The many roles of cyclic di-AMP to control the physiology of Bacillus subtilis

Abstract

The dinucleotide cyclic di-AMP (c-di-AMP) is synthesized as a second messenger in the Gram-positive model bacterium Bacillus subtilis as well as in many bacteria and archaea. B. subtilis possesses three diadenylate cyclases and two phosphodiesterases that synthesize and degrade the molecule, respectively. Among the second messengers, c-di-AMP is unique since it is essential for B. subtilis on one hand, but toxic upon accumulation on the other. This role as an “essential poison” is related to the function of c-di-AMP in the control of potassium homeostasis. C-di-AMP inhibits the expression and activity of potassium uptake systems by binding to riboswitches and transporters and activates the activity of potassium exporters. In this way, c-di-AMP allows the adjustment of uptake and export systems to achieve a balanced intracellular potassium concentration. C-di-AMP also binds to two dedicated signal transduction proteins, DarA and DarB. Both proteins seem to interact with other proteins in their apo state, i.e. in the absence of c-di-AMP. For DarB, the (p)ppGpp synthetase/hydrolase Rel and the pyruvate carboxylase PycA have been identified as targets. The interactions trigger the synthesis of the alarmone (p)ppGpp and of the acceptor molecule for the citric acid cycle, oxaloacetate, respectively. In the absence of c-di-AMP, many amino acids inhibit the growth of B. subtilis. This feature can be used to identify novel players in amino acid homeostasis. In this review, we discuss the different functions of c-di-AMP and their physiological relevance.

Control of asparagine homeostasis in Bacillus subtilis : identification of promiscuous amino acid importers and exporters

“…2 ). We made, therefore, use of the observation that a strain that is unable to produce c-di-AMP due to the deletion of the three genes encoding the diadenylate cyclases (Δ dac ) is sensitive to glutamate and several other amino acids ( 4 , 17 ). As shown in Fig.…”

“…Some amino acids become toxic if they accumulate due to the lack of the corresponding catabolic enzymes. Similarly, strains lacking the essential second messenger c-di-AMP are highly sensitive to multiple amino acids ( 4 , 11 , 17 ), probably resulting from the formation of glutamate which drastically increases the affinity of the the potassium channel KtrCD for potassium, thus supporting potassium uptake which is toxic for such mutants ( 18 – 20 ). Finally, many d -amino acids are toxic for the cells, and toxic analogs exist for many amino acids, such as 4-azaleucine ( 21 , 22 ).…”

The second messenger c-di-AMP controls natural competence via ComFB signaling protein

“…Cyclic di-AMP is one of the recently discovered di-nucleotide-type second messengers only present in prokaryotes (Stülke & Krüger 2020; He et al 2020; Yin et al 2020; Mantovani et al 2023a). Its functions have been mainly studied in firmicutes, where it plays an important role in osmo-adaptation by controlling potassium homeostasis and influencing transcription of genes related to osmosis and cell wall metabolism (Stülke & Krüger 2020; He et al 2020; Yin et al 2020; Herzberg et al 2023; Nelson et al 2013; Ren & Patel 2014). In cyanobacteria, c-di-AMP seems to control additional processes, including the diurnal metabolism via its binding to the carbon control protein SbtB to regulate glycogen metabolism (Rubin et al 2018; Selim et al 2021a).…”

Control of asparagine homeostasis inBacillus subtilis: Identification of promiscuous amino acid importers and exporters

“…2). We made therefore use of the observation that a strain that is unable to produce c-di-AMP due to the deletion of the three genes encoding the diadenylate cyclases (Δdac) is sensitive to glutamate and several other amino acids (4,17). As shown in Fig.…”

“…Some amino acids become toxic if they accumulate due to the lack of the corresponding catabolic enzymes. Similarly, strains lacking the essential second messenger c-di-AMP are highly sensitive to multiple amino acids (4,11,17), probably resulting from the formation of glutamate which drastically increases the affinity of the the potassium channel KtrCD for potassium thus supporting potassium uptake which is toxic for such mutants (18,19,20). Finally, many D-amino acids are toxic for the cells, and toxic analogs exist for many amino acids, such as 4-azaleucine (21,22).…”