ArticleMolecular cell2016
ppGpp Binding to a Site at the RNAP-DksA Interface Accounts for Its Dramatic Effects on Transcription Initiation during the Stringent Response.
Article in Molecular cell, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 171 papers.
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Who cites it
171 citing papers in PubMed, 251 citations in OpenAlex.
- Bacterial growth rate in populations and single cells.Nature microbiology · 2026Review
- The alarmone pGpp inhibits translation through GTP depletion.Nucleic acids research · 2026Article
- Phage portal proteins counteract stringent-response-mediated restriction.Nature communications · 2026Article
- Sustained ppGpp production underpins months-long survival of a bacterium in growth arrest.mBio · 2026Article
- Role of starvation survival response mechanisms on ribosome integrity, antibiotic tolerances, and virulence of Pseudomonas aeruginosa biofilms.NPJ biofilms and microbiomes · 2026Article
- The ω subunit stabilizes transcribing RNA polymerase to balance processivity and collision resolution.bioRxiv : the preprint server for biology · 2026Article
- ppGpp regulates transcription elongation via direct and indirect inputs to RNA polymerase pausing and nucleotide addition.bioRxiv : the preprint server for biology · 2026Article
- Omega stabilizes RNA polymerase condensates and contributes to cellular fitness during acid stress.bioRxiv : the preprint server for biology · 2026Article
- Mike Cashel: magic spot magician.Journal of bacteriology · 2026Article
- 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
- The bacterial RNA polymerase-associated CarD protein couples promoter activity to DNA supercoiling.Nature communications · 2026Article
- Non-canonical stringent response signaling mediates antimicrobial fatty acid sensitivity inbioRxiv : the preprint server for biology · 2026Article
- Enzymatic activity of PBP1B is required for growth rate-independent ppGpp-mediated resistance to PBP2 inhibitors inJournal of bacteriology · 2026Article
- Starvation-independent alarmone production inhibits translation through GTP depletion.bioRxiv : the preprint server for biology · 2026Article
- Suppressor analysis inFrontiers in microbiology · 2026Article
- Functional interplay between (p)ppGpp and RNAP in Acinetobacter baumannii.PLoS pathogens · 2025Article
- Characterization of a Novel RNA Polymerase Mutant of Escherichia coli That Confers Thermotolerance and Chaperone Independence.Molecular microbiology · 2025Article
- Bacterial alarmone (p)ppGpp mediates the pathogenicity ofmSystems · 2025Article
- Virulence Regulation inMicroorganisms · 2025Review
111 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Throughout the bacterial domain, the alarmone ppGpp dramatically reprograms transcription following nutrient limitation. This "stringent response" is critical for survival and antibiotic tolerance and is a model for transcriptional regulation by small ligands. We report that ppGpp binds to two distinct sites 60 Å apart on E. coli RNA polymerase (RNAP), one characterized previously (site 1) and a second identified here at an interface of RNAP and the transcription factor DksA (site 2). The location and unusual tripartite nature of site 2 account for the DksA-ppGpp synergism and suggest mechanisms for ppGpp enhancement of DksA's effects on RNAP. Site 2 binding results in the majority of ppGpp's effects on transcription initiation in vitro and in vivo, and strains lacking site 2 are severely impaired for growth following nutritional shifts. Filling of the two sites at different ppGpp concentrations would expand the dynamic range of cellular responses to changes in ppGpp levels.
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