Nature Structural & Molecular Biology
- 13, 806 - 814 (2006)
Published online: 6 August 2006; | doi:10.1038/nsmb1130
Extensive functional overlap between  factors in Escherichia coliJoseph T Wade1, Daniel Castro Roa2, David C Grainger3, Douglas Hurd4, Stephen J W Busby3, Kevin Struhl1 & Evgeny Nudler21
Department of Biological Chemistry and Molecular Pharmacology, Harvard University, Boston, Massachusetts 02115, USA. 2
Department of Biochemistry, New York University School of Medicine, New York, New York 10016, USA. 3
School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK. 4
Oxford Gene Technology, Begbroke Science Park, Sandy Lane, Yarnton, Oxford OX5 1PF, UK.
Correspondence should be addressed to Evgeny Nudler evgeny.nudler@med.nyu.edu or Kevin Struhl kevin@hms.harvard.edu Bacterial core RNA polymerase (RNAP) must associate with a  factor to recognize promoter sequences. Escherichia coli encodes seven factors, each believed to be specific for a largely distinct subset of promoters. Using microarrays representing the entire E. coli genome, we identify 87 in vivo targets of
32, the heat-shock factor, and estimate that there are 120–150 32 promoters in total. Unexpectedly, 25% of these 32 targets are located within coding regions, suggesting novel regulatory roles for 32. The majority of 32 promoter targets overlap with those of 70, the housekeeping factor. Furthermore, their DNA sequence motifs are often interdigitated, with RNAP70 and RNAP32 initiating transcription in vitro with similar efficiency and from identical positions. E-regulated promoters also overlap extensively with those for 70. These results suggest that extensive functional overlap between factors is an important phenomenon.
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