Genome sequences of Escherichia coli B strains REL606 and BL21(DE3).
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.
Jeong
Haeyoung
H
Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong, Daejeon 305-806, Korea.
Barbe
Valérie
V
Lee
Choong Hoon
CH
Vallenet
David
D
Yu
Dong Su
DS
Choi
Sang-Haeng
SH
Couloux
Arnaud
A
Lee
Seung-Won
SW
Yoon
Sung Ho
SH
Cattolico
Laurence
L
Hur
Cheol-Goo
CG
Park
Hong-Seog
HS
Ségurens
Béatrice
B
Kim
Sun Chang
SC
Oh
Tae Kwang
TK
Lenski
Richard E
RE
Studier
F William
FW
Daegelen
Patrick
P
Kim
Jihyun F
JF
D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics*; D016680:Genome, Bacterial; D020071:Interspersed Repetitive Sequences; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic; D039002:Prophages / Q000235:genetics; D017422:Sequence Analysis, DNA
D004269:DNA, Bacterial