Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

The plastid clpP1 protease gene is essential for plant development

Nature volume 425, pages 86–89 (2003)Cite this article

Abstract

Plastids of higher plants are semi-autonomous cellular organelles that have their own genome and transcription–translation machinery1. Examples of plastid functions are photosynthesis and biosynthesis of starch, amino acids, lipids and pigments2. Plastid functions are encoded in ∼120 plastid genes1 and ∼3,000 nuclear genes2,3. Although many embryo and seedling lethal nuclear genes are required for chloroplast biogenesis4,5,6, until now deletion of plastid genes either had no phenotypic consequence (8 genes), or caused a mutant phenotype but did not affect viability (13 genes)7,8,9,10. Here we identify an essential plastid gene. By using the CRE–lox site-specific recombination system11,12 we have deleted clpP1 (caseinolytic protease P1), one of the three genes (clpP1, ycf1 and ycf2) whose disruption had previously only been possible in a fraction of the 1,000–10,000 plastid genome copies in a cell7,13. Loss of the clpP1 gene product, the ClpP1 protease subunit14, results in ablation of the shoot system of tobacco plants, suggesting that ClpP1-mediated protein degradation is essential for shoot development.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Strategy for deletion of the plastid clpP1 gene by the CRE recombinase.
Figure 2: Maps of transformation vectors and plastid DNA.
Figure 3: CRE-mediated excision of clpP1 in the seed progeny.
Figure 4: Seedling phenotypes in crosses between Nt-pHK85 clpP1fl plants as maternal parent and nuclear Cre pollen parents.
Figure 5: Immunoblot to detect accumulation of ClpP1 in seedling cotyledons20.

Similar content being viewed by others

References

  1. Sugiura, M. The chloroplast genome. Plant Mol. Biol. 19, 149–168 (1992)

    Article  CAS  Google Scholar 

  2. Leister, D. Chloroplast research in the genomic era. Trends Genet. 19, 47–56 (2003)

    Article  CAS  Google Scholar 

  3. 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 

  4. McElver, J. et al. Insertional mutagenesis of genes required for seed development in Arabidopsis thaliana. Genetics 159, 1751–1763 (2001)

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Budziszewski, G. J. et al. Arabidopsis genes essential for seedling viability: Isolation of insertional mutants and molecular cloning. Genetics 159, 1765–1778 (2001)

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Maréchal, E. Chloroplast biogenesis and function are first in the list of essential Arabidopsis genes. Trends Plant Sci. 7, 99–100 (2002)

    Article  Google Scholar 

  7. Bock, R. in Progress in Botany (eds Esser, K., Lüttge, U., Beyschlag, W. & Hellwig, F.) 106–131 (Springer, Berlin, 2002)

    Book  Google Scholar 

  8. Hager, M., Hermann, M., Biehler, K., Krieger-Liszkay, A. & Bock, R. Lack of the small plastid-encoded PsbJ polypeptide results in a defective water-splitting apparatus of photosystem II, reduced photosystem I levels, and hypersensitivity to light. J. Biol. Chem. 277, 14031–14039 (2002)

    Article  CAS  Google Scholar 

  9. Swiatek, M. et al. Effects of selective inactivation of individual genes for low-molecular-mass subunits on the assembly of photosystem II, as revealed by chloroplast transformation: The psbEFLJ operon in Nicotiana tabacum. Mol. Genet. Genomics 268, 699–710 (2003)

    CAS  PubMed  Google Scholar 

  10. Swiatek, M. et al. PCR analysis of pulse-field gel electrophoresis-purified plastid DNA, a sensitive tool to judge the hetero-/homoplastomic status of plastid transformants. Curr. Genet. 43, 45–53 (2003)

    CAS  PubMed  Google Scholar 

  11. Corneille, S., Lutz, K., Svab, Z. & Maliga, P. Efficient elimination of selectable marker genes from the plastid genome by the CRE–lox site-specific recombination system. Plant J. 72, 171–178 (2001)

    Article  Google Scholar 

  12. Hajdukiewicz, P. T. J., Gilbertson, L. & Staub, J. M. Multiple pathways for Cre/lox-mediated recombination in plastids. Plant J. 27, 161–170 (2001)

    Article  CAS  Google Scholar 

  13. Shikanai, T. et al. The chloroplast clpP gene, encoding a proteolytic subunit of ATP-dependent protease, is indispensable for chloroplast development in tobacco. Plant Cell Physiol. 42, 264–273 (2001)

    Article  CAS  Google Scholar 

  14. Adam, Z. & Clarke, A. K. Cutting edge of chloroplast proteolysis. Trends Plant Sci. 7, 451–456 (2002)

    Article  CAS  Google Scholar 

  15. Ow, D. W. Recombinase-directed plant transformation for the post-genomic era. Plant Mol. Biol. 48, 183–200 (2002)

    Article  CAS  Google Scholar 

  16. Peltier, J. B., Ytterberg, J., Liberles, D. A., Roepstroff, P. & van Wijk, K. J. Identification of a 350 kDa ClpP protease complex with 10 different Clp isoforms in chloroplasts of Arabidopsis thaliana. J. Biol. Chem. 276, 16318–16327 (2001)

    Article  CAS  Google Scholar 

  17. Svab, Z. & Maliga, P. High-frequency plastid transformation in tobacco by selection for a chimeric aadA gene. Proc. Natl Acad. Sci. USA 90, 913–917 (1993)

    Article  ADS  CAS  Google Scholar 

  18. Springer, P. S. Gene traps: Tools for plant development and genomics. Plant Cell 12, 1007–1020 (2000)

    Article  CAS  Google Scholar 

  19. Corneille, S., Lutz, K. A., Azhagiri, A. K. & Maliga, P. Identification of functional lox sites in the plastid genome. Plant J. (in the press)

  20. Kuroda, H. & Maliga, P. Overexpression of the clpP 5′-untranslated region in a chimeric context causes a mutant phenotype, suggesting competition for a clpP-specific RNA maturation factor in tobacco chloroplasts. Plant Physiol. 129, 1600–1606 (2002)

    Article  CAS  Google Scholar 

  21. Zubko, M. K. & Day, A. Stable albinism induced without mutagenesis: A model for ribosome-free plastid inheritance. Plant J. 15, 265–271 (1998)

    Article  CAS  Google Scholar 

  22. Walbot, V. & Coe, E. H. J. Nuclear gene iojap conditions a programmed change to ribosome-less plastids in Zea mays. Proc. Natl Acad. Sci. USA 76, 2760–2764 (1979)

    Article  ADS  CAS  Google Scholar 

  23. Han, C. D., Coe, E. H. J. & Martienssen, R. A. Molecular cloning and characterization of the maize iojap (ij), a pattern striping in maize. EMBO J. 11, 4037–4046 (1992)

    Article  CAS  Google Scholar 

  24. Hess, W. R., Prombona, A., Fieder, B., Subramanian, A. R. & Börner, T. Chloroplast rps15 and the rpoB/C1/C2 gene cluster are strongly transcribed in ribosome-deficient plastids: Evidence for a functioning non-chloroplast-encoded RNA polymerase. EMBO J. 12, 563–571 (1993)

    Article  CAS  Google Scholar 

  25. Cahoon, A. B., Cunningham, K. A. & Stern, D. B. The plastid clpP gene may not be essential for plant cell viability. Plant Cell Physiol. 44, 93–95 (2003)

    Article  CAS  Google Scholar 

  26. Wolfe, K. H., Morden, C. W. & Palmer, J. D. Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant. Proc. Natl Acad. Sci. USA 89, 10648–10652 (1992)

    Article  ADS  CAS  Google Scholar 

  27. Wickner, S., Maurizi, M. R. & Gottesman, S. Posttranslational quality control: Folding, refolding, and degrading proteins. Science 286, 1888–1893 (1999)

    Article  CAS  Google Scholar 

  28. Flynn, J. M., Neher, S. B., Kim, Y.-I., Sauer, R. T. & Baker, T. A. Proteomic discovery of cellular substrates of the ClpXP protease reveals five classes of ClpX-recognition signals. Mol. Cell 11, 671–683 (2003)

    Article  CAS  Google Scholar 

  29. Zhou, Y., Gottesman, S., Hoskins, J. R., Maurizi, M. R. & Wickner, S. The RssB response regulator directly targets σS for degradation by ClpXP. Genes Dev. 15, 627–637 (2001)

    Article  CAS  Google Scholar 

  30. Staub, J. M. & Maliga, P. Accumulation of D1 polypeptide in tobacco plastids is regulated via the untranslated region of the psbA mRNA. EMBO J. 12, 601–606 (1993)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank K. Lutz and S. Corneille for the nuclear Cre plants, and Z. Adam for the ClpP1 antibody. This research was supported by a Rutgers F&A special project grant.

Author information

Authors and Affiliations

  1. Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, New Jersey, 08854-8020, USA

    Hiroshi Kuroda & Pal Maliga

  2. Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Jersey, 08901, New Brunswick, USA

    Pal Maliga

Authors
  1. Hiroshi Kuroda
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Pal Maliga
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Pal Maliga.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kuroda, H., Maliga, P. The plastid clpP1 protease gene is essential for plant development. Nature 425, 86–89 (2003). https://doi.org/10.1038/nature01909

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature01909

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing