Synthesis and characterization of a fluorescent analogue of cyclic di-GMP

Biochemistry

Volumn 51, Issue 27, 2012, Pages 5443-5453

  Sharma, Indra Mani ^a   Dhanaraman, Thillaivillalan ^a,b   Mathew, Ritta ^b   Chatterji, Dipankar ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

^b INSTITUTE OF LIFE SCIENCES   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEINS; BIOLOGICAL PROCESS; CYCLASE ACTIVITY; CYCLASES; DOMAIN-CONTAINING PROTEINS; IN-VITRO; MECHANISTIC ASPECTS; MICROENVIRONMENTS; PHOSPHODIESTERASES; RESEARCH TOOLS; SECOND MESSENGER; SPECTRAL BEHAVIORS;

ESTERS; FLUORESCENCE;

MOLECULAR BIOLOGY;

ACID ANHYDRIDE; BACTERIAL PROTEIN; BACTERIAL PROTEIN MSDGC1; BACTERIAL PROTEIN YCGR; BINDING PROTEIN; CYCLIC DI GMP; CYCLIC GMP; DIGUANYLATE CYCLASE; GUANYLATE CYCLASE; N METHYLISATOIC ANHYDRIDE; N METHYLISATOIC ANHYDRIDE CYCLIC DI GMP; PHOSPHODIESTERASE; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CONTROLLED STUDY; ENERGY TRANSFER; ENZYME INHIBITION; ENZYME KINETICS; FLUORESCENCE SPECTROSCOPY; HYDROLYSIS; MICROENVIRONMENT; NONHUMAN; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN PURIFICATION; PROTEIN STRUCTURE; SYNTHESIS;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CHEMISTRY TECHNIQUES, SYNTHETIC; CYCLIC GMP; FLUORESCENCE RESONANCE ENERGY TRANSFER; FLUORESCENT DYES; HYDROLYSIS; KINETICS; MOLECULAR SEQUENCE DATA; REPRODUCIBILITY OF RESULTS;

BACTERIA (MICROORGANISMS);

EID: 84863772351     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi3003617     Document Type: Article

References (36)

1. Hengge, R. (2009) Principles of c-di-GMP signalling in bacteria Nat. Rev. Microbiol. 7, 263-273
2. Schirmer, T. and Jenal, U. (2009) Structural and mechanistic determinants of c-di-GMP signalling Nat. Rev. Microbiol. 7, 724-735
3. Nakayama, S., Kelsey, I., Wang, J., Roelofs, K., Stefane, B., Luo, Y., Lee, V. T., and Sintim, H. O. (2011) Thiazole orange-induced c-di-GMP quadruplex formation facilitates a simple fluorescent detection of this ubiquitous biofilm regulating molecule J. Am. Chem. Soc. 133, 4856-4864
4. Wang, J., Zhou, J., Donaldson, G. P., Nakayama, S., Yan, L., Lam, Y. F., Lee, V. T., and Sintim, H. O. (2011) Conservative change to the phosphate moiety of cyclic diguanylic monophosphate remarkably affects its polymorphism and ability to bind DGC, PDE, and PilZ proteins J. Am. Chem. Soc. 133, 9320-9330
5. 2-biotinylated analogs of c-di-GMP with c-di-GMP riboswitches and binding proteins Mol. BioSyst. 8, 772-778
6. Chatterji, D. and Gopal, V. (1996) Fluorescence spectroscopy analysis of active and regulatory sites of RNA polymerase Methods Enzymol. 274, 456-478 (Pubitemid 26353097)
7. Hiratsuka, T. (1982) New fluorescent analogs of cAMP and cGMP available as substrates for cyclic nucleotide phosphodiesterase J. Biol. Chem. 257, 13354-13358 (Pubitemid 13188950)
8. Reddy, P. S., Raghavan, A., and Chatterji, D. (1995) Evidence for a ppGpp-binding site on Escherichia coli RNA polymerase: Proximity relationship with the rifampicin-binding domain Mol. Microbiol. 15, 255-265
9. Newton, M., Niewczas, I., Clark, J., and Bellamy, T. C. (2010) A real-time fluorescent assay of the purified nitric oxide receptor, guanylyl cyclase Anal. Biochem. 402, 129-136
10. Johnson, J. D., Walters, J. D., and Mills, J. S. (1987) A continuous fluorescence assay for cyclic nucleotide phosphodiesterase hydrolysis of cyclic GMP Anal. Biochem. 162, 291-295 (Pubitemid 17064328)
11. Ren, J. and Goss, D. J. (1996) Synthesis of a fluorescent 7-methylguanosine analog and a fluorescence spectroscopic study of its reaction with wheatgerm cap binding proteins Nucleic Acids Res. 24, 3629-3634 (Pubitemid 26315778)
12. Pisareva, V. P., Pisarev, A. V., Hellen, C. U. T., Rodnina, M. V., and Pestova, T. V. (2006) Kinetic analysis of interaction of eukaryotic release factor 3 with guanine nucleotides J. Biol. Chem. 281, 40224-40235 (Pubitemid 46043300)
13. 2)-substituted purine and pyrimidine nucleotides J. Pharmacol. Exp. Ther. 336, 234-241
14. Rensland, H., John, J., Linke, R., Simon, I., Schlichting, I., Wittinghofer, A., and Goody, R. S. (1995) Substrate and product structural requirements for binding of nucleotides to H-ras p21: The mechanism of discrimination between guanosine and adenosine nucleotides Biochemistry 34, 593-599
15. Lenzen, C., Cool, R. H., and Wittinghofer, A. (1995) Analysis of intrinsic and CDC25 stimulated guanine nucleotide exchange of p21ras-nucleotide complexes by fluorescence measurements Methods Enzymol. 255, 95-109
16. Stryer, L. (1978) Fluorescence energy transfer as a spectroscopic ruler Annu. Rev. Biochem. 47, 819-846
17. Kumar, K. P. and Chatterji, D. (1990) Resonance energy transfer study on the proximity relationship between the GTP binding site and the rifampicin binding site of Escherichia coli RNA polymerase Biochemistry 29, 317-322 (Pubitemid 20037635)
18. Sullivan, S. M., Mishra, R., Neubig, R. R., and Maddock, J. R. (2000) Analysis of guanine nucleotide binding and exchange kinetics of the Escherichia coli GTPase Era J. Bacteriol. 182, 3460-3466 (Pubitemid 30341609)
19. Chan, C., Paul, R., Samoray, D., Amiot, N. C., Giese, B., Jenal, U., and Schirmer, T. (2004) Structural basis of activity and allosteric control of diguanylate cyclase Proc. Natl. Acad. Sci. U.S.A. 101, 17084-17089 (Pubitemid 39627778)
20. Arnold, K., Bordoli, L., Kopp, J., and Schwede, T. (2006) The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling Bioinformatics 22, 195-201 (Pubitemid 43205406)
21. Lasckowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) PROCHECK: A program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26, 283-291
22. Simm, R., Morr, M., Kader, A., Nimtz, M., and RöÂ̂mling, U. (2004) GGDEF and EAL domains inversely regulate cyclic di-GMP levels and transition from sessility to motility Mol. Microbial. 53, 1123-34 (Pubitemid 39120434)
23. Woodward, J. J., Iavarone, A. T., and Portnoy, D. A. (2010) c-di AMP secreted by intracellular Listeria monocytogenes activates a host type I interferon response Science 328, 1703-1705
24. Kamegaya, T., Kuroda, K., and Hayakawa, Y. (2011) Identification of a Streptococcus pyogenes SF370 gene involved in production of c-di-AMP Nagoya J. Med. Sci. 73, 49-57
25. Christen, B., Christen, M., Paul, R., Schmid, F., Folcher, M., Jenoe, P., Meuwly, M., and Jenal, U. (2006) Structural basis of activity and allosteric control of diguanylate cyclase J. Biol. Chem. 281, 32015-32024
26. --modified response regulator PleD: Implications for diguanylate cyclase activation, catalysis, and feedback inhibition Structure 15, 915-927 (Pubitemid 47212753)
27. Ching, S. M., Tan, W. J., Chua, K. L., and Lam, Y. (2010) Synthesis of cyclic dinucleotidic acids as potential inhibitors targeting diguanylate cyclase Bioorg. Med. Chem. 18, 6657-6665
28. Bharati, B. K., Sharma, I. M., Kasetty, S., Kumar, M., Mukherjee, R., and Chatterji, D. (2012) A full length bifunctional protein involved in c-di-GMP turnover is required for long term survival under nutrient starvation in Mycobacterium smegmatis Microbiology 158, 1415-1427
29. Rao, F., Yang, Y., Qi, Y., and Liang, Z. X. (2008) Catalytic mechanism of cyclic di-GMP specific phosphodiesterase: A study of the EAL domain-containing RocR from Pseudomonas aeruginosa J. Bacteriol. 190, 3622-3631
30. Amikam, D. and Galperin, M. Y. (2006) PilZ domain is part of the bacterial c-di-GMP binding protein Bioinformatics 22, 3-6 (Pubitemid 43057001)
31. Ryjenkov, D. A., Simm, R., RöÂ̂mling, U., and Gomelsky, M. (2006) The PilZ domain is a receptor for the second messenger c-di-GMP J. Biol. Chem. 281, 30310-30314
32. Pratt, J. T., Tamayo, R., Tischler, A. D., and Camilli, A. (2007) PilZ domain proteins bind cyclic digyanylate and regulate diverse processes in Vibrio cholera J. Biol. Chem. 282, 12860-12870 (Pubitemid 47100636)
33. Benach, J., Swaminathan, S. S., Tamayo, R., Handelman, S. K., Folta-Stogniew, E., Ramos, J. E., Forouhar, F., Neely, H., Seetharaman, J., Camilli, A., and Hunt, J. F. (2007) The structural basis of cyclic diguanylate signal transduction by PilZ domains EMBO J. 26, 5153-5166 (Pubitemid 350261281)
34. Friedman, M. L., Schlueter, K. T., Kirley, T. L., and Halsall, H. B. (1985) Fluorescence quenching of human orosomucoid. Accessibility to drugs and small quenching agents Biochem. J. 232, 863-867 (Pubitemid 16207327)
35. Tamayo, R., Tischler, A. D., and Camilli, A. (2005) The EAL domain protein VieA is a cyclic diguanylate phosphodiesterase J. Biol. Chem. 280, 33324-33330 (Pubitemid 41397129)
36. Christen, M., Christen, B., Folcher, M., Schauerte, A., and Jenal, U. (2005) Identification and characterization of a cyclic di-GMP-specific phosphodiesterase and its allosteric control by GTP J. Biol. Chem. 280, 30829-30837 (Pubitemid 41291813)