Probing the Cl − -pumping photocycle of pharaonis halorhodopsin: Examinations with bacterioruberin, an intrinsic dye, and membrane potential-induced modulation of the photocycle

Structural changes of Natronomonas pharaonis halorhodopsin in its late photocycle revealed by solid-state NMR spectroscopy

Natronomonas pharaonis halorhodopsin (NpHR) is a light-driven Cl- inward pump that is widely used as an optogenetic tool. Although NpHR is previously extensively studied, its Cl- uptake process is not well understood from the protein structure perspective, mainly because in crystalline lattice, it has been difficult to analyze the structural changes associated with the Cl- uptake process. In this study, we used solid-state NMR to analyze NpHR both in the Cl--bound and -free states under near-physiological transmembrane condition. Chemical shift perturbation analysis suggested that while the structural change caused by the Cl- depletion is widespread over the NpHR molecule, residues in the extracellular (EC) part of helix D exhibited significant conformational changes that may be related to the Cl- uptake process. By combining photochemical analysis and dynamic nuclear polarization (DNP)-enhanced solid-state NMR measurement on NpHR point mutants for the suggested residues, we confirmed their importance in the Cl- uptake process. In particular, we found the mutation at Ala165 position, located at the trimer interface, to an amino acid with bulky sidechain (A165V) significantly perturbs the late photocycle and disrupts its trimeric assembly in the Cl--free state as well as during the ion-pumping cycle under the photo-irradiated condition. This strongly suggested an outward movement of helix D at EC part, disrupting the trimer integrity. Together with the spectroscopic data and known NpHR crystal structures, we proposed a model that this helix movement is required for creating the Cl- entrance path on the extracellular surface of the protein and is crucial to the Cl- uptake process.

Direct detection of the chloride release and uptake reactions of Natronomonas pharaonis halorhodopsin

Membrane transport proteins undergo multistep conformational changes to fulfill the transport of substrates across biological membranes. Substrate release and uptake are the most important events of these multistep reactions that accompany significant conformational changes. Thus, their relevant structural intermediates should be identified to better understand the molecular mechanism. However, their identifications have not been achieved for most transporters due to the difficulty of detecting the intermediates. Herein, we report the success of these identifications for a light-driven chloride transporter halorhodopsin (HR). We compared the time course of two flash-induced signals during a single transport cycle. One is a potential change of Cl--selective membrane, which enabled us to detect tiny Cl--concentration changes due to the Cl- release and the subsequent Cl--uptake reactions by HR. The other is the absorbance change of HR reflecting the sequential formations and decays of structural intermediates. Their comparison revealed not only the intermediates associated with the key reactions but also the presence of two additional Cl--binding sites on the Cl--transport pathways. The subsequent mutation studies identified one of the sites locating the protein surface on the releasing side. Thus, this determination also clarified the Cl--transport pathway from the initial binding site until the release to the medium.

Multistep conformational changes leading to the gate opening of light-driven sodium pump rhodopsin

Membrane transport proteins require a gating mechanism that opens and closes the substrate transport pathway to carry out unidirectional transport. The "gating" involves large conformational changes and is achieved via multistep reactions. However, these elementary steps have not been clarified for most transporters due to the difficulty of detecting the individual steps. Here, we propose these steps for the gate opening of the bacterial Na+ pump rhodopsin, which outwardly pumps Na+ upon illumination. We herein solved an asymmetric dimer structure of Na+ pump rhodopsin from the bacterium Indibacter alkaliphilus. In one protomer, the Arg108 sidechain is oriented toward the protein center and appears to block a Na+ release pathway to the extracellular (EC) medium. In the other protomer, however, this sidechain swings to the EC side and then opens the release pathway. Assuming that the latter protomer mimics the Na+-releasing intermediate, we examined the mechanism for the swing motion of the Arg108 sidechain. On the EC surface of the first protomer, there is a characteristic cluster consisting of Glu10, Glu159, and Arg242 residues connecting three helices. In contrast, this cluster is disrupted in the second protomer. Our experimental results suggested that this disruption is a key process. The cluster disruption induces the outward movement of the Glu159-Arg242 pair and simultaneously rotates the seventh transmembrane helix. This rotation resultantly opens a space for the swing motion of the Arg108 sidechain. Thus, cluster disruption might occur during the photoreaction and then trigger sequential conformation changes leading to the gate-open state.

The preferential transport of NO3- by full-length Guillardia theta anion channelrhodopsin 1 is enhanced by its extended cytoplasmic domain

Previous research of anion channelrhodopsins (ACRs) has been performed using cytoplasmic domain (CPD)-deleted constructs and therefore have overlooked the native functions of full-length ACRs and the potential functional role(s) of the CPD. In this study, we used the recombinant expression of full-length Guillardia theta ACR1 (GtACR1_full) for pH measurements in Pichia pastoris cell suspensions as an indirect method to assess its anion transport activity and for absorption spectroscopy and flash photolysis characterization of the purified protein. The results show that the CPD, which was predicted to be intrinsically disordered and possibly phosphorylated, enhanced NO3- transport compared to Cl- transport, which resulted in the preferential transport of NO3-. This correlated with the extended lifetime and large accumulation of the photocycle intermediate that is involved in the gate-open state. Considering that the depletion of a nitrogen source enhances the expression of GtACR1 in native algal cells, we suggest that NO3- transport could be the natural function of GtACR1_full in algal cells.

Mutations conferring SO42- pumping ability on the cyanobacterial anion pump rhodopsin and the resultant unique features of the mutant

Membrane transport proteins can be divided into two types: those that bind substrates in a resting state and those that do not. In this study, we demonstrate that these types can be converted by mutations through a study of two cyanobacterial anion-pumping rhodopsins, Mastigocladopsis repens halorhodopsin (MrHR) and Synechocystis halorhodopsin (SyHR). Anion pump rhodopsins, including MrHR and SyHR, initially bind substrate anions to the protein center and transport them upon illumination. MrHR transports only smaller halide ions, Cl^- and Br^-, but SyHR also transports SO₄^2-, despite the close sequence similarity to MrHR. We sought a determinant that could confer SO₄^2- pumping ability on MrHR and found that the removal of a negative charge at the anion entrance is a prerequisite for SO₄^2- transport by MrHR. Consistently, the reverse mutation in SyHR significantly weakened SO₄^2- pump activity. Notably, the MrHR and SyHR mutants did not show SO₄^2- induced absorption spectral shifts or changes in the photoreactions, suggesting no bindings of SO₄^2- in their initial states or the bindings to the sites far from the protein centers. In other words, unlike wild-type SyHR, these mutants take up SO₄^2- into their centers after illumination and release it before the ends of the photoreactions.

Unique Cl- pump rhodopsin with close similarity to H+ pump rhodopsin

Microbial rhodopsin is a ubiquitous membrane protein in unicellular microorganisms. Similar to animal rhodopsin, this protein consists of seven transmembrane helices and the chromophore retinal. However, unlike animal rhodopsin, microbial rhodopsin acts as not only a photosignal receptor but also a light-activated ion transporter and light-switchable enzyme. In this article, the third Cl- pump microbial rhodopsin will be introduced. The physiological importance of Cl- pumps has not been clarified. Despite this, their mechanisms, especially that of the first Cl- pump halorhodopsin (HR), have been studied to characterize them as model proteins for membrane anion transporters. The third Cl- pump defines a phylogenetic cluster distinct from other microbial rhodopsins. However, this Cl- pump conserves characteristic residues for not only the Cl- pump HR but also the H+ pump bacteriorhodopsin (BR). Reflecting close similarity to BR, the third Cl- pump begins to pump H+ outwardly after single amino acid replacement. This mutation activates several residues that have no roles in the original Cl- pump function but act as important H+ relay residues in the H+ pump mutant. Thus, the third Cl- pump might be the model protein for functional differentiation because this rhodopsin seems to be the Cl- pump occurring immediately after functional differentiation from the BR-type H+ pump.

Replaceability of Schiff base proton donors in light-driven proton pump rhodopsins

Many H⁺-pump rhodopsins conserve “H⁺ donor” residues in cytoplasmic (CP) half channels to quickly transport H⁺ from the CP medium to Schiff bases at the center of these proteins. For conventional H⁺ pumps, the donors are conserved as Asp or Glu but are replaced by Lys in the minority, such as Exiguobacterium sibiricum rhodopsin (ESR). In dark states, carboxyl donors are protonated, whereas the Lys donor is deprotonated. As a result, carboxyl donors first donate H⁺ to the Schiff bases and then capture the other H⁺ from the medium, whereas the Lys donor first captures H⁺ from the medium and then donates it to the Schiff base. Thus, carboxyl and Lys-type H⁺ pumps seem to have different mechanisms, which are probably optimized for their respective H⁺-transfer reactions. Here, we examined these differences via replacement of donor residues. For Asp-type deltarhodopsin (DR), the embedded Lys residue distorted the protein conformation and did not act as the H⁺ donor. In contrast, for Glu-type proteorhodopsin (PR) and ESR, the embedded residues functioned well as H⁺ donors. These differences were further examined by focusing on the activation volumes during the H⁺-transfer reactions. The results revealed essential differences between archaeal H⁺ pump (DR) and eubacterial H⁺ pumps PR and ESR. Archaeal DR requires significant hydration of the CP channel for the H⁺-transfer reactions; however, eubacterial PR and ESR require the swing-like motion of the donor residue rather than hydration. Given this common mechanism, donor residues might be replaceable between eubacterial PR and ESR.

Real-time identification of two substrate-binding intermediates for the light-driven sodium pump rhodopsin

Membrane transport proteins undergo critical conformational changes during substrate uptake and release, as the substrate-binding site is believed to switch its accessibility from one side of the membrane to the other. Thus, at least two substrate-binding intermediates should appear during the process, that is, after uptake and before the release of the substrate. However, this view has not been verified for most transporters because of the difficulty in detecting short-lived intermediates. Here, we report real-time identification of these intermediates for the light-driven outward current-generating Na⁺-pump rhodopsin. We triggered the transport cycle of Na⁺-pump rhodopsin using a short laser pulse, and subsequent formation and decay of various intermediates was detected by time-resolved measurements of absorption changes. We used this method to analyze transport reactions and elucidated the sequential formation of the Na⁺-binding intermediates O1 and O2. Both intermediates exhibited red-shifted absorption spectra and generated transient equilibria with short-wavelength intermediates. The equilibria commonly shifted toward O1 and O2 with increasing Na⁺ concentration, indicating that Na⁺ is bound to these intermediates. However, these equilibria were formed independently; O1 reached equilibrium with preceding intermediates, indicating Na⁺ uptake on the cytoplasmic side. In contrast, O2 reached equilibrium with subsequent intermediates, indicating Na⁺ release on the extracellular side. Thus, there is an irreversible switch in “accessibility” during the O1 to O2 transition, which could represent one of the key processes governing unidirectional Na⁺ transport.

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.

Direct Detection of the Substrate Uptake and Release Reactions of the Light-Driven Sodium-Pump Rhodopsin

For membrane transporters, substrate uptake and release reactions are major events during their transport cycles. Despite the functional importance of these events, it is difficult to identify their relevant structural intermediates because of the requirements of the experimental methods, which are to detect the timing of the formation and decay of intermediates and to detect the timing of substrate uptake and release. We report successfully achieving this for the light-driven Na⁺ pump rhodopsin (NaR). Here, a Na⁺-selective membrane, which consists of polyvinyl chloride and a Na⁺ ionophore, was employed to detect Na⁺ uptake and release. When one side of the membrane was covered by the lipid-reconstituted NaR, continuous illumination induced an increase in membrane potential, which reflected Na⁺ uptake by the photolyzed NaR. Via use of nanosecond laser pulses, two kinds of data were obtained during a single transport cycle: one was the flash-induced absorbance change in NaR to detect the formation and decay of structural intermediates, and the other was the flash-induced change in membrane potential, which reflects the transient Na⁺ uptake and release reactions. Their comparison clearly indicated that Na⁺ is captured and released during the formation and decay of the O intermediate, the red-shifted intermediate that appears in the latter half of the transport cycle.

Spectroscopic Characterization of Halorhodopsin Reconstituted into Nanodisks Using Native Lipids

We successfully reconstituted single Natronomonas pharaonis halorhodopsin (NpHR) trimers into a nanodisk (ND) using the native archaeal lipid (NL) and an artificial lipid having a zwitterionic headgroup, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). Incorporation of single trimeric NpHR into NDs was confirmed by sodium dodecyl sulfate polyacrylamide gel electrophoresis, size-exclusion chromatography, and visible circular dichroism spectroscopy. The Cl^- binding affinity of NpHR in NDs using NL (NL-ND NpHR) or POPC (POPC-ND NpHR) was examined by absorption spectroscopy, showing that the Cl^--releasing affinities (K_d,N↔O) of these ND-reconstituted NpHRs are more than 10 times higher than that obtained from native NpHR membrane fragments (MFs) harvested from a NpHR-overexpressing archaeal strain (MF NpHR). The photoreaction kinetics of these ND-reconstituted NpHRs revealed that the Cl^- uptake was faster than that of MF NpHR. These differences in the Cl^--releasing and uptake properties of ND-reconstituted NpHRs and MF NpHR may arise from suppression of protein conformational changes associated with Cl^- release from the trimeric NpHR caused by ND reconstitution, conformational perturbation in the trimeric state, and loss of the trimer-trimer interactions. On the other hand, POPC-ND NpHR demonstrated accelerated Cl^- uptake compared to NL-ND NpHR, suggesting that the negative charge on the archaeal membrane surface regulates the photocycle of NpHR. Although NL-ND NpHR and MF NpHR are embedded in the same lipid, the lower Cl^--binding affinity at the initial state (K_d,initial) and faster recovering from the NpHR' state to the original state of the photoreaction cycle were observed for NL-ND NpHR, probably because of insufficient interactions with a chromophore in the native membrane, bacterioruberin in reconstituted NDs. Our results indicate that specific interactions of NpHR with surrounding lipids and bacterioruberin, structural flexibility of the membrane, and interactions between trimeric NpHRs may be necessary for efficient Cl^- pumping.

Comparison of low-power, high-frequency and temporally precise optogenetic inhibition of spiking in NpHR, eNpHR3.0 and Jaws-expressing neurons

A detailed theoretical analysis of low-power, high-frequency and temporally precise optogenetic inhibition of neuronal spiking, with red-shifted opsins namely, NpHR, eNpHR3.0 and Jaws, has been presented. An accurate model for inhibition of spiking in these opsins expressed hippocampal neurons that includes the important rebound activity of chloride ions across the membrane has been formulated. The effect of various parameters including irradiance, pulse width, frequency, opsin-expression density and chloride concentration has been studied in detail. Theoretical simulations are in very good agreement with reported experimental results. The chloride concentration gradient directly affects the photocurrent and inhibition capacity in all three variants. eNpHR3.0 shows smallest inhibitory post-synaptic potential plateau at higher frequencies. The time delay between light stimulus and target spike is crucial to minimize irradiance and expression density thresholds for suppressing individual spike. Good practical values of photostimulation parameters have been obtained empirically for peak photocurrent, time delay and 100% spiking inhibition, at continuous and pulsed illumination. Under continuous illumination, complete inhibition of neural activity in Jaws-expressing neurons takes place at minimum irradiance of 0.2 mW mm^-2 and expression density of 0.2 mS cm^-2, whereas for pulsed stimulation, it is at minimum irradiance of 0.6 mW mm^-2 and 5 ms pulse width, at 10 Hz. It is shown that Jaws and eNpHR3.0 are able to invoke single spike precise inhibition up to 160 and 200 Hz, respectively. The study is useful in designing new experiments, understanding temporal spike coding and bidirectional control, and curing neurological disorders.

Natronomonas salsuginis sp. nov., a New Inhabitant of a Marine Solar Saltern

A halophilic archaeon, strain F20-122^T, was isolated from a marine saltern of Isla Bacuta (Huelva, Spain). Cells were Gram-stain-negative, aerobic, and coccoid in morphology. It grew at 25–50 °C (optimum 37 °C), pH 6.5–9.0 (optimum pH 8.0), and 10–30% (w/v) total salts (optimum 25% salts). The phylogenetic analyses based on the 16S rRNA and rpoB’ genes showed its affiliation with the genus Natronomonas and suggested its placement as a new species within this genus. The in silico DNA–DNA hybridization (DDH) and average nucleotide identity (ANI) analyses of this strain against closely related species supported its placement in a new taxon. The DNA G + C content of this isolate was 63.0 mol%. The polar lipids of strain F20-122^T were phosphatidylglycerol phosphate methyl ester (PGP-Me), phosphatidylglycerol (PG), and phosphatidylglycerol sulfate (PGS). Traces of biphosphatidylglycerol (BPG) and other minor phospholipids and unidentified glycolipids were also present. Based on the phylogenetic, genomic, phenotypic, and chemotaxonomic characterization, we propose strain F20-122^T (= CCM 8891^T = CECT 9564^T = JCM 33320^T) as the type strain of a new species within the genus Natronomonas, with the name Natronomonas salsuginis sp. nov. Rhodopsin-like sequence analysis of strain F20-122^T revealed the presence of haloarchaeal proton pumps, suggesting a light-mediated ATP synthesis for this strain and a maximum wavelength absorption in the green spectrum.

Protochromic absorption changes in the two-cysteine photocycle of a blue/orange cyanobacteriochrome

Cyanobacteriochromes (CBCRs) are phytochrome-related photosensors with diverse spectral sensitivities spanning the entire visible spectrum. They covalently bind bilin chromophores via conserved cysteine residues and undergo 15Z/15E bilin photoisomerization upon light illumination. CBCR subfamilies absorbing violet-blue light use an additional cysteine residue to form a second bilin-thiol adduct in a two-Cys photocycle. However, the process of second thiol adduct formation is incompletely understood, especially the involvement of the bilin protonation state. Here, we focused on the Oscil6304_2705 protein from the cyanobacterium Oscillatoria acuminata PCC 6304, which photoconverts between a blue-absorbing 15Z state ( ^15Z Pb) and orange-absorbing 15E state ( ^15E Po). pH titration analysis revealed that ^15Z Pb was stable over a wide pH range, suggesting that bilin protonation is stabilized by a second thiol adduct. As revealed by resonance Raman spectroscopy, ^15E Po harbored protonated bilin at both acidic and neutral pH, but readily converted to a deprotonated green-absorbing 15Z state ( ^15Z Pg) at alkaline pH. Site-directed mutagenesis revealed that the conserved Asp-71 and His-102 residues are required for second thiol adduct formation in ^15Z Pb and bilin protonation in ^15E Po, respectively. An Oscil6304_2705 variant lacking the second cysteine residue, Cys-73, photoconverted between deprotonated ^15Z Pg and protonated ^15E Pr, similarly to the protochromic photocycle of the green/red CBCR subfamily. Time-resolved spectroscopy revealed ^15Z Pg formation as an intermediate in the ^15E Pr-to- ^15Z Pg conversion with a significant solvent-isotope effect, suggesting the sequential occurrence of 15EP-to-15Z photoisomerization, deprotonation, and second thiol adduct formation. Our findings uncover the details of protochromic absorption changes underlying the two-Cys photocycle of violet-blue-absorbing CBCR subfamilies.

Functional importance of the oligomer formation of the cyanobacterial H+ pump Gloeobacter rhodopsin

Many microbial rhodopsins self-oligomerize, but the functional consequences of oligomerization have not been well clarified. We examined the effects of oligomerization of a H⁺ pump, Gloeobacter rhodopsin (GR), by using nanodisc containing trimeric and monomeric GR. The monomerization did not appear to affect the unphotolyzed GR. However, we found a significant impact on the photoreaction: The monomeric GR showed faint M intermediate formation and negligible H⁺ transfer reactions. These changes reflected the elevated pKa of the Asp121 residue, whose deprotonation is a prerequisite for the functional photoreaction. Here, we focused on His87, which is a neighboring residue of Asp121 and conserved among eubacterial H⁺ pumps but replaced by Met in an archaeal H⁺ pump. We found that the H87M mutation removes the “monomerization effects”: Even in the monomeric state, H87M contained the deprotonated Asp121 and showed both M formation and distinct H⁺ transfer reactions. Thus, for wild-type GR, monomerization probably strengthens the Asp121-His87 interaction and thereby elevates the pKa of Asp121 residue. This strong interaction might occur due to the loosened protein structure and/or the disruption of the interprotomer interaction of His87. Thus, the trimeric assembly of GR enables light-induced H⁺ transfer reactions through adjusting the positions of key residues.

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.

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

The anion pumping cycle of halorhodopsin from Natronomonas pharaonis ( pHR) is initiated when the all- trans/15- anti isomer of retinal is photoisomerized into the 13- cis/15- anti configuration. A recent crystallographic study suggested that a reaction state with 13- cis/15- syn retinal occurred during the anion release process, i.e., after the N state with the 13- cis/15- anti retinal and before the O state with all- trans/15- anti retinal. In this study, we investigated the retinal isomeric composition in a long-living reaction state at various bromide ion concentrations. It was found that the 13- cis isomer (^csHR'), in which the absorption spectrum was blue-shifted by ∼8 nm compared with that of the trans isomer (^taHR), accumulated significantly when a cold suspension of pHR-rich claret membranes in 4 M NaBr was illuminated with continuous light. Analysis of flash-induced absorption changes suggested that the branching of the trans photocycle into the 13- cis isomer (^csHR') occurs during the decay of an O-like state (O') with 13- cis/15- syn retinal; i.e., O' can decay to either ^csHR' or O with all- trans/15- anti retinal. The efficiency of the branching reaction was found to be dependent on the bromide ion concentration. At a very high bromide ion concentration, the anion pumping cycle is described by the scheme ^taHR -( hν) → K → L_1a ↔ L_1b ↔ N ↔ N' ↔ O' ↔ ^csHR' ↔ ^taHR. At a low bromide ion concentration, on the other hand, O' decays into ^taHR via O.

Implications for the impairment of the rapid channel closing of Proteomonas sulcata anion channelrhodopsin 1 at high Cl- concentrations

Natural anion channelrhodopsins (ACRs) have recently received increased attention because of their effectiveness in optogenetic manipulation for neuronal silencing. In this study, we focused on Proteomonas sulcata ACR1 (PsuACR1), which has rapid channel closing kinetics and a rapid recovery to the initial state of its anion channel function that is useful for rapid optogenetic control. To reveal the anion concentration dependency of the channel function, we investigated the photochemical properties of PsuACR1 using spectroscopic techniques. Recombinant PsuACR1 exhibited a Cl⁻ dependent spectral red-shift from 531 nm at 0.1 mM to 535 nm at 1000 mM, suggesting that it binds Cl⁻ in the initial state with a K_d of 5.5 mM. Flash-photolysis experiments revealed that the photocycle was significantly changed at high Cl⁻ concentrations, which led not only to suppression of the accumulation of the M-intermediate involved in the Cl⁻ non-conducting state but also to a drastic change in the equilibrium state of the other photo-intermediates. Because of this, the Cl⁻ conducting state is protracted by one order of magnitude, which implies an impairment of the rapid channel closing of PsuACR1 in the presence of high concentrations of Cl⁻.

Presence of a Haloarchaeal Halorhodopsin-Like Cl- Pump in Marine Bacteria

Light-driven ion-pumping rhodopsins are widely distributed among bacteria, archaea, and eukaryotes in the euphotic zone of the aquatic environment. H⁺-pumping rhodopsin (proteorhodopsin: PR), Na⁺-pumping rhodopsin (NaR), and Cl^--pumping rhodopsin (ClR) have been found in marine bacteria, which suggests that these genes evolved independently in the ocean. Putative microbial rhodopsin genes were identified in the genome sequences of marine Cytophagia. In the present study, one of these genes was heterologously expressed in Escherichia coli cells and the rhodopsin protein named Rubricoccus marinus halorhodopsin (RmHR) was identified as a light-driven inward Cl^- pump. Spectroscopic assays showed that the estimated dissociation constant (K_d,int.) of this rhodopsin was similar to that of haloarchaeal halorhodopsin (HR), while the Cl^--transporting photoreaction mechanism of this rhodopsin was similar to that of HR, but different to that of the already-known marine bacterial ClR. This amino acid sequence similarity also suggested that this rhodopsin is similar to haloarchaeal HR and cyanobacterial HRs (e.g., SyHR and MrHR). Additionally, a phylogenetic analysis revealed that retinal biosynthesis pathway genes (blh and crtY) belong to a phylogenetic lineage of haloarchaea, indicating that these marine Cytophagia acquired rhodopsin-related genes from haloarchaea by lateral gene transfer. Based on these results, we concluded that inward Cl^--pumping rhodopsin is present in genera of the class Cytophagia and may have the same evolutionary origins as haloarchaeal HR.

Membrane Independence of Ultrafast Photochemistry in Pharaonis Halorhodopsin: Testing the Role of Bacterioruberin

Ultrafast photochemistry of pharaonis halorhodopsin (p-HR) in the intact membrane of Natronomonas pharaonis has been studied by photoselective femtosecond pump-hyperspectral probe spectroscopy with high time resolution. Two variants of this sample were studied, one with wild-type retinal prosthetic groups and another after shifting the retinal absorption deep into the blue range by reducing the Schiff base linkage, and the results were compared to a previous study on detergent-solubilized p-HR. This comparison shows that retinal photoisomerization dynamics is identical in the membrane and in the solubilized sample. Selective photoexcitation of bacterioruberin, which is associated with the protein in the native membrane, in wild-type and reduced samples, demonstrates conclusively that unlike the carotenoids associated with some bacterial retinal proteins the carrotenoid in p-HR does not act as a light-harvesting antenna.

Implications for the Light-Driven Chloride Ion Transport Mechanism of Nonlabens marinus Rhodopsin 3 by Its Photochemical Characteristics

Several new retinal-based photoreceptor proteins that act as light-driven electrogenic halide ion pumps have recently been discovered. Some of them, called "NTQ" rhodopsins, contain a conserved Asn-Thr-Gln motif in the third or C-helix. In this study, we investigated the photochemical characteristics of an NTQ rhodopsin, Nonlabens marinus rhodopsin 3 (NM-R3), which was discovered in the N. marinus S1-08^T strain, using static and time-resolved spectroscopic techniques. We demonstrate that NM-R3 binds a Cl^- in the vicinity of the retinal chromophore accompanied by a spectral blueshift from 568 nm in the absence of Cl^- to 534 nm in the presence of Cl^-. From the Cl^- concentration dependence, we estimated the affinity (dissociation constant, K_d) for Cl^- in the original state as 24 mM, which is ca. 10 times weaker than that of archaeal halorhodopsins but ca. 3 times stronger than that of a marine bacterial Cl^- pumping rhodopsin (C1R). NM-R3 showed no dark-light adaptation of the retinal chromophore and predominantly possessed an all-trans-retinal, which is responsible for the light-driven Cl^- pump function. Flash-photolysis experiments suggest that NM-R3 passes through five or six photochemically distinct intermediates (K, L(N), O₁, O₂, and NM-R3'). From these results, we assume that the Cl^- is released and taken up during the L(N)-O₁ transition from a transiently formed cytoplasmic (CP) binding site and the O₂-NM-R3' or the NM-R3'-original NM-R3 transitions from the extracellular (EC) side, respectively. We propose a mechanism for the Cl^- transport by NM-R3 based on our results and its recently reported crystal structure.

Photochemical characterization of actinorhodopsin and its functional existence in the natural host

Actinorhodopsin (ActR) is a light-driven outward H⁺ pump. Although the genes of ActRs are widely spread among freshwater bacterioplankton, there are no prior data on their functional expression in native cell membranes. Here, we demonstrate ActR phototrophy in the native actinobacterium. Genome analysis showed that Candidatus Rhodoluna planktonica, a freshwater actinobacterium, encodes one microbial rhodopsin (RpActR) belonging to the ActR family. Reflecting the functional expression of RpActR, illumination induced the acidification of the actinobacterial cell suspension and then elevated the ATP content inside the cells. The photochemistry of RpActR was also examined using heterologously expressed RpActR in Escherichia coli membranes. The purified RpActR showed λ_max at 534nm and underwent a photocycle characterized by the very fast formation of M intermediate. The subsequent intermediate, named P₆₂₀, could be assigned to the O intermediate in other H⁺ pumps. In contrast to conventional O, the accumulation of P₆₂₀ remains prominent, even at high pH. Flash-induced absorbance changes suggested that there exists only one kind of photocycle at any pH. However, above pH7, RpActR shows heterogeneity in the H⁺ transfer sequences: one first captures H⁺ and then releases it during the formation and decay of P₆₂₀, while the other first releases H⁺ prior to H⁺ uptake during P₆₂₀ formation.