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Published online 10 February 2004

Nucleic Acids Research, 2004, Vol. 32, No. 3 1083-1090
© 2004 Oxford University Press

Interactions among CII protein, RNA polymerase and the {lambda} PRE promoter: contacts between RNA polymerase and the –35 region of PRE are identical in the presence and absence of CII protein

Michael T. Marr1, Jeffrey W. Roberts1, Susan E. Brown2, Matthew Klee2 and Gary N. Gussin*,2

1 Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA and 2 Department of Biological Sciences, University of Iowa, Iowa City, IA, USA

*To whom correspondence should be addressed. Tel: +1 319 335 1113; Fax: +1 319 335 1069; Email: gary-gussin{at}uiowa.edu
Present address: Michael T. Marr, Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA

The DNA recognition sequence for the transcriptional activator, CII protein, which is critical for lysogenization by bacteriophage {lambda}, overlaps the –35 region of the PRE promoter. Data presented here show that activation by CII does not change the pattern of cleavage of the –35 region of PRE by iron (S)-1-(p-bromoacetamidobenzyl)-EDTA (Fe-BABE) conjugated to the {sigma} subunit of RNA polymerase (RNAP). Thus, the overall interaction between {sigma} and the –35 region of PRE is not significantly altered by CII. Therefore, the effects of the activator on RNAP binding to the promoter and formation of open complexes do not reflect a large-scale qualitative change in the nature of the interaction between RNAP and promoter DNA. The ability of CII to stimulate lysogenization is reduced in the presence of plasmid-borne rpoA variants encoding alanine substitutions at several positions in the C-terminal domain of the {alpha} subunit. However, it has not been possible to identify residues that directly affect the interaction between the activator and RNA polymerase.


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