ArticleJournal of molecular biology2008
Still looking for the magic spot: the crystallographically defined binding site for ppGpp on RNA polymerase is unlikely to be responsible for rRNA transcription regulation.
Article in Journal of molecular biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 41 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
41 citing papers in PubMed, 80 citations in OpenAlex.
- Control of transcription elongation and DNA repair by alarmone ppGpp.Nature structural & molecular biology · 2023Article
- Protein-Ligand Interactions in Scarcity: The Stringent Response from Bacteria to Metazoa, and the Unanswered Questions.International journal of molecular sciences · 2023Review
- The extended (p)ppGpp family: New dimensions in Stress response.Current research in microbial sciences · 2021Review
- The Stringent Response Inhibits DNA Replication Initiation in E. coli by Modulating Supercoiling ofmBio · 2019Article
- The Link between Purine Metabolism and Production of Antibiotics inAntibiotics (Basel, Switzerland) · 2019Review
- Transcriptional Responses to ppGpp and DksA.Annual review of microbiology · 2018Review
- Affinity Selection-Mass Spectrometry Identifies a Novel Antibacterial RNA Polymerase Inhibitor.ACS chemical biology · 2017Article
- ppGpp Binding to a Site at the RNAP-DksA Interface Accounts for Its Dramatic Effects on Transcription Initiation during the Stringent Response.Molecular cell · 2016Article
- Mycobacterium tuberculosis Transcription Machinery: Ready To Respond to Host Attacks.Journal of bacteriology · 2016Review
- CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex.eLife · 2015Article
- Structural biology of bacterial RNA polymerase.Biomolecules · 2015Review
- Recent functional insights into the role of (p)ppGpp in bacterial physiology.Nature reviews. Microbiology · 2015Review
- Diversity in (p)ppGpp metabolism and effectors.Current opinion in microbiology · 2015Review
- Molecular mechanism and evolution of guanylate kinase regulation by (p)ppGpp.Molecular cell · 2015Article
- Basal levels of (p)ppGpp in Enterococcus faecalis: the magic beyond the stringent response.mBio · 2013Article
- Characterization of a novel RNA polymerase mutant that alters DksA activity.Journal of bacteriology · 2013Article
- Differential regulation by ppGpp versus pppGpp in Escherichia coli.Nucleic acids research · 2013Article
- The mechanism of E. coli RNA polymerase regulation by ppGpp is suggested by the structure of their complex.Molecular cell · 2013Article
- The magic spot: a ppGpp binding site on E. coli RNA polymerase responsible for regulation of transcription initiation.Molecular cell · 2013Article
- X-ray crystal structure of Escherichia coli RNA polymerase σ70 holoenzyme.The Journal of biological chemistry · 2013Article
Corrections and comments
- Erratum issued
Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Identification of the RNA polymerase (RNAP) binding site for ppGpp, a central regulator of bacterial transcription, is crucial for understanding its mechanism of action. A recent high-resolution X-ray structure defined a ppGpp binding site on Thermus thermophilus RNAP. We report here effects of ppGpp on 10 mutant Escherichia coli RNAPs with substitutions for the analogous residues within 3-4 A of the ppGpp binding site in the T. thermophilus cocrystal. None of the substitutions in E. coli RNAP significantly weakened its responses to ppGpp. This result differs from the originally reported finding of a substitution in E. coli RNAP eliminating ppGpp function. The E. coli RNAPs used in that study likely lacked stoichiometric amounts of omega, an RNAP subunit required for responses of RNAP to ppGpp, in part explaining the discrepancy. Furthermore, we found that ppGpp did not inhibit transcription initiation by T. thermophilus RNAP in vitro or shorten the lifetimes of promoter complexes containing T. thermophilus RNAP, in contrast to the conclusion in the original report. Our results suggest that the ppGpp binding pocket identified in the cocrystal is not the one responsible for regulation of E. coli ribosomal RNA transcription initiation and highlight the importance of inclusion of omega in bacterial RNAP preparations.
Indexed as
Identifiers
What OpenQuestion holds
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.