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J. Biol. Chem., Vol. 280, Issue 18, 17758-17768, May 6, 2005

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The Global Transcriptional Response of Escherichia coli to Induced ³² Protein Involves ³² Regulon Activation Followed by Inactivation and Degradation of ³² in Vivo^*

Kai Zhao, Mingzhu Liu¶, and Richard R. Burgess||

From the McArdle Laboratory for Cancer Research, the Department of Genetics, and the ^¶Department of Computer Science, University of Wisconsin, Madison, Wisconsin 53706

³² is the first alternative factor discovered in Escherichia coli and can direct transcription of many genes in response to heat shock stress. To define the physiological role of ³², we have used transcription profiling experiments to identify, on a genome-wide basis, genes under the control of ³² in E. coli by moderate induction of a plasmid-borne rpoH gene under defined, steady-state growth conditions. Together with a bioinformatics approach, we successfully confirmed genes known previously to be directly under the control of ³² and also assigned many additional genes to the ³² regulon. In addition, to understand better the functional relevance of the increased amount of ³² to changes in the transcriptional level of ³²-dependent genes, we measured the protein level of ³² both before and after induction by a newly developed quantitative Western blot method. At a normal constant growth temperature (37 °C), we found that the ³² protein level rapidly increased, plateaued, and then gradually decreased after induction, indicating ³² can be regulated by genes in its regulon and that the mechanisms of ³² synthesis, inactivation, and degradation are not strictly temperature-dependent. The decrease in the transcriptional level of ³²-dependent genes occurs earlier than the decrease in full-length ³² in the wild type strain, and the decrease in the transcriptional level of ³²-dependent genes is greatly diminished in a DnaK strain, suggesting that DnaK can act as an anti- factor to functionally inactivate ³² and thus reduce ³²-dependent transcription in vivo.

Received for publication, January 12, 2005

^* This work was supported by NIGMS Grant GM28575 from the National Institutes of Health (to R. R. B.). In compliance with the University of Wisconsin, Madison, Conflict of Interest Committee Policy, R. R. B. acknowledges financial interest in NeoClone, LLC. (Madison, WI), which markets the proteins and mAbs in this study. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

^|| To whom correspondence should be addressed: McArdle Laboratory for Cancer Research, University of Wisconsin, Madison, 1400 University Ave., Madison, WI 53706. Tel.: 608-263-2635; Fax: 608-262-2824; E-mail: rburgess{at}wisc.edu.

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