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Related Concept Videos

Bacterial RNA Polymerase00:43

Bacterial RNA Polymerase

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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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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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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) 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.
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Updated: Mar 25, 2026

Artificial RNA Polymerase II Elongation Complexes for Dissecting Co-transcriptional RNA Processing Events
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Functional Evolution in Orthologous Cell-encoded RNA-dependent RNA Polymerases.

Xinlei Qian1, Fursham M Hamid1, Abbas El Sahili1

  • 1From the Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 138673 Singapore, Singapore.

The Journal of Biological Chemistry
|February 25, 2016
PubMed
Summary

RNA-dependent RNA polymerases (RdRPs) rapidly evolved distinct functions after gene duplication. Structural analysis reveals conserved protein fold and dimer formation despite functional divergence in RNA synthesis.

Keywords:
RNA interference (RNAi)RNA polymeraseRNA-dependent RNA polymeraseelectron microscopy (EM)protein evolutionx-ray crystallography

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Area of Science:

  • Molecular Biology
  • Biochemistry
  • Evolutionary Biology

Background:

  • Eukaryotes possess multiple RNA-dependent RNA polymerases (RdRPs), often arising from gene duplication.
  • These RdRP paralogs are implicated in diverse RNA silencing pathways and exhibit varied enzymatic activities.
  • The extent of functional adaptation in RdRPs during speciation is not well understood.

Purpose of the Study:

  • To investigate the evolutionary divergence and functional changes in QDE-1 orthologs, RNA-dependent RNA polymerases involved in RNA silencing.
  • To compare the enzymatic activities and structural properties of QDE-1 proteins from different fungal species.

Main Methods:

  • Comparative analysis of amino acid sequences of QDE-1 orthologs.
  • Biochemical characterization of purified QDE-1 enzymes from Neurospora crassa, Thielavia terrestris, and Myceliophthora thermophila.
  • X-ray crystallography and electron microscopy to determine protein structure and quaternary organization.

Main Results:

  • QDE-1 orthologs show rapid amino acid sequence divergence.
  • All three enzymes synthesize RNA, but with distinct modes of action: N. crassa's QDE-1 favors processive synthesis, while T. terrestris and M. thermophila's QDE-1 enzymes produce short RNAs via primer-independent initiation.
  • Crystal structure of T. terrestris QDE-1 reveals a dimer, confirmed by electron microscopy in solution and during template interaction, similar to N. crassa's QDE-1.

Conclusions:

  • Orthologous RNA-dependent RNA polymerases can undergo significant functional innovation during evolution.
  • This functional divergence can occur while maintaining the overall protein fold and quaternary structure, such as dimer formation.