Book of Abstracts: Albany 2007
June 19-23 2007
Transcription and Translation Regulating Riboswitches. Structure of the Guanine Sensing Riboswitch in its Guanine-Free and -Bound Forms and Comparison with the SAM Riboswitch Type II
Riboswitches are regulatory mRNA elements that influence the expression -via transcription or translation - of certain genes by binding to specific ligands. They have been found in bacteria, plants and fungi and are located within the 5?-untranslated mRNA region. For their function they require no protein assistance. Riboswitches generally consist of two domains: a ligand-binding aptamer domain, and a so-called expression platform. Binding of the specific ligand molecule to the aptamer domain causes a structural rearrangement in the expression platform leading to modulation of transcription or translation. The SAM Riboswitch type II, regulates translation by binding SAM to the aptamer causing a structural rearrangement in the expression platform that masks the Shine-Dalgarno sequence thereby halting translation. The guanine riboswitch regulates transcription by binding guanine or hypoxanthine to the aptamer causing the expression platform to fold into a stable hairpin, which signals the RNA polymerase to stop the transcription. Solution-state structural information on the aptamers of the SAM Riboswitch and G-riboswitch will be presented.
For the G-riboswitch aptamer solution-state structural information is presented in both guanine-free and guanine-bound states. Crystal structures of aptamer in the guanine/hypoxanthine-bound states show that it folds into a three-way junction. Two of the three stems form a pseudoknot interaction and the ligand binds inside the junction. NMR chemical shift and RDC analyses show that in this ligand-bound state the solution structure of the aptamer closely resembles the crystal structure. The NMR data also show that in its ligand-free state the global structure of the RNA is highly similar to that in the ligand-bound state. For instance, the pseudoknot interaction between the two stems is already present. Also, the binding pocket is already partly ordered. However, the lower part of the binding pocket, which includes the upper part of the lower stem, as well as a 5-residue loop that closes off the binding pocket, is largely disordered. Thus, the ligand binds via an induced-fit mechanism, where a previously unstructured 5-residue loop folds over the ligand, thereby almost fully enclosing it and stabilizing the upper part of the lower stem. This stabilization of the lower stem is expected to promote the formation of the transcription-termination signal in the expression platform, thereby stopping the gene transcription. The structural information on the G-riboswitch will be compared with the structural data on the SAM Riboswitch.