There is a clear consensus in the community of pre-biotic chemistry and in Synthetic Biology that compartments are essential for the apparition of life [Mann 2013] as “all life on Earth is cellular, namely based on closed compartments” [Luisi 2006].
The role of compartments in the apparition of life has been clearly stated by Oparin [Oparin 1965]. Even if prebiotic chemistry would enable the synthesis of macromolecules, the sole synthesis of the molecules is not sufficient: “if mononucleotides are polymerized in isolated solution, we simply get an accumulation of polynucleotides which under natural conditions would yield deposits of the substances” [Oparin 1965]. However, in the presence of other polymers such as polypeptides, “individual systems” or compartments can be found in suspension. These are denoted as protenoids (or Fox) microsphere, have a size of a few microns and a double membrane-like structure [Oparin 1965]. Already then, Oparin proposed a Synthetic Biology approach of this observation and produced coacervate droplets as artificial minimal models for the Fox microspheres up to the point where these coacervate droplets could grow, driven by enzymatic synthesis of starch [Oparin 1965]. Coacervates provide means to increase the concentrations from dilute solutions thereby enhancing the efficiency of chemical reactions. As a note, cells make use of this property with the P-granules, which will be one of the ingredients studied in this project cluster (see Work Package WP A1). In the past 50 years, progress beyond was hindered by challenges both in biochemistry and in the fabrication and manipulation techniques for micro-compartments. The advent of modern microfluidics combined with the rapid advances in biophysics and biochemistry now allow for the first time a systematic approach.
Another important property of compartments is to provide boundaries and hence means to avoid diffusion and dilution of products. For example, interfacial catalysis or evaporation processes leading to the decrease of the size of the micro-compartment also increase concentration, thereby favouring reactions [Dobson 2000]. At a later stage of evolution, it also provides a link between the genotype and the phenotype when the catalytic molecules (e.g. enzymes) are different from the replicating molecules (carrying the information). Such a link is required to guarantee that the encoding molecules are selected when they provide a selective (catalytic) advantage.
In a Bottom-up Synthetic Biology approach, controlling micro-compartments is essential. Sub-project A deals with the formation, characterisation and manipulation of biomimetic micro-compartments. We will use microfluidic technology to produce these compartments from a library of chemical systems that includes emulsions, vesicles and polymersomes. We will generate, understand and control individual compartments with well-defined and well-controlled physico-chemical properties and functions. We will design artificial systems with minimal but sufficient functions to serve as artificial biomimetic compartments with cell-like properties. In our bottom-up approach, the complexity of the compartment will be gradually increased. We start from functionalized interfaces in droplets (most basic micro-compartments), vesicles (membrane-based micro-compartments) or polymersomes (synthetic membranes usable for controlled chemical functionalization). Emphasize with be given to control the (bio-)chemistry and the physical properties of their interfaces. We will integrate the microfluidic scheme for the controlled, reproducible and high-throughput production of the compartments. We then quantify and characterize the physico-chemical properties with established techniques for colloids and interfaces characterization, and theoretical modelling.
Essential to living systems is the necessity to exchange materials with its surrounding [Luisi 2006]. Micro-compartments therefore need not to be closed, but the selective transport in and out of the compartments is crucial. Energy supply, metabolism, chemical sensing, and compartment-compartment communication must be possible while not losing essential inter-compartmental functions. We shall design and investigate different transport mechanisms, characterise these in detail and use this information to improve our design. We will for example design systems where the interfacial properties of a micro-compartment can be externally controlled through light, temperature or electric field. The understanding and control of the interfacial properties will be a key for the optimal design of non-equilibrium and self-organized systems [see Project Clusters B and C, respectively].