Laboratory strains of Escherichia coli K-12: things are seldom what they seem

Abstract

Escherichia coli K-12 was originally isolated 100 years ago and since then it has become an invaluable model organism and a cornerstone of molecular biology research. However, despite its pedigree, since its initial isolation E. coli K-12 has been repeatedly cultured, passaged and mutagenized, resulting in an organism that carries many genetic changes. To understand more about this important model organism, we have sequenced the genomes of two ancestral K-12 strains, WG1 and EMG2, considered to be the progenitors of many key laboratory strains. Our analysis confirms that these strains still carry genetic elements such as bacteriophage lambda (λ) and the F plasmid, but also indicates that they have undergone extensive laboratory-based evolution. Thus, scrutinizing the genomes of ancestral E. coli K-12 strains leads us to examine whether E. coli K-12 is a sufficiently robust model organism for 21st century microbiology.

Keywords: Escherichia coli K-12; F plasmid; bacteriophage lambda; genomic analysis; laboratory-based evolution.

Fig. 1.

The pedigree of E. coli K-12 strains. The figure details the pathway of E. coli K-12 evolution from its isolation in 1922 to the generation of MG1655 and W3100 strains [1, 3, 4, 12]. Blood agar indicates selection on blood agar plates; UV indicates irradiation with ultraviolet light; EMB-gal indicates selection for utilization of galactose on eosin methylene blue indicator plates. Dotted lines represent uncertain evolutionary lineage events.

Fig. 2.

Genome comparison of different E. coli K-12 strains. The figure shows the comparison of the WG1 chromosome (contig 1) and F plasmid (contig 2) with the genomes of EMG2, MG1655 (NC_000913.3) and W3110 (NC_007779.1), using the Proksee server [19]. The outer two rings display the genes and features of the WG1 genome, with selected genes and differences labelled. The green, brown and blue rings illustrate the blast results when the genome sequences of E. coli K-12 strains EMG2, MG1655 (NC_000913.3) and W3110 (NC_007779.1), respectively, are compared to that of WG1.

Fig. 3.

Comparison of the F plasmids from different E. coli K-12 strains. The figure shows the comparison of the F plasmid (AP001918.1) with that from EMG2 and WG1 using Proksee [19]. The outer two rings display the genes and features of the F plasmid, with selected genes labelled. The green and brown rings illustrate the blast results when the F plasmid sequences from EMG2 and WG1, respectively, are compared to the original F plasmid sequence.