Abstract
We report the cloning and nucleotide sequence analysis ofpsbD/C operon from a dicotyledonous tree species,Populus deltoides (poplar). The coding regions ofpsbD andpsbC and deduced amino acid sequences show very high homology with those from other higher plants. In pairwise alignment of the gene sequences,P. deltoides clustered with dicotyledonous annuals rather than withPinus, the only other tree whosepsbD/C nucleotide sequence is available. Comparison of several reported sequences showed that synonymous substitutions were distributed in bothpsbD andpsbC uniformly, throughout the length of the genes. The frequency of nonsynonymous substitutions located in the amino-terminal endof psbD was distinctly higher, suggesting a lower degree of structural constraints in this region of the encoded D2 protein. The arrangement of reading frames and Northern analysis suggest that organization and expression ofpsbD/C operon inP. deltoides is similar to that in other higher plants.
Similar content being viewed by others
References
Barkan A., Voelker R., Mendel-Hartvig J., Johnson D. and Walker M. 1995 Genetic analysis of chloroplast biogenesis in higher plants.Physiol. Plantarum 93, 163–170.
Chase M. W. and Palmer J. D. 1989 Chloroplast DNA systematics of lilioid monocots: Resources, feasibility and an example from the Orchidaceae.Am. J. Bot. 76, 1720–1730.
Chen S.-C. G., Lu J.-H., Cheng M.-C., Chen L.-F. O. and Lo C. P.-K. 1994 Four promoters in the rice plastidpsbK-psbI-psbD-psbC operon.Plant Sci. 99, 171–182.
Christopher D. A., Kim M. and Mullet J. E. 1992 A novel light-regulated promoter is conserved in cereal and dicot chloroplasts.The Plant Cell 4, 785–798.
De Heij, H. T., Lustig H., Moeskops D.-J. M., Bovenberg W. A., Bisanz C. and Grott G. S. P. 1983 Chloroplast DNAs ofSpinacia, Petunia andSpirodela have a similar gene organization.Curr. Genet. 7, 1–6.
Golden S. S., Cho D.-S. C. and Nalty M. S. 1989 Two functionalpsbD genes in the cyanobacteriumSynechococcus sp. strain PCC7942.J. Bacteriol. 171, 4707–4713.
Habeshausen G., Valentin K. and Zetsche K. 1992 Organization and sequence of photosynthetic genes from the plastid genome of the holoparasitic flowering plantCuscuta reflexa. Mol. Gen. Genet. 232, 154–161.
Hiratsuka J., Shimada H., Whittier R., Ishibashi T., Sakamoto M., Mori M., Kondo C., Honji Y., Sun C. R., Meng B. Y., Li Y. Q., Kanno A., Nishikawa Y., Hirai A., Shinozaki K. and Sugiura M. 1989 The complete sequence of the rice (Oryza sativa) chloroplast genome: Intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals.Mol. Gen. Genet. 217, 185–194.
Ikemura T. 1985 Codon usage and tRNA content in unicellular and multicellular organisms.Mol. Biol. Evol. 2, 13–34.
Leonhardt K. and Straus N. A. 1994 Photosystem II genesisiA, psbDI andpsbC inAnabaena sp. PCC 7120: cloning, sequencing and the transcriptional regulation in iron-stressed and iron-repleted cells.Plant Mol. Biol. 24, 63–73.
Meng B. Y., Wakasugi T. and Sugiura M. 1991 Two promoters within thepsbK-psbI-trnG gene cluster in tobacco chloroplast DNA.Curr. Genet. 20, 259–264.
Morton B. R. 1993 Chloroplast DNA codon use: evidence for selection at thepsbA locus based on tRNA availability.J. Mol. Evol. 37, 273–280.
Morton B. R. 1994 Codon use and the rate of divergence of land plant chloroplast genes.Mol. Biol. Evol. 11, 231–238.
Naithani S., Trivedi P. K., Tuli R. and Sane P. V. 1997a ThepsbE-F-L-J operon from chloroplast genome ofPopulus deltoides: cloning, nucleotide sequence and transcript analysis.J. Genet. 76, 61–72.
Naithani S., Trivedi P. K. and Sane P. V. 1997b Characterization oforf31-petG gene cluster from plastid genome ofPopulus deltoides.Biochem. Mol. Biol. Int. 43, 433–442.
Nath P., Sane A. P., Bijola V., Trivedi P. K., Arora J. and Sane P. V. 1993 A simple method for purification of organelle DNA of plants.J. Plant Biochem. Biotechnol. 2, 117–120.
Orsat B., Spielmann A., Marc-Martin S., Lemberger T. and Stutz E. 1994 Analysis of the 22 kbp longpsbD-psbC gene cluster ofEuglena gracilis chloroplast DNA: evidence for overlapping transcription units undergoing differential processing.Biochim. Biophys. Acta 1218, 75–81.
Pakrasi H. B. and Vermaas W. F. J. 1992 InThe photosystems: structure, function and molecular biology (ed. J. Barber), pp. 231- 257. Elsevier, Amsterdam.
Rochaix J.-D., Kuchka M., Mayfield S., Schirmer-Rahire M., Girard-Bascou J. and Bennoun P. 1989 Nuclear and chloroplast mutations affect the synthesis or stability of the chloroplastpsbC gene product inChlamydomonas reinhardtii.EMBO J. 84, 1013–1021.
Sambrook T., Fritsch E. F. and Maniatis T. 1989Molecular cloning—a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
Sexton T. B., Christopher D. A. and Mullet J. E. 1990 Light induced switch in barleypsbD-psbC promoter utilization: A novel mechanism regulating chloroplast gene expression.EMBO J. 9, 4485–4494.
Sharp P. M. 1991 Determinants of DNA sequence divergence betweenEscherichia coli andSalmonella typhimurium: codon usage, map position and concerted evolution.J. Mol. Evol. 33, 23–33.
Sharp P. M. and Li W. H. 1987 The codon adaptation index — a measure of directional synonymous codon usage bias and its potential applications.Nucl. Acids Res. 15, 1281–1295.
Trivedi P. K., Nath P. and Sane P. V. 1994 Characterization of thepsbA gene from chloroplasts ofPopulus deltoides.J. Plant Biochem. Biotechnol. 3, 97–102.
Van Slogteren C. M. S., Hoge J. H. C., Hooykaas P. J. J. and Schilperoot R. A. 1983 Clonal analysis of heterogeneous crown gall tumor tissues induced by wild-type and shooter mutant strains ofAgrobacterium tumefaciens expression of T-DNA genes.Plant Mol. Biol. 2, 321–333.
Wakasugi T., Tsudzuki J., Ito S., Nakashima K., Tsudzuki T. and Sugiura M. 1994 Loss of allndh genes as determined by sequencing the entire chloroplast genome of the black pinePinus thunbergii.Proc. Natl. Acad. Sci. USA 91, 9794–9798.
Wolfe K. H. and Sharp P. M. 1988 Identification of functional open reading frames in chloroplast genomes.Gene 66, 215–222.
Wolfe K. H., Morden C. W. and Palmer J. D. 1992 Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant.Proc. Natl. Acad. Sci. USA 89, 10648–10652.
Yao W. B., Meng B. Y., Tanaka M. and Sugiura M. 1989 An additional promoter within the protein-coding region of thepsbD-psbC gene cluster in tobacco chloroplast DNA.Nucl. Acids Res. 17, 9583–9591.
Yu J. and Vermaas W. F. J. 1990 Transcript levels and synthesis of photosystem II components in cyanobacterial mutants with inactivated photosystem II genes.The Plant Cell 2, 315–322.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Reddy, M.S.S., Trivedi, P.K., Tuli, R. et al. Cloning and nucleotide sequence analysis ofpsbD/C operon from chloroplasts ofPopulus deltoides . J. Genet. 77, 77–83 (1998). https://doi.org/10.1007/BF02966593
Received:
Revised:
Issue Date:
DOI: https://doi.org/10.1007/BF02966593