Date of Completion

Spring 5-6-2012

Thesis Advisor(s)

R. Thane Papke


Biology | Other Ecology and Evolutionary Biology


Rhodopsins are among the most studied protein families. They all incorporate a light based chromophore and an opsin. They are found in all three domains of life and can be found in diverse environments, such as the membrane of the haloarchaea, Haloarcula (Haa) marismortui, growing on salt flats in Death Valley, to within human tissues and deep sea water (Briggs and Spudich 2005). Rhodopsins can serve multifarious purposes, from phototaxis away from harmful light to efficient energy generation. Bacteriorhodopsin is the best studied rhodopsin in haloarchaea. The evolutionary pattern of bacteriorhodopsin through its gene, bop, is the main focus of this study. Planned as a comparative study of bop against expected phylogeny constructed on 16S rRNA gene sequences, as well as phylogeny based on a tree constructed from core genes; this study also hoped to find possible examples of Horizontal Gene Transfer (HGT). The bop gene was amplified and sequenced from multiple strains, and additional sequences were gathered from the National Center for Biotechnology Information (NCBI), bringing a total of 51 sequences from 41 strains covering 15 recognized genera. Additionally, three sensory rhodopsins were included to serve as an out-group. A phylogeny was reconstructed using Maximum Likelihood (ML) with the GTR plus gamma model, creating an ML tree of bop based off of bootstrapped multiple sequence alignment.