Date of Award


Document Type

Honors Thesis (Open Access)


Colby College. Biology Dept.


Ronald Peck

Second Advisor

Russell Johnson

Third Advisor

Kevin Rice


Organisms have evolved numerous specialized molecules for constantly responding to environmental changes. Examples of such molecules are the light-driven proton-pump rhodopsins, such as bacteriorhodopsin (BR) and cruxrhodopsin (cR), and the carotenoid pigments, such as retinal and bacterioruberin. In halophilic Archaea, retinal can covalently bind bacterioopsin (BO) and cruxopsin (CO) to form the corresponding protein complexes, and its biosynthesis is indirectly controlled by the activity of the lycopene elongase (Lye) enzyme, which converts lycopene, a retinal precursor, to a form of bacterioruberin. Interestingly, opsins were shown to inhibit the activity of Lye, thereby promoting retinal biosynthesis and indirectly regulating the apoprotein-cofactor stoichiometry. This is a newly described regulatory mechanism, and, considering the importance of the problem it addresses, we set to determine the protein domains involved in the opsin-Lye inhibition. Using a fusion protein approach, we determined that a 52 amino acid domain in Lye, a 2 amino acid section in BO, and 34 and 43 amino acid regions in CO are required for the studied interaction. Furthermore, we compared the proteins’ tertiary structures and found supporting evidence for the validity of our identified regions and for the localization of the interaction at the interface of the lipid bilayer and the cytoplasm. Future studies could further investigate this recently discovered regulatory mechanism by identifying the participating protein amino acids more precisely and by searching for homologous domains in other biological systems.


opsin, carotenoid, protein complex, gene shuffling, fusion protein, similarity optimized backtranslation