Nucleic Acids Research, 2001, Vol. 29, No. 20 4166-4178
© 2001 Oxford University Press
UP element-dependent transcription at the Escherichia coli rrnB P1 promoter: positional requirements and role of the RNA polymerase 
subunit linker
Laboratory of Molecular Microbiology, Division of Genomic Medicine, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, UK, 1School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK, 2Department of Biochemistry, University of Bristol, School of Medical Sciences, University Walk, Bristol BS8 1TD, UK and 3Department of Bacteriology, University of Wisconsin, 1550 Linden Drive, Madison, WI 53706, USA
The UP element stimulates transcription from the rrnB P1 promoter through a direct interaction with the C-terminal domain of the RNA polymerase 
subunit (CTD). We investigated the effect on transcription from rrnB P1 of varying both the location of the UP element and the length of the subunit interdomain linker, separately and in combination. Displacement of the UP element by a single turn of the DNA helix resulted in a large decrease in transcription from rrnB P1, while displacement by half a turn or two turns totally abolished UP element-dependent transcription. Deletions of six or more amino acids from within the subunit linker resulted in a decrease in UP element-dependent stimulation, which correlated with decreased binding of CTD to the UP element. Increasing the linker length was less deleterious to RNA polymerase function at rrnB P1 but did not compensate for the decrease in activation that resulted from displacing the UP element. Our results suggest that the location of the UP element at rrnB P1 is crucial to its function and that the natural length of the subunit linker is optimal for utilisation of the UP element at this promoter.
* To whom correspondence should be addressed. Tel: +44 114 271 2834; Fax: +44 114 273 9926; Email: m.s.thomas{at}shef.ac.uk Correspondence may also be addressed to Richard L. Gourse. Tel: +1 608 262 2914; Fax: +1 608 262 9865; Email: rgourse{at}bact.wisc.eduPresent address:Wenmao Meng, School of Biochemistry and Genetics, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK
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