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Related Concept Videos

RNA Polymerase II Accessory Proteins02:36

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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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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.
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Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
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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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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.
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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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Characterization of RNA polymerase II trigger loop mutations using molecular dynamics simulations and machine

Bercem Dutagaci1, Bingbing Duan2, Chenxi Qiu3

  • 1Department of Molecular and Cell Biology, University of California Merced, Merced, California, United States of America.

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Summary

Machine learning predicts RNA Polymerase II trigger loop (TL) mutations

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Area of Science:

  • Molecular biology
  • Biophysics
  • Computational biology

Background:

  • The trigger loop (TL) is crucial for RNA Polymerase II (Pol II) catalysis and fidelity.
  • TL mutations impact enzyme activity and accuracy.
  • Understanding these impacts requires linking mutations to structural changes.

Purpose of the Study:

  • To characterize TL mutations in Saccharomyces cerevisiae Pol II.
  • To correlate mutations with observed phenotypes.
  • To link phenotypes to structural alterations identified via molecular dynamics (MD) simulations.

Main Methods:

  • Applied molecular dynamics (MD) simulations.
  • Utilized machine learning (ML) techniques, including a variational auto-encoder.
  • Modeled mutant phenotypes using fitness values under stress conditions.

Main Results:

  • ML models predicted phenotypes from amino acid sequences with 0.68 R2 correlation.
  • MD data integration into ML predictions proved challenging due to noise and incompleteness.
  • A variational auto-encoder clustered mutants by phenotype based on structural details.

Conclusions:

  • Loss-of-function (LOF) and lethal mutations often increase distances between TL residues and NTP substrates or the bridge helix (BH).
  • Gain-of-function (GOF) mutants may disrupt hydrophobic contacts within the TL.
  • Structural insights from MD, despite noise, aid in classifying mutant phenotypes.