RT Journal Article SR Electronic T1 Laboratory evolution of multiple E. coli strains reveals unifying principles of adaptation but diversity in driving genotypes JF bioRxiv FD Cold Spring Harbor Laboratory SP 2020.05.19.104992 DO 10.1101/2020.05.19.104992 A1 Erol S. Kavvas A1 Maciek Antoniewicz A1 Christopher Long A1 Yang Ding A1 Jonathan M. Monk A1 Bernhard O. Palsson A1 Adam M. Feist YR 2020 UL http://biorxiv.org/content/early/2020/05/20/2020.05.19.104992.abstract AB Fitness landscapes are a central concept in evolutionary biology and have been thoroughly detailed in terms of genotypes. However, our understanding of the selected metabolic and gene expression adaptations, and their dependence on genetic background, remains limited. Here, we reveal multi-scale adaptation principles in the E. coli species by taking multi-omics measurements of six different strains throughout their adaptive evolution to glucose minimal media. Statistics and matrix factorization is applied to yield four key results. First, analysis of the metabolic and physiological data shows evolutionary convergence in growth rate, glucose uptake rate, glycolytic ATP and NADH production but divergence in NADPH production strategies. Second, factorization-based analysis of the transcriptome revealed six conserved transcriptomic adaptations describing increased expression of ribosome and amino acid biosynthetic genes and decreased expression of stress response and structural genes. Third, correlation analysis identifies five tradeoffs underlying the transcriptomic profiles. Fourth, statistical tests leveraging ALE design identify four mutation-flux correlates and eight mutation-transcriptomic correlates that link mutations to systems level adaptation principles. Our total results reveal the dominant metabolic and regulatory constraints governing E. coli growth adaptation that either distinguish strains or are conserved principles.Competing Interest StatementThe authors have declared no competing interest.