Systems-level response to point mutations in a core metabolic enzyme modulates genotype-phenotype relationship

Cell Rep. 2015 Apr 28;11(4):645-56. doi: 10.1016/j.celrep.2015.03.051. Epub 2015 Apr 16.


Linking the molecular effects of mutations to fitness is central to understanding evolutionary dynamics. Here, we establish a quantitative relation between the global effect of mutations on the E. coli proteome and bacterial fitness. We created E. coli strains with specific destabilizing mutations in the chromosomal folA gene encoding dihydrofolate reductase (DHFR) and quantified the ensuing changes in the abundances of 2,000+ E. coli proteins in mutant strains using tandem mass tags with subsequent LC-MS/MS. mRNA abundances in the same E. coli strains were also quantified. The proteomic effects of mutations in DHFR are quantitatively linked to phenotype: the SDs of the distributions of logarithms of relative (to WT) protein abundances anticorrelate with bacterial growth rates. Proteomes hierarchically cluster first by media conditions, and within each condition, by the severity of the perturbation to DHFR function. These results highlight the importance of a systems-level layer in the genotype-phenotype relationship.

Publication types

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

MeSH terms

  • Escherichia coli / enzymology
  • Escherichia coli / genetics*
  • Escherichia coli / growth & development
  • Escherichia coli / metabolism
  • Genetic Fitness
  • Genotype*
  • Phenotype*
  • Point Mutation*
  • Proteome / genetics
  • Proteome / metabolism
  • Tetrahydrofolate Dehydrogenase / genetics*
  • Tetrahydrofolate Dehydrogenase / metabolism


  • Proteome
  • Tetrahydrofolate Dehydrogenase

Associated data

  • BioProject/PRJNA277706
  • SRA/SAMN03393359
  • SRA/SRX951916
  • SRA/SRX951945
  • SRA/SRX951946
  • SRA/SRX951950
  • SRA/SRX951951