**1.3. Regulation of alternative transcriptions by secondary structure**

These observations suggest translational activity of mitochondrial tRNAs with anticodons matching stop codons [3] templated by antisense strands of regular mitochondrial tRNAs [4, 5]. Predicted occurrences of mitochondrial stop suppressor (antiterminator) tRNAs coevolve with stop codon usages in predicted off-frame protein coding genes in all analyzed mitochondria (primates and Drosophila [6, 7], including their ribosomal RNAs [8], turtles [9] and Chaetognaths [10]), and in a peptide detected by specific monoclonal immunolocalization in human mitochondria [11]. Hence, there are probably more mitochondrion-encoded genes than usually accepted [12, 13]. Mitogenome size reduction probably causes gene multifunc-

Translation of stop codons occurs in different organisms [22, 23], but seems particularly widespread in mitochondria [2, 3] as reflected by the evolution of mitochondrial genetic codes [1]. Nuclear genetic codes lacking dedicated stop codons have been described in protists [24–27]

Switching between regular and stopless genetic codes is not the only strategy increasing dramatically information encoded by genomes. Isolated tetracodons, codons expanded by a fourth silent nucleotide, are known since the dawn of molecular biology [29]. These are sometimes translated by tRNAs with expanded anticodons [30, 31]. It seems probable that systematic frameshifts produce stretches of tetracodons that code for (yet) undetected peptides ([32–34]). Some evidence suggests that tetracoding occurs especially at high environmental temperatures [35] and is predicted by genetic code optimization [36]: codonanticodon interactions are more stable when four rather than only three base pairs hybridize. Other theoretical considerations suggest that the mitochondrial vertebrate genetic code evolved from a specific subset of 64 tetracodons, the tesserae, chosen on the basis of sym-

Indeed, analyses of mitochondrial mass spectra searching for peptides matching translations assuming tetra- and pentacodons, codons expanded by one or two silent nucleotides, detected

Further little known mechanisms increase numbers of proteins potentially coded by single sequences. Polymerization occasionally exchanges systematically between nucleotides during DNA replication [44–46] or RNA transcription [47–53] for long sequence stretches (23 exchange rules are possible, nine symmetric, e.g., A<>C, and fourteen asymmetric, e.g., A > C > G > A), producing swinger sequences. Swinger replication, in particular the double symmetric exchange A<>T + C<>G, seems most frequent for mitochondrial ribosomal RNAs [46]. This increases the coding potential of rRNAs, strengthening the hypothesis that rRNAs are modern remnants of protogenomes that templated for translational molecules (tRNA-like and rRNA-like) and protein coding genes [54–58] by dense overlap coding. This is compatible

I stress here that the exchange A<>T + C<>G is not trivial: this creates the complement of the template sequence, which is not the regular inverse (or reverse) complement. "Complement"

with the occurrence of protein coding regions within modern rRNAs [8, 59–61].

tionality, including mt tDNAs functioning as replication origins [14–21].

and fungi [28].

58 Mitochondrial DNA - New Insights

metry principles [37].

**1.1. Alternative coding by expanded codons**

numerous tetra- and pentacoded peptides [38–43].

**1.2. Alternative coding by swinger polymerization**

Secondary structures are important components of RNA function and evolution [64, 65]. Secondary structures formed by tRNA sequences punctuate posttranscriptional processing of mitochondrial transcripts [66–68]. Palindromes potentially forming secondary structures after sequence swinger-tranformation associate with detected mitochondrial swinger RNAs [69]. This is similar to what is known from regular RNA processing in mitochondria and, surprisingly, giant viruses [70] which bear also other striking resemblances with mitogenomes, including similar gene order [71]. Transcription sometimes deletes systematically mono- or dinucleotides after transcribing trinucleotides (del-transcription), translated into peptides that in part converge with peptides translated from regular RNAs by expanded anticodons [38]. Del-transcription, or at least detection of delRNAs, seems downregulated by secondary structures formed after transformation of the sequence by systematic deletions [72].
