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Nucleobase modification by an RNA enzyme.

Raghav R Poudyal1,2, Phuong D M Nguyen1,2, Melissa P Lokugamage2,3

  • 1Dept. of Biochemistry, University of Missouri, Columbia, MO, USA.

Nucleic Acids Research
|February 10, 2017
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Summary
This summary is machine-generated.

A novel ribozyme performs both phosphoryl and nucleotidyl transfer reactions, modifying a nucleobase instead of a ribose hydroxyl. This discovery expands our understanding of ribozyme capabilities and their potential roles in early RNA evolution.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Origin of Life

Background:

  • Ribozymes are RNA molecules with catalytic activity, known to perform phosphoryl or nucleotidyl transfer reactions.
  • Kinase ribozyme K28 was investigated for its catalytic mechanisms involving ribose hydroxyl groups.

Purpose of the Study:

  • To investigate the catalytic mechanism of kinase ribozyme K28.
  • To identify the specific site of reaction and the type of transfer catalyzed by K28.
  • To characterize a novel ribozyme with dual catalytic functions.

Main Methods:

  • Site-directed mutagenesis using 2'-fluoro analogs to probe ribose hydroxyl requirements.
  • Analysis of two-stranded K28 variants with oligodeoxynucleotide acceptors lacking 2'-hydroxyl groups.
  • Mass spectrometry to determine product composition and structure.
  • Radiolabeling studies to trace phosphate transfer from donor molecules.
  • Periodate reactivity assays to confirm the presence of a ribose sugar with intact vicinal diols.

Main Results:

  • The ribozyme K28 does not require specific 2'-hydroxyl groups for activity, indicating a non-ribose hydroxyl catalytic site.
  • Modification occurs on an internal guanosine N-2, not a ribose hydroxyl.
  • The ribozyme catalyzes both phosphoryl and nucleotidyl transfer reactions, forming a GDP(S) adduct and undergoing thiophosphorylation.
  • Evidence from radiolabeling and periodate reactivity confirms dual transfer and acquisition of a ribose sugar.

Conclusions:

  • A single ribozyme (K28) has been identified that catalyzes both phosphoryl and nucleotidyl transfer reactions, with a nucleobase as the acceptor.
  • This represents a first-in-class kinase ribozyme capable of base modification and nucleotidyl transfer.
  • Such base-modifying ribozymes could have been crucial for enhancing nucleic acid functions in the early RNA world.