Modification of complex microbial cellular processes is often necessary to obtain organisms with particularly favorable characteristics, but such experiments can take many generations to achieve. In the present article, we accelerated the experimental evolution of Escherichia coli populations under selection for improved growth using one of the restriction-modification systems, which have shaped bacterial genomes. This resulted in faster evolutionary changes in both the genome and bacterial growth. Transcriptome/genome analysis at various stages enabled prompt identification of sequential genome rearrangements and dynamic gene-expression changes associated with growth improvement. The changes were related to cell-to-cell communication, the cell death program, as well as mass production and energy consumption. These observed changes imply that improvements in microorganism population growth can be achieved by inactivating the cellular mechanisms regulating fraction of active cells in a population. Some of the mutations were shown to have additive effects on growth. These results open the way for the application of evolutionary genome engineering to generate organisms with desirable properties.