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Korean Society for Biochemistry and Molecular Biology (생화학분자생물학회)
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Comprehensive analysis of AHL homologous genes encoding AT-hook motif nuclear localized protein in rice

  • Kim, Ho-Bang (The Natural Science Research Institute, Myongji University) ;
  • Oh, Chang-Jae (School of Biological Sciences, College of Natural Sciences, Seoul National University) ;
  • Park, Yung-Chul (Department of Forest Environment Protection, College of Forest & Environmental Sciences, Kangwon National University) ;
  • Lee, Yi (Department of Industrial Plant Science & Technology, Chungbuk National University) ;
  • Choe, Sung-Hwa (School of Biological Sciences, College of Natural Sciences, Seoul National University) ;
  • An, Chung-Sun (School of Biological Sciences, College of Natural Sciences, Seoul National University) ;
  • Choi, Sang-Bong (Department of Biological Sciences, Myongji University)
  • Received : 2011.06.13
  • Accepted : 2011.07.11
  • Published : 2011.10.31
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Abstract

The AT-hook motif is a small DNA-binding protein motif that has been found in the high mobility group of non-histone chromosomal proteins. The Arabidopsis genome contains 29 genes encoding the AT-hook motif DNA-binding protein (AHL). Recent studies of Arabidopsis genes (AtAHLs) have revealed that they might play diverse functional roles during plant growth and development. In this report, we mined 20 AHL genes (OsAHLs) from the rice genome database using AtAHL genes as queries and characterized their molecular features. A phylogenetic tree revealed that OsAHL proteins can be classified into 2 evolutionary clades. Tissue expression pattern analysis revealed that all of the OsAHL genes might be functionally expressed genes with 3 distinct expression patterns. Nuclear localization analysis using transgenic Arabidopsis showed that several OsAHL proteins are exclusively localized in the nucleus, indicating that they may act as architectural transcription factors to regulate expression of their target genes during plant growth and development.

Keywords

References

  1. Sikder, D. and Kodadek, T. (2005) Genomic studies of transcription factor-DNA interactions. Curr. Opin. Chem. Biol. 9, 38-45. https://doi.org/10.1016/j.cbpa.2004.12.008
  2. Zhao, K., Kas, E., Gonzales, E. and Laemmli, U. K. (1993) SAR-dependent mobilization of histone H1 by HMG-I/Y in vitro: HMG-I/Y is enriched in H1-depleted chromatin. EMBO J. 12, 3237-3247.
  3. Rajeswari, M. R. and Jain, A. (2002) High-mobility-group chromosomal proteins, HMGA1 as potential tumour markers. Current Sci. 82, 838-844.
  4. Grasser, K. D. (2003) Chromatin-associated HMGA and HMGB proteins: versatile co-regulators of DNA-dependent processes. Plant Mol. Biol. 53, 281-295. https://doi.org/10.1023/B:PLAN.0000007002.99408.ba
  5. Aravind, L. and Landsman, D. (1998) AT-hook motifs identified in a wide variety of DNA-binding proteins. Nucleic Acids Res. 26, 4413-4421. https://doi.org/10.1093/nar/26.19.4413
  6. Reeves, R. and Beckerbauer, L. (2001) HMGI/Y proteins: flexible regulators of transcription and chromatin structure. Biochim. Biophys. Acta. 1519, 13-29. https://doi.org/10.1016/S0167-4781(01)00215-9
  7. Strick, R. and Laemmli, U. K. (1995) SARs are cis DNA elements of chromosome dynamics: synthesis of a SAR repressor protein. Cell 83, 1137-1148. https://doi.org/10.1016/0092-8674(95)90140-X
  8. Morisawa, G., Han-Yama, A., Moda, I., Tamai, A., Iwabuchi, M. and Meshi, T. (2000) AHM1, a novel type of nuclear matrix-localized, MAR binding protein with a single AT hook and a J domain-homologous region. Plant Cell 12, 1903-1916. https://doi.org/10.1105/tpc.12.10.1903
  9. Fujimoto, S., Matsunaga, S., Yonemura, M., Uchiyama, S., Azuma, T. and Fukui, K. (2004) Identification of a novel plant MAR DNA binding protein localized on chromosomal surfaces. Plant Mol. Biol. 56, 225-239. https://doi.org/10.1007/s11103-004-3249-5
  10. Matsushita, A., Furumoto, T., Ishida, S. and Takahashi, Y. (2007) AGF1, an AT-hook protein, is necessary for the negative feedback of AtGA3ox1 encoding GA 3-oxidase. Plant Physiol. 143, 1152-1162. https://doi.org/10.1104/pp.106.093542
  11. Vom Endt, D., Soares e Silva, M., Kijne, J. W., Pasquali, G. and Memelink, J. (2007) Identification of a bipartite jasmonate-responsive promoter element in the Catharanthus roseus ORCA3 transcription factor gene that interacts specifically with AT-Hook DNA-binding proteins. Plant Physiol. 144, 1680-1689. https://doi.org/10.1104/pp.107.096115
  12. Lim, P. O., Kim, Y., Breeze, E., Koo, J. C., Woo, H. R., Ryu, J. S., Park, D. H., Beynon, J., Tabrett, A., Buchanan- Wollsston, V. and Nam, H. G. (2007) Overexpression of a chromatin architecture-controlling AT-hook protein extends leaf longevity and increases the post-harvest storage life of plants. Plant J. 52, 1140-1153. https://doi.org/10.1111/j.1365-313X.2007.03317.x
  13. Street, I. H., Shah, P. K., Smith, A. M., Avery, N. and Neff, M. M. (2008) The AT-hook-containing proteins SOB3/AHL29 and ESC/AHL27 are negative modulators of hypocotyl growth in Arabidopsis. Plant J. 54, 1-14.
  14. Xiao, C., Chen, F., Yu, X., Lin, C. and Fu, Y. -F. (2009) Over-expression of an AT-hook gene, AHL22, delays flowering and inhibits the elongation of the hypocotyl in Arabidopsis thaliana. Plant Mol. Biol. 71, 39-50. https://doi.org/10.1007/s11103-009-9507-9
  15. Ng, K.-H., Yu, H. and Ito, T (2009) AGAMOUS controls GIANT KILLER, a multifunctional chromatin modifier in reproductive organ patterning and differentiation. PLoS Biol. 7(11), e1000251. doi:10,1371/journal.pbio.1000251. https://doi.org/10.1371/journal.pbio.1000251
  16. Nieto-Sotelo, J., Ichida, A. and Quail, P. H. (1994) PF1: an A-T hook-containing DNA binding protein from rice that interacts with a functionally defined d(AT)-rich element in the oat phytochrome A3 gene promoter. Plant Cell 6, 287-301. https://doi.org/10.1105/tpc.6.2.287
  17. Meijer, A. H., van Dijk, E. L. and Hoge, J. H. (1996) Novel members of a family of AT hook-containing DNA-binding proteins from rice are identified through their in vitro interaction with consensus target sites of plant and animal homeodomain proteins. Plant Mol. Biol. 31, 607-618. https://doi.org/10.1007/BF00042233
  18. Gupta, R., Webster, C. I., Walker, A. and Gray, J. C. (1997) Chromosomal location and expression of the single-copy gene encoding high-mobility-group protein HMG-I/Y in Arabidopsis thaliana. Plant Mol. Biol. 34, 529-536. https://doi.org/10.1023/A:1005828430861
  19. Gupta, R., Webster, C. I. and Gray, J. C. (1998) Characterization and promoter analysis of the Arabidopsis gene encoding high-mobility-group protein HMG-I/Y. Plant Mol. Biol. 36, 897-907. https://doi.org/10.1023/A:1005928219895
  20. Zhao, J., Paul, L. K. and Grafi, G. (2009) The maize HMGA protein is localized to the nucleolus, can be acetylated in vitro at its globular domain and phosphorylation by CDK reduces its binding activity to AT-rich DNA. BBA - Gene Regulatory Mechanisms 1789, 751-757.
  21. Yamamoto, S. and Minamikawa, T. (1997) The high mobility group protein HMG-Y binds to promoter regions of seed storage protein genes from Canavalia gladiata D.C. Plant Sci. 124, 165-173. https://doi.org/10.1016/S0168-9452(97)04611-6
  22. Zhang, W., Wu, Q., Pwee, K. -H. and Kini, R. M. (2003) Interaction of wheat high-mobility-group proteins with four-way-junction DNA and characterization of the structure and expression of HMGA gene. Arch. Biochem. Biophys. 409, 357-366. https://doi.org/10.1016/S0003-9861(02)00630-6
  23. Zhao, J. and Grafi, G. (2000) The high mobility group I/Y protein is hypophosphorylated in endoreduplicating maize endosperm cells and is involved in alleviating histone H1-mediated transcriptional repression. J. Biol. Chem. 275, 27494-27499.
  24. Jung, K. -H., Jeon, J. -S. and An, G (2011) Web tools for rice transcriptome analyses. J. Plant Biol. 54, 65-80. https://doi.org/10.1007/s12374-011-9146-y
  25. Altschul, S. F., Gish, W., Miller, W., Meyers, E. W. and Lipman, D. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403-410. https://doi.org/10.1016/S0022-2836(05)80360-2
  26. Tamura, K., Dudley, J., Nei, M. and Kumar, S. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596-1599. https://doi.org/10.1093/molbev/msm092
  27. Clough, S. J. and Bent, A. F. (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735-743. https://doi.org/10.1046/j.1365-313x.1998.00343.x

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