Updated project metadata. Acetylation on ε-amino groups of lysine residues (N-ε-lysine acetylation) represents an important mechanism of post-translational regulation of protein function. However, its role and extent in the whooping cough agent Bordetella pertussis remain unknown. In this study, we analyzed the acetylomes of two bacterial mutants lacking putative lysine deacetylases encoded by genes BP0960 and BP3063 and compared them with the acetylome of wild-type B. pertussis. The results suggest that acetylation on lysine residues may modulate the activities of proteins involved in bacterial virulence and of multiple histone-like proteins.