Comparative multi-omics systems analysis of Escherichia coli strains B and K-12

We present a comprehensive analysis of genome-wide measurements incorporating multifaceted holistic data - genome, transcriptome, proteome, and phenome - to determine the differences between Escherichia coli B and K-12 strains. A genome-scale metabolic network of E. coli B was reconstructed and used to identify genetic bases of the phenotypes unique to B compared with K-12 through in silico complementation testing. This systems analysis revealed that E. coli B is well-suited for production of recombinant proteins due to a greater capacity for amino acid biosynthesis, fewer proteases, and lack of flagella. Furthermore, E. coli B has an additional type II secretion system and a different cell wall and outer membrane composition predicted to be more favorable for protein secretion. In contrast, E. coli K-12 showed a higher expression of heat shock genes and was less susceptible to certain stress conditions.This integrative systems approach provides a high-resolution system-wide view and insights into why two closely related strains of E. coli, B and K-12, manifest distinct phenotypes. Therefore, systematic understanding of cellular physiology and metabolism of the strains is essential not only to determine culture conditions but also to design recombinant hosts.Escherichia coli is one of the most intensively studied organisms and has been widely employed in scientific studies and industrial applications. The most widely used E. coli have been those derived from strains B and K-12, the result of pioneering work using K-12 for genetic and biochemical studies and B for studying virulent bacteriophages, restriction systems, mutagenic assays, and bacterial evolution [1,2]. The first whole-genome sequence of strain K-12, MG1655, was determined [3] and compared in detail with another K-12 strain, W3110 [4]. We have determined genome sequences of B strains [5,6] - REL606, which has been applied to the study of long-term experimental evolution, and BL21(DE3), which has been use