Title |
Local Gene Regulation Details a Recognition Code within the LacI Transcriptional Factor Family
|
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Published in |
PLoS Computational Biology, November 2010
|
DOI | 10.1371/journal.pcbi.1000989 |
Pubmed ID | |
Authors |
Francisco M. Camas, Eric J. Alm, Juan F. Poyatos |
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. |
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Spain | 1 | 3% |
United States | 1 | 3% |
Unknown | 26 | 84% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 10 | 32% |
Student > Ph. D. Student | 8 | 26% |
Professor > Associate Professor | 4 | 13% |
Student > Bachelor | 3 | 10% |
Professor | 2 | 6% |
Other | 2 | 6% |
Unknown | 2 | 6% |
Readers by discipline | Count | As % |
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Environmental Science | 2 | 6% |
Immunology and Microbiology | 1 | 3% |
Social Sciences | 1 | 3% |
Other | 2 | 6% |
Unknown | 2 | 6% |