Research

Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations

Tom M Conrad¹ , Andrew R Joyce² , M Kenyon Applebee¹ , Christian L Barrett² , Bin Xie³ , Yuan Gao^3,4 and Bernhard Ø Palsson³

¹  Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093-0332, USA

²  Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California, 92093-0412, USA

³  Department of Computer Science, Virginia Commonwealth University, 401 West Main Street, Richmond, Virginia, 23284-3019, USA

⁴  Center for the Study of Biological Complexity, Virginia Commonwealth University, 1000 W. Cary St., Richmond, Virginia, 23284-3068, USA

author email corresponding author email

Genome Biology 2009, 10:R118doi:10.1186/gb-2009-10-10-r118

Published:	22 October 2009

Subject areas: Evolution, Genetics, Microbiology and parasitology

Abstract

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.