Mechanism divergence in microbial rhodopsins

Abstract

A fundamental design principle of microbial rhodopsins is that they share the same basic light-induced conversion between two conformers. Alternate access of the Schiff base to the outside and to the cytoplasm in the outwardly open "E" conformer and cytoplasmically open "C" conformer, respectively, combined with appropriate timing of pKa changes controlling Schiff base proton release and uptake make the proton path through the pumps vectorial. Phototaxis receptors in prokaryotes, sensory rhodopsins I and II, have evolved new chemical processes not found in their proton pump ancestors, to alter the consequences of the conformational change or modify the change itself. Like proton pumps, sensory rhodopsin II undergoes a photoinduced E→C transition, with the C conformer a transient intermediate in the photocycle. In contrast, one light-sensor (sensory rhodopsin I bound to its transducer HtrI) exists in the dark as the C conformer and undergoes a light-induced C→E transition, with the E conformer a transient photocycle intermediate. Current results indicate that algal phototaxis receptors channelrhodopsins undergo redirected Schiff base proton transfers and a modified E→C transition which, contrary to the proton pumps and other sensory rhodopsins, is not accompanied by the closure of the external half-channel. The article will review our current understanding of how the shared basic structure and chemistry of microbial rhodopsins have been modified during evolution to create diverse molecular functions: light-driven ion transport and photosensory signaling by protein-protein interaction and light-gated ion channel activity. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.

Keywords: Microbial rhodopsins; Optogenetics; Photosensory transduction; Phototaxis; Proton transfer; Schiff base connectivity.

Figure 1. Microbial rhodopsin conformers

The figure depicts light-induced conformer transitions in the indicated microbial rhodopsins in their native functional state. BR, bacteriorhodopsin; HR, halorhodopsin; SRI, sensory rhodopsin I; SRII, sensory rhodopsin II; ChR, channelrhodopsin. E (green), conformer with externally-connected Schiff base and exterior half-channelopen; C (red), conformer with cytoplasmically-connected Schiff base and cytoplasmic half-channel open; C/E (purple), conformer with an open channel from the extracellular to cytoplasmic surfaces of the protein.

Figure 2. Photoisomerization-induced steric-trigger in the SRII-HtrII complex

SRII, sensory rhodopsin II; HtrII, haloarchaeal transducer for SRII. The three residues in SRII circled in red are those which, when engineered into bacteriorhodopsin, enable bacteriorhodopsin-mediated phototaxis signaling through HtrII [36]. Redrawn from reference .

Figure 3. Channelrhodopsin functions in vivo

The figure depicts conclusions from studies of ChRfunction in Chlamydomonas reinhardtii and related algae (reviewed in [, –83]) that ChRs depolarize algal plasma membranes with two distinct mechanisms, a direct light-gated channel activity as depicted in Figure 1 attributable to the 7-helix domain, and an amplified current dependent on an unidentified Ca²⁺ channel activated by ChRs either by direct protein-protein interaction or through intermediare components.