Secondary structure analysis of the 5′ ends of mitochondrial mRNAs

The mRNAs in mammalian mitochondria are quite unusual in that they have an almost complete lack of 5′ and 3′ untranslated regions. The start codons of the mRNAs are usually within the first 8 nucleotides of the 5′ end. Since mammalian mitochondrial mRNAs do not have a Shine‐Dalgarno sequence as in prokaryotes nor a 5′ cap as in the cytoplasm of eukaryotes, a different mechanism must be used for start codon recognition. As a first step in understanding how the start codon of mitochondrial mRNAs is recognized we have used Selective 2′‐Hydroxyl Acylation analyzed by Primer Extension (SHAPE) to map the secondary structure of the 5′ ends of the mRNAs for cytochrome oxidase subunits II and III. SHAPE chemistry is used to analyze nucleotide flexibility in RNA molecules. The overall structure of the 50 or more residues near the 5′ end of the cytochrome oxidase subunit II and III mRNAs is quite flexible. However, all or part of the start codons of these RNAs are predicted to be base paired. The free energy of the structures predicted range from −0.5 to −7 kcal/mol, suggesting that the start codons will be accessible to the mitochondrial ribosome during initiation. The structures of the 5′ ends of additional mitochondrial mRNAs are currently being studied. This work was supported by NIH grant GM32734.