- About this Journal ·
- Abstracting and Indexing ·
- Advance Access ·
- Aims and Scope ·
- Annual Issues ·
- Article Processing Charges ·
- Articles in Press ·
- Author Guidelines ·
- Bibliographic Information ·
- Citations to this Journal ·
- Contact Information ·
- Editorial Board ·
- Editorial Workflow ·
- Free eTOC Alerts ·
- Publication Ethics ·
- Reviewers Acknowledgment ·
- Submit a Manuscript ·
- Subscription Information ·
- Table of Contents
BioMed Research International
Volume 2013 (2013), Article ID 630803, 11 pages
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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- E. Reisler, “Actin molecular structure and function,” Current Opinion in Cell Biology, vol. 5, no. 1, pp. 41–47, 1993.
- 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.
- D. A. Schafer and T. A. Schroer, “Actin-related proteins,” Annual Review of Cell and Developmental Biology, vol. 15, pp. 341–363, 1999.
- L. M. Machesky and R. C. May, “Arps: actin-related proteins,” Results and Problems in Cell Differentiation, vol. 32, pp. 213–229, 2001.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- R. C. Hightower and R. B. Meagher, “The molecular evolution of actin,” Genetics, vol. 114, no. 1, pp. 315–332, 1986.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- G. P. Smith, “Mouse immunoglobulin kappa chain MPC 11: extra amino terminal residues,” Science, vol. 181, no. 4103, pp. 941–943, 1973.
- 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.
- 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.