ArticleNucleic acids research2013
Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 51 citations in OpenAlex.
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- The emergence and diversification of a zoonotic pathogen from within the microbiota of intensively farmed pigs.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Human Milk Oligosaccharide Utilization in Intestinal Bifidobacteria Is Governed by Global Transcriptional Regulator NagR.mSystems · 2022Article
- Genomic and transcriptomic dissection of Theionarchaea in marine ecosystem.Science China. Life sciences · 2022Article
- Novel functional insights into a modified sugar-binding protein from Synechococcus MITS9220.Scientific reports · 2022Article
- Transcriptional Regulation of Plant Biomass Degradation and Carbohydrate Utilization Genes in the Extreme ThermophilemSystems · 2021Article
- Secretome Analysis ofProteomes · 2021Article
- Gene Regulation and Transcriptomics.Current issues in molecular biology · 2021Article
- A genome-wide approach for identification and characterisation of metabolite-inducible systems.Nature communications · 2020Article
- In vivo biosensors: mechanisms, development, and applications.Journal of industrial microbiology & biotechnology · 2018Article
- Comparative Genomics Reveals the Regulatory Complexity of Bifidobacterial Arabinose and Arabino-Oligosaccharide Utilization.Frontiers in microbiology · 2018Article
- Substrate adaptabilities of Thermotogae mannan binding proteins as a function of their evolutionary histories.Extremophiles : life under extreme conditions · 2016Article
- Two Novel Glycoside Hydrolases Responsible for the Catabolism of Cyclobis-(1→6)-α-nigerosyl.The Journal of biological chemistry · 2016Article
- Simultaneous achievement of high ethanol yield and titer in Clostridium thermocellum.Biotechnology for biofuels · 2016Article
- Characterization of DNA Binding Sites of RokB, a ROK-Family Regulator from Streptomyces coelicolor Reveals the RokB Regulon.PloS one · 2016Article
- Adaptive Evolution of Thermotoga maritima Reveals Plasticity of the ABC Transporter Network.Applied and environmental microbiology · 2015Article
- Operator recognition by the ROK transcription factor family members, NagC and Mlc.Nucleic acids research · 2015Article
- Multiple regulatory mechanisms control the expression of the Geobacillus stearothermophilus gene for extracellular xylanase.The Journal of biological chemistry · 2014Article
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Large and functionally heterogeneous families of transcription factors have complex evolutionary histories. What shapes specificities toward effectors and DNA sites in paralogous regulators is a fundamental question in biology. Bacteria from the deep-branching lineage Thermotogae possess multiple paralogs of the repressor, open reading frame, kinase (ROK) family regulators that are characterized by carbohydrate-sensing domains shared with sugar kinases. We applied an integrated genomic approach to study functions and specificities of regulators from this family. A comparative analysis of 11 Thermotogae genomes revealed novel mechanisms of transcriptional regulation of the sugar utilization networks, DNA-binding motifs and specific functions. Reconstructed regulons for seven groups of ROK regulators were validated by DNA-binding assays using purified recombinant proteins from the model bacterium Thermotoga maritima. All tested regulators demonstrated specific binding to their predicted cognate DNA sites, and this binding was inhibited by specific effectors, mono- or disaccharides from their respective sugar catabolic pathways. By comparing ligand-binding domains of regulators with structurally characterized kinases from the ROK family, we elucidated signature amino acid residues determining sugar-ligand regulator specificity. Observed correlations between signature residues and the sugar-ligand specificities provide the framework for structure functional classification of the entire ROK family.
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