A protein adaptor mediating Ap4A-dependent control of protein acetylation.

Reversible lysine acetylation is a highly conserved post-translational modification across all domains of life, modulating diverse cellular processes. However, the regulatory mechanisms governing this modification remain poorly understood. Here, we uncover a novel regulatory system in Bacillus subtilis involving the histone deacetylase (HDAC)-like protein AcuC, which targets multiple substrates, including acetyl-CoA synthetase and translation elongation factor. We show that AcuC is inhibited through complex formation with AcuB, a previously uncharacterized protein. We further demonstrate that the alarmone diadenosine tetraphosphate (Ap4A) binds to the cystathionine beta-synthase (CBS) domain of AcuB, stabilizing the AcuB-AcuC complex and enhancing AcuC inhibition. This study identify AcuB as an Ap4A-enhanced deacetylation inhibitor, revealing a new regulatory mechanism for HDAC-like proteins. Our findings also provide the first direct evidence that the secondary messenger Ap4A modulates protein (de)acetylation, highlighting a regulatory network linking cell stress, proteome acetylation, and acetyl-CoA availability. These insights advance our understanding of protein acetylation control.