Detection of Cyclic Diguanylate G-octaplex Assembly and Interaction with Proteins

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2013 Jan 12

PMID 23308275

Citations 1

Authors

Ori J Lieberman

Jeffrey J DeStefano

Vincent T Lee

Affiliations

Soon will be listed here.

Abstract

Bacterial signaling networks control a wide variety of cellular processes including growth, metabolism, and pathogenesis. Bis-(3'-5')-cyclic dimeric guanosine monophosphate (cdiGMP) is a secondary signaling nucleotide that controls cellulose synthesis, biofilm formation, motility and virulence in a wide range of gram-negative bacterial species. CdiGMP is a dynamic molecule that forms different tertiary structures in vitro, including a trans-monomer, cis-monomer, cis-dimer and G-octaplex (G8). Although the monomer and dimer have been shown to be physiologically relevant in modulating protein activity and transcription, the biological effects of the cdiGMP G8 has not yet been described. Here, we have developed a TLC-based assay to detect radiolabeled cdiGMP G8 formation. Utilizing the radiolabeled cdiGMP G8, we have also shown a novel inhibitory interaction between the cdiGMP G8 and HIV-1 reverse transcriptase and that the cdiGMP G8 does not interact with proteins from Pseudomonas aeruginosa known to bind monomeric and dimeric cdiGMP. These results suggest that the radiolabeled cdiGMP G8 can be used to measure interactions between the cdiGMP G8 and cellular proteins, providing an avenue through which the biological significance of this molecule could be investigated.

Citing Articles

High-throughput screening using the differential radial capillary action of ligand assay identifies ebselen as an inhibitor of diguanylate cyclases.

Lieberman O, Orr M, Wang Y, Lee V ACS Chem Biol. 2013; 9(1):183-92.

PMID: 24134695 PMC: 4545405. DOI: 10.1021/cb400485k.

References

Merighi M, Lee V, 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. 2007; 65(4):876-95. DOI: 10.1111/j.1365-2958.2007.05817.x. View

Smith K, Shanahan C, Moore E, Simon A, Strobel S . Structural basis of differential ligand recognition by two classes of bis-(3'-5')-cyclic dimeric guanosine monophosphate-binding riboswitches. Proc Natl Acad Sci U S A. 2011; 108(19):7757-62. PMC: 3093532. DOI: 10.1073/pnas.1018857108. View

Schirmer T, Jenal U . Structural and mechanistic determinants of c-di-GMP signalling. Nat Rev Microbiol. 2009; 7(10):724-35. DOI: 10.1038/nrmicro2203. View

Horvath M, SCHULTZ S . DNA G-quartets in a 1.86 A resolution structure of an Oxytricha nova telomeric protein-DNA complex. J Mol Biol. 2001; 310(2):367-77. DOI: 10.1006/jmbi.2001.4766. View

Smith K, Lipchock S, Ames T, Wang J, Breaker R, Strobel S . Structural basis of ligand binding by a c-di-GMP riboswitch. Nat Struct Mol Biol. 2009; 16(12):1218-23. PMC: 2850612. DOI: 10.1038/nsmb.1702. View

Brooks T, Kendrick S, Hurley L . Making sense of G-quadruplex and i-motif functions in oncogene promoters. FEBS J. 2010; 277(17):3459-69. PMC: 2971675. DOI: 10.1111/j.1742-4658.2010.07759.x. View

De N, Navarro M, Raghavan R, Sondermann H . Determinants for the activation and autoinhibition of the diguanylate cyclase response regulator WspR. J Mol Biol. 2009; 393(3):619-33. PMC: 2760619. DOI: 10.1016/j.jmb.2009.08.030. View

Qin Y, Hurley L . Structures, folding patterns, and functions of intramolecular DNA G-quadruplexes found in eukaryotic promoter regions. Biochimie. 2008; 90(8):1149-71. PMC: 2585383. DOI: 10.1016/j.biochi.2008.02.020. View

Donaldson G, Roelofs K, Luo Y, Sintim H, Lee V . A rapid assay for affinity and kinetics of molecular interactions with nucleic acids. Nucleic Acids Res. 2012; 40(7):e48. PMC: 3326337. DOI: 10.1093/nar/gkr1299. View

10.

Christen B, Christen M, Paul R, Schmid F, Folcher M, Jenoe P . Allosteric control of cyclic di-GMP signaling. J Biol Chem. 2006; 281(42):32015-24. DOI: 10.1074/jbc.M603589200. View

11.

Romling U, Gomelsky M, Galperin M . C-di-GMP: the dawning of a novel bacterial signalling system. Mol Microbiol. 2005; 57(3):629-39. DOI: 10.1111/j.1365-2958.2005.04697.x. View

12.

Gatto B, Palumbo M, Sissi C . Nucleic acid aptamers based on the G-quadruplex structure: therapeutic and diagnostic potential. Curr Med Chem. 2009; 16(10):1248-65. DOI: 10.2174/092986709787846640. View

13.

Nakayama S, Kelsey I, Wang J, Sintim H . c-di-GMP can form remarkably stable G-quadruplexes at physiological conditions in the presence of some planar intercalators. Chem Commun (Camb). 2011; 47(16):4766-8. DOI: 10.1039/c0cc05432a. View

14.

Cotter P, Stibitz S . c-di-GMP-mediated regulation of virulence and biofilm formation. Curr Opin Microbiol. 2007; 10(1):17-23. DOI: 10.1016/j.mib.2006.12.006. View

15.

Navarro M, De N, Bae N, Wang Q, Sondermann H . Structural analysis of the GGDEF-EAL domain-containing c-di-GMP receptor FimX. Structure. 2009; 17(8):1104-16. PMC: 2747306. DOI: 10.1016/j.str.2009.06.010. View

16.

Amikam D, Galperin M . PilZ domain is part of the bacterial c-di-GMP binding protein. Bioinformatics. 2005; 22(1):3-6. DOI: 10.1093/bioinformatics/bti739. View

17.

Cahoon L, Seifert H . An alternative DNA structure is necessary for pilin antigenic variation in Neisseria gonorrhoeae. Science. 2009; 325(5941):764-7. PMC: 2803317. DOI: 10.1126/science.1175653. View

18.

Fukuda H, Katahira M, Tsuchiya N, Enokizono Y, Sugimura T, Nagao M . Unfolding of quadruplex structure in the G-rich strand of the minisatellite repeat by the binding protein UP1. Proc Natl Acad Sci U S A. 2002; 99(20):12685-90. PMC: 130521. DOI: 10.1073/pnas.152456899. View

19.

Barends T, Hartmann E, Griese J, Beitlich T, Kirienko N, Ryjenkov D . Structure and mechanism of a bacterial light-regulated cyclic nucleotide phosphodiesterase. Nature. 2009; 459(7249):1015-8. DOI: 10.1038/nature07966. View

20.

Paul R, Weiser S, Amiot N, Chan C, Schirmer T, Giese B . Cell cycle-dependent dynamic localization of a bacterial response regulator with a novel di-guanylate cyclase output domain. Genes Dev. 2004; 18(6):715-27. PMC: 387245. DOI: 10.1101/gad.289504. View