Structure Modeling of Small Subunit Ribosomal RNA of Copper Resistant Ciliates

The most suitable secondary structures of SSU rRNA of Euplotes adiculatus lahorensis and two new subspecies Tetrahymena tropicalis lahorensis subsp. nov. and Euplotes muscicola SBSrc subsp. nov. are being proposed based on minimum free energy. These ciliates were highly resistant to copper with minimum inhibitory concentration of 50 ppm. T. t. lahorensis SSU rRNA structure with 564 base pairs consists of 117 stems while the free energy of the structure is -380.71 kcal at 37 C. The SS rRNA structure of E. muscicola SBSrc has 126 stems and 606 base pairs with -396.17 kcal free energy whereas E. adiculatus lahorensis has 121 stems 609 base pairs and the free energy of its structure is -425.23 kcal at 37 C. There are number of salient features located in all the three rRNA secondary structures. Most important are the sequence complementary to ribosome binding site (RBS) of mRNA and the variable regions (V1V9). Alignments of these regions indicate noticeable variation in sequence which may be considered as basis for classification of ciliates.