ArticleJournal of molecular biology2007
Effects of DksA, GreA, and GreB on transcription initiation: insights into the mechanisms of factors that bind in the secondary channel of RNA polymerase.
Article in Journal of molecular biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
79 citing papers in PubMed, 123 citations in OpenAlex.
- NAD+ capping of sibD transcripts in E. coli is mediated by its minimal promoter and enhanced by ppGpp.Nucleic acids research · 2026Article
- Targeting Bacterial RNA Polymerase: Harnessing Simulations and Machine Learning to Design Inhibitors for Drug-Resistant Pathogens.Biochemistry · 2025Review
- Article
- DksA, ppGpp, and RegAB Regulate Nitrate Respiration in Paracoccus denitrificans.Journal of bacteriology · 2023Article
- Article
- Expression and structure of the Chlamydia trachomatis DksA ortholog.Pathogens and disease · 2022Article
- Three Microbial Musketeers of the Seas:International journal of molecular sciences · 2022Article
- Mutational analysis of Escherichia coli GreA protein reveals new functional activity independent of antipause and lethal when overexpressed.Scientific reports · 2020Article
- Interactions between DksA and Stress-Responsive Alternative Sigma Factors Control Inorganic Polyphosphate Accumulation in Escherichia coli.Journal of bacteriology · 2020Article
- Conditional down-regulation of GreA impacts expression of rRNA and transcription factors, affecting Mycobacterium smegmatis survival.Scientific reports · 2020Article
- Transcriptome analysis reveals that the RNA polymerase-binding protein DksA1 has pleiotropic functions inThe Journal of biological chemistry · 2020Article
- Chromosomal Organization and Regulation of Genetic Function inEcoSal Plus · 2020Article
- Guanosine Tetraphosphate Has a Similar Affinity for Each of Its Two Binding Sites onFrontiers in microbiology · 2020Article
- Gre-family factors modulate DNA damage sensing byRNA biology · 2019Article
- Autoregulation ofInternational journal of molecular sciences · 2019Article
- The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase.Journal of molecular biology · 2019Review
- Structural Basis of Transcription: RNA Polymerase Backtracking and Its Reactivation.Molecular cell · 2019Article
- Inorganic Polyphosphate Accumulation in Escherichia coli Is Regulated by DksA but Not by (p)ppGpp.Journal of bacteriology · 2019Article
- DksA-RNA polymerase interactions support new origin formation and DNA repair in Escherichia coli.Molecular microbiology · 2019Article
- Genome-wide effects onProceedings of the National Academy of Sciences of the United States of America · 2019Article
19 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Escherichia coli DksA, GreA, and GreB have similar structures and bind to the same location on RNA polymerase (RNAP), the secondary channel. We show that GreB can fulfil some roles of DksA in vitro, including shifting the promoter-open complex equilibrium in the dissociation direction, thus allowing rRNA promoters to respond to changes in the concentration of ppGpp and NTPs. However, unlike deletion of the dksA gene, deletion of greB had no effect on rRNA promoters in vivo. We show that the apparent affinities of DksA and GreB for RNAP are similar, but the cellular concentration of GreB is much lower than that of DksA. When over-expressed and in the absence of competing GreA, GreB almost completely complemented the loss of dksA in control of rRNA expression, indicating its inability to regulate rRNA transcription in vivo results primarily from its low concentration. In contrast to GreB, the apparent affinity of GreA for RNAP was weaker than that of DksA, GreA affected rRNA promoters only modestly in vitro and, even when over-expressed, GreA did not affect rRNA transcription in vivo. Thus, binding in the secondary channel is necessary but insufficient to explain the effect of DksA on rRNA transcription. Neither Gre factor was capable of fulfilling two other functions of DksA in transcription initiation: co-activation of amino acid biosynthetic gene promoters with ppGpp and compensation for the loss of the omega subunit of RNAP in the response of rRNA promoters to ppGpp. Our results provide important clues to the mechanisms of both negative and positive control of transcription initiation by DksA.
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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.