coli K-12 derivatives. The comparative proteomic and genetic analyses revealed an IS5 disruption of the kdgR gene in two commonly used derivative strains of E. coli K-12, XL1-Blue and DH5α, compared with K-12 wild-type strain

W3110. In addition, a controversial deoR mutation was clarified as a wild type in E. coli DH5α using Inhibitor Library purchase the same approach. This approach should be useful in characterizing the unknown mutations in various mutant strains developed. At the same time, comparative proteomic analysis also revealed the distinct metabolic characteristic of the two derivatives: higher biosynthetic flux to purine nucleotides. This is potentially beneficial for the synthesis of plasmid DNA. Escherichia coli is widely used in laboratory and industry for producing diverse products such as biochemicals, biopolymers, plasmid DNA, and recombinant proteins (Lee et al., 2005; Park et al., 2008). In particular, plasmid DNA production Natural Product Library has attracted considerable attention with the

recent increasing demand for plasmid DNA for gene therapies and vaccination (Kutzler & Weiner, 2008). Although numerous E. coli strains are available as potential host strains including XL1-Blue and DH5α, their genetic and metabolic characteristics remain inadequately studied. This might be explained by the fact that the generation of these strains usually involves random mutations, followed by the selection of a particularly Casein kinase 1 wanted phenotype, and often requires many steps of transfer or the deletion of undefined DNA fragments, thus leading to some unintentional and/or undiscovered mutations. These complex genotypes have often been ignored, but they are becoming increasingly important as we are moving into systems-level studies on these strains (Lee et al., 2005; Park et al., 2008). Comparative proteomics offers a powerful platform technology to study the differentially expressed proteins in response to various genetic and environmental perturbations

(Han & Lee, 2003, 2006). This technology has been used for the study of cell physiology and the identification of new biomarkers (Han & Lee, 2003; Meng & Veenstra, 2007). However, to date, there has been no report on the use of comparative proteomics to identify genetic mutations. It was reasoned that mutations in the structural as well as the regulatory genes could be identified by examining the differentially expressed proteins, which can be confirmed by further genetic analysis such as PCR and DNA sequencing. To demonstrate a proof of concept, we performed a comparative proteomic analysis of two E. coli K-12 derivatives XL1-Blue and DH5α with the sequenced wild-type strain. An unknown kdgR mutation was identified in the two derivatives. In addition, a controversial deoR mutation was clarified as a wild type in E. coli DH5α using the same approach. The wild-type E. coli K-12 W3110 (Korean Collection for Type Cultures number 2223, Daejeon, Korea) was used as a reference.