PMID:19786035
| Citation |
Jeong, H, Barbe, V, Lee, CH, Vallenet, D, Yu, DS, Choi, SH, Couloux, A, Lee, SW, Yoon, SH, Cattolico, L, Hur, CG, Park, HS, Ségurens, B, Kim, SC, Oh, TK, Lenski, RE, Studier, FW, Daegelen, P and Kim, JF (2009) Genome sequences of Escherichia coli B strains REL606 and BL21(DE3). J. Mol. Biol. 394:644-52 |
|---|---|
| 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 lambda 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 approximately 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. |
| Links |
PubMed Online version:10.1016/j.jmb.2009.09.052 |
| Keywords |
DNA, Bacterial/chemistry; DNA, Bacterial/genetics; Escherichia coli/genetics; Genome, Bacterial; Interspersed Repetitive Sequences; Molecular Sequence Data; Polymorphism, Genetic; Prophages/genetics; Sequence Analysis, DNA |
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