Fluoride Action Network

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Abstract

Fluoride exporter genes (FEX) are known for the expulsion of cytoplasmic fluoride, thus preventing fluoride toxicity in plants. In this study, 31 FEX genes were identified across 19 plant species. Camphor Resistance (CrcB) domain was found to be present in all the identified FEX genes in plants. FEX genes were sequentially very conserved among the plants and are located mostly in chloroplast and mitochondria. The tertiary structure (3D) of AtFEX1 suggests that FEX genes of plants possess pore I and pore II, necessary for fluoride export. The TTFSGWNQ and GCLSTVSTF motifs were found to be well conserved in pore I and pore II. Phenylalanine (Phe/F) was also present in both the motifs, necessary for fluoride ions recognition and export. Cis-acting analysis in promoter sequences of plant FEX revealed several elements associated with various functions such as phytohormone signaling, integrating biotic and abiotic stress responses in plants. Prolong fluoride exposure causes necrosis in young leaves in Vigna radiata. Expression of VrFEX1 and VrFEX2 were highly induced under exogenous fluoride, thus suggesting a possible role in fluoride detoxification.

Supplementary Information

*Original abstract online at https://link.springer.com/article/10.1007%2Fs13205-021-02677-z

 

Excerpt:

References

  1. Altschul SF, Gish W, Miller W (1990) Basic local alignment search tool. J MolBiol 215(3):403–410. https://doi.org/10.1016/S0022-2836(05)80360-2

    CAS  Article  Google Scholar

  2. Armenteros JJA, Salvatore M, Emanuelsson O (2019) Detecting sequence signals in targeting peptides using deep learning. Life Sci Alliance 2:1–14. https://doi.org/10.26508/lsa.201900429

    Article  Google Scholar

  3. Bailey TL, Boden M, Buske FA (2009) MEME Suite: tools for motif discovery and searching. Nucleic Acids Res 37:202–208. https://doi.org/10.1093/nar/gkp335

    CAS  Article  Google Scholar

  4. Baker JL, Sudarsan N, Weinberg Z (2012) Widespread genetic switches and toxicity resistance proteins for fluoride. Science 335(6065):233–235. https://doi.org/10.1126/science.1215063

    CAS  Article  PubMed  Google Scholar

  5. Banerjee A, Roychoudhury A (2019) Structural introspection of a putative fluoride transporter in plants. Biotech 9:103. https://doi.org/10.1007/s13205-019-1629-4

    Article  Google Scholar

  6. Berardini TZ, Reiser L, Li D (2015) The arabidopsis information resource: making and mining the “gold standard” annotated reference plant genome. Genesis 53:474–485. https://doi.org/10.1002/dvg.22877

    CAS  Article  PubMed  PubMed Central  Google Scholar

  7. Berbasova T, Nallur S, Sells T (2017) Fluoride export (FEX) proteins from fungi, plants and animals are “single barreled” channels containing one functional and one vestigial ion pore. PLoS ONE 12:1–20. https://doi.org/10.1371/journal.pone.0177096

    CAS  Article  Google Scholar

  8. Bhargava D, Bhardwaj N, Bhardwaj Effect N (2010) Effect of sodium fluoride on seed g ermination and seedling growth of triticumaestivum VAR. RAJ. 4083. J Phytol 2010:41–43

    Google Scholar

  9. Bolser D, Staines DM, Pritchard E, Kersey P et al (2016) Ensembl plants: integrating tools for visualizing, mining, and analyzing plant genomics data. Methods MolBiol 1374:115–140. https://doi.org/10.1007/978-1-4939-3167-5_6

    CAS  Article  Google Scholar

  10. Chakrabarti S, Patra PK (2015) Biochemical and antioxidant responses of paddy (Oryza sativa L.) to fluoride stress. Fluoride 48:56

    Google Scholar

  11. Chakrabarti S, Patra PK, Mandal B, Mahato D et al (2012) Effect of sodium fluoride on germination, seedling growth, and biochemistry of Bengal gram (Cicerarieninum). Fluoride 45:257–262

    Google Scholar

  12. Choudhuri S (2014) Fundamentals of genes and genomes. Bioinforma Beginners. https://doi.org/10.1016/b978-0-12-410471-6.00001-3

    Article  Google Scholar

  13. Chow CN, Lee TY, Hung YC (2019) Plantpan3.0: a new and updated resource for reconstructing transcriptional regulatory networks from chip-seq experiments in plants. Nucleic Acids Res 47:D1155–D1163. https://doi.org/10.1093/nar/gky1081

    Article  PubMed  Google Scholar

  14. Davieson G, Murray F, Wilson S (1990) Effects of sulphur dioxide and hydrogen fluoride, singly and in combination, on growth and yield of wheat in open-top chambers. AgricEcosyst Environ 30:317–325. https://doi.org/10.1016/0167-8809(90)90113-R

    CAS  Article  Google Scholar

  15. DeLano WL (2002) Pymol: An open-source molecular graphics tool. CCP4 Newsl Protein Crystallogr 40:82–92

    Google Scholar

  16. Deshmukh A, Wadaskar P, Malpe D (1995) Fluorine in environment: a review. GondwanaGeol Mag 9:1–20

    Article  Google Scholar

  17. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797. https://doi.org/10.1093/nar/gkh340

    CAS  Article  PubMed  PubMed Central  Google Scholar

  18. Edler D, Klein J, Antonelli A, Silvestro D et al (2019) raxmlGUI 20 beta: a graphical interface and toolkit for phylogenetic analyses using RAxML. bioRxiv. https://doi.org/10.1101/800912

    Article  Google Scholar

  19. Elloumi N, Ben Abdallah F, Mezghani I (2005) Effect of flouride on almond seedlings in culture solution. Fluoride 38:193–198

    CAS  Google Scholar

  20. Fornasiero RB (2001) Phytotoxic effects of fluorides. Plant Sci 161:979–985. https://doi.org/10.1016/S0168-9452(01)00499-X

    CAS  Article  Google Scholar

  21. Gilbert D (2003) Sequence file format conversion with command-line readseq. CurrProtocBioinforma Appendix. https://doi.org/10.1002/0471250953.bia01es00

    Article  Google Scholar

  22. Goodstein DM, Shu S, Howson R (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40:1178–1186. https://doi.org/10.1093/nar/gkr944

    CAS  Article  Google Scholar

  23. Götz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talon M, Dopazo J, Conesa A (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36(10):3420–3435

    Article  Google Scholar

  24. Gupta S, Banerjee S, Mondal S (2009) Phytotoxicity of fluoride in the germination of paddy (Oryzasativa) and its effect on the physiology and biochemistry of germinated seedlings. Fluoride 42:142–146

    CAS  Google Scholar

  25. Hu B, Jin J, Guo AY (2015) GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics 31:1296–1297. https://doi.org/10.1093/bioinformatics/btu817

    Article  PubMed  Google Scholar

  26. Jacobson JS, Weinstein LH, Mccune DC, Hitchcock AE et al (1966) The accumulation of fluorine by plants. J Air Pollut Control Assoc 16:412–417. https://doi.org/10.1080/00022470.1966.10468494

    CAS  Article  PubMed  Google Scholar

  27. Karmakar S, Mukherjee J, Mukherjee S (2016) Removal of fluoride contamination in water by three aquatic plants. Int J Phytoremediation 18:222–227. https://doi.org/10.1080/15226514.2015.1073676

    CAS  Article  PubMed  Google Scholar

  28. Karolewski P, Siepak J, Gramowska H (2000) Response scots pine (Pinussylvestris), Norway spruce (Piceaabies) and Douglas fir (Pseudotsugamenziesii) needles to environment pollution with flourine compounds. Dendrobiology 45:41–46

    CAS  Google Scholar

  29. Kim DE, Chivian D, Baker D (2004) Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res 32:526–531. https://doi.org/10.1093/nar/gkh468

    CAS  Article  Google Scholar

  30. Kozlov AM, Darriba D, Flouri T (2019) RAxML-NG: A fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35:4453–4455. https://doi.org/10.1093/bioinformatics/btz305

    CAS  Article  PubMed  PubMed Central  Google Scholar

  31. Kumar K (2017) Effects of fluoride on respiration and photosynthesis in plants: an overview. Peertechz J Environ SciToxicol 2:43–47. https://doi.org/10.17352/pjest.000011

    Article  Google Scholar

  32. Kumar S, Singh M (2015) Effect of fluoride contaminated irrigation water on Eco-physiology, biomass and yield in Gossypium hirsutum L. Tropical Plant Res 2(2):134–142

    Google Scholar

  33. Lescot M (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 30:325–327. https://doi.org/10.1093/nar/30.1.325

    CAS  Article  PubMed  PubMed Central  Google Scholar

  34. Li S, Smith KD, Davis JH (2013) Eukaryotic resistance to fluoride toxicity mediated by a widespread family of fluoride export proteins. ProcNatlAcadSci USA 110:19018–19023. https://doi.org/10.1073/pnas.1310439110

    CAS  Article  Google Scholar

  35. Li QS, Lin XM, Qiao RY (2017) Effect of fluoride treatment on gene expression in tea plant (Camellia sinensis). Sci Rep 7:1–8. https://doi.org/10.1038/s41598-017-08587-6

    Article  Google Scholar

  36. Li S, Wang R, Jin H, Ding Y, Cai C (2019) Molecular characterization and expression profile analysis of heat shock transcription factors in mungbean. Front Gene 9:736. https://doi.org/10.3389/fgene.2018.00736

    CAS  Article  Google Scholar

  37. Miller MA, Pfeiffer W, Schwartz T (2010) Creating the CIPRES science gateway for inference of large phylogenetic trees mark. GatewComput Environ Work GCE 2:4

    Google Scholar

  38. Pulyaevskaya MA, Varakina NN, Gamburg KZ, Rusaleva TM, Stepanov AV, Voinikov VK et al (2011) Sodium fluoride inhibits HSP synthesis in heat-stressed cultured cells of Arabidopsis thaliana. Russ J Plant Physiol 58(4):589–596

    CAS  Article  Google Scholar

  39. R Core Team (2013) R: A language and environment for statistical computing. R Foundation for Statistical Computing.

  40. Robert X, Gouet P (2014) Deciphering key features in protein structures with the new ENDscript server. Nucl Acids Res 42(W1):W320–W324. https://doi.org/10.1093/nar/gku316

    CAS  Article  PubMed  Google Scholar

  41. Schultz J (2000) SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Res 28:231–234. https://doi.org/10.1093/nar/28.1.231

    CAS  Article  PubMed  PubMed Central  Google Scholar

  42. Smith KD, Gordon PB, Rivetta A (2015a) Yeast fexp is a constitutively expressed fluoride channel with functional asymmetry of its two. Homologous 290:19874–19887

    CAS  Google Scholar

  43. Smith KD, Gordon PB, Rivetta A (2015b) Yeast Fex1p is a constitutively expressed fluoride channel with functional asymmetry of its two homologous domains. J BiolChem 290:19874–19887. https://doi.org/10.1074/jbc.M115.651976

    CAS  Article  Google Scholar

  44. Stockbridge RB, Lim HH, Otten R (2012) Fluoride resistance and transport by riboswitch-controlled CLC antiporters. ProcNatlAcadSci USA 109:15289–15294. https://doi.org/10.1073/pnas.1210896109

    Article  Google Scholar

  45. Stockbridge RB, Robertson JL, Kolmakova-Partensky L, Miller C et al (2013) A family of fluoride-specific ion channels with dual-topology architecture. Elife 2:1–14. https://doi.org/10.7554/elife.01084

    Article  Google Scholar

  46. Takmaz-Nisancioglu SD, Davison AW (1988) Effects of Al on fluoride uptake by plants. New Phytol 109:149–155. https://doi.org/10.1111/j.1469-8137.1988.tb03702.x

    CAS  Article  Google Scholar

  47. Taylor SC, Nadeau K, Abbasi M, Lachance C, Nguyen M, Fenrich J (2019) The ultimate qpcr experiment: producing publication quality, reproducible data the first time. Trends Biotech 37(7):761–774. https://doi.org/10.1016/j.tibtech.2018.12.002

    CAS  Article  Google Scholar

  48. Wickham H (2016) ggplot2: elegant graphics for data analysis. Springer-Verlag, New York

    Google Scholar

  49. Zhang L, Li Q, Ma L, Ruan J et al (2013) Characterization of fluoride uptake by roots of tea plants (Camellia sinensis (L.) O. Kuntze). Plant Soil 366:659–669. https://doi.org/10.1007/s11104-012-1466-2

    CAS  Article  Google Scholar

  50. Zhu J, Xing A, Wu Z (2019) CsFEX, a fluoride export protein gene from camellia sinensis, alleviates fluoride toxicity in transgenic escherichia coli and Arabidopsis thaliana. J Agric Food Chem 67:5997–6006. https://doi.org/10.1021/acs.jafc.9b00509

    CAS  Article  PubMed  Google Scholar

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Author information

Affiliations

  1. Department of Biochemistry, Central University of Rajasthan, Bandar Sindri, Ajmer, Rajasthan, 305817, India

    Samridhi Agarwal & Sanjib Kumar Panda

  2. Department of Life Science and Bioinformatics, Assam University, Silchar, Assam, 788011, India

    Preetom Regon

  3. Department of Botany, Gauhati University, Gauhati, Assam, 781014, India

    Mehzabin Rehman & Bhaben Tanti

Corresponding author

Correspondence to Sanjib Kumar Panda.

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