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Volume 165, Issue 12

Shotgun proteomic analysis of nanoparticle-synthesizing in response to platinum and palladium Open Access

Abstract

Platinum and palladium are much sought-after metals of critical global importance in terms of abundance and availability. At the nano-scale these metals are of even higher value due to their catalytic abilities for industrial applications. is able to capture ionic forms of both of these metals, reduce them and synthesize elemental nanoparticles. Despite this ability, very little is known about the biological pathways involved in the formation of these nanoparticles. Proteomic analysis of in response to platinum and palladium has highlighted those proteins involved in both the reductive pathways and the wider stress-response system. A core set of 13 proteins was found in both treatments and consisted of proteins involved in metal transport and reduction. There were also seven proteins that were specific to either platinum or palladium. Overexpression of one of these platinum-specific genes, a NiFe hydrogenase small subunit (Dde_2137), resulted in the formation of larger nanoparticles. This study improves our understanding of the pathways involved in the metal resistance mechanism of and is informative regarding how we can tailor the bacterium for nanoparticle production, enhancing its application as a bioremediation tool and as a way to capture contaminant metals from the environment.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Desulfovibrio , nanoparticle , palladium , platinum and proteomics
© 2019 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2019-12-01
2024-04-26
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References

  1. Gordon RB, Bertram M, Graedel TE. Metal stocks and sustainability. Proc Natl Acad Sci U S A 2006; 103:0509498103 [pii]1209–1214 [View Article]
     [Google Scholar]
  2. Pantidos N, Horsfall LE. Biological synthesis of metallic nanoparticles by bacteria, fungi and plants. J Nanomed Nanotechnol 2014; 05: [View Article]
     [Google Scholar]
  3. Hulkoti NI, Taranath TC. Biosynthesis of nanoparticles using microbes—a review. Colloids Surf B Biointerfaces 2014; 121:474–483 [View Article]
     [Google Scholar]
  4. Porcel E, Liehn S, Remita H, Usami N, Kobayashi K et al. Platinum nanoparticles: a promising material for future cancer therapy?. Nanotechnology 2010; 21:85103 [View Article]
     [Google Scholar]
  5. Balaz P, Sedlak J, Pastorek M, Cholujova D, Vignarooban K et al. Arsenic sulphide As4S4 nanoparticles: physico-chemical properties and anticancer effects. J Nano Res-Sw 2012; 18-19:149–155
     [Google Scholar]
  6. Gong P, HM L, XX H, Wang KM, JB H et al. Preparation and antibacterial activity of Fe3O4@Ag nanoparticles. Nanotechnology 2007; 18:Artn 285604
     [Google Scholar]
  7. Yong P, Rowson NA, Farr JPG, Harris IR, Macaskie LE. Bioreduction and biocrystallization of palladium byDesulfovibrio desulfuricans NCIMB 8307. Biotechnol Bioeng 2002; 80:369–379 [View Article]
     [Google Scholar]
  8. Martins M, Mourato C, Sanches S, Noronha JP, Crespo MTB et al. Biogenic platinum and palladium nanoparticles as new catalysts for the removal of pharmaceutical compounds. Water Res 2017; 108:160–168 [View Article]
     [Google Scholar]
  9. Delay M, Frimmel FH. Nanoparticles in aquatic systems. Anal Bioanal Chem 2012; 402:583–592 [View Article]
     [Google Scholar]
  10. Lovley DR, Phillips EJ. Reduction of uranium by Desulfovibrio desulfuricans . Appl Environ Microbiol 1992; 58:850–856
     [Google Scholar]
  11. Lloyd JR, Yong P, Macaskie LE. Enzymatic recovery of elemental palladium by using sulfate-reducing bacteria. Appl Environ Microbiol 1998; 64:4607–4609
     [Google Scholar]
  12. Lloyd JR, Ridley J, Khizniak T, Lyalikova NN, Macaskie LE. Reduction of technetium by Desulfovibrio desulfuricans: biocatalyst characterization and use in a flowthrough bioreactor. Appl Environ Microbiol 1999; 65:2691–2696
     [Google Scholar]
  13. Chardin B, Dolla A, Chaspoul F, Fardeau ML, Gallice P et al. Bioremediation of chromate: thermodynamic analysis of the effects of Cr(VI) on sulfate-reducing bacteria. Appl Microbiol Biotechnol 2002; 60:352–360 [View Article]
     [Google Scholar]
  14. Payne RB, Gentry DM, Rapp-Giles BJ, Casalot L, Wall JD. Uranium reduction by Desulfovibrio desulfuricans strain G20 and a cytochrome C3 mutant . Appl Environ Microbiol 2002; 68:3129–3132 [View Article]
     [Google Scholar]
  15. Capeness MJ, Edmundson MC, Horsfall LE. Nickel and platinum group metal nanoparticle production by Desulfovibrio alaskensis G20 . N Biotechnol 2015; 32:727–731 [View Article]
     [Google Scholar]
  16. Capeness MJ, Echavarri-Bravo V, Horsfall LE. Production of biogenic nanoparticles for the reduction of 4-nitrophenol and oxidative Laccase-Like reactions. Front Microbiol 2019; 10:997 [View Article]
     [Google Scholar]
  17. Lovley DR, Widman PK, Woodward JC, Phillips EJ. Reduction of uranium by cytochrome c3 of Desulfovibrio vulgaris . Appl Environ Microbiol 1993; 59:3572–3576
     [Google Scholar]
  18. De Luca G, de Philip P, Dermoun Z, Rousset M, Verméglio A. Reduction of technetium(VII) by Desulfovibrio fructosovorans is mediated by the nickel-iron hydrogenase. Appl Environ Microbiol 2001; 67:4583–4587 [View Article]
     [Google Scholar]
  19. Mikheenko IP, Rousset M, Dementin S, Macaskie LE. Bioaccumulation of palladium by Desulfovibrio fructosivorans wild-type and hydrogenase-deficient strains. Appl Environ Microbiol 2008; 74:6144–6146 [View Article]
     [Google Scholar]
  20. Deplanche K, Woods RD, Mikheenko IP, Sockett RE, Macaskie LE. Manufacture of stable palladium and gold nanoparticles on native and genetically engineered flagella scaffolds. Biotechnol Bioeng 2008; 101:873–880 [View Article]
     [Google Scholar]
  21. Dundas CM, Graham AJ, Romanovicz DK, Keitz BK. Extracellular Electron Transfer by Shewanella oneidensis Controls Palladium Nanoparticle Phenotype. ACS Synth Biol 2018; 7:27262736 [View Article]
     [Google Scholar]
  22. Foulkes JM, Deplanche K, Sargent F, Macaskie LE, Lloyd JR. A Novel Aerobic Mechanism for Reductive Palladium Biomineralization and Recovery by Escherichia coli . Geomicrobiol J 2016; 33:230–236 [View Article]
     [Google Scholar]
  23. Qian C, Chen H, Johs A, Lu X, An J et al. Quantitative Proteomic Analysis of Biological Processes and Responses of the Bacterium Desulfovibrio desulfuricans ND132 upon Deletion of Its Mercury Methylation Genes. Proteomics 2018; 18:ARTN 1700479 [View Article]
     [Google Scholar]
  24. Poirier I, Hammann P, Kuhn L, Bertrand M. Strategies developed by the marine bacterium Pseudomonas fluorescens BA3SM1 to resist metals: a proteome analysis. Aquat Toxicol 2013; 128-129:215–232 [View Article]
     [Google Scholar]
  25. Zakeri F, Sadeghizadeh M, Kardan MR, Shahbani Zahiri H, Ahmadian G et al. Differential proteome analysis of a selected bacterial strain isolated from a high background radiation area in response to radium stress. J Proteomics 2012; 75:4820–4832 [View Article]
     [Google Scholar]
  26. Daware V, Kesavan S, Patil R, Natu A, Kumar A et al. Effects of arsenite stress on growth and proteome of Klebsiella pneumoniae. J Biotechnol 2012; 158:8–16 [View Article]
     [Google Scholar]
  27. Postgate JR, Kent HM, Robson RL, Chesshyre JA. The genomes of Desulfovibrio gigas and D. vulgaris. Microbiology 1984; 130:1597–1601 [View Article]
     [Google Scholar]
  28. Le Bihan T, Grima R, Martin S, Forster T, Le Bihan Y. Quantitative analysis of low-abundance peptides in HeLa cell cytoplasm by targeted liquid chromatography/mass spectrometry and stable isotope dilution: emphasising the distinction between peptide detection and peptide identification. Rapid Commun Mass Spectrom 2010; 24:1093–1104 [View Article]
     [Google Scholar]
  29. Hauser LJ, Land ML, Brown SD, Larimer F, Keller KL et al. Complete genome sequence and updated annotation of Desulfovibrio alaskensis G20. J Bacteriol 2011; 193:4268–4269 [View Article]
     [Google Scholar]
  30. Vizcaino JA, Csordas A, del-Toro N, Dianes JA, Griss J et al. 2016 update of the pride database and its related tools (Vol 44, PG D447, 2016). Nucleic Acids Res 2016; 44:11033
     [Google Scholar]
  31. Keller KL, Rapp-Giles BJ, Semkiw ES, Porat I, Brown SD et al. New model for electron flow for sulfate reduction in Desulfovibrio alaskensis G20 . Appl Environ Microbiol 2014; 80:855–868 [View Article]
     [Google Scholar]
  32. Li X, Krumholz LR. Regulation of arsenate resistance in Desulfovibrio desulfuricans G20 by an arsRBCC operon and an arsC gene. J Bacteriol 2007; 189:3705–3711 [View Article]
     [Google Scholar]
  33. Queiroz PS, Ruas FAD, Barboza NR, de Castro Borges W, Guerra-Sá R. Alterations in the proteomic composition of Serratia marcescens in response to manganese (II). BMC Biotechnol 2018; 18:ARTN 83 [View Article]
     [Google Scholar]
  34. Stefanopoulou M, Kokoschka M, Sheldrick WS, Wolters DA. Cell response of Escherichia coli to cisplatin-induced stress. Proteomics 2011; 11:4174–4188 [View Article]
     [Google Scholar]
  35. Zane GM, Yen HB, Wall JD. Effect of the deletion of qmoABC and the promoter-distal gene encoding a hypothetical protein on sulfate reduction in Desulfovibrio vulgaris Hildenborough. Appl Environ Microbiol 2010; 76:5500–5509 [View Article]
     [Google Scholar]
  36. Li X, Luo Q, Wofford NQ, Keller KL, McInerney MJ et al. A molybdopterin oxidoreductase is involved in H2 oxidation in Desulfovibrio desulfuricans G20. J Bacteriol 2009; 191:2675–2682 [View Article]
     [Google Scholar]
  37. Krumholz LR, Bradstock P, Sheik CS, Diao Y, Gazioglu O et al. Syntrophic growth of Desulfovibrio alaskensis requires genes for H2 and formate metabolism as well as those for flagellum and biofilm formation. Appl Environ Microbiol 2015; 81:2339–2348 [View Article]
     [Google Scholar]
  38. Kubacka A, Diez MS, Rojo D, Bargiela R, Ciordia S et al. Understanding the antimicrobial mechanism of TiO2-based nanocomposite films in a pathogenic bacterium. Sci Rep 2015; 4:4134 [View Article]
     [Google Scholar]
  39. Hong R, Kang TY, Michels CA, Gadura N. Membrane lipid peroxidation in copper alloy-mediated contact killing of Escherichia coli . Appl Environ Microbiol 2012; 78:1776–1784 [View Article]
     [Google Scholar]
  40. Johnstone TC, Alexander SM, Lin W, Lippard SJ. Effects of monofunctional platinum agents on bacterial growth: a retrospective study. J Am Chem Soc 2014; 136:116–118 [View Article]
     [Google Scholar]
  41. Pierik AJ, Wolbert RB, Portier GL, Verhagen MF, Hagen WR. Nigerythrin and rubrerythrin from Desulfovibrio vulgaris each contain two mononuclear iron centers and two dinuclear iron clusters. Eur J Biochem 1993; 212:237–245 [View Article]
     [Google Scholar]
  42. Lumppio HL, Shenvi NV, Summers AO, Voordouw G, Kurtz DM. Rubrerythrin and rubredoxin oxidoreductase in Desulfovibrio vulgaris: a novel oxidative stress protection system. J Bacteriol 2001; 183:101–108 [View Article]
     [Google Scholar]
  43. Cadby IT, Faulkner M, Cheneby J, Long J, van Helden J et al. Coordinated response of the Desulfovibrio desulfuricans 27774 transcriptome to nitrate, nitrite and nitric oxide. Sci Rep 2017; 7:16228 [View Article]
     [Google Scholar]
  44. Figueiredo MCO, Lobo SAL, Sousa SH, Pereira FP, Wall JD et al. Hybrid cluster proteins and flavodiiron proteins afford protection to Desulfovibrio vulgaris upon macrophage infection. J Bacteriol 2013; 195:2684–2690 [View Article]
     [Google Scholar]
  45. Wang J, Vine CE, Balasiny BK, Rizk J, Bradley CL et al. The roles of the hybrid cluster protein, HCP and its reductase, HCR, in high affinity nitric oxide reduction that protects anaerobic cultures of Escherichia coli against nitrosative stress. Mol Microbiol 2016; 100:877–892 [View Article]
     [Google Scholar]
  46. Gur E, Biran D, Ron EZ. Regulated proteolysis in Gram-negative bacteria--how and when?. Nat Rev Microbiol 2011; 9:839–848 [View Article]
     [Google Scholar]
  47. Slavin YN, Asnis J, Häfeli UO, Bach H. Metal nanoparticles: understanding the mechanisms behind antibacterial activity. J Nanobiotechnology 2017; 15:65 [View Article]
     [Google Scholar]
  48. Rensing C, Fan B, Sharma R, Mitra B, Rosen BP. CopA: An Escherichia coli Cu(I)-translocating P-type ATPase. Proc Natl Acad Sci U S A 2000; 97:652–656 [View Article]
     [Google Scholar]
  49. Rensing C, Grass G. Escherichia coli mechanisms of copper homeostasis in a changing environment. FEMS Microbiol Rev 2003; 27:197–213 [View Article]
     [Google Scholar]
  50. Argüello JM, González-Guerrero M, Raimunda D. Bacterial transition metal P(1B)-ATPases: transport mechanism and roles in virulence. Biochemistry 2011; 50:9940–9949 [View Article]
     [Google Scholar]
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Shotgun proteomic analysis of nanoparticle-synthesizing Desulfovibrio alaskensis in response to platinum and palladium
Microbiology 165, 1282 (2019); https://doi.org/10.1099/mic.0.000840
/content/journal/micro/10.1099/mic.0.000840
/content/journal/micro/10.1099/mic.0.000840
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