Sensing intracellular signatures with synthetic mRNAs

Abstract

The bottom-up assembly of biological components in synthetic biology has contributed to a better understanding of natural phenomena and the development of new technologies for practical applications. Over the past few decades, basic RNA research has unveiled the regulatory roles of RNAs underlying gene regulatory networks; while advances in RNA biology, in turn, have highlighted the potential of a wide variety of RNA elements as building blocks to construct artificial systems. In particular, synthetic mRNA-based translational regulators, which respond to signals in cells and regulate the production of encoded output proteins, are gaining attention with the recent rise of mRNA therapeutics. In this Review, we discuss recent progress in RNA synthetic biology, mainly focusing on emerging technologies for sensing intracellular protein and RNA molecules and controlling translation.

Synthetic RNA biology

“…In this special focus, different strategies for RNA-based regulatory systems will be discussed. They use RNA binding proteins (RBPs) [ 1 ] and small molecules [ 2 , 3 ] as triggers, or RNA molecules expressed in the cell that affect a target RNA by base pairing [ 4–6 ]. Thereby multiple mechanisms can be used to regulate gene expression, ranging from the control of translation and splicing to the precise control of mRNA stability [ 1–6 ].…”

“…RNA-RBP pairs can be used to create regulatory systems and are derived either from natural counterparts or from RNA partners newly generated by an in vitro selection process called SELEX. However, the number of available RNA partners is still limited, which currently inhibits multiplexing [ 1 ]. One way of solving this problem is by redesigning existing RNA-RBPs.…”

“…Variations in protein expression underlie cellular states and identities. Therefore, sensors that detect proteins and generate measurable outputs are indispensable tools for cellular engineering applications [ 1 ].…”

Advancing in vivo reprogramming with synthetic biology

“…RNA is single-stranded and has the unique ability to base-pair with itself to form complex structures that enable the engineering of RNA-based tools to function by coupling the binding of a target molecule to alter its shape and facilitate translation [ 45 , 46 ]. This approach has been used to regulate the translation of mRNAs based on the presence or absence of RNA–protein interactions within the cytoplasm [ 47 – 52 ].…”