ArticleGenes & development2012
Direct interactions between the coiled-coil tip of DksA and the trigger loop of RNA polymerase mediate transcriptional regulation.
Article in Genes & development, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
56 citing papers in PubMed, 81 citations in OpenAlex.
- Promoter contacts by TFB and TFEα during archaeal transcription initiation.Transcription · 2026Article
- Widespread epistasis shapes RNA polymerase II active site function and evolution.Nature communications · 2025Article
- Regulation of the transcription factor CdnL promotes adaptation to nutrient stress inPNAS nexus · 2024Article
- Structure of the recombinant RNA polymerase from African Swine Fever Virus.Nature communications · 2024Article
- DksA, ppGpp, and RegAB Regulate Nitrate Respiration in Paracoccus denitrificans.Journal of bacteriology · 2023Article
- Protein-Ligand Interactions in Scarcity: The Stringent Response from Bacteria to Metazoa, and the Unanswered Questions.International journal of molecular sciences · 2023Review
- How to Shut Down Transcription in Archaea during Virus Infection.Microorganisms · 2022Review
- Expression and structure of the Chlamydia trachomatis DksA ortholog.Pathogens and disease · 2022Article
- The structure of an Hsp90-immunophilin complex reveals cochaperone recognition of the client maturation state.Molecular cell · 2021Article
- Rhodobacter sphaeroides CarD Negatively Regulates Its Own Promoter.Journal of bacteriology · 2021Article
- TheMicroorganisms · 2020Article
- Article
- Diversity, versatility and complexity of bacterial gene regulation mechanisms: opportunities and drawbacks for applications in synthetic biology.FEMS microbiology reviews · 2019Review
- DksA Controls the Response of the Lyme Disease SpirocheteJournal of bacteriology · 2019Article
- Delayed inhibition mechanism for secondary channel factor regulation of ribosomal RNA transcription.eLife · 2019Article
- Region 3.2 of the σ factor controls the stability of rRNA promoter complexes and potentiates their repression by DksA.Nucleic acids research · 2018Article
- Transcriptional Responses to ppGpp and DksA.Annual review of microbiology · 2018Review
- The stringent response and Mycobacterium tuberculosis pathogenesis.Pathogens and disease · 2018Review
- Guanosine tetraphosphate relieves the negative regulation of Salmonella pathogenicity island-2 gene transcription exerted by the AT-rich ssrA discriminator region.Scientific reports · 2018Article
- Article
Corrections and comments
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
Abstract
Escherichia coli DksA is a transcription factor that binds to RNA polymerase (RNAP) without binding to DNA, destabilizing RNAP-promoter interactions, sensitizing RNAP to the global regulator ppGpp, and regulating transcription of several hundred target genes, including those encoding rRNA. Previously, we described promoter sequences and kinetic properties that account for DksA's promoter specificity, but how DksA exerts its effects on RNAP has remained unclear. To better understand DksA's mechanism of action, we incorporated benzoyl-phenylalanine at specific positions in DksA and mapped its cross-links to RNAP, constraining computational docking of the two proteins. The resulting evidence-based model of the DksA-RNAP complex as well as additional genetic and biochemical approaches confirmed that DksA binds to the RNAP secondary channel, defined the orientation of DksA in the channel, and predicted a network of DksA interactions with RNAP that includes the rim helices and the mobile trigger loop (TL) domain. Engineered cysteine substitutions in the TL and DksA coiled-coil tip generated a disulfide bond between them, and the interacting residues were absolutely required for DksA function. We suggest that DksA traps the TL in a conformation that destabilizes promoter complexes, an interaction explaining the requirement for the DksA tip and its effects on transcription.
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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.