title: Nuclease-Resistant c-di-AMP Derivatives That Differentially Recognize RNA and Protein Receptors.
abstract: The ability of bacteria to sense environmental cues and adapt is essential for their survival. The use of second-messenger signaling molecules to translate these cues into a physiological response is a common mechanism employed by bacteria. The second messenger 3'-5'-cyclic diadenosine monophosphate (c-di-AMP) has been linked to a diverse set of biological processes involved in maintaining cell viability and homeostasis, as well as pathogenicity. A complex network of both protein and RNA receptors inside the cell activates specific pathways and mediates phenotypic outputs in response to c-di-AMP. Structural analysis of these RNA and protein receptors has revealed the different recognition elements employed by these effectors to bind the same small molecule. Herein, using a series of c-di-AMP analogues, we probed the interactions made with a riboswitch and a phosphodiesterase protein to identify the features important for c-di-AMP binding and recognition. We found that the ydaO riboswitch binds c-di-AMP in two discrete sites with near identical affinity and a Hill coefficient of 1.6. The ydaO riboswitch distinguishes between c-di-AMP and structurally related second messengers by discriminating against an amine at the C2 position more than a carbonyl at the C6 position. We also identified phosphate-modified analogues that bind both the ydaO RNA and GdpP protein with high affinity, whereas symmetrically modified ribose analogues exhibited a substantial decrease in ydaO affinity but retained high affinity for GdpP. These ligand modifications resulted in increased resistance to enzyme-catalyzed hydrolysis by the GdpP enzyme. Together, these data suggest that these c-di-AMP analogues could be useful as chemical tools to specifically target subsections of second-messenger signaling pathways.
authors.forename: Robert E
authors.initials: RE
authors.lastname: Meehan
authors.forename: Chad D
authors.initials: CD
authors.lastname: Torgerson
authors.affiliation: Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey , Piscataway, New Jersey 08854, United States.
authors.forename: Barbara L
authors.initials: BL
authors.lastname: Gaffney
authors.affiliation: Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey , Piscataway, New Jersey 08854, United States.
authors.forename: Roger A
authors.initials: RA
authors.lastname: Jones
authors.forename: Scott A
authors.initials: SA
authors.lastname: Strobel
mesh_terms: D001412:Bacillus subtilis / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism*; D018360:Crystallography, X-Ray; D015226:Dinucleoside Phosphates / Q000737:chemistry* / Q000378:metabolism*; D010727:Phosphoric Diester Hydrolases / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding / Q000502:physiology; D017433:Protein Structure, Secondary; D012329:RNA, Bacterial / Q000737:chemistry* / Q000378:metabolism*; D012260:Ribonucleases / Q000737:chemistry / Q000378:metabolism; D058928:Riboswitch / Q000502:physiology; D015290:Second Messenger Systems / Q000502:physiology
chemical_list: D001426:Bacterial Proteins; D015226:Dinucleoside Phosphates; D012329:RNA, Bacterial; D058928:Riboswitch; C528998:cyclic diadenosine phosphate; D012260:Ribonucleases; D010727:Phosphoric Diester Hydrolases