## 2 Second Messengers in Cyanobacteria
### Cyclic Dimeric Guanosine 3',5'-Monophosphate, c-di-GMP  
Cyclic di-GMP is synthesized from two GTP molecules by diguanylate cyclase (DGC) (Pfam 00990) activity, whereas c-di-GMP-specific PDE (Pfam00563 and Pfam01966) proteins degrade the molecule into pGpG or GMP (Figure 6). Proteins that can impact the synthesis or degradation of c-di-GMP and c-di-GMP-based signaling exist in a range of cyanobacterial species, yet are largely underexplored in these systems relative to their characterization in pathogenic bacteria [16]. Many cyanobacterial proteins contain light-responsive domains linked to domains that can impact c-di-GMP synthesis or degradation, suggesting that light is an important signal for altering c-di-GMP homeostasis and associated development, physiology and metabolism in cyanobacteria [16]. Among the species present in the CyanoBase database [87], the only species found to lack c-di-GMP signaling systems were _Prochlorococcus_ and some strains of _Synechococcus_[16], similar to a report for cAMP [17]. DGC and PDE domain sequences (_i.e.,_ Pfam00990 and Pfam00563) were used to identify conserved c-di-GMP domains in the 83 finished genomes in IMG (Table 1; Tables S5 and S6). These new results confirmed that only _Prochlorococcus_ and some strains of _Synechococcus_ lack c-di-GMP domains, with the exception of UCYN-A, an uncultured unicellular cyanobacterium associated with a eukaryotic cell [88] (Table S7). Similar to cAMP receptors [17], species adapted to stable habitats may have lost genes encoding c-di-GMP-modulating proteins [16]. Figure 5: External factors controlling intracellular levels of cGMP and phenotypes or processes that are controlled by cGMP in cyanobacteria. Cyclic GMP is synthesized by guanylyl cyclases and degraded by cGMP-specific phosphodiesterase. –, indicates process inhibited by increased cGMP levels. To date, the protein encoded by gene _all2874_ in _Anabaena_, the phytochrome-like protein Cph2 in _Synechocystis_, and the cyanobacterium SesA in _Thermosynechococcus elongatus_ are the only reported cyanobacterial proteins with a functional DGC activity characterized _in vitro_[89, 90, 91]. Mutation of the gene _all2874_ resulted in decreased heterocyst differentiation and reduced vegetative cell size under relatively high light intensity [91]. Cph2 has three GAF domains, two DGCs and one PDE domain. GAF domains bind a light-absorbing chromophore in phytochrome family proteins [92, 93]. Cph2 has been studied for its involvement in inhibiting phototaxis toward blue light in _Synechocystis_[89]. Although wild-type _Synechocystis_ cells did not move toward blue light, mutants lacking Cph2 showed phototaxis toward the light source. Covalent binding of a tetrapyrrole to conserved cysteine residues has been shown for two of the GAF domains of Cph2, as has light-induced photoconversion [89, 94]. The DGC SesA possesses one GAF domain that can sense green and blue light [90]. SesA is responsible for cell aggregation under blue light at relatively low temperature [90]. Although c-di-GMP levels were not measured _in vivo_ in any of these studies, these results suggest that light can serve as a signal for regulating c-di-GMP levels in these three species. Recently, we demonstrated that intracellular levels of c-di-GMP are regulated by light in some cyanobacteria _in vivo_[16]. Levels of c-di-GMP were higher under blue light than other qualities of light in _Synechocystis_, whereas c-di-GMP levels were lower under blue light and higher under white and red light in the chromatically-acclimating _Fremyella diplosiphon_. Intracellular c-di-GMP levels in  
Figure 6: External factors controlling intracellular levels of c-di-GMP and phenotypes or processes that are controlled by c-di-GMP in cyanobacteria. Cyclic di-GMP is synthesized from two GTP by diguanylate cyclases and degraded to two GMP or pGpG by phosphodiesterase (PDE).