Local Gene Regulation Details a Recognition Code within the LacI Transcriptional Factor Family
Name
Camas-2010-Local Gene Regulation Details a Recognition Code within the LacI Transcriptional Factor Family.pdf
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1.12 MB
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Adobe PDF
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61da1da56686719620c1418e6247f554
Author(s)
Camas, Francisco M.
Alm, Eric J.
Poyatos, Juan F.
Date Issued
November 2010
Journal
PLoS Computational Biology
Publisher
Public Library of Science
Citation
Camas, Francisco M., Eric J. Alm, and Juan F. Poyatos. "Local Gene Regulation Details a Recognition Code within the LacI Transcriptional Factor Family." PLoS Computational Biology 6(11): e1000989.
Version
Final published version
Abstract
The specific binding of regulatory proteins to DNA sequences exhibits no clear patterns of association between amino acids (AAs) and nucleotides (NTs). This complexity of protein-DNA interactions raises the question of whether a simple set of wide-coverage recognition rules can ever be identified. Here, we analyzed this issue using the extensive LacI family of transcriptional factors (TFs). We searched for recognition patterns by introducing a new approach to phylogenetic footprinting, based on the pervasive presence of local regulation in prokaryotic transcriptional networks. We identified a set of specificity correlations –determined by two AAs of the TFs and two NTs in the binding sites– that is conserved
throughout a dominant subgroup within the family regardless of the evolutionary distance, and that act as a relatively consistent recognition code. The proposed rules are confirmed with data of previous experimental studies and by events of convergent evolution in the phylogenetic tree. The presence of a code emphasizes the stable structural context of the LacI family, while defining a precise blueprint to reprogram TF specificity with many practical applications.
MIT Department
Massachusetts Institute of Technology. Department of Biological Engineering
Massachusetts Institute of Technology. Department of Civil and Environmental Engineering
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Creative Commons Attribution
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DOI of Published Version
https://doi.org/10.1371/journal.pcbi.1000989
