Bioinformatic, structural, and functional analyses support release factor-like MTRF1 as a protein able to decode nonstandard stop codons beginning with adenine in vertebrate mitochondria

• DOI: 10.1261/rna.1970310
• Publication Date: 2010-04-27T01:07:29Z
• Authors: David J. Young; Christina D. Edgar; Jennifer Murphy; Johannes Fredebohm; Elizabeth S. Poole; Warren P. Tate
• Keywords: Release factor; Stop codon; Mitochondrial ribosome

Vertebrate mitochondria use stop codons UAA and UAG decoded by the release factor (RF) MTRF1L two reassigned arginine codons, AGA AGG. A second highly conserved RF-like factor, MTRF1, which evolved from a gene duplication of an ancestral mitochondrial RF1 not RF2, is good candidate for recognizing nonstandard codons. MTRF1 differs other RFs having insertions in external loops important codon recognition (tip helix alpha5 loop) key substitutions that are involved interactions eubacterial RF/ribosome structures. These changes may allow larger purine base first position AGA/G and, uniquely RFs, only G at 2. In contrast, residues support third as would be required Since assay with vertebrate ribosomes has been established, we modified Escherichia coli loop regions to mimic MTRF1. There was loss peptidyl-tRNA hydrolysis activity standard beginning U (e.g., UAG), but gain (AAG particular). lower level could enhanced solvent modification. observations imply characteristics recognize decode