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Related Concept Videos

Translesion DNA Polymerases02:10

Translesion DNA Polymerases

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.
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...
Eukaryotic RNA Polymerases00:58

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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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Eukaryotic RNA Polymerases00:58

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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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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 Proteins02:36

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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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Artificial RNA Polymerase II Elongation Complexes for Dissecting Co-transcriptional RNA Processing Events
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RNA polymerase II flexibility during translocation from normal mode analysis.

Michael Feig1, Zachary F Burton

  • 1Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA. feig@msu.edu

Proteins
|August 29, 2009
PubMed
Summary

Computational analysis reveals how eukaryotic RNA polymerase II (RNAPII) moves during transcription. Specific enzyme motions coupled with nucleic acid movement are key for efficient DNA and RNA translocation.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • Eukaryotic RNA polymerase II (RNAPII) is crucial for gene expression.
  • Understanding RNAPII's dynamic structural changes during transcription is essential for elucidating its mechanism.

Purpose of the Study:

  • To investigate the structural dynamics of RNAPII during nucleic acid translocation using computational normal mode analysis.
  • To identify conserved motions and their role in the transcription cycle.

Main Methods:

  • Normal Mode Analysis (NMA) applied to crystal structures of RNAPII in various functional states (pre- and post-translocated, open/closed trigger loops).
  • Analysis of conserved vibrational modes and root mean square fluctuations (RMSF) to assess enzyme flexibility.

Main Results:

  • Identified conserved dynamic modes involving coupled motions of RNAPII domains (clamp, jaw) and nucleic acid translocation.
  • NMA suggests downstream DNA translocation can be distinct from DNA:RNA hybrid translocation.
  • Enzyme flexibility analysis indicates an open trigger loop is necessary for productive translocation, while NTP presence inhibits it.

Conclusions:

  • A combination of conserved dynamic modes likely drives active transcription.
  • Productive RNAPII translocation is regulated by trigger loop conformation and active site occupancy.