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

Abstract

BackgroundElucidation of a genotype-phenotype relationship is critical to understand an organism at the whole-system level. Here, we demonstrate that comparative analyses of multi-omics data combined with a computational modeling approach provide a framework for elucidating the phenotypic characteristics of organisms whose genomes are sequenced.ResultsWe 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.ConclusionsThis 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.

Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli

“…3D). REL607 displays severe growth defects on succinate, as noted previously in a comparison of E. coli B and K12 strains (24). CZB154 does, however, show growth on succinate, and addition of the dctA* mutation to REL607 enables it to grow on succinate.…”

“…Unlike most strains of E. coli K-12, the ancestral strain of E.coli B used in the LTEE cannot use C 4 -dicarboxylates (24). This difference has been attributed an inactivating mutation in the gene for DcuS (24), the sensor kinase in the DcuSR two-component system that regulates genes involved in C 4 -dicarboxylate transport and utilization (25,26). The dctA* promoter mutation apparently enables this gene to be expressed in the absence of activation by DcuSR, permitting transport of C 4 -dicarboxylates.…”

Proteome-wide Subcellular Topologies of E. coli Polypeptides Database (STEPdb)

“…The "basic" K-12 proteome comprises 3897 proteins (supplemental Table S4A). The transcripts encoding 3849 of these polypeptides (42)(43)(44)(45) as well as 3178 of these polypeptides have been detected in cells grown in LB broth (48,49).…”

“…transcribed at mRNA level) were considered to be all genes that have transcripts identified as "present" at either of four microarray datasets (42)(43)(44)(45)(46) or quantified in single cell analyses (44).…”

“…BL21(DE3) is the most widely employed host for the production of recombinant proteins and is considered more robust than K12 strains because of reduced acetate production and absence of some proteases (42,78). More than 90% of each proteome is "common," leaving 266 and 359 proteins unique to K-12 and BL21(DE3) respectively (supplemental Table S1).…”