Temperature-based variation of rRNA secondary structure models: a case study in the insectDrosophila simulans, the land snailIsabellaria adriani, and the crustaceanDaphnia pulex

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Abstract
The influence of a temperature default on ribosomal RNA (rRNA) secondary structure models was studied with the "Mfold" energy-optimization program. Folding models of the internal transcribed spacer (ITS) 1 rRNA for both Drosophila simulans (Insecta) and Isabellaria adriani (Gastropoda) were generated at two different temperatures. The folding models are compared with the models previously shown for the ITS-1 of D. melanogaster Oregon R strain and I. adriani. A search for phylogenetically informative ITS-1 folding motifs was conducted for D. simulans. In I. adriani, a new approach for ITS-1 secondary structure analyses is suggested. The paper also elucidates results inferred from three energy-optimizing programs (Mfold, GeneBee, and STAR). These three folding programs give different information on the structure and free energy of a ITS-1 rRNA molecule. Furthermore, secondary-structure models of the small subunit (ssu) rRNA of Daphnia pulex (Crustacea: Cladocera) were investigated. The ssu rRNA molecule is usually folded according to alignment information. Here, ssu folding patterns are computed with Mfold using two temperature conditions. The two Mfold models are compared with the alignment model previously suggested for D. pulex. Three cladoceran-specific motifs and a short stem motif within the ssu rRNA of eukaryotes are discussed with respect to structure and phylogenetic information.