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

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Title
Genome sequences of Escherichia coli B strains REL606 and BL21(DE3)
Author(s)
Haeyoung Jeong; V Barbe; Choong Hoon Lee; D Ballenet; Dong Su Yu; Sang-Haeng Choi; A Couloux; Seung-Won Lee; Sung Ho Yoon; L Cattolico; Cheol-Goo Hur; Hong-Seog Park; B Segurens; S C Kim; Tae Kwang Oh; R E Lenski; F W Studier; P Daegelen; Jihyun Kim
Bibliographic Citation
Journal of Molecular Biology, vol. 394, no. 4, pp. 644-652
Publication Year
2009
Abstract
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.
Keyword
BL21(DE3)Comparative genomicsE. coli BREL606Similarity of E. coli B and K-12
ISSN
0022-2836
Publisher
Elsevier
DOI
http://dx.doi.org/10.1016/j.jmb.2009.09.052
Type
Article
Appears in Collections:
Division of Research on National Challenges > Infectious Disease Research Center > 1. Journal Articles
Division of Biomedical Research > Metabolic Regulation Research Center > 1. Journal Articles
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