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Analysis of Escherichia coli Global Gene Expression Profiles in Response to Overexpression and Deletion of CspC and CspE

Department of Biochemistry, Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, New Jersey 08854,¹ BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey, 110 Frelinghuysen Road, Piscataway, New Jersey 08854,² Korea Intellectual Property Office, Gov. Complex Darjeon Bldg. 4, Dunsan-dong, Seo-gu, 302-701, Daejeon City, Korea,³ Department of Physics and Astronomy, Rutgers, The State University of New Jersey, 136 Frelinghuysen Road, Piscataway, New Jersey 08854,⁴ Waksman Institute, Department of Biochemistry and Molecular Biology, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, New Jersey 08854⁵

Received 15 December 2005/ Accepted 18 January 2006

The Escherichia coli cold shock protein CspA family consists of nine proteins (CspA to CspI), of which two, CspE and CspC, are constitutively produced at 37°C and are involved in regulation of expression of genes encoding stress response proteins but can also perform an essential function during cold acclimation. In this study, we analyzed global transcript profiles of cells lacking cspE and cspC as well as cells individually overexpressing these proteins or a CspE mutant that is unable to melt nucleic acids and is defective in cold acclimation. The analysis reveals sets of genes whose expression (i) is regulated by CspC and CspE at physiological temperature or cold shock conditions and (ii) depends on the nucleic acid melting function of CspE. Bioinformatic analysis of the latter group reveals that many of those genes contain promoter-proximal sequences that can block transcript elongation and may be targeted by the nucleic acid melting function of CspE.

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