# Nucleotides as Bacterial Second Messengers
#### Similarities and Differences between c-di-Nucleotides  
Cyclic AMP (cAMP) was initially described in glycogen metabolism in animals. In bacteria, cAMP is involved in biofilm formation, virulence, and in central metabolism [3; 4]. The substantial difference between signaling in prokaryotic and eukaryotic cells is that cAMP directly binds to target proteins to function in bacteria. In contrast, cAMP requires intermediates of the protein kinase A (PKA) complex in eukaryotic cells.  
The second messenger c-di-GMP subsequently was discovered. From studies of bacterial genomes, it was found that diguanylate cyclase (DGCs) enzymes have a conserved domain known as the \"GGDEF\" domain [5]. In the case of c-di-GMP phosphodiesterase (PDE), enzymes that degrade c-di-GMP have a highly conserved enzymatic domain known as the \"EAL\" domain [6]. However, a second domain with c-di-GMP degrading activity was determined in PDEs corresponding to the HD-GYP domain. In most bacteria, enzymes that participate in c-di-GMP synthesis/degradation have GGDEF, EAL, and HD-GYP domains, which are widely conserved. Other bacteria have up to dozens of enzymes associated with the synthesis/degradation of c-di-GMP [7].  
The c-di-AMP was the next cyclic dinucleotide discovered [8] in several bacterial and archaeal species. Adenylate cyclases (DACs) are involved in the synthesis of c-di-AMP, and their degradation is by specific PDEs; the DAC domain is in DAC enzymes and the DHH-DHHA1 domain in PDE enzymes, degradation of c-di-AMP by PDE enzymes produces pApA [9].  
There are differences between c-di-AMP and c-di-GMP. For example, one of the few genes that encode DAC enzymes is present in most bacteria. In contrast, genes for DGC enzymes are more abundant in both quantity and variety. Additionally, c-di-AMP participates in the process of bacterial growth that is essential in many bacterial species but not all [10].  
Gram-positive bacteria, such as the phyla Actinobacteria and Firmicutes, frequently have DAC domain-containing proteins. On the other hand, members of phyla Fusobacteria, Bacteroidetes, Chlamydia, Cyanobacteria, and the class Deltaproteobacteria, all Gram-negative bacteria, possess DAC domain proteins. As was mentioned, one DAC enzyme is present in most organisms. However, _Bacillus_ spp. and _Clostridium_ are bacteria that have two or three DAC enzymes. In contrast to c-di-GMP, most organisms can have multiple DGC enzymes.  
The c-di-AMP and c-di-GMP synthesis or degradation enzymes are distributed differently among bacteria. The phylum Proteobacteria are especially abundant in c-di-GMP synthesis enzymes. The classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria have c-di-GMP synthesis enzymes but they do not possess a c-di-AMP signaling system. Instead, enzymes to synthesize both c-di-GMP and c-di-AMP are present in the class Deltaproteobacteria. In contrast, c-di-GMP-producing enzymes are absent in phyla Fusobacteria and Bacteroidetes, and in the order Chlamydomonasiales [11]. On the other hand, _Clostridium_, _Streptomyces_ spp., _Mycobacterium_, _Listeria_, and _Bacillus_, members of the phyla Actinobacteria and Firmicutes, contain both cellular signaling systems, whereas _Corynebacterium_ spp., _Streptococcus_, and _Staphylococcus_ have the c-di-AMP system but not the c-di-GMP system. Although the GGDEF domain is representative of the DGCs, it has been reported that the c-di-AMP synthesis or degradation enzymes in _Streptococcus_ spp. and _Staphylococcus_ have the degenerate GGDEF domains with the capacity to synthesize c-di-AMP or the YybT protein of _B. subtilis_ that has GGDEF domain-containing PDE activity (GdpP) [12].