Compared are involved in aerobic respiration (also called oxidative

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Last updated: September 9, 2019

Compared to mitochondria found inother eukaryotic kingdoms, those of metazoan are massively reduced in theirgenetic structure (Berntet al., 2013) . Their mtDNAis a short, circular molecule that generally contains about 13 intronless,protein-coding genes, all of which are involved in aerobic respiration (also calledoxidative 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 maturemRNA and rRNA by precise cleavage of the 5? and 3?-termini of the flankingtRNAs. 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 beinvolved in the processing of liberation of RNAs.

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Besides,in several taxa mt-mRNAs, rRNAs and even tRNAs may be oligo- orpoly-adenylated (Kyriakouet al., 2014) . The consequence of this process is numerous, thiscould have a dual and opposite role: it promotes the stability of transcriptsor offers a target for the initiation of degradation. Overlapping genes on the same DNA strand have long been knownthroughout metazoans (Fiedler et al.

, 2015) . So, the termination points of the protein-encoding genes couldbe difficult to infer as stop codons (generally UAA or UAG) may be absent. Itis accepted that abbreviated stop codons (U or UA) are converted to UAA codonsby polyadenylation after transcript cleavage, and this has been confirmed byanalyses of transcripts in some cases (Wolstenholme, 1992) . Althoughmore rarely, the initiation codon may also not have been determined. For several protein-encoding genes, the question of apossible overlapping with adjacentdownstream or upstream trn genes isoften raised.Incidentally, in 2004, when lookingfor chaetognath mt-trn genes (Faure and Casanova, 2006) , it was seen that tRNAs bear nt tripletscorresponding to stop or start codons at precise positions, this unpublishedobservation is the topic of this article.

2. Material and methodsMost of the research was done in two databases which include primarysequences 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 toprokaryotes and eukaryotes whereas in mitotRNAdb (http://mttrna.

bioinf.uni-leipzig.de/mtDataOutput/) were recorded 30,525 metazoan mt-trngenes belongingto 1418 species (Jühlinget al., 2009) . Despite a bias for metazoan, these two databases provide powerful andfast search engines.

Alignments were generated by Clustal W (www.ebi.ac.uk/clustalw/) whereassecondary 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 discussion3.1Frequencies of TAR10 and ATR49 triplets in various taxaVisual observations oftRNA deduced 2D structures suggested that nt triplets which could correspond tostop or start codons seemed to be particularly represented at specificpositions.

These are the UAR (R for purine) triplets at position 8-10 in the standard numberingand therefore will be named UAR10 while initiation codons whose the last nt is atthe position 49 will called AUR49 (Figure 1). However, itwould most often be written TAR or ATR instead of UAR or AUR because generally theanalyzes focus on DNA. All the tRNAs which bear one or both of thesecodons 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 investigatedin different taxa including nuclear and organelles genomes for eukaryotes (Table 1). Excluding taxa forwhich the number of trn genes is too lowto 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 oftRNA combined, the percentage of TAG10 triplets is always significantly higherthan those of TAA10.

The differences are very important in prokaryotes andnuclear genomes since the percentage of TAA10 is always less than 1 while thatof TAG10 is at least 40%. Within the organelle genomes, the difference issmaller but can vary from a factor of 2.5 to 22.

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