Escherichia coli K-12 and B have been the subjects of classical experiments from which much of our understanding of molecular genetics has emerged. We present here complete genome sequences of two E. coli B strains, REL606, used in a long-term evolution experiment, and BL21(DE3), widely used to express recombinant proteins. The two genomes differ in length by 72,304 bp and have 426 single base pair differences, a seemingly large difference for laboratory strains having a common ancestor within the last 67 years. Transpositions by IS1 and IS150 have occurred in both lineages. Integration of the DE3 prophage in BL21(DE3) apparently displaced a defective prophage in the λ attachment site of B. As might have been anticipated from the many genetic and biochemical experiments comparing B and K-12 over the years, the B genomes are similar in size and organization to the genome of E. coli K-12 MG1655 and have > 99% sequence identity over ∼ 92% of their genomes. E. coli B and K-12 differ considerably in distribution of IS elements and in location and composition of larger mobile elements. An unexpected difference is the absence of a large cluster of flagella genes in B, due to a 41 kbp IS1-mediated deletion. Gene clusters that specify the LPS core, O antigen, and restriction enzymes differ substantially, presumably because of horizontal transfer. Comparative analysis of 32 independently isolated E. coli and Shigella genomes, both commensals and pathogenic strains, identifies a minimal set of genes in common plus many strain-specific genes that constitute a large E. coli pan-genome.
Bibliographical noteFunding Information:
We thank Jae-Pil Choi, Hyun-Jin Kim, Soo-Yeon Kim, Benoît Vacherie, and other members of GEM and the KRIBB/CNS sequencing team for technical assistance; the late Michel Blot and Dominique Schneider for samples of REL606 DNA and culture; and Sang Yup Lee, Seung-Hwan Park, and Jean Weissenbach for valuable comments. This work was supported by the 21C Frontier Microbial Genomics and Applications Center Program of the Korean Ministry of Education, Science and Technology, and the KRIBB Research Initiative Program (to J.F.K.); Consortium National de Recherche en Génomique (to P.D.); the GTL Program of the Office of Biological and Environmental Sciences of the U.S. Department of Energy and internal research funding from Brookhaven National Laboratory (to F.W.S.); and the U.S. National Science Foundation and DARPA 'Fun Bio' program (to R.E.L.).
All Science Journal Classification (ASJC) codes
- Structural Biology
- Molecular Biology