Genomic analysis of high-cell-density recombinant Escherichia coli fermentation and "cell conditioning" for improved recombinant protein yield

The Escherichia coli stress gene transcription profile and response to reco mbinant protein overexpression were substantially altered at high cell dens ity when compared with low cell density. Reverse transcription-polymerase c hain reaction RT-PCR-amplified mRNA from low (4 g[DCW]/L) and high-cell-den sity 143.5 g [DCW]/L) conditions were hybridized with a DNA microarray of K ohara clones encompassing 16% of the E. coli genome, and differentially dis played genes were identified. Transcript-specific RNA dot blots indicated t hat molecular chaperones (groEL, ibpA, degP), proteases (degP, ftsH), the l ysis gene mltB, and DNA damage/bacteriophaae-associated gene transcript lev els (ftsH, recA, alpA, uvrB) increased 10- to 43-fold at high cell density. In addition, overexpression of recombinant green fluorescent protein (GFP( uv))/chloramphenicol acetyltransferase (CAT) fusion protein did not change the rates of cell growth or cell lysis. The stress gene transcription profi le at high cell density was used to evaluate "cell conditioning" strategies to alter the levels of chaperones, proteases, and other intracellular prot eins prior to recombinant protein overexpression. Interestingly, the additi on of 1 g/L dithiothreitol (DTT) 20 min prior to induction of a GFP(uv)/CAT fusion protein resulted in a twofold increase in CAT activity when compare d with the unconditioned controls. In addition, RNA dot blots of five stres s genes confirmed that cell conditioning strategies significantly altered t he dyn a mic stress ge ne response to foreign protein overexpression. (C) 2 001 John Wiley & Sons, Inc.