Journal: BMC Evolutionary Biology

Article Title: Phenotypic convergence in bacterial adaptive evolution to ethanol stress

doi: 10.1186/s12862-015-0454-6

Figure Lengend Snippet: Time-series transcriptome analysis for adaptive evolution of E. coli to ethanol stress. Expression changes of representative genes in the central metabolic pathway including glycolysis, the pentose phosphate pathway, and TCA cycle are shown. In each inset, the horizontal axis shows time (hours), and the vertical axis shows expression level (a.u.). Expression levels of 0 h in each gene represent the ones of parent strain. Asterisks (*) indicate expression levels of parent strain obtained without adding ethanol as a reference. The numbers of generations from 0 to 2000 h were strain A:1025, B:1002, C:950, D:990, E:954, and F:938, respectively. Abbreviations: 2PG, 2-Phosphoglyceric acid; 3PG, 3-phosphoglycerate; AcCoA, acetyl-CoA; αKG, α-ketoglutarate; BPG, 1,3-bisphosphoglycerate; Cit, citrate; E4P, erythrose4-phosphate; F6P, fructose 6-phosphate; FBP, fructose 1,6-bisphosphate; GAP, glyceraldehyde 3-phosphate; G6P, glucose 6-phosphate; Oxa, oxaloacetate; PEP, phosphoenolpyruvate; Pyr, pyruvate; R5P, ribose 5-phosphate; S7P, sedoheptulose 7-phosphate; Suc, succinate; X5P, xylulose 5-phosphate

Article Snippet: For transcriptome analysis, a custom-designed tilling microarray of E. coli W3110 in Affymetrix platform was used.

Techniques: Expressing

Journal: BMC Evolutionary Biology

Article Title: Phenotypic convergence in bacterial adaptive evolution to ethanol stress

doi: 10.1186/s12862-015-0454-6

Figure Lengend Snippet: Metabolome analysis of ethanol tolerant E. coli strains under ethanol stress conditions. a Concentration of amino acids in ethanol tolerant strains. In each inset, the vertical axis shows the log-transformed absolute concentration (μM). The blue bar and red bars indicate the data of the parent strain and tolerant strains, respectively. b Correlation between metabolite concentration changes in strains E and F. Horizontal and vertical axes represent log-transformed concentration ratios with the parent strain, and each dot represents the concentration change of the metabolites

Article Snippet: For transcriptome analysis, a custom-designed tilling microarray of E. coli W3110 in Affymetrix platform was used.

Techniques: Concentration Assay, Transformation Assay

Journal: BMC Evolutionary Biology

Article Title: Phenotypic convergence in bacterial adaptive evolution to ethanol stress

doi: 10.1186/s12862-015-0454-6

Figure Lengend Snippet: Time-series analysis of the mutation fixation. a Timing of mutation fixation events in strain F. To identify the timing of mutation fixation, genomic DNA samples obtained at 12 different time points (216, 384, 576, 744, 888, 1056, 1224, 1392, 1584, 1824, 1968, and 2232 h after inoculation) were applied to Sanger sequencing. For each of the 5 identified mutations, the results of the Sanger sequencing is presented as a solid or dotted line. The solid line indicates that the mutation was fixed in the population at the corresponding time point, while the dashed line indicates the case of two peak signals, which indicates polymorphism in the population with and without the mutation. For example, in cells at 576 h after inoculation, only some have mutations in relA and cspC. b Specific growth rates of cloned E. coli cells with and without cspC and relA mutations under ethanol stress condition. Each bar represents the specific growth rate of an isolated clone, which were obtained from strain F cell populations at 576 h. " + " and "-" mean with and without the corresponding mutation, respectively. Blue, green, and red bars represent the growth rates of clones without mutations, that with cspC mutation only, and with cspC and relA mutations, respectively. Error bars indicate standard deviations calculated from three independent cultures

Article Snippet: For transcriptome analysis, a custom-designed tilling microarray of E. coli W3110 in Affymetrix platform was used.

Techniques: Mutagenesis, Sequencing, Clone Assay, Isolation