Abstract
Adaptive laboratory evolution (ALE) has been used to study and solve pressing questions about evolution, especially for the study of the development of mutations that confer increased fitness during evolutionary processes. In this contribution, we investigated how the evolutionary process conducted with the PTS− mutant of Escherichia coli PB11 in three parallel batch cultures allowed the restoration of rapid growth with glucose as the carbon source. The significant findings showed that genomic sequence analysis of a set of newly evolved mutants isolated from ALE experiments 2–3 developed some essential mutations, which efficiently improved the fast-growing phenotypes throughout different fitness landscapes. Regulator galR was the target of several mutations such as SNPs, partial and total deletions, and insertion of an IS1 element and thus indicated the relevance of a null mutation of this gene in the adaptation of the evolving population of PB11 during the parallel ALE experiments. These mutations resulted in the selection of MglB and GalP as the primary glucose transporters by the evolving population, but further selection of at least a second adaptive mutation was also necessary. We found that mutations in the yfeO, rppH, and rng genes improved the fitness advantage of evolving PTS− mutants and resulted in amplification of leaky activity in Glk for glucose phosphorylation and upregulation of glycolytic and other growth-related genes. Notably, we determined that these mutations appeared and were fixed in the evolving populations between 48 and 72 h of cultivation, which resulted in the selection of fast-growing mutants during one ALE experiments in batch cultures of 80 h duration.
Key points
• ALE experiments selected evolved mutants through different fitness landscapes in which galR was the target of different mutations: SNPs, deletions, and insertion of IS.
• Key mutations in evolving mutants appeared and fixed at 48–72 h of cultivation.
• ALE experiments led to increased understanding of the genetics of cellular adaptation to carbon source limitation.
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Acknowledgments
We thank Paul Gaytán, Jorge Yáñez, and Eugenio López for the synthesis of oligonucleotides and Sanger DNA sequencing. We thank Georgina Hernández, Luz María Martínez, and Alfredo Mendoza for their technical assistance.
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This study was funded by the Consejo Nacional de Ciencia y Tecnología (CONACYT, México) Ciencia Básica grant 240519.
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SBC has a major contribution to the conception and design of the study, the acquisition, analysis, interpretation of the data, and writing the manuscript. NF has a major contribution to the acquisition of RT-qPCR data. EMR, GG, and FB have a major contribution to the design of the study and review of the manuscript. AE has a major contribution to the conception and design of the study, interpretation of data, and writing of the manuscript.
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Carmona, S.B., Flores, N., Martínez-Romero, E. et al. Evolution of an Escherichia coli PTS− strain: a study of reproducibility and dynamics of an adaptive evolutive process. Appl Microbiol Biotechnol 104, 9309–9325 (2020). https://doi.org/10.1007/s00253-020-10885-5
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DOI: https://doi.org/10.1007/s00253-020-10885-5