U. Jenal and J. Malone, Mechanisms of Cyclic-di-GMP Signaling in Bacteria, Annual Review of Genetics, vol.40, issue.1, pp.385-407, 2006.
DOI : 10.1146/annurev.genet.40.110405.090423

R. Hengge, Principles of c-di-GMP signalling in bacteria, Nature Reviews Microbiology, vol.178, issue.4, pp.263-273, 2009.
DOI : 10.1038/nrmicro2109

R. P. Ryan, T. Tolker-nielsen, and J. M. Dow, When the PilZ don???t work: effectors for cyclic di-GMP action in bacteria, Trends in Microbiology, vol.20, issue.5, pp.235-242, 2012.
DOI : 10.1016/j.tim.2012.02.008

Z. Zhang, B. L. Gaffney, and R. A. Jones, c-di-GMP Displays A Monovalent Metal Ion-Dependent Polymorphism, Journal of the American Chemical Society, vol.126, issue.51, pp.16700-16701, 2004.
DOI : 10.1021/ja0449832

Z. Zhang, S. Kim, B. L. Gaffney, and R. A. Jones, Polymorphism of the Signaling Molecule c-di-GMP, Journal of the American Chemical Society, vol.128, issue.21, pp.7015-7024, 2006.
DOI : 10.1021/ja0613714

M. Gentner, M. G. Allan, F. Zaehringer, T. Schirmer, and S. Grzesiek, Oligomer Formation of the Bacterial Second Messenger c-di-GMP: Reaction Rates and Equilibrium Constants Indicate a Monomeric State at Physiological Concentrations, Journal of the American Chemical Society, vol.134, issue.2, pp.1019-1029, 2012.
DOI : 10.1021/ja207742q

S. Nakayama, I. Kelsey, J. Wang, K. Roelofs, B. Stefane et al., Thiazole Orange-Induced c-di-GMP Quadruplex Formation Facilitates a Simple Fluorescent Detection of This Ubiquitous Biofilm Regulating Molecule, Journal of the American Chemical Society, vol.133, issue.13, pp.4856-4864, 2011.
DOI : 10.1021/ja1091062

S. Nakayama, I. Kelsey, J. Wang, and H. O. Sintim, c-di-GMP can form remarkably stable G-quadruplexes at physiological conditions in the presence of some planar intercalators, Chemical Communications, vol.17, issue.16, pp.4766-4768, 2011.
DOI : 10.1039/c0cc05432a

J. Ko, K. S. Ryu, H. Kim, J. S. Shin, J. O. Lee et al., Structure of PP4397 Reveals the Molecular Basis for Different c-di-GMP Binding Modes by Pilz Domain Proteins, Journal of Molecular Biology, vol.398, issue.1, pp.97-110, 2010.
DOI : 10.1016/j.jmb.2010.03.007

J. Benach, S. S. Swaminathan, R. Tamayo, S. K. Handelman, E. Folta-stogniew et al., The structural basis of cyclic diguanylate signal transduction by PilZ domains, The EMBO Journal, vol.73, issue.24, pp.5153-5166, 2007.
DOI : 10.1038/sj.emboj.7601918

J. Duvel, D. Bertinetti, S. Moller, F. Schwede, M. Morr et al., A chemical proteomics approach to identify c-di-GMP binding proteins in Pseudomonas aeruginosa, Journal of Microbiological Methods, vol.88, issue.2, pp.229-236, 2012.
DOI : 10.1016/j.mimet.2011.11.015

C. Y. Yang, K. H. Chin, M. L. Chuah, Z. X. Liang, A. H. Wang et al., at the active site, Acta Crystallographica Section D Biological Crystallography, vol.67, issue.12, pp.997-1008, 2011.
DOI : 10.1107/S090744491104039X/rr5003sup1.pdf

N. De, M. Pirruccello, P. V. Krasteva, N. Bae, R. V. Raghavan et al., Phosphorylation-Independent Regulation of the Diguanylate Cyclase WspR, PLoS Biology, vol.17, issue.3, p.67, 2008.
DOI : 10.1371/journal.pbio.0060067.st001

C. Chan, R. Paul, D. Samoray, N. C. Amiot, B. Giese et al., Structural basis of activity and allosteric control of diguanylate cyclase, Proc. Natl Acad. Sci. USA, pp.17084-17089, 2004.

G. Minasov, S. Padavattan, L. Shuvalova, J. S. Brunzelle, D. J. Miller et al., Crystal Structures of YkuI and Its Complex with Second Messenger Cyclic Di-GMP Suggest Catalytic Mechanism of Phosphodiester Bond Cleavage by EAL Domains, Journal of Biological Chemistry, vol.284, issue.19, pp.13174-13184, 2009.
DOI : 10.1074/jbc.M808221200

M. V. Navarro, N. De, N. Bae, Q. Wang, and H. Sondermann, Structural Analysis of the GGDEF-EAL Domain-Containing c-di-GMP Receptor FimX, Structure, vol.17, issue.8, pp.1104-1116, 2009.
DOI : 10.1016/j.str.2009.06.010

J. Wang, J. Zhou, G. P. Donaldson, S. Nakayama, L. Yan et al., Conservative Change to the Phosphate Moiety of Cyclic Diguanylic Monophosphate Remarkably Affects Its Polymorphism and Ability To Bind DGC, PDE, and PilZ Proteins, Journal of the American Chemical Society, vol.133, issue.24, pp.9320-9330, 2011.
DOI : 10.1021/ja1112029

R. Paul, S. Weiser, N. C. Amiot, C. Chan, T. Schirmer et al., Cell cycle-dependent dynamic localization of a bacterial response regulator with a novel di-guanylate cyclase output domain, Genes & Development, vol.18, issue.6, pp.715-727, 2004.
DOI : 10.1101/gad.289504

R. Paul, S. Abel, P. Wassmann, A. Beck, H. Heerklotz et al., Activation of the Diguanylate Cyclase PleD by Phosphorylation-mediated Dimerization, Journal of Biological Chemistry, vol.282, issue.40, pp.29170-29177, 2007.
DOI : 10.1074/jbc.M704702200

B. Christen, M. Christen, R. Paul, F. Schmid, M. Folcher et al., Allosteric Control of Cyclic di-GMP Signaling, Journal of Biological Chemistry, vol.281, issue.42, pp.32015-32024, 2006.
DOI : 10.1074/jbc.M603589200

J. R. Tuckerman, G. Gonzalez, E. H. Sousa, X. Wan, J. A. Saito et al., An Oxygen-Sensing Diguanylate Cyclase and Phosphodiesterase Couple for c-di-GMP Control, Biochemistry, vol.48, issue.41, pp.9764-9774, 2009.
DOI : 10.1021/bi901409g

M. R. Neunuebel and J. W. Golden, The Anabaena sp. Strain PCC 7120 Gene all2874 Encodes a Diguanylate Cyclase and Is Required for Normal Heterocyst Development under High-Light Growth Conditions, Journal of Bacteriology, vol.190, issue.20, pp.6829-6836, 2008.
DOI : 10.1128/JB.00701-08

M. Christen, B. Christen, M. Folcher, A. Schauerte, and U. Jenal, Identification and Characterization of a Cyclic di-GMP-specific Phosphodiesterase and Its Allosteric Control by GTP, Journal of Biological Chemistry, vol.280, issue.35, pp.30829-30837, 2005.
DOI : 10.1074/jbc.M504429200

S. Z. Sultan, J. E. Pitzer, T. Boquoi, G. Hobbs, M. R. Miller et al., Analysis of the HD-GYP Domain Cyclic Dimeric GMP Phosphodiesterase Reveals a Role in Motility and the Enzootic Life Cycle of Borrelia burgdorferi, Infection and Immunity, vol.79, issue.8, pp.3273-3283, 2011.
DOI : 10.1128/IAI.05153-11

P. Wassmann, C. Chan, R. Paul, A. Beck, H. Heerklotz et al., Structure of BeF3???-Modified Response Regulator PleD: Implications for Diguanylate Cyclase Activation, Catalysis, and Feedback Inhibition, Structure, vol.15, issue.8, pp.915-927, 2007.
DOI : 10.1016/j.str.2007.06.016

T. H. Lai, Y. Kumagai, M. Hyodo, Y. Hayakawa, and Y. Rikihisa, PleC Histidine Kinase and PleD Diguanylate Cyclase Two-Component System and Role of Cyclic Di-GMP in Host Cell Infection, Journal of Bacteriology, vol.191, issue.3, pp.693-700, 2009.
DOI : 10.1128/JB.01218-08

H. Sawai, S. Yoshioka, T. Uchida, M. Hyodo, Y. Hayakawa et al., Molecular oxygen regulates the enzymatic activity of a heme-containing diguanylate cyclase (HemDGC) for the synthesis of cyclic di-GMP, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, vol.1804, issue.1, pp.1804-166, 2010.
DOI : 10.1016/j.bbapap.2009.09.028

F. Rao, S. Pasunooti, Y. Ng, W. Zhuo, L. Lim et al., Enzymatic synthesis of c-di-GMP using a thermophilic diguanylate cyclase, Analytical Biochemistry, vol.389, issue.2, pp.138-142, 2009.
DOI : 10.1016/j.ab.2009.03.031

Y. W. He, C. Boon, L. Zhou, and L. H. Zhang, virulence by quorum sensing and a novel two-component regulatory system RavS/RavR, Molecular Microbiology, vol.51, issue.6, pp.1464-1476, 2009.
DOI : 10.1111/j.1365-2958.2009.06617.x

F. Rao, Y. Yang, Y. Qi, and Z. X. Liang, Catalytic Mechanism of Cyclic Di-GMP-Specific Phosphodiesterase: a Study of the EAL Domain-Containing RocR from Pseudomonas aeruginosa, Journal of Bacteriology, vol.190, issue.10, pp.3622-3631, 2008.
DOI : 10.1128/JB.00165-08

T. R. Barends, E. Hartmann, J. J. Griese, T. Beitlich, N. V. Kirienko et al., Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase, Nature, vol.2, issue.7249, pp.1015-1018, 2009.
DOI : 10.1038/nature07966

F. Rao, Y. Qi, H. S. Chong, M. Kotaka, B. Li et al., The Functional Role of a Conserved Loop in EAL Domain-Based Cyclic di-GMP-Specific Phosphodiesterase, Journal of Bacteriology, vol.191, issue.15, pp.4722-4731, 2009.
DOI : 10.1128/JB.00327-09

R. P. Ryan, Y. Fouhy, J. F. Lucey, L. C. Crossman, S. Spiro 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, pp.6712-6717, 2006.
DOI : 10.1073/pnas.0600345103

I. M. Sharma, T. Dhanaraman, R. Mathew, and D. Chatterji, Synthesis and Characterization of a Fluorescent Analogue of Cyclic di-GMP, Biochemistry, vol.51, issue.27, pp.51-5443, 2012.
DOI : 10.1021/bi3003617

M. Egli, R. V. Gessner, L. D. Williams, G. J. Quigley, G. A. Van-der-marel et al., Atomic-resolution structure of the cellulose synthase regulator cyclic diguanylic acid., Proc. Natl Acad. Sci. USA, pp.3235-3239, 1990.
DOI : 10.1073/pnas.87.8.3235

A. Altomare, M. C. Burla, M. Camalli, G. Cascarano, C. Giacovazzo et al., 97: a new tool for crystal structure determination and refinement, Journal of Applied Crystallography, vol.32, issue.1, pp.115-119, 1999.
DOI : 10.1107/S0021889898007717

S. M. Kelly and N. C. Price, The Use of Circular Dichroism in the Investigation of Protein Structure and Function, Current Protein & Peptide Science, vol.1, issue.4, pp.349-384, 2000.
DOI : 10.2174/1389203003381315

Y. C. Liaw, Y. G. Gao, H. Robinson, G. M. Sheldrick, L. A. Sliedregt et al., Cyclic diguanylic acid behaves as a host molecule for planar intercalators, FEBS Letters, vol.107, issue.2, pp.223-227, 1990.
DOI : 10.1016/0014-5793(90)80253-F

Y. Zhang and K. Huang, On the interactions of hydrated metal cations (Mg2+, Mn2+, Ni2+, Zn2+) with guanine???cytosine Watson???Crick and guanine???guanine reverse-Hoogsteen DNA base pairs, Journal of Molecular Structure: THEOCHEM, vol.812, issue.1-3, pp.51-62, 2007.
DOI : 10.1016/j.theochem.2007.02.009

G. L. Eichhorn and Y. A. Shin, Interaction of metal ions with polynucleotides and related compounds. XII. The relative effect of various metal ions on DNA helicity, Journal of the American Chemical Society, vol.90, issue.26, pp.7323-7328, 1968.
DOI : 10.1021/ja01028a024

J. E. Sponer, V. Sychrovsky, P. Hobza, and J. Sponer, Interactions of hydrated divalent metal cations with nucleic acid bases. How to relate the gas phase data to solution situation and binding selectivity in nucleic acids, Phys. Chem. Chem. Phys., vol.100, issue.10, pp.2772-2780, 2004.
DOI : 10.1039/B404306P

D. Antoniani, P. Bocci, A. Maciag, N. Raffaelli, and P. Landini, Monitoring of diguanylate cyclase activity and of cyclic-di-GMP biosynthesis by whole-cell assays suitable for high-throughput screening of biofilm inhibitors, Applied Microbiology and Biotechnology, vol.39, issue.4, pp.1095-1104, 2009.
DOI : 10.1007/s00253-009-2199-x

J. G. Malone, T. Jaeger, P. Manfredi, A. Do¨tschdo¨tsch, A. Blanka et al., The YfiBNR Signal Transduction Mechanism Reveals Novel Targets for the Evolution of Persistent Pseudomonas aeruginosa in Cystic Fibrosis Airways, PLoS Pathogens, vol.14, issue.Pt 5, p.1002760, 2012.
DOI : 10.1371/journal.ppat.1002760.s009

J. P. Massie, E. L. Reynolds, B. J. Koestler, J. P. Cong, M. Agostoni et al., Quantification of high-specificity cyclic diguanylate signaling, Proc. Natl Acad. Sci. USA, pp.12746-12751, 2012.
DOI : 10.1073/pnas.1115663109