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Nucleic Acids Res. 2019 Jul 26;47(13):6858-6870. doi: 10.1093/nar/gkz517.

Coding palindromes in mitochondrial genes of Nematomorpha.

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Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskiye Gory 1-40, Moscow 119991, Russian Federation.
Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russian Federation.
Severtsov Institute of Ecology and Evolution, Moscow 119071, Russian Federation.
Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow 119991, Russian Federation.
Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143028, Russian Federation.


Inverted repeats are common DNA elements, but they rarely overlap with protein-coding sequences due to the ensuing conflict with the structure and function of the encoded protein. We discovered numerous perfect inverted repeats of considerable length (up to 284 bp) embedded within the protein-coding genes in mitochondrial genomes of four Nematomorpha species. Strikingly, both arms of the inverted repeats encode conserved regions of the amino acid sequence. We confirmed enzymatic activity of the respiratory complex I encoded by inverted repeat-containing genes. The nucleotide composition of inverted repeats suggests strong selection at the amino acid level in these regions. We conclude that the inverted repeat-containing genes are transcribed and translated into functional proteins. The survey of available mitochondrial genomes reveals that several other organisms possess similar albeit shorter embedded repeats. Mitochondrial genomes of Nematomorpha demonstrate an extraordinary evolutionary compromise where protein function and stringent secondary structure elements within the coding regions are preserved simultaneously.

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