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Mol Syst Biol. 2017 Oct 23;13(10):949. doi: 10.15252/msb.20177819.

Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in Arabidopsis.

Author information

Plant Proteomics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
Plant Molecular Biology, Department Biology I, Ludwig-Maximilians-University Munich, Martinsried, Germany.
Mass Spectrometry Facility, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria.
Plant Physiology, Institute of Plant Biology and Biotechnology, University of Muenster, Muenster, Germany.
Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany.
Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.
Department of Biological Sciences, University of Calgary, Calgary, AB, Canada.
US Department of Agriculture, Agricultural Research Service, Arid-Land Agricultural Research Center, Maricopa, AZ, USA.
Plant Proteomics, Max Planck Institute for Plant Breeding Research, Cologne, Germany


Histone deacetylases have central functions in regulating stress defenses and development in plants. However, the knowledge about the deacetylase functions is largely limited to histones, although these enzymes were found in diverse subcellular compartments. In this study, we determined the proteome-wide signatures of the RPD3/HDA1 class of histone deacetylases in Arabidopsis Relative quantification of the changes in the lysine acetylation levels was determined on a proteome-wide scale after treatment of Arabidopsis leaves with deacetylase inhibitors apicidin and trichostatin A. We identified 91 new acetylated candidate proteins other than histones, which are potential substrates of the RPD3/HDA1-like histone deacetylases in Arabidopsis, of which at least 30 of these proteins function in nucleic acid binding. Furthermore, our analysis revealed that histone deacetylase 14 (HDA14) is the first organellar-localized RPD3/HDA1 class protein found to reside in the chloroplasts and that the majority of its protein targets have functions in photosynthesis. Finally, the analysis of HDA14 loss-of-function mutants revealed that the activation state of RuBisCO is controlled by lysine acetylation of RuBisCO activase under low-light conditions.


Arabidopsis ; RuBisCO activase; histone deacetylases; lysine acetylation; photosynthesis

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