Remodeling Cells with RNA

A recent issue of Science featured on its cover an image of sheets and tubes made entirely of building blocks of RNA. In the accompanying article, the authors reported successfully building these biological scaffolds using genetically encoded instructions in bacteria, and found that these scaffolds enhance the efficiency of producing hydrogen fuel¹. Hydrogen is an appealing alternative energy source because the sole waste product of its combustion is ordinary water. Producing hydrogen in large quantities efficiently remains a challenge, however. Engineering cells to do it for us is an attractive option.

Being a nucleic acid, we usually think of RNA in terms of its information storage: mRNAs carry the protein-encoding information from genes, and tRNAs act as adapters in synthesizing these proteins. But we've also learned that RNAs can have primitive catalytic functions in nature, which has important implications for the origin of life. More recently, scientists working at the interface between biology and nanotechnology have used the base-pairing properties of nucleic acids to build interesting 2D and 3D shapes, known as DNA origami^2–3. Besides making pretty shapes (smiley faces, maps of the world, etc.), the technology can also be used for building molecular scaffolds to position other objects, such as nanoparticles or proteins³, with atomic precision.

The eukaryotic cell is distinguished from the prokaryotic cell largely by its extensive use of internal membranes. By compartmentalizing its interior, the eukaryotic cell can designate particular 3D spaces for specialized chemical reactions, such as cellular respiration in the mitochondria. This strategy works because enzymes and protein complexes that are involved with the same function are in close physical proximity to one another within the overall cell. In other words, the intermediate product of one enzyme needn't venture far before bumping into the next enzyme in the chain. This same principle makes molecular scaffolds a very attractive engineering pursuit. If two (or more) related, useful proteins are forced into close proximity by being bound to a scaffold, the efficiency of the overall reaction pathway should go way up. Delebecque et al. applied this strategy to improve the efficiency of a hydrogen production system in bacterial cells.

The authors of the paper designed RNA strands that piece together to form (1) a long hollow tube, (2) a flat two-dimensional sheet, or (3) a discrete, unbound unit. For each of the three, the RNAs contained sequences where two particular protein domains can bind. They fused these domains to two proteins that, together, enable the cells to produce hydrogen gas (H₂) from hydrogen ions (H⁺). Since all of this information is genetically encoded, the cells synthesize the RNA scaffold as well as the "chimera" proteins (a fusion of a domain that binds to RNA and a domain that makes H₂). In the strains containing instructions for building a discrete scaffold, H₂ production improved 4-fold. The one-dimensional hollow tube raised production 11-fold, and the 2D sheet a whopping 48-fold.

Clearly, RNA scaffolds have enormous potential for improving the efficiency of biosynthesis operations, whether it is hydrogen fuel, a drug, or something else. An intriguing extension of this idea is to program RNA scaffolds to assemble or disassemble based on environmental cues and internal cellular conditions⁴. Using existing parts within the synthetic biology toolkit, it isn't hard to imagine programming bacteria to assemble particular molecules on demand, choosing from a genetically encoded suite of pathways. By adding an inducer, such as lactose, you could prompt an entire vat of cell-factories to begin synthesizing a molecule of your choice. Incorporating intricate RNA and protein regulatory mechanisms, which we are beginning to make ourselves, would allow for even greater control and tuning of these living chemical factories.

Image Credits: My own sketch (free to reproduce without attribution)

References:

1. Delebecque, C. J. et al. Organization of Intracellular Reactions with Rationally Designed RNA Assemblies. Science 333, 470–474 (2011).

2. Rothemund, P. W. K. Folding DNA to Create Nanoscale Shapes and Patterns. Nature 440, 297–302 (2006).

3. Lin, C., Liu, Y., & Yan, H. Designer DNA Nanoarchitectures. Biochemistry 48, 1663–1674 (2009).

4. Thodey, K. & Smolke, C. D. Bringing It Together with RNA. Science 333, 412–413 (2011).