Adaptation to mutational inactivation of an essential gene converges to an accessible suboptimal fitness peak

Abstract
Data availability
Article and author information
Metrics

Abstract

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.

Data availability

All data are presented in supplementary datasets S1-S4

The following data sets were generated

1. Rodrigues JR
2. Shakhnovich ES
(2019) Resequencing evolved folA D27 mutant strains
NCBI Bioproject, PRJNA566398.

https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA566398

Article and author information

Author details

João V Rodrigues

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States

Competing interests
The authors declare that no competing interests exist.
Eugene I Shakhnovich

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States

For correspondence
shakhnovich@chemistry.harvard.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-4769-2265

Funding

National Institute of General Medical Sciences (068670)

João V Rodrigues

National Institute of General Medical Sciences (068670)

Eugene I Shakhnovich

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.