H-085. Genome-Wide Transcriptional Responses of Different Escherichia coli Strains to Recombinant Protein Overproduction

M. Kim, S. Park, D-B. Oh, H. Kang, O. Kwon;
Korea Res. Inst. of Bioscience and Biotechnology, Daejeon, REPUBLIC OF KOREA.

The Gram-negative bacterium Escherichia coli is one of the most widely used hosts for heterologous protein expression and perhaps the best characterized organism for genetic and molecular biology studies. In this study, we investigated the global transcriptome profiles of four commonly used E. coli strains, JM109(DE3), BL21(DE3), C41(DE3), and C43(DE3), in response to overproduction of heterologous cytosolic or secretory proteins. When a secretory protein was overexpressed in JM109(DE3) or BL21(DE3), between 120 and 150 genes in each strain were either up- or down-regulated by at least twofold. However, in cases of cytosolic protein overexpression, the numbers of up- or down-regulated genes were between 170 and 200. Interestingly, the numbers of differently expressed genes in both C41(DE3) and C43(DE3) strains were less than half compared to those observed in JM109(DE3) or BL21(DE3). Even though more than 20% of the differently expressed genes in each case were found to encode proteins of hypothetical or unknown functions, In brief, the majority of up-regulated genes upon recombinant protein overexpression were functionally grouped into those responsible for translation and post-translational modification, and cell processes. In contrast, the majority of down-regulated genes were functionally categorized into transport and binding proteins, and amino acid biosynthesis and metabolism. It is noteworthy that various stress responsive genes, such as heat shock and phage shock were commonly induced irregardless of the type of overexpressed proteins. However, the secretory protein overproduction specifically induced genes involved in the envelop stress response. Since our transcriptome profiling data also include various target or strain specific genes, it will provide useful information to understand and to develop E. coli as an efficient cell factory for recombinant protein production. This work was supported by the 21st Century Frontier R&D Program grant of the Ministry of Science and Technology (MOST) and by the Basic Research Program grant (R01-2005-000-10288-0) of the Korea Science & Engineering Foundation (KOSEF).