Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch
Open Access
- 8 November 2009
- journal article
- research article
- Published by Springer Nature in Nature Structural & Molecular Biology
- Vol. 16 (12), 1212-1217
- https://doi.org/10.1038/nsmb.1701
Abstract
C-di-GMP is a bacterial second messenger implicated in processes such as biofilm formation and switches between motile and sedentary lifestyles. The structure of the c-di-GMP–binding GEMM riboswitch is now presented with ligand and the large conformational changes between ligand-bound and unbound forms analyzed by small-angle X-ray scattering. The cyclic diguanylate (bis-(3′-5′)-cyclic dimeric guanosine monophosphate, c-di-GMP) riboswitch is the first known example of a gene-regulatory RNA that binds a second messenger. c-di-GMP is widely used by bacteria to regulate processes ranging from biofilm formation to the expression of virulence genes. The cocrystal structure of the c-di-GMP responsive GEMM riboswitch upstream of the tfoX gene of Vibrio cholerae reveals the second messenger binding the RNA at a three-helix junction. The two-fold symmetric second messenger is recognized asymmetrically by the monomeric riboswitch using canonical and noncanonical base-pairing as well as intercalation. These interactions explain how the RNA discriminates against cyclic diadenylate (c-di-AMP), a putative bacterial second messenger. Small-angle X-ray scattering and biochemical analyses indicate that the RNA undergoes compaction and large-scale structural rearrangement in response to ligand binding, consistent with organization of the core three-helix junction of the riboswitch concomitant with binding of c-di-GMP.Keywords
This publication has 57 references indexed in Scilit:
- Adaptive Ligand Binding by the Purine Riboswitch in the Recognition of Guanine and Adenine AnalogsStructure, 2009
- The long and the short of riboswitchesCurrent Opinion in Structural Biology, 2009
- Cocrystal structure of a class I preQ1 riboswitch reveals a pseudoknot recognizing an essential hypermodified nucleobaseNature Structural & Molecular Biology, 2009
- Structural Basis for Specific, High-Affinity Tetracycline Binding by an In Vitro Evolved Aptamer and Artificial RiboswitchChemistry & Biology, 2008
- Crystal Structure of the Lysine Riboswitch Regulatory mRNA ElementJournal of Biological Chemistry, 2008
- Ligand recognition determinants of guanine riboswitchesNucleic Acids Research, 2007
- Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipelineNucleic Acids Research, 2007
- Structural Transitions and Thermodynamics of a Glycine-Dependent Riboswitch from Vibrio choleraeJournal of Molecular Biology, 2007
- UCSF Chimera—A visualization system for exploratory research and analysisJournal of Computational Chemistry, 2004
- [20] Processing of X-ray diffraction data collected in oscillation modeMethods in Enzymology, 1997