Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in Arabidopsis

TY - JOUR

T1 - Lysine acetylome profiling uncovers novel histone deacetylase substrate proteins in Arabidopsis

AU - Hartl, Markus

AU - Füßl, Magdalena

AU - Boersema, Paul J.

AU - Jost, Jan-Oliver

AU - Kramer, Katharina

AU - Bakirbas, Ahmet

AU - Sindlinger, Julia

AU - Plöchinger, Magdalena

AU - Leister, Dario

AU - Uhrig, Glen

AU - Moorhead, Greg Bg

AU - Cox, Jürgen

AU - Salvucci, Michael E

AU - Schwarzer, Dirk

AU - Mann, Matthias

AU - Finkemeier, Iris

N1 - © 2017 The Authors. Published under the terms of the CC BY 4.0 license.

PY - 2017/10

Y1 - 2017/10

N2 - 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.

AB - 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.

KW - Journal Article

U2 - 10.15252/msb.20177819

DO - 10.15252/msb.20177819

M3 - Journal article

C2 - 29061669

SN - 1744-4292

VL - 13

JO - Molecular Systems Biology

JF - Molecular Systems Biology

IS - 10

M1 - 949

ER -