Growth adaptation ofgndandsdhCB Escherichia colideletion strains diverges from a similar initial perturbation of the transcriptome

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 rerouting 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.All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx

Multiplex Design of the Metabolic Network for Production of l -Homoserine in Escherichia coli

“…However, the diversion of flux away from forming oxaloacetate from fumaric acid by deletion of fumarase genes or overexpression of aspA dramatically reduced the production of L-homoserine, which may attribute to the toxicity of fumaric acids(41).on October 31, 2020 by guest http://aem.asm.org/Downloaded fromIn addition to above rather obvious genetic modifications, we also tested the impact of other different genes on L-homoserine production by using CRISPRi-based gene repression methodology.The results of gene repression indicated that CRISPRi system was a feasible method to regulate gene expression with less labor and time consumption. Specifically, down-regulation of the phosphotransferase system (PTS) is widely approved for reinforcing the biosynthesis of phosphoenolpyruvate (PEP)-derived products(42,43). The repression of zwf, tktA, rpe and talB disrupted the pentose phosphate pathway, which can direct more carbon to the synthesis of precursors in glycolytic pathway.…”