Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Structural and mechanistic determinants of c-di-GMP signalling

Key Points

  • Bis-(3′-5′)-cyclic dimeric GMP (c-di-GMP) is a ubiquitous bacterial second messenger that is involved in the regulation of virulence, cell surface-associated traits and biofilm formation. Recently, our structural and functional knowledge of key protein domains that are involved in c-di-GMP metabolism and recognition has increased considerably, such that an atomic description of the molecular events has become possible.

  • Diguanylate cyclases (DGCs) with GGDEF domains catalyse the condensation reaction of two GTP molecules to form c-di-GMP. Although their fold is similar to adenylyl cyclases, they operate as homodimers. Activation by dimerization has been shown for PleD, a response regulator from Caulobacter crescentus with a GGDEF output domain, and may also be the mechanism for signal-induced activation of other DGCs. A large subclass of DGCs seems to be subject to allosteric product inhibition through c-di-GMP-mediated domain immobilization.

  • c-di-GMP specific phosphodiesterases (PDEs) typically contain EAL domains. They exhibit a TIM-barrel fold, and catalysis seems to be assisted by two magnesium ions. Possible mechanisms for their regulation by accessory domains have been proposed.

  • GGDEF- and EAL-containing proteins with degenerated active sites have evolved to act as c-di-GMP receptors or have acquired c-di-GMP-unrelated functions. New data also provide first insights into the various functions of GGDEF–EAL-containing composite proteins, a large subclass of EAL-containing proteins.

  • The small PilZ domain, folded as a six-stranded antiparallel β-barrel, is the best-characterized c-di-GMP receptor. Ligand binding results in fixation of the amino-terminal PilZ segment or in domain rearrangement in the case of multi-domain PilZ-containing receptors.

  • c-di-GMP is an multivalent molecule that is perfectly suited to not only act as a domain cross-linker but also to immobilize disordered regions in polypeptides. This property is used for feedback inhibition of DGCs and probably for the downstream signaling by PilZ receptors.

Abstract

Bis-(3′-5′)-cyclic dimeric GMP (c-di-GMP) is a ubiquitous second messenger that regulates cell surface-associated traits in bacteria. Components of this regulatory network include GGDEF and EAL domain-containing proteins that determine the cellular concentrations of c-di-GMP by mediating its synthesis and degradation, respectively. Crystal structure analyses in combination with functional studies have revealed the catalytic mechanisms and regulatory principles involved. Downstream, c-di-GMP is recognized by PilZ domain-containing receptors that can undergo large-scale domain rearrangements on ligand binding. Here, we review recent data on the structure and functional properties of the protein families that are involved in c-di-GMP signalling and discuss the mechanistic implications.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Components of c-di-GMP signalling pathways.
Figure 2: Domain organization of selected functionally and/or structurally well-characterized GGDEF- and EAL-containing proteins.
Figure 3: Active and regulatory sites of activated PleD from Caulobacter crescentus.
Figure 4: Crystal structures of diguanylate cyclases and an activated REC domain.
Figure 5: Crystal structures of EAL-containing proteins BlrP1 and YkuI.
Figure 6: PilZ-containing proteins and c-di-GMP binding.

Similar content being viewed by others

References

  1. Potrykus, K. & Cashel, M. (p)ppGpp: still magical? Annu. Rev. Microbiol. 62, 35–51 (2008).

    Article  CAS  PubMed  Google Scholar 

  2. Srivatsan, A. & Wang, J. D. Control of bacterial transcription, translation and replication by (p)ppGpp. Curr. Opin. Microbiol. 11, 100–105 (2008).

    Article  CAS  PubMed  Google Scholar 

  3. Shenoy, A. R. & Visweswariah, S. S. New messages from old messengers: cAMP and mycobacteria. Trends Microbiol. 14, 543–550 (2006).

    Article  CAS  PubMed  Google Scholar 

  4. Shenoy, A. R. & Visweswariah, S. S. Mycobacterial adenylyl cyclases: biochemical diversity and structural plasticity. FEBS Lett. 580, 3344–3352 (2006).

    Article  CAS  PubMed  Google Scholar 

  5. Galperin, M. Y. A census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial IQ, extroverts and introverts. BMC Microbiol. 5, 35 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Rauch, A., Leipelt, M., Russwurm, M. & Steegborn, C. Crystal structure of the guanylyl cyclase Cya2. Proc. Natl Acad. Sci. USA 105, 15720–15725 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Ausmees, N. et al. Genetic data indicate that proteins containing the GGDEF domain possess diguanylate cyclase activity. FEMS Microbiol. Lett. 204, 163–167 (2001).

    Article  CAS  PubMed  Google Scholar 

  8. Paul, R. et al. Cell cycle-dependent dynamic localization of a bacterial response regulator with a novel di-guanylate cyclase output domain. Genes Dev. 18, 715–727 (2004). Biochemical analysis that shows that GGDEF domains have DGC activity.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Bobrov, A. G., Kirillina, O. & Perry, R. D. The phosphodiesterase activity of the HmsP EAL domain is required for negative regulation of biofilm formation in Yersinia pestis. FEMS Microbiol. Lett. 247, 123–130 (2005).

    Article  CAS  PubMed  Google Scholar 

  10. 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). First example of a composite protein with a GGDEF domain that allosterically controls the PDE activity of the EAL domain.

    Article  CAS  PubMed  Google Scholar 

  11. Schmidt, A. J., Ryjenkov, D. A. & Gomelsky, M. The ubiquitous protein domain EAL is a cyclic diguanylate-specific phosphodiesterase: enzymatically active and inactive EAL domains. J. Bacteriol. 187, 4774–4781 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Tamayo, R., Tischler, A. D. & Camilli, A. The EAL domain protein VieA is a cyclic diguanylate phosphodiesterase. J. Biol. Chem. 280, 33324–33330 (2005).

    Article  CAS  PubMed  Google Scholar 

  13. Ryan, R. P. et al. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Galperin, M. Y. Structural classification of bacterial response regulators: diversity of output domains and domain combinations. J. Bacteriol. 188, 4169–4182 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Nakhamchik, A., Wilde, C. & Rowe-Magnus, D. A. Cyclic-di-GMP regulates extracellular polysaccharide production, biofilm formation, and rugose colony development by Vibrio vulnificus. Appl. Environ. Microbiol 74, 4199–4209 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Monds, R. D., Newell, P. D., Gross, R. H. & O'Toole, G. A. Phosphate-dependent modulation of c-di-GMP levels regulates Pseudomonas fluorescens Pf0–1 biofilm formation by controlling secretion of the adhesin LapA. Mol. Microbiol. 63, 656–679 (2007).

    Article  CAS  PubMed  Google Scholar 

  17. Merritt, J. H., Brothers, K. M., Kuchma, S. L. & O'Toole, G. A. SadC reciprocally influences biofilm formation and swarming motility via modulation of exopolysaccharide production and flagellar function. J. Bacteriol. 189, 8154–8164 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Meissner, A. et al. Pseudomonas aeruginosa cupA-encoded fimbriae expression is regulated by a GGDEF and EAL domain-dependent modulation of the intracellular level of cyclic diguanylate. Environ. Microbiol. 9, 2475–2485 (2007).

    Article  CAS  PubMed  Google Scholar 

  19. Merighi, M., Lee, V. T., Hyodo, M., Hayakawa, Y. & Lory, S. The second messenger bis-(3′-5′)-cyclic-GMP and its PilZ domain-containing receptor Alg44 are required for alginate biosynthesis in Pseudomonas aeruginosa. Mol. Microbiol. 65, 876–895 (2007).

    Article  CAS  PubMed  Google Scholar 

  20. Pesavento, C. et al. Inverse regulatory coordination of motility and curli-mediated adhesion in Escherichia coli. Genes Dev. 22, 2434–2446 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Lee, V. T. et al. A cyclic-di-GMP receptor required for bacterial exopolysaccharide production. Mol. Microbiol. 65, 1474–1484 (2007). Identification of a new c-di-GMP receptor protein, PelD, that is involved in PEL polysaccharide biosynthesis. Analysis of the conserved secondary structure elements and c-di-GMP-binding site suggests that PelD carries a degenerate GGDEF domain.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Jenal, U. & Malone, J. Mechanisms of cyclic-di-GMP signaling in bacteria. Annu. Rev. Genet. 40, 385–407 (2006).

    Article  CAS  PubMed  Google Scholar 

  23. Hengge, R. Principles of c-di-GMP signalling in bacteria. Nature Rev. Microbiol. 7, 263–273 (2009).

    Article  CAS  Google Scholar 

  24. Girgis, H. S., Liu, Y., Ryu, W. S. & Tavazoie, S. A comprehensive genetic characterization of bacterial motility. PLoS Genet. 3, 1644–1660 (2007).

    Article  CAS  PubMed  Google Scholar 

  25. Wolfe, A. J. & Visick, K. L. Get the message out: cyclic-di-GMP regulates multiple levels of flagellum-based motility. J. Bacteriol. 190, 463–475 (2008).

    Article  CAS  PubMed  Google Scholar 

  26. Klebensberger, J., Lautenschlager, K., Bressler, D., Wingender, J. & Philipp, B. Detergent-induced cell aggregation in subpopulations of Pseudomonas aeruginosa as a preadaptive survival strategy. Environ. Microbiol 9, 2247–2259 (2007).

    Article  PubMed  Google Scholar 

  27. Kumar, M. & Chatterji, D. Cyclic di-GMP: a second messenger required for long-term survival, but not for biofilm formation, in Mycobacterium smegmatis. Microbiology 154, 2942–2955 (2008). In vitro demonstration of bifunctionality of a protein containing GGDEF and EAL domains.

    Article  CAS  PubMed  Google Scholar 

  28. Sabirova, J. S., Chernikova, T. N., Timmis, K. N. & Golyshin, P. N. Niche-specificity factors of a marine oil-degrading bacterium Alcanivorax borkumensis SK2. FEMS Microbiol. Lett. 285, 89–96 (2008).

    Article  CAS  PubMed  Google Scholar 

  29. Fineran, P. C., Williamson, N. R., Lilley, K. S. & Salmond, G. P. Virulence and prodigiosin antibiotic biosynthesis in Serratia are regulated pleiotropically by the GGDEF/EAL domain protein, PigX. J. Bacteriol. 189, 7653–7662 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Duerig, A. et al. Second messenger-mediated spatiotemporal control of protein degradation regulates bacterial cell cycle progression. Genes Dev. 23, 93–104 (2009). First demonstration that GGDEF domains can act as c-di-GMP effectors through a conserved inhibition site. This study also provides the evidence that c-di-GMP interferes with bacterial cell cycle control.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Tamayo, R., Schild, S., Pratt, J. T. & Camilli, A. Role of cyclic di-GMP during el tor biotype Vibrio cholerae infection: characterization of the in vivo-induced cyclic di-GMP phosphodiesterase CdpA. Infect. Immun. 76, 1617–1627 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Chatterjee, S., Wistrom, C. & Lindow, S. E. A cell-cell signaling sensor is required for virulence and insect transmission of Xylella fastidiosa. Proc. Natl Acad. Sci. USA 105, 2670–2675 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. McCarthy, Y. et al. The role of PilZ domain proteins in the virulence of Xanthomonas campestris pv. campestris. Mol. Plant Pathol. 9, 819–824 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Hammer, B. K. & Bassler, B. L. Distinct sensory pathways in Vibrio cholerae El Tor and classical biotypes modulate cyclic dimeric GMP levels to control biofilm formation. J. Bacteriol. 191, 169–177 (2009).

    Article  CAS  PubMed  Google Scholar 

  35. Lai, T. H., Kumagai, Y., Hyodo, M., Hayakawa, Y. & Rikihisa, Y. The Anaplasma phagocytophilum PleC histidine kinase and PleD diguanylate cyclase two-component system and role of cyclic Di-GMP in host cell infection. J. Bacteriol. 191, 693–700 (2009).

    Article  CAS  PubMed  Google Scholar 

  36. Tamayo, R., Pratt, J. T. & Camilli, A. Roles of cyclic diguanylate in the regulation of bacterial pathogenesis. Annu. Rev. Microbiol. 61, 131–148 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Cotter, P. A. & Stibitz, S. C-di-GMP-mediated regulation of virulence and biofilm formation. Curr. Opin. Microbiol 10, 17–23 (2007).

    Article  CAS  PubMed  Google Scholar 

  38. Brouillette, E., Hyodo, M., Hayakawa, Y., Karaolis, D. K. & Malouin, F. 3′, 5′-cyclic diguanylic acid reduces the virulence of biofilm-forming Staphylococcus aureus strains in a mouse model of mastitis infection. Antimicrob. Agents Chemother. 49, 3109–3113 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Ogunniyi, A. D. et al. c-di-GMP is an effective immunomodulator and vaccine adjuvant against pneumococcal infection. Vaccine 26, 4676–4685 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Karaolis, D. K. et al. Bacterial c-di-GMP is an immunostimulatory molecule. J. Immunol. 178, 2171–2181 (2007).

    Article  CAS  PubMed  Google Scholar 

  41. Newell, P. D., Monds, R. D. & O'Toole, G. A. LapD is a bis-(3′, 5′)-cyclic dimeric GMP-binding protein that regulates surface attachment by Pseudomonas fluorescens Pf0–1. Proc. Natl Acad. Sci. USA 106, 3461–3466 (2009). First example of a GGDEF- and EAL-containing protein with a regulatory activity that does not involve c-di-GMP metabolism.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Suzuki, K., Babitzke, P., Kushner, S. R. & Romeo, T. Identification of a novel regulatory protein (CsrD) that targets the global regulatory RNAs CsrB and CsrC for degradation by RNase E. Genes Dev. 20, 2605–2617 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Tschowri, N., Busse, S. & Hengge, R. The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli. Genes Dev. 23, 522–534 (2009). First example of a regulatory function of an EAL-containing protein that does not rely on c-di-GMP hydrolysis or binding, but on protein–protein interactions.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Yildiz, F. H. Cyclic dimeric GMP signaling and regulation of surface-associated developmental programs. J. Bacteriol. 190, 781–783 (2008).

    Article  CAS  PubMed  Google Scholar 

  45. Sinha, S. C. & Sprang, S. R. Structures, mechanism, regulation and evolution of class III nucleotidyl cyclases. Rev. Physiol. Biochem. Pharmacol. 157, 105–140 (2007).

    Google Scholar 

  46. Chan, C. et al. Structural basis of activity and allosteric control of diguanylate cyclase. Proc. Natl Acad. Sci. USA 101, 17084–17089 (2004). Crystal structure of the DGC PleD that reveals the fold of the GGDEF domain and a new allosteric c-di-GMP-binding site that is involved in product inhibition.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. 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). Crystal structure of activated PleD that gives solid evidence for an activation by dimerization mechanism and unveils a second mode of allosteric product inhibition.

    Article  CAS  PubMed  Google Scholar 

  48. Paul, R. et al. Activation of the diguanylate cyclase PleD by phosphorylation-mediated dimerization. J. Biol. Chem. 282, 29170–29177 (2007).

    Article  CAS  PubMed  Google Scholar 

  49. Bachhawat, P. & Stock, A. M. Crystal structures of the receiver domain of the response regulator PhoP from Escherichia coli in the absence and presence of the phosphoryl analog beryllofluoride. J. Bacteriol. 189, 5987–5995 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Gao, R., Mack, T. R. & Stock, A. M. Bacterial response regulators: versatile regulatory strategies from common domains. Trends Biochem. Sci. 32, 225–234 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Malone, J. G. et al. The structure-function relationship of WspR, a Pseudomonas fluorescens response regulator with a GGDEF output domain. Microbiology 153, 980–994 (2007).

    Article  CAS  PubMed  Google Scholar 

  52. Güvener, Z. T. & Harwood, C. S. Subcellular location characteristics of the Pseudomonas aeruginosa GGDEF protein, WspR, indicate that it produces cyclic-di-GMP in response to growth on surfaces. Mol. Microbiol. 66, 1459–1473 (2007).

    PubMed  PubMed Central  Google Scholar 

  53. Ryjenkov, D. A., Tarutina, M., Moskvin, O. V. & Gomelsky, M. Cyclic diguanylate is a ubiquitous signaling molecule in bacteria: insights into biochemistry of the GGDEF protein domain. J. Bacteriol. 187, 1792–1798 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. De, N. et al. Phosphorylation-independent regulation of the diguanylate cyclase WspR. PLoS Biol. 6, e67 (2008). Crystal structure of a DGC with REC– GGDEF organization suggesting that activation proceeds by REC dimerization and reveals c-di-GMP binding to the I site.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Hickman, J. W., Tifrea, D. F. & Harwood, C. S. A chemosensory system that regulates biofilm formation through modulation of cyclic diguanylate levels. Proc. Natl Acad. Sci. USA 102, 14422–14427 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Christen, B. et al. Allosteric control of cyclic di-GMP signaling. J. Biol. Chem. 281, 32015–32024 (2006).

    Article  CAS  PubMed  Google Scholar 

  57. Boehm, A. et al. Second messenger signaling governs Escherichia coli biofilm induction upon ribosomal stress. Mol. Microbiol. 72, 1500–1516 (2009).

    Article  CAS  PubMed  Google Scholar 

  58. Schmid, F. F. & Meuwly, M. All-atom simulations of structures and energetics of c-di-GMP-bound and free PleD. J. Mol. Biol. 374, 1270–1285 (2007).

    Article  CAS  PubMed  Google Scholar 

  59. Dow, J. M., Fouhy, Y., Lucey, J. F. & Ryan, R. P. The HD-GYP domain, cyclic di-GMP signaling, and bacterial virulence to plants. Mol. Plant Microbe Interact. 19, 1378–1384 (2006).

    Article  CAS  PubMed  Google Scholar 

  60. Rao, F., Yang, Y., Qi, Y. & Liang, Z. X. Catalytic mechanism of cyclic di-GMP-specific phosphodiesterase: a study of the EAL domain-containing RocR from Pseudomonas aeruginosa. J. Bacteriol. 190, 3622–3631 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Minasov, G. et al. Crystal structures of YkuI and its complex with second messenger c-di-GMP suggests catalytic mechanism of phosphodiester bond cleavage by EAL domains. J. Biol. Chem. 284, 13174–13184 (2009). EAL structure that revealed the c-di-GMP binding mode and inspired discussion of its regulation.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Barends, T. et al. Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase. Nature 459, 1015–1018 (2009). Crystal structure of a BLUF–EAL-containing protein that suggests a two-metal assisted catalytic mechanism and a communication route between the BLUF domain and the active site of the EAL domain.

    Article  CAS  PubMed  Google Scholar 

  63. Chang, A. L. et al. Phosphodiesterase A1, a regulator of cellulose synthesis in Acetobacter xylinum, is a heme-based sensor. Biochemistry 40, 3420–3426 (2001).

    Article  CAS  PubMed  Google Scholar 

  64. Sasakura, Y., Yoshimura-Suzuki, T., Kurokawa, H. & Shimizu, T. Structure-function relationships of EcDOS, a heme-regulated phosphodiesterase from Escherichia coli. Acc. Chem. Res. 39, 37–43 (2006).

    Article  CAS  PubMed  Google Scholar 

  65. Sasakura, Y. et al. Characterization of a direct oxygen sensor heme protein from Escherichia coli. Effects of the heme redox states and mutations at the heme-binding site on catalysis and structure. J. Biol. Chem. 277, 23821–23827 (2002).

    Article  CAS  PubMed  Google Scholar 

  66. Tanaka, A., Takahashi, H. & Shimizu, T. Critical role of the heme axial ligand, Met95, in locking catalysis of the phosphodiesterase from Escherichia coli (Ec DOS) toward cyclic diGMP. J. Biol. Chem. 282, 21301–21307 (2007).

    Article  CAS  PubMed  Google Scholar 

  67. 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).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Jung, A., Reinstein, J., Domratcheva, T., Shoeman, R. L. & Schlichting, I. Crystal structures of the AppA BLUF domain photoreceptor provide insights into blue light-mediated signal transduction. J. Mol. Biol. 362, 717–732 (2006).

    Article  CAS  PubMed  Google Scholar 

  69. Rao, F. et al. The functional role of a conserved loop in EAL domain-based c-di-GMP specific phosphodiesterase. J. Bacteriol. 191, 4722–4731 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Nakasone, Y., Ono, T. A., Ishii, A., Masuda, S. & Terazima, M. Transient dimerization and conformational change of a BLUF protein: YcgF. J. Am. Chem. Soc. 129, 7028–7035 (2007). Spectroscopic study that suggests light-induced dimerization of a BLUF–EAL-containing protein.

    Article  CAS  PubMed  Google Scholar 

  71. Rajagopal, S., Key, J. M., Purcell, E. B., Boerema, D. J. & Moffat, K. Purification and initial characterization of a putative blue light-regulated phosphodiesterase from Escherichia coli. Photochem. Photobiol. 80, 542–547 (2004).

    Article  CAS  PubMed  Google Scholar 

  72. Tal, R. et al. Three cdg operons control cellular turnover of cyclic di-GMP in Acetobacter xylinum: genetic organization and occurrence of conserved domains in isoenzymes. J. Bacteriol. 180, 4416–4425 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  73. Garcia, B. et al. Role of the GGDEF protein family in Salmonella cellulose biosynthesis and biofilm formation. Mol. Microbiol. 54, 264–277 (2004).

    Article  CAS  PubMed  Google Scholar 

  74. Weber, H., Pesavento, C., Possling, A., Tischendorf, G. & Hengge, R. Cyclic-di-GMP-mediated signalling within the sigma network of Escherichia coli. Mol. Microbiol. 62, 1014–1034 (2006).

    Article  CAS  PubMed  Google Scholar 

  75. Holland, L. M. et al. A staphylococcal GGDEF domain protein regulates biofilm formation independently of cyclic dimeric GMP. J. Bacteriol. 190, 5178–5189 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Tarutina, M., Ryjenkov, D. A. & Gomelsky, M. An unorthodox bacteriophytochrome from Rhodobacter sphaeroides involved in turnover of the second messenger c-di-GMP. J. Biol. Chem. 281, 34751–34758 (2006).

    Article  CAS  PubMed  Google Scholar 

  77. Ferreira, R. B., Antunes, L. C., Greenberg, E. P. & McCarter, L. L. Vibrio parahaemolyticus ScrC modulates cyclic dimeric GMP regulation of gene expression relevant to growth on surfaces. J. Bacteriol. 190, 851–860 (2008).

    Article  CAS  PubMed  Google Scholar 

  78. Boles, B. R. & McCarter, L. L. Vibrio parahaemolyticus scrABC, a novel operon affecting swarming and capsular polysaccharide regulation. J. Bacteriol. 184, 5946–5954 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Hogg, T., Mechold, U., Malke, H., Cashel, M. & Hilgenfeld, R. Conformational antagonism between opposing active sites in a bifunctional RelA/SpoT homolog modulates (p)ppGpp metabolism during the stringent response. Cell 117, 57–68 (2004).

    Article  CAS  PubMed  Google Scholar 

  80. Hickman, J. W. & Harwood, C. S. Identification of FleQ from Pseudomonas aeruginosa as a c-di-GMP-responsive transcription factor. Mol. Microbiol. 69, 376–389 (2008). Identification of the first transcription factor that is regulated directly by c-di-GMP binding.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Sudarsan, N. et al. Riboswitches in eubacteria sense the second messenger cyclic di-GMP. Science 321, 411–413 (2008). Identification of the first c-di-GMP-dependent riboswitch that is involved in gene expression control at the translational level.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Ryjenkov, D. A., Simm, R., Römling, U. & Gomelsky, M. The PilZ domain is a receptor for the second messenger c-di-GMP: the PilZ domain protein YcgR controls motility in enterobacteria. J. Biol. Chem. 281, 30310–30314 (2006).

    Article  CAS  PubMed  Google Scholar 

  83. Amikam, D. & Galperin, M. Y. PilZ domain is part of the bacterial c-di-GMP binding protein. Bioinformatics 22, 3–6 (2006). In silico identification of PilZ-containing proteins, the first family of c-di-GMP effector proteins.

    Article  CAS  PubMed  Google Scholar 

  84. Ross, P. et al. Regulation of cellulose synthesis in Acetobacter xylinum by cyclic diguanylic acid. Nature 325, 279–281 (1987).

    Article  CAS  PubMed  Google Scholar 

  85. Pratt, J. T., Tamayo, R., Tischler, A. D. & Camilli, A. PilZ domain proteins bind cyclic diguanylate and regulate diverse processes in Vibrio cholerae. J. Biol. Chem. 282, 12860–12870 (2007).

    Article  CAS  PubMed  Google Scholar 

  86. Christen, M. et al. DgrA is a member of a new family of cyclic diguanosine monophosphate receptors and controls flagellar motor function in Caulobacter crescentus. Proc. Natl Acad. Sci. USA 104, 4112–4117 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Ramelot, T. A. et al. NMR structure and binding studies confirm that PA4608 from Pseudomonas aeruginosa is a PilZ domain and a c-di-GMP binding protein. Proteins 66, 266–271 (2007).

    Article  CAS  PubMed  Google Scholar 

  88. Benach, J. et al. The structural basis of cyclic diguanylate signal transduction by PilZ domains. EMBO J. 26, 5153–5166 (2007). Crystal structure of a PilZ-containing protein in complex with c-di-GMP, showing ligand-induced domain rearrangement.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Luscombe, N. M., Laskowski, R. A. & Thornton, J. M. Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res. 29, 2860–2874 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Beyhan, S., Odell, L. S. & Yildiz, F. H. Identification and characterization of cyclic diguanylate signaling systems controlling rugosity in Vibrio cholerae. J. Bacteriol. 190, 7392–7405 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Aloni, Y., Delmer, D. P. & Benziman, M. Achievement of high rates of in vitro synthesis of 1, 4-beta-D-glucan: activation by cooperative interaction of the Acetobacter xylinum enzyme system with GTP, polyethylene glycol, and a protein factor. Proc. Natl Acad. Sci. USA 79, 6448–6452 (1982).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Frederick, C. A., Coll, M., van der Marel, G. A., van Boom, J. H. & Wang, A. H. Molecular structure of cyclic deoxydiadenylic acid at atomic resolution. Biochemistry 27, 8350–8361 (1988).

    Article  CAS  PubMed  Google Scholar 

  93. Blommers, M. J. et al. Solution structure of the 3′-5′ cyclic dinucleotide d(pApA). A combined NMR, UV melting, and molecular mechanics study. Biochemistry 27, 8361–8369 (1988).

    Article  CAS  PubMed  Google Scholar 

  94. Egli, M. et al. Atomic-resolution structure of the cellulose synthase regulator cyclic diguanylic acid. Proc. Natl Acad. Sci. USA 87, 3235–3239 (1990).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Guan, Y., Gao, Y. G., Liaw, Y. C., Robinson, H. & Wang, A. H. Molecular structure of cyclic diguanylic acid at 1 A resolution of two crystal forms: self-association, interactions with metal ion/planar dyes and modeling studies. J. Biomol. Struct. Dyn. 11, 253–276 (1993).

    Article  CAS  PubMed  Google Scholar 

  96. Zhang, Z., Kim, S., Gaffney, B. L. & Jones, R. A. Polymorphism of the signaling molecule c-di-GMP. J. Am. Chem. Soc. 128, 7015–7024 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Simm, R., Morr, M., Remminghorst, U., Andersson, M. & Römling, U. Quantitative determination of cyclic diguanosine monophosphate concentrations in nucleotide extracts of bacteria by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry. Anal. Biochem. 386, 53–58 (2009).

    Article  CAS  PubMed  Google Scholar 

  98. Paul, R. et al. Allosteric regulation of histidine kinases by their cognate response regulator determines cell fate. Cell 133, 452–461 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. 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). Discovery of c-di-AMP as a putative second messenger.

    Article  CAS  PubMed  Google Scholar 

  100. Römling, U. Great times for small molecules: c-di-AMP, a second messenger candidate in Bacteria and Archaea. Sci. Signal. 1, pe39 (2008).

    Article  PubMed  Google Scholar 

Download references

Acknowledgements

We thank A. Böhm, J. Malone and C. Massa for critical reading and comments. Work carried out in the authors' laboratories and cited in this Review has been supported by the Swiss National Science Foundation.

Author information

Authors and Affiliations

Authors

Related links

Supplementary information

Supplementary information S1 (figure)

Domain organisation of a selection of functionally and/or structurally well characterized GGDEF and EAL proteins. (PDF 257 kb)

Supplementary information S2 (figure)

Domain organisation and signature motifs of selected PilZ proteins. (PDF 148 kb)

Glossary

Alarmone

A stress-induced hormone that switches bacterial cells from a growth state to a survival state.

Response regulator

Part of bacterial two-component systems, which comprise a response regulator and a histidine kinase. The cognate kinase can phosphorylate the response regulator at an asparate residue in its receiver domain. This elicits a response in the output (or effector) domain, which is usually involved in transcription, but can also have enzymatic function.

Product inhibition

Inhibition of an enzymatic reaction by re-binding of the catalytic product, often to an allosteric site on the enzyme.

Macrocycle

Ring-like substructure of c-di-GMP that is composed of the ribose and phosphate moieties.

Structural genomics

Large scale, systematic approach to determine the three-dimensional structures of proteins.

Hypochromic shift

Reduction of the optical extinction coefficient of nucleic acids on base stacking.

Isothermal titration calorimetry

Biophysical technique that is used for the determination of thermodynamic parameters of a non-covalent molecular interaction.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Schirmer, T., Jenal, U. Structural and mechanistic determinants of c-di-GMP signalling. Nat Rev Microbiol 7, 724–735 (2009). https://doi.org/10.1038/nrmicro2203

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrmicro2203

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing