ArticlePLoS computational biology2010
Local gene regulation details a recognition code within the LacI transcriptional factor family.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 22 citations in OpenAlex.
- Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability.Briefings in bioinformatics · 2024Article
- Comparative Analysis of the IclR-Family of Bacterial Transcription Factors and Their DNA-Binding Motifs: Structure, Positioning, Co-Evolution, Regulon Content.Frontiers in microbiology · 2021Article
- Mapping DNA sequence to transcription factor binding energy in vivo.PLoS computational biology · 2019Article
- Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants.Microbial biotechnology · 2018Article
- The LacI-Family Transcription Factor, RbsR, Is a Pleiotropic Regulator of Motility, Virulence, Siderophore and Antibiotic Production, Gas Vesicle Morphogenesis and Flotation inFrontiers in microbiology · 2017Article
- Networks analysis of genes and microRNAs in human Wilms' tumors.Oncology letters · 2016Article
- Regulation of Streptococcus mutans PTS Bio by the transcriptional repressor NigR.Molecular oral microbiology · 2015Article
- GntR Family of Bacterial Transcription Factors and Their DNA Binding Motifs: Structure, Positioning and Co-Evolution.PloS one · 2015Article
- The LacI-Type transcriptional regulator AraR acts as an L-arabinose-responsive repressor of L-arabinose utilization genes in Corynebacterium glutamicum ATCC 31831.Journal of bacteriology · 2014Article
- Comparative genomics and evolution of regulons of the LacI-family transcription factors.Frontiers in microbiology · 2014Article
- IpsA, a novel LacI-type regulator, is required for inositol-derived lipid formation in Corynebacteria and Mycobacteria.BMC biology · 2013Article
- Evolution of transcriptional regulation in closely related bacteria.BMC evolutionary biology · 2012Article
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Corrections and comments
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Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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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