Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations.
BACKGROUND
Short-term laboratory evolution of bacteria followed by genomic sequencing provides insight into the mechanism of adaptive evolution, such as the number of mutations needed for adaptation, genotype-phenotype relationships, and the reproducibility of adaptive outcomes.


RESULTS
In the present study, we describe the genome sequencing of 11 endpoints of Escherichia coli that underwent 60-day laboratory adaptive evolution under growth rate selection pressure in lactate minimal media. Two to eight mutations were identified per endpoint. Generally, each endpoint acquired mutations to different genes. The most notable exception was an 82 base-pair deletion in the rph-pyrE operon that appeared in 7 of the 11 adapted strains. This mutation conferred an approximately 15% increase to the growth rate when experimentally introduced to the wild-type background and resulted in an approximately 30% increase to growth rate when introduced to a background already harboring two adaptive mutations. Additionally, most endpoints had a mutation in a regulatory gene (crp or relA, for example) or the RNA polymerase.


CONCLUSIONS
The 82 base-pair deletion found in the rph-pyrE operon of many endpoints may function to relieve a pyrimidine biosynthesis defect present in MG1655. In contrast, a variety of regulators acquire mutations in the different endpoints, suggesting flexibility in overcoming regulatory challenges in the adaptation.
Conrad
Tom M
TM
Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093-0332, USA. tconrad@ucsd.edu
Joyce
Andrew R
AR
Applebee
M Kenyon
MK
Barrett
Christian L
CL
Xie
Bin
B
Gao
Yuan
Y
Palsson
Bernhard Ø
BØ
D000222:Adaptation, Physiological / Q000187:drug effects* / Q000235:genetics; D001483:Base Sequence; D003470:Culture Media / Q000494:pharmacology; D019020:Directed Molecular Evolution; D004926:Escherichia coli / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development; D020440:Gene Duplication / Q000187:drug effects; D005798:Genes, Bacterial; D016680:Genome, Bacterial / Q000235:genetics*; D019344:Lactic Acid / Q000494:pharmacology*; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009154:Mutation / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D013997:Time Factors
D003470:Culture Media; D019344:Lactic Acid