**1.4. Mechanisms that switch between genetic codes?**

Phenomena systematically exchanging nucleotides remind more specific mechanisms that alter the genetic code according to which a protein is coded, from a regular genetic code to a stopless genetic code, and/or vice versa. Indeed, previous analyses of mitogenomes revealed that in one GenBank mitogenome (from a marine turtle, the Olive Ridley, *Lepidochelys olivacea*), following GenBank's annotations, several regular protein coding genes do not code for the regular proteins essential for mitochondrial metabolism and usually encoded at these genomic locations. These essential proteins are indeed coded by the corresponding sequences, but only after a frameshift, and only if stops in that frame are translated, explaining the erroneous annotation of stopless ORFs (abbreviation for open reading frames) that do not code for recognized mitochondrial proteins [9].

This was originally interpreted as resulting from directed selection on stop codons. Observations of systematic mutations in contexts creating stop codons in ORFs of HIV genes specifically in elite controllers immune to HIV [73, 74] suggests that enzymatically directed mutagenesis during DNA replication and/or edition could transform ORFs coded according to a regular genetic code into one coded by a stopless genetic code, and vice versa, as observed in several mitochondrial genes of the Olive Ridley. For HIV, introducing stops presumably drastically reduces viral production and contributes to immunity.

This hypothesis of mutations directed at stop codons is in line with observations that polymerase errors are more frequent in stop codon contexts, interpreted as an adaptational bias to introduce mutations in stops [75]. In the next section, GenBank is explored to detect further mitogenomes in which genetic codes were switched by producing stop codons in ORFs and stop-depletion in other frames.

coding genes. These unusual CDs in this insect mitogenome remind previous descriptions of other unusual CDs in the mitogenome of the marine turtle *Lepidochelys olivacea*. This justifies detailed analyses of peptides translated from the six frames of the 13 protein coding genes of the mitogenomes of *Aleurodicus dispersus* (JX566506), and, for comparative purpose, of its closest relative with a complete mitogenome in GenBank, *Aleurodicus dugesii* (NC\_005939),

Directed Mutations Recode Mitochondrial Genes: From Regular to Stopless Genetic Codes

http://dx.doi.org/10.5772/intechopen.80871

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All six frames of the 13 mitochondrial protein coding genes of *Aleurodicus dispersus* were translated according to the regular invertebrate mitochondrial genetic code. First, BLAST analyzed peptides translated from GenBank-annotated, stopless ORFs to verify which of these peptides are "normal," i.e., have regular homologies with the corresponding protein predicted for the

These analyses confirm that GenBank annotations of the six *Aleurodicus dispersus* mitogenes COI, COII, AT6, COIII, ND3, and ND2 code for typical invertebrate proteins homologous with corresponding proteins in regular insect mitogenomes, notably *Aleurodicus dugesii*. The remaining seven genes follow different coding structures described below, based on frameshifts and/or stop depletion/translation. Blastp does not detect any homologies for proteins predicted according to GenBank annotations for genes AT8, ND1, ND6, ND5, ND4, and ND4l,

Mitochondrial metabolism without the regular proteins usually translated from these seven genes seems impossible. Regular analyses of the mitogenome of *Aleurodicus dugesii* detect these proteins as they are annotated in GenBank. The possibility that these genes were transferred in *Aleurodicus dispersus* to the nucleus and that proteins are imported to the mitochondrion seems unlikely as ORFs occur at positions corresponding to gene locations coding for

The case of the missing ATP synthetase subunit 8 is solved by Blastp analysis of the peptide coded by the +2 frameshifted sequence of gene AT8. Residues at positions 8–48 (the gene has 49 codons including stop codon) in frame +2 have 75% similarity with congeneric mitochondrial ATP synthetase subunit 8 of *Aleurodicus dugesii* (YP\_026055, e value 2 × 10−<sup>9</sup>

alignment in **Figure 1**). It seems likely that the regular AT8 gene codes for the corresponding protein. This frame does not contain stops, implying that this gene has two stopless ORFs. The GenBank-annotated ORF does not correspond to the regular AT8, which is the +2 frame-

For gene ND6, the stopless ORF annotated in GenBank does not align with any ND6-like protein. This conundrum is solved by Blastp analysis of the peptide translated from the +1

, see

the seven missing proteins in the predicted mitoproteome of *Aleurodicus dispersus*.

whose predicted proteome seems coded according to regular rules.

**3.2.** *Aleurodicus dispersus* **protein coding genes**

regular ORF of the mitogenome of *Aleurodicus dugesii*.

**3.3. Recoding of mitogenes in** *Aleurodicus dispersus*

and only partial homology for CytB.

*3.3.1. Two ORFs on the same strand: AT8*

shifted sequence of the annotated sequence.

*3.3.2. Stop codon translation after frameshift: ND6*
