A high-throughput percentage-of-binding strategy to measure binding energies in DNA–protein interactions: application to genome-scale site discovery

Wang, Xiaohu; Gao, Haichun; Shen, Yufeng; Weinstock, George M.; Zhou, Jizhong; Palzkill, Timothy

doi:10.1093/nar/gkn477

A high-throughput percentage-of-binding strategy to measure binding energies in DNA–protein interactions: application to genome-scale site discovery

Journal Article · Wed Jul 23 00:00:00 EDT 2008 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkn477· OSTI ID:1625449

Wang, Xiaohu ^[1]; Gao, Haichun ^[2]; Shen, Yufeng ^[3]; Weinstock, George M. ^[4]; Zhou, Jizhong ^[5]; Palzkill, Timothy ^[5]

Baylor Univ., Houston, TX (United States); DOE/OSTI
Univ. of Oklahoma, Norman, OK (United States). Inst. for Environmental Genomics. Dept. of Botany and Microbiology; Zhejiang Univ. of Technology, Hangzhou (China)
Baylor Univ., Houston, TX (United States). College of Medicine. Human Genome Sequencing Center
Univ. of Oklahoma, Norman, OK (United States). Inst. for Environmental Genomics. Dept. of Botany and Microbiology
Baylor Univ., Houston, TX (United States)

Quantifying the binding energy in DNA–protein interactions is of critical importance to understand transcriptional regulation. Based on a simple computational model, this study describes a high-throughput percentage-of-binding strategy to measure the binding energy in DNA–protein interactions between the Shewanella oneidensis ArcA two-component transcription factor protein and a systematic set of mutants in an ArcA-P (phosphorylated ArcA) binding site. The binding energies corresponding to each of the 4 nt at each position in the 15-bp binding site were used to construct a position-specific energy matrix (PEM) that allowed a reliable prediction of ArcA-P binding sites not only in Shewanella but also in related bacterial genomes.

View Accepted Manuscript (DOE)

Research Organization:: Baylor University, Houston, TX (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

OSTI ID:: 1625449

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: 15 Vol. 36; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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The Influence of Repressor DNA Binding Site Architecture on Transcriptional Control Park, Dan M.; Kiley, Patricia J. mBio, Vol. 5, Issue 5 https://doi.org/10.1128/mbio.01684-14	journal	August 2014
Inference of Self-Regulated Transcriptional Networks by Comparative Genomics Cornish, Joseph P.; Matthews, Fialelei; Thomas, Julien R. SAGE https://doi.org/10.13016/m2zmzn-jazc	collection	January 2012
The Bacterial Response Regulator ArcA Uses a Diverse Binding Site Architecture to Regulate Carbon Oxidation Globally Park, Dan M.; Akhtar, Md. Sohail; Ansari, Aseem Z. PLoS Genetics, Vol. 9, Issue 10 https://doi.org/10.1371/journal.pgen.1003839	journal	October 2013
Modeling the Quantitative Specificity of DNA-Binding Proteins from Example Binding Sites Homsi, Dana S. F.; Gupta, Vineet; Stormo, Gary D. PLoS ONE, Vol. 4, Issue 8 https://doi.org/10.1371/journal.pone.0006736	journal	August 2009
Physiological Roles of ArcA, Crp, and EtrA and Their Interactive Control on Aerobic and Anaerobic Respiration in Shewanella oneidensis Gao, Haichun; Wang, Xiaohu; Yang, Zamin K. PLoS ONE, Vol. 5, Issue 12 https://doi.org/10.1371/journal.pone.0015295	journal	December 2010
Endogenous generation of hydrogen sulfide and its regulation in Shewanella oneidensis Wu, Genfu; Li, Ning; Mao, Yinting Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00374	journal	April 2015
Evolutionary meandering of intermolecular interactions along the drift barrier Lynch, Michael; Hagner, Kyle Proceedings of the National Academy of Sciences, Vol. 112, Issue 1 https://doi.org/10.1073/pnas.1421641112	journal	December 2014

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