Escherichia coli str. K-12 substr. MG1655 - EcoliWT (GSM576634-39 WT – WT E.coli EcNR1, no isobutanol)

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Description

Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli

Platform organism: Escherichia coli str. K-12 substr. MG1655
Sample organism: Escherichia coli
Experiment type: Expression profiling by array
Summary

BACKGROUND: Isobutanol is a promising next generation biofuel with demonstrated high yield microbial production, but the toxicity of this molecule reduces fermentation volumetric productivity and final titers. Organic solvent tolerance is a complex, multigenic phenotype that has been recalcitrant to rational engineering approaches. We apply experimental evolution followed by genome resequencing and a gene expression study to elucidate genetic bases on adaptation to exogenous isobutanol stress.

RESULTS: The adaptations acquired in our evolved lineages exhibit antagonistic pleiotropy between minimal and rich medium, and appear to be specific to the effects of longer chain alcohols. By examining genotypic adaptation in multiple independent lineages, we find evidence of parallel evolution in hfq, mdh, acrAB, gatYZABCD, and rph genes. Many isobutanol tolerant lineages show reduced rpoS activity, perhaps related to mutations in hfq or acrAB. Consistent with the complex, multigenic nature of solvent tolerance, we observe adaptations in a diversity of cellular processes. Many adaptations appear to involve epistasis between different mutations, implying a rugged fitness landscape for isobutanol tolerance. We observe a trend of evolution targeting post-transcriptional regulation and high centrality nodes of biochemical networks. Collectively, the genotypic adaptations we observe suggest mechanisms of adaptation to isobutanol stress based on remodelling the cell envelope and surprisingly, stress response attenuation.

CONCLUSIONS: We have discovered a set of genotypic adaptations that confer increased tolerance to exogenous isobutanol stress. Our results are immediately useful to efforts to engineer more isobutanol tolerant host strains of E. coli for isobutanol production. We suggest that rpoS and post-transcriptional regulators, such as hfq, RNA helicases, and sRNAs may be interesting mutagenesis targets for futurue global phenotype engineering.

Overall design
Two strains (WT strain and G3.2 mutant strain), each with two culture conditions (with and without isobutanol in medium). Three biological replicates for each strain/culture condition. Twelve samples in total.

  • GSM576634 – WT E.coli EcNR1, no isobutanol – EcoliWT

  • GSM576635 – WT E.coli EcNR1, no isobutanol

  • GSM576636 – WT E.coli EcNR1, no isobutanol

  • GSM576637 – WT E.coli EcNR1, 0.5 % isobutanol

  • GSM576638 – WT E.coli EcNR1, 0.5 % isobutanol

  • GSM576639 – WT E.coli EcNR1, 0.5 % isobutanol

  • GSM576640 – G3.2 mutant of E.coli EcNR1, no isobutanol

  • GSM576641 – G3.2 mutant of E.coli EcNR1, no isobutanol

  • GSM576642 – G3.2 mutant of E.coli EcNR1, no isobutanol

  • GSM576643 – G3.2 mutant of E.coli EcNR1, 0.5 % isobutanol

  • GSM576644 – G3.2 mutant of E.coli EcNR1, 0.5 % isobutanol

  • GSM576645 – G3.2 mutant of E.coli EcNR1, 0.5 % isobutanol

Correponding dataset
EcoliWT – GSM576634-39 WT

Usage

1

Format

A 7 column table defined as such:

  • the first column containing the names of the probes

  • columns 2-4 contain the gene expression values of three replicates for the initial conditions of the experiment

  • columns 5-7 contain the gene expression values of three replicates for the final conditions of the experiment

Source

Geo Accession #Series GSE23526

References

Minty, J. J., Lesnefsky, A. A., Lin, F., Chen, Y., Zaroff, T. A., Veloso, A. B., Xie, B., McConnell, C. A.,Ward, R. J., Schwartz, D. R., Rouillard, J. M., Gao, Y., Gulari, E., Lin, X.N. (March 2011) “Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli.” Microb Cell Fact. Vol. 10, p. 18. doi: 10.1186/1475-2859-1 0-18.