The Cell Built from Scratch That Will Change How Biology Is Engineered

No living cell is fully understood. In E. coli, the organism biologists have studied the most, roughly 1/3rd of its genes still have no experimental evidence of what they do [1]. The most minimal cell ever built, the JCVI minimal cell, has about 90 of its 452 protein-coding genes with no known function [2]. The known genes are only half the story, because how they are regulated is also largely uncharted. In E. coli, as little as 10 to 30% of the regulation controlling E. coli gene expression is mapped.[3]

This black box nature makes biology hard to engineer. While powerful, biology often cannot be reliably re-engineered and scaled with the confidence engineers in other fields take for granted. Kate Adamala, a synthetic biologist at the University of Minnesota, has dedicated her career to a different approach, building cells from the bottom up out of fully defined parts. Her latest work discloses SpudCell, a minimal synthetic cell that can express proteins, grow, divide, and undergo Darwinian selection. Together with synthetic biology pioneer Drew Endy, Jan Jedryszek, and Chris Raggio, she has launched a nonprofit named Biotic to standardize this new chassis and build on it. We sat down with Kate to talk about the work and what it means for engineering biology.

SpudCell is simpler than any living cell in nature, and the team does not claim it is alive. They call it constructed rather than created. Without steady feeding and tightly controlled lab conditions, it runs out of resources and stops. Every component, though, is known and placed on purpose, so any one of them can be changed at a time.

The 90-kilobase genome, spread across seven DNA molecules, sits inside a lipid membrane. To express the DNA, the team uses the PURE system, a defined mixture of 36 purified proteins that can run transcription and translation outside a living cell. The genome is replicated by the phage enzyme Phi29 DNA polymerase.

SpudCell differs from the infamous JCVI minimal cell, which was made at the J. Craig Venter Institute by deleting as many genes as possible from Mycoplasma mycoides without killing it. Where the JCVI minimal cell was built top down from something already alive, SpudCell was built from the bottom up from parts that are fully specified and understood.

The team started by encapsulating PURE inside liposomes, then worked out how to feed them. SpudCells grow by fusing with small feeder liposomes that resupply fresh PURE, containing ribosomes, enzymes, and small molecules, along with lipids for the membrane. The feeders carry no DNA of their own. Fusion is made possible by an alpha-hemolysin membrane protein with a polyhistidine tag encoded in the SpudCell genome. The tag sits on the cell surface and binds to nickel atoms held by lipids on the feeder cell membrane, pulling the two liposomes together until they merge. Because the genome controls how much alpha-hemolysin the cell makes, it sets whether the cell feeds, how fast it grows, and how large it gets.

More surprising is that SpudCell divides without a cytoskeleton. The same His-tagged alpha-hemolysin anchors a linker and the protein streptavidin to the outside of the membrane. That load crowds the surface until mechanical stress buds off a piece of the cell. Cells that make more alpha-hemolysin build up more crowding and divide more readily, so division too is encoded in the genome.

This sets the ground for Darwinian selection. The researchers introduced a mutation that increases the production of alpha-hemolysin, then made the mutated and standard SpudCells compete in an environment with fewer feeders. Cells carrying the mutation fed faster, grew faster, and produced more offspring, outcompeting the standard version within five generations. 

It is an early prototype, and it still has a way to go to become a fully autonomous synthetic cell. The system relies on feeder liposomes and streptavidin supplied from outside. Without a cytoskeleton to organize the DNA, the seven DNA molecules do not yet pass reliably to every daughter, and after five generations only about a third of offspring carry the full set. The E. coli ribosomes it borrows degrade after five to ten generations, and SpudCell cannot yet make its own.

Sharing methods and data is a barrier that runs deeper than any single technical advance. Individual labs can solve technical problems, but academia provides little incentive to make interoperable and standardized solutions. What works in one lab in Minnesota has trouble transferring cleanly to another lab, and groups keep rebuilding the same translation systems, membranes, and energy modules in incompatible ways, so progress does not add up. Closing that gap is the reason for Biotic, a public-benefit institution launching alongside the work, co-founded by Adamala, Drew Endy, Jan Jedryszek, and Chris Raggio to build shared infrastructure for synthetic cell engineering and keep it open.

SpudCell provides the field with a common chassis. It is still weaker than a natural cell, but it is fully defined. Any group can improve one module at a time, and Biotic will help ensure the improvements are easy to share with the community. Biotic rests on the idea that shared foundations, released in the open, tend to compound across a whole field, as they did for the Human Genome Project, the early internet, and the Protein Data Bank.

The work is being released as a preprint, shared early so other labs can test and replicate it, with protocols and sequences posted at biotic.org/research/spudcell/. Researchers who want to build on it can find the wider effort through Build-a-Cell, the open community Adamala helped start.

The longer goal is a biology that can be engineered the way computers are. A computer chip is built from defined parts, stacked into layers of abstraction that each hide the complexity beneath them, so a new designer can easily contribute at any layer. Cells offer nothing like that today, because their genomes are highly evolved and only partly understood. A fully defined synthetic cell changes this. If every component is known and every change can be measured, biology can be built up in the same modular layers, one interoperable part at a time. SpudCell is a rough first version of such a part, and Biotic aims to turn it into a foundation the whole field can stand on.

References

1. Ghatak S, King ZA, Sastry A, Palsson BO. The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function. Nucleic Acids Research. 2019;47(5):2446-2454. https://doi.org/10.1093/nar/gkz030

2. Breuer M, Earnest TM, Merryman C, et al. Essential metabolism for a minimal cell. eLife. 2019;8:e36842. https://doi.org/10.7554/eLife.36842

3. Santos-Zavaleta A, Salgado H, Gama-Castro S, et al. RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12. Nucleic Acids Research. 2019;47(D1):D212-D220. https://doi.org/10.1093/nar/gky1077