Russian Journal of Plant Physiology

, Volume 56, Issue 6, pp 838–845 | Cite as

Rapid evolution of promoters for the plastome gene ndhF in flowering plants

  • A. V. Seliverstov
  • E. A. LysenkoEmail author
  • V. A. Lyubetsky
Research Papers


Plastome is thought to be a very conservative part of plant genome but little is known about the evolution of plastome promoters. It was previously shown that one light-regulated promoter (LRPpsbD) is highly conserved in different flowering plant species and in black pine. We have undertaken search and demonstrated that gene ndhF is located in a plastome region that rarely underwent substantial rearrangements in terrestrial plants. However, alignment of sequences upstream ndhF suggests that promoters of this gene underwent comparatively rapid evolution in flowering plants. Probably, the ancestor of two basal Magnoliophyta branches (magnoliids and eudicotyledons) had the promoter PA-ndhF, which was substituted with other promoters—PB-ndhF and PC-ndhF—in some phylogenetic lineages of dicots. We failed to reveal conservative sequences with potential promoters of −10/−35 type upstream ndhF genes of monocotyledonous plants, including nine representatives of the grass family (Poaceae). Multiple alignments of sequences from related taxa showed that the predicted ndhF promoters (A–C) underwent frequent mutations and these mutations are not only nucleotide substitutions but also small insertions and deletions. Thus, we can assume that at least some plastome promoters evolve rapidly.

Key words

flowering plants plastome promoter evolution ndhF 



insertion or deletion


inverted repeat


light-regulated promoter of psbD gene


nucleus-encoded plastid RNA polymerase


plastid-encoded RNA polymerase


plastid DNA


small single-copy region (in plastome).


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  1. 1.
    Allen, J.F., The Function of Genomes in Bioenergetic Organelles, Phil. Trans. R. Soc. Lond., B. Biol. Sci., 2003, vol. 358, pp. 19–37.CrossRefGoogle Scholar
  2. 2.
    Turmel, M., Otis, C., and Lemieux, C., The Chloroplast and Mitochondrial Genome Sequences of the Charophyte Chaetosphaeridium globosum: Insights into the Timing of the Events That Restructured Organelle DNAs within the Green Algal Lineage That Led to Land Plants, Proc. Natl. Acad. Sci. USA, 2002, vol. 99, pp. 11275–11280.CrossRefPubMedGoogle Scholar
  3. 3.
    Palmer, J.D., Comparison of Chloroplast and Mitochondrial Genome Evolution in Plants, Cell Organelles, Herrmann, R.G., Ed., Wien: Springer-Verlag, 1992, pp. 99–136.Google Scholar
  4. 4.
    Sorhannus, U. and Fox, M., Synonymous and Nonsynonymous Substitution Rates in Diatoms: A Comparison between Chloroplast and Nuclear Genes, J. Mol. Evol., 1999, vol. 48, pp. 209–212.CrossRefPubMedGoogle Scholar
  5. 5.
    Seliverstov, A. and Lyubetsky, V., Translation Regulation of Intron Containing Genes in Chloroplasts, J. Bioinform. Comput. Biol., 2006, vol. 4, pp. 783–790.CrossRefPubMedGoogle Scholar
  6. 6.
    Berg, S., Krupinska, K., and Krause, K., Plastids of Three Cuscuta Species Differing in Plastid Coding Capacity Have a Common Parasite-Specific RNA Composition, Planta, 2003, vol. 218, pp. 135–142.CrossRefPubMedGoogle Scholar
  7. 7.
    Hess, W.R. and Borner, T., Organellar RNA Polymerases of Higher Plants, Int. Rev. Cytol., 1999, vol. 190, pp. 1–59.CrossRefPubMedGoogle Scholar
  8. 8.
    Lysenko, E.A. and Kusnetsov, V.V., Plastid RNA Polymerases, Mol. Biol. (Moscow), 2005, vol. 39, pp. 661–674.CrossRefGoogle Scholar
  9. 9.
    Kung, S.D. and Lin, C.M., Chloroplast Promoters from Higher Plants, Nucleic Acids Res., 1985, vol. 13, pp. 7543–7549.CrossRefPubMedGoogle Scholar
  10. 10.
    Hoffer, P.H. and Christopher, D.A., Structure and Blue-Light-Responsive Transcription of a Chloroplast psbD Promoter from Arabidopsis thaliana, Plant Physiol., 1997, vol. 115, pp. 213–222.CrossRefPubMedGoogle Scholar
  11. 11.
    Lerbs-Mache, S., Regulation of rDNA Transcription in Plastids of Higher Plants, Biochimie, 2000, vol. 82, pp. 525–535.CrossRefPubMedGoogle Scholar
  12. 12.
    Swiatecka-Hagenbruch, M., Liere, K., and Börner, T., High Diversity of Plastidial Promoters in Arabidopsis thaliana, Mol. Genet. Genom., 2007, vol. 277, pp. 725–734.CrossRefGoogle Scholar
  13. 13.
    Peltier, G. and Cournac, L., Chlororespiration, Annu. Rev. Plant Biol., 2002, vol. 53, pp. 523–550.CrossRefPubMedGoogle Scholar
  14. 14.
    Wang, P., Duan, W., Takabayashi, A., Endo, T., Shikanai, T., Ye, J.Y., and Mi, H., Chloroplastic NAD(P)H Dehydrogenase in Tobacco Leaves Functions in Alleviation of Oxidative Damage Caused by Temperature Stress, Plant Physiol., 2006, vol. 141, pp. 465–474.CrossRefPubMedGoogle Scholar
  15. 15.
    Wakasugi, T., Tsudzuki, J., Ito, S., Nakashima, K., Tsudzuki, T., and Sugiura, M., Loss of All ndh Genes as Determined by Sequencing the Entire Chloroplast Genome of the Black Pine Pinus thunbergii, Proc. Natl. Acad. Sci. USA, 1994, vol. 91, pp. 9794–9798.CrossRefPubMedGoogle Scholar
  16. 16.
    Kim, K.-J. and Jansen, R.K., NdhF Sequence Evolution and the Major Classes in the Sunflower Family, Proc. Natl. Acad. Sci. USA, 1995, vol. 92, pp. 10379–10383.CrossRefPubMedGoogle Scholar
  17. 17.
    Favory, J.-J., Kobayshi, M., Tanaka, K., Peltier, G., Kreis, M., Valay, J.-G., and Lerbs-Mache, S., Specific Function of a Plastid Sigma Factor for ndhF Gene Transcription, Nucleic Acids Res., 2005, vol. 33, pp. 5991–5999.CrossRefPubMedGoogle Scholar
  18. 18.
    Greiner, S., Wang, X., Rauwolf, U., Silber, M.V., Mayer, K., Meurer, J., Haberer, G., and Herrmann, R.G., The Complete Nucleotide Sequences of the Five Genetically Distinct Plastid Genomes of Oenothera, Subsection Oenotera: I. Sequence Evaluation and Plastome Evolution, Nucleic Acids Res., 2008, vol. 36, pp. 2366–2378.CrossRefPubMedGoogle Scholar
  19. 19.
    Yamane, K., Yano, K., and Kawahara, T., Pattern and Rate of Indel Evolution Inferred from Whole Chloroplast Intergenic Regions in Sugarcane, Maize and Rice, DNA Res., 2006, vol. 13, pp. 197–204.CrossRefPubMedGoogle Scholar
  20. 20.
    Kanno, A. and Hirai, A., A Transcription Map of the Chloroplast Genome from Rice (Oryza sativa), Curr. Genet., 1993, vol. 23, pp. 166–174.CrossRefPubMedGoogle Scholar
  21. 21.
    Zubo, Ya.O., Lysenko, E.A., Aleinikova, A.Yu., Kusnetsov, V.V., and Pshibytko, N.L., Changes in the Transcriptional Activity of Barley Plastome Genes under Heat Shock, Russ. J. Plant Physiol., 2008, vol. 55, pp. 293–300.CrossRefGoogle Scholar
  22. 22.
    Kim, M., Thum, K.E., Morishige, D.T., and Mullet, J.E., Detailed Architecture of the Barley Chloroplast psbD-psbC Blue Light-Responsive Promoter, J. Biochem., 1999, vol. 274, pp. 4684–4692.Google Scholar

Copyright information

© Pleiades Publishing, Ltd. 2009

Authors and Affiliations

  • A. V. Seliverstov
    • 1
  • E. A. Lysenko
    • 1
    • 2
    Email author
  • V. A. Lyubetsky
    • 2
  1. 1.Kharkevich Institute for Information Transmission ProblemsRussian Academy of SciencesMoscowRussia
  2. 2.Timiryazev Institute of Plant PhysiologyRussian Academy of SciencesMoscowRussia

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