About this Journal Submit a Manuscript Table of Contents
BioMed Research International
Volume 2013 (2013), Article ID 630803, 11 pages
http://dx.doi.org/10.1155/2013/630803
Research Article

Dynamic Actin Gene Family Evolution in Primates

1Institute of System Biology, Shanghai University, Shanghai 200444, China
2Yangzhou Breeding Biological Agriculture Technology Co. Ltd., Yangzhou 225200, China
3School of Life Sciences, Shanghai University, Shanghai 200444, China
4State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China

Received 10 April 2013; Revised 17 May 2013; Accepted 18 May 2013

Academic Editor: Tao Huang

Copyright © 2013 Liucun Zhu 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. I. M. Sehring, J. Mansfeld, C. Reiner, E. Wagner, H. Plattner, and R. Kissmehl, “The actin multigene family of Paramecium tetraurelia,” BMC Genomics, vol. 8, article 82, 2007. View at Publisher · View at Google Scholar · View at Scopus
  2. J. F. Morrow, R. S. Stearman, C. G. Peltzman, and D. A. Potter, “Induction of hepatic synthesis of serum amyloid A protein and actin,” Proceedings of the National Academy of Sciences of the United States of America, vol. 78, no. 8, pp. 4718–4722, 1981. View at Scopus
  3. J. L. Degen, M. G. Neubauer, S. J. Degen, C. E. Seyfried, and D. R. Morris, “Regulation of protein synthesis in mitogen-activated bovine lymphocytes. Analysis of actin-specific and total mRNA accumulation and utilization,” The Journal of Biological Chemistry, vol. 258, no. 20, pp. 12153–12162, 1983. View at Scopus
  4. C. J. Staiger, Y. Ming, R. Valenta, P. J. Shaw, R. M. Warn, and C. W. Lloyd, “Microinjected profilin affects cytoplasmic streaming in plant cells by rapidly depolymerizing actin microfilaments,” Current Biology, vol. 4, no. 3, pp. 215–219, 1994. View at Publisher · View at Google Scholar · View at Scopus
  5. J. Snider, F. Lin, N. Zahedi, V. Rodionovt, C. C. Yu, and S. P. Gross, “Intracellular actin-based transport: how far you go depends on how often you switch,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 36, pp. 13204–13209, 2004. View at Publisher · View at Google Scholar · View at Scopus
  6. M. Ghosh, X. Song, G. Mouneimne, M. Sidani, D. S. Lawrence, and J. S. Condeelis, “Cofilin promotes actin polymerization and defines the direction of cell motility,” Science, vol. 304, no. 5671, pp. 743–746, 2004. View at Publisher · View at Google Scholar · View at Scopus
  7. K. L. Hill, N. L. Catlett, and L. S. Weisman, “Actin and myosin function in directed vacuole movement during cell division in Saccharomyces cerevisiae,” The Journal of Cell Biology, vol. 135, no. 6, pp. 1535–1549, 1996. View at Publisher · View at Google Scholar · View at Scopus
  8. M. S. Otegui, K. J. Verbrugghe, and A. R. Skop, “Midbodies and phragmoplasts: analogous structures involved in cytokinesis,” Trends in Cell Biology, vol. 15, no. 8, pp. 404–413, 2005. View at Publisher · View at Google Scholar · View at Scopus
  9. E. Reisler, “Actin molecular structure and function,” Current Opinion in Cell Biology, vol. 5, no. 1, pp. 41–47, 1993. View at Scopus
  10. P. K. Howard, B. M. Sefton, and R. A. Firtel, “Tyrosine phosphorylation of actin in Dictyostelium associated with cell-shape changes,” Science, vol. 259, no. 5092, pp. 241–244, 1993. View at Scopus
  11. D. A. Schafer and T. A. Schroer, “Actin-related proteins,” Annual Review of Cell and Developmental Biology, vol. 15, pp. 341–363, 1999. View at Publisher · View at Google Scholar · View at Scopus
  12. L. M. Machesky and R. C. May, “Arps: actin-related proteins,” Results and Problems in Cell Differentiation, vol. 32, pp. 213–229, 2001. View at Scopus
  13. J. Muller, Y. Oma, L. Vallar, E. Friederich, O. Poch, and B. Winsor, “Sequence and comparative genomic analysis of actin-related proteins,” Molecular Biology of the Cell, vol. 16, no. 12, pp. 5736–5748, 2005. View at Publisher · View at Google Scholar · View at Scopus
  14. H. V. Goodson and W. F. Hawse, “Molecular evolution of the actin family,” Journal of Cell Science, vol. 115, no. 13, pp. 2619–2622, 2002. View at Scopus
  15. M. K. Kandasamy, R. B. Deal, E. C. McKinney, and R. B. Meagher, “Plant actin-related proteins,” Trends in Plant Science, vol. 9, no. 4, pp. 196–202, 2004. View at Publisher · View at Google Scholar · View at Scopus
  16. J. L. Hodgkinson, C. Peters, S. A. Kuznetsov, and W. Steffen, “Three-dimensional reconstruction of the dynactin complex by single-particle image analysis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 10, pp. 3667–3672, 2005. View at Publisher · View at Google Scholar · View at Scopus
  17. A. Efstratiadis, J. W. Posakony, T. Maniatis, et al., “The structure and evolution of the human β-globin gene family,” Cell, vol. 21, no. 3, pp. 653–668, 1980. View at Scopus
  18. G. G. Brown, J. S. Lee, N. Brisson, and D. P. S. Verma, “The evolution of a plant globin gene family,” Journal of Molecular Evolution, vol. 21, no. 1, pp. 19–32, 1984. View at Scopus
  19. J. N. Engel, P. W. Gunning, and L. Kedes, “Isolation and characterization of human actin genes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 78, no. 8, pp. 4674–4678, 1981. View at Scopus
  20. E. A. Fyrberg, B. J. Bond, N. D. Hershey, K. S. Mixter, and N. Davidson, “The actin genes of drosophila: protein coding regions are highly conserved but intron positions are not,” Cell, vol. 24, no. 1, pp. 107–116, 1981. View at Scopus
  21. R. Zakut, M. Shani, D. Givol, S. Neuman, D. Yaffe, and U. Nudel, “Nucleotide sequence of the rat skeletal muscle actin gene,” Nature, vol. 298, no. 5877, pp. 857–859, 1982. View at Scopus
  22. J. G. Files, S. Carr, and D. Hirsh, “Actin gene family of Caenorhabditis elegans,” Journal of Molecular Biology, vol. 164, no. 3, pp. 355–375, 1983. View at Scopus
  23. J. A. Fornwald, G. Kuncio, I. Peng, and C. P. Ordahl, “The complete nucleotide sequence of the chick a-actin gene and its evolutionary relationship to the actin gene family,” Nucleic Acids Research, vol. 10, no. 13, pp. 3861–3876, 1982. View at Publisher · View at Google Scholar · View at Scopus
  24. R. C. Hightower and R. B. Meagher, “The molecular evolution of actin,” Genetics, vol. 114, no. 1, pp. 315–332, 1986. View at Scopus
  25. M. Wu, J. M. Comeron, H. S. Yoon, and D. Bhattacharya, “Unexpected dynamic gene family evolution in algal actins,” Molecular Biology and Evolution, vol. 26, no. 2, pp. 249–253, 2009. View at Publisher · View at Google Scholar · View at Scopus
  26. S. Kim, T. R. Bachvaroff, S. M. Handy, and C. F. Delwiche, “Dynamics of actin evolution in dinoflagellates,” Molecular Biology and Evolution, vol. 28, no. 4, pp. 1469–1480, 2011. View at Publisher · View at Google Scholar · View at Scopus
  27. R. J. Kinsella, A. Kahari, S. Haider, et al., “Ensembl BioMarts: a hub for data retrieval across taxonomic space,” Database, vol. 2011, Article ID bar030, 2011.
  28. A. Marchler-Bauer, J. B. Anderson, P. F. Cherukuri et al., “CDD: a conserved domain database for protein classification,” Nucleic Acids Research, vol. 33, pp. D192–D196, 2005. View at Publisher · View at Google Scholar · View at Scopus
  29. K. Tamura, J. Dudley, M. Nei, and S. Kumar, “MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0,” Molecular Biology and Evolution, vol. 24, no. 8, pp. 1596–1599, 2007. View at Publisher · View at Google Scholar · View at Scopus
  30. 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 Scopus
  31. M. Lynch and T. J. Crease, “The analysis of population survey data on DNA sequence variation,” Molecular Biology and Evolution, vol. 7, no. 4, pp. 377–394, 1990. View at Scopus
  32. M. Nei and T. Gojobori, “Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions,” Molecular Biology and Evolution, vol. 3, no. 5, pp. 418–426, 1986. View at Scopus
  33. P. M. Sharp, T. M. F. Tuohy, and K. R. Mosurski, “Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes,” Nucleic Acids Research, vol. 14, no. 13, pp. 5125–5143, 1986. View at Publisher · View at Google Scholar · View at Scopus
  34. T. Zhou, W. Gu, J. Ma, X. Sun, and Z. Lu, “Analysis of synonymous codon usage in H5N1 virus and other influenza A viruses,” BioSystems, vol. 81, no. 1, pp. 77–86, 2005. View at Publisher · View at Google Scholar · View at Scopus
  35. I. Ahn, B. J. Jeong, S. E. Bae, J. Jung, and H. S. Son, “Genomic analysis of influenza A viruses, including avian flu (H5N1) strains,” European Journal of Epidemiology, vol. 21, no. 7, pp. 511–519, 2006. View at Publisher · View at Google Scholar · View at Scopus
  36. G. Perrière and J. Thioulouse, “Use and misuse of correspondence analysis in codon usage studies,” Nucleic Acids Research, vol. 30, no. 20, pp. 4548–4555, 2002. View at Scopus
  37. P. Khaitovich, I. Hellmann, W. Enard et al., “Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees,” Science, vol. 309, no. 5742, pp. 1850–1854, 2005. View at Publisher · View at Google Scholar · View at Scopus
  38. R. Percudani and S. Ottonello, “Selection at the wobble position of codons read by the same tRNA in Saccharomyces cerevisiae,” Molecular Biology and Evolution, vol. 16, no. 12, pp. 1752–1762, 1999. View at Scopus
  39. S. Kanaya, Y. Yamada, M. Kinouchi, Y. Kudo, and T. Ikemura, “Codon usage and tRNA genes in eukaryotes: correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis,” Journal of Molecular Evolution, vol. 53, no. 4-5, pp. 290–298, 2001. View at Publisher · View at Google Scholar · View at Scopus
  40. G. Sánchez, A. Bosch, and R. M. Pintó, “Genome variability and capsid structural constraints of hepatitis A virus,” Journal of Virology, vol. 77, no. 1, pp. 452–459, 2003. View at Publisher · View at Google Scholar · View at Scopus
  41. L. A. Shackelton, C. R. Parrish, and E. C. Holmes, “Evolutionary basis of codon usage and nucleotide composition bias in vertebrate DNA viruses,” Journal of Molecular Evolution, vol. 62, no. 5, pp. 551–563, 2006. View at Publisher · View at Google Scholar · View at Scopus
  42. C. T. Tsai, C. H. Lin, and C. Y. Chang, “Analysis of codon usage bias and base compositional constraints in iridovirus genomes,” Virus Research, vol. 126, no. 1-2, pp. 196–206, 2007. View at Publisher · View at Google Scholar · View at Scopus
  43. K. M. Pepin, J. Domsic, and R. McKenna, “Genomic evolution in a virus under specific selection for host recognition,” Infection, Genetics and Evolution, vol. 8, no. 6, pp. 825–834, 2008. View at Publisher · View at Google Scholar · View at Scopus
  44. S. Oota and N. Saitou, “Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees,” Molecular Biology and Evolution, vol. 16, no. 6, pp. 856–867, 1999. View at Scopus
  45. D. Zhang, Q. Du, B. Xu, Z. Zhang, and B. Li, “The actin multigene family in Populus: organization, expression and phylogenetic analysis,” Molecular Genetics and Genomics, vol. 284, no. 2, pp. 105–119, 2010. View at Publisher · View at Google Scholar · View at Scopus
  46. K. Slajcherova, J. Fiserova, L. Fischer, and K. Schwarzerova, “Multiple actin isotypes in plants: diverse genes for diverse roles?” Frontiers in Plant Science, vol. 3, article 226, 2012.
  47. P. Gunning, P. Ponte, L. Kedes, R. J. Hickey, and A. I. Skoultchi, “Expression of human cardiac actin in mouse L cells: a sarcomeric actin associates with a nonmuscle cytoskeleton,” Cell, vol. 36, no. 3, pp. 709–715, 1984. View at Scopus
  48. J. Vandekerckhove and K. Weber, “At least six different actins are expressed in a higher mammal: an analysis based on the amino acid sequence of the amino-terminal tryptic peptide,” Journal of Molecular Biology, vol. 126, no. 4, pp. 783–802, 1978. View at Scopus
  49. A. S. Tsang, H. Mahbubani, and J. G. Williams, “Cell-type specific actin mRNA populations in dictyostelium discoideum,” Cell, vol. 31, no. 2, pp. 375–382, 1982. View at Scopus
  50. E. A. Fyrberg, J. W. Mahaffey, B. J. Bond, and N. Davidson, “Transcripts of the six Drosophila actin genes accumulate in a stage- and tissue-specific manner,” Cell, vol. 33, no. 1, pp. 115–123, 1983. View at Scopus
  51. Y. Lee, T. Ise, D. Ha et al., “Evolution and expression of chimeric POTE-actin genes in the human genome,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 47, pp. 17885–17890, 2006. View at Publisher · View at Google Scholar · View at Scopus
  52. T. K. Bera, D. B. Zimonjic, N. C. Popescu et al., “POTE, a highly homologous gene family located on numerous chromosomes and expressed in prostate, ovary, testis, placenta, and prostate cancer,” Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 26, pp. 16975–16980, 2002.
  53. A. P. Rooney and T. J. Ward, “Birth-and-death evolution of the internalin multigene family in Listeria,” Gene, vol. 427, no. 1-2, pp. 124–128, 2008. View at Publisher · View at Google Scholar · View at Scopus
  54. M. Nei, X. Gu, and T. Sitnikova, “Evolution by the birth-and-death process in multigene families of the vertebrate immune system,” Proceedings of the National Academy of Sciences of the United States of America, vol. 94, no. 15, pp. 7799–7806, 1997. View at Publisher · View at Google Scholar · View at Scopus
  55. G. P. Smith, “Mouse immunoglobulin kappa chain MPC 11: extra amino terminal residues,” Science, vol. 181, no. 4103, pp. 941–943, 1973. View at Scopus
  56. E. A. Zimmer, S. L. Martin, S. M. Beverley, Y. W. Kan, and A. C. Wilson, “Rapid duplication and loss of genes coding for the α chains of hemoglobin,” Proceedings of the National Academy of Sciences of the United States of America, vol. 77, no. 4, pp. 2158–2162, 1980. View at Scopus
  57. D. M. Irwin and A. C. Wilson, “Concerted evolution of ruminant stomach lysozymes. Characterization of lysozyme cDNA clones from sheep and deer,” The Journal of Biological Chemistry, vol. 265, no. 9, pp. 4944–4952, 1990. View at Scopus