Three-Step Isomerization of the Retinal Chromophore during the Anion Pumping Cycle of Halorhodopsin

Existence of two substates in the O intermediate of the bacteriorhodopsin photocycle

The proton pumping cycle of bacteriorhodopsin (bR) is initiated when the retinal chromophore with the 13-trans configuration is photo-isomerized into the 13-cis configuration. To understand the recovery processes of the initial retinal configuration that occur in the late stage of the photocycle, we have performed a comprehensive analysis of absorption kinetics data collected at various pH levels and at different salt concentrations. The result of analysis revealed the following features of the late stages of the trans photocycle. i) Two substates occur in the O intermediate. ii) The visible absorption band of the first substate (O1) appears at a much shorter wavelength than that of the late substate (O2). iii) O1 is in rapid equilibrium with the preceding state (N), but O1 becomes less stable than N when an ionizable residue (X₁) with a pKa value of 6.5 (in 2 M KCl) is deprotonated. iv) At a low pH and at a low salt concentration, the decay time constant of O2 is longer than those of the preceding states, but the relationship between these time constants is altered when the medium pH or the salt concentration is increased. On the basis of the present observations and previous studies on the structure of the chromophore in O, we suspect that the retinal chromophore in O1 takes on a distorted 13-cis configuration and the O1-to-O2 transition is accompanied by cis-to-trans isomerization about C13C14 bond.

Functional Mechanism of Cl--Pump Rhodopsin and Its Conversion into H+ Pump

Cl^--pump rhodopsin is the second discovered microbial rhodopsin. Although its physiological role has not been fully clarified, its functional mechanism has been studied as a model for anion transporters. After the success of neural activation by channel rhodopsin, the first Cl^--pump halorhodopsin (HR) had become widely used as a neural silencer. The emergence of artificial and natural anion channel rhodopsins lowered the importance of HRs. However, the longer absorption maxima of approximately 585-600 nm for HRs are still advantageous for applications in mammalian brains and collaborations with neural activators possessing shorter absorption maxima. In this chapter, the variation and functional mechanisms of Cl^- pumps are summarized. After the discovery of HR, Cl^--pump rhodopsins were confined to only extremely halophilic haloarchaea. However, after 2014, two Cl^--pump groups were newly discovered in marine and terrestrial bacteria. These Cl^- pumps are phylogenetically distinct from HRs and have unique characteristics. In particular, the most recently identified Cl^- pump has close similarity with the H⁺ pump bacteriorhodopsin and was converted into the H⁺ pump by a single amino acid replacement.

Photochemical study of a cyanobacterial chloride-ion pumping rhodopsin

Mastigocladopsis repens halorhodopsin (MrHR) is a Cl^--pumping rhodopsin that belongs to a distinct cluster far from other Cl^- pumps. We investigated its pumping function by analyzing its photocycle and the effect of amino acid replacements. MrHR can bind I^- similar to Cl^- but cannot transport it. I^--bound MrHR undergoes a photocycle but lacks the intermediates after L, suggesting that, in the Cl^--pumping photocycle, Cl^- moves to the cytoplasmic (CP) channel during L decay. A photocycle similar to that of the I^--bound form was also observed for a mutant of the Asp200 residue, which is superconserved and assumed to be deprotonated in most microbial rhodopsins. This residue is probably close to the Cl^--binding site and the protonated Schiff base, in which a chromophore retinal binds to a specific Lys residue. However, the D200N mutation affected neither the Cl^--binding affinity nor the absorption spectrum, but completely eliminated the Cl^--pumping function. Thus, the Asp200 residue probably protonates in the dark state but deprotonates during the photocycle. Indeed, a H⁺ release was detected for photolyzed MrHR by using an indium‑tin oxide electrode, which acts as a good time-resolved pH sensor. This H⁺ release disappeared in the I^--bound form of the wild-type and Cl^--bound form of the D200N mutant. Thus, Asp200 residue probably deprotonates during L decay and then drives the Cl^- movement to the CP channel.