Identification of a Functionally Efficient and Thermally Stable Outward Sodium-Pumping Rhodopsin (BeNaR) from a Thermophilic Bacterium

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Rhodopsins are transmembrane proteins with retinal chromophores that are involved in photo-energy conversion and photo-signal transduction in diverse organisms. In this study, we newly identified and characterized a rhodopsin from a thermophilic bacterium, Bellilinea sp. Recombinant Escherichia coli cells expressing the rhodopsin showed light-induced alkalization of the medium only in the presence of sodium ions (Na⁺), and the alkalization signal was enhanced by addition of a protonophore, indicating an outward Na⁺ pump function across the cellular membrane. Thus, we named the protein Bellilinea Na⁺-pumping rhodopsin, BeNaR. Of note, its Na⁺-pumping activity is significantly greater than that of the known Na⁺-pumping rhodopsin, KR2. We further characterized its photochemical properties as follows: (i) Visible spectroscopy and HPLC revealed that BeNaR has an absorption maximum at 524 nm with predominantly (>96%) the all-trans retinal conformer. (ii) Time-dependent thermal denaturation experiments revealed that BeNaR showed high thermal stability. (iii) The time-resolved flash-photolysis in the nanosecond to millisecond time domains revealed the presence of four kinetically distinctive photointermediates, K, L, M and O. (iv) Mutational analysis revealed that Asp101, which acts as a counterion, and Asp230 around the retinal were essential for the Na⁺-pumping activity. From the results, we propose a model for the outward Na⁺-pumping mechanism of BeNaR. The efficient Na⁺-pumping activity of BeNaR and its high stability make it a useful model both for ion transporters and optogenetics tools.