Table of Contents Author Guidelines Submit a Manuscript
Enzyme Research
Volume 2011, Article ID 543912, 8 pages
http://dx.doi.org/10.4061/2011/543912
Research Article

Specific and Nonhomologous Isofunctional Enzymes of the Genetic Information Processing Pathways as Potential Therapeutical Targets for Tritryps

1Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz/FIOCRUZ, 21045-900 Rio de Janeiro, RJ, Brazil
2Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz/FIOCRUZ, 21045-900 Rio de Janeiro, RJ, Brazil

Received 15 January 2011; Revised 22 March 2011; Accepted 5 May 2011

Academic Editor: Ariel M. Silber

Copyright © 2011 Monete Rajão Gomes 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. U. González, M. Pinart, M. Rengifo-Pardo, A. Macaya, J. Alvar, and J. A. Tweed, “Interventions for American cutaneous and mucocutaneous leishmaniasis,” Cochrane Database of Systematic Reviews, no. 2, article CD004834, 2009. View at Google Scholar · View at Scopus
  2. World Health Organization, “African trypanosomiasis (sleeping sickness),” Fact sheet N°259, October 2010, http://www.who.int/mediacentre/factsheets/fs259/.
  3. World Health Organization, “Chagas disease (American trypanosomiasis),” Fact sheet N°340, June 2010, http://www.who.int/mediacentre/factsheets/fs340/.
  4. M. P. Barrett, R. J. S. Burchmore, A. Stich et al., “The trypanosomiases,” The Lancet, vol. 362, no. 9394, pp. 1469–1480, 2003. View at Publisher · View at Google Scholar · View at Scopus
  5. WHO, Global Plan to Combat Neglected Diseases 2008–2015, WHO, Geneva, Switzerland, 2007, WHO/CDS/NTD/2007.2003.
  6. M. P. Barrett and I. H. Gilbert, “Perspectives for new drugs against trypanosomiasis and leishmaniasis,” Current Topics in Medicinal Chemistry, vol. 2, no. 5, pp. 471–482, 2002. View at Google Scholar · View at Scopus
  7. C. R. Caffrey and D. Steverding, “Recent initiatives and strategies to developing new drugs for tropical parasitic diseases,” Expert Opinion on Drug Discovery, vol. 3, no. 2, pp. 173–186, 2008. View at Publisher · View at Google Scholar · View at Scopus
  8. M. P. Barrett, G. H. Coombs, and J. C. Mottram, “Recent advances in identifying and validating drug targets in trypanosomes and leishmanias,” Trends in Microbiology, vol. 7, no. 2, pp. 82–88, 1999. View at Publisher · View at Google Scholar · View at Scopus
  9. M. Berriman, E. Ghedin, C. Hertz-Fowler et al., “The genome of the African trypanosome Trypanosoma brucei,” Science, vol. 309, no. 5733, pp. 416–422, 2005. View at Publisher · View at Google Scholar · View at Scopus
  10. N. M. A. El-Sayed, P. Myler, D. C. Bartholomeu et al., “The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease,” Science, vol. 309, no. 5733, pp. 409–415, 2005. View at Publisher · View at Google Scholar · View at Scopus
  11. A. C. Ivens, C. S. Peacock, E. A. Worthey et al., “The genome of the kinetoplastid parasite, Leishmania major,” Science, vol. 309, no. 5733, pp. 436–442, 2005. View at Publisher · View at Google Scholar · View at Scopus
  12. S. Kaur, A. V. Shivange, and N. Roy, “Structural analysis of trypanosomal sirtuin: an insight for selective drug design,” Molecular Diversity, vol. 14, no. 1, pp. 169–178, 2010. View at Publisher · View at Google Scholar · View at Scopus
  13. H. Ma and A. P. Zeng, “Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms,” Bioinformatics, vol. 19, no. 2, pp. 270–277, 2003. View at Publisher · View at Google Scholar · View at Scopus
  14. B. Ø. Palsson, Systems Biology: Properties of Reconstructed Networks, Cambridge University Press, New York, NY, USA, 1st edition, 2006.
  15. A. M. Feist, M. J. Herrgård, I. Thiele, J. L. Reed, and B. Ø. Palsson, “Reconstruction of biochemical networks in microorganisms,” Nature Reviews Microbiology, vol. 7, no. 2, pp. 129–143, 2009. View at Publisher · View at Google Scholar · View at Scopus
  16. J. A. Papin, N. D. Price, S. J. Wiback, D. A. Fell, and B. Ø. Palsson, “Metabolic pathways in the post-genome era,” Trends in Biochemical Sciences, vol. 28, no. 5, pp. 250–258, 2003. View at Publisher · View at Google Scholar · View at Scopus
  17. M. Kanehisa, S. Goto, M. Furumichi, M. Tanabe, and M. Hirakawa, “KEGG for representation and analysis of molecular networks involving diseases and drugs,” Nucleic Acids Research, vol. 38, no. 1, pp. D355–D360, 2010. View at Publisher · View at Google Scholar · View at Scopus
  18. P. D. Karp, M. Krummenacker, S. Paley, and J. K. Wagg, “Integrated pathway-genome databases and their role in drug discovery,” Trends in Biotechnology, vol. 17, no. 7, pp. 275–281, 1999. View at Publisher · View at Google Scholar · View at Scopus
  19. C. A. Ouzounis, R. M. R. Coulson, A. J. Enright, V. Kunin, and J. B. Pereira-Leal, “Classification schemes for protein structure and function,” Nature Reviews Genetics, vol. 4, no. 7, pp. 508–519, 2003. View at Publisher · View at Google Scholar · View at Scopus
  20. D. L. Nelson and M. M. Cox, Lehninger—Principles of Biochemistry, W. H. Freeman & Company, New York, NY, USA, 4th edition, 2004.
  21. A. C. Guimarães, T. D. Otto, M. Alves-Ferreira, A. B. de Miranda, and W. M. Degrave, “In silico reconstruction of the amino acid metabolic pathways of Trypanosoma cruzi,” Genetics and Molecular Research, vol. 7, no. 3, pp. 872–882, 2008. View at Google Scholar · View at Scopus
  22. T. D. Otto, A. C. Guimarães, W. M. Degrave, and A. B. de Miranda, “AnEnPi: identification and annotation of analogous enzymes,” BMC Bioinformatics, vol. 9, p. 544, 2008. View at Publisher · View at Google Scholar · View at Scopus
  23. P. V. Capriles, A. C. Guimarães, T. D. Otto, A. B. Miranda, L. E. Dardenne, and W. M. Degrave, “Structural modelling and comparative analysis of homologous, analogous and specific proteins from Trypanosoma cruzi versus Homo sapiens: putative drug targets for chagas' disease treatment,” BMC Genomics, vol. 11, p. 610, 2010. View at Publisher · View at Google Scholar · View at Scopus
  24. M. Y. Galperin, D. R. Walker, and E. V. Koonin, “Analogous enzymes: independent inventions in enzyme evolution,” Genome Research, vol. 8, no. 8, pp. 779–790, 1998. View at Google Scholar · View at Scopus
  25. M. V. Omelchenko, M. Y. Galperin, Y. I. Wolf, and E. V. Koonin, “Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution,” Biology Direct, vol. 5, p. 31, 2010. View at Publisher · View at Google Scholar · View at Scopus
  26. Y. I. Pavlov, P. V. Shcherbakova, and I. B. Rogozin, “Roles of DNA polymerases in replication, repair, and recombination in eukaryotes,” International Review of Cytology, vol. 255, pp. 41–132, 2006. View at Publisher · View at Google Scholar · View at Scopus
  27. B. Lewin, Genes IX, Jones & Bartlett, Sudbury, Mass, USA, 9th edition, 2007.
  28. 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
  29. M. M. Klingbeil, P. Burton, R. Barnes, and R. McCulloch, “The three R's of the trypanosomatid genomes: replication, recombination and repair,” in Trypanosomes: After the Genome, D. Barry, R. McCulloch, J. Mottram, and A. Acosta-Serrano, Eds., pp. 133–175, Horizon Bioscience, Norfolk, UK, 1st edition, 2007. View at Google Scholar
  30. M. Alves-Ferreira, A. C. Guimarães, P. V. Capriles, L. E. Dardenne, and W. M. Degrave, “A new approach for potential drug target discovery through in silico metabolic pathway analysis using Trypanosoma cruzi genome information,” Memorias do Instituto Oswaldo Cruz, vol. 104, no. 8, pp. 1100–1110, 2009. View at Google Scholar · View at Scopus
  31. K. Vickerman, “The diversity of the kinetoplastid flagellates,” in Biology of the Kinetoplastida, W. H. R. Lumsden and D. A. Evans, Eds., pp. 1–34, Academic Press, London, UK, 1976. View at Google Scholar
  32. C. R. Davies, P. Kaye, S. L. Croft, and S. Sundar, “Leishmaniasis: new approaches to disease control,” The British Medical Journal, vol. 326, no. 7385, pp. 377–382, 2003. View at Google Scholar · View at Scopus
  33. J. E. Donelson, M. J. Gardner, and N. M. El-Sayed, “More surprises from Kinetoplastida,” Proceedings of the National Academy of Sciences of the United States of America, vol. 96, no. 6, pp. 2579–2581, 1999. View at Publisher · View at Google Scholar · View at Scopus
  34. M. Kanehisa, M. Araki, S. Goto et al., “KEGG for linking genomes to life and the environment,” Nucleic Acids Research, vol. 36, no. 1, pp. D480–D484, 2008. View at Publisher · View at Google Scholar · View at Scopus
  35. R. Fukunaga and S. Yokoyama, “Structural insights into the first step of RNA-dependent cysteine biosynthesis in archaea,” Nature Structural and Molecular Biology, vol. 14, no. 4, pp. 272–279, 2007. View at Publisher · View at Google Scholar · View at Scopus
  36. S. I. Hauenstein and J. J. Perona, “Redundant synthesis of cysteinyl-tRNACys in Methanosarcina mazei,” Journal of Biological Chemistry, vol. 283, no. 32, pp. 22007–22017, 2008. View at Publisher · View at Google Scholar · View at Scopus
  37. F. Charrière, T. H. Tan, and A. Schneider, “Mitochondrial initiation factor 2 of Trypanosoma brucei binds imported formylated elongator-type tRNA(Met),” Journal of Biological Chemistry, vol. 280, no. 16, pp. 15659–15665, 2005. View at Publisher · View at Google Scholar · View at Scopus
  38. S. Adhya, “Leishmania mitochondrial tRNA importers,” International Journal of Biochemistry and Cell Biology, vol. 40, no. 12, pp. 2681–2685, 2008. View at Publisher · View at Google Scholar · View at Scopus
  39. T. J. Vickers, S. M. Murta, M. A. Mandell, and S. M. Beverley, “The enzymes of the 10-formyl-tetrahydrofolate synthetic pathway are found exclusively in the cytosol of the trypanosomatid parasite Leishmania major,” Molecular and Biochemical Parasitology, vol. 166, no. 2, pp. 142–152, 2009. View at Publisher · View at Google Scholar · View at Scopus
  40. C. D. Mol, D. J. Hosfield, and J. A. Tainer, “Abasic site recognition by two apurinic/apyrimidinic endonuclease families in DNA base excision repair: the 3' ends justify the means,” Mutation Research, vol. 460, no. 3-4, pp. 211–229, 2000. View at Publisher · View at Google Scholar · View at Scopus
  41. A. Memisoglu and L. D. Samson, “Base excision repair in yeast and mammals,” Mutation Research, vol. 451, no. 1-2, pp. 39–51, 2000. View at Publisher · View at Google Scholar · View at Scopus
  42. J. M. Egly, “The 14th Datta Lecture. TFIIH: from transcription to clinic,” FEBS Letters, vol. 498, no. 2-3, pp. 124–128, 2001. View at Publisher · View at Google Scholar · View at Scopus
  43. L. C. Chen, K. M. Trujillo, W. Ramos, P. Sung, and A. E. Tomkinson, “Promotion of Dnl4-catalyzed DNA end-joining by the Rad50/Mre11/Xrs2 and Hdf1/Hdf2 complexes,” Molecular Cell, vol. 8, no. 5, pp. 1105–1115, 2001. View at Publisher · View at Google Scholar · View at Scopus
  44. T. A. Dobbs, J. A. Tainer, and S. P. Lees-Miller, “A structural model for regulation of NHEJ by DNA-PKcs autophosphorylation,” DNA Repair, vol. 9, no. 12, pp. 1307–1314, 2010. View at Publisher · View at Google Scholar · View at Scopus
  45. C. Kühne, M. L. Tjörnhammar, S. Pongor, L. Banks, and A. Simoncsits, “Repair of a minimal DNA double-strand break by NHEJ requires DNA-PKcs and is controlled by the ATM/ATR checkpoint,” Nucleic Acids Research, vol. 31, no. 24, pp. 7227–7237, 2003. View at Publisher · View at Google Scholar · View at Scopus
  46. E. A. Worthey and P. J. Myler, “Protozoan genomes: gene identification and annotation,” International Journal for Parasitology, vol. 35, no. 5, pp. 495–512, 2005. View at Publisher · View at Google Scholar · View at Scopus
  47. L. H. Harrison, K. L. Brame, L. E. Geltz, and A. M. Landry, “Closely opposed apurinic/apyrimidinic sites are converted to double strand breaks in Escherichia coli even in the absence of exonuclease III, endonuclease IV, nucleotide excision repair and AP lyase cleavage,” DNA Repair, vol. 5, no. 3, pp. 324–335, 2006. View at Publisher · View at Google Scholar · View at Scopus
  48. J. D. Hoheisel, “On the activities of Escherichia coli exonuclease III,” Analytical Biochemistry, vol. 209, no. 2, pp. 238–246, 1993. View at Publisher · View at Google Scholar · View at Scopus
  49. Z. Yang, A. M. Sismour, and S. A. Benner, “Nucleoside alpha-thiotriphosphates, polymerases and the exonuclease III analysis of oligonucleotides containing phosphorothioate linkages,” Nucleic Acids Research, vol. 35, no. 9, pp. 3118–3127, 2007. View at Publisher · View at Google Scholar · View at Scopus
  50. W. Sun and A. W. Nicholson, “Mechanism of action of Escherichia coli ribonuclease III. Stringent chemical requirement for the glutamic acid 117 side chain and Mn2+ rescue of the Glu117Asp mutant,” Biochemistry, vol. 40, no. 16, pp. 5102–5110, 2001. View at Publisher · View at Google Scholar · View at Scopus
  51. C. C. Richardson, I. R. Lehman, and A. Kornberg, “A deoxyribonucleic acid phosphatase-exonuclease from Escherichia coli. II. Characterization of the exonuclease activity,” Journal of Biological Chemistry, vol. 239, pp. 251–258, 1964. View at Google Scholar
  52. A. Slaitas, C. Ander, Z. Földes-Papp, R. Rigler, and E. Yeheskiely, “Suppression of exonucleolytic degradation of double-stranded DNA and inhibition of exonuclease III by PNA,” Nucleosides, Nucleotides and Nucleic Acids, vol. 22, no. 5–8, pp. 1603–1605, 2003. View at Publisher · View at Google Scholar · View at Scopus
  53. D. M. Kirtikar, G. R. Cathcart, and D. A. Goldthwait, “Endonuclease II, apurinic acid endonuclease, and exonuclease III,” Proceedings of the National Academy of Sciences of the United States of America, vol. 73, no. 12, pp. 4324–4328, 1976. View at Google Scholar · View at Scopus
  54. L. L. Souza, I. R. Eduardo, M. D. Pádula, and A. C. Leitão, “Endonuclease IV and exonuclease III are involved in the repair and mutagenesis of DNA lesions induced by UVB in Escherichia coli,” Mutagenesis, vol. 21, no. 2, pp. 125–130, 2006. View at Publisher · View at Google Scholar · View at Scopus
  55. T. Takemoto, Q. M. Zhang, Y. Matsumoto et al., “3'-blocking damage of DNA as a mutagenic lesion caused by hydrogen peroxide in Escherichia coli,” Journal of Radiation Research, vol. 39, no. 2, pp. 137–144, 1998. View at Google Scholar · View at Scopus
  56. D. M. Serafini and H. E. Schellhorn, “Endonuclease III and endonuclease IV protect Escherichia coli from the lethal and mutagenic effects of near-UV irradiation,” The Canadian Journal of Microbiology, vol. 45, no. 7, pp. 632–637, 1999. View at Google Scholar · View at Scopus
  57. N. R. Asad, L. M. Asad, A. B. Silva, I. Felzenszwalb, and A. C. Leitão, “Hydrogen peroxide effects in Escherichia coli cells,” Acta Biochimica Polonica, vol. 45, no. 3, pp. 677–690, 1998. View at Google Scholar
  58. A. P. Guedes, V. N. Cardoso, J. C. De Mattos et al., “Cytotoxic and genotoxic effects induced by stannous chloride associated to nuclear medicine kits,” Nuclear Medicine and Biology, vol. 33, no. 7, pp. 915–921, 2006. View at Publisher · View at Google Scholar · View at Scopus
  59. H. E. Krokan, R. Standal, and G. Slupphaug, “DNA glycosylases in the base excision repair of DNA,” Biochemical Journal, vol. 325, no. 1, pp. 1–16, 1997. View at Google Scholar · View at Scopus
  60. M. D. Wyatt, J. M. Allan, A. Y. Lau, T. E. Ellenberger, and L. D. Samson, “3-Methyladenine DNA glycosylases: structure, function, and biological importance,” BioEssays, vol. 21, no. 8, pp. 668–676, 1999. View at Publisher · View at Google Scholar · View at Scopus
  61. K. Sheppard, J. Yuan, M. J. Hohn, B. Jester, K. M. Devine, and D. Söll, “From one amino acid to another: tRNA-dependent amino acid biosynthesis,” Nucleic Acids Research, vol. 36, no. 6, pp. 1813–1825, 2008. View at Publisher · View at Google Scholar · View at Scopus
  62. F. Agüero, B. Al-Lazikani, M. A. Aslett et al., “Genomic-scale prioritization of drug targets: the TDR Targets database,” Nature Reviews Drug Discovery, vol. 7, no. 11, pp. 900–907, 2008. View at Publisher · View at Google Scholar · View at Scopus