Numerous small hammerhead ribozyme variants associated with Penelope-like retrotransposons cleave RNA as dimers

RNA Biol. 2017 Nov 2;14(11):1499-1507. doi: 10.1080/15476286.2016.1251002. Epub 2017 Nov 3.


Hammerhead ribozymes represent the most common of the 9 natural classes of self-cleaving RNAs. The hammerhead catalytic core includes 11 highly-conserved nucleotides located largely within the unpaired regions of a junction formed by stems I, II and III. The vast majority of previously reported examples carry an additional pseudoknot or other tertiary interactions between nucleotides that precede stem I and nucleotides in the loop of stem II. These extra contacts are critical for high-speed RNA catalysis. Herein, we report the discovery of ∼150,000 additional variant hammerhead representatives that exhibit diminished stem III substructures. These variants are frequently associated with Penelope-like retrotransposons, which are a type of mobile genetic element. Kinetic analyses indicate that these RNAs form dimers to cleave RNA.

Keywords: Penelope-like retrotransposon; Phosphoester transfer; self-cleaving.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Base Pairing
  • Base Sequence
  • Biocatalysis
  • Catalytic Domain
  • Dimerization
  • Isoptera / chemistry
  • Kinetics
  • Nucleic Acid Conformation
  • RNA / chemistry
  • RNA / genetics
  • RNA / metabolism*
  • RNA Cleavage*
  • RNA, Catalytic / chemistry*
  • RNA, Catalytic / genetics
  • RNA, Catalytic / isolation & purification
  • RNA, Catalytic / metabolism
  • RNA, Protozoan / genetics
  • RNA, Protozoan / metabolism
  • Retroelements*
  • Soil / chemistry
  • Urochordata / chemistry


  • RNA, Catalytic
  • RNA, Protozoan
  • Retroelements
  • Soil
  • hammerhead ribozyme
  • RNA