title: Systems-level response to point mutations in a core metabolic enzyme modulates genotype-phenotype relationship.
abstract: 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.
authors.affiliation: Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA; Department of Life Sciences, Ben-Gurion University of the Negev, P.O. Box 653, Beer-Sheva 8410501, Israel.
authors.forename: Shimon
authors.initials: S
authors.lastname: Bershtein
authors.affiliation: Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
authors.forename: Jeong-Mo
authors.initials: JM
authors.lastname: Choi
authors.affiliation: Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
authors.forename: Sanchari
authors.initials: S
authors.lastname: Bhattacharyya
authors.affiliation: MSPRL, Center of Systems Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
authors.forename: Bogdan
authors.initials: B
authors.lastname: Budnik
authors.affiliation: Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA. Electronic address: shakhnovich@chemistry.harvard.edu.
authors.forename: Eugene
authors.initials: E
authors.lastname: Shakhnovich
mesh_terms: D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D056084:Genetic Fitness; D005838:Genotype; D010641:Phenotype; D017354:Point Mutation; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D013762:Tetrahydrofolate Dehydrogenase / Q000235:genetics* / Q000378:metabolism
chemical_list: D020543:Proteome; D013762:Tetrahydrofolate Dehydrogenase