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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

Transcription Initiation

Transcription Initiation

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.
The promoters and enhancers and their accessory proteins allow tight regulation of...

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

Bacterial Transcription

Bacterial Transcription

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:

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Related Experiment Video

Updated: May 3, 2026

High-throughput Purification of Affinity-tagged Recombinant Proteins

High-throughput Purification of Affinity-tagged Recombinant Proteins

Published on: August 26, 2012

Structural basis for multi-subunit DNA-dependent RNA polymerase catalytic activity.

Andreas U Mueller¹, Seth A Darst¹

¹Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA.

|May 1, 2026

Summary

Researchers visualized bacterial RNA polymerase (RNAP) during transcription initiation. This revealed key structural details of the enzyme

Keywords:

Michaelis complex RNA polymerase catalytic mechanism cryo-electron microscopy nucleotide addition cycle transcription trigger loop

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Last Updated: May 3, 2026

High-throughput Purification of Affinity-tagged Recombinant Proteins

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Published on: August 26, 2012

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Chemical Triphosphorylation of Oligonucleotides

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Published on: June 2, 2022

Area of Science:

Biochemistry
Molecular Biology
Structural Biology

Background:

DNA-dependent RNA polymerase (RNAP) is essential for gene expression.
The catalytic mechanism of RNAP remains poorly understood due to a lack of high-resolution intermediate structures.

Purpose of the Study:

To visualize E. coli RNAP during initial transcription using cryo-electron microscopy.
To elucidate the catalytic mechanism of RNAP by obtaining high-resolution structures of key intermediates.

Main Methods:

Cryo-electron microscopy (cryo-EM) was used to visualize E. coli RNAP.
High-resolution structures of initial transcribing complexes were determined.

Main Results:

Five high-resolution structures of initial transcribing complexes were obtained, including Michaelis complex (MC) and post-catalytic product complex (PC).
The MC structure revealed critical conformational transitions during catalysis.
Conserved water molecules in MC and PC structures suggest functional importance.

Conclusions:

RNAP catalyzes nucleotidyl transfer via a positional (entropic) mechanism.
Structural determinants for the initial step of gene expression were identified.