Cotranscriptional folding of single riboswitches

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 DESCRIPTION (provided by applicant): The ultimate goal of this proposal is to unravel the coupling between RNA transcription and folding. It is well known that nascent RNA secondary structure can have a significant impact on transcription, as exemplified by the hairpin that acts as a key component of intrinsic terminators. Furthermore, the time-ordered, directional RNA synthesis that occurs during transcription often yields RNA folds other than the most thermodynamically stable structure of the full-length transcript. This coupling between transcription and functional RNA folding is merely one example in an emerging field that seeks to understand the relationship between gene expression and RNA structure. In an elegant example of this relationship, bacterial riboswitches contain non-coding RNA "aptamers" whose secondary and tertiary structures re-fold in response to binding of a small metabolite, leading to a change in expression of the downstream gene through effects on transcription termination or translation initiation. Riboswitches are a key mechanism of gene regulation in bacteria where, in some species, they are responsible for the regulation of up to 4% of all genes, rendering them excellent model systems with potential for real-world impact as drug targets. The study of riboswitches has so far been divided into two separate areas of inquiry: the structural and biophysical studies of isolated aptamer domains, and in vivo studies of gene regulation using riboswitches incorporated into reporter constructs. While this has led to extensive knowledge of the mechanisms by which aptamers sense their ligands and the discovery of many new regulatory RNA sequences, precious little is still known about riboswitch behavior in the context of the macromolecular complexes that they regulate. We will fill this gap through study of a favorably small riboswitch that regulates the efficiency of transcription termination in response t 7-aminomethyl-7-deazaguanine (preQ1) binding. To do so, we will leverage a unique combination of biophysical and biochemical tools to study the riboswitch in active transcription complexes. We will perform single molecule fluorescence resonance energy transfer (smFRET) measurements on paused transcription complexes consisting of a DNA bubble and a fluorophore-labeled nascent riboswitch transcript bound to RNA polymerase, determining the effects of downstream RNA sequence and polymerase on aptamer structure and dynamics (Specific Aim 1). We will use a technique we recently developed termed Single Molecule Kinetic Analysis of RNA Transient Structure (SiM-KARTS) to probe the relative formation of terminator and antiterminator hairpins in the expression platforms of pre-synthesized as well as actively transcribed RNA, determining the role of co-transcriptional folding in riboswitch function (Specific Aim 2). Finally, we will combine in vitro transcription assays and smFRET to study the termination effects of transcription factors NusA and RfaH, which have been shown to affect nascent RNA structure formation (Specific Aim 3). In addition to advancing our understanding of riboswitches, these studies have the potential to transform our understanding of RNA structure formation in general, and of how RNA structure is coupled to the function of macromolecular machines.