Molecular Evolution of Rhodopsin Protein

Rhodopsins are light-sensitive proteins which universally exist in prokaryotes and eukaryotes. Type I rhodopsins exist in microbes and are known as microbial rhodopsins, which include various kinds such as bacteriorhodopsins (BR), halorhodopsins (HR), and sensory rhodopsins (SR). Type II rhodopsins, which belong to G-protein-coupled receptors (GPCR), exist in animals, and are collectively known as animal rhodopsins. Type III rhodopsins, also known as heliorhodopsins discovered by Alina Pushkarev in 2018, are distributed globally and exist in eukaryotes, prokaryotes, and even some viruses. Since type III rhodopsin is distinct in its protein sequence when compared to type I and II rhodopsins, it is not considered in this research. Past research has shown that there exists a clear evolution relationship between different kinds of microbial rhodopsins. However, the evolutionary relationship between microbial and animal rhodopsins hasn’t been verified yet due to the huge difference between their sequences. Thus, this paper aims to explore the evolution process within microbial rhodopsins as well as the evolutionary relationship between microbial and animal rhodopsins, utilizing phylogenetic trees and transmembrane domain analysis. Results show that HR and SR both evolved from BR. Additionally, by comparing the phylogenetic tree of BR with phylogenetic tree of microbial 16S rRNA, it is discovered that evolution of microbial rhodopsins is significantly different from their host microbes.