Developmental design of synthetic bacterial architectures by morphogenetic engineering

Pascalie, J, Potier, M, Kowaliw, T, Giavitto, JL, Michel, O, Spicher, A and Doursat, R (2016) Developmental design of synthetic bacterial architectures by morphogenetic engineering. ACS Synthetic Biology, 5 (8). pp. 842-861. ISSN 2161-5063

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Abstract

Synthetic biology is an emerging scientific field that promotes the standardized manufacturing of biological components without natural equivalents. Its goal is to create artificial living systems that can meet various needs in health care or energy domains. While most works are focused on the individual bacterium as a chemical reactor, our project, SynBioTIC, addresses a novel and more complex challenge: shape engineering, i.e. the redesign of natural morphogenesis toward a new kind of "developmental 3D printing". Potential applications include organ growth, natural computing in biocircuits, or future vegetal houses. To create in silico multicellular organisms that exhibit specific shapes, we construe their development as an iterative process combining fundamental collective phenomena such as homeostasis, patterning, segmentation, and limb growth. Our numerical experiments rely on the existing Escherichia coli simulator Gro, a physico-chemical computation platform offering reaction-diffusion and collision dynamics solvers. The synthetic "bioware" of our model executes a set of rules, or "genome", in each cell. Cells can differentiate into several predefined types associated with specific actions (divide, emit signal, detect signal, die). Transitions between types are triggered by conditions involving internal and external sensors that detect various protein levels inside and around the cell. Indirect communication between bacteria is relayed by morphogen diffusion and the mechanical constraints of 2D packing. Starting from a single bacterium, the overall architecture emerges in a purely endogenous fashion through a series of developmental stages, inlcuding proliferation, differentiation, morphogen diffusion and synchronization. The genome can be parametrized to control the growth and features of appendages individually. As exemplified by the L and T shapes that we obtain, certain precursor cells can be inhibited while others can create limbs of varying size ("divergence of the homology"). Such morphogenetic phenotypes open the way to more complex shapes made of a recursive array of core bodies and limbs and, most importantly, to an evolutionary developmental ("evo-devo") exploration of unplanned functional forms.