Fig. 1.

Adaptive laboratory evolution (ALE) of a genome-reduced strain (MS56). a Growth profiles of genome-reduced strain MS56 (red line) and wild-type E. coli MG1655 (black line) in LB medium. μ indicates specific growth rate. Error bars indicate standard deviation (s.d.) of two biological replicates. b Growth profiles of genome-reduced strain MS56 (red line) and wild-type E. coli MG1655 (black line) in M9 minimal medium. Error bars indicate s.d. of three biological replicates. c Cell growth trajectory showing changes in fitness during the ALE of MS56 in M9 minimal medium with supplementation of LB medium. Cell density was measured after 12 h of three individual batch cultivation (circles) and error bars indicate the s.d. of three individual cultures. LB supplementation was stepwise reduced from 0.1 to 0% over time (orange line). At the end of the ALE experiment, the evolved population exhibited restored growth rate in M9 minimal medium without any nutrient supplementation. d Growth profiles of a clone eMS57 (red line) isolated from the ALE population and wild-type E. coli MG1655 (black line) in M9 minimal medium. Error bars indicate s.d. of three biological replicates. e Morphological changes between MG1655, MS56, and eMS57. Upper panel, TEM images. Lower panel, SEM images. f Phenotype microarray characterization of MG1655 and eMS57 showing different nutrient utilization capability. Various carbon sources (red circle), phosphorus sources (black circles), nitrogen sources (yellow circles), and sulfur sources (blue circles). g Intracellular and extracellular pyruvate concentrations for MG1655 and eMG57 at 4, 6, and 8 h after inoculation. Int: intracellular pyruvate concentration. Ext: pyruvate concentration in the medium. Black (MG1655) and red (eMS57) lines show cell density at 4, 6, and 8 h after inoculation. Intracellular pyruvate level is presented as mole pyruvate per 10⁹ cells and extracellular pyruvate level was measured in molar concentration. Individual data points are shown as blue circles and error bars indicate the s.d. of two biological replicates. h Pyruvate uptake function in MG1655 and eMS57 was examined by growth inhibition induced by a toxic pyruvate analog (3-fluoropyruvate, FP). Error bars indicate s.d. of three biological replicates. Source data are provided as a Source Data file