Abstract
The multiple copies of the chloroplast genome (plastome) are condensed and organized into nucleoids by a set of proteins. One of these, the DNA-binding protein DCP68 from soybean, has previously been shown to compact DNA and to inhibit DNA synthesis in vitro. N-terminal amino acid analysis and the absorption spectrum of the purified protein suggest that DCP68 is the siroheme protein sulfite reductase, a ferredoxin-dependent enzyme that participates in sulfur assimilation for cysteine and methionine biosynthesis. The in vivoassociation of this protein with chloroplast nucleoids was confirmed by immuno-colocalization with antibodies against sulfite reductase from Arabidopsis thaliana. These results suggest that DCP68 is a bifunctional chloroplast protein that participates in reductive sulfur assimilation and plays a role in organellar nucleoid organization. The fact that dephosphorylation by alkaline phosphatase affects the binding of purified DCP68 to DNA in vitro might be indicative of the way the interaction of the protein with the nucleoid is regulated in vivo.
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Ach, R.A., Taranto, P. and Gruissem, W. 1997. A conserved family of WD-40 proteins binds to the retinoblastoma protein in both plants and animals. Plant Cell 9: 1595–606.
Akashi, T., Matsumura, T., Ideguchi, T., Iwakiri, K., Kawakatsu, T., Taniguchi, I. and Hase, T. 1999. Comparison of the electrostatic binding sites on the surface of ferredoxin for two ferredoxindependent enzymes, ferredoxin-NADP+ reductase and sulfite reductase. J. Biol. Chem. 274: 29399–29405.
Allen, J.F. 1993. Redox control of transcription: sensors, response regulators, activators and repressors. FEBS Lett. 332: 203–207.
Ausubel, F., Brent, R., Kingston, R., Moore, D., Seidman, J.G., Smith, J. and Struhl, K. 1994. Isolation of proteins for microsequence analysis. In: K. Janssen (Ed.) Current Protocols in Molecular Biology, John Wiley, New York, pp. 10.19.1–10.19.4.
Baginsky, S., Tiller, K. and Link, G. 1997. Transcription factor phosphorylation by a protein kinase associated with chloroplast RNA polymerase from mustard (Sinapis alba). Plant Mol. Biol. 34: 181–189.
Baginsky, S., Tiller, K., Pfannschmidt, T. and Link, G. 1999. PTK, the chloroplast RNA polymerase-associated protein kinase from mustard (Sinapis alba), mediates redox control of plastid in vitro transcription. Plant Mol. Biol. 39: 1013–1023.
Boffey, S.A. and Leech, R.M. 1982. Chloroplast DNA levels and the control of chloroplast division in light-grown wheat leaves. Plant Physiol. 69: 1387–1391.
Bradford, M. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72: 248–254.
Briat, J., Letoffe, S., Mache, R. and Rouviere-Yaniv, J. 1984. Similarity between the bacterial histone-like protein HU and a protein from spinach chloroplasts. FEBS Lett. 172: 75–79.
Bruhl, A., Haverkamp, T., Gisselmann, G. and Schwenn, J. 1996. A cDNA clone from Arabidopsis thaliana encoding plastidic ferredoxin:sulfite reductase. Biochim. Biophys. Acta 1295: 119–124.
Brunold, C. and Suter, M. 1989. Localization of enzymes of assimilatory sulfate reduction in pea roots. Planta 179: 228–234.
Cannon, G.C., Ward, L.N., Case, C.I. and Heinhorst, S. 1999. The 68 kDa DNA compacting nucleoid protein from soybean chloroplasts inhibits DNA synthesis in vitro. Plant Mol. Biol. 39: 835–845.
Chi-Ham, C.L., Keaton, M.A., Cannon, G.C. and Heinhorst, S. 2000. Soybean chloroplast nucleoid proteins and their interactions with DNA. Sixth International Congress of Plant Molecular Biology, Quebec, Canada, p. S19-7.
Danon, A. and Mayfield, S.P. 1994. Light-regulated translation of chloroplast messenger RNAs through redox potential. Science 266: 1717–1719.
Diffley, J.F. and Stillman, B. 1991. A close relative of the nuclear, chromosomal high-mobility group protein HMG1 in yeast mitochondria. Proc. Natl. Acad. Sci. USA 88: 7864–7868.
Grasser, K.D., Ritt, C., Krieg, M., Fernandez, S., Alonso, J.C. and Grimm, R. 1997. The recombinant product of the Chryptomonas Φ plastid gene hlpA is an architectural HU-like protein that promotes the assembly of complex nucleoprotein structures. Eur. J. Biochem. 249: 70–76.
Hansmann, P., Falk, H., Ronai, K. and Sitte, P. 1985. Structure, composition, and distribution of plastid nucleoids in Narcissus pseudonarcissus. Planta 164: 459–472.
Hashimoto, H. 1985. Changes in distribution of nucleoids in developing and dividing chloroplast and etioplasts of Avena sativa. Protoplasma 127: 119–127.
Heinhorst, S., Cannon, G.C. and Weissbach, A. 1990. Chloroplast and mitochondrial DNA polymerases from cultured soybean cells. Plant Physiol. 92: 939–945.
Horn, M.E., Sherrard, J.H. and Widholm, J.M. 1983. Photoautotrophic growth of soybean cells in suspension culture. Plant Physiol. 72: 426–429.
Houben, A., Wako, T., Furushima-Shimogawara, R., Presting, G., Kunzel, G., Schubert, I.I. and Fukui, K. 1999. Short communication: the cell cycle dependent phosphorylation of histone H3 is correlated with the condensation of plant mitotic chromosomes. Plant J. 18: 675–679.
Ideguchi, T., Akashi, T., Onda, Y. and Hase, T. 1995. cDNA cloning and functional expression of ferredoxin-dependent sulfite reductase from maize in E. coli cells. In: R. Mathis (Ed.) Photosynthesis: From Light to Biosphere, Vol. II, Kluwer Academic Publishers, Dordrecht, Netherlands, pp. 713–716.
Irihimovitch, V. and Shapira, M. 2000. Glutathione redox potential modulated by reactive oxygen species regulates translation of Rubisco large subunit in the chloroplast. J. Biol. Chem. 275: 16289–16295.
Ito, K. and Kawanishi, S. 1991. Site-specific fragmentation and modification of albumin by sulfite in the presence of metal ions or peroxidase/H2O2: role of sulfate radical. Biochem. Biophys. Res. Commun. 176: 1306–1312.
Kaufman, B.A., Newman, S.M., Hallberg, R.L., Slaughter, C.A., Perlman, P.S. and Butow, R.A. 2000. In organello formaldehyde crosslinking of proteins to mtDNA: Identification of bifunctional proteins. Proc. Natl. Acad. Sci. USA 97: 7772–7777.
Kim, M., Christopher, D.A. and Mullet, J.E. 1999. ADP-dependent phosphorylation regulates association of a DNA-binding complex with the barley chloroplast psbD blue-light-responsive promoter. Plant Physiol. 119: 663–670.
Kleinschmidt, J.A. and Steinbeisser, H. 1991. DNA-dependent phosphorylation of histone H2A.X during nucleosome assembly in Xenopus laevis oocytes: involvement of protein phosphorylation in nucleosome spacing. EMBO J. 10: 3043–3050.
Kleinschmidt, J.A., Seiter, A. and Zentgraf, H. 1990. Nucleosome assembly in vitro: separate histone transfer and synergistic interaction of native histone complexes purified from nuclei of Xenopus laevis oocytes. EMBO J. 9: 1309–1318.
Krueger, R.J. and Siegel, L.M. 1982. Spinach siroheme enzymes: isolation and characterization of ferredoxin-sulfite reductase and comparison of properties with ferredoxin-nitrite reductase. Biochemistry 21: 2892–2904.
Kuroiwa, T. 1991. The replication, differentiation, and inheritance of plastids with emphasis on the concept of organelle nuclei. Int. Rev. Cytol. 128: 1–62.
Lamppa, G. and Bendich, A. 1979. Changes in chloroplast DNA levels during development of pea (Pisum sativum). Plant Physiol. 64: 126–130.
Lau, K.W., Ren, J. and Wu, M. 2000. Redox modulation of chloroplast DNA replication in Chlamydomonas reinhardtii. Antioxid. Redox Signal 2: 529–235.
Lawrence, M.E. and Possingham, J.V. 1986. Microspectrofluorometric measurement of chloroplast DNA in dividing and expanding leaf cells of Spinacea oleracea. Plant Physiol. 81: 708–710.
Leustek, T. and Saito, K. 1999. Sulfate transport and assimilation in plants. Plant Physiol. 120: 637–644.
Levings, C.S. and Siedow, J.N. 1995. Regulation by redox poise in chloroplasts. Science 268: 609–772.
MacAlpine, D.M., Perlman, P.S. and Butow, R.A. 1998. The high mobility group protein Abf2p influences the level of yeast mitochondrial DNA recombination intermediates in vivo. Proc. Natl. Acad. Sci. USA 95: 6739–6743.
MacAlpine, D.M., Perlman, P.S. and Butow, R.A. 2000. The numbers of individual mitochondrial DNA molecules and mitochondrial DNA nucleoids in yeast are co-regulated by the general amino acid control pathway. EMBO J. 19: 767–775.
Meeusen, S., Tieu, Q., Wong, E., Weiss, E., Schieltz, D., Yates, J.R. and Nunnari, J. 1999. Mgm101p is a novel component of the mitochondrial nucleoid that binds DNA and is required for the repair of oxidatively damaged mitochondrial DNA. J. Cell Biol. 145: 291–304.
Megraw, T. and Chae, C.-B. 1993. Functional complementarity between the HMG1-like yeast mitochondrial histone HM and the bacterial histone-like protein HU. J. Biol. Chem. 268: 12758–12763.
Mottley, C. and Mason, R.P. 1988. Sulfate anion free radical formation by the peroxidation of (bi)sulfite and its reaction with hydroxyl radical scavengers. Arch. Biochem. Biophys. 267: 681–689.
Mullet, J. 1988. Chloroplast development and gene expression. Annu. Rev. Plant Physiol. 39: 475–502.
Murakami, S., Kondo, Y., Nakano, T. and Sato, F. 2000. Protease activity of CND41, a chloroplast nucleoid DNA-binding protein, isolated from cultured tobacco cells. FEBS Lett. 468: 15–18.
Nakano, T., Sato, F. and Yamada, Y. 1993. Analysis of nucleoidproteins in tobacco chloroplasts. Plant Cell Physiol. 34: 873–880.
Nakano, T., Murakami, S., Shoji, T., Yoshida, S., Yamada, Y. and Sato, F. 1997. A novel protein with DNA binding activity from tobacco chloroplast nucleoids. Plant Cell 9: 1673–1682.
Nakano, T., Nagata, N., Kimura, T., Sekimoto, M., Hiroshi, K., Murakami, S., Kamiya, Y. and Sato, F. 2000. Abstracts 6th International Congress of Plant Molecular Biology, Quebec, Canada, pp. S19-S36.
Nemoto, Y., Kawano, S., Nakamura, S., Mita, T., Nagata, T. and Kuroiwa, T. 1988. Studies on plastid-nuclei (nucleoids) in Nicotiana tabacum L. I. Isolation of proplastid-nuclei from cultured cells and identification of proplastid-nuclear proteins. Plant Cell Physiol. 29: 167–177.
Nemoto, Y., Nagata, T. and Kuroiwa, T. 1989. Studies on plastidnuclei (nucleoids) in Nicotiana tabacum L. II. Disassembly and reassembly of proplastid-nuclei isolated from cultured cells. Plant Cell Physiol. 30: 445–454.
Nemoto, Y., Kawano, S., Kondoh, K., Nagata, T. and Kuroiwa, T. 1990. Studies on plastid-nuclei (nucleoids) in Nicotiana tabacum L. III. Isolation of chloroplast-nuclei from mesophyll protoplasts and identification of chloroplast DNA-binding proteins. Plant Cell Physiol. 31: 767–776.
Newman, S.M., Zelenaya-Troitskaya, O., Perlman, P.S. and Butow, R.A. 1996. Analysis of mitochondrial DNA nucleoids in wildtype and a mutant strain of Saccharomyces cerevisiae that lacks the mitochondrial HMG box protein Abf2p. Nucl. Acids Res. 24: 386–393.
Nie, Z.Q., Chang, D.Y. and Wu, M. 1987. Protein-DNA interaction within one cloned chloroplast DNA replication origin of Chlamydomonas. Mol. Gen. Genet. 209: 265–269.
Pfannschmidt, T., Nilsson, A. and Allen, J. 1999. Photosynthetic control of chloroplast gene expression. Nature 397: 625–628.
Rose, R.J., Cran, D.G. and Possingham, J.V. 1975. Changes in DNA synthesis during cell growth and chloroplast replication in greening spinach leaf disks. J. Cell Sci. 17: 27–41.
Saito, K. 2000. Regulation of sulfate transport and synthesis of sulfur-containing amino acids. Curr. Opin. Plant Biol. 3: 188–195.
Salvador, M.L. and Klein, U. 1999. The redox state regulates RNA degradation in the chloroplast of Chlamydomonas reinhardtii. Plant Physiol. 121: 1367–1374.
Sato, N., Albrieux, C., Joyard, J., Douce, R. and Kuroiwa, T. 1993. Detection and characterization of a plastid envelope DNA-binding protein which may anchor plastid nucleoids. EMBO J. 12: 555–561.
Sato, N., Misumi, O., Shinada, Y., Sasaki, M. and Yoine, M. 1997. Dynamics of localization and protein composition of plastid nucleoids in light-grown pea seedlings. Protoplasma 200: 163–173.
Sato, N., Ohshima, K., Watanabe, A., Ohta, N., Nishiyama, Y., Joyard, J. and Douce, R. 1998. Molecular characterization of the PEND protein, a novel bZIP protein present in the envelope membrane that is the site of nucleoid replication in developing plastids. Plant Cell 10: 859–872.
Sato, N., Rolland, N., Block, M.A. and Joyard, J. 1999. Do plastid envelope membranes play a role in the expression of the plastid genome? Biochimie 81: 619–629.
Sato, N., Nakayama, M. and Hase, T. 2001. The 70-kDa major DNA-compacting protein of the chloroplast nucleoid is sulfite reductase. FEBS Lett. 487: 347–350.
Scott, N.S. and Possingham, J.V. 1983. Changes in chloroplast DNA levels during growth of spinach leaves. J. Exp. Bot. 34: 1756–1767.
Shi, X. and Mao, Y. 1994. 8-Hydroxy-2'-deoxyguanosine formation and DNA damage induced by sulfur trioxide anion radicals. Biochem. Biophys. Res. Commun. 205: 141–147.
Sun, X., Shi, X. and Dalal, N.S. 1992. Xanthine oxidase/hydrogen peroxide generates sulfur trioxide anion radical (SO .??3 ) from sulfite (SO 2?3 ). FEBS Lett. 303: 213–216.
Tiller, K. and Link, G. 1993. Phosphorylation and dephosphorylation affect functional characteristics of chloroplast and etioplast transcription systems from mustard (Sinapis alba L.). EMBO J. 12: 1745–1753.
Tymms, M.J., Scott, N.S. and Possingham, J.V. 1983. DNA content of Beta vulgaris chloroplasts during leaf cell expansion. Plant Physiol. 71: 785–788.
Van den Broeck, D., Van der Straeten, D., Van Montagu, M. and Caplan, A. 1994. A group of chromosomal proteins is specifically released by spermine and loses DNA-binding activity upon phosphorylation. Plant Physiol. 106: 559–566.
Wu, M., Nie, Z.Q. and Yang, J. 1989. The 18-kD protein that binds to the chloroplast DNA replicative origin is an iron-sulfur protein related to a subunit of NADH dehydrogenase. Plant Cell 1: 551–557.
Yonekura-Sakakibara, K., Ashikari, T., Tanaka, Y., Kusumi, T. and Hase, T. 1998. Molecular characterization of tobacco sulfite reductase: enzyme purification, gene cloning, and gene expression analysis. J. Biochem. (Tokyo) 124: 615–621.
Yonekura-Sakakibara, K., Onda, Y., Ashikari, T., Tanaka, Y., Kusumi, T. and Hase, T. 2000. Analysis of reductant supply systems for ferredoxin-dependent sulfite reductase in photosynthetic and nonphotosynthetic organs of maize. Plant Physiol. 122: 887–894.
Yurina, N., Belkina, G., Karapetyan, N. and Odintsova, M. 1995. Nucleoids of pea chloroplasts: microscopic and chemical characterization, occurrence of histone-like proteins. Biochem. Mol. Biol. Int. 36: 145–154.
Zelenaya-Troitskaya, O., Perlman, P.S. and Butow, R.A. 1995. An enzyme in yeast mitochondria that catalyzes a step in branchedchain amino acid biosynthesis also functions in mitochondrial DNA stability. EMBO J. 14: 3268–3276.
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Chi-Ham, C.L., Keaton, M.A., Cannon, G.C. et al. The DNA-compacting protein DCP68 from soybean chloroplasts is ferredoxin:sulfite reductase and co-localizes with the organellar nucleoid. Plant Mol Biol 49, 621–630 (2002). https://doi.org/10.1023/A:1015500431421
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DOI: https://doi.org/10.1023/A:1015500431421