MaxSynBio: Design of Artificial Cells from Functional Modules
The exciting field of Synthetic Biology focuses on producing engineered, predictable cells or other biological systems to carry out desired functions, whereby these functions can be modified, enhanced or entirely new. Conceptually, Synthetic Biology relies on breaking down the complexity of biological systems into smaller subsystems and functional modules, followed by (re-)designing and (re-)assembling them into larger units. This can be considered as an analogue to the design of a biotechnological or chemical plant (Rollié et al., 2012). With respect to this, the PSE Group has introduced its expertise in the assembly and control of chemical, energy and production processes in MaxSynBio– a research consortium with eight other Max Planck Institutes and research groups from the Friedrich-Alexander University in Erlangen-Nuremberg and the University of Bordeaux, which is jointly funded by the Max Planck Society and the Federal Ministry of Education and Research in Germany.
The primary scientific goal of MaxSynBio is a true bottom-up engineering approach for mimicking the fundamental structural and functional principles of real cells towards better understanding of living systems (Fig. 1). The near future in Synthetic Biology will still lean heavily on the top-down approach, i.e. minimal systems derived from an existing organism. The bottom-up approach however – starting from first principles – might allow us to refine and further improve these minimal systems with alternative synthetic or biological components and pave the way for establishing a radically new generation of biotechnological production processes.
The MaxSynBio consortium focuses on selected life processes, which are of fundamental importance for the replication and functionality of living cells, such as growth, division, morphogenesis, signaling and motility, summarized under the umbrella term “proliferome” (Schwille et al., 2018). The specific responsibilities of the PSE group within the MaxSynBio consortium include:
- Compartmentalization and growth (tools for production, functionalization, characterization, and controlled increase of compartment size)
- Establishment and characterization of energy and cofactor regeneration modules for artificial cells (light- or chemically-driven)
- Establishment and characterization of metabolic (e.g. for CO2 fixation) and transport modules
- Coupling of the energy supply modules with different energy sink subsystems
- General methodology for integration of functional parts and modules and modular design of synthetic cells, based on assembly standards and mathematical modeling
and the general workflow is depicted in Fig. 2.
Compartmentalization is a major landmark of living systems – to establish gradients for energy generation or to spatially segregate metabolic reactions from the environment – and therefore the reconstitution of living processes is inherently associated with the creation and manipulation of compartments. Phospholipid membranes closely imitate the architecture and function of natural membranes and they have been widely used in planar (e.g. as supported bilayers) and closed (vesicles) architectures as model systems. Recently, amphiphilic copolymer-based analogues of cellular membranes have expanded the chemical dimensions of supramolecular structures, which allows for further tailoring to technological, biological and medical applications. Within the compartmentalization technology platform, we are developing various methods for production and characterization of nano- and microcompartments of different chemical compositions, including conventional and microfluidic tools (Weiss et al., 2018). In addition, we establish different protocols for membrane functionalization and studying the respective interactions (e.g. with membrane proteins) (Fig. 3).
Active processes in living systems need continuous supply of energy and materials and the energy supply and storage are closely connected to the cellular metabolism. Following the bottom-up approach, we have obtained and characterized the basic biochemical machinery for energy transduction and conversion – light- and chemically-driven proton pumps and ATP synthase – and are constantly expanding the library of purified membrane proteins (other oxidases, porins, fusogenic peptides, etc.). We are integrating energy-converting parts in three types of nano- and microcompartments – liposomes, hybrid vesicles and polymersomes – and characterizing them with respect to activity, reconstitution efficiency and orientation, whereby experimental optimization resulted in retention of enzymatic activity in semisynthetic and synthetic nanocompartments (Fig. 4, Otrin et al., 2017). We have also demonstrated encapsulated cofactor regeneration by a hydrophobic redox mediator as a synthetic analog for NADH dehydrogenase and cytochrome c reductase (Fig. 5, Wang et al., 2018). We are also exploring various metabolic pathways and ways to integrate them with energy supply modules. In parallel, we use the respiratory chain from E. coli membranes as a natural counterpart of bottom-up-assembled modules and combine it with a simple metabolism (Beneyton et al., 2018). Additionally, we describe the energy and metabolic modules through mathematical models, which provides possibilities for optimization and a quantitative framework for their integration.
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Dr. Rumiana Dimova, Prof. Reinhard Lipowsky, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
Prof. Jean-Christophe Baret, University of Bordeaux, Bordeaux, France
Prof. Tobias Erb, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
Prof. Katharina Landfester, Max Planck Institute for Polymer Research, Mainz, Germany
Prof. Reinhard Jahn, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
Prof. Robert J. Flassig, Brandenburg University of Applied Sciences, Brandenburg, Germany
Prof. Ramin Golestanian, Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany
Prof. Michael Börsch, Jena University Hospital, Jena, Germany
Prof. Panagiotis L. Kastritis, Martin Luther University Halle-Wittenberg, Halle, Germany
Prof. Seraphine Wegner, Institute of Physiological Chemistry and Phatobiochemistry, Münster, Germany
Prof. Eberhard Bodenschatz, Max Planck Institute for Dynamics and Self-organization, Göttingen, Germany