Aptamers, Riboswitches, and Ribozymes in S. cerevisiae Synthetic Biology

Abstract

Among noncoding RNA sequences, riboswitches and ribozymes have attracted the attention of the synthetic biology community as circuit components for translation regulation. When fused to aptamer sequences, ribozymes and riboswitches are enabled to interact with chemicals. Therefore, protein synthesis can be controlled at the mRNA level without the need for transcription factors. Potentially, the use of chemical-responsive ribozymes/riboswitches would drastically simplify the design of genetic circuits. In this review, we describe synthetic RNA structures that have been used so far in the yeast Saccharomyces cerevisiae. We present their interaction mode with different chemicals (e.g., theophylline and antibiotics) or proteins (such as the RNase III) and their recent employment into clustered regularly interspaced short palindromic repeats–CRISPR-associated protein 9 (CRISPR-Cas) systems. Particular attention is paid, throughout the whole paper, to their usage and performance into synthetic gene circuits.

Synthetic Genetic Elements, Devices, and Systems

“…Aptamers interact with specific molecules, and riboswitches and ribozymes can be fused with aptamers to express their functions in a conditional manner. Ge and Marchisio present a comprehensive review of the aptamers, riboswitches, and ribozymes used in yeast synthetic biology [ 2 ].…”

In vivo, in vitro and in silico: an open space for the development of microbe‐based applications of synthetic biology

“…A most important sequel of Spiegelman’s early experiment has been the systematic evolution of ligands by exponential enrichment (SELEX) procedure devised by Larry Gold and his colleagues (Tuerk et al ., 1992). After the discovery of ribozymes, it was clear that RNA molecules could fold into complex structures able to bind foreign molecules [aptamers, riboswitches and ribozymes (Ge and Marchisio, 2021)]. This prompted exploration of novel RNA‐based activities, substrate‐dependent ribozymes in particular.…”

Integration of an Expression Platform in the SELEX Cycle to Select DNA Aptamer Binding to a Disease Biomarker

“…Since the invention of SELEX, many aptamers have been discovered and applied in various research fields, including biosensors, 4 − 7 gene-expression regulators, 8 − 11 and therapeutic reagents. 12 Two well-known aptamers that are applied as biosensors and gene-expression regulators are the theophylline aptamer and the VEGF aptamer.…”

“…Since the invention of SELEX, many aptamers have been discovered and applied in various research fields, including biosensors, − gene-expression regulators, − and therapeutic reagents . Two well-known aptamers that are applied as biosensors and gene-expression regulators are the theophylline aptamer and the VEGF aptamer. , Theophylline is a natural drug used to treat asthma, bronchitis, and emphysema; however, serum levels must be monitored carefully to avoid serious toxicity .…”