Skip to main content
SpringerLink
Log in

Application of bioinformatics tools and databases in microbial dehalogenation research: A review

  • Published:
Applied Biochemistry and Microbiology Aims and scope Submit manuscript

Abstract

Microbial dehalogenation is a biochemical process in which the halogenated substances are catalyzed enzymatically in to their non-halogenated form. The microorganisms have a wide range of organohalogen degradation ability both explicit and non-specific in nature. Most of these halogenated organic compounds being pollutants need to be remediated; therefore, the current approaches are to explore the potential of microbes at a molecular level for effective biodegradation of these substances. Several microorganisms with dehalogenation activity have been identified and characterized. In this aspect, the bioinformatics plays a key role to gain deeper knowledge in this field of dehalogenation. To facilitate the data mining, many tools have been developed to annotate these data from databases. Therefore, with the discovery of a microorganism one can predict a gene/protein, sequence analysis, can perform structural modelling, metabolic pathway analysis, biodegradation study and so on. This review highlights various methods of bioinformatics approach that describes the application of various databases and specific tools in the microbial dehalogenation fields with special focus on dehalogenase enzymes. Attempts have also been made to decipher some recent applications of in silico modeling methods that comprise of gene finding, protein modelling, Quantitative Structure Biodegradibility Relationslup (QSBR) study and reconstruction of metabolic pathways employed in dehalogenation research area.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Gribble, G.W., Environ. Sci. Technol., 1994, vol. 28, no. 7, pp. 310–319.

    Article  Google Scholar 

  2. Song, B., Palleroni, N.J., and Häggblom, M.M., Appl. Environ. Microbiol., 2000, vol. 66, no.8, pp. 3446–3453.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  3. Perocco, P., Bolognesi, S., and Alberghini, W., Toxicol. Lett., 1983, vol. 16, nos. 1–2, pp. 69–75.

    Article  CAS  PubMed  Google Scholar 

  4. Rees, H.C., Oswald, S.E., Banwart, S.A., Pickup, R.W., and Lerner, D.N, Appl. Environ. Microbiol., 2007, vol. 73, no. 12, pp. 3865–3876.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  5. van Wyk, E., Bouwman, H., van der Bank, H., Verdoorn, G.H., and Hofmann, D., Comp. Biochem. Physiol. C Toxicol. Pharmacol., 2001, vol. 129, no.3, pp. 243–264.

    Article  PubMed  Google Scholar 

  6. Chunjiao, L., Lirong, Y., Gang, X., and Jianping, W., Appl. Microbiol. Biotechnol., 2011, vol. 90, no.2, pp. 689–696.

    Article  Google Scholar 

  7. Asgard, S., Ulrike, J., Elke, H., and Frieder, S., Appl. Environ. Microbiol., 2001, vol. 67, no. 9, pp. 4377–4381.

    Article  Google Scholar 

  8. Janssen, D.B, Pries, F., and Van der Ploeg, J.R., Ann. Rev. Microbiol., 1994, vol. 48, pp. 163–191.

    Article  CAS  Google Scholar 

  9. Chaudhry, G.R. and Chapalamadugu, S., Microbiol. Mol. Biol. Rev., 1991, vol. 55, no. 1, pp. 59–79.

    CAS  Google Scholar 

  10. Heinz van Pee, K. and Unversucht, S., Chemosphere, 2003, vol. 52, no.2, pp. 299–312.

    Article  Google Scholar 

  11. Fishbein, L., Sci. Total Environ., 1979, vol. 11, no. 3, pp. 259–278.

    Article  CAS  PubMed  Google Scholar 

  12. Lee, M.D., Odom, J.M., and Buchanan, R.J., Ann. Rev. Microbiol., 1998, vol. 52, pp. 423–452.

    Article  CAS  Google Scholar 

  13. Singh, A. and Ward, O.P., Biodegradation and Bioremediation, Heidelberg: Soil Biology, Springer, 2004. doi: 10.1007/978-3-662-06066-7-1

    Book  Google Scholar 

  14. Janssen, D.B., Oppentocht, J.E., and Poelarends, G.J., Curr. Opin. Biotechnol., 2001, vol. 12, no.3, pp. 254–258.

    Article  CAS  PubMed  Google Scholar 

  15. Nagata, Y., Prokop, Z., Sato, Y., Jerabek, P., Kumar, A., Ohtsubo Y, Tsuda M, and Damborsky J., Appl. Environ. Microbiol., 2005, vol. 71, no.4, pp. 2183–2185.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  16. Kaminski, N., Am. J. Respir. Cell Mol. Biol., 2000, vol. 23, no.6, pp. 705–711.

    Article  CAS  PubMed  Google Scholar 

  17. Altman, R.B., Brief Bioinformatics, 2004, vol. 5, no. 1, pp. 4–5.

    Article  PubMed  Google Scholar 

  18. Hogeweg, P., PLoS Comput. Biol., 2011, vol. 7, p. e1002021. doi: 10.1371/journal.pcbi.1002021

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  19. Teufel, A., Krupp, M., Weinmann, A., and Galle, P.R., Int. J. Mol.Med., 2006, vol. 17 no. 6, pp. 967–973.

    CAS  PubMed  Google Scholar 

  20. Johnson, A.D., Circ. Cardiovasc. Genet., 2009, vol. 2, no. 5, pp. 530–536.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  21. Baker, P.G., Goble, C.A., Bechhofer, S., Paton, N.W., Stevens, R., and Brass A., Bioinformatics, 1999, vol.15, no. 6, pp. 510–520.

    Article  CAS  PubMed  Google Scholar 

  22. Francois, B. and Kroger, P., Distributed Parallel Data-bases, 2003, vol. 13, no.1, pp. 7–42.

    Article  Google Scholar 

  23. Liu, Y. and Zhao, H., BMC Bioinformatics, 2004, vol. 25, pp. 158.

    Article  Google Scholar 

  24. Bansal, A.K., Microb. Cell Fact., vol. 4, p. 19. doi: 10.1186/1475-2859-4-19

  25. Moore, J.H., Asselbergs, F.W, and Williams, S.M., Bioinformatics, 2010, vol. 26, no. 4, pp. 445–455.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  26. Zhang, S., Golbraikh, A., and Tropsha, A., J. Med. Chem., 2006, vol. 49, no.9, pp. 2713–2724.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  27. Rastogi, S. and Rost, B., Methods Mol. Biol., 2010, vol. 619, pp. 285–305.

    Article  CAS  PubMed  Google Scholar 

  28. Rapin, N., Lund, O., Bernaschi, M., and Castiglione, F., Plos One, 2010, vol. 5, p. e9862. doi:10.1371/journal.pone.0009862

    Article  PubMed Central  PubMed  Google Scholar 

  29. Huang, H., Patskovsky, Y., Toro, R., Farelli, J.D., Pandya, C., Almo, S.C. et al., Biochemistry, 2011, vol. 50, no. 41, pp. 8937–8949.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  30. Novak, H.R., Sayer, C., Isupov, M.N, Paszkiewicz, K., Gotz, D., Spragg, A.M, and Littlechild, J.A., FEBS J., 2013, vol. 280, no. 7, pp. 1664–1680.

    Article  CAS  PubMed  Google Scholar 

  31. Ryu, D.D. and Nam, D.H., Biotechnol Prog., 2000, vol. 16, no.1, pp. 2–16.

    Article  CAS  PubMed  Google Scholar 

  32. Yu, H.M, Luo, H., Shi, Y., Sun, X.D, and Shen, Z.Y., Sheng Wu Gong Cheng Xue Bao, 2004, vol. 20, no.3, pp. 325–331.

    PubMed  Google Scholar 

  33. Karp, P.D., Paley, S., and Romero, P., Bioinformatics, 2002, vol.18, pp. 225–232.

    Article  Google Scholar 

  34. Caspi, R. and Karp, P.D., Curr. Protoc. Bioinformatics, 2007. doi: 10.1002/0471250953.bi0117s20

    Google Scholar 

  35. Aguda, B.D. and Goryachev, A.B., PLoS Comput. Biol., 2007, vol.3, pp. 1674–1678.

    Article  CAS  PubMed  Google Scholar 

  36. Murzin, A.G., Brenner, S.E., Hubbard, T., and Chothia, C., J. Mol. Biol., 1995, vol. 247, no.4, pp. 536–540.

    CAS  PubMed  Google Scholar 

  37. Lord, P.W., Stevens, R.D., Brass, A., and Goble, C.A., Bioinformatics, 2003, vol. 19, no.10, pp. 1275–1283.

    Article  CAS  PubMed  Google Scholar 

  38. Bray J.E., Todd, A.E., Pearl, F.M., Thornton, J.M., and Orengo, C.A., Protein Eng., 2000, vol.13, no. 3, pp. 153–165.

    Article  CAS  PubMed  Google Scholar 

  39. Casbon, J. and Saqi, M.A., Nucleic Acids Res., 2005, vol. 33, pp. 219–222.

    Article  Google Scholar 

  40. He, J., Qin, W., Zhang, X., Wen, Y., Su, L., and Zhao, Y., Sci. Total Environ., 2013, vol. 444, pp. 392–400.

    Article  CAS  PubMed  Google Scholar 

  41. Aworska, J.S., Boethling, R.S., and Howard, P.H., Environ. Toxicol. Chem., 2003, vol. 22, no.8, pp. 1710–1723.

    Article  Google Scholar 

  42. Chaffron, S., Rehrauer, H., Pernthaler, J., and von Mering, C., Genome Res., 2010, vol. 20, no.7, pp. 947–959.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  43. Ilić, M., Antić, M., Antić, V., Schwarzbauer, J., Vrvić, M., and Jovančcićević, B., Environ. Chem. Lett., 2011, vol. 9, no.1, pp.133–140.

    Article  Google Scholar 

  44. Ecker, D.J., Sampath, R., Willett, P., Wyatt. J.R., Samant, V., Massire, C., et al., BMC Microbiol., 2005, vol. 25, pp. 5–19.

    Google Scholar 

  45. Hocquette, J.F., J. Physiol. Pharmacol., 2005, vol. 56, no. 3, pp. 37–70.

    PubMed  Google Scholar 

  46. Noguchi, H., Park, J., and Takagi, T., Nucleic Acids Res., 2006, vol. 34, no. 19, pp. 5623–5630.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  47. Rho, M., Tang, H., and Ye, Y., Nucleic Acids Res., 2010, vol. 38, no. 20. doi: 10.1093/nar/gkq747

    Google Scholar 

  48. Ter-Hovhannisyan, V., Lomsadze, A., Chernoff, Y.O., and Borodovsky, M., Genome Res., 2008, vol. 18, no.12, pp. 1979–1790.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  49. Nayarisseri, A., Yadav, M., Lokhande, V., Patidar, R., and Mayna, M., Nature Precedings, 2011. doi:10.1038/npre.2011.5806.1

    Google Scholar 

  50. Mathe, C., Sagot M.F, Schiex T., and Rouzé, P., Nucleic Acids Res., 2002, vol. 30, no.19, pp. 4103–4117.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  51. Kim, S.H., Harzman, C., Davis, J.K., Hutcheson, R., Broderick, J.B., Marsh, T.L., and Tiedje, J.M., BMC Microbiol., 2012, vol. 12, p. 21. doi: 10.1186/1471-2180-12-21

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  52. Sudi, I.Y., Wong, E.L., Joyce-Tan, K.H., Shamsir, M.S., Jamaluddin, H., and Huyop, F., Int. J. Mol. Sci., 2012, vol.13, no.12, pp. 15724–15754.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  53. Zhang, Y., Li, Z.S, Wu, J.Y, Sun., M, Zheng, Q.C., and Sun, C.C., Biochem. Biophys. Res. Commun., 2004, vol. 325, no.2, pp.414–420.

    Article  CAS  PubMed  Google Scholar 

  54. Marsh, A., and Ferguson, D.M., Proteins, 1997, vol. 28, no.2, pp. 217–226.

    Article  CAS  PubMed  Google Scholar 

  55. Krooshof, G.H., Kwant, E.M., Damborsky, J., Koca, J., and Janssen, D.B., Biochemistry, 1997, vol. 36, no.31, pp. 9571–9580.

    Article  CAS  PubMed  Google Scholar 

  56. Ichiyama, S., Kurihara, T., Miyagi, M., Galkin, A., Tsunasawa. S., Kawasaki, H., and Esaki, N., J. Biochem., 2002, vol. 131, no.5, pp. 671–677.

    Article  CAS  PubMed  Google Scholar 

  57. Rai, AR., Singh, R.P., Srivastava, A.K., and Dubey, R.C., Bioinformation, 2012, vol. 8, no.22, pp. 1111–1113.

    Article  PubMed Central  PubMed  Google Scholar 

  58. Poelarends, G.J., Serrano, H., Huddleston, J.P., Johnson, W.H., Jr., and Whitman, C.P., FEBS Lett., 2013, vol. 587, no. 17, pp. 2842–2850.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  59. Hasan, K., Gora, A., Brezovsky, J., Chaloupkova, R., Moskalikova, H., Fortova, A., et al., FEBS J., 2013, vol. 280, no. 13, pp. 3149–3159.

    Article  CAS  PubMed  Google Scholar 

  60. Hamid, A. A. A., Tengku Abdul Hamid, T. H., Wahab, R. A., and Huyop, F., J. Basic Microbiol., 2013. doi: 10.1002/jobm.201300526

    Google Scholar 

  61. Elenkov, M.M., Primožič, I., Hrenar, T., Smolko, A., Dokli, I., Salopek-Sondi, B., and Tang L., Org. Biomol. Chem., 2012, vol. 10, no. 26, pp. 5063–5072.

    Article  Google Scholar 

  62. Kmunícek, J., Bohác, M., Luengo, S., Gago, F., Wade, R.C., and Damborsky, J., J. Comput.-Aided Mol. Des., 2003, vol. 17, no. 5–6, pp.299–311.

    Article  PubMed  Google Scholar 

  63. Robert, D., Gironés, X., and Carbó-Dorca, R., J. Chem. Inf. Comput. Sci., 2000, vol. 40, no. 3, pp. 839–846.

    Article  CAS  PubMed  Google Scholar 

  64. Kmunícek J., Hynková K., Jedlicka T., Nagata Y., Negri A., Gago F., et al., Biochemistry, 2005, vol. 44, no. 9, pp. 3390–3401.

    Article  PubMed  Google Scholar 

  65. Pieper, D.H., Martins dos Santos, V.A., Golyshin, P.N., Curr. Opin. Biotechnol., 2004, vol. 15, no. 3, pp. 215–224.

    Article  CAS  PubMed  Google Scholar 

  66. Seo, J.S., Keum, Y.S., and Li, Q.X., Int. J. Environ. Res. Public Health, 2009, vol. 6, no. 1, pp. 278–309.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  67. Finley S.D., Broadbelt, L.J., and Hatzimanikatis, V., Biotechnol. Bioeng., 2009, vol. 104, no. 6, pp. 1086–1097.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  68. Finley, S.D., Broadbelt, L.J., and Hatzimanikatis, V., Biotechnol. Bioeng., 2009, vol. 103, no. 3, pp. 532–541.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  69. Philipp, B., Hoff, M., Germa, F., Schink, B., Beimborn, D., and Mersch-Sundermann, V., Environ. Sci. Technol., 2007, vol. 41, no. 4, pp.1390–1398.

    Article  CAS  PubMed  Google Scholar 

  70. Zhang, S., Golbraikh, A., and Tropsha, A., J. Med. Chem., 2006, vol. 49, no. 9, pp. 2713–2724.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  71. Yi-Jun, C., Zun-Ya, W., Liang, M., Shi-Xiang, G., Chin. J. Struct. Chem., 2010, vol. 29, pp. 895–899.

    Google Scholar 

  72. Dai, Y., Yang, D., Zhu, F., Wu, L., Yang, X., and Li, J., Chemosphere, 2006, vol. 65, no. 11, pp. 2427–2433.

    Article  CAS  PubMed  Google Scholar 

  73. Dearden, J.C., SAR QSAR Environ. Res., 1996, vol. 5, no. 1, pp. 17–26.

    Article  CAS  PubMed  Google Scholar 

  74. Matthews E.J., Kruhlak N.L., Daniel Benz R., Ivanov J., Klopman G., and Contrera, J.F., Regul. Toxicol. Pharm., 2007, vol. 47, no. 2, pp. 136–155.

    Article  CAS  Google Scholar 

  75. Alikhanidi, S. and Takahashi, Y., J. Comput. Chem., Jpn., 2004, vol. 3, no. 2, pp. 59–70.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. School of Life science, Sambalpur University, Jyoti vihar, Burla, Odisha, 768019, India

    R. Satpathy & J. Ratha

  2. School of Biological Sciences, National Institute of Science Education and Research (NISER), Bhubaneswar, Odisha, 751005, India

    V. B. Konkimalla

Authors
  1. R. Satpathy
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. V. B. Konkimalla
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. J. Ratha
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to R. Satpathy.

Additional information

The article is published in the original.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Satpathy, R., Konkimalla, V.B. & Ratha, J. Application of bioinformatics tools and databases in microbial dehalogenation research: A review. Appl Biochem Microbiol 51, 11–20 (2015). https://doi.org/10.1134/S0003683815010147

Download citation

  • Received:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S0003683815010147

Keywords

Search

Navigation