Highly accurate genome sequences of<i>Escherichia coli</i>K‐12 strains MG1655 and W3110

Hayashi, Koji; Morooka, Naoki; Yamamoto, Yoshihiro; Fujita, Katsutoshi; Isono, Katsumi; Choi, Sunju; Ohtsubo, Eiichi; Baba, Tomoya; Wanner, Barry L.; Mori, Hirotada; Horiuchi, Takashi

doi:10.1038/msb4100049

Cited by 442 publications

(399 citation statements)

References 35 publications

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“…To study species-wide competitiveness, we used MG1655 as a reference; this is a much used laboratory K-12 strain of E. coli (Hayashi et al, 2006). In Figure 2, we investigated fitness with mixtures of substrates (either LSLB or mixtures of sugars) as limiting nutrients in chemostats.…”

Section: Resultsmentioning

confidence: 99%

A design-constraint trade-off underpins the diversity in ecologically important traits in species Escherichia coli

Phan

Ferenci

2013

The ISME Journal

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Bacterial species are internally diverse in genomic and multi-locus gene comparisons. The ecological causes of phenotypic and genotypic diversity within species are far less well understood. Here, we focus on the competitive fitness for growth on nutrients within Escherichia coli, an internally rich species. Competition experiments in nutrient-limited chemostats revealed that members of the ECOR collection exhibited a wide continuum of competitive abilities, with some fitter and some less fit than the lab strain MG1655. We observed an inverse relationship between competitiveness and the resistance of strains to detergent and antibiotic, consistent with the notion that membrane permeability and competitive fitness are linked by a trade-off between selfpreservation and nutritional competence (SPANC); high permeability has a postulated cost in antibacterial sensitivity whereas a low permeability has a cost in nutrient affinity. Isolates moved along the markedly nonlinear trade-off curve by mutational adaptation; an ECOR strain sensitive to antibacterials and a good competitor was easily converted by mutation into a mutant with higher resistance but poorer competition in the presence of low antibiotic concentrations. Conversely, a resistant ECOR strain changed into a better competitor after a short period of selection under nutrient limitation. In both directions, mutations can affect porin proteins and outer membrane permeability, as indicated by protein analysis, gene sequencing and an independent assay of outer membrane permeability. The extensive, species-wide diversity of E. coli in ecologically important traits can thus be explained as an evolutionary consequence of a SPANC trade-off driven by antagonistic pleiotropy.

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Section: Resultsmentioning

confidence: 99%

A design-constraint trade-off underpins the diversity in ecologically important traits in species Escherichia coli

Phan

Ferenci

2013

The ISME Journal

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“…Note that the commonly used strain MG1655 (CGSC#6300) is closely related to ancestral E. coli K12 (EMG2 or WG1) (Hayashi et al 2006). The strain was obtained from IMTECH, Chandigarh, India.…”

Section: Methodsmentioning

confidence: 99%

Variation of swimming speed enhances the chemotactic migration of Escherichia coli

et al. 2015

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Studies on chemotaxis of Escherichia coli have shown that modulation of tumble frequency causes a net drift up the gradient of attractants. Recently, it has been demonstrated that the bacteria is also capable of varying its runs speed in uniform concentration of attractant. In this study, we investigate the role of swimming speed on the chemotactic migration of bacteria. To this end, cells are exposed to gradients of a non-metabolizable analogue of glucose which are sensed via the Trg sensor. When exposed to a gradient, the cells modulate their tumble duration, which is accompanied with variation in swimming speed leading to drift velocities that are much higher than those achieved through the modulation of the tumble duration alone. We use an existing intra-cellular model developed for the Tar receptor and incorporate the variation of the swimming speed along with modulation of tumble frequency to predict drift velocities close to the measured values. The main implication of our study is that E. coli not only modulates the tumble frequency, but may also vary the swimming speed to affect chemotaxis and thereby efficiently sample its nutritionally rich environment.

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“…On the basis of the complete genome sequence of several model Escherichia coli strains, the whole set of about 4600 genes has been predicted to exist in E. coli K-12 (Hayashi et al, 2006;Riley et al, 2006). In growing E. coli cells under laboratory culture conditions, only one-quarter to one-third of the genes on its genome are expressed, the others remaining silent.…”

Section: Introductionmentioning

confidence: 99%

Expression levels of transcription factors in Escherichia coli: growth phase- and growth condition-dependent variation of 90 regulators from six families

Watanabe

Ishihama

2014

Microbiology

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The expression pattern of the genome in Escherichia coli is controlled by regulating the utilization of a limited number of RNA polymerases between a total of 4600 genes on its genome. The distribution pattern of RNA polymerase on the genome changes after two steps of protein-protein interaction with seven sigma subunits and about 300 transcription factors (TFs). Based on a systematic search for the regulation target promoters recognized by each TF, we propose two novel concepts: each TF regulates a number of target promoters; and each promoter is regulated by many TFs. In parallel, attempts have been made to determine the intracellular concentrations of all TFs using two systems: quantitative immunoblot analysis using TF-specific antibodies; and reporter assay of TF promoter activities. The direct measurement of TF protein level has so far been published for a set of 60 regulators with known functions. This study describes the determination of growth phase-dependent expression levels of 90 TFs using the reporter assay system. The translational fusion vector was constructed from the TF promoter sequence including an N-terminal proximal TF segment and the reporter GFP. At the beginning of cell growth, highlevel expression was observed only for a small number of TFs. In the exponential phase, approximately 80 % TFs are expressed, but the expressed TF species change upon transfer to the stationary phase. Significant changes in the pattern of TF expression were observed between aerobic and anaerobic conditions. The list of intracellular levels of TFs provides further understanding to the transcription regulation of the E. coli genome under various stressful conditions. INTRODUCTIONSingle-cell bacteria are directly exposed to frequently changing environments in nature and thus carry sophisticated genetic systems for adaptation to environmental changes (Ishihama, 2010(Ishihama, , 2012Yamamoto, 2014). On the basis of the complete genome sequence of several model Escherichia coli strains, the whole set of about 4600 genes has been predicted to exist in E. coli K-12 (Hayashi et al., 2006;Riley et al., 2006). In growing E. coli cells under laboratory culture conditions, only one-quarter to one-third of the genes on its genome are expressed, the others remaining silent. The majority of these uncharacterized silent genes must be expressed and utilized for adaptation and survival of E. coli under stressful conditions. Thus, even for this well-characterized model organism, the gene functions remain unidentified or unpredicted for approximately one-quarter because expression conditions of these silent genes have not yet been established.As the total number of RNA polymerases (RNAPs) in E. coli K-12 is less than the total number of genes on its genome (Ishihama, 2000), we proposed a model in which the change in genome transcription pattern takes place mainly through controlling the utilization of this limited number of transcription apparatuses between 4600 genes on the genome (Ishihama, 2010(Ishihama, , 2012. Two groups of reg...

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Highly accurate genome sequences ofEscherichia coliK‐12 strains MG1655 and W3110

Cited by 442 publications

References 35 publications

A design-constraint trade-off underpins the diversity in ecologically important traits in species Escherichia coli

A design-constraint trade-off underpins the diversity in ecologically important traits in species Escherichia coli

Variation of swimming speed enhances the chemotactic migration of Escherichia coli

Expression levels of transcription factors in Escherichia coli: growth phase- and growth condition-dependent variation of 90 regulators from six families

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