Chemical proteomics reveals a second family of cyclic-di-AMP hydrolases.

Cyclic-di-AMP is a relative newcomer to the large family of nucleotide-based signaling molecules, which notably includes cyclic-AMP, cyclic-di-GMP, and ppGpp(p) (1). Cyclic-diAMP was first implicated as a possible signaling molecule when it was unexpectedly found bound to the active site of the Bacillus subtilis DisA protein, the prototype for a diverse family of diadenyl cyclases (DAC) (2). Shortly thereafter, cyclic-di-AMP was detected in bacterial cells and shown, in the case of Listeria monocytogenes, to trigger the innate immune response in infected cells (3). To date, all identified cyclic-di-AMP synthases have a DAC domain homologous to that found within DisA (1). Signaling, of course, requires mechanisms for both synthesis and degradation of the signal. The best characterized cyclic-di-AMP phosphodiesterase (PDE) is the B. subtilis GdpP(YybT) protein, which contains an active site structure with DHH-DHHA1 domains (4). All previously characterized cyclic-di-AMP PDEs have a similar catalytic region, although the overall protein architecture varies. In PNAS, Huynh et al. now provide evidence for a new class of cyclic-di-AMP–specific PDE, which functions—together with a GdpP ortholog (PdeA)—to degrade cyclic-di-AMP in L. monocytogenes (5). This enzyme was previously defined as a metal-dependent hydrolase that affected ppGpp levels and was therefore designated PgpH (6). Huynh et al. (5) demonstrate that L. monocytogenes PgpH is the primary cyclic-di-AMP hydrolase during growth in broth, whereas PdeA is the dominant activity during intracellular growth in mammalian cells.