An NAD⁺-dependent sirtuin depropionylase and deacetylase (Sir2La) from the probiotic bacterium Lactobacillus acidophilus NCFM

Sirtuins, a group of NAD⁺-dependent deacylases-have emerged as key in the connection between NAD⁺ metabolism and aging. This class of enzymes hydrolyze a range of ε- N-acyllysine PTMs and determining the repertoire of catalyzed deacylation reactions is of high importance to fully elucidate the roles of a given sirtuin. Here we have identified and produced two potential sirtuins from the probiotic bacterium Lactobacillus acidophilus NCFM and screening more than 80 different substrates, covering 26 acyl groups on five peptide scaffolds, demonstrated that one of the investigated proteins-Sir2La-is a bona fide NAD⁺-dependent sirtuin, catalyzing hydrolysis of acetyl-, propionyl-, and butyryllysine. Further substantiating the identity of Sir2La as a sirtuin, known sirtuin inhibitors nicotinamide and suramin as well as a thioacetyllysine compound inhibit the deacylase activity in a concentration-dependent manner. Based on steady-state kinetics Sir2La showed a slight preference for propionyllysine (Kpro) over acetyllysine (Kac). For non-fluorogenic peptide substrates the preference is driven by a remarkably low K_M (280 nM vs 700 nM, for Kpro and Kac, respectively) whereas k_cat was similar (21 X 10^-3 s^-1). Moreover, while NAD⁺ is a prerequisite for Sir2La-mediated deacylation, Sir2La has very high K_M for NAD⁺ compared to the expected levels of the dinucleotide in L. acidophilus. Sir2La is the first sirtuin from Lactobacillales and of the Gram-positive bacterial subclass of sirtuins to be functionally characterized. The ability to hydrolyze propionyl- and butyryllysine emphasizes the relevance of further exploring the role of other short-chain acyl moieties as PTMs.