Key Points
-
Cyclic di-GMP (c-di-GMP) is a global bacterial second messenger that controls a wide range of cellular processes that contribute to surface adaptation, biofilm formation, cell cycle progression and virulence.
-
Cellular levels of c-di-GMP are controlled by enzyme classes that have antagonistic activities, diguanylate cyclases that synthesize c-di-GMP and phosphodiesterases that degrade c-di-GMP.
-
c-di-GMP controls cellular processes at the transcriptional, translational and post-translational level, and through an increasing number of c-di-GMP-binding proteins and riboswitches.
-
The binding of c-di-GMP to specific proteins can influence their activity, stability, interaction with other proteins or their subcellular localization.
-
c-di-GMP and other bacterial cyclic dinucleotides (CDNs) stimulate the mammalian innate immune response by binding to the stimulator of interferon genes (STING) receptor, thereby converging with the cyclic GMP–AMP synthase (cGAS)–cyclic GMP–AMP (cGAMP) cytosolic DNA-surveillance pathway.
Abstract
Cyclic dinucleotides (CDNs) are highly versatile signalling molecules that control various important biological processes in bacteria. The best-studied example is cyclic di-GMP (c-di-GMP). Known since the late 1980s, it is now recognized as a near-ubiquitous second messenger that coordinates diverse aspects of bacterial growth and behaviour, including motility, virulence, biofilm formation and cell cycle progression. In this Review, we discuss important new insights that have been gained into the molecular principles of c-di-GMP synthesis and degradation, which are mediated by diguanylate cyclases and c-di-GMP-specific phosphodiesterases, respectively, and the cellular functions that are exerted by c-di-GMP-binding effectors and their diverse targets. Finally, we provide a short overview of the signalling versatility of other CDNs, including c-di-AMP and cGMP–AMP (cGAMP).
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Ross, P. et al. Regulation of cellulose synthesis in Acetobacter xylinum by cyclic diguanylic acid. Nature 325, 279–281 (1987).
Witte, G., Hartung, S., Büttner, K. & Hopfner, K.-P. Structural biochemistry of a bacterial checkpoint protein reveals diadenylate cyclase activity regulated by DNA recombination intermediates. Mol. Cell 30, 167–178 (2008).
Davies, B. W., Bogard, R. W., Young, T. S. & Mekalanos, J. J. Coordinated regulation of accessory genetic elements produces cyclic di-nucleotides for V. cholerae virulence. Cell 149, 358–370 (2012). This work discovers cGAMP in bacteria and identifies the first enzyme to synthesize cGAMP from GTP and ATP.
Hornung, V., Hartmann, R., Ablasser, A. & Hopfner, K.-P. OAS proteins and cGAS: unifying concepts in sensing and responding to cytosolic nucleic acids. Nat. Rev. Immunol. 14, 521–528 (2014).
Chan, C. et al. Structural basis of activity and allosteric control of diguanylate cyclase. Proc. Natl Acad. Sci. USA 101, 17084–17089 (2004).
Kranzusch, P. J. et al. Structure-guided reprogramming of human cGAS dinucleotide linkage specificity. Cell 158, 1011–1021 (2014).
Paul, R. Cell cycle-dependent dynamic localization of a bacterial response regulator with a novel di-guanylate cyclase output domain. Genes Dev. 18, 715–727 (2004).
Christen, M., Christen, B., Folcher, M., Schauerte, A. & Jenal, U. Identification and characterization of a cyclic di-GMP-specific phosphodiesterase and its allosteric control by GTP. J. Biol. Chem. 280, 30829–30837 (2005).
Lori, C. et al. Cyclic di-GMP acts as a cell cycle oscillator to drive chromosome replication. Nature 523, 236–239 (2015). This study shows that c-di-GMP directly controls a member of the histidine kinase family to interfere with the two-component phosphorylation network of bacteria.
Srivastava, D. & Waters, C. M. A tangled web: regulatory connections between quorum sensing and cyclic di-GMP. J. Bacteriol. 194, 4485–4493 (2012).
Gupta, K. R., Kasetty, S. & Chatterji, D. Novel functions of (p)ppGpp and cyclic di-GMP in mycobacterial physiology revealed by phenotype microarray analysis of wild-type and isogenic strains of Mycobacterium smegmatis. Appl. Environ. Microbiol. 81, 2571–2578 (2015).
An, S.-Q. et al. A cyclic GMP-dependent signalling pathway regulates bacterial phytopathogenesis. EMBO J. 32, 2430–2438 (2013).
Almblad, H. et al. The cyclic AMP–Vfr signaling pathway in Pseudomonas aeruginosa is inhibited by cyclic di-GMP. J. Bacteriol. 197, 2190–2200 (2015).
Römling, U., Galperin, M. Y. & Gomelsky, M. Cyclic di-GMP: the first 25 years of a universal bacterial second messenger. Microbiol. Mol. Biol. Rev. 77, 1–52 (2013).
Corrigan, R. M. & Gründling, A. Cyclic di-AMP: another second messenger enters the fray. Nat. Rev. Microbiol. 11, 513–524 (2013).
Cai, X., Chiu, Y.-H. & Chen, Z. J. The cGAS–cGAMP–STING pathway of cytosolic DNA sensing and signaling. Mol. Cell 54, 289–296 (2014).
Danilchanka, O. & Mekalanos, J. J. Cyclic dinucleotides and the innate immune response. Cell 154, 962–970 (2013).
Kalia, D. et al. Nucleotide, c-di-GMP, c-di-AMP, cGMP, cAMP, (p)ppGpp signaling in bacteria and implications in pathogenesis. Chem. Soc. Rev. 42, 305–341 (2013).
Schirmer, T. c-di-GMP synthesis: structural aspects of evolution, catalysis and regulation. J. Mol. Biol. 428, 3683–3701 (2016).
Gentner, M., Allan, M. G., Zaehringer, F., Schirmer, T. & Grzesiek, S. Oligomer formation of the bacterial second messenger c-di-GMP: reaction rates and equilibrium constants indicate a monomeric state at physiological concentrations. J. Am. Chem. Soc. 134, 1019–1029 (2012).
Wassmann, P. et al. Structure of BeF3–-modified response regulator PleD: implications for diguanylate cyclase activation, catalysis, and feedback inhibition. Structure 15, 915–927 (2007).
Paul, R. et al. Activation of the diguanylate cyclase PleD by phosphorylation-mediated dimerization. J. Biol. Chem. 282, 29170–29177 (2007).
Christen, B. et al. Allosteric control of cyclic di-GMP signaling. J. Biol. Chem. 281, 32015–32024 (2006).
De, N. et al. Phosphorylation-independent regulation of the diguanylate cyclase WspR. PLoS Biol. 6, e67 (2008).
Zähringer, F., Lacanna, E., Jenal, U., Schirmer, T. & Boehm, A. Structure and signaling mechanism of a zinc-sensory diguanylate cyclase. Structure 21, 1149–1157 (2013).
Dahlstrom, K. M., Giglio, K. M., Sondermann, H. & O'Toole, G. A. The inhibitory site of a diguanylate cyclase is a necessary element for interaction and signaling with an effector protein. J. Bacteriol. 198, 1595–1603 (2016).
Barends, T. R. M. et al. Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase. Nature 459, 1015–1018 (2009).
Sundriyal, A. et al. Inherent regulation of EAL domain-catalyzed hydrolysis of second messenger cyclic di-GMP. J. Biol. Chem. 289, 6978–6990 (2014). This study demonstrates structural coupling between the dimer interface and the catalytic centre of an EAL domain-containing phosphodiesterase.
Winkler, A. et al. Characterization of elements involved in allosteric light regulation of phosphodiesterase activity by comparison of different functional BlrP1 states. J. Mol. Biol. 426, 853–868 (2014).
Rao, F. et al. The functional role of a conserved loop in EAL domain-based cyclic di-GMP-specific phosphodiesterase. J. Bacteriol. 191, 4722–4731 (2009).
Navarro, M. V. et al. Structural basis for c-di-GMP-mediated inside-out signaling controlling periplasmic proteolysis. PLoS Biol. 9, e1000588 (2011).
Ryan, R. P., Fouhy, Y. & Lucey, J. F. Cell–cell signaling in Xanthomonas campestris involves an HD-GYP domain protein that functions in cyclic di-GMP turnover. Proc. Natl Acad. Sci. USA 103, 6712–6717 (2006).
Bellini, D. et al. Crystal structure of an HD-GYP domain cyclic-di-GMP phosphodiesterase reveals an enzyme with a novel trinuclear catalytic iron centre. Mol. Microbiol. 91, 26–38 (2013).
Orr, M. W. et al. Oligoribonuclease is the primary degradative enzyme for pGpG in Pseudomonas aeruginosa that is required for cyclic-di-GMP turnover. Proc. Natl Acad. Sci. USA 112, E5048–E5057 (2015).
Cohen, D. et al. Oligoribonuclease is a central feature of cyclic diguanylate signaling in Pseudomonas aeruginosa. Proc. Natl Acad. Sci. USA 112, 11359–11364 (2015).
García, B. et al. Role of the GGDEF protein family in Salmonella cellulose biosynthesis and biofilm formation. Mol. Microbiol. 54, 264–277 (2004).
Tuckerman, J. R. et al. An oxygen-sensing diguanylate cyclase and phosphodiesterase couple for c-di-GMP control. Biochemistry 48, 9764–9774 (2009).
Plate, L. & Marletta, M. A. Nitric oxide modulates bacterial biofilm formation through a multicomponent cyclic-di-GMP signaling network. Mol. Cell 46, 1–12 (2012).
Basu Roy, A. & Sauer, K. Diguanylate cyclase NicD-based signalling mechanism of nutrient-induced dispersion by Pseudomonas aeruginosa. Mol. Microbiol. 94, 771–793 (2014).
Mills, E., Petersen, E., Kulasekara, B. R. & Miller, S. I. A direct screen for c-di-GMP modulators reveals a Salmonella Typhimurium periplasmic l-arginine-sensing pathway. Sci. Signal. 8, ra57 (2015). This study applies a fluorescence resonance energy transfer (FRET) sensor for c-di-GMP to identify l-arginine as a signal that activates a DGC and leads to biofilm formation.
O'Connor, J. R., Kuwada, N. J., Huangyutitham, V., Wiggins, P. A. & Harwood, C. S. Surface sensing and lateral subcellular localization of WspA, the receptor in a chemosensory-like system leading to c-di-GMP production. Mol. Microbiol. 86, 720–729 (2012).
Hengge, R. et al. Systematic nomenclature for GGDEF and EAL domain-containing cyclic di-GMP turnover proteins of Escherichia coli. J. Bacteriol. 198, 7–11 (2015).
Boehm, A. et al. Second messenger-mediated adjustment of bacterial swimming velocity. Cell 141, 107–116 (2010).
Reinders, A. et al. Expression and genetic activation of cyclic di-GMP-specific phosphodiesterases in Escherichia coli. J. Bacteriol. 198, 448–462 (2016).
Lindenberg, S., Klauck, G., Pesavento, C., Klauck, E. & Hengge, R. The EAL domain protein YciR acts as a trigger enzyme in a c-di-GMP signalling cascade in E. coli biofilm control. EMBO J. 32, 2001–2014 (2013). This work shows that EAL domain-containing PDEs can act both as enzymes and as regulatory triggers, thereby coupling c-di-GMP levels to transcriptional control.
Chou, S.-H. & Galperin, M. Y. Diversity of cyclic di-GMP-binding proteins and mechanisms. J. Bacteriol. 198, 32–46 (2016).
Hengge, R. Cyclic-di-GMP reaches out into the bacterial RNA world. Sci. Signal. 3, pe44 (2010).
Krasteva, P. V. et al. Vibrio cholerae VpsT regulates matrix production and motility by directly sensing cyclic di-GMP. Science 327, 866–868 (2010).
Baraquet, C. & Harwood, C. S. Cyclic diguanosine monophosphate represses bacterial flagella synthesis by interacting with the Walker A motif of the enhancer-binding protein FleQ. Proc. Natl Acad. Sci. USA 110, 18478–18483 (2013).
Tschowri, N. et al. Tetrameric c-di-GMP mediates effective transcription factor dimerization to control Streptomyces development. Cell 158, 1136–1147 (2014). This work identifies c-di-GMP as a main driver of multicellular differentiation in sporulating actinomycete bacteria.
Habazettl, J., Allan, M. G., Jenal, U. & Grzesiek, S. Solution structure of the PilZ domain protein PA4608 complex with cyclic di-GMP identifies charge clustering as molecular readout. J. Biol. Chem. 286, 14304–14314 (2011).
Schumacher, M. A. & Zeng, W. Structures of the activator of K. pneumonia biofilm formation, MrkH, indicates PilZ domains involved in c-di-GMP and DNA binding. Proc. Natl Acad. Sci. USA 113, 10067–10072 (2016).
Duerig, A. et al. Second messenger-mediated spatiotemporal control of protein degradation regulates bacterial cell cycle progression. Genes Dev. 23, 93–104 (2009).
Morgan, J. L. W., McNamara, J. T. & Zimmer, J. Mechanism of activation of bacterial cellulose synthase by cyclic di-GMP. Nat. Struct. Mol. Biol. 21, 489–496 (2014). This study provides the structural basis of c-di-GMP-mediated control of cellulose biosynthesis.
An, S.-Q. et al. Novel cyclic di-GMP effectors of the YajQ protein family control bacterial virulence. PLoS Pathog. 10, e1004429 (2014).
Fazli, M. et al. The CRP/FNR family protein Bcam1349 is a c-di-GMP effector that regulates biofilm formation in the respiratory pathogen Burkholderia cenocepacia. Mol. Microbiol. 82, 327–341 (2011).
Matsuyama, B. Y. et al. Mechanistic insights into c-di-GMP-dependent control of the biofilm regulator FleQ from Pseudomonas aeruginosa. Proc. Natl Acad. Sci. USA 113, E209–E218 (2016).
Skotnicka, D. et al. A minimal threshold of c-di-GMP is essential for fruiting body formation and sporulation in Myxococcus xanthus. PLoS Genet. 12, e1006080 (2016).
Srivastava, D., Hsieh, M.-L., Khataokar, A., Neiditch, M. B. & Waters, C. M. Cyclic di-GMP inhibits Vibrio cholerae motility by repressing induction of transcription and inducing extracellular polysaccharide production. Mol. Microbiol. 90, 1262–1276 (2013).
Roelofs, K. G. et al. Systematic identification of cyclic-di-GMP binding proteins in Vibrio cholerae reveals a novel class of cyclic-di-GMP-binding ATPases associated with type II secretion systems. PLoS Pathog. 11, e1005232 (2015). This study shows that c-di-GMP controls ATPases that are involved in type IV pili biogenesis and in type II secretion.
Jones, C. J. et al. c-di-GMP regulates motile to sessile transition by modulating MshA pili biogenesis and near-surface motility behavior in Vibrio cholerae. PLoS Pathog. 11, e1005068 (2015).
Wang, Y. C. et al. Nucleotide binding by the widespread high-affinity cyclic di-GMP receptor MshEN domain. Nat. Commun. 7, 12481 (2016). By elucidating the structure of the N-terminal domain of the MshE ATPase bound to c-di-GMP, this study defines a large and widespread new family of c-di-GMP-binding proteins.
Moscoso, J. A., Mikkelsen, H., Heeb, S., Williams, P. & Filloux, A. The Pseudomonas aeruginosa sensor RetS switches type III and type VI secretion via c-di-GMP signalling. Environ. Microbiol. 13, 3128–3138 (2011).
Trampari, E. et al. Bacterial rotary export ATPases are allosterically regulated by the nucleotide second messenger cyclic-di-GMP. J. Biol. Chem. 290, 24470–24483 (2015). This study shows that c-di-GMP controls ATPases that are involved in type III secretion.
Kirkpatrick, C. L. & Viollier, P. H. Decoding Caulobacter development. FEMS Microbiol. Rev. 36, 193–205 (2012).
Abel, S. et al. Regulatory cohesion of cell cycle and cell differentiation through interlinked phosphorylation and second messenger networks. Mol. Cell 43, 550–560 (2011).
Abel, S. et al. Bi-modal distribution of the second messenger c-di-GMP controls cell fate and asymmetry during the Caulobacter cell cycle. PLoS Genet. 9, e1003744 (2013).
Christen, M. et al. Asymmetrical distribution of the second messenger c-di-GMP upon bacterial cell division. Science 328, 1295–1297 (2010).
Paul, R. et al. Allosteric regulation of histidine kinases by their cognate response regulator determines cell fate. Cell 133, 452–461 (2008).
Davis, N. J. et al. De− and repolarization mechanism of flagellar morphogenesis during a bacterial cell cycle. Genes Dev. 27, 2049–2062 (2013). This study demonstrates how oscillations of c-di-GMP contribute to flagellar polarity in a simple polarized bacterium.
Ozaki, S. et al. Activation and polar sequestration of PopA, a c-di-GMP effector protein involved in Caulobacter crescentus cell cycle control. Mol. Microbiol. 94, 580–594 (2014).
Smith, S. C. et al. Cell cycle-dependent adaptor complex for ClpXP-mediated proteolysis directly integrates phosphorylation and second messenger signals. Proc. Natl Acad. Sci.USA 111, 14229–14234 (2014).
Dubey, B. N. et al. Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking. Sci. Adv. 2, e1600823 (2016).
Morgan, D. O. Cyclin-dependent kinases: engines, clocks, and microprocessors. Annu. Rev. Cell Dev. Biol. 13, 261–291 (1998).
Chen, Y. E. et al. Spatial gradient of protein phosphorylation underlies replicative asymmetry in a bacterium. Proc. Natl Acad. Sci. USA 108, 1052–1057 (2011).
Tsokos, C. G., Perchuk, B. S. & Laub, M. T. A. Dynamic complex of signaling proteins uses polar localization to regulate cell-fate asymmetry in Caulobacter crescentus. Dev. Cell 20, 329–341 (2011).
Kulasekara, B. R. et al. c-di-GMP heterogeneity is generated by the chemotaxis machinery to regulate flagellar motility. eLife 2, e01402 (2013). This work identifies a PDE that is responsible for the heterogeneous distribution of c-di-GMP following cell division in P. aeruginosa.
Bush, M. J., Tschowri, N., Schlimpert, S., Flärdh, K. & Buttner, M. J. c-di-GMP signalling and the regulation of developmental transitions in streptomycetes. Nat. Rev. Microbiol. 13, 749–760 (2015).
Petters, T. et al. The orphan histidine protein kinase SgmT is a c-di-GMP receptor and regulates composition of the extracellular matrix together with the orphan DNA binding response regulator DigR in Myxococcus xanthus. Mol. Microbiol. 84, 147–165 (2012).
Hobley, L. et al. Discrete cyclic di-GMP-dependent control of bacterial predation versus axenic growth in Bdellovibrio bacteriovorus. PLoS Pathog. 8, e1002493 (2012).
Enomoto, G., Ni-Ni-Win, Narikawa, R. & Ikeuchi, M. Three cyanobacteriochromes work together to form a light color-sensitive input system for c-di-GMP signaling of cell aggregation. Proc. Natl Acad. Sci. USA 112, 8082–8087 (2015).
Valentini, M. & Filloux, A. Biofilms and cyclic di-GMP (c-di-GMP) signaling: lessons from Pseudomonas aeruginosa and other bacteria. J. Biol. Chem. 291, 12547–12555 (2016).
Russell, M. H. et al. Integration of the second messenger c-di-GMP into the chemotactic signaling pathway. mBio 4, e00001-13 (2013).
Paul, K., Nieto, V., Carlquist, W. C., Blair, D. F. & Harshey, R. M. The c-di-GMP binding protein YcgR controls flagellar motor direction and speed to affect chemotaxis by a “backstop brake” mechanism. Mol. Cell 38, 128–139 (2010).
Fang, X. & Gomelsky, M. A post-translational, c-di-GMP-dependent mechanism regulating flagellar motility. Mol. Microbiol. 76, 1295–1305 (2010).
Chen, Y., Chai, Y., Guo, J.-H. & Losick, R. Evidence for cyclic di-GMP-mediated signaling in Bacillus subtilis. J. Bacteriol. 194, 5080–5090 (2012).
Baker, A. E. et al. PilZ domain protein FlgZ mediates cyclic di-GMP-dependent swarming motility control in Pseudomonas aeruginosa. J. Bacteriol. 198, 1837–1846 (2016).
Martínez-Granero, F. et al. Identification of flgZ as a flagellar gene encoding a PilZ domain protein that regulates swimming motility and biofilm formation in Pseudomonas. PLoS ONE 9, e87608 (2014).
Pultz, I. S. et al. The response threshold of Salmonella PilZ domain proteins is determined by their binding affinities for c-di-GMP. Mol. Microbiol. 86, 1424–1440 (2012).
Park, J. H. et al. The cabABC operon essential for biofilm and rugose colony development in Vibrio vulnificus. PLoS Pathog. 11, e1005192 (2015).
Kariisa, A. T., Weeks, K. & Tamayo, R. The RNA domain Vc1 regulates downstream gene expression in response to cyclic diguanylate in Vibrio cholerae. PLoS ONE 11, e0148478 (2016).
Steiner, S., Lori, C., Boehm, A. & Jenal, U. Allosteric activation of exopolysaccharide synthesis through cyclic di-GMP-stimulated protein–protein interaction. EMBO J. 32, 354–368 (2013). This work shows the first example of c-di-GMP stimulating cellular processes by mediating protein–protein interactions.
Skotnicka, D. et al. Cyclic di-GMP regulates type IV pilus-dependent motility in Myxococcus xanthus. J. Bacteriol. 198, 77–90 (2016).
Kazmierczak, B. I., Lebron, M. B. & Murray, T. S. Analysis of FimX, a phosphodiesterase that governs twitching motility in Pseudomonas aeruginosa. Mol. Microbiol. 60, 1026–1043 (2006).
Bordeleau, E. et al. Cyclic di-GMP riboswitch-regulated type IV pili contribute to aggregation of Clostridium difficile. J. Bacteriol. 197, 819–832 (2015).
Serra, D. O., Richter, A. M., Klauck, G., Mika, F. & Hengge, R. Microanatomy at cellular resolution and spatial order of physiological differentiation in a bacterial biofilm. mBio 4, e00103-13 (2013).
Pesavento, C. et al. Inverse regulatory coordination of motility and curli-mediated adhesion in Escherichia coli. Genes Dev. 22, 2434–2446 (2008).
Vakulskas, C. A., Potts, A. H., Babitzke, P., Ahmer, B. M. M. & Romeo, T. Regulation of bacterial virulence by Csr (Rsm) systems. Microbiol. Mol. Biol. Rev. 79, 193–224 (2015).
Chua, S. L. et al. In vitro and in vivo generation and characterization of Pseudomonas aeruginosa biofilm-dispersed cells via c-di-GMP manipulation. Nat. Protoc. 10, 1165–1180 (2015).
Chatterjee, D. et al. Mechanistic insight into the conserved allosteric regulation of periplasmic proteolysis by the signaling molecule cyclic-di-GMP. eLife 3, e03650 (2014).
Malone, J. G. et al. YfiBNR mediates cyclic di-GMP dependent small colony variant formation and persistence in Pseudomonas aeruginosa. PLoS Pathog. 6, e1000804 (2010).
Blanka, A. et al. Constitutive production of c-di-GMP is associated with mutations in a variant of Pseudomonas aeruginosa with altered membrane composition. Sci. Signal. 8, ra36 (2015).
Bordeleau, E., Fortier, L.-C., Malouin, F. & Burrus, V. c-di-GMP turn-over in Clostridium difficile is controlled by a plethora of diguanylate cyclases and phosphodiesterases. PLoS Genet. 7, e1002039 (2011).
Purcell, E. B., McKee, R. W., McBride, S. M., Waters, C. M. & Tamayo, R. Cyclic diguanylate inversely regulates motility and aggregation in Clostridium difficile. J. Bacteriol. 194, 3307–3316 (2012).
Soutourina, O. A. et al. Genome-wide identification of regulatory RNAs in the human pathogen Clostridium difficile. PLoS Genet. 9, e1003493 (2013).
Purcell, E. B., McKee, R. W., Bordeleau, E., Burrus, V. & Tamayo, R. Regulation of type IV pili contributes to surface behaviors of historical and epidemic strains of Clostridium difficile. J. Bacteriol. 198, 565–577 (2015).
McKee, R. W., Mangalea, M. R., Purcell, E. B., Borchardt, E. K. & Tamayo, R. The second messenger cyclic di-GMP regulates Clostridium difficile toxin production by controlling expression of sigD. J. Bacteriol. 195, 5174–5185 (2013).
Peltier, J. et al. Cyclic diGMP regulates production of sortase substrates of Clostridium difficile and their surface exposure through ZmpI protease-mediated cleavage. J. Biol. Chem. 290, 24453–24469 (2015).
Buchholz, U. et al. German outbreak of Escherichia coli O104:H4 associated with sprouts. N. Engl. J. Med. 365, 1763–1770 (2011).
Richter, A. M., Povolotsky, T. L., Wieler, L. H. & Hengge, R. Cyclic-di-GMP signalling and biofilm-related properties of the Shiga toxin-producing 2011 German outbreak Escherichia coli O104:H4. EMBO Mol. Med. 6, 1622–1637 (2014).
Jenal, U. & Malone, J. Mechanisms of cyclic-di-GMP signaling in bacteria. Annu. Rev. Genet. 40, 385–407 (2006).
Hengge, R. Principles of c-di-GMP signalling in bacteria. Nat. Rev. Microbiol. 7, 263–273 (2009).
Lee, E. R., Baker, J. L., Weinberg, Z., Sudarsan, N. & Breaker, R. R. An allosteric self-splicing ribozyme triggered by a bacterial second messenger. Science 329, 845–848 (2010).
Li, L. et al. Hydrolysis of 2′3′-cGAMP by ENPP1 and design of nonhydrolyzable analogs. Nat. Chem. Biol. 10, 1043–1048 (2014).
Ohana, P. et al. Identification of a novel triterpenoid saponin from Pisum sativum as a specific inhibitor of the diguanylate cyclase of Acetobacter xylinum. Plant Cell Physiol. 39, 144–152 (1998).
Lieberman, O. J., Orr, M. W., Wang, Y. & Lee, V. T. High-throughput screening using the differential radial capillary action of ligand assay identifies ebselen as an inhibitor of diguanylate cyclases. ACS Chem. Biol. 9, 183–192 (2014).
He, Q. et al. Structural and biochemical insight into the mechanism of Rv2837c from Mycobacterium tuberculosis as a c-di-NMP phosphodiesterase. J. Biol. Chem. 291, 3668–3681 (2016).
Huynh, T. N. et al. An HD-domain phosphodiesterase mediates cooperative hydrolysis of c-di-AMP to affect bacterial growth and virulence. Proc. Natl Acad. Sci. USA 112, E747–E756 (2015).
Bai, Y. et al. Two DHH subfamily 1 proteins in Streptococcus pneumoniae possess cyclic di-AMP phosphodiesterase activity and affect bacterial growth and virulence. J. Bacteriol. 195, 5123–5132 (2013).
Mehne, F. M. P. et al. Cyclic di-AMP homeostasis in Bacillus subtilis: both lack and high level accumulation of the nucleotide are detrimental for cell growth. J. Biol. Chem. 288, 2004–2017 (2013).
Witte, C. E. et al. Cyclic di-AMP is critical for Listeria monocytogenes growth, cell wall homeostasis, and establishment of infection. mBio 4, e00282–13 (2013).
Whiteley, A. T., Pollock, A. J. & Portnoy, D. A. The PAMP c-di-AMP is essential for Listeria monocytogenes growth in rich but not minimal media due to a toxic increase in (p)ppGpp. Cell Host Microbe 17, 788–798 (2015).
Kaplan Zeevi, M. et al. Listeria monocytogenes multidrug resistance transporters and cyclic di-AMP, which contribute to type I interferon induction, play a role in cell wall stress. J. Bacteriol. 195, 5250–5261 (2013).
Zhu, Y. et al. Cyclic-di-AMP synthesis by the diadenylate cyclase CdaA is modulated by the peptidoglycan biosynthesis enzyme GlmM in Lactococcus lactis. Mol. Microbiol. 99, 1015–1027 (2016).
Luo, Y. & Helmann, J. D. Analysis of the role of Bacillus subtilis σM in β-lactam resistance reveals an essential role for c-di-AMP in peptidoglycan homeostasis. Mol. Microbiol. 83, 623–639 (2012).
Corrigan, R. M., Abbott, J. C., Burhenne, H., Kaever, V. & Gründling, A. c-di-AMP is a new second messenger in Staphylococcus aureus with a role in controlling cell size and envelope stress. PLoS Pathog. 7, e1002217 (2011).
Oppenheimer-Shaanan, Y., Wexselblatt, E., Katzhendler, J., Yavin, E. & Ben-Yehuda, S. c-di-AMP reports DNA integrity during sporulation in Bacillus subtilis. EMBO Rep. 12, 594–601 (2011).
Gándara, C. & Alonso, J. C. DisA and c-di-AMP act at the intersection between DNA-damage response and stress homeostasis in exponentially growing Bacillus subtilis cells. DNA Repair 27, 1–8 (2015).
Zhang, L. & He, Z.-G. Radiation-sensitive gene A (RadA) targets DisA, DNA integrity scanning protein A, to negatively affect cyclic di-AMP synthesis activity in Mycobacterium smegmatis. J. Biol. Chem. 288, 22426–22436 (2013).
Corrigan, R. M. et al. Systematic identification of conserved bacterial c-di-AMP receptor proteins. Proc. Natl Acad. Sci. USA 110, 9084–9089 (2013).
Chin, K.-H. et al. Structural insights into the distinct binding mode of cyclic di-AMP with SaCpaA_RCK. Biochemistry 54, 4936–4951 (2015).
Kim, H. et al. Structural studies of potassium transport protein KtrA regulator of conductance of K+ (RCK) C domain in complex with cyclic diadenosine monophosphate (c-di-AMP). J. Biol. Chem. 290, 16393–16402 (2015).
Moscoso, J. A. et al. Binding of cyclic di-AMP to the Staphylococcus aureus sensor kinase KdpD occurs via the universal stress protein domain and downregulates the expression of the Kdp potassium transporter. J. Bacteriol. 198, 98–110 (2016).
Schuster, C. F. et al. The second messenger c-di-AMP inhibits the osmolyte uptake system OpuC in Staphylococcus aureus. Sci. Signal. 9, ra81 (2016).
Huynh, T. N. et al. Cyclic di-AMP targets the cystathionine β-synthase domain of the osmolyte transporter OpuC. Mol. Microbiol. 102, 233–243 (2016).
Zhang, L., Li, W. & He, Z.-G. DarR, a TetR-like transcriptional factor, is a cyclic di-AMP-responsive repressor in Mycobacterium smegmatis. J. Biol. Chem. 288, 3085–3096 (2013).
Nelson, J. W. et al. Riboswitches in eubacteria sense the second messenger c-di-AMP. Nat. Chem. Biol. 9, 834–839 (2013).
Gundlach, J., Rath, H., Herzberg, C., Mäder, U. & Stülke, J. Second messenger signaling in Bacillus subtilis: accumulation of cyclic di-AMP inhibits biofilm formation. Front. Microbiol. 7, 804 (2016).
Peng, X., Zhang, Y., Bai, G., Zhou, X. & Wu, H. Cyclic di-AMP mediates biofilm formation. Mol. Microbiol. 99, 945–959 (2016).
Mehne, F. M. P. et al. Control of the diadenylate cyclase CdaS in Bacillus subtilis: an autoinhibitory domain limits cyclic di-AMP production. J. Biol. Chem. 289, 21098–21107 (2014).
Sureka, K. et al. The cyclic dinucleotide c-di-AMP is an allosteric regulator of metabolic enzyme function. Cell 158, 1389–1401 (2014). This study links c-di-AMP to metabolic control by identifying pyruvate carboxylase as being regulated by the second messenger in Gram-positive bacterial pathogens.
Dengler, V. et al. Mutation in the c-di-AMP cyclase dacA affects fitness and resistance of methicillin resistant Staphylococcus aureus. PLoS ONE 8, e73512 (2013).
Ablasser, A. et al. cGAS produces a 2′-5′-linked cyclic dinucleotide second messenger that activates STING. Nature 498, 380–384 (2013).
Kato, K., Ishii, R., Hirano, S., Ishitani, R. & Nureki, O. Structural basis for the catalytic mechanism of DncV, bacterial homolog of cyclic GMP–AMP synthase. Structure 23, 843–850 (2015).
Nelson, J. W. et al. Control of bacterial exoelectrogenesis by c-AMP–GMP. Proc. Natl Acad. Sci. USA 112, 5389–5394 (2015).
Kellenberger, C. A. et al. GEMM-I riboswitches from Geobacter sense the bacterial second messenger cyclic AMP–GMP. Proc. Natl Acad. Sci.USA 112, 5383–5388 (2015).
Sun, L., Wu, J., Du, F., Chen, X. & Chen, Z. J. Cyclic GMP–AMP synthase is a cytosolic DNA sensor that activates the type I interferon pathway. Science 339, 786–791 (2013).
Civril, F. et al. Structural mechanism of cytosolic DNA sensing by cGAS. Nature 498, 332–337 (2013).
Diner, E. J. et al. The innate immune DNA sensor cGAS produces a noncanonical cyclic dinucleotide that activates human STING. Cell Rep. 3, 1355–1361 (2013).
Kranzusch, P. J. et al. Ancient origin of cGAS–STING reveals mechanism of universal 2′,3′ cGAMP signaling. Mol. Cell 59, 891–903 (2015).
Karaolis, D. K. R. et al. Bacterial c-di-GMP is an immunostimulatory molecule. J. Immunol. 178, 2171–2181 (2007).
McWhirter, S. M. et al. A host type I interferon response is induced by cytosolic sensing of the bacterial second messenger cyclic-di-GMP. J. Exp. Med. 206, 1899–1911 (2009).
Woodward, J. J., Iavarone, A. T. & Portnoy, D. A. c-di-AMP secreted by intracellular Listeria monocytogenes activates a host type I interferon response. Science 328, 1703–1705 (2010).
Andrade, W. A. et al. Group B Streptococcus degrades cyclic-di-AMP to modulate STING-dependent type I interferon production. Cell Host Microbe 20, 49–59 (2016).
Spangler, C., Böhm, A., Jenal, U., Seifert, R. & Kaever, V. A liquid chromatography-coupled tandem mass spectrometry method for quantitation of cyclic di-guanosine monophosphate. J. Microbiol. Methods 81, 226–231 (2010).
Burhenne, H. & Kaever, V. Quantification of cyclic dinucleotides by reversed-phase LC–MS/MS. Methods Mol. Biol. 1016, 27–37 (2013).
Pawar, S. V. et al. Novel genetic tools to tackle c-di-GMP-dependent signalling in Pseudomonas aeruginosa. J. Appl. Microbiol. 120, 205–217 (2016).
Zhou, H. et al. Characterization of a natural triple-tandem c-di-GMP riboswitch and application of the riboswitch-based dual-fluorescence reporter. Sci. Rep. 6, 20871 (2016).
Kellenberger, C. A., Wilson, S. C., Sales-Lee, J. & Hammond, M. C. RNA-based fluorescent biosensors for live cell imaging of second messengers cyclic di-GMP and cyclic AMP–GMP. J. Am. Chem. Soc. 135, 4906–4909 (2013).
Rybtke, M. T. et al. Fluorescence-based reporter for gauging cyclic di-GMP levels in Pseudomonas aeruginosa. Appl. Environ. Microbiol. 78, 5060–5069 (2012).
Nesper, J., Reinders, A., Glatter, T., Schmidt, A. & Jenal, U. A novel capture compound for the identification and analysis of cyclic di-GMP binding proteins. J. Proteomics 75, 4874–4878 (2012).
Laventie, B.-J. et al. Capture compound mass spectrometry — a powerful tool to identify novel c-di-GMP effector proteins. J. Vis. Exp. 97, e51404 (2015).
Düvel, J. et al. A chemical proteomics approach to identify c-di-GMP binding proteins in Pseudomonas aeruginosa. J. Microbiol. Methods 88, 229–236 (2012).
Rotem, O. et al. An extended cyclic di-GMP network in the predatory Bacterium Bdellovibrio bacteriovorus. J. Bacteriol. 198, 127–137 (2015).
Roelofs, K. G., Wang, J. & Sintim, H. O. Differential radial capillary action of ligand assay for high-throughput detection of protein-metabolite interactions. Proc. Natl Acad. Sci. USA 108, 15528–15533 (2011).
Acknowledgements
The authors thank the reviewers for very constructive comments that have helped to improve both the accuracy and quality of this article. Work in the authors' laboratory was supported by the Swiss National Science Foundation (grant 310030B_147090 to U.J.) and by a European Research Council (ERC) Advanced Research Grant (322809 to U.J.).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Related links
Glossary
- GGDEF domains
-
Catalytic domains of diguanylate cyclases that are responsible for the condensation of two GTP molecules to cyclic di-GMP (c-di-GMP). The domain is named after its conserved signature motif Gly-Gly-Asp-Glu-Phe.
- Receiver domain
-
A conserved amino-terminal domain of response regulators that receives a phosphoryl group from a histidine kinase to activate a carboxy-terminal output domain.
- I site
-
An allosteric binding site for cyclic di-GMP (c-di-GMP) that is responsible for substrate inhibition of diguanylate cyclases.
- EAL domain
-
A catalytic domain of phosphodiesterases that is responsible for the hydrolysis of cyclic di-GMP (c-di-GMP). The EAL domain is named after its conserved signature motif Glu-Ala-Leu and cleaves c-di-GMP into the linear molecule 5′-phosphoguanylyl-(3′-5′)-guanosine (pGpG).
- HD-GYP domain
-
A catalytic domain of phosphodiesterases that is responsible for the cleavage of cyclic di-GMP (c-di-GMP) into two molecules of GMP. The domain belongs to a subclass of HD phosphohydrolases that contain an additional Gly-Tyr-Pro signature motif.
- Riboswitches
-
Regulatory segments of an mRNA that can bind to a small molecule, which results in the altered stability or translation efficiency of the mRNA.
- PilZ domain
-
A small prototypical cyclic di-GMP (c-di-GMP)-binding domain. PilZ domain-containing proteins represent the best-studied class of c-di-GMP effectors.
- YajQ protein family
-
A family of poorly characterized bacterial proteins with motifs that are characteristic of nucleotide-binding or nucleic acid-binding proteins.
- ATPases
-
Enzymes that catalyse the hydrolysis of ATP and harness the energy that is released to drive chemical reactions.
- Mannose-sensitive haemagglutinin pili
-
(MSHA pili). Type IV pili with haemagglutinating activity that are inhibited by mannosides.
- Sensor histidine kinases
-
Enzymes that autophosphorylate a conserved histidine residue and transfer this moiety to the receiver domain of a response regulator.
- Birth scar protein
-
A protein that is positioned at the site of cytokinesis and acts as a marker for the newly formed poles of daughter cells after cell division.
- Vegetative hyphae
-
Filamentous, fungal-like cellular structures in a medium or on a colony surface.
- Adhesins
-
Surface components of bacterial cells that facilitate adherence to other cells or to surfaces.
- Extracellular matrix
-
A self-produced and secreted polymeric matrix that consists of sugars, proteins and DNA, in which bacteria are embedded within a surface-grown biofilm.
- σS
-
A sigma factor in gammaproteobacteria that is a central regulator of the general stress response and of gene expression in stationary phase.
- Haemolytic uraemic syndrome
-
(HUS). A clinical syndrome that is characterized by the destruction of red blood cells and acute kidney failure, and is caused primarily by infection with Shiga toxin-producing Escherichia coli.
- Shiga-toxin
-
A family of related toxins that are expressed and secreted by various enteric pathogens, and inhibit protein synthesis in eukaryotic target cells.
- Stimulator of interferon genes
-
(STING). A receptor that has an important role in innate immunity by inducing the production of type I interferons.
Rights and permissions
About this article
Cite this article
Jenal, U., Reinders, A. & Lori, C. Cyclic di-GMP: second messenger extraordinaire. Nat Rev Microbiol 15, 271–284 (2017). https://doi.org/10.1038/nrmicro.2016.190
Published:
Issue Date:
DOI: https://doi.org/10.1038/nrmicro.2016.190
This article is cited by
-
A c-di-GMP signaling module controls responses to iron in Pseudomonas aeruginosa
Nature Communications (2024)
-
Identification and expression profiling of c-di-GMP signaling genes in the probiotic strain Escherichia coli Nissle 1917 during adhesion to the intestinal epithelial cells
Systems Microbiology and Biomanufacturing (2024)
-
A Novel Bioactive Antimicrobial Film Based on Polyvinyl Alcohol-Protocatechuic Acid: Mechanism and Characterization of Biofilm Inhibition and its Application in Pork Preservation
Food and Bioprocess Technology (2024)
-
Functional diversity of c-di-GMP receptors in prokaryotic and eukaryotic systems
Cell Communication and Signaling (2023)
-
A narrative review on bacterial biofilm: its formation, clinical aspects and inhibition strategies
Future Journal of Pharmaceutical Sciences (2023)