Nucleic Acids Research Advance Access originally published online on December 22, 2006
Nucleic Acids Research 2007 35(3):771-788; doi:10.1093/nar/gkl956
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Nucleic Acids Research, 2007, Vol. 35, No. 3 771-788
Published by Oxford University Press 2006
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Computational Biology |
Anatomy of Escherichia coli 
70 promoters
Center for Cancer Research Nanobiology Program, National Cancer Institute at Frederick PO Box B, Building 469, Room 144, Frederick, MD 21702-1201, USA
*To whom correspondence should be addressed. Tel: +1 301 846 5581; Fax: +1 301 846 5598; Email: toms{at}ncifcrf.gov
Received September 9, 2006. Revised October 23, 2006. Accepted October 24, 2006.
Information theory was used to build a promoter model that accounts for the –10, the –35 and the uncertainty of the gap between them on a common scale. Helical face assignment indicated that base –7, rather than –11, of the –10 may be flipping to initiate transcription. We found that the sequence conservation of 
70 binding sites is 6.5 ± 0.1 bits. Some promoters lack a –35 region, but have a 6.7 ± 0.2 bit extended –10, almost the same information as the bipartite promoter. These results and similarities between the contacts in the extended –10 binding and the –35 suggest that the flexible bipartite factor evolved from a simpler polymerase. Binding predicted by the bipartite model is enriched around 35 bases upstream of the translational start. This distance is the smallest 5' mRNA leader necessary for ribosome binding, suggesting that selective pressure minimizes transcript length. The promoter model was combined with models of the transcription factors Fur and Lrp to locate new promoters, to quantify promoter strengths, and to predict activation and repression. Finally, the DNA-bending proteins Fis, H-NS and IHF frequently have sites within one DNA persistence length from the –35, so bending allows distal activators to reach the polymerase.
Present addresses: Ryan K. Shultzaberger, Department of Molecular and Cell Biology, University of California, 16 Barker Hall, Berkeley, CA 94720-3202, USA
Karen A. Lewis, Department of Physiology, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390-9040, USA
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