ArticleGenome biology2006
Co-evolution of transcription factors and their targets depends on mode of regulation.
Article in Genome biology, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 37 citations in OpenAlex.
- Early Evolution of the Prokaryotic Transcription Factor Repertoire.Genome biology and evolution · 2026Article
- Genome-wide identification of metabolic and regulatory determinants of intracellular growth inbioRxiv : the preprint server for biology · 2026Article
- Modeling binding of the conserved Csr/Rsm protein family across species of the γ-proteobacteria reveals niche-specific adaptation of the post-transcriptional regulon.bioRxiv : the preprint server for biology · 2026Article
- Auxotrophic and prototrophic conditional genetic networks reveal the rewiring of transcription factors in Escherichia coli.Nature communications · 2022Article
- Yeast Crf1p: An activator in need is an activator indeed.Computational and structural biotechnology journal · 2022Review
- The relation between crosstalk and gene regulation form revisited.PLoS computational biology · 2020Article
- An Essential Regulatory System Originating from Polygenic Transcriptional Rewiring of PhoP-PhoQ ofGenetics · 2017Article
- Comprehensive computational analysis of bacterial CRP/FNR superfamily and its target motifs reveals stepwise evolution of transcriptional networks.Genome biology and evolution · 2013Article
- Evolution of transcriptional regulation in closely related bacteria.BMC evolutionary biology · 2012Article
- The evolutionary dynamics of functional modules and the extraordinary plasticity of regulons: the Escherichia coli perspective.Nucleic acids research · 2012Article
- Regulatory network structure as a dominant determinant of transcription factor evolutionary rate.PLoS computational biology · 2012Article
- Deciphering the transcriptional regulatory logic of amino acid metabolism.Nature chemical biology · 2011Article
- Unexpected coregulator range for the global regulator Lrp of Escherichia coli and Proteus mirabilis.Journal of bacteriology · 2011Article
- Dissecting the expression patterns of transcription factors across conditions using an integrated network-based approach.Nucleic acids research · 2010Article
- Gene duplication and the evolution of ribosomal protein gene regulation in yeast.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Stochasticity versus determinism: consequences for realistic gene regulatory network modelling and evolution.Journal of molecular evolution · 2010Article
- Mechanisms and evolution of control logic in prokaryotic transcriptional regulation.Microbiology and molecular biology reviews : MMBR · 2009Review
- Article
- Bioinformatics resources for the study of gene regulation in bacteria.Journal of bacteriology · 2009Review
- Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli.Genome biology · 2008Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDifferences in the transcription regulation network are at the root of much of the phenotypic variation observed among organisms. These differences may be achieved either by changing the repertoire of regulators and/or their targets, or by rewiring the network. Following these changes and studying their logic is crucial for understanding the evolution of regulatory networks.
resultsWe use the well characterized transcription regulatory network of Escherichia coli K12 and follow the evolutionary changes in the repertoire of regulators and their targets across a large number of fully sequenced gamma-proteobacteria. By focusing on close relatives of E. coli K12, we study the dynamics of the evolution of transcription regulation across a relatively short evolutionary timescale. We show significant differences in the evolution of repressors and activators. Repressors are only lost from a genome once their targets have themselves been lost, or once the network has significantly rewired. In contrast, activators are often lost even when their targets remain in the genome. As a result, E. coli K12 repressors that regulate many targets are rarely absent from organisms that are closely related to E. coli K12, while activators with a similar number of targets are often absent in these organisms.
conclusionWe demonstrate that the mode of regulation exerted by transcription factors has a strong effect on their evolution. Repressors co-evolve tightly with their target genes. In contrast, activators can be lost independently of their targets. In fact, loss of an activator can lead to efficient shutdown of an unnecessary pathway.
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