2019/10/01 by João V. Rodrigues, Eugene I. Shakhnovich · 1 voice · 3 citations
Biochemistry, Genetics and Molecular Biology · #Evolution and Genetic Dynamics #CRISPR and Genetic Engineering #Microbial Metabolic Engineering and Bioproduction
paper · doi:10.7554/elife.50509
openalex publication_date 2019/10/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/06/26
The mechanisms of adaptation to inactivation of essential genes remain unknown. Here we inactivate E. coli dihydrofolate reductase (DHFR) by introducing D27G,N,F chromosomal mutations in a key catalytic residue with subsequent adaptation by an automated serial transfer protocol. The partial reversal G27- > C occurred in three evolutionary trajectories. Conversely, in one trajectory for D27G and in all trajectories for D27F,N strains adapted to grow at very low metabolic supplement (folAmix) concentrations but did not escape entirely from supplement auxotrophy. Major global shifts in metabolome and proteome occurred upon DHFR inactivation, which were partially reversed in adapted strains. Loss-of-function mutations in two genes, thyA and deoB, ensured adaptation to low folAmix by rerouting the 2-Deoxy-D-ribose-phosphate metabolism from glycolysis towards synthesis of dTMP. Multiple evolutionary pathways of adaptation converged to a suboptimal solution due to the high accessibility to loss-of-function mutations that block the path to the highest, yet least accessible, fitness peak.