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In silico and in vivo studies of molecular structures and mechanisms of AtPCS1 protein involved in binding arsenite and/or cadmium in plant cells

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Abstract

This paper reports a continuation of our previous research on the phytochelatin synthase1 (PCS1) gene involved in binding and sequestration of heavy metals or metalloids in plant cells [1]. Construction of a 3D structure of the Arabidopsis thaliana PCS1 protein and prediction of gene function by employing iterative implementation of the threading assembly refinement (I-TASSER) revealed that PC ligands (3GC-gamma-glutamylcysteine) and Gln50, Pro53, Ala54, Tyr55, Cys56, Ile102, Gly161, His162, Phe163, Asp204 and Arg211 residues are essential for formation of chelating complex with cadmium (Cd2+) or arsenite (AsIII). This finding suggests that the PCS1 protein might be involved in the production of the enzyme phytochelatin synthase, which might in turn bind, localize, store or sequester heavy metals in plant cells. For validation of the in silico results, we included a T-DNA tagged mutant of Arabidopsis thaliana, SAIL_650_C12, (mutation in AtPCS1 gene) in our investigation. Furthermore, using reverse transcriptase PCR we confirmed that the mutant does not express the AtPCS1 gene. Mutant plants of SAIL_650_C12 were exposed to various amounts of cadmium (Cd2+) and arsenite (AsIII) and the accumulation of these toxic metals in the plant cells was quantified spectrophotometrically. The levels of Cd2+ and AsIII accumulation in the mutant were approximately 2.8 and 1.6 times higher, respectively, than that observed in the wild-type controlled plants. We confirmed that the results obtained in in silico analyses complement those obtained in in vivo experiments.

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References

  1. Lund D, Larsson D, Nahar N, Mandal A (2010) J Biol Syst 18:223–224

    Article  Google Scholar 

  2. Chen Y, Parvez F, Gamble M, Islam T, Ahmed A, Argos M, Graziano JH, Ahsan H (2009) Toxicol Appl Pharmacol 239:184–192

    Article  CAS  Google Scholar 

  3. Zhao FJ, McGrath SP, Meharg A (2010) Annu Rev Plant Biol 61:1–25

    Article  CAS  Google Scholar 

  4. Dhankher OP, Rosen BP, McKinney EC, Meagher RB (2006) Proc Natl Acad Sci USA 103:5413–5418

    Article  CAS  Google Scholar 

  5. Zhu YG, Rosen BP (2009) Curr Opin Biotechnol 20:220–224

    Article  CAS  Google Scholar 

  6. Wu G, Kang H, Zhang X, Shao H, Chu L, Ruan C (2010) J Hazard Mater 174:1–8

    Article  CAS  Google Scholar 

  7. Zhao FJ, Ma JF, Meharg AA, McGrath SP (2009) New Phytol 181:777–794

    Article  CAS  Google Scholar 

  8. Lee DA, Chen A, Schroeder JI (2003) Plant J35:637–646

    Article  CAS  Google Scholar 

  9. Clemens S, Palmgren MG, Krämer U (2002) Trends Plant Sci 7:309–315

    Article  CAS  Google Scholar 

  10. Gasic K, Korban SS (2007) Planta 225:1277–1285

    Article  CAS  Google Scholar 

  11. Tuli R, Chakrabarty D, Trivedi PK, Tripathi RD (2010) Mol Breed 26:307–323

    Article  CAS  Google Scholar 

  12. Cobbett CS, Goldsbrough PB (2002) Annu Rev Plant Biol 53:159–182

    Article  CAS  Google Scholar 

  13. Grill E, Loffler S, Winnacker EL, Zenk MH (1989) Proc Natl Acad Sci USA 86:6838–6842

    Article  CAS  Google Scholar 

  14. Vatamaniuk OK, Mari S, Lang A, Chalasani S, Demkiv L, Rea PA (2004) J Biol Chem 279:22449–22460

    Article  CAS  Google Scholar 

  15. Rea PA (2012) Physiol Plant. doi:10. 1111/j.1399-3054.2012.01571.x

    Google Scholar 

  16. Glaeser H, Coblenz A, Kruczek R, Ruttke I, Ebert-Jung A, Wolf K (1991) Curr Genet 19:207–213

    Article  CAS  Google Scholar 

  17. Cobbett CS (2000) Curr Opin Plant Biol 3:211–216

    Article  CAS  Google Scholar 

  18. Howden R, Goldsbrough PB, Andersen CR, Cobbett CS (1995) Plant Physiol 107:1059–1066

    Article  CAS  Google Scholar 

  19. Brunetti P, Zanella L, Proia A, De Paolis A, Falasca G, Altamura MM, Sanità di Toppi L, Costantino P, Cardarelli M (2011) J Exp Bot 62:5509–5519

    Article  CAS  Google Scholar 

  20. Wojas S, Clemens S, Skłodowska A, Maria Antosiewicz D (2010) J Plant Physiol 167:169–175

    Article  CAS  Google Scholar 

  21. Wojas S, Ruszczyńska A, Bulska E, Clemens S, Antosiewicz DM (2010) J Plant Physiol 167:981–988

    Article  CAS  Google Scholar 

  22. Lee S, Moon JS, Ko TS, Petros D, Goldsbrough PB, Korban SS (2003) Plant Physiol 131:656–663

    Article  CAS  Google Scholar 

  23. Li Y, Dhankher OM, Carreira L, Lee D, Chen A, Schroeder JI, Balish RS, Meagher RB (2004) Plant Cell Physiol 45:1787–1797

    Article  CAS  Google Scholar 

  24. Li J, Guo J, Xu W, Ma M (2006) J Integr Plant Biol 48:928–937

    Article  CAS  Google Scholar 

  25. Liu GY, Zhang YX, Chai TY (2011) Plant Cell Rep 30:1067–1076

    Article  CAS  Google Scholar 

  26. Pittelkow M, Tschapek B, Smits SH, Schmitt L, Bremer E (2011) J Mol Biol 411:53–67

    Article  CAS  Google Scholar 

  27. Lee DS, Kingdon RD, Pacyna JM, Bouwman AF, Tegen I (1999) Atmos Environ 33:2241–2256

    Article  CAS  Google Scholar 

  28. Osguthorpe DJ (2000) Curr Opin Struct Biol 10:146–152

    Article  CAS  Google Scholar 

  29. Browne WJ, North AC, Phillips DC (1969) J Mol Biol 42:65–86

    Article  CAS  Google Scholar 

  30. Sali A, Blundell TL (1993) J Mol Biol 234:779–815

    Article  CAS  Google Scholar 

  31. Sanchez R, Sali A (1997) Proteins 1:50–58

    Article  Google Scholar 

  32. Gerstein M, Levitt M (1997) Proc Natl Acad Sci USA 94:11911–11916

    Article  CAS  Google Scholar 

  33. Fischer D, Eisenberg D (1999) Bioinforma Discov Note 15:759–762

    Article  CAS  Google Scholar 

  34. Roy A, Kucukural A, Zhang Y (2010) Nat Protocols 5:725–738

    Article  CAS  Google Scholar 

  35. McGuffin LJ, Bryson K, Jones DT (2000) Bioinformatics 16:404–405

    Article  CAS  Google Scholar 

  36. Jones DT (1999) J Mol Biol 292:195–202

    Article  CAS  Google Scholar 

  37. Margeleviĉium M, Venclovas C (2005) BMC Bioinforma 6:185

    Article  CAS  Google Scholar 

  38. Eswar N, Marti-Renom MA, Webb B, Madhusudhan MS, Eramian D, Shen M, Pieper U, Sali A (2006) Current Protocols in Bioinformatics. Wiley, New York, Supplement 15, 5.6.1–5.6.30

  39. Kelley LA, Sternberg MJE (2009) Nat Protoc 4(3):363–371

    Article  CAS  Google Scholar 

  40. Xu J, Li M, Kim D, Xu Y (2003) J Bioinforma Comput Biol 1(1):95–117

    Article  CAS  Google Scholar 

  41. Schwede T, Kopp J, Guex N, Peitsch MC (2003) Nucleic Acids Res 31(13):3381–3385

    Article  CAS  Google Scholar 

  42. Wu S, Zhang Y (2007) Nucleic Acids Res 35:3375–3382

    Article  CAS  Google Scholar 

  43. Margeleviĉium M, Laganeckas M, Venclovas C (2010) Bioinformatics 26:1905–1906

    Article  CAS  Google Scholar 

  44. Shi J, Blundell TL, Mizuguchi K (2001) J Mol Biol 310:243–257

    Article  CAS  Google Scholar 

  45. Sording J (2005) Bioinformatics 21:951–960

    Article  Google Scholar 

  46. Wu S, Zhang Y (2008) Proteins Struct Funct Bioinforma 72:547–556

    Article  CAS  Google Scholar 

  47. Xu Y, Xu D (2000) Proteins 40:343–354

    Article  CAS  Google Scholar 

  48. Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diekhans M, Hughey R (2003) Proteins 53:491–496

    Article  CAS  Google Scholar 

  49. Zhou H, Zhou Y (2004) Proteins 55:1005–1013

    Article  CAS  Google Scholar 

  50. Zhou H, Zhou Y (2005) Proteins 58:321–328

    Article  CAS  Google Scholar 

  51. Lee D, Redfern O, Orengo C (2007) Nat Rev Mol Cell Biol 8:995–1005

    Article  CAS  Google Scholar 

  52. Wu S, Zhang Y (2008) Bioinformatics 24:924–931

    Article  CAS  Google Scholar 

  53. Zhang Y, Skolnick J (2004) J Comput Chem 25:865–871

    Article  CAS  Google Scholar 

  54. Holm L, Sander C (1991) J Biol 218:183–194

    Article  CAS  Google Scholar 

  55. McDonald IK, Thornton JM (1994) J Mol Biol 238:777–793

    Article  CAS  Google Scholar 

  56. Bennett MJ, Schlunegger MP, Eisenberg D (1995) Protein Sci 4:2455–2468

    Article  CAS  Google Scholar 

  57. Zhang Y, Skolnick J (2005) Nucleic Acids Res 33:2302–2309

    Article  CAS  Google Scholar 

  58. Li YQ, Zhang Y (2009) Proteins 76:665–676

    Article  CAS  Google Scholar 

  59. Buck M, Bonnet BS, Pastor WR, MacKerell DA (2006) Biophys J 90:36–38

    Article  CAS  Google Scholar 

  60. Lee SY, Skolnick J (2008) Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints. Biophys J 95:1956–1964

    Article  CAS  Google Scholar 

  61. Wiederstein M, Sippl MJ (2007) Nucleic Acids Res 35:407–410

    Article  Google Scholar 

  62. Alonso MJ, Stepanova NA, Leisse JT, Kim JC, Chen H, Shinn P, Stevenson KD, Zimmerman J, Barajas P, Cheuk R et al (2003) Science 301:653–657

    Article  Google Scholar 

  63. Murashige T, Skoog F (1962) Physiol Planta 15:473–497

    Article  CAS  Google Scholar 

  64. Svensson M, Lund D, Ejdebäck M, Mandal A (2004) J Mol Model 10:130–138

    Article  CAS  Google Scholar 

  65. Nahar N, Rahman A, Moś M, Warzecha T, Algerin M, Ghosh S, Johnson-Brousseau S, Mandal A (2012) J Mol Model 18:4249–4262

    Article  CAS  Google Scholar 

  66. Elke M, Lorentzen L, Kingston HM (1996) Anal Chem 68:4316–4320

    Article  Google Scholar 

  67. Kumar R, Kumar S, Sangwan S, Yadav IS, Yadav R (2011) J Mol Graph Model 29:740–746

    Article  CAS  Google Scholar 

  68. Biarnés X, Bongarzone S, Vargiu AV, Carloni P, Ruggerone P (2011) J Comput Aided Mol 25:395–402

    Article  CAS  Google Scholar 

  69. Haq ul Z, Khan W (2011) J Comput Aided Mol 25:81–101

    Article  CAS  Google Scholar 

  70. Cobbett CS (1999) Plant Cell 11:1153–3363

    Google Scholar 

  71. Ruotolo R, Peracchi A, Bolchi A, Infusini G, Amoresano A, Ottonello S (2004) J Biol Chem 279:14686–14693

    Article  CAS  Google Scholar 

  72. Tsuji N, Nishikori S, Iwabe O, Shiraki K, Miyasaka H, Takagi M, Hirata K, Miyamoto K (2004) Biochem Biophys Res Commun 315:751–755

    Article  CAS  Google Scholar 

  73. Maier T, Yu C, Küllertz G, Clemens S (2003) Planta 218:300–308

    Article  CAS  Google Scholar 

  74. Romanyuk ND, Rigden DJ, Vatamaniuk OK, Lang A, Cahoon RE, Jez JM, Rea PA (2006) Plant Physiol 141:858–869

    Article  CAS  Google Scholar 

  75. Liu WJ, Wood BA, Raab A, McGrath SP, Zhao FJ, Feldmann J (2010) Plant Physiol 152:2211–2221

    Article  CAS  Google Scholar 

  76. Shukla D, Kesari R, Mishra S, Dwivedi S, Tripathi RD, Nath P, Trivedi PK (2012) Plant Cell Rep 31:1687–1699

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This present study was supported financially partly by the Swedish International Development Cooperation Agency (SIDA, grant no. AKT-2010-018) and partly by the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (FORMAS, grant no.229-2007-217). We also acknowledge a grant from the Nilsson-Ehle Foundation (The Royal Physiographic Society in Lund). We would like to thank (1) the European Arabidopsis Stock Center, Nottingham (NASC) for providing us with their SAIL mutants, and (2) the I-TASSER server team for providing us with their programs and software for computational analyses.

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Authors and Affiliations

  1. School of Biological Sciences, System Biology Research Center, University of Skövde, PO Box 408, 541 28, Skövde, Sweden

    Noor Nahar, Aminur Rahman & Abul Mandal

  2. Department of Plant Breeding and Seed Science, University of Agriculture in Krakow, Krakow, Poland

    Maria Moś & Tomasz Warzecha

  3. School of Arts and Science, Iona College, New Rochelle, NY, 10801, USA

    Sibdas Ghosh

  4. Department of Biochemistry and Molecular Biology, University of Rajshahi, 6205, Rajshahi, Bangladesh

    Khaled Hossain

  5. Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth University, Tathawade, Pune, 411033, India

    Neelu N. Nawani

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  1. Noor Nahar
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Correspondence to Abul Mandal.

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Nahar, N., Rahman, A., Moś, M. et al. In silico and in vivo studies of molecular structures and mechanisms of AtPCS1 protein involved in binding arsenite and/or cadmium in plant cells. J Mol Model 20, 2104 (2014). https://doi.org/10.1007/s00894-014-2104-0

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