title: Lack of secondary structure characterizes the 5' ends of mammalian mitochondrial mRNAs.
abstract: The mammalian mitochondrial genome encodes 13 proteins, which are synthesized at the direction of nine monocistronic and two dicistronic mRNAs. These mRNAs lack both 5' and 3' untranslated regions. The mechanism by which the specialized mitochondrial translational apparatus locates start codons and initiates translation of these leaderless mRNAs is currently unknown. To better understand this mechanism, the secondary structures near the start codons of all 13 open reading frames have been analyzed using RNA SHAPE chemistry. The extent of structure in these mRNAs as assessed experimentally is distinctly lower than would be predicted by current algorithms based on free energy minimization alone. We find that the 5' ends of all mitochondrial mRNAs are highly unstructured. The first 35 nucleotides for all mitochondrial mRNAs form structures with free energies less favorable than -3 kcal/mol, equal to or less than a single typical base pair. The start codons, which lie at the very 5' ends of these mRNAs, are accessible within single stranded motifs in all cases, making them potentially poised for ribosome binding. These data are consistent with a model in which the specialized mitochondrial ribosome preferentially allows passage of unstructured 5' sequences into the mRNA entrance site to participate in translation initiation.
authors: Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, USA.
authors: Christie N
authors: CN
authors: Jones
authors: Kevin A
authors: KA
authors: Wilkinson
authors: Kimberly T
authors: KT
authors: Hung
authors: Kevin M
authors: KM
authors: Weeks
authors: Linda L
authors: LL
authors: Spremulli
mesh_terms: D000818:Animals; D001483:Base Sequence; D002417:Cattle; D018387:Codon, Initiator / Q000235:genetics; D017931:DNA Primers / Q000235:genetics; D042967:Electron Transport Complex I / Q000235:genetics; D003576:Electron Transport Complex IV / Q000235:genetics; D020869:Gene Expression Profiling; D005796:Genes; D054629:Genome, Mitochondrial; D008957:Models, Genetic; D008958:Models, Molecular; D009245:NADH Dehydrogenase / Q000235:genetics; D009690:Nucleic Acid Conformation; D010442:Peptide Chain Initiation, Translational; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D000077278:RNA, Mitochondrial
chemical_list: D018387:Codon, Initiator; D017931:DNA Primers; D012333:RNA, Messenger; D000077278:RNA, Mitochondrial; C029305:mitochondrial messenger RNA; D009245:NADH Dehydrogenase; D003576:Electron Transport Complex IV; D042967:Electron Transport Complex I