Table of Contents Author Guidelines Submit a Manuscript
Comparative and Functional Genomics
Volume 2009, Article ID 820381, 13 pages
http://dx.doi.org/10.1155/2009/820381
Research Article

A Comprehensive Bioinformatics Analysis of the Nudix Superfamily in Arabidopsis thaliana

1Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
2School of Biological Sciences, University of Sydney, New South Wales 2006, Australia

Received 15 October 2008; Accepted 16 April 2009

Academic Editor: H. Heng

Copyright © 2009 D. Gunawardana 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. S. Sheikh, S. F. O'Handley, C. A. Dunn, and M. J. Bessman, “Identification and characterization of the Nudix hydrolase from the Archaeon, Methanococcus jannaschii, as a highly specific ADP-ribose pyrophosphatase,” The Journal of Biological Chemistry, vol. 273, no. 33, pp. 20924–20928, 1998. View at Publisher · View at Google Scholar
  2. W. Xu, P. Gauss, J. Shen, C. A. Dunn, and M. J. Bessman, “The gene e.1 (nudE.1) of T4 bacteriophage designates a new member of the Nudix hydrolase superfamily active on flavin adenine dinucleotide, adenosine 5-triphospho-5-adenosine, and ADP-ribose,” The Journal of Biological Chemistry, vol. 277, no. 26, pp. 23181–23185, 2002. View at Publisher · View at Google Scholar
  3. W. Xu, C. A. Dunn, C. R. Jones, G. D'Souza, and M. J. Bessman, “The 26 Nudix hydrolases of Bacillus cereus, a close relative of Bacillus anthracis,” The Journal of Biological Chemistry, vol. 279, no. 23, pp. 24861–24865, 2004. View at Publisher · View at Google Scholar
  4. M. J. Bessman, D. N. Frick, and S. F. O'Handley, “The MutT proteins or “Nudix” hydrolases, a family of versatile, widely distributed, “housecleaning” enzymes,” The Journal of Biological Chemistry, vol. 271, no. 41, pp. 25059–25062, 1996. View at Publisher · View at Google Scholar
  5. M. E. Glasner, J. A. Gerlt, and P. C. Babbitt, “Evolution of enzyme superfamilies,” Current Opinion in Chemical Biology, vol. 10, no. 5, pp. 492–497, 2006. View at Publisher · View at Google Scholar
  6. C. Abeygunawardana, D. J. Weber, A. G. Gittis et al., “Solution structure of the MutT enzyme, a nucleoside triphosphate pyrophosphohydrolase,” Biochemistry, vol. 34, no. 46, pp. 14997–15005, 1995. View at Publisher · View at Google Scholar
  7. J. Lin, C. Abeygunawardana, D. N. Frick, M. J. Bessman, and A. S. Mildvan, “The role of Glu 57 in the mechanism of the Escherichia coli MutT enzyme by mutagenesis and heteronuclear NMR,” Biochemistry, vol. 35, no. 21, pp. 6715–6726, 1996. View at Publisher · View at Google Scholar
  8. T. K. Harris, G. Wu, M. A. Massiah, and A. S. Mildvan, “Mutational, kinetic, and NMR studies of the roles of conserved glutamate residues and of lysine-39 in the mechanism of the MutT pyrophosphohydrolase,” Biochemistry, vol. 39, no. 7, pp. 1655–1674, 2000. View at Publisher · View at Google Scholar
  9. A. S. Mildvan, Z. Xia, H. F. Azurmendi et al., “Structures and mechanisms of Nudix hydrolases,” Archives of Biochemistry and Biophysics, vol. 433, no. 1, pp. 129–143, 2005. View at Publisher · View at Google Scholar
  10. F. J. Muñoz, E. Baroja-Fernández, M. T. Morán-Zorzano, N. Alonso-Casajús, and J. Pozueta-Romero, “Cloning, expression and characterization of a Nudix hydrolase that catalyzes the hydrolytic breakdown of ADP-glucose linked to starch biosynthesis in Arabidopsis thaliana,” Plant and Cell Physiology, vol. 47, no. 7, pp. 926–934, 2006. View at Publisher · View at Google Scholar
  11. N. Jambunathan and R. Mahalingam, “Analysis of Arabidopsis Growth Factor Gene 1 (GFG1) encoding a Nudix hydrolase during oxidative signaling,” Planta, vol. 224, no. 1, pp. 1–11, 2006. View at Publisher · View at Google Scholar
  12. M. Bartsch, E. Gobbato, P. Bednarek et al., “Salicylic acid-independent ENHANCED DISEASE SUSCEPTIBILITY1 signaling in Arabidopsis immunity and cell death is regulated by the monooxygenase FMO1 and the Nudix hydrolase NUDT7,” The Plant Cell, vol. 18, no. 4, pp. 1038–1051, 2006. View at Publisher · View at Google Scholar
  13. J. Xu, J.-Y. Yang, Q.-W. Niu, and N.-H. Chua, “Arabidopsis DCP2, DCP1, and VARICOSE form a decapping complex required for postembryonic development,” The Plant Cell, vol. 18, no. 12, pp. 3386–3398, 2006. View at Publisher · View at Google Scholar
  14. C. A. Dunn, S. F. O'Handley, D. N. Frick, and M. J. Bessman, “Studies on the ADP-ribose pyrophosphatase subfamily of the Nudix hydrolases and tentative identification of trgB, a gene associated with tellurite resistance,” The Journal of Biological Chemistry, vol. 274, no. 45, pp. 32318–32324, 1999. View at Publisher · View at Google Scholar
  15. A. G. McLennan, “The Nudix hydrolase superfamily,” Cellular and Molecular Life Sciences, vol. 63, no. 2, pp. 123–143, 2006. View at Publisher · View at Google Scholar
  16. The Arabidopsis Genome Initiative, “Analysis of the genome sequence of the flowering plant Arabidopsis thaliana,” Nature, vol. 408, no. 6814, pp. 796–815, 2000. View at Publisher · View at Google Scholar
  17. S. R. Eddy, “Hidden Markov models,” Current Opinion in Structural Biology, vol. 6, no. 3, pp. 361–365, 1996. View at Publisher · View at Google Scholar
  18. 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 Publisher · View at Google Scholar
  19. X. Xia and Z. Xie, “DAMBE: software package for data analysis in molecular biology and evolution,” The Journal of Heredity, vol. 92, no. 4, pp. 371–373, 2001. View at Publisher · View at Google Scholar
  20. E. Huala, A. W. Dickerman, M. Garcia-Hernandez et al., “The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant,” Nucleic Acids Research, vol. 29, no. 1, pp. 102–105, 2001. View at Publisher · View at Google Scholar
  21. V. Gopalan, T. W. Tan, B. T. K. Lee, and S. Ranganathan, “Xpro: database of eukaryotic protein-encoding genes,” Nucleic Acids Research, vol. 32, database issue, pp. D59–D63, 2004. View at Publisher · View at Google Scholar
  22. G. Basset, E. P. Quinlivan, M. J. Ziemak et al., “Folate synthesis in plants: the first step of the pterin branch is mediated by a unique bimodular GTP cyclohydrolase I,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 19, pp. 12489–12494, 2002. View at Publisher · View at Google Scholar
  23. T. L. Bailey and C. Elkan, “The value of prior knowledge in discovering motifs with MEME,” in Proceedings of the 3rd International Conference on Intelligent Systems for Molecular Biology, vol. 3, pp. 21–29, Cambridge, UK, July 1995.
  24. T. Schwede, J. Kopp, N. Guex, and M. C. Peitsch, “SWISS-MODEL: an automated protein homology-modeling server,” Nucleic Acids Research, vol. 31, no. 13, pp. 3381–3385, 2003. View at Publisher · View at Google Scholar
  25. K. Chen, D. Durand, and M. Farach-Colton, “NOTUNG: a program for dating gene duplications and optimizing gene family trees,” Journal of Computational Biology, vol. 7, no. 3-4, pp. 429–447, 2000. View at Publisher · View at Google Scholar
  26. E. L. L. Sonnhammer, S. R. Eddy, and R. Durbin, “Pfam: a comprehensive database of protein domain families based on seed alignments,” Proteins: Structure, Function and Genetics, vol. 28, no. 3, pp. 405–420, 1997. View at Publisher · View at Google Scholar
  27. C. J. Sigrist, L. Cerutti, N. Hulo et al., “PROSITE: a documented database using patterns and profiles as motif descriptors,” Briefings in Bioinformatics, vol. 3, no. 3, pp. 265–274, 2002. View at Publisher · View at Google Scholar
  28. N. Hulo, A. Bairoch, V. Bulliard et al., “The PROSITE database,” Nucleic Acids Research, vol. 34, database issue, pp. D227–D230, 2006. View at Publisher · View at Google Scholar
  29. 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
  30. D. Gunawardana, H.-C. Cheng, and K. R. Gayler, “Identification of functional domains in Arabidopsis thaliana mRNA decapping enzyme (AtDcp2),” Nucleic Acids Research, vol. 36, no. 1, pp. 203–216, 2008. View at Publisher · View at Google Scholar
  31. B. C. Meyers, A. Kozik, A. Griego, H. Kuang, and R. W. Michelmore, “Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis,” The Plant Cell, vol. 15, no. 4, pp. 809–834, 2003. View at Publisher · View at Google Scholar
  32. N. Tijet, C. Helvig, and R. Feyereisen, “The cytochrome P450 gene superfamily in Drosophila melanogaster: annotation, intron-exon organization and phylogeny,” Gene, vol. 262, no. 1-2, pp. 189–198, 2001. View at Publisher · View at Google Scholar
  33. S. M. J. Klaus, A. Wegkamp, W. Sybesma, J. Hugenholtz, J. F. Gregory III, and A. D. Hanson, “A Nudix enzyme removes pyrophosphate from dihydroneopterin triphosphate in the folate synthesis pathway of bacteria and plants,” The Journal of Biological Chemistry, vol. 280, no. 7, pp. 5274–5280, 2005. View at Publisher · View at Google Scholar
  34. J. D. Swarbrick, T. Bashtannyk, D. Maksel et al., “The three-dimensional structure of the Nudix enzyme diadenosine tetraphosphate hydrolase from Lupinus angustifolius L,” Journal of Molecular Biology, vol. 302, no. 5, pp. 1165–1177, 2000. View at Publisher · View at Google Scholar
  35. J. I. Fletcher, J. D. Swarbrick, D. Maksel, K. R. Gayler, and P. R. Gooley, “The structure of Ap4A hydrolase complexed with ATP-MgFx reveals the basis of substrate binding,” Structure, vol. 10, no. 2, pp. 205–213, 2003. View at Publisher · View at Google Scholar
  36. B. Szurmak, A. Wysłouch-Cieszyńska, M. Wszelaka-Rylik, W. Bal, and M. Dobrzańska, “A diadenosine 5,5-P1P4 tetraphosphate (Ap4A) hydrolase from Arabidopsis thaliana that is activated preferentially by Mn2+ ions,” Acta Biochimica Polonica, vol. 55, no. 1, pp. 151–160, 2008. View at Google Scholar
  37. M. Schneider, A. Bairoch, C. H. Wu, and R. Apweiler, “Plant protein annotation in the UniProt knowledgebase,” Plant Physiology, vol. 138, no. 1, pp. 59–66, 2005. View at Publisher · View at Google Scholar
  38. T. Ogawa, K. Yoshimura, H. Miyake et al., “Molecular characterization of organelle-type Nudix hydrolases in Arabidopsis thaliana,” Plant Physiology, vol. 148, no. 3, pp. 1412–1424, 2008. View at Google Scholar
  39. T. Ogawa, Y. Ueda, K. Yoshimura, and S. Shigeoka, “Comprehensive analysis of cytosolic Nudix hydrolases in Arabidopsis thaliana,” The Journal of Biological Chemistry, vol. 280, no. 26, pp. 25277–25283, 2005. View at Publisher · View at Google Scholar
  40. C. Popovici, R. Roubin, F. Coulier, and D. Birnbaum, “An evolutionary history of the FGF superfamily,” BioEssays, vol. 27, no. 8, pp. 849–857, 2005. View at Publisher · View at Google Scholar
  41. G. Blanc, K. Hokamp, and K. H. Wolfe, “A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome,” Genome Research, vol. 13, no. 2, pp. 137–144, 2003. View at Publisher · View at Google Scholar
  42. G. A. Petsko, G. L. Kenyon, J. A. Gerlt, D. Ringe, and J. W. Kozarich, “On the origin of enzymatic species,” Trends in Biochemical Sciences, vol. 18, no. 10, pp. 372–376, 1993. View at Publisher · View at Google Scholar