Transcriptome, metabolome and suppressor analysis reveal an essential role for the ubiquitin-proteasome system in seedling chloroplast development

BMC Plant Biology, vol. 22, pp. 183

Abstract

BACKGROUND: Many regulatory circuits in plants contain steps of targeted proteolysis, with the ubiquitin proteasome system (UPS) as the mediator of these proteolytic events. In order to decrease ubiquitin-dependent proteolysis, we inducibly expressed a ubiquitin variant with Arg at position 48 instead of Lys (ubK48R). This variant acts as an inhibitor of proteolysis via the UPS, and allowed us to uncover processes that are particularly sensitive to UPS perturbation. RESULTS: Expression of ubK48R during germination leads to seedling death. We analyzed the seedling transcriptome, proteome and metabolome 24 h post ubK48R induction and confirmed defects in chloroplast development. We found that mutations in single genes can suppress seedling lethality, indicating that a single process in seedlings is critically sensitive to decreased performance of the UPS. Suppressor mutations in phototropin 2 (PHOT2) suggest that a contribution of PHOT2 to chloroplast protection is compromised by proteolysis inhibition. CONCLUSIONS: Overall, the results reveal protein turnover as an integral part of a signal transduction chain that protects chloroplasts during development.

Authors 15

1. Prabhavathi Talloji

   University of Vienna · Max Perutz Labs

   Affiliation as printed

   Department of Biochemistry and Cell Biology, Max Perutz Labs/Center for Molecular Biology, University of Vienna, A-1030, Vienna, Austria

2. Lilian Nehlin

   University of Vienna · Max Perutz Labs

   Affiliation as printed

   Department of Biochemistry and Cell Biology, Max Perutz Labs/Center for Molecular Biology, University of Vienna, A-1030, Vienna, Austria

3. Bruno Hüttel

   Max Planck Institute for Plant Breeding Research

   Affiliation as printed

   Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany

4. Nikola Winter

   University of Vienna · Max Perutz Labs

   Affiliation as printed

   Department of Biochemistry and Cell Biology, Max Perutz Labs/Center for Molecular Biology, University of Vienna, A-1030, Vienna, Austria

5. Martin Černý

   Mendel University in Brno

   Affiliation as printed

   Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, CZ-613 00, Brno, Czech Republic

6. Hana Dufková

   Mendel University in Brno

   Affiliation as printed

   Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, CZ-613 00, Brno, Czech Republic

7. Bulut Hamali

   University of Vienna · Oregon State University · Max Perutz Labs

   Affiliation as printed

   Department of Biochemistry and Cell Biology, Max Perutz Labs/Center for Molecular Biology, University of Vienna, A-1030, Vienna, Austria

   Present address: Department of Integrative Biology, Oregon State University, 3029 Cordley Hall, Corvallis, OR, 97331, USA

8. Katarzyna Hanczaryk

   University of Vienna · Max Perutz Labs

   Affiliation as printed

   Department of Biochemistry and Cell Biology, Max Perutz Labs/Center for Molecular Biology, University of Vienna, A-1030, Vienna, Austria

9. Jan Novák

   Mendel University in Brno

   Affiliation as printed

   Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, CZ-613 00, Brno, Czech Republic

10. Monika Hermanns Aachen Institute of Plant Physiology (Bio III)

    RWTH Aachen University

    Affiliation as printed

    Institute of Plant Physiology (Bio III), RWTH-Aachen, 52056, Aachen, Germany

11. Nicole Drexler

    Vienna BioCenter Core Facilities

    Affiliation as printed

    Vienna Biocenter Core Facilities, Electron Microscopy, A-1030, Vienna, Austria

12. Karolin Eifler

    University of Vienna · Max Perutz Labs

    Affiliation as printed

    Department of Biochemistry and Cell Biology, Max Perutz Labs/Center for Molecular Biology, University of Vienna, A-1030, Vienna, Austria

13. Nikolaus L. Schlaich Aachen Institute of Plant Physiology (Bio III)

    RWTH Aachen University

    Affiliation as printed

    Institute of Plant Physiology (Bio III), RWTH-Aachen, 52056, Aachen, Germany

14. Břetislav Brzobohatý

    Central European Institute of Technology · Mendel University in Brno

    Affiliation as printed

    CEITEC - Central European Institute of Technology, Mendel University in Brno, CZ-61300, Brno, Czech Republic

    Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, CZ-613 00, Brno, Czech Republic

    CEITEC – Central European Institute of Technology, Mendel University in Brno, CZ-61300, Brno, Czech Republic

15. Andreas Bachmair corresponding

    University of Vienna · Max Perutz Labs

    Affiliation as printed

    Department of Biochemistry and Cell Biology, Max Perutz Labs/Center for Molecular Biology, University of Vienna, A-1030, Vienna, Austria. andreas.bachmair@univie.ac.at

    Department of Biochemistry and Cell Biology, Max Perutz Labs/Center for Molecular Biology, University of Vienna, A-1030, Vienna, Austria