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Stockbridge RB, Wackett LP. The link between ancient microbial fluoride resistance mechanisms and bioengineering organofluorine degradation or synthesis. Nat Commun 2024; 15:4593. [PMID: 38816380 PMCID: PMC11139923 DOI: 10.1038/s41467-024-49018-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/20/2024] [Indexed: 06/01/2024] Open
Abstract
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.
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Affiliation(s)
- Randy B Stockbridge
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Lawrence P Wackett
- Department of Biochemistry, Biophysics & Molecular Biology and Biotechnology Institute, University of Minnesota, Minneapolis, MN, 55455, USA.
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2
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Singh A, Patani A, Patel M, Vyas S, Verma RK, Amari A, Osman H, Rathod L, Elboughdiri N, Yadav VK, Sahoo DK, Chundawat RS, Patel A. Tomato seed bio-priming with Pseudomonas aeruginosa strain PAR: a study on plant growth parameters under sodium fluoride stress. Front Microbiol 2024; 14:1330071. [PMID: 38239735 PMCID: PMC10794310 DOI: 10.3389/fmicb.2023.1330071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/04/2023] [Indexed: 01/22/2024] Open
Abstract
The primary goal of this experiment is to examine the effectiveness of Pseudomonas aeruginosa strain PAR as a rhizobacterium that promotes plant growth in mitigating the negative effects of fluoride-induced stress in tomato (Lycopersicon esculentum Mill.) plants. A total of 16 rhizobacterial strains were tested for plant growth-promoting (PGP) attributes, with isolates S1, S2, and S3 exhibiting different characteristics. Furthermore, growth kinetics studies revealed that these isolates were resilient to fluoride stress (10, 20, 40, and 80 ppm), with isolate S2 exhibiting notable resilience compared to the other two strains. Phylogenetic analysis revealed isolate S2 as P. aeruginosa strain PAR. Physiological analyses demonstrated that P. aeruginosa strain PAR had a beneficial impact on plant properties under fluoride stress, comprising seed germination, root length, shoot height, relative water content, and leaf area, the strain also impacted the buildup of glycine betaine, soluble sugar, and proline, demonstrating its significance in enhancing plant stress tolerance. In P. aeruginosa strain PAR-treated plants, chlorophyll content increased while malondialdehyde (MDA) levels decreased, indicating enhanced photosynthetic efficiency and less oxidative stress. The strain modified antioxidant enzyme action (catalase, ascorbate, glutathione reductase, peroxidase, and superoxide dismutase), which contributed to improved stress resilience. Mineral analysis revealed a decrease in sodium and fluoride concentrations while increasing magnesium, potassium, phosphorus, and iron levels, emphasizing the strain's significance in nutrient management. Correlation and principal component analysis revealed extensive correlations between physiological and biochemical parameters, underscoring P. aeruginosa strain PAR's multifaceted impact on plant growth and stress response. This study offers valuable information on effectively utilizing PGPR, particularly P. aeruginosa strain PAR, in fluoride-contaminated soils for sustainable agriculture. It presents a promising biological strategy to enhance crop resilience and productivity.
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Affiliation(s)
- Anamika Singh
- School of Liberal Arts and Sciences, Mody University of Science and Technology, Sikar, India
| | - Anil Patani
- Department of Biotechnology, Smt. S. S. Patel Nootan Science and Commerce College, Sankalchand Patel University, Visnagar, India
| | - Margi Patel
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
| | - Suhas Vyas
- Department of Life Sciences, Bhakta Kavi Narsinh Mehta University, Junagadh, Gujarat, India
| | - Rakesh Kumar Verma
- School of Liberal Arts and Sciences, Mody University of Science and Technology, Sikar, India
| | - Abdelfattah Amari
- Department of Chemical Engineering, College of Engineering, King Khalid University, Abha, Saudi Arabia
| | - Haitham Osman
- Department of Chemical Engineering, College of Engineering, King Khalid University, Abha, Saudi Arabia
| | - Lokendra Rathod
- ICMR-National Institute for Research in Environmental Health, Bhopal, India
| | - Noureddine Elboughdiri
- Chemical Engineering Department, College of Engineering, University of Ha'il, Ha'il, Saudi Arabia
- Chemical Engineering Process Department, National School of Engineers Gabes, University of Gabes, Gabes, Tunisia
| | - Virendra Kumar Yadav
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
| | - Dipak Kumar Sahoo
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, United States
| | | | - Ashish Patel
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, India
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Cao Y, Zhang C, Fang Y, Liu Y, Lyu K, Ding J, Wang X. Investigation the global effect of rare earth gadolinium on the budding Saccharomyces cerevisiae by genome-scale screening. Front Microbiol 2022; 13:1022054. [DOI: 10.3389/fmicb.2022.1022054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/11/2022] [Indexed: 11/29/2022] Open
Abstract
IntroductionThe rare earth gadolinium (Gd) is widely used in industry and medicine, which has been treated as an emerging pollutant in environment. The increasing pollution of Gd has potential hazards to living organisms. Thus it is essential to investigate the toxicity and action mechanism of Gd in biological system.MethodsIn this study, the global effect and activation mechanism of Gd on yeast were investigated by genome-scale screening.Results and discussionOur results show that 45 gene deletion strains are sensitive to Gd and 10 gene deletion strains are Gd resistant from the diploid gene deletion strain library of Saccharomyces cerevisiae. The result of localization analysis shows that most of these genes are involved in cell metabolism, cell cycle, transcription, translation, protein synthesis, protein folding, and cell transport. The result of functional analysis shows that four genes (CNB1, CRZ1, VCX1, and GDT1) are involved in the calcium signaling pathway, and four genes (PHO84, PHO86, PHO2, and PHO4) are involved in phosphorus metabolism. For Gd3+ has the similar ion radius with Ca2+ and easily binds to the phosphate radical, it affects Ca2+ signaling pathway and phosphorus metabolism. The genes ARF1, ARL1, ARL3, SYS1, COG5, COG6, YPT6, VPS9, SSO2, MRL1, AKL1, and TRS85 participate in vesicle transport and protein sorting. Thus, Gd accumulation affects the function of proteins related to vesicle transport, which may result in the failure of Gd transport out of cells. In addition, the intracellular Gd content in the 45 sensitive deletion strains is higher than that in the wild type yeast under Gd stress. It suggests that the sensitivity of yeast deletion strains is related to the excessive intracellular Gd accumulation.
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Johnston N, Cline G, Strobel SA. Cells Adapt to Resist Fluoride through Metabolic Deactivation and Intracellular Acidification. Chem Res Toxicol 2022; 35:2085-2096. [PMID: 36282204 PMCID: PMC9683101 DOI: 10.1021/acs.chemrestox.2c00222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Indexed: 01/09/2023]
Abstract
Fluoride is highly abundant in the environment. Many organisms have adapted specific defense mechanisms against high concentrations of fluoride, including the expression of proteins capable of removing fluoride from cells. However, these fluoride transporters have not been identified in all organisms, and even organisms that express fluoride transporters vary in tolerance capabilities across species, individuals, and even tissue types. This suggests that alternative factors influence fluoride tolerance. We screened for adaptation against fluoride toxicity through an unbiased mutagenesis assay conducted on Saccharomyces cerevisiae lacking the fluoride exporter FEX, the primary mechanism of fluoride resistance. Over 80 independent fluoride-hardened strains were generated, with anywhere from 100- to 1200-fold increased fluoride tolerance compared to the original strain. The whole genome of each mutant strain was sequenced and compared to the wild type. The fluoride-hardened strains utilized a combination of phenotypes that individually conferred fluoride tolerance. These included intracellular acidification, cellular dormancy, nutrient storage, and a communal behavior reminiscent of flocculation. Of particular importance to fluoride resistance was intracellular acidification, which served to reverse the accumulation of fluoride and lead to its excretion from the cell as HF without the activity of a fluoride-specific protein transporter. This transport mechanism was also observed in wild-type yeast through a manual mutation to lower their cytoplasmic pH. The results demonstrate that the yeast developed a protein-free adaptation for removing an intracellular toxicant.
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Affiliation(s)
- Nichole
R. Johnston
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven 06477, Connecticut, United States
| | - Gary Cline
- Department
of Internal Medicine, Yale School of Medicine, New Haven 06510, Connecticut, United States
| | - Scott A. Strobel
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven 06477, Connecticut, United States
- Department
of Chemistry, Yale University, New Haven 06477, Connecticut, United States
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Calero P, Gurdo N, Nikel PI. Role of the CrcB transporter of Pseudomonas putida in the multi-level stress response elicited by mineral fluoride. Environ Microbiol 2022; 24:5082-5104. [PMID: 35726888 PMCID: PMC9796867 DOI: 10.1111/1462-2920.16110] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/16/2022] [Accepted: 06/19/2022] [Indexed: 01/07/2023]
Abstract
The presence of mineral fluoride (F- ) in the environment has both a geogenic and anthropogenic origin, and the halide has been described to be toxic in virtually all living organisms. While the evidence gathered in different microbial species supports this notion, a systematic exploration of the effects of F- salts on the metabolism and physiology of environmental bacteria remained underexplored thus far. In this work, we studied and characterized tolerance mechanisms deployed by the model soil bacterium Pseudomonas putida KT2440 against NaF. By adopting systems-level omic approaches, including functional genomics and metabolomics, we gauged the impact of this anion at different regulatory levels under conditions that impair bacterial growth. Several genes involved in halide tolerance were isolated in a genome-wide Tn-Seq screening-among which crcB, encoding an F- -specific exporter, was shown to play the predominant role in detoxification. High-resolution metabolomics, combined with the assessment of intracellular and extracellular pH values and quantitative physiology experiments, underscored the key nodes in central carbon metabolism affected by the presence of F- . Taken together, our results indicate that P. putida undergoes a general, multi-level stress response when challenged with NaF that significantly differs from that caused by other saline stressors. While microbial stress responses to saline and oxidative challenges have been extensively studied and described in the literature, very little is known about the impact of fluoride (F- ) on bacterial physiology and metabolism. This state of affairs contrasts with the fact that F- is more abundant than other halides in the Earth crust (e.g. in some soils, the F- concentration can reach up to 1 mg gsoil -1 ). Understanding the global effects of NaF treatment on bacterial physiology is not only relevant to unveil distinct mechanisms of detoxification but it could also guide microbial engineering approaches for the target incorporation of fluorine into value-added organofluorine molecules. In this regard, the soil bacterium P. putida constitutes an ideal model to explore such scenarios, since this species is particularly known for its high level of stress resistance against a variety of physicochemical perturbations.
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Affiliation(s)
- Patricia Calero
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
| | - Nicolás Gurdo
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
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Biological small-molecule assays using gradient-based microfluidics. Biosens Bioelectron 2021; 178:113038. [PMID: 33556809 DOI: 10.1016/j.bios.2021.113038] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 01/18/2021] [Accepted: 01/23/2021] [Indexed: 12/20/2022]
Abstract
Studying the potency of small-molecules on eukaryotic and prokaryotic cells using conventional biological settings requires time-consuming procedures and large volumes of expensive small-molecules. Microfluidics could significantly expedite these assays by enabling operation in high-throughput and (semi)automated modes. Here, we introduce a microfluidics platform based on multi-volume microchamber arrays that can produce a wide range of small-molecule concentrations with a desired gradient-based profile for rapid and precise biological testing within a single device with minimal hands-on time. The concept behind this device is based on introducing the same amount of a small-molecule into microchambers of different volumes to spontaneously generate a gradient concentration profile via diffusion. This design enables to obtain an unprecedented concentration range (e.g., three orders of magnitude) that can be easily adjusted, allowing us to pinpoint the precise effect of small-molecules on pre-loaded prokaryotic and eukaryotic cells. We also propose a comprehensive relationship for determining the loading time (the only required parameter for implementing this platform) in order to study the effects of any small-molecule on a biological species in a desired test. We demonstrate the versatility of this microfluidics platform by conducting two small-molecule assays-antimicrobial resistance and sugar-phosphate toxicity for both eukaryotic and prokaryotic biological systems.
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Abstract
Microorganisms contend with numerous and unusual chemical threats and have evolved a catalog of resistance mechanisms in response. One particularly ancient, pernicious threat is posed by fluoride ion (F-), a common xenobiotic in natural environments that causes broad-spectrum harm to metabolic pathways. This review focuses on advances in the last ten years toward understanding the microbial response to cytoplasmic accumulation of F-, with a special emphasis on the structure and mechanisms of the proteins that microbes use to export fluoride: the CLCF family of F-/H+ antiporters and the Fluc/FEX family of F- channels.
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Affiliation(s)
- Benjamin C McIlwain
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA;
| | - Michal T Ruprecht
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA;
| | - Randy B Stockbridge
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; .,Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, USA
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Johnston NR, Nallur S, Gordon PB, Smith KD, Strobel SA. Genome-Wide Identification of Genes Involved in General Acid Stress and Fluoride Toxicity in Saccharomyces cerevisiae. Front Microbiol 2020; 11:1410. [PMID: 32670247 PMCID: PMC7329995 DOI: 10.3389/fmicb.2020.01410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 05/29/2020] [Indexed: 11/13/2022] Open
Abstract
Hydrofluoric acid elicits cell cycle arrest through a mechanism that has long been presumed to be linked with the high affinity of fluoride to metals. However, we have recently found that the acid stress from fluoride exposure is sufficient to elicit many of the hallmark phenotypes of fluoride toxicity. Here we report the systematic screening of genes involved in fluoride resistance and general acid resistance using a genome deletion library in Saccharomyces cerevisiae. We compare these to a variety of acids - 2,4-dinitrophenol, FCCP, hydrochloric acid, and sulfuric acid - none of which has a high metal affinity. Pathways involved in endocytosis, vesicle trafficking, pH maintenance, and vacuolar function are of particular importance to fluoride tolerance. The majority of genes conferring resistance to fluoride stress also enhanced resistance to general acid toxicity. Genes whose expression regulate Golgi-mediated vesicle transport were specific to fluoride resistance, and may be linked with fluoride-metal interactions. These results support the notion that acidity is an important and underappreciated principle underlying the mechanisms of fluoride toxicity.
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Affiliation(s)
- Nichole R Johnston
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Sunitha Nallur
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Patricia B Gordon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Kathryn D Smith
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Scott A Strobel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States.,Department of Chemistry, Yale University, New Haven, CT, United States
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Johnston NR, Strobel SA. Principles of fluoride toxicity and the cellular response: a review. Arch Toxicol 2020; 94:1051-1069. [PMID: 32152649 PMCID: PMC7230026 DOI: 10.1007/s00204-020-02687-5] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 02/21/2020] [Indexed: 02/04/2023]
Abstract
Fluoride is ubiquitously present throughout the world. It is released from minerals, magmatic gas, and industrial processing, and travels in the atmosphere and water. Exposure to low concentrations of fluoride increases overall oral health. Consequently, many countries add fluoride to their public water supply at 0.7-1.5 ppm. Exposure to high concentrations of fluoride, such as in a laboratory setting often exceeding 100 ppm, results in a wide array of toxicity phenotypes. This includes oxidative stress, organelle damage, and apoptosis in single cells, and skeletal and soft tissue damage in multicellular organisms. The mechanism of fluoride toxicity can be broadly attributed to four mechanisms: inhibition of proteins, organelle disruption, altered pH, and electrolyte imbalance. Recently, there has been renewed concern in the public sector as to whether fluoride is safe at the current exposure levels. In this review, we will focus on the impact of fluoride at the chemical, cellular, and multisystem level, as well as how organisms defend against fluoride. We also address public concerns about fluoride toxicity, including whether fluoride has a significant effect on neurodegeneration, diabetes, and the endocrine system.
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Affiliation(s)
- Nichole R Johnston
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Scott A Strobel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA.
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