Pervasive Pairwise Intragenic Epistasis among Sequential Mutations in TEM-1 β-Lactamase

J Mol Biol. 2019 May 3;431(10):1981-1992. doi: 10.1016/j.jmb.2019.03.020. Epub 2019 Mar 25.


Interactions between mutations play a central role in shaping the fitness landscape, but a clear picture of intragenic epistasis has yet to emerge. To further reveal the prevalence and patterns of intragenic epistasis, we present a survey of epistatic interactions between sequential mutations in TEM-1 β-lactamase. We measured the fitness effect of ~12,000 pairs of consecutive amino acid substitutions and used our previous study of the fitness effects of single amino acid substitutions to calculate epistasis for over 8000 mutation pairs. Since sequential mutations are prone to physically interact, we postulated that our study would be surveying specific epistasis instead of nonspecific epistasis. We found widespread negative epistasis, especially in beta-strands, and a high frequency of negative sign epistasis among individually beneficial mutations. Negative epistasis (52%) occurred 7.6 times as frequently as positive epistasis (6.8%). Buried residues experienced more negative epistasis that surface-exposed residues. However, TEM-1 exhibited a couple of hotspots for positive epistasis, most notably L221/ R222 at which many combinations of mutations positively interacted. This study is the first to systematically examine pairwise epistasis throughout an entire protein performing its native function in its native host.

Keywords: antibiotic resistance protein; epistasis; fitness landscapes; protein evolution.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Substitution
  • Epistasis, Genetic
  • Escherichia coli / chemistry
  • Escherichia coli / genetics*
  • Escherichia coli Infections / microbiology
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / genetics*
  • Evolution, Molecular
  • Genetic Fitness
  • Humans
  • Models, Molecular
  • Mutation
  • Protein Conformation
  • beta-Lactamases / chemistry
  • beta-Lactamases / genetics*


  • Escherichia coli Proteins
  • beta-Lactamases
  • beta-lactamase TEM-1