Identification of ligand analogues that control c-di-GMP riboswitches.
Riboswitches for the bacterial second messenger c-di-GMP control the expression of genes involved in numerous cellular processes such as virulence, competence, biofilm formation, and flagella synthesis. Therefore, the two known c-di-GMP riboswitch classes represent promising targets for developing novel modulators of bacterial physiology. Here, we examine the binding characteristics of circular and linear c-di-GMP analogues for representatives of both class I and II c-di-GMP riboswitches derived from the pathogenic bacterium Vibrio choleae (class I) and Clostridium difficile (class II). Some compounds exhibit values for apparent dissociation constant (K(D)) below 1 μM and associate with riboswitch RNAs during transcription with a speed that is sufficient to influence riboswitch function. These findings are consistent with the published structural models for these riboswitches and suggest that large modifications at various positions on the ligand can be made to create novel compounds that target c-di-GMP riboswitches. Moreover, we demonstrate the potential of an engineered allosteric ribozyme for the rapid screening of chemical libraries for compounds that bind c-di-GMP riboswitches.
Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA.
Kazuhiro
K
Furukawa
Hongzhou
H
Gu
Narasimhan
N
Sudarsan
Yoshihiro
Y
Hayakawa
Mamoru
M
Hyodo
Ronald R
RR
Breaker
D000495:Allosteric Site; D000890:Anti-Infective Agents / Q000494:pharmacology; D018407:Bacterial Physiological Phenomena; D001665:Binding Sites; D016360:Clostridioides difficile / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D006152:Cyclic GMP / Q000031:analogs & derivatives* / Q000737:chemistry; D007700:Kinetics; D008024:Ligands; D008956:Models, Chemical; D012266:Ribose / Q000737:chemistry*; D015290:Second Messenger Systems; D014158:Transcription, Genetic; D014734:Vibrio cholerae / Q000378:metabolism
D000890:Anti-Infective Agents; D008024:Ligands; C062025:bis(3',5')-cyclic diguanylic acid; D012266:Ribose; D006152:Cyclic GMP