Can we build a minimal form of life from molecular components and control the physicochemistry of the cell
Bert Poolman
Department of Biochemistry, University of Groningen, The Netherlands, Email: b.poolman@rug.nl; http://www.membraneenzymology.com
The biochemical processes that characterize all living cells, such as energy provision, gene expression, and cell division take place in a confined and highly crowded space. High concentrations of macromolecules give rise to the phenomenon of macromolecular crowding, which impacts individual proteins, the formation of protein complexes and the structure of the cytoplasm. The interplay between macromolecular crowding, pH, ionic strength, water activity and osmotic pressure determines the physicochemical state of the cytoplasm. In addition, many processes in biological cells depend on the ability of macromolecules to find each other by translational diffusion, which can limit the tempo of processes. We find that protein diffusion in the crowded cytoplasm depends on the net charge and its distribution over the protein, with positive proteins diffusing up to 100-fold slower than negative ones. The lower mobility is caused by interaction of cationic proteins with ribosomes and strongly dependent on the ionic strength of the cytoplasm, which exemplifies the importance of physicochemical homeostasis.
We have initiated a program to construct minimal forms of life from molecular components to achieve physicochemical homeostasis in synthetic cells. One of the grand challenges in synthetic biology is the construction of far-from-equilibrium molecular systems integrated into cell-like containers with control of solute fluxes and a constant supply of energy to fuel ATP-requiring processes. Such systems should enable long-term metabolic energy conservation and physicochemical homeostasis and a better understanding of how living cells perform these tasks. I will present the assembly of synthetic vesicles containing a pathway for sustained ATP production that performs at least an order of magnitude better than any system described so far. I will also show the bottom-up construction of a volume regulatory network to control the osmotic pressure, ionic strength, pH, and molecular crowding of the synthetic cells.
Recent papers, related to lecture:
van den Berg J, Boersma AJ & Poolman B (2017) Do microorganisms maintain crowding homeostasis? Nat Rev Microbiol 15: 309.
Bianchi F, Syga L, Moiset G, Spakman D, Schavemaker PE, Punter M, Seinen AB, van Oijen AM, Robinson A and Poolman B (2018) Steric exclusion and protein conformation determine the localization of plasma membrane transporters. Nat Comm9: 501. doi: 10.1038/s41467-018-02864-2.
Boersma AJ, Zuhorn I & Poolman B (2015) A sensor for quantification of macromolecular crowding in living cells. Nat Meth 12: 227
Liu B, Poolman B & Boersma AJ (2017) Ionic strength sensing in living cells. ACS Chem. Biol12: 2510. doi: 10.1021/acschembio.7b00348.
Liu B, Åberg C, van Eerden FJ, Marrink SJ, Poolman B & Boersma AJ (2017) Design and properties of genetically encoded probes for sensing macromolecular crowding. Biophys J 122: 1929.
Schavemaker PE, Ĺmigiel WM & Poolman B (2017) Ribosome surface properties may impose limits on the nature of the cytoplasmic proteome. Elife 6. pii: e30084. doi: 10.7554/eLife.30084.
Spitzer J, Pielak G, Poolman B. (2015) Emergence of life: physical chemistry changes the paradigm. Biology Direct 10: 33.
