Table of Contents
ISRN Computational Biology
Volume 2013, Article ID 850179, 6 pages
http://dx.doi.org/10.1155/2013/850179
Research Article

A Whole Genome Pairwise Comparative and Functional Analysis of Geobacter sulfurreducens PCA

Bioinformatics Lab, AU-KBC Research Centre, M.I.T Campus of Anna University, Chromepet, Chennai, Tamil Nadu 600044, India

Received 16 May 2013; Accepted 25 June 2013

Academic Editors: F. Barbault, S. Chavali, G. Colonna, and W. B. Fischer

Copyright © 2013 Ashok Selvaraj et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. C. Leang, L. A. Adams, K.-J. Chin et al., “Adaptation to disruption of the electron transfer pathway for Fe(III) reduction in Geobacter sulfurreducens,” Journal of Bacteriology, vol. 187, no. 17, pp. 5918–5926, 2005. View at Publisher · View at Google Scholar · View at Scopus
  2. D. R. Bond and D. R. Lovley, “Electricity production by Geobacter sulfurreducens attached to electrodes,” Applied and Environmental Microbiology, vol. 69, no. 3, pp. 1548–1555, 2003. View at Publisher · View at Google Scholar · View at Scopus
  3. B. A. Methé, K. E. Nelson, J. A. Eisen et al., “Genome of Geobacter sulfurreducens: metal reduction in subsurface environments,” Science, vol. 302, no. 5652, pp. 1967–1969, 2003. View at Publisher · View at Google Scholar · View at Scopus
  4. R. T. Anderson, H. A. Vrionis, I. Ortiz-Bernad et al., “Stimulating the in situ activity of Geobacter species to remove uranium from the groundwater of a uranium-contaminated aquifer,” Applied and Environmental Microbiology, vol. 69, no. 10, pp. 5884–5889, 2003. View at Publisher · View at Google Scholar · View at Scopus
  5. A. R. Schoen, “Carbon fiber electrode as an electron acceptor for a microbial fuel cell using geobacter,” Cantaurus, vol. 15, pp. 24–26, 2007. View at Google Scholar
  6. W. C. Lin, M. V. Coppi, and D. R. Lovley, “Geobacter sulfurreducens can grow with oxygen as a terminal electron acceptor,” Applied and Environmental Microbiology, vol. 70, no. 4, pp. 2525–2528, 2004. View at Publisher · View at Google Scholar · View at Scopus
  7. W. M. Fitch, “Homologya personal view on some of the problems,” Trends in Genetics, vol. 16, no. 5, pp. 227–231, 2000. View at Publisher · View at Google Scholar · View at Scopus
  8. M. Richter, M. Kube, D. A. Bazylinski et al., “Comparative genome analysis of four magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function,” Journal of Bacteriology, vol. 189, no. 13, pp. 4899–4910, 2007. View at Publisher · View at Google Scholar · View at Scopus
  9. L. Wei, Y. Liu, I. Dubchak, J. Shon, and J. Park, “Comparative genomics approaches to study organism similarities and differences,” Journal of Biomedical Informatics, vol. 35, no. 2, pp. 142–150, 2002. View at Publisher · View at Google Scholar · View at Scopus
  10. G. Sawa, J. Dicks, and I. N. Roberts, “Current approaches to whole genome phylogenetic analysis.,” Briefings in Bioinformatics, vol. 4, no. 1, pp. 63–74, 2003. View at Google Scholar · View at Scopus
  11. J. E. Butler, N. D. Young, and D. R. Lovley, “Evolution from a respiratory ancestor to fill syntrophic and fermentative niches: comparative fenomics of six Geobacteraceae species,” BMC Genomics, vol. 10, article 103, 2009. View at Publisher · View at Google Scholar · View at Scopus
  12. E. W. Sayers, T. Barrett, D. A. Benson et al., “Database resources of the National Center for Biotechnology Information,” Nucleic Acids Research, vol. 39, pp. 38–51, 2011. View at Google Scholar
  13. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic local alignment search tool,” Journal of Molecular Biology, vol. 215, no. 3, pp. 403–410, 1990. View at Publisher · View at Google Scholar · View at Scopus
  14. UniProt Consortium, “Ongoing and future developments at the Universal Protein Resource,” Nucleic Acids Research, vol. 39, pp. D214–D219, 2011. View at Google Scholar
  15. M. A. Larkin, G. Blackshields, N. P. Brown et al., “Clustal W and clustal X version 2.0,” Bioinformatics, vol. 23, no. 21, pp. 2947–2948, 2007. View at Publisher · View at Google Scholar · View at Scopus
  16. J. Felsenstein, “PHYLIP—phylogeny inference package (version 3. 2),” Cladistics, vol. 5, pp. 164–166, 1989. View at Google Scholar
  17. M. V. Han and C. M. Zmasek, “PhyloXML: XML for evolutionary biology and comparative genomics,” BMC Bioinformatics, vol. 10, article 356, 2009. View at Publisher · View at Google Scholar · View at Scopus
  18. D. Lee, O. Redfern, and C. Orengo, “Predicting protein function from sequence and structure,” Nature Reviews Molecular Cell Biology, vol. 8, no. 12, pp. 995–1005, 2007. View at Publisher · View at Google Scholar · View at Scopus
  19. S. J. Callister, L. A. McCue, J. E. Turse et al., “Comparative bacterial proteomics: analysis of the core genome concept,” PLoS ONE, vol. 3, no. 2, Article ID e1542, 2008. View at Publisher · View at Google Scholar · View at Scopus
  20. D. W. Ussery and P. F. Hallin, “Genome update: length distributions of sequenced prokaryotic genomes,” Microbiology, vol. 150, no. 3, pp. 513–516, 2004. View at Google Scholar · View at Scopus
  21. E. S. Shelobolina, H. A. Vrionis, R. H. Findlay, and D. R. Lovley, “Geobacter uraniireducens sp. nov., isolated from subsurface sediment undergoing uranium bioremediation,” International Journal of Systematic and Evolutionary Microbiology, vol. 58, no. 5, pp. 1075–1078, 2008. View at Publisher · View at Google Scholar · View at Scopus
  22. F. Hildebrand, A. Meyer, and A. Eyre-Walker, “Evidence of selection upon genomic GC-content in bacteria,” PLoS Genetics, vol. 6, no. 9, Article ID e1001107, 2010. View at Publisher · View at Google Scholar · View at Scopus
  23. J. E. Clarridge III, “Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases,” Clinical Microbiology Reviews, vol. 17, no. 4, pp. 840–862, 2004. View at Publisher · View at Google Scholar · View at Scopus
  24. N. T. Trinh, J. H. Park, and B. Kim, “Increased generation of electricity in a microbial fuel cell using Geobacter sulfurreducens,” Korean Journal of Chemical Engineering, vol. 26, no. 3, pp. 748–753, 2009. View at Publisher · View at Google Scholar · View at Scopus
  25. G. E. Murphy, J. R. Leadbetter, and G. J. Jensen, “In situ structure of the complete Treponema primitia flagellar motor,” Nature, vol. 442, no. 7106, pp. 1062–1064, 2006. View at Publisher · View at Google Scholar · View at Scopus