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Banerjee A, Kang CY, An M, Koff BB, Sunder S, Kumar A, Tenuta LMA, Stockbridge RB. Fluoride export is required for the competitive fitness of pathogenic microorganisms in dental biofilm models. mBio 2024:e0018424. [PMID: 38624207 DOI: 10.1128/mbio.00184-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/20/2024] [Indexed: 04/17/2024] Open
Abstract
Microorganisms resist fluoride toxicity using fluoride export proteins from one of several different molecular families. Cariogenic species Streptococcus mutans and Candida albicans extrude intracellular fluoride using a CLCF F-/H+ antiporter and FEX fluoride channel, respectively, whereas oral commensal eubacteria, such as Streptococcus gordonii, export fluoride using a Fluc fluoride channel. In this work, we examine how genetic knockout of fluoride export impacts pathogen fitness in single-species and three-species dental biofilm models. For biofilms generated using S. mutans with the genetic knockout of the CLCF transporter, exposure to low fluoride concentrations decreased S. mutans counts, synergistically reduced the populations of C. albicans, increased the relative proportion of oral commensal S. gordonii, and reduced properties associated with biofilm pathogenicity, including acid production and hydroxyapatite dissolution. Biofilms prepared with C. albicans with genetic knockout of the FEX channel also exhibited reduced fitness in the presence of fluoride but to a lesser degree. Imaging studies indicate that S. mutans is highly sensitive to fluoride, with the knockout strain undergoing complete lysis when exposed to low fluoride for a moderate amount of time. Biochemical purification of the S. mutans CLCF transporter and functional reconstitution establishes that the functional protein is a dimer encoded by a single gene. Together, these findings suggest that fluoride export by oral pathogens can be targeted by specific inhibitors to restore biofilm symbiosis in dental biofilms and that S. mutans is especially susceptible to fluoride toxicity. IMPORTANCE Dental caries is a globally prevalent condition that occurs when pathogenic species, including Streptococcus mutans and Candida albicans, outcompete beneficial species, such as Streptococcus gordonii, in the dental biofilm. Fluoride is routinely used in oral hygiene to prevent dental caries. Fluoride also has antimicrobial properties, although most microbes possess fluoride exporters to resist its toxicity. This work shows that sensitization of cariogenic species S. mutans and C. albicans to fluoride by genetic knockout of fluoride exporters alters the microbial composition and pathogenic properties of dental biofilms. These results suggest that the development of drugs that inhibit fluoride exporters could potentiate the anticaries effect of fluoride in over-the-counter products like toothpaste and mouth rinses. This is a novel strategy to treat dental caries.
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Affiliation(s)
- Aditya Banerjee
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Chia-Yu Kang
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | - Minjun An
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - B Ben Koff
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sham Sunder
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Anuj Kumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Livia M A Tenuta
- School of Dentistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Randy B Stockbridge
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA
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Banerjee A, Kang CY, An M, Koff BB, Sunder S, Kumar A, Tenuta LMA, Stockbridge RB. Fluoride export is required for competitive fitness of pathogenic microorganisms in dental biofilm models. bioRxiv 2024:2024.01.18.576223. [PMID: 38293214 PMCID: PMC10827179 DOI: 10.1101/2024.01.18.576223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Microorganisms resist fluoride toxicity using fluoride export proteins from one of several different molecular families. Cariogenic species Streptococcus mutans and Candida albicans extrude intracellular fluoride using a CLCF F-/H+ antiporter and FEX fluoride channel, respectively, whereas commensal eubacteria, such as Streptococcus gordonii, export fluoride using a Fluc fluoride channel. In this work, we examine how genetic knockout of fluoride export impacts pathogen fitness in single-species and three-species dental biofilm models. For biofilms generated using S. mutans with genetic knockout of the CLCF transporter, exposure to low fluoride concentrations decreased S. mutans counts, synergistically reduced the populations of C. albicans, increased the relative proportion of commensal S. gordonii, and reduced properties associated with biofilm pathogenicity, including acid production and hydroxyapatite dissolution. Biofilms prepared with C. albicans with genetic knockout of the FEX channel also exhibited reduced fitness in the presence of fluoride, but to a lesser degree. Imaging studies indicate that S. mutans is highly sensitive to fluoride, with the knockout strain undergoing complete lysis when exposed to low fluoride for a moderate amount of time, and biochemical purification the S. mutans CLCF transporter and functional reconstitution establishes that the functional protein is a dimer encoded by a single gene. Together, these findings suggest that fluoride export by oral pathogens can be targeted by specific inhibitors to restore biofilm symbiosis in dental biofilms, and that S. mutans is especially susceptible to fluoride toxicity.
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Affiliation(s)
- Aditya Banerjee
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chia-Yu Kang
- Program in Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Minjun An
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - B Ben Koff
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sham Sunder
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anuj Kumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Livia M A Tenuta
- School of Dentistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Randy B Stockbridge
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Program in Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
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Kermani AA, Burata OE, Koff BB, Koide A, Koide S, Stockbridge RB. Crystal structures of bacterial small multidrug resistance transporter EmrE in complex with structurally diverse substrates. eLife 2022; 11:76766. [PMID: 35254261 PMCID: PMC9000954 DOI: 10.7554/elife.76766] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/06/2022] [Indexed: 11/13/2022] Open
Abstract
Proteins from the bacterial small multidrug resistance (SMR) family are proton-coupled exporters of diverse antiseptics and antimicrobials, including polyaromatic cations and quaternary ammonium compounds. The transport mechanism of the Escherichia coli transporter, EmrE, has been studied extensively, but a lack of high-resolution structural information has impeded a structural description of its molecular mechanism. Here, we apply a novel approach, multipurpose crystallization chaperones, to solve several structures of EmrE, including a 2.9 Å structure at low pH without substrate. We report five additional structures in complex with structurally diverse transported substrates, including quaternary phosphonium, quaternary ammonium, and planar polyaromatic compounds. These structures show that binding site tryptophan and glutamate residues adopt different rotamers to conform to disparate structures without requiring major rearrangements of the backbone structure. Structural and functional comparison to Gdx-Clo, an SMR protein that transports a much narrower spectrum of substrates, suggests that in EmrE, a relatively sparse hydrogen bond network among binding site residues permits increased sidechain flexibility.
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Affiliation(s)
- Ali A Kermani
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Olive E Burata
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - B Ben Koff
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Akiko Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, United States
| | - Shohei Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, United States
| | - Randy B Stockbridge
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, United States
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McIlwain BC, Erwin AL, Davis AR, Ben Koff B, Chang L, Bylund T, Chuang GY, Kwong PD, Ohi MD, Lai YT, Stockbridge RB. N-terminal Transmembrane-Helix Epitope Tag for X-ray Crystallography and Electron Microscopy of Small Membrane Proteins. J Mol Biol 2021; 433:166909. [PMID: 33676924 PMCID: PMC8292168 DOI: 10.1016/j.jmb.2021.166909] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 12/21/2022]
Abstract
Structural studies of membrane proteins, especially small membrane proteins, are associated with well-known experimental challenges. Complexation with monoclonal antibody fragments is a common strategy to augment such proteins; however, generating antibody fragments that specifically bind a target protein is not trivial. Here we identify a helical epitope, from the membrane-proximal external region (MPER) of the gp41-transmembrane subunit of the HIV envelope protein, that is recognized by several well-characterized antibodies and that can be fused as a contiguous extension of the N-terminal transmembrane helix of a broad range of membrane proteins. To analyze whether this MPER-epitope tag might aid structural studies of small membrane proteins, we determined an X-ray crystal structure of a membrane protein target that does not crystallize without the aid of crystallization chaperones, the Fluc fluoride channel, fused to the MPER epitope and in complex with antibody. We also demonstrate the utility of this approach for single particle electron microscopy with Fluc and two additional small membrane proteins that represent different membrane protein folds, AdiC and GlpF. These studies show that the MPER epitope provides a structurally defined, rigid docking site for antibody fragments that is transferable among diverse membrane proteins and can be engineered without prior structural information. Antibodies that bind to the MPER epitope serve as effective crystallization chaperones and electron microscopy fiducial markers, enabling structural studies of challenging small membrane proteins.
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Affiliation(s)
- Benjamin C McIlwain
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Amanda L Erwin
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48019, United States
| | - Alexander R Davis
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, United States
| | - B Ben Koff
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Louise Chang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States
| | - Tatsiana Bylund
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, United States
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, United States
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, United States
| | - Melanie D Ohi
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48019, United States.
| | - Yen-Ting Lai
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, United States; Moderna Therapeutics, 200 Technology Square, Cambridge, MA 02139, United States.
| | - Randy B Stockbridge
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, United States; Program in Biophysics, University of Michigan, Ann Arbor, MI 48109, United States.
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McIlwain BC, Gundepudi R, Koff BB, Stockbridge RB. The fluoride permeation pathway and anion recognition in Fluc family fluoride channels. eLife 2021; 10:69482. [PMID: 34250906 PMCID: PMC8315801 DOI: 10.7554/elife.69482] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/09/2021] [Indexed: 11/13/2022] Open
Abstract
Fluc family fluoride channels protect microbes against ambient environmental fluoride by undermining the cytoplasmic accumulation of this toxic halide. These proteins are structurally idiosyncratic, and thus the permeation pathway and mechanism have no analogy in other known ion channels. Although fluoride-binding sites were identified in previous structural studies, it was not evident how these ions access aqueous solution, and the molecular determinants of anion recognition and selectivity have not been elucidated. Using x-ray crystallography, planar bilayer electrophysiology, and liposome-based assays, we identified additional binding sites along the permeation pathway. We used this information to develop an oriented system for planar lipid bilayer electrophysiology and observed anion block at one of these sites, revealing insights into the mechanism of anion recognition. We propose a permeation mechanism involving alternating occupancy of anion-binding sites that are fully assembled only as the substrate approaches.
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Affiliation(s)
- Benjamin C McIlwain
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Roja Gundepudi
- Program in Biophysics, University of Michigan, Ann Arbor, United States
| | - B Ben Koff
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States
| | - Randy B Stockbridge
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, United States.,Program in Biophysics, University of Michigan, Ann Arbor, United States
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