicated to exporting fluoride ions (F-). S. mutans possesses 2 homologous genes, eriCF1 and eriCF2, which encode fluoride exporters, but their function has not been fully clarified. In this work, we constructed the markerless gene deletion mutants, overexpression, and complemented strains of S. mutans UA159. Assessing fluoride sensitivity, intracellular F- levels, and cell membrane permeability revealed that EriCF1 was the major functional unit of the fluoride exporter in S. mutans. To further enhance the antibacterial efficiency of fluoride, we identified 3 diphenylurea derivatives that might target EriCF1 by molecular docking, which significantly enhanced the antibacterial effect of sodium fluoride (NaF) by synergistically impeding fluoride efflux, as demonstrated by chequerboard broth microdilution assays. Moreover, these compounds combined with 1 mM NaF impaired the cariogenicity of S. mutans significantly in vivo and with good biocompatibility, especially compounds 9 and 15. Collectively, these findings suggest that fluoride exporters in S. mutans could serve as a potential target for caries prevention, and the diphenylurea derivatives identified for targeting EriCF1 could be a valuable therapeutic approach when combined with fluoride, providing promising measures for dental caries prevention.

Enhancing Pseudomonas cell growth for the production of medium-chain-length polyhydroxyalkanoates from Antarctic krill shell waste

Antarctic krill shell waste (AKSW), a byproduct of Antarctic krill processing, has substantial quantity but low utilization. Utilizing microbial-based cell factories, with Pseudomonas putida as a promising candidate, offers an ecofriendly and sustainable approach to producing valuable bioproducts from renewable sources. However, the high fluoride content in AKSW impedes the cell growth of P. putida. This study aims to investigate the transcriptional response of P. putida to fluoride stress from AKSW and subsequently conduct genetic modification of the strain based on insights gained from transcriptomic analysis. Notably, the engineered strain KT+16840+03100 exhibited a remarkable 33.7-fold increase in cell growth, capable of fermenting AKSW for medium-chain-length-polyhydroxyalkanoates (mcl-PHA) biosynthesis, achieving a 40.3-fold increase in mcl-PHA yield compared to the control strain. This research advances our understanding of how P. putida responds to fluoride stress from AKSW and provides engineered strains that serve as excellent platforms for producing mcl-PHA through AKSW.

Fluoride Ion Binding and Translocation in the CLCF Fluoride/Proton Antiporter: Molecular Insights from Combined Quantum-Mechanical/Molecular-Mechanical Modeling

CLCF fluoride/proton antiporters move fluoride ions out of bacterial cells, leading to fluoride resistance in these bacteria. However, many details about their operating mechanisms remain unclear. Here, we report a combined quantum-mechanical/molecular-mechanical (QM/MM) study of a CLCF homologue from Enterococci casseliflavus (Eca), in accord with the previously proposed windmill mechanism. Our multiscale modeling sheds light on two critical steps in the transport cycle: (i) the external gating residue E118 pushing a fluoride in the external binding site into the extracellular vestibule and (ii) an incoming fluoride reconquering the external binding site by forcing out E118. Both steps feature competitions for the external binding site between the negatively charged carboxylate of E118 and the fluoride. Remarkably, the displaced E118 by fluoride accepts a proton from the nearby R117, initiating the next transport cycle. We also demonstrate the importance of accurate quantum descriptions of fluoride solvation. Our results provide clues to the mysterious E318 residue near the central binding site, suggesting that the transport activities are unlikely to be disrupted by the glutamate interacting with a well-solvated fluoride at the central binding site. This differs significantly from the structurally similar CLC chloride/proton antiporters, where a fluoride trapped deep in the hydrophobic pore causes the transporter to be locked down. A free-energy barrier of 10-15 kcal/mol was estimated via umbrella sampling for a fluoride ion traveling through the pore to repopulate the external binding site.

Computational approaches to investigate fluoride binding, selectivity and transport across the membrane

The use of molecular dynamics (MD) simulations to study biomolecular systems has proven reliable in elucidating atomic-level details of structure and function. In this chapter, MD simulations were used to uncover new insights into two phylogenetically unrelated bacterial fluoride (F-) exporters: the CLCF F-/H+ antiporter and the Fluc F- channel. The CLCF antiporter, a member of the broader CLC family, has previously revealed unique stoichiometry, anion-coordinating residues, and the absence of an internal glutamate crucial for proton import in the CLCs. Through MD simulations enhanced with umbrella sampling, we provide insights into the energetics and mechanism of the CLCF transport process, including its selectivity for F- over HF. In contrast, the Fluc F- channel presents a novel architecture as a dual topology dimer, featuring two pores for F- export and a central non-transported sodium ion. Using computational electrophysiology, we simulate the electrochemical gradient necessary for F- export in Fluc and reveal details about the coordination and hydration of both F- and the central sodium ion. The procedures described here delineate the specifics of these advanced techniques and can also be adapted to investigate other membrane protein systems.

Fluoride resistance capacity in mammalian cells involves global gene expression changes associate with ferroptosis

OBJECTIVE

The purpose of this study was to understand mouse osteoblast ferroptosis under high fluoride environment by stimulating fluoride levels to corresponding levels. In order to define the underlying mechanism of fluoride resistance in mammals and provide a theoretical basis for fluorosis treatment, high-throughput sequencing was applied to map the genetic changes of fluoride-resistant mouse osteoblasts and analyze the role of ferroptosis-related genes.

METHODS

Cell Counting Kit-8, Reactive Oxygen Species Assay Kit and C11 BODIPY 581/591 were used to monitor proliferation and ferroptosis of mouse osteoblasts MC3T3-E1 under high fluoride environment. Fluoride-tolerant MC3T3-E1 cells were developed by gradient fluoride exposure. The differentially expressed genes of fluorine-resistant MC3T3-E1 cells were identified by high-throughput sequencing.

RESULTS

MC3T3-E1 cells cultured in medium containing 20, 30, 60, 90 ppm F^- exhibited decreased viability and increased reactive oxygen species and lipid peroxidation levels in correlation with F^- concentrations. High-throughput RNA sequencing identified 2702 differentially expressed genes (DEGs) showed more than 2-fold difference in 30 ppm FR MC3T3-E1 cells, of which 17 DEGs were associated with ferroptosis.

CONCLUSION

High fluoride environment affected the content of lipid peroxides in the body and increased the level of ferroptosis, further, ferroptosis-related genes played specific roles in the fluoride resistance of mouse osteoblasts.