Tunable synthetic phenotypic diversification on Waddington’s landscape through autonomous signaling

Abstract

Phenotypic diversification of cells is crucial for developmental and regenerative processes in multicellular organisms. The diversification concept is described as the motion of marbles rolling down Waddington’s landscape, in which the number of stable states changes as development proceeds. In contrast to this simple concept, the complexity of natural biomolecular processes prevents comprehension of their design principles. We have constructed, in Escherichia coli , a synthetic circuit with just four genes, which programs cells to autonomously diversify as the motion on the landscape through cell–cell communication. The circuit design was based on the combination of a bistable toggle switch with an intercellular signaling system. The cells with the circuit diversified into two distinct cell states, “high” and “low,” in vivo and in silico, when all of the cells started from the low state. The synthetic diversification was affected by not only the shape of the landscape determined by the circuit design, which includes the synthesis rate of the signaling molecule, but also the number of cells in the experiments. This cell-number dependency is reminiscent of the “community effect”: The fates of developing cells are determined by their number. Our synthetic circuit could be a model system for studying diversification and differentiation in higher organisms. Prospectively, further integrations of our circuit with different cellular functions will provide unique tools for directing cell fates on the population level in tissue engineering.

A Bacterial Continuous Culture System Based on a Microfluidic Droplet Open Reactor

“…The control of the bacterial cell density, for example, will be helpful to study cell diversification, depending on the cell density. 19 Therefore, our method will contribute to a wide range of fields, such as synthetic biology and metabolic engineering.…”

Effect of timescale on energy landscape: Distinction between free-energy landscape and potential of mean force

“…Its application can be found in the studies of, for example, large molecules, such as clusters [1,2] and proteins [3][4][5][6][7][8][9][10], diffusion in oxide networks [11], fullerene materials [12], formation process of gels and glasses [13], chemical and biological separation through micro-and nanofluidic systems [14], and epigenetics in developmental biology [15][16][17]. Two important roles of the energy landscape can be pointed out.…”

“…The results are expected to provide an important basis for the study of long time scale phenomena in large systems. [15][16][17]. Two important roles of the energy landscape can be pointed out.…”

“…Thus, chemical reactions can be imagined as a point mass moving on the energy surface drawn in the configuration space, and their rate constants can also be calculated from the information of the energy surface [8,[18][19][20][21]. Also, phenotypic diversification of cells can be modeled as the motion of marbles on Waddington's landscape [15][16][17].The other role of the energy landscape is that the probability distribution at the stationary state is given by the energy landscape through the Boltzmann factor. Thus, the stable structures of proteins can be predicted as minima of the free-energy landscape, and it is possible to elucidate specific interactions that give rise to the stable structures [7,[22][23][24].…”

“…Thus, chemical reactions can be imagined as a point mass moving on the energy surface drawn in the configuration space, and their rate constants can also be calculated from the information of the energy surface [8,[18][19][20][21]. Also, phenotypic diversification of cells can be modeled as the motion of marbles on Waddington's landscape [15][16][17].…”