Cyclic Di-GMP Signaling in Bacteria: Recent Advances and New Puzzles

Abstract

Cyclic di-GMP [bis-(3Ј-5Ј)-cyclic di-GMP] (Fig. 1) is a novel second messenger in bacteria that was first described as an allosteric activator of cellulose synthase in Gluconacetobacter xylinus (49). It is now established that this nucleotide is almost ubiquitous in bacteria, where it regulates a range of functions including developmental transitions, aggregative behavior, adhesion, biofilm formation, and the virulence of animal and plant pathogens (for reviews, see references 15, 18, 30, 31, 47, and 48). The level of cyclic di-GMP in bacterial cells is influenced by both synthesis and degradation. The GGDEF protein domain synthesizes cyclic di-GMP, whereas the EAL and HD-GYP domains are involved in cyclic di-GMP hydrolysis (43,50,51,53,54,58). Bacterial genomes encode a number of proteins with GGDEF, EAL, and HD-GYP domains; e.g., in Pseudomonas aeruginosa, there are 40 such proteins. The majority of these proteins contain additional signal input domains. These signaling systems are presumed to use cyclic di-GMP as a second messenger to link the sensing of specific environmental cues to appropriate alterations in bacterial physiology and/or gene expression. Some details about the operation and organization of cyclic di-GMP signaling systems are emerging. Nevertheless, many questions remain to be answered, and new puzzles have arisen as a result of experimental investigations. Here, we review the recent advances and highlight the considerable gaps in our understanding of cyclic di-GMP signaling. In particular, we discuss (i) the protein domains involved in cyclic di-GMP turnover, highlighting HD-GYP, recently described as a novel cyclic di-GMP phosphodiesterase; (ii) signals that are transduced through cyclic di-GMP signaling; (iii) the role of cyclic di-GMP signaling in bacterial virulence; (iv) recent findings addressing the organization of, and interplay between, different cyclic di-GMP signaling systems; (v) the concept of localized pools of cyclic di-GMP within the cell; and (vi) the mechanisms by which cyclic di-GMP exerts its effects on diverse cellular functions.

Cell–cell signal-dependent dynamic interactions between HD-GYP and GGDEF domain proteins mediate virulence in Xanthomonas campestris

“…S6), they act to regulate motility positively. Such divergences from the general correlation between enzymatic activities of specific cyclic di-GMP signaling proteins and their regulatory functions have been noted previously (10,20). These observations, taken together with the identification of dedicated tasks for particular signaling proteins, have suggested the existence of discrete pools of cyclic di-GMP that may be generated and act in a highly localized fashion (21).…”

“…The role of RpfG in DSF signal transduction is poorly understood, and relatively little is known about the function of the HD-GYP domain (9,10). Although it is established that the enzymatic and regulatory activities of the HD-GYP domain depend upon the HD dyad, the role of other conserved residues, including the GYP motif, is unknown.…”

LapD is a bis-(3′,5′)-cyclic dimeric GMP-binding protein that regulates surface attachment by Pseudomonas fluorescens Pf0–1

“…In contrast, relatively few c-di-GMP-binding proteins have been characterized, leaving open the question of how this signal is received and translated into phenotypic outputs. The occurrence of degenerate GGDEF and EAL domains has led many to speculate that some are inactive and serve as effectors (15,25). LapD provides a key example of an effector protein with degenerate GGDEF and EAL domains that specifically binds c-di-GMP.…”

“…Degenerate GGDEF or EAL domains have been proposed to function as regulatory domains through the binding of c-di-GMP or other nucleotides (15,25). To test if LapD could bind c-di-GMP, we evaluated the ability of LapD6H to interact specifically with this nucleotide.…”

Genetic reductionist approach for dissecting individual roles of GGDEF proteins within the c-di-GMP signaling network in Salmonella

“…This network uses a cyclic dinucleotide, 3Ј-5Ј-cyclic diguanylic acid (c-di-GMP), to relay the signal (1)(2)(3)(4)(5)(6). In c-di-GMP signaling, the sensor protein domain seems to react to the stimulus by activating an output domain, usually fused in the same polypeptide, that triggers changes in c-di-GMP levels.…”