Fig. 1
From: Cell-free prediction of protein expression costs for growing cells
A method to measure resource competition using a capacity monitor in cell lysate. a Illustration of resource competition in E. coli between a genome-integrated GFP capacity monitor gene and a plasmid-based gene of interest (GoI) fused to mkate. Graph shows the correlation between the inferred expression capacity (measured as max GFP production rate per cell) and the cell growth rate. b Illustration of resource competition in cell lysates expressing the capacity monitor from a plasmid and the GoI from another plasmid. Graph shows the correlation between the normalized in vitro capacity (measured as max GFP production rate, Supplementary Fig. 1A) and increasing concentrations of a GoI plasmid. c Measured in vitro capacity with the capacity monitor plasmid added at different concentrations in cell lysate. d Normalized in vitro capacity measured in cell lysate containing 30 nM of the capacity monitor plasmid and different concentration plasmids bearing mkate with either a strong (black/orange) or a very weak (black/blue) RBS sequence. The grey area represents the concentration of plasmid where competition is for translational resources. Values are normalised to the in vitro capacity obtained with capacity monitor plasmid alone. e Correlation between normalized in vitro capacity measured in cell lysate and normalized in vivo capacity measured with DH10B cells. The constructs in this experiment all express mkate with different RBS sequences (Supplementary Table 1). f Correlation between normalized in vitro capacity measured in cell lysate and normalized in vivo capacity measured in DH10B using constructs with various genes of different sizes paired with RBS BCD264. g Growth rate of strains growing in different conditions and containing only the capacity monitor. Strains/conditions: DH10B in M9 pyruvate (a, red); DH10B in M9 fructose (b, black); MG1655 in M9 fructose (c, orange); DH10B in M9 glucose (d, purple); DH10B in LB (e, blue). h Correlation between normalized in vitro capacity (from f) and normalized in vivo capacity when constructs with various genes of different sizes paired with RBS BCD2 are expressed in the strains and conditions described in g. Error bars show standard error of three independent repeats
