ArticlePLoS computational biology2007
Orthologous transcription factors in bacteria have different functions and regulate different genes.
Article in PLoS computational biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed, 110 citations in OpenAlex.
- Comprehensive in silico analysis of eggNOG-annotated orthologous genes infers functional dynamics and energy metabolism in the microbiome of Abutilon fruticosum.BMC plant biology · 2026Article
- Early Evolution of the Prokaryotic Transcription Factor Repertoire.Genome biology and evolution · 2026Article
- Interspecies interactions drive bacterial proteome reorganization and emergent metabolism.Nature ecology & evolution · 2026Article
- Molecular Phylogeny of "Chemosensory Proteins" in Bacteria and Arthropods: CSP as an Extremely Ancient Gene.Journal of molecular evolution · 2026Article
- Rewiring of cell morphology by Small protein B enhances stress tolerance and colonization in Aeromonas veronii under adverse conditions.Nucleic acids research · 2025Article
- Targeting bacterial transcription factors for infection control: opportunities and challenges.Transcription · 2025Review
- Diversity of Transcriptional Regulatory Adaptation in E. coli.Molecular biology and evolution · 2024Article
- Functional and regulatory diversity of homeobox-leucine zipper transcription factors BnaHB6 under dehydration and salt stress in Brassica napus L.Plant molecular biology · 2024Article
- Ecophysiological and genomic analyses of a representative isolate of highly abundant Bacillus cereus strains in contaminated subsurface sediments.Environmental microbiology · 2022Article
- Article
- Determination and Dissection of DNA-Binding Specificity for theInternational journal of molecular sciences · 2020Article
- Dynamics of genetic variation in transcription factors and its implications for the evolution of regulatory networks in Bacteria.Nucleic acids research · 2020Article
- Abasy Atlas v2.2: The most comprehensive and up-to-date inventory of meta-curated, historical, bacterial regulatory networks, their completeness and system-level characterization.Computational and structural biotechnology journal · 2020Article
- Assessment of transfer methods for comparative genomics of regulatory networks in bacteria.BMC bioinformatics · 2016Article
- Transcription Factors Exhibit Differential Conservation in Bacteria with Reduced Genomes.PloS one · 2016Article
- Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria.Database : the journal of biological databases and curation · 2016Article
- Following the Footsteps of Chlamydial Gene Regulation.Molecular biology and evolution · 2015Article
- An HcpR paralog of Desulfovibrio gigas provides protection against nitrosative stress.FEBS open bio · 2015Article
- Analysis of Genome-scale Expression Network in Four Major Bacterial Residents of Cystic Fibrosis Lung.Current genomics · 2014Article
- A functional genomics catalogue of activated transcription factors during pathogenesis of pneumococcal disease.BMC genomics · 2014Article
4 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcription factors (TFs) form large paralogous gene families and have complex evolutionary histories. Here, we ask whether putative orthologs of TFs, from bidirectional best BLAST hits (BBHs), are evolutionary orthologs with conserved functions. We show that BBHs of TFs from distantly related bacteria are usually not evolutionary orthologs. Furthermore, the false orthologs usually respond to different signals and regulate distinct pathways, while the few BBHs that are evolutionary orthologs do have conserved functions. To test the conservation of regulatory interactions, we analyze expression patterns. We find that regulatory relationships between TFs and their regulated genes are usually not conserved for BBHs in Escherichia coli K12 and Bacillus subtilis. Even in the much more closely related bacteria Vibrio cholerae and Shewanella oneidensis MR-1, predicting regulation from E. coli BBHs has high error rates. Using gene-regulon correlations, we identify genes whose expression pattern differs between E. coli and S. oneidensis. Using literature searches and sequence analysis, we show that these changes in expression patterns reflect changes in gene regulation, even for evolutionary orthologs. We conclude that the evolution of bacterial regulation should be analyzed with phylogenetic trees, rather than BBHs, and that bacterial regulatory networks evolve more rapidly than previously thought.
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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.