Insights into the DNA-binding mechanism of a LytTR-type transcription regulator
| العنوان: | Insights into the DNA-binding mechanism of a LytTR-type transcription regulator |
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| المؤلفون: | Stefan Behr, Kirsten Jung, Ralf Heermann |
| المصدر: | Bioscience Reports |
| سنة النشر: | 2016 |
| مصطلحات موضوعية: | 0301 basic medicine, DNA, Bacterial, Biophysics, Plasma protein binding, Biology, S8, Biochemistry, 03 medical and health sciences, chemistry.chemical_compound, Escherichia coli, Protein–DNA interaction, Binding site, Promoter Regions, Genetic, Molecular Biology, Transcription factor, response regulator YpdB, Original Paper, Escherichia coli Proteins, S13, Promoter, Cell Biology, Surface Plasmon Resonance, Molecular biology, Original Papers, S10, Cell biology, S34, Response regulator, interaction map® (IM) analysis, 030104 developmental biology, chemistry, surface plasmon resonance (SPR) spectroscopy, protein–DNA interaction, nutrient scavenging, DNA, pyruvate sensing, Binding domain, Protein Binding, Transcription Factors |
| الوصف: | A combination of surface plasmon resonance (SPR) spectroscopy and interaction map® (IM) analysis was used to characterize binding of the LytTR-type response regulator YpdB to promoter DNA. YpdB follows an ‘AB-BA’ mechanism involving sequential and cooperative DNA binding followed by rapid successive promoter clearance. Most bacterial response regulators (RRs) make contact with DNA through a recognition α-helix in their DNA-binding domains. An emerging class of RRs interacts with DNA via a relatively novel type of binding domain, called the LytTR domain, which is mainly composed of β-strands. YpdB belongs to this latter class, is part of a nutrient-sensing network in Escherichia coli and triggers expression of its only target gene, yhjX, in response to extracellular pyruvate. Expression of yhjX mainly occurs in the late exponential growth phase, and in a pulsed manner. Although the DNA-binding sites for YpdB are well defined, exactly how YpdB initiates pulsed gene expression has remained elusive. To address this question, we measured the binding kinetics of wild-type YpdB and the phosphomimetic variant YpdB-D53E to the yhjX promoter region (PyhjX) using surface plasmon resonance (SPR) spectroscopy combined with interaction map® (IM) analysis. Both YpdB and YpdB-D53E bound as monomers to the tandem-repeat sequences in the promoter, with YpdB-D53E displaying a higher maximal binding rate than YpdB. Furthermore, we identified a high-affinity (A-site) and a low-affinity binding site (B-site) within the yhjX promoter. Only YpdB-D53E utilizes an ‘AB-BA’ DNA-binding mechanism, involving sequential and cooperative promoter binding, and rapid, successive promoter clearance. We propose that response regulator phosphorylation, in combination with the cycle of cooperative DNA binding and rapid promoter clearance just described, can account for pulsed gene expression. |
| تدمد: | 1573-4935 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b917db388f2cf84b5dee06dad18173ab https://pubmed.ncbi.nlm.nih.gov/27013338 |
| Rights: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....b917db388f2cf84b5dee06dad18173ab |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 15734935 |
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