ABSTRACT: The transcriptome profiles for wild-type (plasmid-free) and recombinant (plasmid-bearing) Escherichia coli during well-controlled synchronized high-cell-density fed-batch cultures were analyzed by DNA microarrays. It was observed that the growth phase significantly affected the transcriptome profiles, and the transcriptome profiles were significantly different for the recombinant and wild-type cultures. The response of the wild-type and recombinant cultures to an isopropyl-1-thio-β-D-galactopyranoside- (IPTG-) addition was examined, where IPTG induced recombinant protein production in the plasmid-bearing cultures. The IPTG-addition significantly altered the transcriptome response of the wild-type cultures entering the stationary phase. The IPTG-induced recombinant protein production resulted in a significant down-regulation of many energy synthesis genes (atp, nuo, cyo), as well as nearly all transcription- and translation-related genes (rpo, rpl, rpm, rps, rrf, rrl, rrs). Numerous phage (psp, hfl) and transposon-related genes (tra, ins) were significantly regulated in the recombinant cultures due to the IPTG-induction. These results indicate that the signaling mechanism, associated with the recombinant protein production, may induce a metabolic burden in the form of a phage defense mechanism. Taken together, these results indicated that recombinant protein production initiated a cascade of transcriptome responses that down-regulated the very genes needed to sustain productivity. In this study, the transcriptome profiles for recombinant and wild-type E. coli cultures were compared. The recombinant and wild-type cultures were monitored during the exponential growth phase and as the cultures entered the stationary phase. Well-controlled fed-batch fermenters were used to synchronize the high-cell density cultures. E. coli MG1655 [pPROEx-CAT] and E. coli MG1655 (plasmid-free) were exposed to IPTG in the exponential phase, where chloramphenicol acetyltransferase (CAT) expression was induced in the plasmid-bearing cultures. Control cultures, not exposed to IPTG, were also examined. The gene expression profiles were determined using DNA microarrays. Recombinant protein production was shown to result in a metabolic burden due to significant down-regulation of the transcription, translation, and energy synthesis genes. This was the first comprehensive study that has examined the transcriptome of wild-type and recombinant cultures under the same set of conditions. This data indicated that one cannot merely extrapolate the behavior of recombinant cultures from wild-type culture data. Experiment Overall Design: All fermentations were synchronized in time to the time at which the cell density reached approximately 11.5 OD, or roughly 70% of the fermenter’s maximum cell density. IPTG (5 mM) was added when the cell density reached the targeted OD for the cultures to be induced. Cells were harvested at 0, 1, 2, 3, 4, and 5 hours relative to the synchronization time point (identified as Time S0, S1, etc). Each fermentation condition was conducted in duplicate. For the recombinant Control Time S0 sample, triplicate samples were available since prior to the IPTG-addition, all fermentations within a strain were replicates. All fermentation conditions were repeated twice (two biological replicates). RNA from each biological replicate was purified and processed independently. Three biological replicates were obtained from for the recombinant Control sample (Time S0) since the cultures prior to the IPTG-addition were replicates. Prior to hybridization, where only two biological replicates existed, one of the RNA samples was divided into two technical replicates, resulting in three separate hybridized chips. The wild-type Time S0 samples and all Time S1 and S4 samples contained data from three DNA microarrays obtained from two biological duplicates (30 DNA microarrays total).
