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RNA Polymerase II Accessory Proteins

RNA Polymerase II Accessory Proteins

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...

RNA Polymerase II Accessory Proteins

RNA Polymerase II Accessory Proteins

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...

Eukaryotic RNA Polymerases

Eukaryotic RNA Polymerases

RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...

Eukaryotic RNA Polymerases

Eukaryotic RNA Polymerases

RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
All three eukaryotic RNAPs require specific transcription factors, of which the...

Bacterial RNA Polymerase

Bacterial RNA Polymerase

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...

Bacterial RNA Polymerase

Bacterial RNA Polymerase

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...

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Related Experiment Video

Updated: Jun 18, 2026

An Assay for Quantifying Protein-RNA Binding in Bacteria

An Assay for Quantifying Protein-RNA Binding in Bacteria

Published on: June 12, 2019

Structure-function analysis of mutant RNA-dependent RNA polymerase complexes with VPg.

Chaojiang Gu¹, Tao Zeng, Yong Li

¹State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.

Biochemistry. Biokhimiia

|November 18, 2009

Summary

Mutant foot-and-mouth disease virus (FMDV) RNA-dependent RNA polymerases (RdRps) were studied. VPg orientation in the RdRp-VPg1 complex dictates FMDV RdRp activity, guiding antiviral drug design.

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Area of Science:

Virology
Molecular Biology
Biochemistry

Background:

Foot-and-mouth disease virus (FMDV) replication relies on its RNA-dependent RNA polymerase (RdRp).
Understanding RdRp function is key to developing antiviral strategies against FMDV.

Purpose of the Study:

To investigate the structure-function relationship of FMDV RdRp mutants.
To determine how mutations and VPg binding affect RdRp catalytic activity.
To provide a basis for designing novel antiviral agents targeting FMDV replication.

Main Methods:

Isolation and expression of four FMDV RdRp mutants (L123F, T381A, T291I/T381I, L123F/F244L) in E. coli.
Purification of mutant RdRps using His-bind resin chromatography.
Assessment of polymerase activity using an in vitro RNA replication system and real-time RT-PCR.
Structure determination via homology modeling and molecular docking of RdRp-RNA template-primer complexes.
Mathematical analysis of VPg1 orientation within RdRp-VPg1 complexes.

Main Results:

Mutant L123F showed a 0.6-fold decrease in polymerase activity.
Activities of mutants L123F/F244L and T381A were undetectable.
Mutant T291I/T381I exhibited a surprising 0.7-fold increase in polymerase activity.
VPg1 orientation within the RdRp-VPg1 complex was determined and correlated with catalytic activity.

Conclusions:

The orientation of VPg after binding to FMDV RdRp is a critical determinant of its catalytic activity.
These findings offer insights into the mechanism of FMDV RNA replication.
The study provides a foundation for the rational design of new antiviral therapies targeting FMDV.