Abstract
Cyanidioschyzon merolae andCyanidium caldarium are representative species among of the most primitive algae, although the two species are distinctly different in various morphological traits. We determined the nucleotide sequence of therbcL gene and a flanking 8-kb region in the plastid genome of each of these algae. In both algae, 12 genes were identified in this region, in an identical order. This gene order is not conserved in the plastid genomes of other species of the kingdom Plantae that have been sequenced to data. An additional unidentified open reading frame was also found in the two algae that we analyzed, which has not been described in any other species of algae includingPorphyra purpurea. Comparison of the amino acid sequences of selected genes also supported the conclusion thatCyanidioschyzon merolae andCyanidium caldarium are closely related and that they are distinct from other rhodophytes.
Similar content being viewed by others
References
Allen, M.B. 1959. Studies withCyanidium caldarium, an anomalously pigment chlorophyta. Arch. Mikrobiol.32: 270–277.
An, F. andFriesen, J.D. 1976. The nucleotide sequence oftufB and four nearby tRNA structural genes ofEscherichia coli. Gene12: 33–39.
De Luca, P., Taddei, R. andVarano L. 1978.Cyanidioschyzon merolae: a neo alga of thermal acidic environemnts. Webbia33: 37–44.
Delwiche, C.F. andPalmer, J.D. 1996. Rampant horizontal transfer and duplication of RuBisCO genes Eubacteria and Plastids. Mol. Biol. Evol.13: 873–882.
Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol.17: 368–376.
Hallick, R.B., Hong, L., Drager, R.G., Favreat, M.R., Monfort, A., Orsat, B., Spielmann, A. andStutz E. 1993. Complete sequence ofEuglena gracilis chloroplast DNA. Nucleic Acids Res.21: 3537–3544.
Holmgren, R. 1985. Thioredoxin. Annu. Rev. Biochem.54: 237–271.
Huppe, H., Picaud, A., Buchanan, B.B. andMiginiac-Maslow. 1991. Identification of an NADP/thioredoxin system inChlamydomonas reinhardtii. Planta186: 115–121.
Jones, D.T., Taylor, W.R. andThornton, J.M. 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci.8: 275–282.
Kaneko, T., Sato, S., Kotani, H., Tanaka, A., Asamizu, E., Nakamura, Y., Miyajima, N., Hirosawa, M., Sugiura, M., Sasamoto, S., Kimura, T., Hosouchi, T., Matsuno, A., Muraki, A., Nakazaki, N., Naruo, K., Okumura, S., Shimpo, S., Takeuchi, C., Wada, T., Watanabe, A., Yamada, M., Yasuda, M. andTabata, S. 1996. Sequence analysis of the genome of the unicellular cyanobacteriumSynechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res.3: 109–136.
Karlin, S. andAltschul, S.F. 1990. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. USA87: 2264–68.
Kowallik, K.V., Stobe, B., Schaffran, I., Kroth-Pancic, P. andFreier, U. 1995. The chloroplast genome of a chlorophyll a+c-containing alga,Odontella sinensis. Plant Mol. Biol. Rep.13: 336–342.
Kuroiwa, T., Kawazu, T., Takahashi, H., Suzuki, K., Ohta, N. andKuroiwa, H. 1994a. Comparison of ultrastructures between the ultra-small eukaryoteCyanidioschyzon merolae andCyanidium caldarium. Cytologia59: 149–158.
Kuroiwa, T., Kuroiwa, H., Mita, T. andOhta, N. 1994b.Cyanidium caldarium as a model cell for studying division of chloroplasts.In J. Seckbach, ed., Evolutionary Pathways and Enigmatic Algae:Cyanidium caldarium (Rhodophyta) and Related Cells. Kluwer Academic Publishers, Dordrecht. pp. 239–253.
Lima-de-Faria, A. 1983. The evolution of DNA content.In Molecular Evolution and Organization of the Chromosome. Elsevier Science, Amsterdam. pp 275–294.
Mazzala, G.P. andMcClain, W.H. 1977. Cysteine transfer RNA ofEscherichia coli: Nucleotide sequence and unusual metabolic properties of the 3′c-c-a terminus. J. Mol. Biol.117: 1061–1079.
Meijer, W.G., Arnberg, A.C., Enequist, H.G. andTerpstra, P. 1991. Identification and organization of carbon dioxide fixation genes inXanthobacter flavus H4-14. Mol. Gen. Genet.225: 320–330.
Merola, A., Castaldo, R., De Luca, P., Gambardella, R., Musacchio, A. andTaddei, R. 1981. Revision ofCyanidium caldarium. Three species of acidophilic algae. G. Bot. Ital.115: 189–195.
Nagashima, H., Sakai, K., Kamo, M. andTsugita, A. 1989. Amino acid sequence of ferredoxin isolated fromCyanidium caldarium strain RK-1. Protein Seq. Data Anal.2: 457–460.
Ohta, N., Kawano, S. andKuroiwa, T. 1994b. Physical map of the plastid genome of the unicellular red algaCyanidium caldarium strain RK-1. Curr. Genet.26: 136–138.
Ohta, N., Nagashima, H., Kawano, S. andKuroiwa, T. 1992. Isolation of the chloroplast DNA and the sequence oftrnK gene ofCyanidium caldarium strain RK-1. Plant Cell Physiol.33: 657–661.
Ohta, N., Sato, N., Kawano, S. andKuroiwa, T. 1994a. ThetrpA gene on the plastid genome ofCyanidium caldarium strain RK-1. Curr. Genet.25: 357–361.
Ohta, N., Suzuki, K., Kawano, S. andKuroiwa, T. 1993. Direct evidence of mitochondrial nuclear division in the ultra-micro algaCyanidioschyzon merolae. Cytologia58: 471–476.
Reith, M. andMunholland, J. 1995. Complete nucleotide sequence of thePorphyra purpurea chloroplast genome. Plant Mol. Biol. Rep.13: 333–335.
Saitou, N. andNei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol.4: 406–425.
Sambrook, J., Fritsch, E.F. andManiatis, T. 1989. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
Seckbach, J. 1992. The Cyanidiophyceae and the anomalous symbiosis ofCyanidium caldarium.In W. Reisser, ed., Algae and Symbioses: Plants, Animals, Fungi, Viruses, Interactions Explored. Biopress, Bristol. pp. 400–426.
Seckback, J. 1996. Biological aspects of the origin of life.In J. Chela-Flores and F. Raulin, eds., Chemical Evolution: Physics of the Origin and Evolution of Life, Kluwer Academic Publishers, Dordrecht, pp. 197–213.
Shinozaki, K., Ohme, M., Tanaka, M., Wakasugi, T., Hayashida, N., Matsubayashi, T., Zaita, N., Chunwongse, J., Obokata, J., Shinozaki, K.Y., Ohta, C., Torazawa, K., Meng, B.Y., Sugita, M., Deno, H., Kamogashira, T., Yamada, K., Kusuda, J., Takaiwa, F., Kata, A., Tohdoh, N., Shimada, H. andSugiura, M. 1986. The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J.5: 2043–2069.
Stirewalt, V.L., Michalowski, C.B., Loffelhardt, W., Bohnert, H.J. andBryant, D.A. 1995. Nucleotide sequence of the cyanelle genome fromCyanophora paradoxa. Plant Mol. Biol. Rep.13: 327–332.
Strimmer, K. andvon Haeseler, A. 1996. Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol.13: 964–969.
Suzuki, K., Ohta, N. andKuroiwa, T. 1992. Isolation of the cell-nuclear, mitochondrial and chloroplast DNA from the ultra-small eukaryoteCyanidioschyzon merolae. Protoplasma171: 80–84.
Takahashi, H., Suzuki, K., Ohta, N., Suzuki, T., Takano, H., Kawano, S. andKuroiwa, T. 1993. An electrophoretic Karyotype ofCyanidioschyzon merolae. Cytologia58: 477–482.
Thompson, J.D., Higgins, D.G. andGibson, T.J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res.22: 4673–4680.
Van den Eynde, H., De Baere, R., De Roeck, E., Van de Peer, Y., Bandenberghe, A., Willekens, P. andDe Wachter, R. 1988. The 5S ribosomal RNA sequences of a red algal rhodoplast and a gymnosperm chloroplast. Implications for the evolution of plastids and cyanobacteria. J. Mol. Evol.27: 126–132.
Yamaizumi, Z., Kuchino, Y., Harada F., Nishimura, S. andMcCloskey, J.A. 1980. Primary structure ofEscherichia coli Leu-tRNA-UUR: Presence of an unknown adenosine derivative in the first position of the anticodon which recognizes the UU codon series. J. Biol. Chem.255: 2220–2225.
Yoshimura, M., Kimura, M., Ohno, M., Inokuchi, H. andOzeki, H. 1984. Identification of transfer RNA suppressers inEscherichia coli. J. Mol. Biol.177: 609–625.
Author information
Authors and Affiliations
Corresponding author
Additional information
The nucleotide sequence data reported in this paper will appear in the DDBJ, EMBL and GenBank Nucleotide Sequence Databases under the accession numbers D63675 and D63676.
Rights and permissions
About this article
Cite this article
Ohta, N., Sato, N., Ueda, K. et al. Analysis of a plastid gene cluster reveals a close relationship betweenCyanidioschyzon andCyanidium . J. Plant Res. 110, 235–245 (1997). https://doi.org/10.1007/BF02509312
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/BF02509312