Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110

Abstract

With the goal of solving the whole-cell problem with Escherichia coli K-12 as a model cell, highly accurate genomes were determined for two closely related K-12 strains, MG1655 and W3110. Completion of the W3110 genome and comparison with the MG1655 genome revealed differences at 267 sites, including 251 sites with short, mostly single-nucleotide, insertions or deletions (indels) or base substitutions (totaling 358 nucleotides), in addition to 13 sites with an insertion sequence element or defective prophage in only one strain and two sites for the W3110 inversion. Direct DNA sequencing of PCR products for the 251 regions with short indel and base disparities revealed that only eight sites are true differences. The other 243 discrepancies were due to errors in the original MG1655 sequence, including 79 frameshifts, one amino-acid residue deletion, five amino-acid residue insertions, 73 missense, and 17 silent changes within coding regions. Errors in the original MG1655 sequence (<1 per 13,000 bases) were mostly within portions sequenced with out-dated technology based on radioactive chemistry.

Figure 1

E. coli K-12 pedigree. The relationships of E. coli K-12 MG1655 and W3110 with wild-type E. coli K-12 (EMG2 or WG1) have been described (Bachmann, 1972, 1996). Wild-type K-12 was cured of phage λ to make W1485 prior to 1954 (Step 1), which in turn was cured of the F⁺ factor to make W2637 (Step 2), from which W3110 was selected for a strongly galactose-fermenting strain in 1956 (Step 3). More recently, W1485 was cured of the F⁺ factor to make MG1655 (Guyer et al, 1981). E. coli K-12 EMG2, W1485, W2637, and W3110 have the same rpoS396(Am) allele (codon 33, TAG (Am); Rod et al, 1988; Atlung et al, 2002; KA Datsenko and BL Wanner, unpublished data), while MG1655 has the pseudorevertant Q33 allele (Atlung et al, 2002).

Figure 2

Resolution of E. coli K-12 W3110 and MG1655 sequence differences. See text.

Figure 3

IS element and defective phage differences. Locus names and genome locations on the left side are based on the MG1655 genome. IS1A, IS1B, IS1C, etc. are named alphabetically to distinguish individual insertions (Supplementary Figure 1). IS elements, black arrows; sites, red arrowheads; six ISs disrupt orfs, red bars (alsK, dcuA, gatA, rcsC, tdcD, and tnaB); and phage genes, green arrows.