Engineering biological systems with synthetic RNA molecules

Abstract

RNA molecules play diverse functional roles in natural biological systems. There has been growing interest in designing synthetic RNA counterparts for programming biological function. The design of synthetic RNA molecules that exhibit diverse activities, including sensing, regulatory, information processing, and scaffolding activities, has highlighted the advantages of RNA as a programmable design substrate. Recent advances in implementing these engineered RNA molecules as key control elements in synthetic genetic networks are highlighting the functional relevance of this class of synthetic elements in programming cellular behaviors.

Figure 1

RNA components used to engineer synthetic control functions can be harvested from natural systems or generated using molecular evolution and computational approaches. These components, encoding sensing, actuation, and information transmission activities, can then be assembled into RNA devices using various molecular engineering strategies to link one or more inputs of interest, such as temperature, RNA, small molecules, or proteins, to desired regulatory activities.

Figure 2

RNA-based controllers have been integrated into engineered biological systems for applications spanning biosynthesis, bioremediation, to health and medicine. A metabolite-responsive ribozyme-based device linked to a fluorescent reporter output was demonstrated in yeast as a noninvasive sensor of metabolite concentration (top panel). A pollutant-responsive RBS-based device linked to a motility gene output was demonstrated in bacteria to program the cells to move along a gradient of the pollutant (middle panel). A disease marker-responsive alternative splicing-based device linked to a suicide gene output was demonstrated in human cells to target cell death to cells exhibiting increased signaling through disease pathways (bottom panel). These examples highlight the power of RNA controllers that enable researchers to access, transmit, and act on information within biological systems.