ArticleBiophysical journal2013
Partitioning of RNA polymerase activity in live Escherichia coli from analysis of single-molecule diffusive trajectories.
Article in Biophysical journal, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 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
36 citing papers in PubMed, 73 citations in OpenAlex.
- Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions.Chemical reviews · 2024Review
- Recycling of bacterial RNA polymerase by the Swi2/Snf2 ATPase RapA.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- RNAP Promoter Search and Transcription Kinetics in LiveThe journal of physical chemistry. B · 2023Article
- Recycling of Bacterial RNA Polymerase by the Swi2/Snf2 ATPase RapA.bioRxiv : the preprint server for biology · 2023Article
- Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins.Molecular cell · 2021Article
- Bacterial Vivisection: How Fluorescence-Based Imaging Techniques Shed a Light on the Inner Workings of Bacteria.Microbiology and molecular biology reviews : MMBR · 2020Review
- Clusters of bacterial RNA polymerase are biomolecular condensates that assemble through liquid-liquid phase separation.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Article
- Establishing Live-Cell Single-Molecule Localization Microscopy Imaging and Single-Particle Tracking in the ArchaeonFrontiers in microbiology · 2020Article
- Complex Diffusion in Bacteria.Advances in experimental medicine and biology · 2020Review
- Transcription and translation contribute to gene locus relocation to the nucleoid periphery in E. coli.Nature communications · 2019Article
- Spatial organization of RNA polymerase and its relationship with transcription inProceedings of the National Academy of Sciences of the United States of America · 2019Article
- From single bacterial cell imaging towardsEssays in biochemistry · 2019Review
- Added value of autoregulation and multi-step kinetics of transcription initiation.Royal Society open science · 2018Article
- Homeostasis of protein and mRNA concentrations in growing cells.Nature communications · 2018Article
- The transcription-repair coupling factor Mfd associates with RNA polymerase in the absence of exogenous damage.Nature communications · 2018Article
- How to switch the motor on: RNA polymerase initiation steps at the single-molecule level.Protein science : a publication of the Protein Society · 2017Review
- Taking chances and making mistakes: non-genetic phenotypic heterogeneity and its consequences for surviving in dynamic environments.Journal of the Royal Society, Interface · 2017Review
- Single-molecule and super-resolution imaging of transcription in living bacteria.Methods (San Diego, Calif.) · 2017Review
- Reduction of Confinement Error in Single-Molecule Tracking in Live Bacterial Cells Using SPICER.Biophysical journal · 2017Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Superresolution fluorescence microscopy is used to locate single copies of RNA polymerase (RNAP) in live Escherichia coli and track their diffusive motion. On a timescale of 0.1-1 s, most copies separate remarkably cleanly into two diffusive states. The "slow" RNAPs, which move indistinguishably from DNA loci, are assigned to specifically bound copies (with fractional population ftrxn) that are initiating transcription, elongating, pausing, or awaiting termination. The "mixed-state" RNAP copies, with effective diffusion constant Dmixed = 0.21 μm(2) s(-1), are assigned as a rapidly exchanging mixture of nonspecifically bound copies (fns) and copies undergoing free, three-dimensional diffusion within the nucleoids (ffree). Longer trajectories of 7-s duration reveal transitions between the slow and mixed states, corroborating the assignments. Short trajectories of 20-ms duration enable direct observation of the freely diffusing RNAP copies, yielding Dfree = 0.7 μm(2) s(-1). Analysis of single-particle trajectories provides quantitative estimates of the partitioning of RNAP into different states of activity: ftrxn = 0.54 ± 0.07, fns = 0.28 ± 0.05, ffree = 0.12 ± 0.03, and fnb = 0.06 ± 0.05 (fraction unable to bind to DNA on a 1-s timescale). These fractions disagree with earlier estimates.
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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.