Thermostable light-driven inward proton pump rhodopsins

Structural Evolution of Retinal Chromophore in Early Intermediates of Inward and Outward Proton-Pumping Rhodopsins

Proton-pumping rhodopsins, which consist of seven transmembrane helices and have a retinal chromophore bound to a lysine side chain through a Schiff base linkage, offer valuable insights for developing unidirectional ion transporters. Despite identical overall structures and membrane topologies of outward and inward proton-pumping rhodopsins, these proteins transport protons in opposing directions, suggesting a rational mechanism that enables protons to move in different directions within similar protein structures. In the present study, we clarified the chromophore structures in early intermediates of inward and outward proton-pumping rhodopsins. Most importantly, common to both pumps, the hydrogen bond of the Schiff base became stronger in the L intermediate than in the unphotolyzed state. Experimental data on the chromophore structures of the L intermediates and proton-pumping activities indicated that the direction of proton release from the Schiff base during the L-to-M transition is determined not by the structure of the retinal chromophore but by the number of negative charges on the extracellular side of the Schiff base. This is in contrast to the idea that the chromophore configuration is a determinant for the direction of proton uptake. The present study, together with our previous studies, clarifies the determining factors of the transport direction in inward and outward proton-pumping rhodopsins.

Origin of the Difference in Proton Transport Direction between Inward and Outward Proton-Pumping Rhodopsins

Active transport is a vital and ubiquitous process in biological phenomena. Ion-pumping rhodopsins are light-driven active ion transporters that share a heptahelical transmembrane structural scaffold in which the all-trans retinal chromophore is covalently bonded through a Schiff base to a conserved lysine residue in the seventh transmembrane helix. Bacteriorhodopsin from Halobacterium salinarum was the first ion-pumping rhodopsin to be discovered and was identified as an outward proton-pumping rhodopsin. Since the discovery of bacteriorhodopsin in 1971, many more ion-pumping rhodopsins have been isolated from diverse microorganisms spanning three domains (bacteria, archaea, and eukaryotes) and giant viruses. In addition to proton-pumping rhodopsins, chloride ion- and sodium ion-pumping rhodopsins have also been discovered. Furthermore, diversity of ion-pumping rhodopsins was found in the direction of ion transport; i.e., rhodopsins that pump protons inward have recently been discovered. Very intriguingly, the inward proton-pumping rhodopsins share structural features and many conserved key residues with the outward proton-pumping rhodopsins. However, a central question remains unchanged despite the increasing variety: how and why do the ion-pumping rhodopsins undergo interlocking conformational changes that allow unidirectional ion transfer within proteins? In this regard, it is an effective strategy to compare the structures and their evolutions in the proton-pumping processes of both inward and outward proton-pumping rhodopsins because the comparison sheds light on key elements for the unidirectional proton transport. We elucidated the proton-pumping mechanism of the inward and outward proton-pumping rhodopsins by time-resolved resonance Raman spectroscopy, a powerful technique for tracking the structural evolutions of proteins at work that are otherwise inaccessible. In this Account, we primarily review our endeavors in the elucidation of the proton-pumping mechanisms and determination factors for the transport directions of inward and outward proton-pumping rhodopsins. We begin with a brief summary of previous findings on outward proton-pumping rhodopsins revealed by vibrational spectroscopy. Next, we provide insights into the mechanism of inward proton-pumping rhodopsins, schizorhodopsins, obtained in our studies. Time-resolved resonance Raman spectroscopy provided valuable information about the structures of the retinal chromophore in the unphotolyzed state and intermediates of schizorhodopsins. As we ventured further into our investigations, we succeeded in uncovering the factors determining the directions of proton release and uptake in the retinal Schiff base. While it is intriguing that the proton-pumping rhodopsins actively transport protons against a concentration gradient, it is even more curious that proteins with structural similarities transport protons in opposite directions. Solving the second mystery led to solving the first. When we considered our findings, we realized that we would probably not have been able to elucidate the mechanism if we had studied only the outward pump. Our Account concludes by outlining future opportunities and challenges in the growing research field of ion-pumping rhodopsins, with a particular emphasis on elucidating their sequence-structure-function relationships. We aim to inspire further advances toward the understanding and creation of light-driven active ion transporters.

Chromophore-Protein Interactions Affecting the Polyene Twist and π-π* Energy Gap of the Retinal Chromophore in Schizorhodopsins

The properties of a prosthetic group are broadened by interactions with its neighboring residues in proteins. The retinal chromophore in rhodopsins absorbs light, undergoes structural changes, and drives functionally important structural changes in proteins during the photocycle. It is therefore crucial to understand how chromophore-protein interactions regulate the molecular structure and electronic state of chromophores in rhodopsins. Schizorhodopsin is a newly discovered subfamily of rhodopsins found in the genomes of Asgard archaea, which are extant prokaryotes closest to the last common ancestor of eukaryotes and of other microbial species. Here, we report the effects of a hydrogen bond between a retinal Schiff base and its counterion on the twist of the polyene chain and the color of the retinal chromophore. Correlations between spectral features revealed the unexpected fact that the twist of the polyene chain is reduced as the hydrogen bond becomes stronger, suggesting that the twist is caused by tight atomic contacts between the chromophore and nearby residues. In addition, the strength of the hydrogen bond is the primary factor affecting the color-tuning of the retinal chromophore in schizorhodopsins. The findings of this study are valuable for manipulating the molecular structure and electronic state of the chromophore by controlling chromophore-protein interactions.

Multiple Roles of a Conserved Glutamate Residue for Unique Biophysical Properties in a New Group of Microbial Rhodopsins Homologous to TAT Rhodopsin

TAT rhodopsin, a microbial rhodopsin found in the marine SAR11 bacterium HIMB114, uniquely possesses a Thr-Ala-Thr (TAT) motif in the third transmembrane helix. Because of a low pKa value of the retinal Schiff base (RSB), TAT rhodopsin exhibits both a visible light-absorbing state with the protonated RSB and a UV-absorbing state with the deprotonated RSB at a neutral pH. The UV-absorbing state, in contrast to the visible light-absorbing one, converts to a long-lived photointermediate upon light absorption, implying that TAT rhodopsin functions as a pH-dependent light sensor. Despite detailed biophysical characterization and mechanistic studies on the TAT rhodopsin, it has been unknown whether other proteins with similarly unusual features exist. Here, we identified several new rhodopsin genes homologous to the TAT rhodopsin of HIMB114 (TATHIMB) from metagenomic data. Based on the absorption spectra of expressed proteins from these genes with visible and UV peaks similar to that of TATHIMB, they were classified as Twin-peaked Rhodopsin (TwR) family. TwR genes form a gene cluster with a set of 13 ORFs conserved in subclade IIIa of SAR11 bacteria. A glutamic acid in the second transmembrane helix, Glu54, is conserved in all of the TwRs. We investigated E54Q mutants of two TwRs and revealed that Glu54 plays critical roles in regulating the RSB pKa, oligomer formation, and the efficient photoreaction of the UV-absorbing state. The discovery of novel TwRs enables us to study the universality and individuality of the characteristics revealed so far in the original TATHIMB and contributes to further studies on mechanisms of unique properties of TwRs.

Cis-Trans Reisomerization Preceding Reprotonation of the Retinal Chromophore Is Common to the Schizorhodopsin Family: A Simple and Rational Mechanism for Inward Proton Pumping

The creation of unidirectional ion transporters across membranes represents one of the greatest challenges in chemistry. Proton-pumping rhodopsins are composed of seven transmembrane helices with a retinal chromophore bound to a lysine side chain via a Schiff base linkage and provide valuable insights for designing such transporters. What makes these transporters particularly intriguing is the discovery of both outward and inward proton-pumping rhodopsins. Surprisingly, despite sharing identical overall structures and membrane topologies, these proteins facilitate proton transport in opposite directions, implying an underlying rational mechanism that can transport protons in different directions within similar protein structures. In this study, we unraveled this mechanism by examining the chromophore structures of deprotonated intermediates in schizorhodopsins, a recently discovered subfamily of inward proton-pumping rhodopsins, using time-resolved resonance Raman spectroscopy. The photocycle of schizorhodopsins revealed the cis-trans thermal isomerization that precedes reprotonation at the Schiff base of the retinal chromophore. Notably, this order has not been observed in other proton-pumping rhodopsins, but here, it was observed in all seven schizorhodopsins studied across the archaeal domain, strongly suggesting that cis-trans thermal isomerization preceding reprotonation is a universal feature of the schizorhodopsin family. Based on these findings, we propose a structural basis for the remarkable order of events crucial for facilitating inward proton transport. The mechanism underlying inward proton transport by schizorhodopsins is straightforward and rational. The insights obtained from this study hold great promise for the design of transmembrane unidirectional ion transporters.

Kinetic study on the molecular mechanism of light-driven inward proton transport by schizorhodopsins

Schizorhodopsins (SzRs) are light-driven inward proton pumping membrane proteins. A H⁺ is released to the cytoplasmic solvent from the chromophore, retinal Schiff base (RSB), after light absorption, and then another H⁺ is bound to the RSB at the end of photocyclic reaction. However, the mechanistic detail of H⁺ transfers in SzR is almost unknown. Here we studied the deuterium isotope effect and the temperature dependence of the reaction rate constants of elementary steps in the photocycles of SzRs. The former indicated that deprotonation and reprotonation of RSB is mainly accomplished by H⁺ hopping between heavy atoms with similar H⁺ affinity. Furthermore, the temperature dependence of the rate constants revealed that most of H⁺ transfer events have a high entropy barrier. In contrast, the activation enthalpy and entropy of extremely thermostable SzR (MsSzR) are significantly higher than other types of SzRs (SzR1 and MtSzR) suggesting that its highly thermostable structure is optimized with at the cost of slower reaction rates at ambient temperatures.

Asgard archaea in saline environments

Members of candidate Asgardarchaeota superphylum appear to share numerous eukaryotic-like attributes thus being broadly explored for their relevance to eukaryogenesis. On the contrast, the ecological roles of Asgard archaea remains understudied. Asgard archaea have been frequently associated to low-oxygen aquatic sedimentary environments worldwide spanning a broad but not extreme salinity range. To date, the available information on diversity and potential biogeochemical roles of Asgardarchaeota mostly sourced from marine habitats and to a much lesser extend from true saline environments (i.e., > 3% w/v total salinity). Here, we provide an overview on diversity and ecological implications of Asgard archaea distributed across saline environments and briefly explore their metagenome-resolved potential for osmoadaptation. Loki-, Thor- and Heimdallarchaeota are the dominant Asgard clades in saline habitats where they might employ anaerobic/microaerophilic organic matter degradation and autotrophic carbon fixation. Homologs of primary solute uptake ABC transporters seemingly prevail in Thorarchaeota, whereas those putatively involved in trehalose and ectoine biosynthesis were mostly inferred in Lokiarchaeota. We speculate that Asgardarchaeota might adopt compatible solute-accumulating ('salt-out') strategy as response to salt stress. Our current understanding on the distribution, ecology and salt-adaptive strategies of Asgardarchaeota in saline environments are, however, limited by insufficient sampling and incompleteness of the available metagenome-assembled genomes. Extensive sampling combined with 'omics'- and cultivation-based approaches seem, therefore, crucial to gain deeper knowledge on this particularly intriguing archaeal lineage.

Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering

The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.

Light-driven proton transfers and proton transport by microbial rhodopsins - A biophysical perspective

In the last twenty years, our understanding of the rules and mechanisms for the outward light-driven proton transport (and underlying proton transfers) by microbial rhodopsins has been changing dramatically. It transitioned from a very detailed atomic-level understanding of proton transport by bacteriorhodopsin, the prototypical proton pump, to a confounding variety of sequence motifs, mechanisms, directions, and modes of transport in its newly found homologs. In this review, we will summarize and discuss experimental data obtained on new microbial rhodopsin variants, highlighting their contribution to the refinement and generalization of the ideas crystallized in the previous century. In particular, we will focus on the proton transport (and transfers) vectoriality and their structural determinants, which, in many cases, remain unidentified.

Development of an Outward Proton Pumping Rhodopsin with a New Record in Thermostability by Means of Amino Acid Mutations

We have developed a methodology for identifying further thermostabilizing mutations for an intrinsically thermostable membrane protein. The methodology comprises the following steps: (1) identifying thermostabilizing single mutations (TSSMs) for residues in the transmembrane region using our physics-based method; (2) identifying TSSMs for residues in the extracellular and intracellular regions, which are in aqueous environment, using an empirical force field FoldX; and (3) combining the TSSMs identified in steps (1) and (2) to construct multiple mutations. The methodology is illustrated for thermophilic rhodopsin whose apparent midpoint temperature of thermal denaturation T_m is ∼91.8 °C. The TSSMs previously identified in step (1) were F90K, F90R, and Y91I with ΔT_m ∼5.6, ∼5.5, and ∼2.9 °C, respectively, and those in step (2) were V79K, T114D, A115P, and A116E with ΔT_m ∼2.7, ∼4.2, ∼2.6, and ∼2.3 °C, respectively (ΔT_m denotes the increase in T_m). In this study, we construct triple and quadruple mutants, F90K+Y91I+T114D and F90K+Y91I+V79K+T114D. The values of ΔT_m for these multiple mutants are ∼11.4 and ∼13.5 °C, respectively. T_m of the quadruple mutant (∼105.3 °C) establishes a new record in a class of outward proton pumping rhodopsins. It is higher than T_m of Rubrobacter xylanophilus rhodopsin (∼100.8 °C) that was the most thermostable in the class before this study.