title: Triplex DNA:RNA, 3'-to-5' inverted RNA and protein coding in mitochondrial genomes.
abstract: Triple-stranded DNA:RNA helices of unknown function in vertebrate mitochondria associate with replication and transcription. Antiparallel Hoogsteen pairings form triplexes at physiological conditions. Intermolecular antiparallel triplexes require inverted 3'-to-5' RNA polymerization, which was never observed. Three rare, long natural 3'-to-5' inverted GenBank RNAs from mice mitochondria suggest occasional inverted transcription, putatively coding for proteins. BLAST aligns 18 GenBank-stored proteins with hypothetical proteins translated from the 3'-to-5' inverted Mus musculus mitochondrial genome. Three are DNA-binding, five are membrane proteins. 25% of main frame codons contribute to their 3'-to-5' overlap coding. Properties of these codons match those of overlap coding protein genes, as compared to codons not expected involved in inverted coding: a) nucleotide contents at synonymous codon positions in mitochondrial genomes fit replicational deamination gradients (A->G and C->T), but digress from gradients when functioning as nonsynonymous positions in putative 3'-to-5' overlapping genes; b) bias against 'circular code' codons (codon groups creating unambiguity between frames), and favouring homogenous codons (AAA, CCC, GGG, TTT) characterize overlapping genes, including putative 3'-to-5' overlapping genes, as compared to nonoverlapping coding sequences from the same main frame gene. This signature correlates with digression from deamination gradients. Deamination and circular code tests confirm independently alignment-based predictions of overlapping 3'-to-5' protein coding genes. Results indicate varying expression for different 3'-to-5' overlapping genes. Inverted 3'-to-5' RNA is produced, perhaps by an unknown RNA polymerase (invertase) putatively coded by 3'-to-5' inverted RNA.
authors.affiliation: National Natural History Museum Collections, The Hebrew University of Jerusalem, Jerusalem, Israel. podarcissicula@gmail.com
authors.forename: Hervé
authors.initials: H
authors.lastname: Seligmann
mesh_terms: D000818:Animals; D003062:Codon / Q000737:chemistry / Q000235:genetics; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics*; D054629:Genome, Mitochondrial / Q000502:physiology*; D051379:Mice; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry / Q000235:genetics*; D012313:RNA / Q000737:chemistry / Q000235:genetics*; D000077278:RNA, Mitochondrial
chemical_list: D003062:Codon; D004272:DNA, Mitochondrial; D009692:Nucleic Acid Heteroduplexes; D000077278:RNA, Mitochondrial; D012313:RNA