ArticleNucleic acids research2015
New insights into the regulatory mechanisms of ppGpp and DksA on Escherichia coli RNA polymerase-promoter complex.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 29 citations in OpenAlex.
- DksA-Dependent Stringent Stress Response Drives Virulence and Gastrointestinal Persistence ofbioRxiv : the preprint server for biology · 2026Article
- NAD+ capping of sibD transcripts in E. coli is mediated by its minimal promoter and enhanced by ppGpp.Nucleic acids research · 2026Article
- Evolutionary trajectories determine feasibility of collateral sensitivity-based antibiotic treatment strategies in critical bacterial pathogens.Communications biology · 2025Article
- Virulence Regulation inMicroorganisms · 2025Review
- Review
- Similar and Divergent Roles of Stringent Regulator (p)ppGpp and DksA on Pleiotropic Phenotype of Yersinia enterocolitica.Microbiology spectrum · 2022Article
- Functional characterization and transcriptional repression by Lacticaseibacillus paracasei DinJ-YafQ.Applied microbiology and biotechnology · 2022Article
- Atomic Force Microscopy Investigation of the Interactions between the MCM Helicase and DNA.Materials (Basel, Switzerland) · 2021Article
- Microbial Musings - February 2021.Microbiology (Reading, England) · 2021Article
- Structural basis of ribosomal RNA transcription regulation.Nature communications · 2021Article
- CarD contributes to diverse gene expression outcomes throughout the genome ofProceedings of the National Academy of Sciences of the United States of America · 2019Article
- Studying protein-DNA interactions using atomic force microscopy.Seminars in cell & developmental biology · 2018Review
- Sleeper cells: the stringent response and persistence in the Borreliella (Borrelia) burgdorferi enzootic cycle.Environmental microbiology · 2017Review
- Peptide-nucleotide antibiotic Microcin C is a potent inducer of stringent response and persistence in both sensitive and producing cells.Molecular microbiology · 2017Article
- Fluorescence Resonance Energy Transfer Characterization of DNA Wrapping in Closed and Open Escherichia coli RNA Polymerase-λP(R) Promoter Complexes.Biochemistry · 2016Article
- Article
- Chemical inhibitors of the conserved bacterial transcriptional regulator DksA1 suppressed quorum sensing-mediated virulence of Pseudomonas aeruginosa.The Journal of biological chemistryArticle
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Authors and funding
7 authors at 4 institutions in 3 countries.
Funding
Abstract
The stringent response modulators, guanosine tetraphosphate (ppGpp) and protein DksA, bind RNA polymerase (RNAP) and regulate gene expression to adapt bacteria to different environmental conditions. Here, we use Atomic Force Microscopy and in vitro transcription assays to study the effects of these modulators on the conformation and stability of the open promoter complex (RPo) formed at the rrnA P1, rrnB P1, its discriminator (dis) variant and λ pR promoters. In the absence of modulators, RPo formed at these promoters show different extents of DNA wrapping which correlate with the position of UP elements. Addition of the modulators affects both DNA wrapping and RPo stability in a promoter-dependent manner. Overall, the results obtained under different conditions of ppGpp, DksA and initiating nucleotides (iNTPs) indicate that ppGpp allosterically prevents the conformational changes associated with an extended DNA wrapping that leads to RPo stabilization, while DksA interferes directly with nucleotide positioning into the RNAP active site. At the iNTPs-sensitive rRNA promoters ppGpp and DksA display an independent inhibitory effect, while at the iNTPs-insensitive pR promoter DksA reduces the effect of ppGpp in accordance with their antagonistic role.
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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.