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Identification of a novel plant MAR DNA binding protein localized on chromosomal surfaces

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Abstract

We identified a novel nucleoplasm localized protein in Arabidopsis called AT-hook motif nuclear localized protein 1 (AHL1), which was isolated by visual screening of transformants using random GFP::cDNA fusions. AHL1 contains an AT-hook motif and unknown conserved PPC (plants and prokaryotes conserved) domain that includes a hydrophobic region. Approximately 30 paralogues were identified in the Arabidopsis genome. Proteins with PPC-like domains are found in Bacteria, Archaea and the plant kingdom, but in Bacteria and Archaea the PPC containing proteins of do not have an AT-hook motif. Thus, the PPC domain is evolutionary conserved and has a new function such as AT-rich DNA binding. AHL1 was mainly localized in the nucleoplasm, but little in the nucleolus and heterochromatic region, and was concentrated in the boundary region between euchromatin and heterochromatin. Biochemically, AHL1 was also found in the nuclear matrix fraction. In the M phase, AHL1 was localized on the chromosomal surface. The AT-hook motif was essential for matrix attachment region (MAR) binding, and the hydrophobic region of the PPC was indispensable for nuclear localization. Our results suggest that AHL1 is a novel plant MAR binding protein, which is related to the positioning of chromatin fibers in the nucleus by the presence of an AT-hook motif and PPC domain. In addition, AHL1 is located on the surface of chromosomes during mitosis.

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References

  • Adachi, Y., Kas, E. and Laemmli, U. K. 1989. Preferential, cooperative binding of DNA topoisomerase II to scaffold associated regions. EMBO J. 8: 3997-4006.

    PubMed  Google Scholar 

  • Agard, D. A., Hiraoka, Y., Shaw, P. and Sedat, J. W. 1989. Fluorescence microscopy in three dimensions. Methods Cell Biol. 30: 353-377.

    PubMed  Google Scholar 

  • An, G. 1987. Binary Ti vectors for plant transformation and promoter analysis. Methods Enzymol. 153: 292-305.

    Google Scholar 

  • Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.

    Google Scholar 

  • Aravind, L. and Landsman, D. 1998. AT-hook motifs identified in a wide variety of DNA-binding proteins. Nucleic Acids Res. 26: 4413-4421.

    PubMed  Google Scholar 

  • Ashida, H., Saito, Y., Kojima, C., Kobayashi, K., Ogasawara, N. and Yokota, A. 2003. A functional link between RuBisCOlike protein of Bacillus and photosynthetic RuBisCO. Science 302: 286-290.

    PubMed  Google Scholar 

  • Berezney, R. and Coffey, D. S. 1974. Identification of a nuclear protein matrix. Biochem. Biophys. Res. Commun. 60: 1410-1417.

    PubMed  Google Scholar 

  • Calikowski, T. T., Meulia, T. and Meier, I. 2003. A proteomic study of the Arabidopsis nuclear matrix. J. Cell. Biochem. 90: 361-378.

    PubMed  Google Scholar 

  • Chaly, N., Bladon, T., Setterfield, G., Little, J. E., Kaplan, J. G. and Brown, D. L. 1984. Changes in distribution of nuclear matrix antigens during the mitotic cell cycle. J. Cell Biol. 99: 661-671.

    PubMed  Google Scholar 

  • Chiu, W., Niwa, Y., Zeng, W., Hirano, T., Kobayashi, H. and Sheen, J. 1996. Engineered GFP as a vital reporter in plants. Curr. Biol. 6: 325-330.

    PubMed  Google Scholar 

  • 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.

    PubMed  Google Scholar 

  • Cutler, S. R., Ehrhardt, D. W., Griffitts, J. S. and Somerville, C. R. 2000. Random GFP:: cDNA fusions enable visualization of subcellular structures in cells of Arabidopsis at a high frequency. Proc. Natl. Acad. Sci. USA 97: 3718-3723.

    PubMed  Google Scholar 

  • Dickinson, L. A., Joh, T., Kohwi, Y. and Kohwi-Shigematsu, T. 1992. A tissue-specific MAR/SAR DNA-binding protein with unusual binding site recognition. Cell 70: 631-645.

    PubMed  Google Scholar 

  • Fackelmayer, F. O., Dahm, K., Renz, A., Ramsperger, U. and Richter, A. 1994. Nucleic-acid-binding properties of hnRNP-U/SAF-A, a nuclear-matrix protein which binds DNA and RNA in vivo and in vitro. Eur. J. Biochem. 221: 749-757.

    PubMed  Google Scholar 

  • Gasser, S. M. and Laemmli, U. K. 1987. Improved methods for the isolation of individual and clustered mitotic chromosomes. Exp. Cell Res. 173: 85-98.

    PubMed  Google Scholar 

  • Gautier, T., Masson, C., Quintana, C., Arnoult, J. and Hernandez-Verdun, D. 1992a. The ultrastructure of the chromosome periphery in human cell lines. An in situ study using cryomethods in electron microscopy. Chromosoma 101: 502-510.

    PubMed  Google Scholar 

  • Gautier, T., Robert-Nicoud, M., Guilly, M. N. and HernandezVerdun, D. 1992b. Relocation of nucleolar proteins around chromosomes at mitosis. A study by confocal laser scanning microscopy. J. Cell Sci. 102 (Pt 4): 729-737.

    PubMed  Google Scholar 

  • Gerace, L. and Blobel, G. 1980. The nuclear envelope lamina is reversibly depolymerized during mitosis. Cell 19: 277-287.

    PubMed  Google Scholar 

  • Gindullis, F. and Meier, I. 1999. Matrix attachment region binding protein MFP1 is localized in discrete domains at the nuclear envelope. Plant Cell 11: 1117-1128.

    PubMed  Google Scholar 

  • Gindullis, F., Peffer, N. J. and Meier, I. 1999. MAF1, a novel plant protein interacting with matrix attachment region binding protein MFP1, is located at the nuclear envelope. Plant Cell 11: 1755-1768.

    PubMed  Google Scholar 

  • Glass, J. R. and Gerace, L. 1990. Lamins A and C bind and assemble at the surface of mitotic chromosomes. J. Cell Biol. 111: 1047-1057.

    PubMed  Google Scholar 

  • Hatton, D. and Gray, J. C. 1999. Two MAR DNA-binding proteins of the pea nuclear matrix identify a new class of DNA-binding proteins. Plant J. 18: 417-429.

    PubMed  Google Scholar 

  • He, D. C., Nickerson, J. A. and Penman, S. 1990. Core laments of the nuclear matrix. J. Cell Biol. 110: 569-580.

    PubMed  Google Scholar 

  • Hernandez-Verdun, D. and Gautier, T. 1994. The chromosome periphery during mitosis. Bioessays 16: 179-185.

    PubMed  Google Scholar 

  • Hood, E. E., Helmer, G. L., Fraley, R. T. and Chilton, M. 1986. The hypervirulence of Agrobacterium tumefaciens A281 is encoded in a region of pTiBo542 outside of TDNA. J. Bacteriol. 168: 1291-1301.

    PubMed  Google Scholar 

  • Houben, A., Demidov, D., Gernand, D., Meister, A., Leach, C. R. and Schubert, I. 2003. Methylation of histone H3 in euchromatin of plant chromosomes depends on basic nuclear DNA content. Plant J. 33: 967-973.

    PubMed  Google Scholar 

  • Huth, J. R., Bewley, C. A., Nissen, M. S., Evans, J. N., Reeves, R., Gronenborn, A. M. and Clore, G. M. 1997. The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif. Nat. Struct. Biol. 4: 657-665.

    PubMed  Google Scholar 

  • Izaurralde, E., Kas, E. and Laemmli, U. K. 1989. Highly preferential nucleation of histone H1 assembly on scaffold associated regions. J. Mol. Biol. 210: 573-585.

    PubMed  Google Scholar 

  • Kieber, J. J., Rothenberg, M., Roman, G., Feldmann, K. A. and Ecker, J. R. 1993. CTR1, a negative regulator of the ethylene response pathway in Arabidopsis, encodes a member of the raf family of protein kinases. Cell 72: 427-441.

    PubMed  Google Scholar 

  • Kikuchi, S., Satoh, K., Nagata, T., Kawagashira, N., Doi, K., Kishimoto, N., Yazaki, J., Ishikawa, M., Yamada, H., Ooka, H., Hotta, I., Kojima, K., Namiki, T., Ohneda, E., Yahagi, W., Suzuki, K., Li, C. J., Ohtsuki, K., Shishiki, T., Otomo, Y., Murakami, K., Iida, Y., Sugano, S., Fujimura, T., Suzuki, Y., Tsunoda, Y., Kurosaki, T., Kodama, T., Masuda, H., Kobayashi, M., Xie, Q., Lu, M., Narikawa, R., Sugiyama, A., Mizuno, K., Yokomizo, S., Niikura, J., Ikeda, R., Ishibiki, J., Kawamata, M., Yoshimura, A., Miura, J., Kusumegi, T., Oka, M., Ryu, R., Ueda, M., Matsubara, K., Kawai, J., Carninci, P., Adachi, J., Aizawa, K., Arakawa, T., Fukuda, S., Hara, A., Hashidume, W., Hayatsu, N., Imotani, K., Ishii, Y., Itoh, M., Kagawa, I., Kondo, S., Konno, H., Miyazaki, A., Osato, N., Ota, Y., Saito, R., Sasaki, D., Sato, K., Shibata, K., Shinagawa, A., Shiraki, T., Yoshino, M. and Hayashizaki, Y. 2003. Collection, mapping, and annotation of over 28, 000 cDNA clones from japonica rice. Science 301: 376-379.

    PubMed  Google Scholar 

  • Lude ´rus, M. E., de Graaf, A., Mattia, E., den Blaauwen, J. L., Grande, M. A., de Jong, L. and van Driel, R. 1992. Binding of matrix attachment regions to lamin B1. Cell 70: 949-959.

    PubMed  Google Scholar 

  • Lude ´rus, M. E., den Blaauwen, J. L., de Smit, O. J., Compton, D. A. and van Driel, R. 1994. Binding of matrix attachment regions to lamin polymers involves single-stranded regions and the minor groove. Mol. Cell Biol. 14: 6297-6305.

    PubMed  Google Scholar 

  • Masuda, K., Xu, Z. J., Takahashi, S., Ito, A., Ono, M., Nomura, K. and Inoue, M. 1997. Peripheral framework of carrot cell nucleus contains a novel protein predicted to exhibit a long alpha-helical domain. Exp. Cell Res. 232: 173-181.

    PubMed  Google Scholar 

  • McKeon, F. D., Tuffanelli, D. L., Kobayashi, S. and Kirschner, M. W. 1984. The redistribution of a conserved nuclear envelope protein during the cell cycle suggests a pathway for chromosome condensation. Cell 36: 83-92.

    PubMed  Google Scholar 

  • McNulty, A. K. and Saunders, M. J. 1992 Purification and immunological detection of pea nuclear intermediate laments: evidence for plant nuclear lamins. J. Cell Sci. 103: 407-414.

    PubMed  Google Scholar 

  • Medina, F. J., Cerdido, A. and Fernandez-Gomez, M. E. 1995. Components of the nucleolar processing complex (PrerRNA, brillarin, and nucleolin) colocalize during mitosis and are incorporated to daughter cell nucleoli. Exp. Cell Res. 221: 111-125.

    PubMed  Google Scholar 

  • Meier, I., Phelan, T., Gruissem, W., Spiker, S. and Schneider, D. 1996. MFP1, a novel plant lament-like protein with a. nity for matrix attachment region DNA. Plant Cell 8: 2105-2115.

    PubMed  Google Scholar 

  • Merdes, A., Ramyar, K., Vechio, J. D. and Cleveland, D. W. 1996. A complex of NuMA and cytoplasmic dynein is essential for mitotic spindle assembly. Cell 87: 447-458.

    PubMed  Google Scholar 

  • Mimori, T., Hardin, J. A. and Steitz, J. A. 1986. Characterization of the DNA-binding protein antigen Ku recognized by autoantibodies from patients with rheumatic disorders. J. Biol. Chem. 261: 2274-2278.

    PubMed  Google Scholar 

  • Minguez, A. and Moreno Diaz de la Espina, S. 1993. Immunological characterization of lamins in the nuclear matrix of onion cells. J. Cell Sci. 106: 431-439.

    PubMed  Google Scholar 

  • Mirkovitch, J., Mirault, M. E. and Laemmli, U. K. 1984. Organization of the higher-order chromatin loop: specific DNA attachment sites on nuclear scaffold. Cell 39: 223-232.

    PubMed  Google Scholar 

  • 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.

    PubMed  Google Scholar 

  • Nakai, K. and Kanehisa, M. 1992. A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics 14: 897-911.

    PubMed  Google Scholar 

  • Olins, A. L. and Olins, D. E. 1974. Spheroid chromatin units (v bodies). Science 183: 330-332.

    PubMed  Google Scholar 

  • Penman, S. 1995. Rethinking cell structure. Proc. Natl. Acad. Sci. USA 92: 5251-5257.

    PubMed  Google Scholar 

  • Pienta, K. J., Getzenberg, R. H. and Coffey, D. S. 1991. Cell structure and DNA organization. Crit. Rev. Eukaryot. Gene Expr. 1: 355-385.

    PubMed  Google Scholar 

  • Reeves, R. and Nissen, M. S. 1990. The AT-DNA-binding domain of mammalian high mobility group I chromosomal proteins. A novel peptide motif for recognizing DNA structure. J. Biol. Chem. 265: 8573-8582.

    PubMed  Google Scholar 

  • Sambrook, J., Fritsch, E. F. and Maniatis, T. 1989. Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor.

    Google Scholar 

  • Shi, L. J., Ni, Z. M., Zhao, S., Wang, G. and Yang, Y. 1987. Involvement of a nucleolar component, perichromonucleolin, in the condensation and decondensation of chromosomes. Proc. Natl. Acad. Sci. USA 84: 7953-7956.

    PubMed  Google Scholar 

  • Schubert, I., Dolezel, J., Houben, A., Scerthan, H. and Wanner, G. 1993. Refined examination of plant metaphase chromosome structure at different levels made feasible by new isolation methods. Chromosoma 102: 96-101.

    Google Scholar 

  • Strahl, B. D. and Allis, C. D. 2000. The language of covalent histone modifications. Nature 403: 41-45.

    PubMed  Google Scholar 

  • Sumner, A. T. 1996. The distribution of topoisomerase II on mammalian chromosomes. Chromosome Res. 4: 5-14.

    PubMed  Google Scholar 

  • Swedlow, J. R., Sedat, J. W. and Agard, D. A. 1993. Multiple chromosomal populations of topoisomerase II detected in vivo by time-lapse, three-dimensional wide-field microscopy. Cell 73: 97-108.

    PubMed  Google Scholar 

  • Tsutsui, K., Tsutsui, K., Okada, S., Watarai, S., Seki, S., Yasuda, T. and Shohmori, T. 1993. Identi cation and characterization of a nuclear scaffold protein that binds the matrix attachment region DNA. J. Biol. Chem. 268: 12886-12894.

    PubMed  Google Scholar 

  • van Drunen, C. M., Oosterling, R. W., Keultjes, G. M., Weisbeek, P. J., van Driel, R. and Smeekens, S. C. M. 1997. Analysis of the chromatin domain organisation around the plastocyanin gene reveals an MAR-specific sequence element in Arabidopsis thaliana. Nucleic Acids Res. 25: 3904-3911.

    PubMed  Google Scholar 

  • van Holde, K. and Zlatanova, J. 1995. Chromatin higher order structure: chasing a mirage? J. Biol. Chem. 270: 8373-8376.

    PubMed  Google Scholar 

  • Verheijen, R., Kuijpers, H. J., van Driel, R., Beck, J. L., van Dierendonck, J. H., Brakenho., G. J. and Ramaekers, F. C. 1989. Ki-67 detects a nuclear matrix-associated proliferationrelated antigen. II. Localization in mitotic cells and association with chromosomes. J. Cell Sci. 92 (Pt 4): 531-540.

    PubMed  Google Scholar 

  • von Kries, J. P., Buck, F. and Stratling, W. H. 1994. Chicken MAR binding protein p120 is identical to human heterogeneous nuclear ribonucleoprotein (hnRNP)U. Nucleic Acids Res. 22: 1215-1220.

    PubMed  Google Scholar 

  • Wako, T., Fukuda, M., Furushima-Shimogawara, R., Belyaev, N. D. and Fukui, K. 2002. Cell cycle-dependent and lysine residue-specific dynamic changes of histone H4 acetylation in barley. Plant Mol. Biol. 49: 645-653.

    PubMed  Google Scholar 

  • Xia, Y., Nikolau, B. J. and Schnable, P. S. 1997. Developmental and hormonal regulation of the Arabidopsis CER2 gene that codes for a nuclear-localized protein required for the normal accumulation of cuticular waxes. Plant Physiol. 115: 925-937.

    PubMed  Google Scholar 

  • Yu, W. and Moreno Diaz de la Espina, S. 1999. The plant nucleoskeleton: ultrastructural organization and identi cation of NuMA homologues in the nuclear matrix and mitotic spindle of plant cells. Exp. Cell Res. 246: 516-526.

    PubMed  Google Scholar 

  • Zhao, K., Kas, E., Gonzalez, 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

    PubMed  Google Scholar 

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  1. Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka, 565-0871, Japan

    Satoru Fujimoto, Sachihiro Matsunaga, Masataka Yonemura, Susumu Uchiyama, Takachika Azuma & Kiichi Fukui

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  1. Satoru Fujimoto
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  2. Sachihiro Matsunaga
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Fujimoto, S., Matsunaga, S., Yonemura, M. et al. Identification of a novel plant MAR DNA binding protein localized on chromosomal surfaces. Plant Mol Biol 56, 225–239 (2004). https://doi.org/10.1007/s11103-004-3249-5

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