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Single Mutation in Hammerhead Ribozyme Favors Cleavage Activity with Manganese over Magnesium.

Mohammad Reza Naghdi1, Emilie Boutet1, Clarisse Mucha1

  • 1Institut National de la Recherche Scientifique (INRS), Centre Armand Frappier Santé Biotechnologie, 531 boul. des Prairies, Laval, QB H7V 1B7, Canada.

Non-Coding RNA
|April 5, 2020
PubMed
Summary

Hammerhead ribozymes require cations for activity. A natural A6C variation in hammerhead ribozymes enhances manganese (Mn2+) ion activity over other cations, revealing catalytic core flexibility.

Keywords:
A6C6 hammerhead variantsRNA variantscationmagnesiummanganese

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Enzymology

Background:

  • Hammerhead ribozymes are extensively studied RNA enzymes crucial for various biological processes.
  • Their catalytic activity is largely dependent on divalent cations, with magnesium (Mg2+) being the most prevalent intracellularly.
  • While Mg2+ is primary, other cations like manganese (Mn2+) can also support cleavage, suggesting potential cation selectivity.

Purpose of the Study:

  • To investigate the impact of a naturally occurring variation (A6C) in the hammerhead ribozyme catalytic core.
  • To determine if this variation influences cation preference during RNA cleavage.
  • To explore the adaptability of hammerhead ribozyme function to different ionic environments.

Main Methods:

  • Site-directed mutagenesis was used to introduce the A6C variation into the hammerhead ribozyme sequence.
  • In vitro cleavage assays were performed using the wild-type and A6C mutant ribozymes.
  • Assays were conducted across a range of concentrations for various divalent cations, including Mg2+ and Mn2+.

Main Results:

  • The A6C variant exhibited significantly altered cation preference compared to the wild-type ribozyme.
  • Specifically, the A6C mutant showed enhanced catalytic activity in the presence of Mn2+ compared to Mg2+ and other tested cations.
  • This indicates a functional adaptation driven by the specific sequence variation in the catalytic core.

Conclusions:

  • The catalytic core of hammerhead ribozymes is not rigidly specific for Mg2+ and can be modulated by sequence variations.
  • The A6C mutation confers a preference for Mn2+, demonstrating the potential for fine-tuning ribozyme activity through natural variations.
  • This finding has implications for understanding ribozyme evolution and designing artificial ribozymes with specific ionic requirements.