Nucleobase modification by an RNA enzyme

Nucleic Acids Res. 2017 Feb 17;45(3):1345-1354. doi: 10.1093/nar/gkw1199.

Abstract

Ribozymes can catalyze phosphoryl or nucleotidyl transfer onto ribose hydroxyls of RNA chains. We report a single ribozyme that performs both reactions, with a nucleobase serving as initial acceptor moiety. This unprecedented combined reaction was revealed while investigating potential contributions of ribose hydroxyls to catalysis by kinase ribozyme K28. For a 58nt, cis-acting form of K28, each nucleotide could be replaced with the corresponding 2΄F analog without loss of activity, indicating that no particular 2΄OH is specifically required. Reactivities of two-stranded K28 variants with oligodeoxynucleotide acceptor strands devoid of any 2΄OH moieties implicate modification on an internal guanosine N-2, rather than a ribose hydroxyl. Product mass suggests formation of a GDP(S) adduct along with a second thiophosphorylation, implying that the ribozyme catalyzes both phosphoryl and nucleotidyl transfers. This is further supported by transfer of radiolabels into product from both α and γ phosphates of donor molecules. Furthermore, periodate reactivity of the final product signifies acquisition of a ribose sugar with an intact 2΄-3΄ vicinal diol. Neither nucleobase modification nor nucleotidyl transfer has previously been reported for a kinase ribozyme, making this a first-in-class ribozyme. Base-modifying ribozymes may have played important roles in early RNA world evolution by enhancing nucleic acid functions.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Binding Sites
  • Catalysis
  • Evolution, Molecular
  • Guanosine / chemistry
  • Hydrogen-Ion Concentration
  • Kinetics
  • Nucleic Acid Conformation
  • Phosphorylation
  • RNA / chemistry*
  • RNA / metabolism*
  • RNA Stability
  • RNA, Catalytic / chemistry*
  • RNA, Catalytic / metabolism*
  • Substrate Specificity
  • Synthetic Biology
  • Temperature

Substances

  • RNA, Catalytic
  • Guanosine
  • RNA