The biochemical architecture of an ancient adaptive landscape

Science. 2005 Oct 21;310(5747):499-501. doi: 10.1126/science.1115649.

Abstract

Molecular evolution is moving from statistical descriptions of adaptive molecular changes toward predicting the fitness effects of mutations. Here, we characterize the fitness landscape of the six amino acids controlling coenzyme use in isopropylmalate dehydrogenase (IMDH). Although all natural IMDHs use nicotinamide adenine dinucleotide (NAD) as a coenzyme, they can be engineered to use nicotinamide adenine dinucleotide phosphate (NADP) instead. Intermediates between these two phenotypic extremes show that each amino acid contributes additively to enzyme function, with epistatic contributions confined to fitness. The genotype-phenotype-fitness map shows that NAD use is a global optimum.

Publication types

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

MeSH terms

  • 3-Isopropylmalate Dehydrogenase / chemistry*
  • 3-Isopropylmalate Dehydrogenase / genetics
  • 3-Isopropylmalate Dehydrogenase / metabolism*
  • Amino Acid Substitution
  • Analysis of Variance
  • Catalysis
  • Epistasis, Genetic
  • Escherichia coli / enzymology
  • Evolution, Molecular*
  • Genotype
  • Kinetics
  • Leucine / biosynthesis
  • Mathematics
  • Models, Chemical
  • Mutation
  • NAD / metabolism*
  • NADP / metabolism*
  • Oxidation-Reduction
  • Phenotype
  • Protein Engineering
  • Selection, Genetic
  • Thermodynamics

Substances

  • NAD
  • NADP
  • 3-Isopropylmalate Dehydrogenase
  • Leucine