Transcription profiling of recombinant E. coli to heat-shock and dual heat-shock recombinant protein induction


Recombinant Escherichia coli cultures are used to manufacture numerous therapeutic proteins and industrial enzymes, where many of these processes use elevated temperatures to induce recombinant protein production. The heat-shock response in wild-type E. coli has been well studied. In this study, the transcriptome profiles of recombinant E. coli subjected to a heat-shock and to a dual heat-shock recombinant protein induction were examined. Most classical heat-shock protein genes were identified as regulated in both conditions. The major transcriptome differences between the recombinant and reported wild-type cultures were heavily populated by hypothetical and putative genes, which indicates recombinant cultures utilize many unique genes to respond to a heat-shock. Comparison of the dual stressed culture data with literature recombinant protein induced culture data revealed numerous differences. The dual stressed response encompassed three major response patterns: induced-like, in-between, and greater than either individual stress response. Also, there were no genes that only responded to the dual stress. The most interesting difference between the dual stressed and induced cultures was the amino acid-tRNA gene levels. The amino acid-tRNA genes were elevated for the dual cultures compared to the induced cultures. Since tRNAs facilitate protein synthesis via translation, this observed increase in amino acid-tRNA transcriptome levels, in concert with elevated heat-shock chaperones, might account for improved productivities often observed for thermo-inducible systems. Most importantly, the response of the recombinant cultures to a heat-shock was more profound than wild-type cultures, and further, the response to recombinant protein induction was not a simple additive response of the individual stresses. The objective of the present work is to gain a better understanding of the heat-shock response in recombinant cultures and how this response might impact recombinant protein production. To accomplish this objective, the transcriptome response of recombinant cultures subjected to a heat-shock and a dual heat-shock recombinant protein induction were analyzed. The transcriptome levels were determined using Affymetrix E. coli Antisense DNA microarrays, such that the entire genome was evaluated. These two transcriptome responses were also compared to recombinant cultures at normal growth temperature that were not over-expressing the recombinant protein and a set of literature recombinant culture data that were chemically induced to over-express the recombinant protein. Additionally, the heat-shock response of the recombinant cultures was compared to the literature report of the heat-shock response in wild-type cultures. The results of the global transcriptome analysis demonstrated that recombinant cultures respond differently to a heat-shock stress than wild-type cultures, where the transcriptome response of the recombinant cultures is further modified by production of a recombinant protein. Experiment Overall Design: The heat-shock and recombinant protein production phases were synchronized to the cell density of 11.5 OD, which is referred to as Sample Time 0. For the heat-shocked cultures, the temperature was increased from 37°C to 50°C over 8 minutes beginning at Sample Time 0. The temperature and duration used in this study are the same conditions used to evaluate the heat-shock in wild-type cultures. The temperature was then decreased from 50°C to 37°C over 4 minutes. For the dual heat-shocked recombinant protein production cultures, 5 mM IPTG was added 8 minutes after Sample Time 0. The unstressed recombinant cultures were conducted similarly, except without the heat-shock or IPTG-addition. Each sample condition was obtained from at least two separate fermentations (two biological replicates). RNA from each biological replicate was purified and processed independently. Prior to hybridization, where only two biological replicates existed, one of the processed samples was divided (two technical replicates), resulting in three separate hybridized chips. The heat-shocked and dual stressed culture samples all consisted of three technical replicates from two biological duplicates. For the unstressed culture samples, triplicate samples were obtained for the 11.5 OD and duplicates for the 14 OD conditions. There were no statistical differences between the 11.5 and 14 OD unstressed samples (p ≤ 0.001). Thus, the unstressed culture transcriptome profile consisted of six technical replicates from five biological replicates and four independent fermentations.

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