Fig. 2: A synthetic genotype network of GREEN-stripe (bottom) and BLUE-stripe (top) GRNs.
From: Robustness and innovation in synthetic genotype networks
Starting from a CRISPRi-based GREEN-stripe incoherent feed-forward loop (IFFL-2, design 1.1), we introduced quantitative (gray) or qualitative (black) changes to produce a genotype network of synthetic GREEN-stripe GRNs. Single changes enabled the transition from GREEN-stripe GRNs to BLUE-stripe GRNs. We then explored this BLUE-stripe genotype network through parameter (gray) or topology (black) changes, up to the GRN with the maximum number of repressions for a 3-node GRN without self-repression, GRN 4.1. Dashed lines represent the boundaries of the GREEN-stripe and BLUE-stripe genotype networks. Each design is denoted with a unique code displayed in an ellipse (color-coded according to the phenotype), with the details of the design provided in the diagrams below. The GRN code denotes both the complexity (i.e. number of interactions) and the topology, as well as the specific implementation. A higher starting number of the GRN (e.g. 2 vs. 1) reflects an increased complexity, while different topologies sharing the same complexity are denoted with different letters (e.g. 2a vs. 2b). Lastly, the final number (e.g. 2b.1 vs. 2b.2) distinguishes specific implementations within the same topology. Numbers by the repressions indicate the identity of the sgRNAs, while PH, PM, and PL represent constitutive promoters (BBa_J23100, BBa_J23102, and BBa_J23150, respectively). Small GRNs by the arrows display the changes (in red) between the connected GRNs: topology changes (T) or changes in the promoter strength (P) or in the identity of the sgRNAs (sg). The phenotype of each GRN was characterized in a microplate reader by determining the fluorescence of the three protein reporters (mKO2 (orange), sfGFP (green), and mKate2 (red, here depicted in blue for clarity)) as a function of arabinose (Ara) concentration. Data show the mean of three biological replicates, with error bars depicting the s.d. of normalized replicates (n = 3). GRNs sharing a common topology are grouped with a colored background. The dashed arrow indicates the transition towards another synthetic genotype network (that of oscillators, Fig. 7).
