Bershtein Shimon, Choi Jeong-Mo, Bhattacharyya Sanchari, Budnik Bogdan, Shakhnovich Eugene
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.
Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
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.
将突变的分子效应与适应性联系起来是理解进化动力学的核心。在此，我们建立了突变对大肠杆菌蛋白质组的全局效应与细菌适应性之间的定量关系。我们构建了在编码二氢叶酸还原酶（DHFR）的染色体folA基因中具有特定去稳定化突变的大肠杆菌菌株，并使用串联质量标签及随后的液相色谱-串联质谱法对突变菌株中2000多种大肠杆菌蛋白质丰度的后续变化进行了定量分析。同时还对相同大肠杆菌菌株中的mRNA丰度进行了定量分析。DHFR突变的蛋白质组学效应与表型在数量上相关联：相对（相对于野生型）蛋白质丰度对数分布的标准差与细菌生长速率呈反相关。蛋白质组首先按培养基条件进行分层聚类，并且在每种条件下，再按对DHFR功能的扰动严重程度进行聚类。这些结果突出了系统层面在基因型-表型关系中的重要性。
