We have characterized a homodimeric tRNA endonuclease from the euryarchaeota  Ferroplasma acidarmanus  (FERAC), a facultative anaerobe which can grow at temperatures ranging from 35 to 42 °C. This enzyme, contrary to the eukaryal tRNA endonucleases and the homotetrameric  Methanocaldococcus jannaschii  (METJA) homologs, is able to cleave minimal BHB (bulge-helix-bulge) substrates at 30 °C. The expression of this enzyme in  Schizosaccharomyces pombe  (SCHPO) enables the use of its properties as effectors by inserting BHB motif introns into hairpin loops normally seen in mRNA transcripts. In addition, the FERAC endonuclease can create proteins with new functionalities through the recombination of protein domains.