1. Changes to the growth conditions break the circuit by changing host gene expression
Changes to the growth conditions break the circuit by changing host gene expression Doubling times for cells carrying the circuit grown in culture tubes (gray) and Erlenmeyer flasks (white). Error bars are calculated as the standard deviation from three biological replicates performed on different days.Comparison of host gene expression under culture tube conditions for sets of input states with differing numbers of expressed circuit genes (including yfp): two = −/−/−, three = +/−/−, and four = −/+/−, +/+/−, −/−/+, +/−/+, −/+/+ and +/+/+ (0.5 mM IPTG/22 nM aTc/5 mM arabinose). The baseline is calculated from RNA‐seq data collected from cells harboring an empty circuit plasmid backbone (pAN1201). Points show the mean expression level of each gene. Red points denote genes with statistically significantly differential expression in comparison with the baseline (P < 0.01; Dataset EV2).Flow cytometry data of the YFP output for the circuit grown in Erlenmeyer flasks (filled gray distributions) and the predicted output distributions from Cello (blue is on and red is off).Comparison of transcription profiles for the circuit when cells are grown in culture tubes (black line; data for biological replicate 1) and Erlenmeyer flasks. If the profile obtained from Erlenmeyer flasks is higher the difference is shown in red and if it is lower the difference is shown in blue.Fold‐change analysis of differentially expressed sugar transport‐related genes (P < 0.003) compared between Erlenmeyer flask and culture tube growth conditions (Dataset EV2).
Thomas E Gorochowski et al. Mol Syst Biol 2017;13:952
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