Project description: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.

Project description: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).

Project description:For over 30 years, serine hydroxamate has been used to chemically stimulate a stringent response in Escherichia coli and other bacteria. These studies have elucidated numerous characteristics of the classical stringent response beyond the simple cellular response to an amino acid shortage, including phospholipid synthesis and protease up-regulation. In this study, the effects of a serine hydroxamate addition on high cell density recombinant E. coli were examined and compared to the effects of recombinant protein production to determine overlaps, as recombinant protein production stress has often been attributed to amino acid shortages. Both the transcriptome and growth characteristics were evaluated and compared. The serine hydroxamate addition profoundly decreased the culture growth rate, whereas, recombinant protein production did not. Conversely, the transcriptome profile of the recombinant E. coli cultures were relatively unaffected by the serine hydroxamate addition, yet recombinant protein production dramatically changed the transcriptome profile. A subset of the classical stringent response genes were effected by the serine hydroxamate addition, whereas, recombinant protein production regulated numerous classical stringent response genes; however, not all. The genes that were regulated by the serine hydroxamate addition include numerous fatty acid synthesis genes, in agreement with altered phospholipids synthesis reports. These results indicate that recombinant protein production and the stringent response have many overlapping responses; however, are far from identical. It was hypothesized that recombinant protein production leads to a stringent response due to the high amino acid synthesis demands related to recombinant protein synthesis. A comparison of the transcriptomes during recombinant protein production and a chemical imposed stringent response would assist with determining what portion of the “metabolic burden” associated with recombinant protein production is due to amino acid shortages. In this study, the transcriptome profiles of recombinant E. coli were examined and compared for the three culture conditions: 1) Normal growth, no external stress; 2) L-serine hydroxamate addition (to mediate a stringent response); and 3) IPTG-induction to produce the recombinant protein chloramphenicol acetyltransferase (CAT). The transcriptome profiles from these three conditions were analyzed using Affymetrix Anti-sense E. coli GeneChip® microarrays. Experiment Overall Design: For the serine hydroxamate fermentations, cells were harvested immediately prior to the serine hydroxamate-addition (Time S0) and 1-hour post serine hydroxamate-addition (Time S1). For the IPTG-induced fermentations, cells were harvested immediately prior to the IPTG-addition (Time S0) and 1-hour post-induction (Time S1). For the uninduced (unstressed) fermentations, cells were harvested at Time S0 and Time S1, for which the timing was synchronized with the serine hydroxamate and IPTG fermentations based on OD for Time S0 and time for Time S1. Each fermentation condition was repeated (two biological replicates). RNA from each biological replicates was purified and processed independently. Three biological replicates were obtained for the control condition (Time S0), since prior the serine hydroxamate- or IPTG- addition all fermentations were replicates. Prior to DNA microarray hybridization, where only two biological replicates existed, one of the processed samples was divided into two technical replicates, resulting in three separate hybridized chips. All Time S1 samples contained three technical replicates from two biological duplicates, whereas the control Time S0 measurement contained three biological replicates.

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Metabolomic analysis of riboswitch containing E. coli recombinant expression system

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Metabolomic analysis of riboswitch containing E. coli recombinant expression system.

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