Fig. 7: A synthetic genotype network of oscillatory GRNs.
From: Robustness and innovation in synthetic genotype networks
a Starting from the GREEN-stripe GRN 2b.2, a stronger promoter for the blue node leads to a GRN that displays oscillatory expression. Few changes suffice to transition to the CRISPRlator51, with all intermediates showing the oscillatory phenotype. Bacteria carrying the indicated GRNs were grown in continuous exponential phase in a microfluidic device and imaged every 10 min for up to two days. Oscillations are shown as kymographs: images of the microfluidic chamber (hosting ~100 cells) are displayed in order in a timeline montage. Due to an overlap of mKO2 and mKate2 in the same channel, red color for 2-OS.1 and 1-OS.1 (top) represents both mKO2 and mKate2, while green corresponds to sfGFP. Different fluorescent reporters mCherry (red), mCitrine (yellow) and Cerulean (blue) allowed us to characterize the dynamics of all three nodes (1-OS.2 and 1-OS.3; bottom). b Part of network topologies (schemes as in Fig. 1) and their neighbor relations predicted by the mathematical framework. Similar to Fig. 4a, the pie charts indicate fractions of GRNs (genotypes) with oscillatory (orange) and non-functional (NF; grey) phenotypes per topology. Numbers: percentages of occurrences of the oscillatory topologies. c Similar to Fig. 4d, transition frequencies between the neighboring indicated phenotypes.
