Emerging applications of riboswitches – from antibacterial targets to molecular tools

Abstract

The ability to precisely regulate gene expression is one of the most important features of the living cells as it enables the adaptation and survival in different environmental conditions. The majority of regulatory mechanisms involve protein action, however, multiple genes are controlled by nucleic acids. Among RNA-based regulators, the riboswitches present a large group of specific domains within messenger RNAs able to respond to small metabolites, tRNA, secondary messengers, ions, vitamins or amino acids. A simple, accurate, and efficient mechanism of action as well as easiness in handling and engineering make the riboswitches a potent practical tool in industry, medicine, pharmacy or environmental protection. Hereby, we summarize the current achievements and challenges in designing and practical employment of the riboswitch-based tools.

Discovery of Small‐Molecule Antibiotics against a Unique tRNA‐Mediated Regulation of Transcription in Gram‐Positive Bacteria

“…Riboswitches are ideal targets because analogues of small‐molecule metabolites can be used to disrupt normal riboswitch regulation of the gene expression. Riboswitch inhibitors have been found . While inhibitors of metabolic riboswitches are promising sites for the design of new antibiotics, they are still prone to induce bacterial resistance because the drug binds to a single target molecule that could readily be mutated to decrease drug efficacy.…”

“…Riboswitch inhibitors have been found. [58][59][60] While inhibitors of metabolic riboswitches are promisings ites for the designo fn ew antibiotics, they are still prone to induce bacterial resistance because the drug binds to as ingle target molecule that could readily be mutated to decrease drug efficacy.I nc ontrast, T-box riboswitches are redundantly used to regulate multiple essential operons within asinglec ell.…”

Crowding Shifts the FMN Recognition Mechanism of Riboswitch Aptamer from Conformational Selection to Induced Fit

“…[2,3] Bacteria sense the decrease in Mg 2+ levels to achieve temporal and spatial expression of virulence genes. [5] Affinities of riboswitches for their anionic ligands such as thiamine pyrophosphate, [8] glucosamine-6-phosphate, [9] and flavin mono nucleotide (FMN) [10] are decreased by up to 1000-fold upon disruption of the Mg 2+ -mediated interactions.S ince metabolite-sensing riboswitches are promising antibacterial drug targets, [11] understanding how riboswitchligand interactions respond to Mg 2+ concentration fluctuations is crucial for development of antibacterial drugs.Most structural and ligand binding studies of riboswitches have been performed in dilute solutions [12] that substantially differ from the intracellular environment in which riboswitches function. [5] Thus,t he fluctuation of intracellular Mg 2+ concentration during bacterial pathogenesis will have significant impacts on regulatory RNAc onformations and functions.Indeed, Mg 2+ -sensing riboswitches modulate expression of genes responsible for magnesium transport across the membrane as well as of genes involved in virulence.…”

“…[5] Thus,t he fluctuation of intracellular Mg 2+ concentration during bacterial pathogenesis will have significant impacts on regulatory RNAc onformations and functions.Indeed, Mg 2+ -sensing riboswitches modulate expression of genes responsible for magnesium transport across the membrane as well as of genes involved in virulence. [5] Affinities of riboswitches for their anionic ligands such as thiamine pyrophosphate, [8] glucosamine-6-phosphate, [9] and flavin mono nucleotide (FMN) [10] are decreased by up to 1000-fold upon disruption of the Mg 2+ -mediated interactions.S ince metabolite-sensing riboswitches are promising antibacterial drug targets, [11] understanding how riboswitchligand interactions respond to Mg 2+ concentration fluctuations is crucial for development of antibacterial drugs. Metabolite-sensing riboswitches depend on Mg 2+ to stabilize tertiary structures indispensable for function.…”

Systematic optimization of L‐tryptophan riboswitches for efficient monitoring of the metabolite in Escherichia coli

“…Potential of the riboswitches as in vivo metabolite sensors has been highlighted because monitoring of metabolite concentration can help various applications and RNA aptamers could be created for almost every molecule in principle (Machtel, Bąkowska-Żywicka, & Żywicki, 2016). To maximize the performance of the riboswitches as metabolite sensors, several requirements should be addressed, which could be described using a dose-response curve (Figure 1a) (Link & Breaker, 2009).…”