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Related Concept Videos

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Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
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Initiation is the first step of transcription in eukaryotes. Prokaryotic RNA Polymerase (RNAP) can bind to the template DNA and start transcribing. On the other hand, transcription in eukaryotes requires additional proteins, called transcription factors, to first bind to the promoter region in the DNA template. This binding helps recruit the specific RNAP that can assemble on the DNA and start transcription.
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The organization of prokaryotic genes in their genome is notably different from that of eukaryotes. Prokaryotic genes are organized, such that the genes for proteins involved in the same biochemical process or function are located together in groups. This group of genes, along with their regulatory elements, are collectively known as an operon. The functional genes in an operon are transcribed together to give a single strand of mRNA known as polycistronic mRNA.
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Related Experiment Video

Updated: Apr 17, 2026

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
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Structural basis for transcription reactivation by RapA.

Bin Liu1, Yuhong Zuo1, Thomas A Steitz2

  • 1Department of Molecular Biophysics and Biochemistry.

Proceedings of the National Academy of Sciences of the United States of America
|February 4, 2015
PubMed
Summary

Researchers discovered how ATPase RapA reactivates stalled RNA polymerase (RNAP) by binding to the RNA exit channel. This binding facilitates backward DNA translocation, crucial for efficient transcription.

Keywords:
DNA translocaseRNA polymeraseRapAbacktranslocationtranscription

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • RNA polymerase (RNAP) can stall during transcription, leading to loss of activity and reduced RNA synthesis efficiency.
  • Reactivation of stalled RNAPs is critical for maintaining robust transcriptional output.

Purpose of the Study:

  • To elucidate the structural mechanism by which ATPase RapA reactivates stalled RNAPs.
  • To understand the role of RapA in transcriptional regulation and RNAP translocation.

Main Methods:

  • Determined the crystal structure of the Escherichia coli RNAP core enzyme in complex with ATPase RapA at 4.7-Å resolution.

Main Results:

  • The structure shows RapA binds to the RNA exit channel of RNAP, preventing RNA hairpin formation.
  • RapA's orientation suggests it utilizes ATPase activity to induce backward translocation of RNAP along the DNA template.

Conclusions:

  • The RapA-RNAP structure provides key insights into the reactivation mechanism of stalled RNA polymerases.
  • Supports ATP-driven backward translocation as a fundamental mechanism for transcriptional regulation.