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

Abstract

N e -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 ∼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. acetylation | histone | nucleoid compaction | acetylase | GNAT

The Major Chromosome Condensation Factors Smc, HBsu, and Gyrase in Bacillus subtilis Operate via Strikingly Different Patterns of Motion

“…To investigate the interaction with DNA of a third DNA-architectural protein, we chose the histone-like protein HBsu. The role of this protein and of other nucleoid-associated proteins (NAPs) in DNA compaction has been investigated extensively both in vitro (34,35) and in vivo (13), but its mode of interaction with DNA has not been investigated in vivo.…”

“…Interestingly, HBsu is acetylated in vivo and this acetylation influences DNA compaction (13). Possibly, the fraction of acetylated HBsu and therefore its residence time are altered in differentiated cells, as in competent and sporulating cells.…”

“…It has been suggested that these proteins are functional homologs of histones, despite the absence of sequence or structural homology (12). Like histones, HBsu engages nonspecifically with DNA and its compaction ability is regulated by acetylation (13). Therefore, it has been hypothesized that a histone-like code exists also in prokaryotes (13).…”

“…Like histones, HBsu engages nonspecifically with DNA and its compaction ability is regulated by acetylation (13). Therefore, it has been hypothesized that a histone-like code exists also in prokaryotes (13). HBsu's role in DNA compaction has been extensively characterized in vitro (14,15).…”

New AMP‐forming acid:CoA ligases from Streptomyces lividans, some of which are posttranslationally regulated by reversible lysine acetylation

“…One possible explanation for this observation could be that Sl PatA somehow controls patB transcription . Control of gene expression by RLA is not unprecedented in actinobacteria (Ghosh et al , ) gamma‐ and alpha‐proteobacteria (Thao et al , ; Lima et al , ; Christensen et al , ) and Firmicutes (Carabetta et al , ). If in fact Sl PatA somehow affects the patB transcription, the newly identified Sl PatB substrates would not be acetylated in a Δ patA strain of S. lividans.…”