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

Shimon Bershtein,Bogdan Budnik,Jeong-Mo Choi,Eugene Shakhnovich,Sanchari Bhattacharyya

doi:10.1016/j.celrep.2015.03.051

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.

Highlights

Understanding the genotype-phenotype relationship requires vantage points from multiple scales, ranging from the molecular, through the systems, to the cellular/organismal (Lehner, 2013)
The key objective of the present study is to understand to what extent point mutations in a metabolic enzyme and/or variations in the media affect the proteome composition in the bacterial cytoplasm and how these changes are related to the fitness effects of such mutations
Effect of dihydrofolate reductase (DHFR) mutations and media variations on E. coli fitness folA is an optimal target for studying the genotype-phenotype relationship

Summary

Introduction

Understanding the genotype-phenotype relationship requires vantage points from multiple scales, ranging from the molecular, through the systems, to the cellular/organismal (Lehner, 2013). In most cases a direct link between the mutational effects on protein function and organismal phenotype is not obvious due to pleiotropic effects, such as protein aggregation (Drummond and Wilke, 2008) and formation of functional and non-functional multimers (Bershtein et al, 2012; Lynch, 2013; Zhang et al, 2008). Earlier studies showed that bulk characteristics of the macromolecular composition in the cell cytoplasm, e.g., the total protein concentration or the ratio of proteins to RNA, are sensitive to changes in growth conditions, such as the availability of nutrients (Ehrenberg et al, 2013; Klumpp et al, 2009). The key objective of the present study is to understand to what extent point mutations in a metabolic enzyme and/or variations in the media affect the proteome composition in the bacterial cytoplasm and how these changes are related to the fitness effects of such mutations

Objectives

Results

Discussion

Conclusion