Functional Comparative Analysis of Proteorhodopsin and Sodium ion rhodopsin from Isolates of Marine Flavobacteria

Abstract

Since the proteorhodopsin (PR) was first discovered from gamma-proteobacteria, SAR86 group and recently reported the new type of rhodopsins (NaR and ClR) that function as a light-driven ion-pump in PR-containing one bacteria, Nonlabens marinus S1-08T. In the present study, we investigated novel NaR and ClR from previously reported PR-containing Flavobacteria isolates which were isolated from marine samples such as water, sediment, organisms, etc. Out of 16 PR-containing isolates, 4 contained NaR gene and 1 of these contained ClR gene. On the basis of NaR and ClR sequences, it was confirmed that the key active site residues (Asp85, Asp96 and D216 in Bacteriorhodopsin (BR)) necessary for energy generation are conserved among rhodopsins functioning as proton or ion pumps. Phylogenetic analysis indicated that our NaR and ClR formed with each clade of previously reported NaR and ClR. The light-driven proton pump activity of native cell suspensions from marine Flavobacteia isolates containing both PR and NaR genes was discriminated depending upon the culture time. This study shows the involvement of NaR light-driven energy synthesis might more actively function in the early growth phase (exponential) of cells before PR gene function becomes active in the late growth phase (stationary) of cells and the NaR-containing Flavobacteria might ubiquitously present in marine environment.nus S1-08T. In the present study, we investigated novel NaR and ClR from previously reported PR-containing Flavobacteria isolates which were isolated from marine samples such as water, sediment, organisms, etc. Out of 16 PR-containing isolates, 4 contained NaR gene and 1 of these contained ClR gene. On the basis of NaR and ClR sequences, it was confirmed that the key active site residues (Asp85, Asp96 and D216 in Bacteriorhodopsin (BR)) necessary for energy generation are conserved among rhodopsins functioning as proton or ion pumps. Phylogenetic analysis indicated that our NaR and ClR formed with each clade of previously reported NaR and ClR. The light-driven proton pump activity of native cell suspensions from marine Flavobacteia isolates containing both PR and NaR genes was discriminated depending upon the culture time. This study shows the involvement of NaR light-driven energy synthesis might more actively function in the early growth phase (exponential) of cells before PR gene function becomes active in the late growth phase (stationary) of cells and the NaR-containing Flavobacteria might ubiquitously present in marine environment.