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",
pmid = "17189297",
pmcid = "PMC1807945",
note = "\htmladdnormallink
{https://alum.mit.edu/www/toms/papers/f{l}exprom/}
{https://alum.mit.edu/www/toms/papers/f{l}exprom/}",
\htmladdnormallink
{http://dx.doi.org/10.1093/nar/gkl956}
{http://dx.doi.org/10.1093/nar/gkl956}",
year = "2007"}

• 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.

Confirmation of Base Flipping in Transcriptional Initiation
Predicted by Information Theory!

In this paper we predicted that base +4 (conventional base number -7) flips out of the DNA to initiate transcription. This was confirmed by two papers:

@article{Feklistov.Darst2011,
author = "A. Feklistov
 and S. A. Darst",
title = "{Structural basis for promoter -10 element recognition by
the bacterial RNA polymerase sigma subunit}",
journal = "Cell",
volume = "147",
pages = "1257--1269",
pmid = "22136875",
pmcid = "PMC3245737",
year = "2011"}
(see Figure 1)

@article{Zhang.Ebright2012,
author = "Y. Zhang
 and Y. Feng
 and S. Chatterjee
 and S. Tuske
 and M. X. Ho
 and E. Arnold
 and R. H. Ebright",
title = "{Structural basis of transcription initiation}",
journal = "Science",
volume = "338",
pages = "1076--1080",
pmid = "23086998",
year = "2012"}
(see reference 11)

@article{Liu.Kornberg2011,
author = "X. Liu
 and D. A. Bushnell
 and R. D. Kornberg",
title = "{Lock and key to transcription: sigma-DNA interaction}",
journal = "Cell",
volume = "147",
pages = "1218--1219",
pmid = "22153066",
year = "2011"}

@article{Darst.Gross2014,
author = "S. A. Darst
 and A. Feklistov
 and C. A. Gross",
title = "{Promoter melting by an alternative sigma, one base at a
time}",
journal = "Nat Struct Mol Biol",
volume = "21",
pages = "350--351",
pmid = "24699085",
comment = "reference 9 cites Shultzaberger.Schneider-flexprom2007",
year = "2014"}

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.

Logo for the sigma⁷⁰ model with conventional numbering.

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: 2017 Jul 14