Compared are involved in aerobic respiration (also called oxidative

Compared to mitochondria found in
other eukaryotic kingdoms, those of metazoan are massively reduced in their
genetic structure (Bernt
et al., 2013) . Their mtDNA
is a short, circular molecule that generally contains about 13 intronless,
protein-coding genes, all of which are involved in aerobic respiration (also called
oxidative phosphorylation) (Ladoukakis and Zouros, 2017) . Moreover,
the coding sequences of genes are usually separated by at most a few nts and long polycistronic precursor transcripts may be processed into mature
mRNA and rRNA by precise cleavage of the 5? and 3?-termini of the flanking
tRNAs. This processing, which is known as the RNA punctuation model (Ojala et al., 1980) ,
is mediated by RNase P and Z endonucleases, respectively (Levinger et al., 2004) .
However, this model is not always applicable, genes are not bounded by trn genes or these latter may not be
involved in the processing of liberation of RNAs. Besides,
in several taxa mt-mRNAs, rRNAs and even tRNAs may be oligo- or
poly-adenylated (Kyriakou
et al., 2014) . The consequence of this process is numerous, this
could have a dual and opposite role: it promotes the stability of transcripts
or offers a target for the initiation of degradation. Overlapping genes on the same DNA strand have long been known
throughout metazoans (Fiedler et al., 2015) . So, the termination points of the protein-encoding genes could
be difficult to infer as stop codons (generally UAA or UAG) may be absent. It
is accepted that abbreviated stop codons (U or UA) are converted to UAA codons
by polyadenylation after transcript cleavage, and this has been confirmed by
analyses of transcripts in some cases (Wolstenholme, 1992) . Although
more rarely, the initiation codon may also not have been determined. For several protein-encoding genes, the question of a
possible overlapping with adjacent
downstream or upstream trn genes is
often raised.

Incidentally, in 2004, when looking
for chaetognath mt-trn genes (Faure and Casanova, 2006) , it was seen that tRNAs bear nt triplets
corresponding to stop or start codons at precise positions, this unpublished
observation is the topic of this article.

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2. Material and methods

Most of the research was done in two databases which include primary
sequences and graphical representations of tRNA 2D structures, tRNAdb (http://trna.bioinf.uni-leipzig.de/DataOutput/) contained more than 12,000 trn genes from 579 species belonging to
prokaryotes and eukaryotes whereas in mitotRNAdb (http://mttrna.bioinf.uni-leipzig.de/mtDataOutput/) were recorded 30,525 metazoan mt-trn
genes belonging
to 1418 species (Jühling
et al., 2009) . Despite a bias for metazoan, these two databases provide powerful and
fast search engines. Alignments were generated by Clustal W (www.ebi.ac.uk/clustalw/) whereas
secondary structures were predicted by tRNAscan-SE
(http://lowelab.ucsc.edu/tRNAscan-SE/) (Lowe and Eddy, 1997) . BLAST analyses were conducted using the website:
https://blast.ncbi.nlm.nih.gov/Blast.cgi.

3.
Results and discussion

3.1
Frequencies of TAR10 and ATR49 triplets in various taxa

Visual observations of
tRNA deduced 2D structures suggested that nt triplets which could correspond to
stop or start codons seemed to be particularly represented at specific
positions. These are the UAR (R for purine) triplets at position 8-10 in the standard numbering
and therefore will be named UAR10 while initiation codons whose the last nt is at
the position 49 will called AUR49 (Figure 1). However, it
would most often be written TAR or ATR instead of UAR or AUR because generally the
analyzes focus on DNA. All the tRNAs which bear one or both of these
codons are named ss-tRNAs (ss for stop and start) or ss-trn for the corresponding genes. Using tRNAdb and mitotRNAdb databases, the frequency of these triplets was investigated
in different taxa including nuclear and organelles genomes for eukaryotes (Table 1). Excluding taxa for
which the number of trn genes is too low
to have a statistical value, the TAR10 are always present at high frequencies,
whether in prokaryotes, nuclear or organelle genomes. Values range from 36.5%
for Cnidaria to 81.6% for pseudocoelomates. In all the taxa and all types of
tRNA combined, the percentage of TAG10 triplets is always significantly higher
than those of TAA10. The differences are very important in prokaryotes and
nuclear genomes since the percentage of TAA10 is always less than 1 while that
of TAG10 is at least 40%. Within the organelle genomes, the difference is
smaller but can vary from a factor of 2.5 to 22.