Light-driven Proton Research Articles

Vectorial Proton Transport Mechanism of RxR, a Phylogenetically Distinct and Thermally Stable Microbial Rhodopsin

Rubrobacter xylanophilus rhodopsin (RxR) is a phylogenetically distinct and thermally stable seven-transmembrane protein that functions as a light-driven proton (H+) pump with the chromophore retinal. To characterize its vectorial proton transport mechanism, mutational and theoretical investigations were performed for carboxylates in the transmembrane region of RxR and the sequential proton transport steps were revealed as follows: (i) a proton of the retinylidene Schiff base (Lys209) is transferred to the counterion Asp74 upon formation of the blue-shifted M-intermediate in collaboration with Asp205, and simultaneously, a respective proton is released from the proton releasing group (Glu187/Glu197) to the extracellular side, (ii) a proton of Asp85 is transferred to the Schiff base during M-decay, (iii) a proton is taken up from the intracellular side to Asp85 during decay of the red-shifted O-intermediate. This ion transport mechanism of RxR provides valuable information to understand other ion transporters since carboxylates are generally essential for their functions.

Light-Driven Sodium-Pumping Rhodopsin: A New Concept of Active Transport.

Ion pumps perform active transport of ions by using energy. The active transport mechanism can be illustrated by the Panama Canal model, which considers two gates and a gain in energy. The Panama Canal model is consistent with the alternating access model that is used to describe active transport, in which the substrate ion is bound, energized, and released. It was generally accepted that energization occurs only for an ion-bound protein but not for an ion-unbound protein. Light-driven proton and chloride pumps, two of the best studied pumps, are represented by the Panama Canal model. In this case, light absorption takes place for the bound state of ions (proton and chloride ions) in the active center (protonated Schiff base of the retinal chromophore). In contrast, a recently discovered light-driven sodium pump, Krokinobacter eikastus rhodopsin 2 (KR2), is a unique active transporter that does not bind the transport substrate, the sodium ion, in its resting state. The molecular architecture and photoreaction cycle of the light-driven sodium pump are very similar to those of proton and chloride pumps, although sodium ions are actively transported without initial binding. Sodium uptake is a diffusive process, but the presence of two gates allows the unidirectional transport of sodium ions. In this sense, the light-driven sodium pump is also represented by a modified Panama Canal model. Current understanding of the light-driven sodium pump is reviewed.

Microbial Rhodopsins.

Microbial rhodopsins (MRs) are a large family of photoactive membrane proteins, found in microorganisms belonging to all kingdoms of life, with new members being constantly discovered. Among the MRs are light-driven proton, cation and anion pumps, light-gated cation and anion channels, and various photoreceptors. Due to their abundance and amenability to studies, MRs served as model systems for a great variety of biophysical techniques, and recently found a great application as optogenetic tools. While the basic aspects of microbial rhodopsins functioning have been known for some time, there is still a plenty of unanswered questions. This chapter presents and summarizes the available knowledge, focusing on the functional and structural studies.

An evolutionary optimization of a rhodopsin-based phototrophic metabolism in Escherichia coli

BackgroundThe expression of the Gloeobacter rhodopsin (GR) in a chemotrophic Escherichia coli enables the light-driven phototrophic energy generation. Adaptive laboratory evolution has been used for acquiring desired phenotype of microbial cells and for the elucidation of basic mechanism of molecular evolution. To develop an optimized strain for the artificially acquired phototrophic metabolism, an ancestral E. coli expressing GR was adaptively evolved in a chemostat reactor with constant illumination and limited glucose conditions. This study was emphasized at an unexpected genomic mutation contributed to the improvement of microbial performance.ResultsDuring the chemostat culture, increase of cell size was observed, which were distinguished from that of the typical rod-shaped ancestral cells. A descendant ET5 strain was randomly isolated from the chemostat culture at 88-days. The phototrophic growth and the light-induced proton pumping of the ET5 strain were twofold and eightfold greater, respectively, than those of the ancestral E. coli strain. Single point mutation of C1082A at dgcQ gene (encoding diguanylate cyclase, also known as the yedQ gene) in the chromosome of ET5 strain was identified from whole genome sequencing analysis. An ancestral E. coli complemented with the same dgcQ mutation from the ET5 was repeated the subsequently enhancements of light-driven phototrophic growth and proton pumping. Intracellular c-di-GMP, the product of the diguanylate cyclase (dgcQ), of the descendant ET5 strain was suddenly increased while that of the ancestral strain was negligible.ConclusionsNewly acquired phototrophic metabolism of E. coli was further improved via adaptive laboratory evolution by the rise of a point mutation on a transmembrane cell signaling protein followed by increase of signal molecule that eventually led an increase proton pumping and phototrophic growth.

Retinol as electron carrier in redox signaling, a new frontier in vitamin A research.

Nature uses carotenoids and retinoids as chromophores for diverse energy conversion processes. The key structural feature enabling the interaction with light and other manifestations of electro-magnetism is the conjugated double-bond system that all members of this superfamily share in common. Among retinoids, retinaldehyde alone was long known as the active chromophore of vision in vertebrates and invertebrates, as well of various light-driven proton and ion pumps in Archaea. Until now, vitamin A (retinol) was solely regarded as a biochemical precursor for bioactive retinoids such as retinaldehyde and retinoic acid (RA), but recent results indicate that this compound has its own physiology. It functions as an electron carrier in mitochondria. By electronically coupling protein kinase Cδ (PCKδ) with cytochrome c, vitamin A enables the redox activation of this enzyme. This review focuses on the biochemistry and biology of the PCKδ signaling system, comprising PKCδ, the adapter protein p66Shc, cytochrome c and retinol. This complex positively regulates the conversion of pyruvate to acetyl-coenzyme A (CoA) by the pyruvate dehydrogenase enzyme. Vitamin A therefore plays a key role in glycolytic energy generation. The emerging paradigm of retinol as electron-transfer agent is potentially transformative, opening new frontiers in retinoid research.

Protein-Bound Water as the Determinant of Asymmetric Functional Conversion between Light-Driven Proton and Chloride Pumps

Bacteriorhodopsin (BR) and halorhodopsin (HR) are light-driven outward proton and inward chloride pumps, respectively. They have similar protein architecture, being composed of seven-transmembrane helices that bind an all-trans-retinal. BR can be converted into a chloride pump by a single amino acid replacement at position 85, suggesting that BR and HR share a common transport mechanism, and the ionic specificity is determined by the amino acid at that position. However, HR cannot be converted into a proton pump by the corresponding reverse mutation. Here we mutated 6 and 10 amino acids of HR into BR-like, whereas such multiple HR mutants never pump protons. Light-induced Fourier transform infrared spectroscopy revealed that hydrogen bonds of the retinal Schiff base and water are both strong for BR and both weak for HR. Multiple HR mutants exhibit strong hydrogen bonds of the Schiff base, but the hydrogen bond of water is still weak. We concluded that the cause of nonfunctional conversion of HR is the lack of strongly hydrogen-bonded water, the functional determinant of the proton pump.

Hydrogen-Bonding Interaction of the Protonated Schiff Base with Halides in a Chloride-Pumping Bacteriorhodopsin Mutant

Bacteriorhodopsin (BR) and halorhodopsin (HR) are light-driven proton and chloride ion pumps, respectively, in Halobacterium salinarum. The amino acid identity of these proteins is about 25%, suggesting that each has been optimized for their own functions during evolution. However, it is known that the BR mutants, D85T and D85S, can pump chloride ions. This fact implies that the Schiff base region is important in determining ionic selectivity. The X-ray crystallographic structure of D85S(Br(-)) showed the presence of a bromide ion in the Schiff base region (Facciotti, M. T., Cheung, V. S., Nguyen, D., Rouhani, S., and Glaeser, R. M. (2003) Biophys. J. 85, 451-458). In this article, we report on the study of hydrogen bonds of the Schiff base and water molecules in D85S in the absence and presence of various halides, assigning their N-D and O-D stretching vibrations in D(2)O, respectively, in low-temperature Fourier-transform infrared (FTIR) spectroscopy. We found that the hydrogen bond of the Schiff base in D85S(Cl(-)) is much stronger than that in HR, being as strong as that in wild-type BR. Similar halide dependence in D85S and in solution implies that the Schiff base forms a direct hydrogen bond with a halide, consistent with the X-ray structure. Photoisomerization causes a weakened hydrogen bond of the Schiff base, and halide dependence on the stretching frequency is lost. These spectral features are similar to those in the photocycle of proton-pumping BR, though the weakened hydrogen bond is more significant for BR. However, the spectral features of water bands in D85S are closer to chloride-pumping HR because O-D stretching vibrations of water are observed only at >2500 cm(-)(1). Unlike in BR, we did not observe strongly hydrogen-bonded water molecules for halide-pumping D85S mutants. This observation agrees with our recent hypothesis that strongly hydrogen-bonded water molecules are required for the proton-pumping activity of archaeal rhodopsins. Hydrogen-bonding conditions in the Schiff base region of D85S are discussed on the basis of the spectral comparison with those of wild-type BR and HR.

Coupling Proton Movement to ATP Synthesis in the Chloroplast ATP Synthase

The chloroplast F(0)F(1)-ATP synthase-ATPase is a tiny rotary motor responsible for coupling ATP synthesis and hydrolysis to the light-driven electrochemical proton gradient. Reversible oxidation/reduction of a dithiol, located within a special regulatory domain of the gamma subunit of the chloroplast F(1) enzyme, switches the enzyme between an inactive and an active state. This regulatory mechanism is unique to the ATP synthases of higher plants and its physiological significance lies in preventing nonproductive depletion of essential ATP pools in the dark. The three-dimensional structure of the chloroplast F(1) gamma subunit has not yet been solved. To examine the mechanism of dithiol regulation, a model of the chloroplast gamma subunit was obtained through segmental homology modeling based on the known structures of the mitochondrial and bacterial gamma subunits, together with de novo construction of the unknown regulatory domain. The model has provided considerable insight into how the dithiol might modulate catalytic function. This has, in turn, suggested a mechanism by which rotation of subunits in F(0), the transmembrane proton channel portion of the enzyme, can be coupled, via the epsilon subunit, to rotation of the gamma subunit of F(1) to achieve the 120 degrees (or 90 degrees +30 degrees) stepping action that is characteristic of F(1) gamma subunit rotation.

Structural Determinants of Spectral Tuning in Retinal ProteinsBacteriorhodopsin vs Sensory Rhodopsin II

The mechanism of spectral tuning in the rhodopsin family of proteins, that act as light-driven proton (ion) pumps and light detectors, has been investigated by a combined ab initio quantum mechanical/molecular mechanical technique. Calculations are performed on two members of the family, bacteriorhodopsin (bR) and sensory rhodopsin II (sRII), for which crystal structures of high resolution are available, to explore the physical mechanisms of spectral tuning. Despite a high degree of similarity in the three-dimensional structure, electrostatic environments in bR and sRII differ sufficiently to shift absorption maxima of their common chromophore, a retinal bound to a lysine via a protonated Schiff base, from 568 nm in bR to 497 nm in sRII. This spectral shift, involving the electronical ground state (S0) and first excited state (S1) of retinal, is predicted correctly within 10 nm. The spectral shift can be attributed predominantly to a change in polarization of the S1 state, and is induced predominantly by a shift of the G helix that renders the distance between the Schiff base nitrogen of retinal and the Asp201 counterion shorter in sRII than in bR. A second, weakly allowed excited state, S2, is predicted to lie energetically close to S1, at 474 nm. Its energetic proximity to the S1 state suggests strong vibronic coupling and explains a shoulder observed at 457 nm in the sRII spectrum.

Light-driven proton or chloride pumping by halorhodopsin.

Halorhodopsin from Halobacterium halobium was purified and reconstituted with lipids from purple membranes. The resulting protein-containing membrane sheets were adsorbed to a planar lipid membrane and photoelectric properties were analyzed. Depending on light conditions, halorhodopsin acted either as a light-driven chloride pump or as a proton pump: green light caused chloride transport and additional blue light induced proton pumping. In the living cell, both to these vectorial processes would be directed toward the cytoplasm and, compared to ion transport by bacteriorhodopsin, this is an inversed proton flow. Azide, a catalyst for reversible deprotonation of halorhodopsin, enhanced proton transport, and the deprotonated Schiff base in the 13-cis configuration (H410) was identified as the key intermediate of this alternative catalytic cycle in halorhodopsin. While chloride transport in halorhodopsin is mediated by a one-photon process, proton transport requires the absorption of two photons: one photon for formation of H410 and release of a proton, and one photon for photoisomerization of H410 and re-formation of H578 with concomitant uptake of a proton by the Schiff base.