Genome Sequences of Escherichia coli B strains REL606 and BL21(DE3)

Haeyoung Jeong, Valérie Barbe, Choong Hoon Lee, David Vallenet, Dong Su Yu, Sang Haeng Choi, Arnaud Couloux, Seung Won Lee, Sung Ho Yoon, Laurence Cattolico, Cheol Goo Hur, Hong Seog Park, Béatrice Ségurens, Sun Chang Kim, Tae Kwang Oh, Richard E. Lenski, F. William Studier, Patrick Daegelen, Jihyun F. Kim

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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.

Original languageEnglish
Pages (from-to)644-652
Number of pages9
JournalJournal of Molecular Biology
Issue number4
Publication statusPublished - 2009 Dec 11

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

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    Jeong, H., Barbe, V., Lee, C. H., Vallenet, D., Yu, D. S., Choi, S. H., Couloux, A., Lee, S. W., Yoon, S. H., Cattolico, L., Hur, C. G., Park, H. S., Ségurens, B., Kim, S. C., Oh, T. K., Lenski, R. E., Studier, F. W., Daegelen, P., & Kim, J. F. (2009). Genome Sequences of Escherichia coli B strains REL606 and BL21(DE3). Journal of Molecular Biology, 394(4), 644-652.