Temperature-dependent structural variability of RNAs: spliced leader RNAs and their evolutionary history.
The structures attained by RNA molecules depend not only on their sequence but also on environmental parameters such as their temperature. So far, this effect has been largely neglected in bioinformatics studies. Here, we show that structural comparisons can be facilitated and more coherent structural models can be obtained when differences in environmental parameters are taken into account. We re-evaluate the secondary structures of the spliced leader (SL) RNAs from the seven eukaryotic phyla in which SL RNA trans-splicing has been described. Adjusting structure prediction to the natural growth temperatures and considering energetically similar secondary structures, we observe striking similarities among Euglenida, Kinetoplastida, Dinophyceae, Cnidaria, Rotifera, Nematoda, Platyhelminthes, and Tunicata that cannot be explained easily by the independent innovation of SL RNAs in each of these phyla. Supplementary Table is available at http://www.worldscinet.com/jbcb/.
Marz
Manja
M
Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.
Vanzo
Nathalie
N
Stadler
Peter F
PF
D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D019295:Computational Biology; D056890:Eukaryota; D019143:Evolution, Molecular; D006801:Humans; D008954:Models, Biological; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012326:RNA Splicing; D020038:RNA, Spliced Leader / Q000737:chemistry* / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid; D013696:Temperature; D013816:Thermodynamics
D020038:RNA, Spliced Leader