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Direct measurement of the transfer rate of chloroplast DNA into the nucleus


Gene transfer from the chloroplast to the nucleus has occurred over evolutionary time1. Functional gene establishment in the nucleus is rare, but DNA transfer without functionality is presumably more frequent. Here, we measured directly the transfer rate of chloroplast DNA (cpDNA) into the nucleus of tobacco plants (Nicotiana tabacum). To visualize this process, a nucleus-specific neomycin phosphotransferase gene (neoSTLS2) was integrated into the chloroplast genome, and the transfer of cpDNA to the nucleus was detected by screening for kanamycin-resistant seedlings in progeny. A screen for kanamycin-resistant seedlings was conducted with about 250,000 progeny produced by fertilization of wild-type females with pollen from plants containing cp-neoSTLS2. Sixteen plants of independent origin were identified and their progenies showed stable inheritance of neoSTLS2, characteristic of nuclear genes. Thus, we provide a quantitative estimate of one transposition event in about 16,000 pollen grains for the frequency of transfer of cpDNA to the nucleus. In addition to its evident role in organellar evolution, transposition of cpDNA to the nucleus in tobacco occurs at a rate that must have significant consequences for existing nuclear genes.

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Figure 1: Introduction of aadA and neoSTLS2 genes into the tobacco plastid genome by homologous recombination.
Figure 2: Seedling tests for resistance to spectinomycin and kanamycin.
Figure 3: Analysis of kanamycin-resistant plants and three transplastomic/nuclear junctions.


  1. Martin, W. et al. Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc. Natl Acad. Sci. USA 99, 12246–12251 (2002)

    Article  ADS  CAS  Google Scholar 

  2. Kaneko, T. et al. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res. 3, 109–136 (1996)

    Article  CAS  Google Scholar 

  3. Gray, M. W. The endosymbiont hypothesis revisited. Int. Rev. Cytol. 141, 233–357 (1992)

    Article  CAS  Google Scholar 

  4. Adams, K. L., Daley, D. O., Qiu, Y. L., Whelan, J. & Palmer, J. D. Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants. Nature 408, 354–357 (2000)

    Article  ADS  CAS  Google Scholar 

  5. Millen, R. S. et al. Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus. Plant Cell 13, 645–658 (2001)

    Article  ADS  CAS  Google Scholar 

  6. Stupar, R. M. et al. Complex mtDNA constitutes an approximate 620-kb insertion on Arabidopsis thaliana chromosome 2: implication of potential sequencing errors caused by large-unit repeats. Proc. Natl Acad. Sci. USA 98, 5099–5103 (2001)

    Article  ADS  CAS  Google Scholar 

  7. Yuan, Q. et al. Genome sequencing of 239-kb region of rice chromosome 10L reveals a high frequency of gene duplication and a large chloroplast DNA insertion. Mol. Genet. Gen. 267, 713–720 (2002)

    Article  CAS  Google Scholar 

  8. Timmis, J. N. & Scott, N. S. Spinach nuclear and chloroplast DNAs have homologous sequences. Nature 205, 65–67 (1983)

    Article  ADS  Google Scholar 

  9. Mourier, T., Hansen, A. J., Willerslev, E. & Arctander, P. The human genome project reveals a continuous transfer of large mitochondrial fragments to the nucleus. Mol. Biol. Evol. 18, 1833–1837 (2001)

    Article  CAS  Google Scholar 

  10. Ricchetti, M., Fairhead, C. & Dujon, B. Mitochondrial DNA repairs double-strand breaks in yeast chromosomes. Nature 402, 96–100 (1998)

    Article  ADS  Google Scholar 

  11. Ayliffe, M. A. & Timmis, J. N. Tobacco nuclear DNA contains long tracts of homology to chloroplast DNA. Theor. Appl. Genet. 85, 229–238 (1992)

    Article  CAS  Google Scholar 

  12. Thorsness, P. E. & Fox, T. D. Escape of DNA from the mitochondria to the nucleus in the yeast, Saccharomyces cerevisiae. Nature 346, 376–379 (1990)

    Article  ADS  CAS  Google Scholar 

  13. Maas, C. et al. Expression of intron modified NPTII genes in monocotyledonous and dicotyledonous plant cells. Mol. Breed. 3, 15–28 (1997)

    Article  CAS  Google Scholar 

  14. Zoubenko, O. V., Allison, L. A., Svab, Z. & Maliga, P. Efficient targeting of foreign genes into the tobacco plastid genome. Nucleic Acids Res. 22, 3819–3824 (1994)

    Article  CAS  Google Scholar 

  15. Benfey, P. N. & Chua, N. H. The cauliflower mosaic virus 35S promoter: combinatorial regulation of transcription in plants. Science 250, 959–966 (1990)

    Article  ADS  CAS  Google Scholar 

  16. Eckes, P., Rosahl, S., Schell, J. & Willmitzer, L. Isolation and characterization of a light-inducible, organ-specific gene from potato and analysis of its expression after tagging and transfer into tobacco and potato shoots. Mol. Gen. Genet. 205, 14–22 (1986)

    Article  CAS  Google Scholar 

  17. Whitney, S. M. & Andrews, T. J. The gene for the ribulose-1, 5-bisphosphate carboxylase/oxygenase (Rubisco) small subunit relocated to the plastid genome of tobacco directs the synthesis of small subunits that assemble into Rubisco. Plant Cell 13, 193–205 (2001)

    Article  CAS  Google Scholar 

  18. Horser, C., Abbott, D., Wesley, V., Smith, N. & Waterhouse, P. Gene silencing—principles and application. Genet. Eng. Principles Meth. 24, 239–256 (2002)

    CAS  Google Scholar 

  19. Daniell, H., Datta, R., Varma, S., Gray, S. & Lee, S. B. Containment of herbicide resistance through genetic engineering of the chloroplast genome. Nature Biotechnol. 16, 345–348 (1998)

    Article  CAS  Google Scholar 

  20. Fagard, M. & Vaucheret, H. (Trans)gene silencing in plants: how many mechanisms? Annu. Rev. Plant Physiol. Plant Mol. Biol. 51, 167–194 (2000)

    Article  CAS  Google Scholar 

  21. Babiychuk, E., Fuangthong, M., van Montagu, M., Inzé, D. & Kushnir, S. Efficient gene tagging in Arabidopsis thaliana using a gene trap approach. Proc. Natl Acad. Sci. USA 94, 12722–12727 (1997)

    Article  ADS  CAS  Google Scholar 

  22. Maliga, P. Engineering the plastid genome of higher plants. Curr. Opin. Plant Biol. 5, 164–172 (2002)

    Article  CAS  Google Scholar 

  23. Daniell, H., Khan, M. S. & Allison, L. Milestones in chloroplast genetic engineering: an environmentally friendly era in biotechnology. Trends Plant Sci. 7, 84–91 (2002)

    Article  CAS  Google Scholar 

  24. Scott, S. E. & Wilkinson, M. J. Low probability of chloroplast movement from oilseed rape (Brassica napus) into wild Brassica rapa. Nature Biotechnol. 17, 390–392 (1999)

    Article  CAS  Google Scholar 

  25. Murashige, T. & Skoog, F. A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol. Plant 15, 473–497 (1962)

    Article  CAS  Google Scholar 

  26. Huang, C. Y., Barker, S. J., Langridge, P., Smith, F. W. & Graham, R. D. Zinc deficiency up-regulates expression of high-affinity phosphate transporter genes in both phosphate-sufficient and -deficient barley roots. Plant Physiol. 124, 415–422 (2000)

    Article  CAS  Google Scholar 

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We thank the Australian Research Council for financial support; P. Maliga for pPRV111A; S. Whitney and J. Andrews for facilities and advice on chloroplast transformation, for SSuH2 seeds and for comments on the manuscript; T. J. Higgins, P. Whitfeld, W. Martin and R. Lockington for discussion; C. Maas for pCMneoSTLS2; N. Smith for the NS23 seeds; and S. Elts for technical assistance.

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Correspondence to Jeremy N. Timmis.

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Huang, C., Ayliffe, M. & Timmis, J. Direct measurement of the transfer rate of chloroplast DNA into the nucleus. Nature 422, 72–76 (2003).

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