Introduction

Mobile group II introns are catalytic RNA encoding retroelements found in all branches of life. They were first identified in mitochondrial DNA of fungi where sequences were separated into two groups based on common features. Since then, many more group II introns have been found and three major subclasses identified, denoted as group II intron types A-C. Group II introns are self-catalytic ribozymes composed of highly structured RNA capable of splicing out of a precursor transcript. The intron structure contains six domains (DI-VI) that radiate outwards from a central core with most group II introns containing a conserved open reading frame (ORF) in DIV encoding the associated RT. The RT serves as a maturase that aids in stabilizing the catalytically active intron structure, RNA splicing, and reverse transcription to integrate the intron into a new genomic location.

The reverse transcriptase encoded in introns are difficult to purify because they are tightly bound to their encoding intron, which aids in their solubility. Therefore, introns are complete in and of themselves and do not rely on endogenous proteins for successful splicing. This made the group II intron found in thermacetogenium phaeum an interesting find because within the T. phaeum genome there are multiple group II introns with only one copy encoding the RT. This suggests that the intron copies maintain mobility with a single encoded RT implying that the must must be able to dissociate from its encoding intron and aid in splicing of the copies. It is possible that the T. phaeum RT is more soluble than other RTs, particularly the RT found in Geobacillus stearothermophillus which readily aggregates in solutions even with high ionic strength. I will predict the structure of T. pheum using several modeling programs to compare results and gain confidence in structural features. These models will be used to visualize the electrostatic surface of the predicted structure and determine if there are noticeable differences that might indicate solubility of protein. I will also investigate the N-terminal extension and try to determine whether it is part of the structure.