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Transcriptional analysis and adaptive evolution of Escherichia coli strains growing on acetate

  • Bioenergy and biofuels
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An Erratum to this article was published on 07 April 2017

Abstract

Eighteen strains of Escherichia coli were compared for maximum specific growth rate (μ MAX) on 85 mM acetate as the sole carbon source. The C strain ATCC8739 had the greatest growth rate (0.41 h−1) while SCS-1 had the slowest growth rate (0.15 h−1). Transcriptional analysis of three of the strains (ATCC8739, BL21, SMS-3-5) was conducted to elucidate why ATCC8739 had the greatest maximum growth rate. Seventy-one genes were upregulated 2-fold or greater in ATCC8739, while 128 genes were downregulated 2-fold or greater in ATCC8739 compared to BL21 and SMS-3-5. To generate a strain that could grow more quickly on acetate, ATCC8739 was cultured in a chemostat using a progressively increasing dilution rate. When the dilution rate reached 0.50 h−1, three isolated colonies each grew faster than ATCC8739 on 85 mM acetate, with MEC136 growing the fastest with a growth rate of 0.51 h−1, about 25 % greater than ATCC8739. Transcriptional analysis of MEC136 showed that eight genes were downregulated 2-fold or greater and one gene was upregulated 2-fold or greater compared to ATCC8739. Genomic sequencing revealed that MEC136 contained a single mutation, causing a serine to proline change in amino acid 266 of RpoA, the α subunit of the RNA polymerase core enzyme. The 260–270 amino acid region of RpoA has been shown to be a key region of the protein that affects the interaction of the α subunit of the RNA polymerase core enzyme with several global transcriptional activators, such as CRP and FNR.

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Acknowledgments

MAE and EA acknowledge the Consortium for Biotechnology Research (DOE Prime Agreement DE-FG36-02GO12026), Southeastern Sun Grant Center under Prime Award No. DTOS59-07-G-00050 and NSF (CBET-0929893) for financial support of portions of this research. The authors also acknowledge Sarah A. Lee and Afaq M. M. Niyas for assistance with growth studies and Ronni Altman for strain construction.

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Correspondence to Mark A. Eiteman.

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Ankit Agarwal and Jacob Crigler contributed equally to this work.

An erratum to this article is available at http://dx.doi.org/10.1007/s00253-017-8271-z.

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Table S1: Genes which are two-fold or more upregulated in ATCC8739 compared to SMS-3-5 and BL21. Table S2: Genes which are two-fold or more downregulated in ATCC8739 compared to SMS-3-5 and BL21. (PDF 95 kb)

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Rajaraman, E., Agarwal, A., Crigler, J. et al. Transcriptional analysis and adaptive evolution of Escherichia coli strains growing on acetate. Appl Microbiol Biotechnol 100, 7777–7785 (2016). https://doi.org/10.1007/s00253-016-7724-0

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