High-order epistasis in catalytic power of dihydrofolate reductase gives rise to a rugged fitness landscape in the presence of trimethoprim selection

Tamer, Yusuf Talha and Gazsek, Ilona K. and Abdizadeh, Haleh and Batur, Tuğçe and Reynolds, Kimberly and Atılgan, Ali Rana and Atılgan, Canan and Toprak, Erdal (2019) High-order epistasis in catalytic power of dihydrofolate reductase gives rise to a rugged fitness landscape in the presence of trimethoprim selection. Molecular Biology and Evolution, 36 (7). pp. 1533-1550. ISSN 0737-4038 (Print) 1537-1719 (Online)

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Abstract

Evolutionary fitness landscapes of several antibiotic target proteins have been comprehensively mapped showing strong high-order epistasis between mutations, but understanding these effects at the biochemical and structural levels remained open. Here, we carried out an extensive experimental and computational study to quantitatively understand the evolutionary dynamics of Escherichia coli dihydrofolate reductase (DHFR) enzyme in the presence of trimethopriminduced selection. To facilitate this, we developed a new in vitro assay for rapidly characterizing DHFR steady-state kinetics. Biochemical and structural characterization of resistance-conferring mutations targeting a total of ten residues spanning the substrate binding pocket of DHFR revealed distinct changes in the catalytic efficiencies of mutated DHFR enzymes. Next, we measured biochemical parameters (Km, Ki, and kcat) for a mutant library carrying all possible combinations of six resistance-conferring DHFR mutations and quantified epistatic interactions between them. We found that the high-order epistasis in catalytic power of DHFR (kcat and Km) creates a rugged fitness landscape under trimethoprim selection. Taken together, our data provide a concrete illustration of how epistatic coupling at the level of biochemical parameters can give rise to complex fitness landscapes, and suggest new strategies for developing mutant specific inhibitors.
Item Type: Article
Uncontrolled Keywords: antibiotic resistance; molecular evolution; experimental evolution; epistasis; protein evolution
Subjects: Q Science > Q Science (General)
Divisions: Faculty of Engineering and Natural Sciences > Academic programs > Industrial Engineering
Faculty of Engineering and Natural Sciences > Academic programs > Materials Science & Eng.
Faculty of Engineering and Natural Sciences
Depositing User: Ali Rana Atılgan
Date Deposited: 25 Aug 2019 13:44
Last Modified: 26 Apr 2022 10:06
URI: https://research.sabanciuniv.edu/id/eprint/37619

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