Project 22

RNA studies

 

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Secondary structure prediction reveals extensive variation in higher order structures of mitochondrial tRNAs of four tardigrade species

 

Markus Dicht, Center of Tardigrade Research, Switzerland

 

 

 

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

 

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