Related Experiment Video
Updated: Feb 18, 2026
07:18
Application of Biolayer Interferometry BLI for Studying Protein-Protein Interactions in Transcription
Published on: July 26, 2019
14.6K
Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes
Diego Duchi1, Kristofer Gryte1, Nicole C Robb1
1Gene Machines Group, Biological Physics Research Unit, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK.
Nucleic Acids Research
|November 28, 2017
Summary
Researchers studied transcription initiation in E. coli using single-molecule Förster resonance energy transfer (smFRET). They discovered two stable states and large-scale transitions in RNA polymerase-DNA complexes, revealing key dynamics in gene regulation.
Area of Science:
- Molecular Biology
- Biophysics
- Gene Regulation
Background:
- Transcription initiation is a critical gene regulation step.
- RNA polymerase (RNAP) binding to promoter DNA forms a closed complex, followed by DNA strand separation to form an open complex.
- The precise conformational changes and influencing factors during transcription initiation remain unclear.
Purpose of the Study:
- To investigate the conformational landscape and transitions during transcription initiation.
- To elucidate the dynamics of RNA polymerase-DNA complexes during open complex formation.
Main Methods:
- Single-molecule Förster resonance energy transfer (smFRET) was employed on immobilized Escherichia coli transcription open complexes.
- Mutational studies were conducted to assess the impact of specific RNAP regions on DNA bubble dynamics.
Main Results:
- Two stable states were identified in RNAP-DNA complexes, corresponding to closed and partially open DNA conformations.
- Large-scale transitions were observed where the transcription bubble fluctuated between open and closed states on a 0.1 s timescale.
- The σ70 region 3.2 of RNAP was found to significantly influence transcription bubble dynamics.
Conclusions:
- The findings reveal distinct dynamic states and transitions during transcription initiation.
- A bend-load-open model is supported for the sequence of events leading to transcription bubble opening.
- These insights advance our understanding of gene regulation mechanisms.
Related Concept Videos
01:53Bacterial Transcription
36.9K
RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
36.9K
01:29Coordination of Gene Expression Processes in Bacteria
706
The DNA replication, transcription, and translation processes are intricately coupled in bacteria, allowing efficient gene expression and rapid protein synthesis. While this physical and functional coordination is advantageous, it introduces challenges that bacteria overcome through specific regulatory mechanisms.Coupling of Replication, Transcription, and TranslationThe coupling of replication, transcription, and translation is a hallmark of bacterial gene expression. As the replisome unwinds...
706
00:43Bacterial RNA Polymerase
33.0K
Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
33.0K
00:43Bacterial RNA Polymerase
12.2K
12.2K
02:33Initiation of Translation
39.4K
Initiating translation is complex because it involves multiple molecules. Initiator tRNA, ribosomal subunits, and eukaryotic initiation factors (eIFs) are all required to assemble on the initiation codon of mRNA. This process consists of several steps that are mediated by different eIFs.
First, the initiator tRNA must be selected from the pool of elongator tRNAs by eukaryotic initiation factor 2 (eIF2). The initiator tRNA (Met-tRNAi) has conserved sequence elements including modified bases at...
First, the initiator tRNA must be selected from the pool of elongator tRNAs by eukaryotic initiation factor 2 (eIF2). The initiator tRNA (Met-tRNAi) has conserved sequence elements including modified bases at...
39.4K
01:28Transcription in Prokaryotes
2.7K
Transcription is a highly regulated process that converts genetic information into RNA molecules. The transcription cycle is divided into three key stages: initiation, elongation, and termination, each driven by specific molecular mechanisms.Initiation of TranscriptionIn bacteria, transcription begins when the RNA polymerase core enzyme associates with a sigma factor to form a holoenzyme. For example, the E. coli sigma factor called σ70 forms a holoenzyme, which recognizes the -10 (Pribnow...
2.7K