Journal of Biosciences

, 44:15 | Cite as

Characterization and DNA methylation modulatory activity of gold nanoparticles synthesized by Pseudoalteromonas strain

  • Yugandhara M Patil
  • Shriram N Rajpathak
  • Deepti D DeobagkarEmail author


Marine extremophiles are shown to tolerate extreme environmental conditions and have high metal reducing properties. Here, we report intracellular synthesis of gold nanoparticles (AuNP) by marine extremophilic bacteria Pseudoalteromonas sp. Bac178 which was isolated from the OMZ of Arabian Sea. Preliminary observations suggest that these bacteria use different pathways which may involves the membrane as well as intracellular proteins for the gold salt reduction. Characterization of the biosynthesised nanoparticles by various techniques such as Scanning electron microscopy (SEM), Transmission electron microscopy (TEM), X-ray diffraction (XRD) and Energy-dispersive X-ray spectroscopy (EDS) confirmed the presence of crystalline gold. These biologically synthesized AuNP were investigated for cytotoxicity and oxidative stress generation in human normal fibroblast and melanoma cells (A375). As AuNP are envisaged to find many applications in the medical field, it was of interest to study the effect of AuNP at the epigenetic level. They were found to be non-cytotoxic, non-genotoxic and non-oxidative stress generating over a range of concentrations. Exposure to these AuNP is observed to cause alterations in global DNA methylation as well as in the expression of DNA methyltransferase (DNMT) genes. Since biosynthesized AuNP are being used in various applications and therapies, their epigenetic modulatory activity needs careful consideration.


DNA methylation DNMT epigenetics gold nanoparticles oxygen minimum zone 



This work was funded by Ministry of Earth Sciences (MoES), Government of India (Grant No. GOI-687), under the Microbial Oceanography scheme. The funding agency had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Supplementary material

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  1. Achwal CW, Iyer CA and Chandra HS 1983 Immunochemical evidence for the presence of 5 mC, 6 mA and 7 mG in human, Drosophila and mealybug DNA. FEBS Lett. 158 353–358CrossRefGoogle Scholar
  2. Ahmad A, Senapati S, Khan MI, Kumar R, Ramani R, Srinivas V and Sastry M 2003 Intracellular synthesis of gold nanoparticles by a novel alkalotolerant actinomycete, Rhodococcus species. Nanotechnology 14 824–828CrossRefGoogle Scholar
  3. Amin ZR, Khashyarmanesh Z and Bazzaz BSF 2016 Different behavior of Staphylococcus. World J. Microbiol. Biotechnol. 32 1–11CrossRefGoogle Scholar
  4. Bakr OM, Wunsch BH and Stellacci F 2006 High-Yield Synthesis of multi-branched urchin-like gold nanoparticles. Chem. Mater. 18(14) 3297–3301CrossRefGoogle Scholar
  5. Balansky R, Longobardi M, Ganchev G, Iltcheva M, Nedyalkov N, Atanasov P, et al. 2013 Transplacental clastogenic and epigenetic effects of gold nanoparticles in mice. Mutat. Res. Mol. Mech. Mutagen. 751 42–48CrossRefGoogle Scholar
  6. Balasubramanian SK, Yang L, Yung L-YL, Ong C-N, Ong W-Y and Yu LE 2010 Characterization, purification and stability of gold nanoparticles. Biomaterials 31 9023–9030CrossRefGoogle Scholar
  7. Beeler E and Singh OV 2016 Extremophiles as sources of inorganic bio-nanoparticles. World J. Microbiol. Biotechnol. 32 156CrossRefGoogle Scholar
  8. Binupriya AR, Sathishkumar M and Yun S-I 2009 Myco-crystallization of silver ions to nanosized particles by live and dead cell filtrates of Aspergillus oryzae var. viridis and its bactericidal activity toward Staphylococcus aureus KCCM 12256. Ind. Eng. Chem. Res. 49 852–858CrossRefGoogle Scholar
  9. Bishayee K, Khuda-Bukhsh AR and Huh S-O 2015 PLGA-loaded gold-nanoparticles precipitated with quercetin downregulate HDAC-Akt activities controlling proliferation and activate p53-ROS crosstalk to induce apoptosis in hepatocarcinoma cells. Mol. Cells 38 518CrossRefGoogle Scholar
  10. Chew W-S, Poh K-W, Siddiqi NJ, Alhomida AS, Yu LE and Ong W-Y 2012 Short-and long-term changes in blood miRNA levels after nanogold injection in rats—potential biomarkers of nanoparticle exposure. Biomarkers 17 750–757CrossRefGoogle Scholar
  11. Choi AO, Brown SE, Szyf M and Maysinger D 2008 Quantum dot-induced epigenetic and genotoxic changes in human breast cancer cells. J. Mol. Med. 86 291–302CrossRefGoogle Scholar
  12. Chueh PJ, Liang R-Y, Lee Y-H, Zeng Z-M and Chuang S-M 2014 Differential cytotoxic effects of gold nanoparticles in different mammalian cell lines. J. Hazard. Mater. 264 303–312CrossRefGoogle Scholar
  13. Coates J 2000 Interpretation of infrared spectra, a practical approach. Encycl. Anal. Chem. 1–23.
  14. Correa-Llantén DN, Muñoz-Ibacache SA, Castro ME, Muñoz PA and Blamey JM 2013 Gold nanoparticles synthesized by Geobacillus sp. strain ID17 a thermophilic bacterium isolated from Deception Island, Antarctica. Microb. Cell Factories 12 75CrossRefGoogle Scholar
  15. Debabov VG, Voeikova TA, Shebanova AS, Shaitan KV, Emel’yanova LK, Novikova LM and Kirpichnikov MP 2013 Bacterial synthesis of silver sulfide nanoparticles. Nanotechnologies Russ. 8 269–276CrossRefGoogle Scholar
  16. Deobagkar DD, Panikar C, Rajpathak SN, Shaiwale NS and Mukherjee S 2012 An immunochemical method for detection and analysis of changes in methylome. Methods 56 260–267CrossRefGoogle Scholar
  17. Dykman LA and Khlebtsov NG 2011 Gold nanoparticles in biology and medicine: recent advances and prospects. Acta Naturae 3 34–55PubMedPubMedCentralGoogle Scholar
  18. Ehrlich M 2009 DNA hypomethylation in cancer cells. Epigenomics 1 239–259CrossRefGoogle Scholar
  19. Eom H-J, Chatterjee N, Lee J and Choi J 2014 Integrated mRNA and micro RNA profiling reveals epigenetic mechanism of differential sensitivity of Jurkat T cells to AgNPs and Ag ions. Toxicol. Lett. 229 311–318CrossRefGoogle Scholar
  20. Field J, Nikawa J, Broek D, MacDonald B, Rodgers L, Wilson IA, et al. 1988 Purification of a RAS-responsive adenylyl cyclase complex from Saccharomyces cerevisiae by use of an epitope addition method. Mol. Cell. Biol. 8 2159–2165CrossRefGoogle Scholar
  21. Foldbjerg R, Irving ES, Hayashi Y, Sutherland DS, Thorsen K, Autrup H and Beer C 2012 Global gene expression profiling of human lung epithelial cells after exposure to nanosilver. Toxicol. Sci. 130 145–157CrossRefGoogle Scholar
  22. Gong C, Tao G, Yang L, Liu J, Liu Q, Li W and Zhuang Z 2012 Methylation of PARP-1 promoter involved in the regulation of nano-SiO 2-induced decrease of PARP-1 mRNA expression. Toxicol. Lett. 209 264–269CrossRefGoogle Scholar
  23. Gong C, Tao G, Yang L, Liu J, Liu Q and Zhuang Z 2010 SiO 2 nanoparticles induce global genomic hypomethylation in HaCaT cells. Biochem. Biophys. Res. Commun. 397 397–400CrossRefGoogle Scholar
  24. Ho DH and Tollefsbol T 2014 Historical perspective of transgenerational epigenetics. Transgenerational Epigenetics Evid. Debate 17–23.
  25. Horowitz S 2015 Epigenetics and Its Clinical Applications. Altern. Complement. Ther. 21 269–275CrossRefGoogle Scholar
  26. Kelkar A and Deobagkar D 2009 A novel method to assess the full genome methylation profile using monoclonal antibody combined with the high throughput based microarray approach. Epigenetics 4 415–420CrossRefGoogle Scholar
  27. Khlebtsov NG and Dykman LA 2010 Optical properties and biomedical applications of plasmonic nanoparticles. J. Quant. Spectrosc. Radiat. Transf. 111 1–35CrossRefGoogle Scholar
  28. Kulkarni RR, Shaiwale NS, Deobagkar DN and Deobagkar DD 2015 Synthesis and extracellular accumulation of silver nanoparticles by employing radiation-resistant Deinococcus radiodurans, their characterization and determination of bioactivity. Int. J. Nanomedicine 10 963PubMedPubMedCentralGoogle Scholar
  29. Kuo C-H and Huang MH 2005 Synthesis of Branched Gold Nanocrystals by a Seeding Growth Approach. Langmuir 21 2012–2016CrossRefGoogle Scholar
  30. Li M and Yu X 2015 The role of poly (ADP-ribosyl) ation in DNA damage response and cancer chemotherapy. Oncogene 34 3349CrossRefGoogle Scholar
  31. Li P, Shi Y, Li B, Xu W, Shi Z, Zhou C and Fu S 2015 Photo-thermal effect enhances the efficiency of radiotherapy using Arg-Gly-Asp peptides-conjugated gold nanorods that target αvβ3 in melanoma cancer cells. J. Nanobiotechnology 13 52CrossRefGoogle Scholar
  32. Li S, Wang, Yong, Wang H, Bai Y, Liang G, Wang, Yuanyuan, et al. 2011 MicroRNAs as participants in cytotoxicity of CdTe quantum dots in NIH/3T3 cells. Biomaterials 32 3807–3814CrossRefGoogle Scholar
  33. Lindsay S 2009 Introduction to Nanoscience (Oxford University Press, Oxford, New York)Google Scholar
  34. Ma Y, Fu H, Zhang C, Cheng S, Gao J, Wang Z, et al. 2016 Chiral antioxidant-based gold nanoclusters reprogram DNA epigenetic patterns. Sci. Rep. 6 33436CrossRefGoogle Scholar
  35. Mahdieh M, Zolanvari A and Azimee AS 2012 Green biosynthesis of silver nanoparticles by Spirulina platensis. Sci. Iran. 19 926–929CrossRefGoogle Scholar
  36. Mateo D, Morales P, Ávalos A and Haza AI 2015 Comparative cytotoxicity evaluation of different size gold nanoparticles in human dermal fibroblasts. J. Exp. Nanosci. 10 1401–1417CrossRefGoogle Scholar
  37. Mosmann T 1983 Rapid colorimetric assay for cellular growth and survival: Application to proliferation and cytotoxicity assays. J. Immunol. Methods 65 55–63CrossRefGoogle Scholar
  38. Mukherjee P, Ahmad A, Mandal D, Senapati S, Sainkar SR, Khan MI, et al. 2001 Bioreduction of AuCl4− Ions by the Fungus, Verticillium sp. and Surface Trapping of the Gold Nanoparticles Formed. Angew. Chem. Int. Ed. 40 3585–3588CrossRefGoogle Scholar
  39. Mytych J, Zebrowski J, Lewinska A and Wnuk M 2017 Prolonged effects of silver nanoparticles on p53/p21 pathway-mediated proliferation, DNA damage response and methylation parameters in HT22 hippocampal neuronal cells. Mol. Neurobiol. 54 1285–1300CrossRefGoogle Scholar
  40. Ng C-T, Dheen ST, Yip W-CG., Ong C-N, Bay B-H and Yung L-YL. 2011 The induction of epigenetic regulation of PROS1 gene in lung fibroblasts by gold nanoparticles and implications for potential lung injury. Biomaterials 32 7609–7615CrossRefGoogle Scholar
  41. Oelshlegel FJ, Schroeder JR and Stahmann MA 1970 A simple procedure for basic hydrolysis of proteins and rapid determination of tryptophan using a starch column. Anal. Biochem. 34 331–337CrossRefGoogle Scholar
  42. Pages D, Rose J, Conrod S, Cuine S, Carrier P, Heulin T and Achouak W 2008 Heavy Metal Tolerance in Stenotrophomonas maltophilia. PLoS ONE 3 e1539CrossRefGoogle Scholar
  43. Patil NA, Gade W and Deobagkar DD 2016 Epigenetic modulation upon exposure of lung fibroblasts to TiO2 and ZnO nanoparticles: alterations in DNA methylation. Int. J. Nanomedicine 11 4509–4519CrossRefGoogle Scholar
  44. Pinto VV, Ferreira MJ, Silva R, Santos HA, Silva F and Pereira CM 2010 Long time effect on the stability of silver nanoparticles in aqueous medium: Effect of the synthesis and storage conditions. Colloids Surf. Physicochem. Eng. Asp. 364 19–25CrossRefGoogle Scholar
  45. Polverino A, Longo A, Donizetti A, Drongitis D, Frucci M, Schiavo L, et al. 2014 Molecular responses of cells to 2-mercapto-1-methylimidazole gold nanoparticles (AuNPs)-mmi: investigations of histone methylation changes. J. Nanoparticle Res. 16 2516CrossRefGoogle Scholar
  46. Prakash A, Sharma S, Ahmad N, Ghosh A and Sinha P 2011 Synthesis of AgNps By Bacillus cereus bacteria and their antimicrobial potential. J. Biomater. Nanobiotechnology 2 156CrossRefGoogle Scholar
  47. Qian Y, Zhang J, Hu Q, Xu M, Chen Y, Hu G, et al. 2015 Silver nanoparticle-induced hemoglobin decrease involves alteration of histone 3 methylation status. Biomaterials 70 12–22CrossRefGoogle Scholar
  48. Schmittgen TD and Livak KJ 2008 Analyzing real-time PCR data by the comparative CT method. Nat. Protoc. 3 1101CrossRefGoogle Scholar
  49. Schneider CA, Rasband WS and Eliceiri KW 2012 NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9 671–675CrossRefGoogle Scholar
  50. Senut M-C, Zhang Y, Liu F, Sen A, Ruden DM and Mao G 2016 Size-Dependent Toxicity of Gold Nanoparticles on Human Embryonic Stem Cells and Their Neural Derivatives. Small 12 631–646CrossRefGoogle Scholar
  51. Serpooshan V, Sheibani S, Pushparaj P, Wojcik M, Jang AY, Santoso MR, et al. 2018 Effect of Cell Sex on Uptake of Nanoparticles: The Overlooked Factor at the Nanobio Interface. ACS Nano 12(3) 2253–2266CrossRefGoogle Scholar
  52. Seshadri S, Prakash A and Kowshik M 2012 Biosynthesis of silver nanoparticles by marine bacterium, Idiomarina sp. PR58-8. Bull. Mater. Sci. 35 1201–1205CrossRefGoogle Scholar
  53. Shah R, Oza G, Pandey S and Sharon M 2017 Biogenic Fabrication of Gold Nanoparticles using Halomonas salina. J. Microbiol. Biotechnol. Res. 2 485–492Google Scholar
  54. Shankar SS, Rai A, Ahmad A and Sastry M 2004 Rapid synthesis of Au, Ag and bimetallic Au core–Ag shell nanoparticles using Neem (Azadirachta indica) leaf broth. J. Colloid Interface Sci. 275 496–502CrossRefGoogle Scholar
  55. Sharma N, Pinnaka AK, Raje M, Ashish FNU., Bhattacharyya MS and Choudhury AR 2012 Exploitation of marine bacteria for production of gold nanoparticles. Microb. Cell Factories 11 86CrossRefGoogle Scholar
  56. Stalin Dhas T, Ganesh Kumar V, Stanley Abraham L, Karthick V and Govindaraju K 2012 Sargassum myriocystum mediated biosynthesis of gold nanoparticles. Spectrochim. Acta. A. Mol. Biomol. Spectrosc. 99 97–101CrossRefGoogle Scholar
  57. Suman TY, Rajasree SR, Ramkumar R, Rajthilak C and Perumal P 2014 The Green synthesis of gold nanoparticles using an aqueous root extract of Morinda citrifolia L. Spectrochim. Acta. A. Mol. Biomol. Spectrosc. 118 11–16CrossRefGoogle Scholar
  58. Toyooka T, Amano T and Ibuki Y 2012 Titanium dioxide particles phosphorylate histone H2AX independent of ROS production. Mutat. Res. Toxicol. Environ. Mutagen. 742 84–91CrossRefGoogle Scholar
  59. Tsoli M, Kuhn H, Brandau W, Esche H and Schmid G 2005 Cellular Uptake and Toxicity of Au55 Clusters. Small 1 841–844CrossRefGoogle Scholar
  60. Wang C-Y, Wu S-J, Ng C-C, Tzeng W-S and Shyu Y-T 2012 Halomonas beimenensis sp. nov., isolated from an abandoned saltern. Int. J. Syst. Evol. Microbiol. 62 3013–3017CrossRefGoogle Scholar
  61. Xia Q, Li H, Liu Y, Zhang S, Feng Q and Xiao K 2017 The effect of particle size on the genotoxicity of gold nanoparticles: the effect of particle size on the genotoxicity of gold nanoparticles. J. Biomed. Mater. Res. A 105 710–719CrossRefGoogle Scholar
  62. Xu W, Luo T, Li P, Zhou C, Cui D, Pang B, et al. 2012 RGD-conjugated gold nanorods induce radiosensitization in melanoma cancer cells by downregulating αvβ3 expression. Int. J. Nanomed 7 915Google Scholar

Copyright information

© Indian Academy of Sciences 2019

Authors and Affiliations

  • Yugandhara M Patil
    • 1
  • Shriram N Rajpathak
    • 1
  • Deepti D Deobagkar
    • 1
    • 2
    Email author
  1. 1.Molecular Biology Research Laboratory, Centre of Advanced Studies, Department of ZoologySavitribai Phule Pune UniversityPuneIndia
  2. 2.ISRO Chair ProfessorSavitribai Phule Pune UniversityPuneIndia

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