Adaptive laboratory evolution of a genome-reduced Escherichia coli

Abstract

Synthetic biology aims to design and construct bacterial genomes harboring the minimum number of genes required for self-replicable life. However, the genome-reduced bacteria often show impaired growth under laboratory conditions that cannot be understood based on the removed genes. The unexpected phenotypes highlight our limited understanding of bacterial genomes. Here, we deploy adaptive laboratory evolution (ALE) to re-optimize growth performance of a genome-reduced strain. The basis for suboptimal growth is the imbalanced metabolism that is rewired during ALE. The metabolic rewiring is globally orchestrated by mutations in rpoD altering promoter binding of RNA polymerase. Lastly, the evolved strain has no translational buffering capacity, enabling effective translation of abundant mRNAs. Multi-omic analysis of the evolved strain reveals transcriptome- and translatome-wide remodeling that orchestrate metabolism and growth. These results reveal that failure of prediction may not be associated with understanding individual genes, but rather from insufficient understanding of the strain’s systems biology.

Rapid and assured genetic engineering methods applied to Acinetobacter baylyi ADP1 genome streamlining

“…The overall worse growth of the MGD strains may be the result from metabolic imbalances that result from genome reduction (66) or deletion of quasi-essential genes (18). The deletions most detrimental to growth were in the MGD15 and MGD9 strains.…”

Engineering of membrane complex sphingolipids improves osmotic tolerance of Saccharomyces cerevisiae

“…ALE is a very efficient way to improve industrial strain phenotypes (27, 28). For example, ALE was used to increase the specific growth rate for some genes deletion S. cerevisiae or genome-reduced E.coli with glucose as energy sources (29, 30), or to improve glycerol assimilation ability of S. cerevisiae (31), or enhance Schizochytrium sp. tolerance to high salinity stress (32).…”

Enhancement of Sphingolipid Synthesis Improves Osmotic Tolerance of Saccharomyces cerevisiae

“…ALE is a very efficient way to improve the phenotype of industrial strain (24). For example, ALE has been used to increase the specific growth rate for the deletion of some genes in S. cerevisiae or genome-reduced E. coli with glucose as the energy source (25,26), or enhance Schizochytrium sp. tolerance to high salinity stress (27).…”