Serial adaptation of E. coli under glycerol and lactate reveals order-independent fitness landscape

Abstract

To reveal the genotype-phenotype correlation during evolution, “Fitness Landscape” concept has been proposed. This shape was suggested to be rugged due to the epistatic interaction between genes and fitness trade-offs in bacteria (Rugged Fitness Landscape). However, when bacteria adapt to multiple conditions serially, the fitness landscape had not been understood. To identify the fitness landscape in serial adaptation, E. coli MG1655 was sequentially adapted to glycerol and lactate in different orders during Serial Adaptive Laboratory Evolution (ALE) for 1400~1600 generations. The phenotype of E. coli in glycerol and lactate which evolved during the Serial ALE depends on the order of serial adaptation. To identify the genotype related to this phenotype, population genome sequencing was performed. Then, only 10 mutations appeared at glycerol-lactate Serial ALE, however, 206 mutations were found at lactate-glycerol Serial ALE and they caused by unexpected mutation of mutT. Its hypermutable effect was considered to occur a phenotypic difference in the order of serial adaptation by increasing mutant pools. Although the hypermutator phenotype of lactate-glycerol Serial ALE, repeated mutations were found during whole Serial ALE through population genome sequencing at 50 generation intervals and they were order-independent and carbon-specific. Glycerol-specific mutation, glpK and lactate-specific mutations, ppsA, ydcI, and rph were identified and their effects were confirmed by reverse engineering and precedent research data. In contrast, there was no repeated mutation depending on the only order of Serial adaptation. In summary, the phenotype can be influenced by the order of serial adaptation, however, the carbon-specific genotypes change the phenotype regardless of the order. The fitness landscape in serial adaptation is order-independent.