Chapter 3 : Ubiquity of Cyclic Di-GMP Pathways: a Bioinformatic Analysis

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In this chapter, the author shows how the bioinformatic tools have contributed to the studies of the c-di-GMP-mediated signaling pathways—and continue to do so. A brief discussion of the roles of the GGDEF, EAL, and HD-GYP domains in c-di-GMP turnover and the role of the PilZ domain as a c-di-GMP adaptor protein is followed by an analysis of the phylogenetic distribution of these domains and a listing of the most common domain architectures that involve these four domains. The identification of the GGDEF domain as a component of DGCs and c-di-GMP-specific phosphodiesterases, participating in c-di-GMP turnover, by Benziman and his colleagues was a watershed event in at least three important aspects. This work provided the first evidence of an enzymatic function for this widespread protein domain and paved the way to the experimental demonstration that the GGDEF domain alone was responsible for the DGC activity. Second, linking this widespread domain with c-di-GMP turnover provided evidence for the participation of c-di-GMP in a variety of signaling processes. Third, the presence of the GGDEF domain in DGCs and in c-di-GMP-specific phosphodiesterases, two kinds of enzymes with opposing activities, suggested that this domain had allosteric functions that regulate c-di-GMP turnover. Experimental characterization of the most widespread combinations of c-di- GMP-related domains, including those described above, remains a promising venue of research that can be expected to provide much-needed insights into the functioning of this fascinating signaling system and its role in bacterial adaptation mechanisms.

Citation: Galperin M. 2010. Ubiquity of Cyclic Di-GMP Pathways: a Bioinformatic Analysis, p 24-36. In Wolfe A, Visick K (ed), The Second Messenger Cyclic Di-GMP. ASM Press, Washington, DC. doi: 10.1128/9781555816667.ch3

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Figure 1.

Growth of the number of c-di-GMP-related protein domains in the public protein databases. The numbers of proteins containing GGDEF domains but no EAL domains (open circles), both GGDEF and EAL domains (grey circles), only EAL domains (open squares), HD-GYP domains (diamonds), and PilZ domains (triangles) are indicated.

Citation: Galperin M. 2010. Ubiquity of Cyclic Di-GMP Pathways: a Bioinformatic Analysis, p 24-36. In Wolfe A, Visick K (ed), The Second Messenger Cyclic Di-GMP. ASM Press, Washington, DC. doi: 10.1128/9781555816667.ch3
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Table 1

General properties of c-di-GMP-related signaling domains

Citation: Galperin M. 2010. Ubiquity of Cyclic Di-GMP Pathways: a Bioinformatic Analysis, p 24-36. In Wolfe A, Visick K (ed), The Second Messenger Cyclic Di-GMP. ASM Press, Washington, DC. doi: 10.1128/9781555816667.ch3
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Table 2

Distribution of genes encoding GGDEF, EAL, HD-GYP, and PilZ domain proteins in completely sequenced genomes of selected model organisms

Citation: Galperin M. 2010. Ubiquity of Cyclic Di-GMP Pathways: a Bioinformatic Analysis, p 24-36. In Wolfe A, Visick K (ed), The Second Messenger Cyclic Di-GMP. ASM Press, Washington, DC. doi: 10.1128/9781555816667.ch3

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