Artificial cells - what are they and why would we want to make them?
The challenge of creating artificial life is one of the great challenges that scientists are currently grappling with. It’s also one my favourite examples of where popular culture really misrepresents how scientists think. What images does the idea of “creating life in the lab“ evoke to most of you? Probably some amusing images of Dr Frankenstein hoisting up the lightning rod in his spooky lab. But for most of us the motivation is more subtle and a great deal less dramatic. Put simply, the science of living organism is a bloody complex business and we would be much better at understanding it we could study a simplified version of it that we would could control and measure under simple conditions. If that last sentence seems a bit vague, I’ve made it so intentionally because scientists from different fields have different vision of what they want to achieve through creating artificial life. This makes it a great example for understanding how modern collaborative science works. And for that reason this blog post will be a collaborative effort with a friend and fellow-scientist Dr. Anders Aufderhorst-Roberts. Both of us have similar backgrounds, I trained as an engineer, Anders as a physicist. But we also have a lot in common, in fact we’ve worked in the same labs, albeit at different times. And yet when we first got down to discussing the subject over coffee in an Amsterdam cafe a few months back we discovered we have very different preconceptions and different scientific goals when it comes to artificial life.
My interests are in understanding individual proteins, the underlying machinery of life and to be able to determine how they fold themselves. What particularly interests me is how very small subtle changes in protein chemistry and arrangements can lead to much larger implications on a living systems level. For example, how the modification of a single amino acid in a long protein chain can completely 'switch off' a protein and prevent it from functioning in a cell. By contrast Anders’ research involves taking apart cells and examining, in isolation, the polymers that give cells their integrity and structure (so-called cytoskeletal filaments). Both of these approaches are often the termed the “the bottom up” approach because they start with very simple components of life and allow us to work up to more up to more complex systems. Ultimately we want to be able to build these single components into more complex machinery step-by-step and eventually reach the level of complexity of a single cell. Single cells are significant in that they are the smallest and most simple units that can themselves be considered alive.
The flip side of this is the ‘top-down’ approach, where existing living cells have components removed until they have the lowest complexity possible but still have all of the functions needed to stay alive and reproduce. A beautiful example of the top-down approach is the research led by Craig Venter (see for example [1] and [2]). In order to gain an understanding of the function of every gene in a living cell, they produced a microbe called Syn 3.0 which has the smallest genome and the fewest genes of any living organism (just 473 of them, compared to around 5,000 in E. coli and 20,000 in humans). What’s really interesting about this is that with all of the current available biological knowledge, the team were unable to design a minimal genome from scratch - instead, they had to start with an already functioning one and remove genes until they were down to the lowest number that still enabled the organism to survive and reproduce. This means that we still have some way to go before we are able to design functioning genomes ourselves, but what we can learn from the Syn 3.0 project and similar endeavours is certainly accelerating progress in this direction.
At first glance the top-down approach would seem a more exciting route to take than the bottom-up approach, and indeed we can see it already has results. Researchers like us take a different view, and would claim that the scientific rewards of the bottom-up approach are likely to be much richer. For one, building artificial life from the bottom will give us a finer degree of control over artificial biological processes and with it a better understanding of how the cell controls itself. The caveat of course is that it takes longer as multiple and increasingly more difficult steps need to be taken. Most researchers generally agree that the first of these steps is to isolate the building blocks we use by placing them inside container. The most obvious choice is something that resembles the cell membrane, which is composed of fat molecules (lipids), proteins and carbohydrates. When these membrane containers are constructed as spheres and have similar dimensions to living cells we call them vesicles, and they are simply droplets (often of water) surrounded by a thin, evenly distributed layer of lipids. Think of a soap bubble with water inside, but much, much smaller. At this point we’ll take the opportunity to shamelessly plug Anders’ recent article that reviews how vesicles can best be made and the tools that can be used to studying them [3].
Having made our container and selected the components we want to put inside, the next step is working out how we can tweak it to behave like a real cell. This is where there have seen phenomenal results in recent years. Just under a year ago, a technique was demonstrated for getting DNA to self-replicate inside a vesicle container and subsequently undergo gene expression, the first step towards the manufacture of proteins outside of cell [4] This process, known as, so called-cell-free synthesis, has also been demonstrated [5], as has the ability to engineer additional compartments inside vesicles to separate different biological process from each other [6] and the ability to transfer of energy and materials between such compartments [7]. More complex processes such as artificial cell division and movement are also beginning to be possible to engineer. If you haven’t already deduced it, the really exciting science will come about when all of these techniques and processes are combined together into one unit.
Combining these advances will of course not be without its challenges, but the proof of principle exists, which means that the next challenges will be focussed on careful optimisation and fine-tuning. This will require researchers from numerous different backgrounds to work together towards a common goal. There’s also the question of what to do with artificial life once we achieve it. The potential questions from this are as numerous as the contributions needed to reach this stage. While an engineer might be interested in how proteins in the cell respond to applied forces, the physicist might be more interested in the mechanism that causes cells to divide, while a biologist may focus on gene expression or a chemist may wish to understand the control of chemical reactions. The new insights to be gained are exciting indeed!
Image Credit - Philip Bleicher
[1] https://www.sciencemag.org/news/2016/03/synthetic-microbe-lives-fewer-500-genes
[2] http://science.sciencemag.org/content/351/6280/aad6253
[3] http://iopscience.iop.org/article/10.1088/1478-3975/aab923/pdf
[4] van Nies, P., Westerlaken, I., Blanken, D., Salas, M., Mencía, M., & Danelon, C. (2018). Self-replication of DNA by its encoded proteins in liposome-based synthetic cells. Nature communications, 9(1), 1583.
[5] Shimizu, Y., Inoue, A., Tomari, Y., Suzuki, T., Yokogawa, T., Nishikawa, K., & Ueda, T. (2001). Cell-free translation reconstituted with purified components. Nature biotechnology, 19(8), 751.
[6] Sole, R. V. (2009). Evolution and self-assembly of protocells. The international journal of biochemistry & cell biology, 41(2), 274-284.
[7] Yadav, V. G., De Mey, M., Lim, C. G., Ajikumar, P. K., & Stephanopoulos, G. (2012). The future of metabolic engineering and synthetic biology: towards a systematic practice. Metabolic engineering, 14(3), 233-241.