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

Research output: Contribution to journalArticle

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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.

Original languageEnglish
Pages (from-to)644-652
Number of pages9
JournalJournal of Molecular Biology
Volume394
Issue number4
DOIs
Publication statusPublished - 2009 Dec 11

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Genome
Escherichia coli
Multigene Family
Molecular Biology
Lysogeny
Prophages
O Antigens
DNA Transposable Elements
Shigella
Flagella
Recombinant Proteins
Base Pairing
Genes
Enzymes

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

Cite this

Jeong, Haeyoung ; Barbe, Valérie ; Lee, Choong Hoon ; Vallenet, David ; Yu, Dong Su ; Choi, Sang Haeng ; Couloux, Arnaud ; Lee, Seung Won ; Yoon, Sung Ho ; Cattolico, Laurence ; Hur, Cheol Goo ; Park, Hong Seog ; Ségurens, Béatrice ; Kim, Sun Chang ; Oh, Tae Kwang ; Lenski, Richard E. ; Studier, F. William ; Daegelen, Patrick ; Kim, Jihyun F. / Genome Sequences of Escherichia coli B strains REL606 and BL21(DE3). In: Journal of Molecular Biology. 2009 ; Vol. 394, No. 4. pp. 644-652.
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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 & Kim, JF 2009, 'Genome Sequences of Escherichia coli B strains REL606 and BL21(DE3)', Journal of Molecular Biology, vol. 394, no. 4, pp. 644-652. https://doi.org/10.1016/j.jmb.2009.09.052

Genome Sequences of Escherichia coli B strains REL606 and BL21(DE3). / Jeong, Haeyoung; Barbe, Valérie; Lee, Choong Hoon; Vallenet, David; Yu, Dong Su; Choi, Sang Haeng; Couloux, Arnaud; Lee, Seung Won; Yoon, Sung Ho; Cattolico, Laurence; Hur, Cheol Goo; Park, Hong Seog; Ségurens, Béatrice; Kim, Sun Chang; Oh, Tae Kwang; Lenski, Richard E.; Studier, F. William; Daegelen, Patrick; Kim, Jihyun F.

In: Journal of Molecular Biology, Vol. 394, No. 4, 11.12.2009, p. 644-652.

Research output: Contribution to journalArticle

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AU - Lee, Choong Hoon

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AU - Yu, Dong Su

AU - Choi, Sang Haeng

AU - Couloux, Arnaud

AU - Lee, Seung Won

AU - Yoon, Sung Ho

AU - Cattolico, Laurence

AU - Hur, Cheol Goo

AU - Park, Hong Seog

AU - Ségurens, Béatrice

AU - Kim, Sun Chang

AU - Oh, Tae Kwang

AU - Lenski, Richard E.

AU - Studier, F. William

AU - Daegelen, Patrick

AU - Kim, Jihyun F.

PY - 2009/12/11

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N2 - 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.

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Jeong H, Barbe V, Lee CH, Vallenet D, Yu DS, Choi SH et al. Genome Sequences of Escherichia coli B strains REL606 and BL21(DE3). Journal of Molecular Biology. 2009 Dec 11;394(4):644-652. https://doi.org/10.1016/j.jmb.2009.09.052