Table of Contents
International Journal of Evolutionary Biology
Volume 2009, Article ID 715086, 10 pages
http://dx.doi.org/10.4061/2009/715086
Research Article

Divergence of AMP Deaminase in the Ice Worm Mesenchytraeus solifugus (Annelida, Clitellata, Enchytraeidae)

1Department of Biology, University of Milano, via Celoria 26, 20133 Milano, Italy
2Department of Biology, Rutgers The State University of New Jersey, 315 Penn Street, Science Building, Camden, NJ 08102, USA

Received 7 April 2009; Accepted 22 May 2009

Academic Editor: Dan Graur

Copyright © 2009 Roberto Marotta 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. G. F. Wright, “The Muir Glacier,” American Journal of Science, vol. 33, no. 5, 1887. View at Google Scholar
  2. P. S. Welch, “Snow field and Glacier Oligochaeta from Mt. Rainier, Washington,” Transactions of the American Microscopical Society, vol. 35, pp. 85–124, 1916. View at Google Scholar
  3. B. G. M. Jamieson, “Non-leech Clitellata,” in Reproductive Biology and Phylogeny of Annelida, G. Rouse and F. Pleijel, Eds., pp. 235–392, Science, Enfield, NH, USA, 2006. View at Google Scholar
  4. P. L. Hartzell, J. V. Nghiem, K. J. Richio, and D. H. Shain, “Distribution and phylogeny of Glacier ice worms (Mesenchytraeus solifugus and Mesenchytraeus solifugus rainierensis),” Canadian Journal of Zoology, vol. 83, no. 9, pp. 1206–1213, 2005. View at Publisher · View at Google Scholar
  5. Y. L. Liang, C. F. Hsü, and T. N. Chang, “A new genus and species of Enchytraeidae from Tibet,” Acta Zootaxon Sinica, vol. 4, pp. 312–317, 1979. View at Google Scholar
  6. D. Goodman, “Ecological investigations of ice worm on Casement Glacier, Southeast Alaska,” Tech. Rep., Institute for Polar Studies, Ohio State University Research Foundation, Columbus, Ohio, USA, 1979. View at Google Scholar
  7. M. J. Napolitano, R. G. Nagele, and D. H. Shain, “The ice worm, Mesenchytraeus solifugus, elevates adenylate levels at low physiological temperature,” Comparative Biochemistry and Physiology, vol. 137, no. 1, pp. 227–235, 2004. View at Publisher · View at Google Scholar
  8. M. J. Napolitano and D. H. Shain, “Four kingdoms on Glacier ice: convergent energetic processes boost energy levels as temperatures fall,” Proceedings of the Royal Society B, vol. 271, supplement 5, pp. S273–S276, 2004. View at Google Scholar
  9. M. J. Napolitano and D. H. Shain, “Distinctions in adenylate metabolism among organisms inhabiting temperature extremes,” Extremophiles, vol. 9, no. 2, pp. 93–98, 2005. View at Publisher · View at Google Scholar
  10. F. I. Ataullakhanov and V. M. Vitvitsky, “What determines the intracellular ATP concentration,” Bioscience Reports, vol. 22, no. 5-6, pp. 501–511, 2002. View at Publisher · View at Google Scholar
  11. D. G. Hardie and S. A. Hawley, “AMP-activated protein kinase: the energy charge hypothesis revisited,” BioEssays, vol. 23, no. 12, pp. 1112–1119, 2001. View at Publisher · View at Google Scholar
  12. D. J. Merkler and V. L. Schramm, “Catalytic mechanism of yeast adenosine 5-monophosphate deaminase. Zinc content, substrate specificity, pH studies, and solvent isotope effects,” Biochemistry, vol. 32, no. 22, pp. 5792–5799, 1993. View at Google Scholar
  13. D. J. Merkler and V. L. Schramm, “Catalytic and regulatory site composition of yeast AMP deaminase by comparative binding and rate studies. Resolution of the cooperative mechanism,” Journal of Biological Chemistry, vol. 265, no. 8, pp. 4420–4426, 1990. View at Google Scholar
  14. M. T. Bausch-Jurken and R. L. Sabina, “Divergent N-terminal regions in AMP deaminase and isoform-specific catalytic properties of the enzyme,” Archives of Biochemistry and Biophysics, vol. 321, no. 2, pp. 372–380, 1995. View at Publisher · View at Google Scholar
  15. D. H. Shain, M. R. Carter, K. P. Murray et al., “Morphologic characterization of the ice worm Mesenchytraeus solifugus,” Journal of Morphology, vol. 246, no. 3, pp. 192–197, 2000. View at Publisher · View at Google Scholar
  16. K. A. Hohenstein and D. H. Shain, “Divergence of the F1-ATP synthase complex in the ice worm, Mesenchytraeus solifugus (Annelida, Clitellata, Enchytraeidae),” Hydrobiologia, vol. 564, no. 1, pp. 51–58, 2006. View at Publisher · View at Google Scholar
  17. P. Chomczynski and N. Sacchi, “Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction,” Analytical Biochemistry, vol. 162, no. 1, pp. 156–159, 1987. View at Google Scholar
  18. A. H. Farrell, K. A. Hohenstein, and D. H. Shain, “Molecular adaptation in the ice worm, Mesenchytraeus solifugus: divergence of energetic-associated genes,” Journal of Molecular Evolution, vol. 59, no. 5, pp. 666–673, 2004. View at Publisher · View at Google Scholar
  19. 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
  20. R. Chenna, H. Sugawara, T. Koike et al., “Multiple sequence alignment with the Clustal series of programs,” Nucleic Acids Research, vol. 31, no. 13, pp. 3497–3500, 2003. View at Publisher · View at Google Scholar
  21. E. Gasteiger, C. Hoogland, A. Gattiker et al., “Protein identification and analysis tools on the ExPASy server,” in The Proteomics Protocols Handbook, J. M. Walker, Ed., pp. 571–607, Humana Press, Totowa, NJ, USA, 2005. View at Google Scholar
  22. H. M. Berman, J. Westbrook, Z. Feng et al., “The protein data bank,” Nucleic Acids Research, vol. 28, no. 1, pp. 235–242, 2000. View at Google Scholar
  23. J. Kopp and T. Schwede, “The SWISS-MODEL repository of annotated three-dimensional protein structure homology models,” Nucleic Acids Research, vol. 32, pp. D230–D234, 2004. View at Google Scholar
  24. K. Arnold, L. Bordoli, J. Kopp, and T. Schwede, “The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling,” Bioinformatics, vol. 22, no. 2, pp. 195–201, 2006. View at Publisher · View at Google Scholar
  25. C. Frieden, L. C. Kurz, and H. R. Gilbert, “Adenosine deaminase and adenylate deaminase: comparative kinetic studies with transition state and ground state analogue inhibitors,” Biochemistry, vol. 19, no. 23, pp. 5303–5309, 1980. View at Google Scholar
  26. B. W. Han, C. A. Bingman, D. K. Mahnke et al., “Membrane association, mechanism of action, and structure of Arabidopsis embryonic factor 1 (FAC1),” Journal of Biological Chemistry, vol. 281, no. 21, pp. 14939–14947, 2006. View at Publisher · View at Google Scholar
  27. N. Guex and M. C. Peitsch, “SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling,” Electrophoresis, vol. 18, no. 15, pp. 2714–2723, 1997. View at Publisher · View at Google Scholar
  28. W. L. DeLano, The PyMOL Molecular Graphic System, DeLano Scientific, Palo Alto, Calif, USA, 2002.
  29. D. K. Wilson, F. B. Rudolph, and F. A. Quiocho, “Atomic structure of adenosine deaminase complexed with a transition-state analog: understanding catalysis and immunodeficiency mutations,” Science, vol. 252, no. 5010, pp. 1278–1284, 1991. View at Google Scholar
  30. R. A. Laskowski, M. W. MacArthur, D. S. Moss et al., “PROCHECK: a program to check the stereochemical quality of protein structures,” Journal of Applied Crystallography, vol. 26, pp. 283–291, 1993. View at Google Scholar
  31. T. E. English and K. B. Storey, “Enzymes of adenylate metabolism and their role in hibernation of the white-tailed prairie dog, Cynomys leucurus,” Archives of Biochemistry and Biophysics, vol. 376, no. 1, pp. 91–100, 2000. View at Publisher · View at Google Scholar
  32. A. L. Haas and R. L. Sabina, “N-terminal extensions of the human AMPD2 polypeptide influence ATP regulation of isoform L,” Biochemical and Biophysical Research Communications, vol. 305, no. 2, pp. 421–427, 2003. View at Publisher · View at Google Scholar
  33. C. J. Marshall, “Cold-adapted enzymes,” Trends in Biotechnology, vol. 15, no. 9, pp. 359–364, 1997. View at Publisher · View at Google Scholar
  34. G. Gianese, P. Argos, and S. Pascarella, “Structural adaptation of enzymes to low temperatures,” Protein Engineering, vol. 14, no. 3, pp. 141–148, 2001. View at Google Scholar
  35. S. D'Amico, P. Claverie, T. Collins et al., “Molecular basis of cold adaptation,” Philosophical Transactions of the Royal Society B, vol. 357, no. 1423, pp. 917–925, 2002. View at Publisher · View at Google Scholar
  36. I. L. Alberts, K. Nadassy, and S. J. Wodak, “Analysis of zinc binding sites in protein crystal structures,” Protein Science, vol. 7, no. 8, pp. 1700–1716, 1998. View at Google Scholar
  37. F. Tekaia, E. Yeramian, and B. Dujon, “Amino acid composition of genomes, lifestyles of organisms, and evolutionary trends: a global picture with correspondence analysis,” Gene, vol. 297, no. 1-2, pp. 51–60, 2002. View at Publisher · View at Google Scholar
  38. Y. Nishio, Y. Nakamura, Y. Kawarabayasi et al., “Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens,” Genome Research, vol. 13, no. 7, pp. 1572–1579, 2003. View at Publisher · View at Google Scholar
  39. G. Feller, Z. Zekhnini, J. Lamotte-Brasseur, and C. Gerday, “Enzymes from cold-adapted microorganisms. The class C β-lactamase from the antarctic psychrophile Psychrobacter immobilis A5,” European Journal of Biochemistry, vol. 244, no. 1, pp. 186–191, 1997. View at Google Scholar
  40. L. Menéndez-Arias and P. Argosf, “Engineering protein thermal stability,” Journal of Molecular Biology, vol. 206, no. 2, pp. 397–406, 1989. View at Google Scholar
  41. E. Bae and G. N. Phillips Jr., “Structures and analysis of highly homologous psychrophilic, mesophilic, and thermophilic adenylate kinases,” Journal of Biological Chemistry, vol. 279, no. 27, pp. 28202–28208, 2004. View at Publisher · View at Google Scholar
  42. P. A. Fields, “Review: protein function at thermal extremes: balancing stability and flexibility,” Comparative Biochemistry and Physiology A, vol. 129, no. 2-3, pp. 417–431, 2001. View at Publisher · View at Google Scholar
  43. R. J. Bazin, G. A. McDonald, and C. Phillips, UK patent no. GB2373504, September 2003.
  44. B. A. Morrison and D. H. Shain, “An AMP nucleosidase gene knockout in Escherichia coli elevates intracellular ATP levels and increases cold tolerance,” Biology Letters, vol. 4, no. 1, pp. 53–56, 2008. View at Publisher · View at Google Scholar