## 2 Results and Discussion
### XRE-COG2856
#### 2.8.1 XRE-COG2856 of _G. kaustophilus_ HTA426 and _G. thermolevorans_ Gts
This type of enzyme is expected to function as a phosphodiesterase acting on specific cyclic di-nucleotides, not on the cyclic nucleotide monophosphate--as was the case with the CdnP, whose annotation is the same as the protein products of GK3182 and *_35570, but was experimentally proved to hydrolyze the c-di-AMP [102]. Taken together, we could assume that the signal which the 7 TMR domain of GK3183 and *_35610 transmits is the c-di-AMP. The c-di-AMP signaling molecule, a recently discovered second messenger [103], is synthesized by many bacteria and archaea [104]. Among firmicutes, the c-di-AMP was found essential for the _B. subtilis_ growth; and thus, it is the only essential signaling nucleotide reported so far [104]. However, it was found to be an essential signaling nucleotide for the growth of _Listeria monocytogenes_[105] and _Staphylococcus aureus_[106] only under specific growth conditions. Such examples must be considered when experimentally studying the c-di-AMP in a given bacterial strain. The synthesized c-di-AMP molecules are secreted into the extracellular space [101; 102], and this secretion is possibly related to stress responses [107]. The presence of a protein that senses the c-di-AMP molecule in the same operon with the genes coding for the TA pair is unlikely to be a random incidence. There is possibly a functional link between the c-di-AMP and the COG2856-XRE TA pair, especially since several studies reported that the two signaling messengers, c-di-AMP and (p)ppGpp are interconnected via an unknown mechanism [101; 108; 109; 110; 110]. The signaling messenger, (p)ppGpp, also known as the \"stress messenger\" [111], mediates the stringent response, which is the response that allows bacteria to adapt to stresses, by coordinating different biological processes [108; 112]. The activation of the toxins of TA systems is a part of the stringent response activated by the (p)ppGpp [22; 112]. Since stress conditions require the release of bacterial communication signals for regulating the response [113], it is not surprising that the regulation of the TA modules is connected to the cellular signaling pathways [3]. Toxins are target-specific; thus, they are connected to specific cell signals that control their activation [3]. So far, the signal that has been widely reported to control the toxin activation is the (p)ppGpp. High levels of the (p)ppGpp inhibit the exopolynophatase (PPX) [22]. This, in turn, leads to the accumulation of the polyphosphate (PolyP) [22]. The PolyP is a signaling molecule that activates the Lon protease, which degrades the antitoxin, resulting in the release of the active toxin [22]. Accordingly, high levels of (p)ppGpp eventually lead to the toxin activation. Since, the two messengers (p)ppGpp and c-di-AMP have a bidirectional relation, as mentioned above [101; 104; 108; 109; 110], the conditions that raise the (p)ppGpp levels will also raise those of the c-di-AMP. Based on the roles of the c-di-AMP and (p)ppGpp in controlling cellular processes under unfavorable conditions and the reported crosstalk between them, we are proposing a hypothesis for the regulation of the _cog2856-xre_ TA gene expression by these two signaling molecules (Figure 2). We are first presenting the hypothesis and following up with findings of previous studies that we based our hypothesis on. Figure 2: Scheme illustrating the hypothesis proposed in the current study on the regulation of the _xre-cog2856_ expression by the signaling messengers, (p)ppGpp and c-di-AMP. * 3 rd protein represents the protein products of GK3183 and *_35610. QS stands for quorum sensing molecule(s). The black up arrows indicate increased levels, while the black down arrows indicate decreased levels. The small black curved arrow indicates the involvement of the QS molecule(s). The big black curved arrow indicates that the cell could go back to normal conditions. Scheme inspired by a figure in [PERSON] et al., 2006 [111].