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Retroviruses have a single-stranded RNA genome that undergoes a special form of replication. Once the retrovirus has entered the host cell, an enzyme called reverse transcriptase synthesizes double-stranded DNA from the retroviral RNA genome. This DNA copy of the genome is then integrated into the host’s genome inside the nucleus via an enzyme called integrase. Consequently, the retroviral genome is transcribed into RNA whenever the host’s genome is transcribed, allowing the...
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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
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Identification of RNA binding motifs in the R2 retrotransposon-encoded reverse transcriptase.

Varuni K Jamburuthugoda1, Thomas H Eickbush2

  • 1Department of Biology, University of Rochester, Rochester, NY 14627, USA.

Nucleic Acids Research
|June 25, 2014
PubMed
Summary
This summary is machine-generated.

Mutations in conserved motifs of R2 retrotransposons impair RNA binding. These motifs are crucial for R2 protein functions, including DNA target binding and cleavage, essential for retrotransposon integration.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Evolutionary Biology

Background:

  • R2 non-LTR retrotransposons are mobile genetic elements that integrate into specific sites within 28S rRNA genes across diverse animal phyla.
  • The R2 element encodes a single polypeptide possessing reverse transcriptase, endonuclease, and nucleic acid binding activities, essential for its transposition.
  • Integration involves precise cleavage of both DNA strands at the target site, with the 3' ends serving as primers for DNA synthesis.

Purpose of the Study:

  • To investigate the role of conserved motifs N-terminal to the reverse transcriptase domain in R2 protein function.
  • To determine the impact of mutations within these motifs on R2 RNA binding and integration activities.

Main Methods:

  • Alanine scanning mutagenesis was employed to generate mutant R2 proteins.
  • Mobility shift assays were used to assess the RNA binding capabilities of wild-type and mutant proteins.
  • Functional assays were performed to evaluate DNA cleavage, reverse transcription, and primer utilization.

Main Results:

  • Mutant R2 proteins retained DNA cleavage and initial reverse transcription capabilities but showed significantly reduced binding to R2 RNA.
  • The mutant proteins exhibited impaired target DNA priming and second-strand DNA cleavage.
  • These findings indicate that the studied motifs are critical for RNA binding-dependent functions of the R2 protein.

Conclusions:

  • The conserved motifs N-terminal to the reverse transcriptase domain are essential for specific R2 RNA binding.
  • These motifs mediate crucial steps in the R2 retrotransposon integration process, including target DNA utilization and cleavage.
  • The identified RNA binding motifs share similarities with those found in telomerase and group II introns, suggesting conserved mechanisms in nucleic acid binding proteins.