YfmK is an Nε-lysine acetyltransferase that directly acetylates the histone-like protein HBsu in Bacillus subtilis

N-epsilon-lysine acetylation is an abundant and dynamic regulatory posttranslational modification that remains poorly characterized in bacteria. In bacteria, hundreds of proteins are known to be acetylated, but the biological significance of the majority of these events remains unclear. Previously, we characterized the Bacillus subtilis acetylome and found that the essential histone-like protein HBsu contains seven previously unknown acetylation sites in vivo. Here, we investigate whether acetylation is a regulatory component of the function of HBsu in nucleoid compaction. Using mutations that mimic the acetylated and unacetylated forms of the protein, we show that the inability to acetylate key HBsu lysine residues results in a more compacted nucleoid. We further investigated the mechanism of HBsu acetylation. We screened deletions of the similar to 50 putative GNAT domain-encoding genes in B. subtilis for their effects on DNA compaction, and identified five candidates that may encode acetyltransferases acting on HBsu. Genetic bypass experiments demonstrated that two of these, YfmK and YdgE, can acetylate Hbsu, and their potential sites of action on HBsu were identified. Additionally, purified YfmK was able to directly acetylate HBsu in vitro, suggesting that it is the second identified protein acetyltransferase in B. subtilis. We propose that at least one physiological function of the acetylation of HBsu at key lysine residues is to regulate nucleoid compaction, analogous to the role of histone acetylation in eukaryotes.