RNA studies |
Secondary structure prediction reveals extensive
variation in higher order structures of mitochondrial tRNAs of four
tardigrade species Markus Dicht, Abstract Nothing is
known until now about the secondary structure of the mitochondrial tRNAs (mt
-tRNA) of Tardigrada.The purpose of this study was to investigate the
secondary structure of all known mt-tRNAs of four tardigrade species with a
suitable combination of secondary structure prediction servers. Not only
structure variability of tardigrade mitochondrial tRNAs was analyzed, but
also base composition and higher order structures of mt-tRNAs in connection
with phylogenetic relationships, base- or base-pair substitution by
post-transcriptional transitions, gene overlap, the sense-antisense
hypothesis, the possible existence of `pseudogenes`, the accuracy of gene
annotations and the importance of tRNA editing and mitochondrial import of
cytosolic tRNAs into mitochondria. The
secondary structures of 54 mt-tRNAs of Tardigrada were predicted. All
tardigrades show a remarkable large structural diversity of their mt-tRNAs.
57.4 % of the mt-tRNAs possess the common cloverleaf structure with an
acceptor-arm, an anticodon-arm, a T-arm and a D-arm and their associated loop
regions, 18.5 % of the molecules are D-armless, 3.7 % T-armless, and in 5.6 %
of the molecules both, the D- and the T-domain are missed. In 3.7 % of the
mt-tRNAs a T-arm replacement loop instead of a T-arm
was detected. The rest of the annotated mt-tRNA genes are `pseudogenes` or they produce mt-tRNAs with
losses of acceptor-arms due to gene overlap with adjacent genes at the 3`end
and/or the 5`end. The mean
size of the mt-tRNAs of the four tardigrade species is not as small as in
Caenorhabditis elegans (Nematoda). Mean loop sizes (number of nucleotides)
and number of bp/stem were calculated. Structure variability was compared
with that of other invertebrates. It could be shown that some reverse complements of certain
mt-tRNA genes might replace some `pseudogenes` and that the sense-antisense coding might
be more likely in organisms with reduced genomes, such as mitochondria.
C+G(A+T) contents in the loops and stems, GC pair content in the stems and AT
skew and GC skew of unpaired regions in the mt-tRNAs of the four tardigrade
species were compared. All the
results are discussed in connection with
the evolution of tardigrades and their ability to survive under extreme
environmental conditions. Multiple alignment tools gave some new insights
into the phylogenetic relationships of Tardigrada. Further investigations
showed that the different regions within mt-tRNAs have different modes and rates of evolution. If you
need more detailed informations about the original paper of this abstract,
the methods used, the results and the references, please, contact the CTR E-mail
: info@tardires.ch |