Rapid accumulation of motility-activating mutations in resting liquid culture of Escherichia coli

Expression of motility genes is a potentially beneficial but costly process in bacteria. Interestingly, many isolate strains of Escherichia coli possess motility genes but have lost the ability to activate them in conditions in which motility is advantageous, raising the question of how they respond to these situations. Through transcriptome profiling of strains in the E. coli single-gene knockout Keio collection, we noticed drastic upregulation of motility genes in many of the deletion strains as compared to its weakly motile parent strain (BW25113). We show that this switch to a motile phenotype is not a direct consequence of the genes deleted, but is instead due to a variety of secondary mutations that increase the expression of the major motility regulator, FlhDC. Importantly, we find that this switch can be reproduced by growing poorly motile E. coli strains in non-shaking liquid medium overnight but not in shaking liquid medium. Individual isolates after the non-shaking overnight incubations acquired distinct mutations upstream of the flhDC operon, including different insertion sequence (IS) elements and, to a lesser extent, point mutations. The rapid sweep in the non-shaking population shows that poorly motile strains can quickly adapt to a motile lifestyle by genetic rewiring. IMPORTANCE The ability to tune gene expression in times of need outside of preordained regulatory networks is an essential evolutionary process that allows organisms to survive and compete. Here we show that, upon overnight incubation in liquid media without shaking, populations of largely non-motile Escherichia coli can rapidly accumulate mutants that have constitutive motility. This effect contributes to widespread secondary mutations in the single-gene knockout library, the Keio collection. As a result, 49/71 (69%) of the Keio strains tested exhibit varying degrees of motility, whereas their parental strain is poorly motile. These observations highlight the plasticity of gene expression even in the absence of pre-existing regulatory programs and should raise awareness of procedures for handling laboratory strains of E. coli.