A Membrane Photosensor Related to Proteorhodopsin with Unique Motifs for Signal Transduction
Microbial rhodopsins are light-activated retinal-binding membrane proteins, performing a variety of ion transporting and photosensory functions in prokaryotic and eukaryotic cells. They display several cases of convergent evolution, where the same function is produced by unrelated or very distant protein groups. For example, both schizorhodopsins and xenorhodopsins are inward proton pumps, while halorhodopsins and NTQ-rhodopsins are inward chloride pumps. Here we present another possible case of such convergent evolution, describing biophysical properties of a new group of sensory rhodopsins, not related to the well-known haloarchaeal ones. The first representative of this group was identified in 2004 (by Kyndt, Meyer, and Cusanovich) but none of the members had been expressed and characterized. The well-studied haloarchaeal sensory rhodopsins interacting with membrane-embedded methyl-accepting Htr transducers are close relatives of halobacterial proton pump bacteriorhodopsin and have been studied extensively. In contrast, the new group of sensory rhodopsins we describe here is a relative of proteobacterial proton pumps, proteorhodopsins, but appear to interact with Htr-like transducers likewise. This interaction is likely to occur through an unknown mechanism, as they do not conserve the residues found important for interaction of haloarchaeal sensory rhodopsins and their cognate transducers. Moreover, the new sensory rhodopsins have unique structural motifs and many unusual amino acid residues, including those around the retinal chromophore, most strikingly, a tyrosine in place of a carboxyl counterion of the retinal Schiff base on helix C. We describe spectroscopic properties and molecular dynamics simulations of these sensory rhodopsins, which report on their unique structure and hydrogen-bonded networks, their unusual retinal chromophore, and probe their interactions with the transducers. To characterize their unique sequence motifs, we augment the spectroscopy and biochemistry data by structural modeling of the wild type and three mutants. Taken together, the experimental data, bioinformatics sequence analyses, and structural modeling suggest that the tyrosine/aspartate complex counterion contributes to a complex water-mediated hydrogen-bond network that couples the protonated retinal Schiff base to an extracellular carboxylic dyad.