Creating a simplified form of life

It is one of the most fundamental questions in science: how can lifeless molecules come together to form a living cell? Bert Poolman, Professor of Biochemistry at the University of Groningen, has been working on this problem for over twenty years. He aims to understand life by trying to reconstruct it; he is building simplified artificial versions of biological systems that can be used as components for a synthetic cell. Poolman recently published two papers in Nature Nanotechnology and Nature Communications. In the first paper, he describes a system for energy conversion and cross-feeding of products of this reaction between synthetic cells, while he describes a system for concentrating and converting nutrients in cells in the second paper.

Six Dutch research institutes are collaborating in the consortium BaSyc (Building a Synthetic Cell) to build the elements needed for a synthetic cell. Poolman’s group has been working on energy conversion. The real-life equivalents he aims to replicate are mitochondria, the ‘energy factories’ of the cell. These use the molecule ADP to produce ATP, which is the standard ‘fuel’ that cells require to function. When ATP is converted back into ADP, the energy is released and used to drive other processes.

Artificial energy factories

‘Instead of the hundreds of components of mitochondria, our system for energy conversion uses just five,’ says Poolman. ‘We set out to simplify it as much as possible.’ This may sound odd, as evolution has done a great job of producing functional systems. ‘However, evolution is a one-way street, it builds on existing components and this often makes the outcome very complex,’ explains Poolman. An artificial replica, on the other hand, can be designed with a specific outcome in mind.

The five components were placed inside vesicles, tiny cell-like sacs, that can absorb ADP as well as the amino acid arginine from the surrounding fluid. The arginine is ‘burned’ (deaminated) and thus provides the energy to produce ATP, which is secreted from the vesicle. ‘Of course, the simplification comes at a price: we can only use arginine as the energy source, while cells use all kinds of different molecules, such as amino acids, fats, and sugars.’

Next, the Poolman group designed a second vesicle that is able to absorb the secreted ATP and use it to drive an energy-consuming reaction. The energy is provided by turning ATP back into ADP, which is then secreted and can be absorbed by the first vesicle, closing the loop. Such a cycle of ATP production and use is the foundation of metabolism in every living cell and drives the ‘machinery’ for energy-consuming reactions such as growth, cell division, protein synthesis, DNA replication, and more.

An artificial pumping system

The second module that Poolman created was a bit different: a vesicle in which a chemical process causes the interior to build up a negative charge and, in doing so, form an electrical potential, similar to that of an electronic circuit. The electrical potential is used to couple charge movement to the accumulation of nutrients inside the vesicle, which is carried out by transporters. These proteins in the membrane of the vesicle work a bit like a water wheel: positively charged protons ‘flow’ through it from outside the vesicle to the negatively charged interior. This flow drives the transporter, which in this case imports a sugar molecule, lactose. Again, this is a very common process in living cells, requiring many components that Poolman and his team mimicked with just two components.

When he submitted a paper describing this system, a reviewer asked if he couldn’t do something with the lactose that is being transported, as cells use nutrients like this to produce useful building blocks. Poolman took up the challenge and added three more enzymes to the system, which oxidized the sugar and enabled production of the coenzyme NADH. ‘This helper molecule plays an essential role in the proper functioning of all cells,’ explains Poolman. ‘And by adding NADH production, we have shown that it is feasible to expand the system.’

But what about the synthetic cell?

Having a simplified synthetic equivalent of two key features of life is fascinating, but many more steps need to be integrated to form an autonomously growing and dividing synthetic cell. ‘The next step we want to take is adding our metabolic energy producing systems to a synthetic cell division system created by colleagues,’ says Poolman.

The BaSyc programme is entering its final years; funding for a new programme has recently been secured. A large consortium of Dutch groups, in which Poolman is one of the leading scientists, received 40 million euros to create life from non-living modules. This EVOLF project is set to run for another ten years and aims to find out how many more lifeless modules can come together and create living cells. ‘Ultimately, this would give us a blueprint for life, something that is currently lacking in biology,’ concludes Poolman. ‘This may eventually have all kinds of applications, but will also help us to better understand what life is.’

References:
Miyer F. Patiño-Ruiz, Zaid Ramdhan Anshari, Bauke Gaastra, Dirk J. Slotboom & Bert Poolman: Chemiosmotic nutrient transport in synthetic cells powered by electrogenic antiport coupled to decarboxylation . Nature Communications, 12 September 2024

Laura Heinen, Marco van den Noort, Martin S. King, Edmund R.S. Kunji and Bert Poolman: Synthetic syntrophy: Synthetic syntrophy for adenine nucleotide cross-feeding between metabolically active nanoreactors . Nature Nanotechnology 21 October 2024