Table of Contents Author Guidelines Submit a Manuscript
Comparative and Functional Genomics
Volume 2011, Article ID 878973, 13 pages
http://dx.doi.org/10.1155/2011/878973
Research Article

Cross-Genome Comparisons of Newly Identified Domains in Mycoplasma gallisepticum and Domain Architectures with Other Mycoplasma species

1Equipe de Bioinformatique, Laboratoire de Biochimie et Génétique Moléculaire, Université de La Réunion, 15 avenue René Cassin, La Réunion, 97715 Saint Denis Messag Cedex 09, France
2National Centre for Biological Sciences, GKVK Campus, Bellary Road, Bangalore 560065, India

Received 30 July 2010; Revised 21 February 2011; Accepted 23 May 2011

Academic Editor: G. Pesole

Copyright © 2011 Chandra Sekhar Reddy Chilamakuri 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. P. Bork, T. Dandekar, Y. Diaz-Lazcoz, F. Eisenhaber, M. Huynen, and Y. Yuan, “Predicting function: from genes to genomes and back,” Journal of Molecular Biology, vol. 283, no. 4, pp. 707–725, 1998. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  2. D. Eisenberg, E. M. Marcotte, I. Xenarios, and T. O. Yeates, “Protein function the post-genomic era,” Nature, vol. 405, no. 6788, pp. 823–826, 2000. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  3. W. R. Pearson and D. J. Lipman, “Improved tools for biological sequence comparison,” Proceedings of the National Academy of Sciences of the United States of America, vol. 85, no. 8, pp. 2444–2448, 1988. View at Google Scholar · View at Scopus
  4. 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 PubMed · View at Scopus
  5. S. F. Altschul, T. L. Madden, A. A. Schäffer et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Research, vol. 25, no. 17, pp. 3389–3402, 1997. View at Publisher · View at Google Scholar · View at Scopus
  6. W. C. Barker, F. Pfeiffer, and D. G. George, “Superfamily classification in PIR-international protein sequence database,” Methods in Enzymology, vol. 266, pp. 59–70, 1996. View at Google Scholar · View at Scopus
  7. G. Yona, N. Linial, and M. Linial, “ProtoMap: automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space,” Proteins, vol. 37, no. 3, pp. 360–378, 1999. View at Publisher · View at Google Scholar · View at Scopus
  8. E. L. Sonnhammer, S. R. Eddy, E. Birney, A. Bateman, and R. Durbin, “Pfam: multiple sequence alignments and HMM-profiles of protein domains,” Nucleic Acids Research, vol. 26, no. 1, pp. 320–322, 1998. View at Publisher · View at Google Scholar · View at Scopus
  9. J. Schultz, F. Milpetz, P. Bork, and C. P. Ponting, “SMART, a simple modular architecture research tool: identification of signaling domains,” Proceedings of the National Academy of Sciences of the United States of America, vol. 95, no. 11, pp. 5857–5864, 1998. View at Publisher · View at Google Scholar · View at Scopus
  10. N. Hulo, A. Bairoch, V. Bulliard et al., “The PROSITE database,” Nucleic Acids Aesearch, vol. 34, pp. D227–D230, 2006. View at Google Scholar · View at Scopus
  11. T. K. Attwood, M. J. Blythe, D. R. Flower et al., “PRINTS and PRINTS-S shed light on protein ancestry,” Nucleic Acids Research, vol. 30, no. 1, pp. 239–241, 2002. View at Google Scholar · View at Scopus
  12. C. A. Orengo, A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells, and J. M. Thornton, “CATH—a hierarchic classification of protein domain structures,” Structure, vol. 5, no. 8, pp. 1093–1108, 1997. View at Google Scholar · View at Scopus
  13. A. G. Murzin, S. E. Brenner, T. Hubbard, and C. Chothia, “SCOP: a structural classification of proteins database for the investigation of sequences and structures,” Journal of Molecular Biology, vol. 247, no. 4, pp. 536–540, 1995. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  14. L. Holm and C. Sander, “The FSSP database: fold classification based on structure-structure alignment of proteins,” Nucleic Acids Research, vol. 24, no. 1, pp. 206–209, 1996. View at Publisher · View at Google Scholar · View at Scopus
  15. R. Apweiler, T. K. Attwood, A. Bairoch et al., “InterPro—an integrated documentation resource for protein families, domains and functional sites,” Bioinformatics, vol. 16, no. 12, pp. 1145–1150, 2000. View at Google Scholar · View at Scopus
  16. C. H. Wu, H. Huang, L. S. L. Yeh, and W. C. Barker, “Protein family classification and functional annotation,” Computational Biology and Chemistry, vol. 27, no. 1, pp. 37–47, 2003. View at Publisher · View at Google Scholar · View at Scopus
  17. M. Ashburner, C. A. Ball, J. A. Blake et al., “Gene ontology: tool for the unification of biology. The gene ontology consortium,” Nature Genetics, vol. 25, no. 1, pp. 25–29, 2000. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  18. J. Park, S. A. Teichmann, T. Hubbard, and C. Chothia, “Intermediate sequences increase the detection of homology between sequences,” Journal of Molecular Biology, vol. 273, no. 1, pp. 349–354, 1997. View at Publisher · View at Google Scholar · View at PubMed
  19. C. S. Reddy, A. Manonmani, M. Babu, and R. Sowdhamini, “Enhanced structure prediction of gene products containing class III adenylyl cyclase domains,” In Silico Biology, vol. 6, no. 5, pp. 351–362, 2006. View at Google Scholar
  20. C. C. S. Reddy, K. Shameer, B. O. Offmann, and R. Sowdhamini, “PURE: a webserver for the prediction of domains in unassigned regions in proteins,” BMC Bioinformatics, vol. 9, article 281, 2008. View at Publisher · View at Google Scholar · View at PubMed
  21. C. C. Reddy, S. S. Rani, B. Offmann, and R. Sowdhamini, “Systematic search for putative new domain families in Mycoplasma gallisepticum genome,” BMC Research Notes, vol. 3, article 98, 2010. View at Publisher · View at Google Scholar · View at PubMed
  22. M. J. Rogers, J. Simmons, and R. T. Walker, “Construction of the mycoplasma evolutionary tree from 5S rRNA sequence data,” Proceedings of the National Academy of Sciences of the United States of America, vol. 82, no. 4, pp. 1160–1164, 1985. View at Google Scholar
  23. C. R. Woese, J. Maniloff, and L. B. Zablen, “Phylogenetic analysis of the mycoplasmas,” Proceedings of the National Academy of Sciences of the United States of America, vol. 77, no. 1, pp. 494–498, 1980. View at Google Scholar
  24. A. T. R. Vasconcelos, H. B. Ferreira, C. V. Bizarro et al., “Swine and poultry pathogens: the complete genome sequences of two strains of Mycoplasma hyopneumoniae and a strain of Mycoplasma synoviae,” Journal of Bacteriology, vol. 187, no. 16, pp. 5568–5577, 2005. View at Publisher · View at Google Scholar · View at PubMed
  25. J. L. Wang, M. Y. Ho, and E. Y. Shen, “Mycoplasma pneumoniae infection associated with hemolytic anemia—report of one case,” Acta Paediatrica Taiwanica, vol. 45, no. 5, pp. 293–295, 2004. View at Google Scholar
  26. National center for Biotechnology Information, http://www.ncbi.nlm.nih.gov/.
  27. K. Dybvig and L. L. Voelker, “Molecular biology of mycoplasmas,” Annual Review of Microbiology, vol. 50, pp. 25–57, 1996. View at Publisher · View at Google Scholar · View at PubMed
  28. S. R. Eddy, “Profile hidden Markov models,” Bioinformatics, vol. 14, no. 9, pp. 755–763, 1998. View at Google Scholar
  29. G. E. Tusnády and I. Simon, “The HMMTOP transmembrane topology prediction server,” Bioinformatics, vol. 17, no. 9, pp. 849–850, 2001. View at Google Scholar
  30. A. Lupas, M. Van Dyke, and J. Stock, “Predicting coiled coils from protein sequences,” Science, vol. 252, no. 5010, pp. 1162–1164, 1991. View at Google Scholar
  31. D. L. Wheeler, T. Barrett, D. A. Benson et al., “Database resources of the National Center for Biotechnology Information,” Nucleic Acids Research, vol. 34, pp. D173–D180, 2006. View at Google Scholar
  32. L. J. McGuffin, K. Bryson, and D. T. Jones, “The PSIPRED protein structure prediction server,” Bioinformatics, vol. 16, no. 4, pp. 404–405, 2000. View at Google Scholar
  33. J. D. Thompson, D. G. Higgins, and T. J. Gibson, “CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice,” Nucleic Acids Research, vol. 22, no. 22, pp. 4673–4680, 1994. View at Google Scholar
  34. C. R. Woese, “Bacterial evolution,” Microbiological Reviews, vol. 51, no. 2, pp. 221–271, 1987. View at Google Scholar
  35. C. M. Fraser, J. D. Gocayne, O. White et al., “The minimal gene complement of Mycoplasma genitalium,” Science, vol. 270, no. 5235, pp. 397–403, 1995. View at Google Scholar
  36. N. M. Hooper, “Families of zinc metalloproteases,” Federation of European Biochemical Societies Letters, vol. 354, no. 1, pp. 1–6, 1994. View at Publisher · View at Google Scholar
  37. D. A. Dougan, A. Mogk, and B. Bukau, “Protein folding and degradation in bacteria: to degrade or not to degrade? That is the question,” Cellular and Molecular Life Sciences, vol. 59, no. 10, pp. 1607–1616, 2002. View at Google Scholar
  38. F. U. Hartl and M. Hayer-Hartl, “Protein folding. Molecular chaperones in the cytosol: from nascent chain to folded protein,” Science, vol. 295, no. 5561, pp. 1852–1858, 2002. View at Publisher · View at Google Scholar · View at PubMed
  39. P. Wong and W. A. Houry, “Chaperone networks in bacteria: analysis of protein homeostasis in minimal cells,” Journal of Structural Biology, vol. 146, no. 1-2, pp. 79–89, 2004. View at Publisher · View at Google Scholar · View at PubMed
  40. I. Callebaut, D. Moshous, J. P. Mornon, and J. P. De Villartay, “Metallo-β-lactamase fold within nucleic acids processing enzymes: the β-CASP family,” Nucleic Acids Research, vol. 30, no. 16, pp. 3592–3601, 2002. View at Google Scholar
  41. L. Aravind, “An evolutionary classification of the metallo-beta-lactamase fold proteins,” In Silico Biology, vol. 1, no. 2, pp. 69–91, 1999. View at Google Scholar
  42. K. Sjölander, “Phylogenomic inference of protein molecular function: advances and challenges,” Bioinformatics, vol. 20, no. 2, pp. 170–179, 2004. View at Publisher · View at Google Scholar
  43. M. P. S. Brown, W. N. Grundy, D. Lin et al., “Knowledge-based analysis of microarray gene expression data by using support vector machines,” Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 1, pp. 262–267, 2000. View at Publisher · View at Google Scholar
  44. I. Friedberg, “Automated protein function prediction—the genomic challenge,” Briefings in Bioinformatics, vol. 7, no. 3, pp. 225–242, 2006. View at Publisher · View at Google Scholar · View at PubMed