ArticleJournal of molecular biology2008
The role of DNA-binding specificity in the evolution of bacterial regulatory networks.
Article in Journal of molecular biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
32 citing papers in PubMed, 46 citations in OpenAlex.
- The adaptive landscapes of three globaleLife · 2026Article
- PRIMED: predicting DNA binding residues by leveraging pre-trained protein language models.Frontiers in artificial intelligence · 2026Article
- AdpA, a Global Regulator of Hundreds of Genes, Including Those for Secondary Metabolism, inAntibiotics (Basel, Switzerland) · 2025Article
- TheFrontiers in microbiology · 2023Article
- Article
- Article
- RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12.Nucleic acids research · 2019Article
- Article
- Exploring comprehensive within-motif dependence of transcription factor binding in Escherichia coli.Scientific reports · 2015Article
- Transcriptional analysis of the MrpJ network: modulation of diverse virulence-associated genes and direct regulation of mrp fimbrial and flhDC flagellar operons in Proteus mirabilis.Infection and immunity · 2015Article
- Characterization of the SOS meta-regulon in the human gut microbiome.Bioinformatics (Oxford, England) · 2014Article
- Indirect and suboptimal control of gene expression is widespread in bacteria.Molecular systems biology · 2013Article
- Divergence of the SigB regulon and pathogenesis of the Bacillus cereus sensu lato group.BMC genomics · 2012Article
- "Hypothesis for the modern RNA world": a pervasive non-coding RNA-based genetic regulation is a prerequisite for the emergence of multicellular complexity.Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life · 2011Article
- Rational design of an artificial genetic switch: Co-option of the H-NS-repressed proU operon by the VirB virulence master regulator.Journal of bacteriology · 2011Article
- Whole-genome phylogenies of the family Bacillaceae and expansion of the sigma factor gene family in the Bacillus cereus species-group.BMC genomics · 2011Article
- Unraveling networks of co-regulated genes on the sole basis of genome sequences.Nucleic acids research · 2011Article
- Theoretical and empirical quality assessment of transcription factor-binding motifs.Nucleic acids research · 2011Article
- The atypical OmpR/PhoB response regulator ChxR from Chlamydia trachomatis forms homodimers in vivo and binds a direct repeat of nucleotide sequences.Journal of bacteriology · 2011Article
- Dissecting the expression patterns of transcription factors across conditions using an integrated network-based approach.Nucleic acids research · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 2 countries.
Funding
Abstract
Understanding the mechanisms by which transcriptional regulatory networks (TRNs) change through evolution is a fundamental problem.Here, we analyze this question using data from Escherichia coli and Bacillus subtilis, and find that paralogy relationships are insufficient to explain the global or local role observed for transcription factors (TFs) within regulatory networks. Our results provide a picture in which DNA-binding specificity, a molecular property that can be measured in different ways, is a predictor of the role of transcription factors. In particular, we observe that global regulators consistently display low levels of binding specificity, while displaying comparatively higher expression values in microarray experiments. In addition, we find a strong negative correlation between binding specificity and the number of co-regulators that help coordinate genetic expression on a genomic scale. A close look at several orthologous TFs,including FNR, a regulator found to be global in E. coli and local in B.subtilis, confirms the diagnostic value of specificity in order to understand their regulatory function, and highlights the importance of evaluating the metabolic and ecological relevance of effectors as another variable in the evolutionary equation of regulatory networks. Finally, a general model is presented that integrates some evolutionary forces and molecular properties,aiming to explain how regulons grow and shrink, as bacteria tune their regulation to increase adaptation.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.