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Chapter 4 : The Core Pathway: Diguanylate Cyclases, Cyclic Di-GMP-Specific Phosphodiesterases, and Cyclic Di-GMP-Binding Proteins

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Abstract:

This chapter describes the studies that resulted in the experimental verification of the core signaling pathway. It discusses advances in enzymology of c-di-GMP synthesis and hydrolysis, identification and characterization of cyclic di-GMP (c-di-GMP) receptors, end targets, and molecular mechanisms, where these are known. The first line of experimental evidence that supported the prediction that DGC activity resides in the GGDEF domain came from genetic studies. If GGDEF domains were to function as diguanylate cyclase (DGC), the predicted activity of the EAL domains would have to be c-di-GMP hydrolysis. However, it was unclear whether or not EAL domains are sufficient for phosphodiesterase (PDE) activity, or whether GGDEF domains are needed as well. Spatiotemporal and stimulus-specific regulation proved to be crucial for maintaining specificity of responses and avoiding unwanted cross talk in the bacteria that possess vast networks of DGCs and PDEs. Since functional DGCs are present in representatives from various branches of the phylogenetic tree of the , including branches comprised mostly of thermophiles, one can predict that c-di-GMP originated early in bacterial evolution. In vitro studies characterizing c-di-GMP-specific PDE activity were performed on the EAL domain proteins from other sources, CC3396 and VieA, and very similar conclusions regarding the nature of enzymatic activity were reached.

Citation: Gomelsky M. 2010. The Core Pathway: Diguanylate Cyclases, Cyclic Di-GMP-Specific Phosphodiesterases, and Cyclic Di-GMP-Binding Proteins, p 37-56. In Wolfe A, Visick K (ed), The Second Messenger Cyclic Di-GMP. ASM Press, Washington, DC. doi: 10.1128/9781555816667.ch4
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Figures

Image of Figure 1.
Figure 1.

Core c-di-GMP signaling pathway and detours from the core. Shown are key protein domains and domain combinations involved in c-di-GMP signaling. Enzymatically active GGDEF, EAL, and HD-GYP domains are drawn on the white background; enzymatically inactive domains involved in substrate binding are shown as light grey, while domains that are no longer associated with c-di-GMP are shown as dark grey. G, guanine.

Citation: Gomelsky M. 2010. The Core Pathway: Diguanylate Cyclases, Cyclic Di-GMP-Specific Phosphodiesterases, and Cyclic Di-GMP-Binding Proteins, p 37-56. In Wolfe A, Visick K (ed), The Second Messenger Cyclic Di-GMP. ASM Press, Washington, DC. doi: 10.1128/9781555816667.ch4
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Image of Figure 2.
Figure 2.

c-di-GMP-binding domains in exopolysaccharide biosynthetic and translocation machines. Bcs, bacterial cellulose synthase present in and enterobacteria; Alg, alginate synthase; Pel, glucose-based PEL polysaccharide. Both Alg and Pel are from pseudomonads. cytoplasm., cytoplasmic.

Citation: Gomelsky M. 2010. The Core Pathway: Diguanylate Cyclases, Cyclic Di-GMP-Specific Phosphodiesterases, and Cyclic Di-GMP-Binding Proteins, p 37-56. In Wolfe A, Visick K (ed), The Second Messenger Cyclic Di-GMP. ASM Press, Washington, DC. doi: 10.1128/9781555816667.ch4
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Image of Figure 3.
Figure 3.

General principles of c-di-GMP regulation. Various DGCs, c-di-GMP PDEs, and c-di-GMP receptors are shown. A cloud of c-di-GMP generated by a DGC that is activated by an environmental signal is shown to affect a specific target, exopolysaccharide synthase.

Citation: Gomelsky M. 2010. The Core Pathway: Diguanylate Cyclases, Cyclic Di-GMP-Specific Phosphodiesterases, and Cyclic Di-GMP-Binding Proteins, p 37-56. In Wolfe A, Visick K (ed), The Second Messenger Cyclic Di-GMP. ASM Press, Washington, DC. doi: 10.1128/9781555816667.ch4
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References

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