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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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DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with the...

The Replisome

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The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with the...

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Synthesis of new DNA molecules is carried out by the enzyme DNA polymerase, which adds nucleotides on the daughter strand complementary to the template DNA strand. DNA polymerase has a higher affinity to add the correct base and ensures fidelity during DNA replication. Furthermore, it exhibits proofreading activity during replication, using an exonuclease domain that cuts off incorrect nucleotides from the nascent DNA strand.
Errors During Replication are Corrected by the DNA Polymerase Enzyme

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Artificial RNA Polymerase II Elongation Complexes for Dissecting Co-transcriptional RNA Processing Events

Artificial RNA Polymerase II Elongation Complexes for Dissecting Co-transcriptional RNA Processing Events

Published on: May 13, 2019

RNA polymerase pushing.

Eric A Galburt¹, Juan M R Parrondo, Stephan W Grill

¹Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA. egalburt@biochem.wustl.edu

Biophysical Chemistry

|May 10, 2011

Summary

This summary is machine-generated.

Interacting RNA polymerases may use a novel power stroke mechanism, not a Brownian ratchet. This mechanism, identified via a two-dimensional energy landscape, is more effective with an early transition state.

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Artificial RNA Polymerase II Elongation Complexes for Dissecting Co-transcriptional RNA Processing Events

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Published on: May 13, 2019

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Area of Science:

Biophysics
Molecular Biology
Biochemistry

Background:

Molecular motors operate via Brownian ratchet or power stroke mechanisms, differentiated by transition state positions.
Cellular RNA polymerases (RNAPs) are hypothesized to function as ratchets, facilitating forward movement and reducing pausing during transcription.
The transition state position (early vs. late) dictates whether chemical energy is stored for release (stroke) or used to rectify thermal motion (ratchet).

Purpose of the Study:

To investigate the mechanism by which interacting cellular RNA polymerases (RNAPs) move along DNA.
To differentiate between Brownian ratchet and power stroke models for RNAP-RNAP interactions.
To elucidate the role of energy landscapes in RNAP translocation and pausing.

Main Methods:

Construction of a two-dimensional energy landscape by combining individual landscapes of active and backtracked RNAP enzymes.
Analysis of the energy landscape to identify novel translocation mechanisms arising from enzyme-enzyme interactions.
Evaluation of the efficiency of the identified mechanism based on transition state positions.

Main Results:

Identification of a new pushing mechanism resulting from a saddle trajectory in the two-dimensional energy landscape of interacting RNAPs.
Demonstration that this novel mechanism is more efficient when characterized by an early transition state.
Evidence suggests that interacting RNAPs may utilize a power stroke mechanism rather than a Brownian ratchet.

Conclusions:

Interacting cellular RNA polymerases may employ a power stroke mechanism, distinct from the previously proposed Brownian ratchet model.
The newly identified saddle trajectory mechanism in the energy landscape offers a more effective means of translocation for RNAPs.
The findings suggest that the transition state position is critical in determining the translocation strategy of interacting RNAPs, favoring a power stroke mechanism with an early transition state.