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

Jeong, Haeyoung; Barbe, Valérie; Lee, Choong Hoon; Vallenet, David; Dong, Yu; Choi, Sun-Hye; Couloux, Arnaud; Lee, Seungwon; 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.

doi:10.1016/j.jmb.2009.09.052

Cited by 338 publications

(325 citation statements)

References 58 publications

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“…During the 2,000 generations of evolution in the LTEE, REL1206 accumulated seven mutations relative to its progenitor, strain REL606. The complete genome sequence of REL606 has been determined (17), along with its derivation from the E. coli B strain used by Luria and Delbrück (18) and its genomic similarities and differences relative to other B derivatives and to E. coli K-12 (19). The seven LTEE-derived mutations in REL1206 include point mutations in spoT, topA, and yeiB; a 1-bp insertion upstream of glmU; insertion sequence IS150 elements interrupting fimA and pykF; and an IS150-associated deletion of ∼7 kb in the rbs operon.…”

Section: Resultsmentioning

confidence: 99%

Specificity of genome evolution in experimental populations of Escherichia coli evolved at different temperatures

Deatherage

Kepner

Bennett

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Isolated populations derived from a common ancestor are expected to diverge genetically and phenotypically as they adapt to different local environments. To examine this process, 30 populations ofEscherichia coliwere evolved for 2,000 generations, with six in each of five different thermal regimes: constant 20 °C, 32 °C, 37 °C, 42 °C, and daily alternations between 32 °C and 42 °C. Here, we sequenced the genomes of one endpoint clone from each population to test whether the history of adaptation in different thermal regimes was evident at the genomic level. The evolved strains had accumulated ∼5.3 mutations, on average, and exhibited distinct signatures of adaptation to the different environments. On average, two strains that evolved under the same regime exhibited ∼17% overlap in which genes were mutated, whereas pairs that evolved under different conditions shared only ∼4%. For example, all six strains evolved at 32 °C had mutations innadR, whereas none of the other 24 strains did. However, a population evolved at 37 °C for an additional 18,000 generations eventually accumulated mutations in the signature genes strongly associated with adaptation to the other temperature regimes. Two mutations that arose in one temperature treatment tended to be beneficial when tested in the others, although less so than in the regime in which they evolved. These findings demonstrate that genomic signatures of adaptation can be highly specific, even with respect to subtle environmental differences, but that this imprint may become obscured over longer timescales as populations continue to change and adapt to the shared features of their environments.

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Section: Resultsmentioning

confidence: 99%

Specificity of genome evolution in experimental populations of Escherichia coli evolved at different temperatures

Deatherage

Kepner

Bennett

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

120

101

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“…The donor gDNA of the V. cholerae strain A1552-LacZ-Kan (37) lacks this part of the lacZ gene due to replacement with a kanamycin resistance cassette (aph; primers #3 and #4). A chromosomal region specific to E. coli BL21(DE3) gDNA encodes the T7 DNA-directed RNA polymerase (CP001509 [29]; primers #5 and 6); for B. subtilis 168, the spoEIII gene served as a species-specific genome template (primers #7 and #8). The expected PCR fragment sizes are indicated (not to scale).…”

Section: Resultsmentioning

confidence: 99%

Quorum Sensing Contributes to Natural Transformation of Vibrio cholerae in a Species-Specific Manner

2011

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Although it is a human pathogen, Vibrio cholerae is a regular member of aquatic habitats, such as coastal regions and estuaries. Within these environments, V. cholerae often takes advantage of the abundance of zooplankton and their chitinous molts as a nutritious surface on which the bacteria can form biofilms. Chitin also induces the developmental program of natural competence for transformation in several species of the genus Vibrio. In this study, we show that V. cholerae does not distinguish between species-specific and non-species-specific DNA at the level of DNA uptake. This is in contrast to what has been shown for other Gram-negative bacteria, such as Neisseria gonorrhoeae and Haemophilus influenzae. However, species specificity with respect to natural transformation still occurs in V. cholerae. This is based on a positive correlation between quorum sensing and natural transformation. Using mutant-strain analysis, cross-feeding experiments, and synthetic cholera autoinducer-1 (CAI-1), we provide strong evidence that the species-specific signaling molecule CAI-1 plays a major role in natural competence for transformation. We suggest that CAI-1 can be considered a competence pheromone.

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“…Precultures of the sequenced E. coli B strain BL21 [18] were inoculated in 20 ml lysogeny broth (LB) medium from agar plate and were grown over night at 37°C at 200 rpm shaker speed. Shake flask cultures were inoculated from these precultures to OD 600 = 0.02.…”

Section: Cell Culturementioning

confidence: 99%

Real-time detection of central carbon metabolism in livingEscherichia coliand its response to perturbations

2011

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Edited by Christian Griesinger Keywords:In vivo NMR Spectroscopy Metabolism Model organism Escherichia coli a b s t r a c tThe direct tracking of cellular reactions in vivo has been facilitated with recent technologies that strongly enhance NMR signals in substrates of interest. This methodology can be used to assay intracellular reactions that occur within seconds to few minutes, as the NMR signal enhancement typically fades on this time scale. Here, we show that the enhancement of 13 C nuclear spin polarization in deuterated glucose allows to directly follow the flux of glucose signal through rather extended reaction networks of central carbon metabolism in living Escherichia coli. Alterations in central carbon metabolism depending on the growth phase or upon chemical perturbations are visualized with minimal data processing by instantaneous observation of cellular reactions.

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

Cited by 338 publications

References 58 publications

Specificity of genome evolution in experimental populations of Escherichia coli evolved at different temperatures

Specificity of genome evolution in experimental populations of Escherichia coli evolved at different temperatures

Quorum Sensing Contributes to Natural Transformation of Vibrio cholerae in a Species-Specific Manner

Real-time detection of central carbon metabolism in livingEscherichia coliand its response to perturbations

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