flexprom: Anatomy of Escherichia coli sigma⁷⁰ promoters

@article{Shultzaberger.Schneider-flexprom2007,
author = "R. K. Shultzaberger
 and Zehua Chen
 and Karen A. Lewis
 and T. D. Schneider",
title = "{Anatomy of \emph{Escherichia coli} $\sigma^{70}$ promoters}",
journal = "Nucleic Acids Res.",
volume = "35",
pages = "771--788",
note = "\htmladdnormallink
{http://www.ccrnp.ncifcrf.gov/\~{}toms/paper/f{l}exprom/}
{http://www.ccrnp.ncifcrf.gov/\~{}toms/paper/f{l}exprom/}",
comment = "former name Shultzaberger.Schneider-flexprom2005",
year = "2007"}

• PubMed entry
• Links at Nucleic Acids Research:
  • Abstract
  • Full Text
  • PDF
  • Article Data Webpage
• submitted manuscript PDF: flexprom.pdf
• Supplementary data: flexprom-supplement.txt
• Program: The multiscan program is used to generate complex lister maps such as the one shown above.

Start coordinates for sigma⁷⁰ in E. coli accession U00096:
sigma70_start_coords.txt

Components for the sigma⁷⁰ model

prom.eps is the original Figure 1 of the paper.

We used this structure given by Campbell.Darst2002 to determine how the sigma 70 -35 binds to DNA.

@article{Campbell.Darst2002,
author = "E. A. Campbell
and O. Muzzin
and M. Chlenov
and J. L. Sun
and C. A. Olson
and O. Weinman
and M. L. Trester-Zedlitz
and S. A. Darst",
title = "{Structure of the bacterial RNA polymerase promoter
specificity $\sigma$ subunit}",
journal = "Mol Cell",
volume = "9",
pages = "527--539",
pmid = "11931761",
year = "2002"}

These files show how the 4.2 part of the sigma protein binds into the -35 region of a promoter. Run them as:

rasmolscript 1KU7.pdb -script 1KU7.ras
rasmolscript 1KU7-nowater.pdb -script 1KU7-nowater.ras

• 1KU7.pdb original structure from PDB
• 1KU7.ras rasmol controls for original structure from PDB
• 1KU7-nowater.pdb. The waters have been removed, the second copy of 4.2 is removed.
• 1KU7-nowater.ras A series of displays show how the -35 is aligned and then show upstream contact amino acids.

• See also the companion paper, Anatomy of Escherichia coli Ribosome Binding Sites

• The Delila Server allows you to try the model on the E. coli genome.

• Instructions for Refining Binding Sites

Other pointers:

• Primer on information theory
• A Glossary for Molecular Information Theory and the Delila System. A good starting point would be the definition of a bit.

Tom Schneider

Schneider Lab
origin: 2004 May 13
updated: 2010 Jul 02