Mining the diversity of wild-type Escherichia coli strains for stress tolerance phenotypes

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Rebecca Lennen, Mads Bonde, Morten Sommer, Markus Herrgrd

Novo Nordisk Foundation Center for Biosustainability, Denmark

Industrial-scale fed-batch fermentation of Escherichia coli results in numerous imposed stresses to the culture as a result of non-ideal mixing, high cell densities, and maintenance of environmental homeostasis. These stresses include elevated temperature, acetate accumulation, pH fluctuations, high osmolarity, oxidative stress, and product toxicity. A number of diverse non-pathogenic strains have been utilized as platform strains for metabolic engineering, however relatively little is known about differences in their stress tolerance. We first characterized the growth phenotypes of six wild-type E. coli strains under several imposed stresses. Remarkable differences were observed between strains for most stresses, with different strains exhibiting superior growth under different conditions, and genetically very similar strains exhibiting distinct phenotypes. Utilizing a comparative genomics analysis of these strains, we are employing both semi-rational and random strain engineering approaches that target primarily regulatory and membrane-associated genes. It is anticipated that this strategy will assist both in unraveling genetic determinants of strain-dependent phenotypes and in aiding the development of a universally stress-tolerant host strain of E. coli for bioproduction.