ArticleGenome biology2011
Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium.
Article in Genome biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed, 55 citations in OpenAlex.
- Predicting the bacterial host range of plasmid genomes using the language model-based one-class support vector machine algorithm.Microbial genomics · 2025Article
- Analysis of promoter region and regulatory elements of Rhizobium giardinii DNA-binding response regulator A3AY_RS01 genes.Journal, genetic engineering & biotechnology · 2024Article
- Cross-regulation of Aps-promoters in Lacticaseibacillus paracasei by the PsdR response regulator in response to lantibiotics.Scientific reports · 2024Article
- Microbial sensor variation across biogeochemical conditions in the terrestrial deep subsurface.mSystems · 2024Article
- Integration of text mining and biological network analysis: Identification of essential genes in sulfate-reducing bacteria.Frontiers in microbiology · 2023Article
- Large-scale genetic characterization of the model sulfate-reducing bacterium,Frontiers in microbiology · 2023Article
- Tubby-like proteins (TLPs) transcription factor in different regulatory mechanism in plants: a review.Plant molecular biology · 2022Review
- Genome-Wide Analysis Reveals that PhoP Regulates Pathogenicity in Riemerella anatipestifer.Microbiology spectrum · 2022Article
- Advanced transcriptomic analysis reveals the role of efflux pumps and media composition in antibiotic responses of Pseudomonas aeruginosa.Nucleic acids research · 2022Article
- Sensing Host Health: Insights from Sensory Protein Signature of the Metagenome.Applied and environmental microbiology · 2022Article
- Article
- Response to substrate limitation by a marine sulfate-reducing bacterium.The ISME journal · 2022Article
- Genomics Characterization of an EngineeredFrontiers in bioengineering and biotechnology · 2021Article
- Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris.The ISME journal · 2020Article
- Tools to map target genes of bacterial two-component system response regulators.Environmental microbiology reports · 2020Review
- Salinity-Mediated Increment in Sulfate Reduction, Biofilm Formation, and Quorum Sensing: A Potential Connection Between Quorum Sensing and Sulfate Reduction?Frontiers in microbiology · 2019Article
- LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio species.PloS one · 2019Article
- Regulatory Targets of the Response Regulator RR_1586 from Clostridioides difficile Identified Using a Bacterial One-Hybrid Screen.Journal of bacteriology · 2018Article
- Chemoproteomic Profiling of Phosphoaspartate Modifications in Prokaryotes.Angewandte Chemie (International ed. in English) · 2018Article
- Coordinated response of the Desulfovibrio desulfuricans 27774 transcriptome to nitrate, nitrite and nitric oxide.Scientific reports · 2017Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTwo component regulatory systems are the primary form of signal transduction in bacteria. Although genomic binding sites have been determined for several eukaryotic and bacterial transcription factors, comprehensive identification of gene targets of two component response regulators remains challenging due to the lack of knowledge of the signals required for their activation. We focused our study on Desulfovibrio vulgaris Hildenborough, a sulfate reducing bacterium that encodes unusually diverse and largely uncharacterized two component signal transduction systems.
resultsWe report the first systematic mapping of the genes regulated by all transcriptionally acting response regulators in a single bacterium. Our results enabled functional predictions for several response regulators and include key processes of carbon, nitrogen and energy metabolism, cell motility and biofilm formation, and responses to stresses such as nitrite, low potassium and phosphate starvation. Our study also led to the prediction of new genes and regulatory networks, which found corroboration in a compendium of transcriptome data available for D. vulgaris. For several regulators we predicted and experimentally verified the binding site motifs, most of which were discovered as part of this study.
conclusionsThe gene targets identified for the response regulators allowed strong functional predictions to be made for the corresponding two component systems. By tracking the D. vulgaris regulators and their motifs outside the Desulfovibrio spp. we provide testable hypotheses regarding the functions of orthologous regulators in other organisms. The in vitro array based method optimized here is generally applicable for the study of such systems in all organisms.
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