Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome

Douglas McCloskey, Sibei Xu, Troy E. Sandberg, Elizabeth Brunk, Ying Hefner, Richard Szubin, Adam M. Feist, Bernhard O. Palsson*

*Corresponding author for this work

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Abstract

Adaptive laboratory evolution (ALE) has emerged as a new approach with which to pursue fundamental biological inquiries and, in particular, new insights into the systemic function of a gene product. Two E. coli knockout strains were constructed: one that blocked the Pentose Phosphate Pathway (gnd KO) and one that decoupled the TCA cycle from electron transport (sdhCDAB KO). Despite major perturbations in central metabolism, minimal growth rate changes were found in the two knockout strains. More surprisingly, many similarities were found in their initial transcriptomic states that could be traced to similarly perturbed metabolites despite the differences in the network location of the gene perturbations and concomitant re-routing of pathway fluxes around these perturbations. However, following ALE, distinct metabolomic and transcriptomic states were realized. These included divergent flux and gene expression profiles in the gnd and sdhCDAB KOs to overcome imbalances in NADPH production and nitrogen/sulfur assimilation, respectively, that were not obvious limitations of growth in the unevolved knockouts. Therefore, this work demonstrates that ALE provides a productive approach to reveal novel insights of gene function at a systems level that cannot be found by observing the fresh knockout alone.
Original languageEnglish
Article number1793
JournalFrontiers in Microbiology
Volume9
Number of pages16
ISSN1664-302X
DOIs
Publication statusPublished - 2018

Bibliographical note

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY).

Keywords

  • Adaptive laboratory evolution
  • sdhD gene knockouts
  • Systems biology
  • Casual mutations
  • gnd
  • sdhA
  • sdhB
  • sdhC

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