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Title

Local gene regulation details a recognition code within the laci transcriptional factor family

AuthorsCamas, F.M.; Alm, E.J.; Poyatos, Juan F.
Issue Date2010
PublisherPublic Library of Science
CitationPLoS Computational Biology 6 (2010)
AbstractThe 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 © 2010 Camas et al.
URIhttp://hdl.handle.net/10261/96331
DOI10.1371/journal.pcbi.1000989
ISSN1553-734X
Appears in Collections:(CNB) Artículos
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