3. 1. Polyadenylation patterns of gene groups
In particular, the following findings were obtained when each
mitochondrial gene cluster was examined individually.
Polyadenyl length varied from 15.41 (atp8 ) to 41.88 (nd6 ),
and 23.83 adenines for all protein-coding genes were found in sense
transcripts. Antisense transcripts of protein- coding genes had minimum
of 12 (atp6 ), mean of 20.27 and maximum of 56 (cox1 ) bases
polyadenylated (Figure 3, 4e). 11 of 13 protein coding genes seemed to
be transcribed in longer units than monocistrons which include only ORF.
The excessive presence of intergenic regions in both sense and antisense
transcripts indicates that intergenic regions are also transcribed and
therefore may be functional in transcription or translation, like
recommended as a transcription termination signal in Aydemir et al. 2022
and Roberti et al. 2003. We hypothesized that these extra-added
sequences can act as UTRs for mitochondrial mRNAs. Both 5‘ and 3‘ UTRs
are known to play critical roles in the post-transcriptional regulation
of gene expression by modulating the transport of mRNAs. It is known
that 3‘ UTRs regulate translation efficiency and are important in the
intracellular localization and the stability of mRNAs (Van Der Velden
and Thomas, 1999; Bashirullah, Cooperstock and Lipshitz, 2001; Jansen,
2001). Although it is assumed that mitochondrial RNAs do not contain
UTRs, some genes may contain 3‘ or 5‘ UTR sequences (Gagliardi et
al. , 2004; Nagaike et al. , 2005). In general, it has been
suggested that these UTR-containing sequences are the products of
non-canonical processes and may be associated with RNA secondary
structure clusters (Mercer et al. , 2011). 88.03% of antisense
transcripts of Apis have additional genomic sequences in
monocistron, and these can be considered as UTRs for insects, such as in
humans (Temperley et al. , 2010). tRNA sequences can act as 3‘ UTR
through the tRNA punctuation model in human mitogenomes (Temperleyet al. , 2010). Intergenic regions surrounding almost all mRNAs
including tRNAs may also act as UTRs for mRNAs in animal mitogenomes,
unlike that in human. It has been suggested that 3‘ UTR sequences in
sense transcripts may be regulated by post-transcriptional processes and
control the excessive expression of mRNAs in Drosophila and human
(Torres, Dolezal, Schlötterer, Ottenwälder, et al. , 2009; Merceret al. , 2011). We propose that premature stop codons which are
commonly exist in mitochondrial protein coding genes may lead to the
incorporation of additional amino acids to the protein and may produce
canonically longer transcripts, such has been previously detected incox2 gene of D. melanogaster with additional 11 amino
acids (Stewart and Beckenbach, 2009).
Polyadenyl length was varied from 17,49 (rrnS) to 19,35 (rrnL) with an
average of 18.42 bases for sense rRNAs. The shortest polyadenylated gene
group was rRNA transcripts (Figure 4e). This may be the result of the
tendency to economize the mitogenome due to the proportional abundance
of rRNA transcripts.
Polyadenyl length was varied from 11.64 (trnA) to 85 (trnF), and 45.08
adenines for all tRNA genes on average were found in sense transcripts.
Antisense transcripts of tRNAs have minimum of 13.25 (trnT), mean of
28.84 and maximum of 57 (trnF) bases polyadenylated (Figure 4e).
Antisense transcripts of each tRNA were much more intensely detected
than sense transcripts (10 tRNAs of 17 total). Antisense tRNA pool could
generate tRFs (tRNA- derived RNA fragments), which are a group of small
RNAs detected in human and yeast mitochondria (Lee et al. , 2009;
Mercer et al. , 2011; Ro et al. , 2013; Shang et al. ,
2018). Although the biogenesis of these RNA molecules are not known, it
was predicted that they play a role in the regulation of mtDNA gene
expression (Ro et al. , 2013). Since tRNAs are known to be
extensively transported from the nuclear genome into the mitochondria,
the scarcity of sense tRNA molecules does not have the adverse effect on
mitochondrial transcription such as inhibition or reduction of gene
expression (Mercer et al. , 2011).