Purifying selection acting on the sequence of highly expressed proteins in the microevolution

Constraints on the rate of protein sequence evolution have been a central question in evolutionary biology. Orthology analysis between closely related species has revealed that the evolutionary speed is constrained by the expression level, with highly expressed proteins evolving slowly. This negative correlation between expression levels and evolutionary rates (known as the E-R anticorrelation) has already been widely observed in past macroevolution between species, for example, between Escherichia coli and Salmonella. However, it remains unclear whether this seemingly general law also governs microevolution, including past and de novo, within a species. To explore the ubiquitous impact of expression level on molecular evolution in bacteria, we analysed genome sequences for 99 strains of E. coli for microevolution in nature. We also analysed genomic mutations accumulated under laboratory conditions as a model of de novo microevolution. Here, we show that the E-R anticorrelation is significant in both past microevolution and de novo evolution in E. coli. Our data also indicate that purifying selection acting on highly expressed genes contributes to the ubiquity of the E-R anticorrelation. This study confirmed ongoing purifying selection acting on highly expressed genes, and implied that expression level has a ubiquitous impact on the speed of molecular diversification evolution in bacteria. Transcriptomes of the 6 evolved strains and their ancestral strain of E. coli were compared by microarray analysis. Cells were grown on the modified M63 medium and total RNA was extracted from the cells in the exponential growth phase.