Reversible histone deacetylase activity catalyzes lysine acylation

The dynamic modification of proteins by many metabolites suggests an intimate link between energy metabolism and post-translational modifications (PTM). For instance, starvation and low-carbohydrate diets lead to the accumulation of the ketone body, β-hydroxybutyrate (BHB), whose blood concentrations increase more than 10-fold into the millimolar range, concomitant with the accumulation of lysine β-hydroxybutyrylation (Kbhb) of proteins. As with other lysine acylations, Kbhb marks can be removed by histone deacetylases (HDACs). Here, we report that class I HDACs unexpectedly catalyze a reverse reaction that generates the Kbhb modification on target proteins. Through mutational analysis, we show a shared reliance on key active site amino acids for classical deacetylation and non-canonical HDAC-catalyzed β-hydroxybutyrylation. Based on these data, we propose that HDACs catalyze a condensation reaction between the free amine group on lysine and BHB, thereby generating the amide bond required for covalent attachment of BHB. Also consistent with reversible HDAC activity, Kbhb formation is driven by mass action and substrate availability. This reversible HDAC activity is not limited to BHB but also extends to multiple short-chain fatty acids and represents a novel mechanism of PTM deposition relevant to metabolically-sensitive proteome modifications.