ArticleGenome biology and evolution2013
Comprehensive computational analysis of bacterial CRP/FNR superfamily and its target motifs reveals stepwise evolution of transcriptional networks.
Article in Genome biology and evolution, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 46 citations in OpenAlex.
- A Structure-Based Analysis of the Evolution of Transcription Factors of the FNR/CRP Family.Biomolecules · 2026Review
- The Evolution of Function in the DNA-Binding Domain of the CRP/FNR Family.Genome biology and evolution · 2025Article
- From genes to function: regulation, maturation, and evolution of cytochromeApplied and environmental microbiology · 2025Review
- cAMP-independent Crp homolog adds to the multi-layer regulatory network inFrontiers in cellular and infection microbiology · 2025Article
- Transcriptional regulators of secondary metabolite biosynthesis in Streptomyces.World journal of microbiology & biotechnology · 2024Review
- Surface Plasmon Resonance as a Tool to Elucidate the Molecular Determinants of Key Transcriptional Regulators Controlling Rhizobial Lifestyles.Methods in molecular biology (Clifton, N.J.) · 2024Article
- RedB, a Member of the CRP/FNR Family, Functions as a Transcriptional Redox Brake.Microbiology spectrum · 2022Article
- Fine-Tuning Modulation of Oxidation-Mediated Posttranslational Control ofInternational journal of molecular sciences · 2022Article
- Exploring the Meta-regulon of the CRP/FNR Family of Global Transcriptional Regulators in a Partial-Nitritation Anammox Microbiome.mSystems · 2021Article
- Genetic Redundancy in Iron and Manganese Transport in the Metabolically Versatile Bacterium Rhodopseudomonas palustris TIE-1.Applied and environmental microbiology · 2020Article
- Heterologous expression of the gene for chlorite dismutase from Ideonella dechloratans is induced by an FNR-type transcription factor.MicrobiologyOpen · 2020Article
- Hybrid Transcriptional Regulators for the Screening of Target DNA Motifs in Organohalide-Respiring Bacteria.Frontiers in microbiology · 2020Article
- Orb-weaving spider Araneus ventricosus genome elucidates the spidroin gene catalogue.Scientific reports · 2019Article
- Reassessing the Structure and Function Relationship of the OAntioxidants & redox signaling · 2018Review
- Hierarchical interactions between Fnr orthologs allows fine-tuning of transcription in response to oxygen in Herbaspirillum seropedicae.Nucleic acids research · 2018Article
- Novel structural features drive DNA binding properties of Cmr, a CRP family protein in TB complex mycobacteria.Nucleic acids research · 2018Article
- Participation of the arcRACME protein in self-activation of the arc operon located in the arginine catabolism mobile element in pandemic clone USA300.Memorias do Instituto Oswaldo Cruz · 2017Article
- Evolutionary Analysis of HIV-1 Pol Proteins Reveals Representative Residues for Viral Subtype Differentiation.Frontiers in microbiology · 2017Article
- Structural basis for glutathione-mediated activation of the virulence regulatory protein PrfA in Listeria.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Characterization of LnmO as a pathway-specific Crp/Fnr-type positive regulator for leinamycin biosynthesis in Streptomyces atroolivaceus and its application for titer improvement.Applied microbiology and biotechnology · 2016Article
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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
The cAMP receptor protein (CRP)/fumarate and nitrate reduction regulatory protein (FNR)-type transcription factors (TFs) are members of a well-characterized global TF family in bacteria and have two conserved domains: the N-terminal ligand-binding domain for small molecules (e.g., cAMP, NO, or O(2)) and the C-terminal DNA-binding domain. Although the CRP/FNR-type TFs recognize very similar consensus DNA target sequences, they can regulate different sets of genes in response to environmental signals. To clarify the evolution of the CRP/FNR-type TFs throughout the bacterial kingdom, we undertook a comprehensive computational analysis of a large number of annotated CRP/FNR-type TFs and the corresponding bacterial genomes. Based on the amino acid sequence similarities among 1,455 annotated CRP/FNR-type TFs, spectral clustering classified the TFs into 12 representative groups, and stepwise clustering allowed us to propose a possible process of protein evolution. Although each cluster mainly consists of functionally distinct members (e.g., CRP, NTC, FNR-like protein, and FixK), FNR-related TFs are found in several groups and are distributed in a wide range of bacterial phyla in the sequence similarity network. This result suggests that the CRP/FNR-type TFs originated from an ancestral FNR protein, involved in nitrogen fixation. Furthermore, a phylogenetic profiling analysis showed that combinations of TFs and their target genes have fluctuated dynamically during bacterial evolution. A genome-wide analysis of TF-binding sites also suggested that the diversity of the transcriptional regulatory system was derived by the stepwise adaptation of TF-binding sites to the evolution of TFs.
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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.