Transcriptional Riboswitches Integrate Timescales for Bacterial Gene Expression Control

Abstract

Transcriptional riboswitches involve RNA aptamers that are typically found in the 5′ untranslated regions (UTRs) of bacterial mRNAs and form alternative secondary structures upon binding to cognate ligands. Alteration of the riboswitch's secondary structure results in perturbations of an adjacent expression platform that controls transcription elongation and termination, thus turning downstream gene expression “on” or “off.” Riboswitch ligands are typically small metabolites, divalent cations, anions, signaling molecules, or other RNAs, and can be part of larger signaling cascades. The interconnectedness of ligand binding, RNA folding, RNA transcription, and gene expression empowers riboswitches to integrate cellular processes and environmental conditions across multiple timescales. For a successful response to an environmental cue that may determine a bacterium's chance of survival, a coordinated coupling of timescales from microseconds to minutes must be achieved. This review focuses on recent advances in our understanding of how riboswitches affect such critical gene expression control across time.

Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch

“…While studies have extensively characterized the structures of riboswitch ADs (22)(23)(24)(25)(26), current research is only just beginning to understand how structural features induced by ligand binding in the AD can alter the EP structure and determine gene expression outcomes during transcription (27)(28)(29)(30)(31)(32)(33). Extensive progress has come from the study of transcriptional 'ON' riboswitches that contain an overlap in sequence between the AD and EP that lends to mutually exclusive folds of these two domains.…”

Riboswitches for Controlled Expression of Therapeutic Transgenes Delivered by Adeno-Associated Viral Vectors

“…Many bacterial riboswitches operate at the transcriptional level, but differences in transcription mechanisms and greater compartmentalization of transcription and translation present unique challenges in eukaryotic systems [64]. Common bacterial riboswitch mechanisms such as rho-independent termination are ineffective in eukaryotes, although components of bacterial riboswitches have been adapted for use in mammalian cells [65].…”

The Role of RNA Secondary Structure in Regulation of Gene Expression in Bacteria

“…The conformational transition allows the changes in the conformation of RNA between the energy minima of the free energy landscape. The conformational transition occurs when the free energy landscape is disrupted by cellular changes, e.g., the change in metabolite concentration [14,27] or the temperature [28]. Such cellular cues provide the free energy shift necessary to unfold the RNA region and overcome the energy barrier.…”

“…The strategy for ligand binding and modification of the expression platform will depend on the concentration of the target metabolite in the cell. In their recent work [27], Scull et al described two models of the ligand binding: a conformation selection and an induced fit (Figure 1C). The conformation selection mechanism occurs when the ligand binding is preceded by a change in the aptamer conformation between the two states or into an intermediate form.…”

“…However, in the absence of F-, the short-living intermediate conformation with an accessible ion binding site can be observed (so-called "excited state"). The binding of the F-, in a narrow concentration range, stabilizes this structure and triggers the conformational changes in the expression platform [27]. An example of an induced fit mechanism is a guanine sensing riboswitch in which the conformational changes in three-way junctions appear with the ligand binding in the center of this junction [43].…”