Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12

Abstract

The genome of an Escherichia coli MC4100 strain with a lambda placMu50 fusion revealed numerous regulatory differences from MG1655, including one that arose during laboratory storage. The 194 mutational differences between MC4100(MuLac) and other K-12 sequences were mostly allocated to specific lineages, indicating the considerable mutational divergence between K-12 strains.

FIG. 1.

Alignment of the four sequenced E. coli K-12 genomes. Scales are in megabase pairs. The gray- and yellow-shaded regions represent segments present in all strains, with inverted segments shaded in yellow. Red and green boxes within the gray and yellow areas represent major indels (insertions and deletions, respectively) (see Table S4 in the supplemental material), and the event numbering is also shown (see Table S4 in the supplemental material). R indicates the E. coli B segment gained by recombination. Green lines (no numbering) represent small deletions treated as mutations, and red lines represent insertions (see Table S5 in the supplemental material). Full-height blue lines represent nonsynonymous substitutions, half-height blue lines represent synonymous substitutions, and gray lines represent substitutions in noncoding regions. For an expanded version of this figure showing individual genes, see Fig. S1 in the supplemental material.

FIG. 2.

Tree showing the relationships of strains W3310 and MG1655 and strains MC4100(MuLac) and DH10B and the events allocated to the various lineages. The tree topography for HfrC, W1485, MG1655, and W3110 is taken from reference . Note that the W1485 lineage discussed in the text extends from the ancestral K-12 strain through W1485 to the divergence between W3310 and MG1655 and includes any events that occurred after W1485 was isolated but before the generation of W3310 and MG1655. The same is true of the HfrC lineage, which for the present purposes extends to the divergence of MC4100(MuLac) and DH10B. For each lineage, the number of mutations (mut) and insertion or deletion events (indel) is shown, first as a total and then for mutations as intergenic (i), other noncoding (nc), nonsynonymous (ns), or synonymous (s) and for indels as insertions (ins) or deletions (del). One mutation allocated to the divergence between W1485 and HfrC but not to either lineage is shown between the two lineages.