Using in-vivo RNA scaffolds for metabolic substrate channeling towards high value chemicals

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Gairik Sachdeva, Simon Alexander Thomas Kretschmer, Jeff Way, Pamela Silver

Harvard University, United States

While the biosphere is replete with solar energy, the primary challenge is to channel it into molecules usable with current infrastructure, such as liquid fuels and polymers. In addition to traditional genetic engineering techniques, “coercing” cells to produce chemicals of interest requires ability to manipulate naturally evolved regulation and development of tools to enable directed control. Compartmentalization is a powerful strategy for metabolic control used widely in eukaryotes. Our work shows that carefully designed RNA strands expressed genetically can be used as intracellular scaffolds for metabolic enzymes, enhancing pathway fluxes in E coli and Cyanobacteria. These RNA are in-vivo assembled by base-pair interactions and are designed to form precise structures that offer multiple binding sites to specific enzymes. By spatially insulating metabolic reaction centers, the scaffolds can mimic organellar compartmentalization. We are implementing three different kinds of pathways involving alkane fuel synthesis, succinic acid synthesis and carbon dioxide fixation by RubsiCo. This poster presents the various synthetic parts built, the chasses developed, the mechanism and characterization of increase in pathway flux by various scaffold designs. This is also the first example for use of scaffolds to channel metabolic pathway fluxes in cyanobacteria. We believe that this research sets the stage for a creative merger of the nucleic acid nanotechnology field with that of metabolic engineering.