Additional genes increase the length of the cell cycle. (a) The relationship between the number of additional expressed (solid line) and non-expressed (dashed line) lacI genes and the cell cycle length is shown. Cell cycle length (hours) is plotted against the number of added genes, for 1, 5, 10, 20, 50, and 100 genes added. (b) The mean (per time point, averaged over the length of the cell cycle) number of mRNAs produced from the native genome is plotted against the number of added expressed lacI genes for 1, 5, 10, 20, 50, and 100 genes added. 25 in silico cell simulations were performed for each circuit size. Bars indicate the standard error of the mean.
Codon usage minimally affects synthetic gene expression. Black full lines indicate the optimized gene; red dotted lines indicate the unoptimized gene. (a) lacI, (b). araC, (c) tetR, (d) gfp. Thick lines indicate the average; thin lines represent the standard error of the mean. Results are truncated at the length of the shortest cell cycle length. In all cases, complexes denote tetramers to ease comparisons between experiments. Results are an average of 25 in silico simulations.
Codon optimization of synthetic genes differentially affects cell cycle length. The mean cell cycle length is plotted for M. genitalium with the unoptimized gene (solid line), and the codon-optimized gene (dashed line), for 1, 5, 10, 20, 50, and 100 genes added. (a) lacI, (b) araC, (c) tetR, (d) gfp. 25 in silico cell simulations were performed for each circuit size. Bars indicate the standard error of the mean.
Topology of the Goodwin oscillator. (a) LacI forms a tetramer. (b) The Goodwin oscillator is formed by LacI repressing transcription from its own promoter. Adapted from Ref. 31 .
Whole-cell Goodwin oscillator displays noisy and irregular oscillations. (a) LacI tetramer copy number dynamics in two in silico cells, truncated to the length of the shortest cell cycle. (b) Simulations from (a) with a low-pass filter applied (frequencies greater than 0.001 Hz were removed). (c) Experimental in vivo data of the Goodwin oscillator, modified from Stricker et al. 9 [Reproduced with permission from J. Stricker et al., “A fast, robust and tunable synthetic gene oscillator,” Nature 456, 516–U39 (2008). Copyright 2008 Nature Publishing Group] Each line depicts oscillatory data from a separate E. coli cell.
Summary of t-test p-values.
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