Temperature-based variation of rRNA secondary structure models: a case study in the insect Drosophila simulans, the land snail Isabellaria adriani, and the crustacean Daphnia pulex

The influence of a temperature default on ribosomal RNA (rRNA) secondary st ructure models was studied with the "Mfold" energy-optimization program. Fo lding models of the internal transcribed spacer (ITS) 1 rRNA for both Droso phila simulans (Insecta) and Isabellaria adriani (Gastropoda) were generate d at two different temperatures. The folding models are compared with the m odels 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 sec ondary structure analyses is suggested. The paper also elucidates results i nferred from three energy-optimizing programs (Mfold, GeneBee, and STAR). T hese three folding programs give different information on the structure and free energy of a ITS-1 rRNA molecule. Furthermore, secondary-structure mod els of the small subunit (ssu) rRNA of Daphnia pulex (Crustacea: Cladocera) were investigated. The ssu rRNA molecule is usually folded according to al ignment information. Here, ssu folding patterns are computed with Mfold usi ng two temperature conditions. The two Mfold models are compared with the a lignment model previously suggested for D. pulex. Three cladoceran-specific motifs and a short stem motif within the ssu rRNA of eukaryotes are discus sed with respect to structure and phylogenetic information.