ORIGINAL PAPER Sarah W. Harcum Æ Fu’ad T. Haddadin Global transcriptome response of recombinant Escherichia coli to heat-shock and dual heat-shock recombinant protein induction Received: 12 October 2005 / Accepted: 28 February 2006 / Published online: 6 May 2006 Ó Society for Industrial Microbiology 2006 Abstract 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 re- combinant 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 differ- ences. 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 ob- served 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. Keywords Heat-shock response Æ Gene regulation Æ Chloramphenicol acetyltransferase Æ Transcriptome Æ DNA microarrays Æ tRNA Æ Chaperones Introduction Living organisms respond to stressful environmental conditions by redirecting protein synthesis to alleviate cell damage. One of the most widely studied stressful environmental conditions is elevated temperature. The cellular response to elevated temperature is termed the heat-shock response. The heat-shock response in Esc- herichia coli was first described by the Neidhardt and Yura groups in 1978 [26, 46]. These research groups first observed that 20 proteins were very responsive to heat and later determined that the synthesis of these proteins was controlled at the transcription level [13, 23]. Later, these and other researchers identified numerous heat- shock proteins by examining protein levels on two- dimensional electrophoresis gels [20, 46] and RNA levels via hybridization with genomic libraries [4, 5, 29]. These methods provided the foundation for quantifying the heat-shock response and these identification methods have been extended by the complete sequencing of E. coli [2] and the advent of DNA microarrays [13, 31]. Heat-shock proteins are highly conserved across species. Heat-shock proteins monitor and respond to the level of protein folding in the cell [19]. Many heat-shock proteins are chaperones that promote protein folding, while other heat-shock proteins are proteases, which degrade unfolded or damaged proteins [1, 13]. Interest- ingly, many other stresses can also elicit the heat-shock response, such as ethanol, viral infections, and re- combinant protein production [11, 13, 14, 17, 23, 24, 27, 34, 42, 43]. These and other stress response studies S. W. Harcum (&) Department of Bioengineering, Clemson University, 401 Rhodes Engineering Research Center, Clemson SC 29634-0905, USA E-mail: harcum@clemson.edu Tel.: +1-864-6566865 Fax: +1-864-6560567 F. T. Haddadin Department of Chemical and Biomolecular Engineering, Clemson University, 127 Earle Hall, Clemson SC 29634-0910, USA J Ind Microbiol Biotechnol (2006) 33: 801–814 DOI 10.1007/s10295-006-0122-3