Patchy Phylogenetic Distribution and Poor Translational Adaptation of a Nested ORF in the Mammalian Mitochondrial Gene.

BACKGROUND

The mammalian mitochondrial genome has long been considered to encode only 13 proteins. However, a recent study identified a nested alternative open reading frame (nAltORF) within the primate mitochondrial gene, which we designate , that is reportedly translated in the cytosol using the standard genetic code. This discovery challenges conventional understanding and raises questions about the prevalence, conservation, and translational adaptation of such ORFs.

METHODS

This study conducted a comprehensive bioinformatic analysis of nested genes in 289 primate and 380 rodent mitochondrial sequences.

RESULTS

Nested genes meeting the criteria (>150 codons, standard genetic code) were identified in only 10.73% of primate and 20.53% of rodent species, suggesting a patchy phylogenetic distribution. While their encoded proteins showed homology to the previously reported protein encoded by the nested gene, overall amino acid conservation was low, and characteristic protein domains or signal peptides were generally not predicted. Crucially, the Kozak consensus sequences surrounding the putative start codons of these genes were exclusively "weak" or "adequate", with none classified as "strong" or "optimal". Codon Adaptation Index (CAI) and Relative Codon Deoptimization Index (RCDI) analyses of the nested genes revealed neither significant adaptation nor deoptimization to the codon usage of nuclear and mitochondrial genes. Furthermore, cosine similarity analysis indicated that genes exhibit significantly lower codon usage similarity to both nuclear and mitochondrial gene sets compared to their host genes.

CONCLUSIONS

These findings collectively suggest that while genes exist in some mammals, their inconsistent presence, weak translational initiation signals, and lack of adaptation to cytosolic codon usage characterize them as dispensable genetic elements rather than core functional genes.