Similarity of the Escherichia coli proteome upon completion of different biopharmaceutical fermentation processes

A comprehensive view of the physiological state of Escherichia coli cells a t the completion of fermentation processes for biopharmaceutical production was attained via two-dimensional gel electrophoretic analysis of cellular proteins. For high cell density fermentations in which phosphate is deplete d to induce recombinant protein expression from the alkaline phosphatase pr omoter, proteome analysis confirms that phosphate limitation occurs. Known phosphate starvation inducible proteins are observed at high levels; these include the periplasmic phosphate binding protein and the periplasmic phosp honate binding protein. The phn (EcoK) locus of these E coli K-12 strains r emains cryptic, as demonstrated by failure to grow with phosphonate as the sole phosphorus source. Proteome analysis also provided evidence that cells utilize alternative carbon and energy sources during these fermentation pr ocesses. To address regulatory issues in the biopharmaceutical industry, co mparative electrophoretic analyses were conducted on a qualitative basis fo r four different fermentation processes. Using this approach, the protein p rofiles for these processes were found to be highly similar, with the vast majority (85-90%) of proteins detected in all profiles. The observed simila rity in proteomes suggests that multiproduct host cell protein immunoassays are a feasible means of quantifying host-derived polypeptides from a varie ty of biopharmaceutical fermentation processes.