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The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions.

Shimada, Tomohiro and Ishihama, Akira and Busby, Stephen J. W. and Grainger, David C. (2008) The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions. Nucleic Acids Research, 36 (12). pp. 3950-3955. ISSN 0305-1048

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URL of Published Version: http://nar.oxfordjournals.org/cgi/content/full/36/12/3950

Identification Number/DOI: 10.1093/nar/gkn339

The Escherichia coli RutR protein is the master regulator of genes involved in pyrimidine catabolism. Here we have used chromatin immunoprecipitation in combination with DNA microarrays to measure the binding of RutR across the chromosome of exponentially growing E. coli cells. Twenty RutR-binding targets were identified and analysis of these targets generated a DNA consensus logo for RutR binding. Complementary in vitro binding assays showed high-affinity RutR binding to 16 of the 20 targets, with the four low-affinity RutR targets lacking predicted key binding determinants. Surprisingly, most of the DNA targets for RutR are located within coding segments of the genome and appear to have little or no effect on transcript levels in the conditions tested. This contrasts sharply with other E. coli transcription factors whose binding sites are primarily located in intergenic regions. We suggest that either RutR has yet undiscovered function or that evolution has been slow to eliminate non-functional DNA sites for RutR because they do not have an adverse effect on cell fitness.

Type of Work:Article
Date:30 May 2008 (Publication)
School/Faculty:Schools (1998 to 2008) > School of Biosciences
Department:Molecular Microbiology
Subjects:QR Microbiology
Institution:University of Birmingham
Copyright Holders:Oxford journals
ID Code:90
Refereed:YES
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