Rhodopsin and bacteriorhodopsin: structure-function relationships

Arrestins: A Small Family of Multi-Functional Proteins

The first member of the arrestin family, visual arrestin-1, was discovered in the late 1970s. Later, the other three mammalian subtypes were identified and cloned. The first described function was regulation of G protein-coupled receptor (GPCR) signaling: arrestins bind active phosphorylated GPCRs, blocking their coupling to G proteins. It was later discovered that receptor-bound and free arrestins interact with numerous proteins, regulating GPCR trafficking and various signaling pathways, including those that determine cell fate. Arrestins have no enzymatic activity; they function by organizing multi-protein complexes and localizing their interaction partners to particular cellular compartments. Today we understand the molecular mechanism of arrestin interactions with GPCRs better than the mechanisms underlying other functions. However, even limited knowledge enabled the construction of signaling-biased arrestin mutants and extraction of biologically active monofunctional peptides from these multifunctional proteins. Manipulation of cellular signaling with arrestin-based tools has research and likely therapeutic potential: re-engineered proteins and their parts can produce effects that conventional small-molecule drugs cannot.

Localization of multiple opsins in ocular and non-ocular tissues of deep-sea shrimps and the first evidence of co-localization in a rhabdomeric R8 cell (Caridea: Oplophoroidea)

Bioluminescence is a prevalent phenomenon throughout the marine realm and is often the dominant source of light in mesophotic and aphotic depth horizons. Shrimp belonging to the superfamily Oplophoroidea are mesopelagic, perform diel vertical migration, and secrete a bright burst of bioluminescent mucous when threatened. Species in the family Oplophoridae also possess cuticular light-emitting photophores presumably for camouflage via counter-illumination. Many species within the superfamily express a single visual pigment in the retina, consistent with most other large-bodied mesopelagic crustaceans studied to date. Photophore-bearing species have an expanded visual opsin repertoire and dual-sensitivity visual systems, as evidenced by transcriptomes and electroretinograms. In this study, we used immunohistochemistry to describe opsin protein localization in the retinas of four species of Oplophoroidea and non-ocular tissues of Janicella spinicauda. Our results show that Acanthephyra purpurea (Acanthephyridae) retinas possess LWS-only photoreceptors, consistent with the singular peak sensitivity previously reported. Oplophoridae retinas contain two opsin clades (LWS and MWS) consistent with dual-sensitivity. Oplophorus gracilirostris and Systellaspis debilis have LWS in the proximal rhabdom (R1-7 cells) and MWS2 localized in the distal rhabdom (R8 cell). Surprisingly, Janicella spinicauda has LWS in the proximal rhabdom (R1-7) and co-localized MWS1 and MWS2 opsin paralogs in the distal rhabdom, providing the first evidence of co-localization of opsins in a crustacean rhabdomeric R8 cell. Furthermore, opsins were found in multiple non-ocular tissues of J. spinicauda, including nerve, tendon, and photophore. These combined data demonstrate evolutionary novelty and opsin duplication within Oplophoridae, with implications for visual ecology, evolution in mesophotic environments, and a mechanistic understanding of adaptive counter-illumination using photophore bioluminescence.

Counterion at an atypical position: Investigating the mechanism of photoisomerization in jellyfish rhodopsin

The position of the counterion in animal rhodopsins plays a crucial role in maintaining visible light sensitivity and facilitating the photoisomerization of their retinal chromophore. The counterion displacement is thought to be closely related to the evolution of rhodopsins, with different positions found in invertebrates and vertebrates. Interestingly, box jellyfish rhodopsin (JelRh) acquired the counterion in transmembrane 2 (TM2) independently. This is a unique feature, as in most animal rhodopsins, the counterion is found in a different location. In this study, we used Fourier Transform Infrared spectroscopy to examine the structural changes that occur in the early photointermediate state of JelRh. We aimed to determine whether the photochemistry of JelRh is similar to that of other animal rhodopsins by comparing its spectra to those of vertebrate bovine rhodopsin (BovRh) and invertebrate squid rhodopsin (SquRh). We observed that the N-D stretching band of the retinal Schiff base was similar to that of BovRh, indicating the interaction between the Schiff base and the counterion is similar in both rhodopsins, despite their different counterion positions. Furthermore, we found that the chemical structure of the retinal in JelRh is similar to that in BovRh, including the changes in the hydrogen-out-of-plane band that indicates a retinal distortion. Overall, the protein conformational changes induced by the photoisomerization of JelRh yielded spectra that resemble an intermediate between BovRh and SquRh, suggesting a unique spectral property of JelRh, and making it the only animal rhodopsin with a counterion in TM2 and an ability to activate G_s protein.

Placing human gene families into their evolutionary context

Following the draft sequence of the first human genome over 20 years ago, we have achieved unprecedented insights into the rules governing its evolution, often with direct translational relevance to specific diseases. However, staggering sequence complexity has also challenged the development of a more comprehensive understanding of human genome biology. In this context, interspecific genomic studies between humans and other animals have played a critical role in our efforts to decode human gene families. In this review, we focus on how the rapid surge of genome sequencing of both model and non-model organisms now provides a broader comparative framework poised to empower novel discoveries. We begin with a general overview of how comparative approaches are essential for understanding gene family evolution in the human genome, followed by a discussion of analyses of gene expression. We show how homology can provide insights into the genes and gene families associated with immune response, cancer biology, vision, chemosensation, and metabolism, by revealing similarity in processes among distant species. We then explain methodological tools that provide critical advances and show the limitations of common approaches. We conclude with a discussion of how these investigations position us to gain fundamental insights into the evolution of gene families among living organisms in general. We hope that our review catalyzes additional excitement and research on the emerging field of comparative genomics, while aiding the placement of the human genome into its existentially evolutionary context.

Crustacean conundrums: a review of opsin diversity and evolution

Knowledge of crustacean vision is lacking compared to the more well-studied vertebrates and insects. While crustacean visual systems are typically conserved morphologically, the molecular components (i.e. opsins) remain understudied. This review aims to characterize opsin diversity across crustacean lineages for an integrated view of visual system evolution. Using publicly available data from 95 species, we identified opsin sequences and classified them by clade. Our analysis produced 485 putative visual opsins and 141 non-visual opsins. The visual opsins were separated into six clades: long wavelength sensitive (LWS), middle wavelength sensitive (MWS) 1 and 2, short wavelength or ultraviolet sensitive (SWS/UVS) and a clade of thecostracan opsins, with multiple LWS and MWS opsin copies observed. The SWS/UVS opsins were relatively conserved in most species. The crustacean classes Cephalocarida, Remipedia and Hexanauplia exhibited reduced visual opsin diversity compared to others, with the malacostracan decapods having the highest opsin diversity. Non-visual opsins were identified from all investigated classes except Cephalocarida. Additionally, a novel clade of non-visual crustacean-specific, R-type opsins (Rc) was discovered. This review aims to provide a framework for future research on crustacean vision, with an emphasis on the need for more work in spectral characterization and molecular analysis. This article is part of the theme issue 'Understanding colour vision: molecular, physiological, neuronal and behavioural studies in arthropods'.

The Gluopsins: Opsins without the Retinal Binding Lysine

Opsins allow us to see. They are G-protein-coupled receptors and bind as ligand retinal, which is bound covalently to a lysine in the seventh transmembrane domain. This makes opsins light-sensitive. The lysine is so conserved that it is used to define a sequence as an opsin and thus phylogenetic opsin reconstructions discard any sequence without it. However, recently, opsins were found that function not only as photoreceptors but also as chemoreceptors. For chemoreception, the lysine is not needed. Therefore, we wondered: Do opsins exists that have lost this lysine during evolution? To find such opsins, we built an automatic pipeline for reconstructing a large-scale opsin phylogeny. The pipeline compiles and aligns sequences from public sources, reconstructs the phylogeny, prunes rogue sequences, and visualizes the resulting tree. Our final opsin phylogeny is the largest to date with 4956 opsins. Among them is a clade of 33 opsins that have the lysine replaced by glutamic acid. Thus, we call them gluopsins. The gluopsins are mainly dragonfly and butterfly opsins, closely related to the RGR-opsins and the retinochromes. Like those, they have a derived NPxxY motif. However, what their particular function is, remains to be seen.

Spectral tuning and deactivation kinetics of marine mammal melanopsins

In mammals, the photopigment melanopsin (Opn4) is found in a subset of retinal ganglion cells that serve light detection for circadian photoentrainment and pupil constriction (i.e., mydriasis). For a given species, the efficiency of photoentrainment and length of time that mydriasis occurs is determined by the spectral sensitivity and deactivation kinetics of melanopsin, respectively, and to date, neither of these properties have been described in marine mammals. Previous work has indicated that the absorbance maxima (λmax) of marine mammal rhodopsins (Rh1) have diversified to match the available light spectra at foraging depths. However, similar to the melanopsin λmax of terrestrial mammals (~480 nm), the melanopsins of marine mammals may be conserved, with λmax values tuned to the spectrum of solar irradiance at the water's surface. Here, we investigated the Opn4 pigments of 17 marine mammal species inhabiting diverse photic environments including the Infraorder Cetacea, as well as the Orders Sirenia and Carnivora. Both genomic and cDNA sequences were used to deduce amino acid sequences to identify substitutions most likely involved in spectral tuning and deactivation kinetics of the Opn4 pigments. Our results show that there appears to be no amino acid substitutions in marine mammal Opn4 opsins that would result in any significant change in λmax values relative to their terrestrial counterparts. We also found some marine mammal species to lack several phosphorylation sites in the carboxyl terminal domain of their Opn4 pigments that result in significantly slower deactivation kinetics, and thus longer mydriasis, compared to terrestrial controls. This finding was restricted to cetacean species previously found to lack cone photoreceptor opsins, a condition known as rod monochromacy. These results suggest that the rod monochromat whales rely on extended pupillary constriction to prevent photobleaching of the highly photosensitive all-rod retina when moving between photopic and scotopic conditions.

Supramolecular organization of rhodopsin in rod photoreceptor cell membranes

Rhodopsin is the light receptor in rod photoreceptor cells that initiates scotopic vision. Studies on the light receptor span well over a century, yet questions about the organization of rhodopsin within the photoreceptor cell membrane still persist and a consensus view on the topic is still elusive. Rhodopsin has been intensely studied for quite some time, and there is a wealth of information to draw from to formulate an organizational picture of the receptor in native membranes. Early experimental evidence in apparent support for a monomeric arrangement of rhodopsin in rod photoreceptor cell membranes is contrasted and reconciled with more recent visual evidence in support of a supramolecular organization of rhodopsin. What is known so far about the determinants of forming a supramolecular structure and possible functional roles for such an organization are also discussed. Many details are still missing on the structural and functional properties of the supramolecular organization of rhodopsin in rod photoreceptor cell membranes. The emerging picture presented here can serve as a springboard towards a more in-depth understanding of the topic.

Differential Aggregation Properties of Mutant Human and Bovine Rhodopsin

Rhodopsin is the light receptor required for the function and health of photoreceptor cells. Mutations in rhodopsin can cause misfolding and aggregation of the receptor, which leads to retinal degeneration. Bovine rhodopsin is often used as a model to understand the effect of pathogenic mutations in rhodopsin due to the abundance of structural information on the bovine form of the receptor. It is unclear whether or not the bovine rhodopsin template is adequate in predicting the effect of these mutations occurring in human retinal disease or in predicting the efficacy of therapeutic strategies. To better understand the extent to which bovine rhodopsin can serve as a model, human and bovine P23H rhodopsin mutants expressed heterologously in cells were examined. The aggregation properties and cellular localization of the mutant receptors were determined by Förster resonance energy transfer and confocal microscopy. The potential therapeutic effects of the pharmacological compounds 9-cis retinal and metformin were also examined. Human and bovine P23H rhodopsin mutants exhibited different aggregation properties and responses to the pharmacological compounds tested. These observations would lead to different predictions on the severity of the phenotype and divergent predictions on the benefit of the therapeutic compounds tested. The bovine rhodopsin template does not appear to adequately model the effects of the P23H mutation in the human form of the receptor.

Expansion of the "Sodium World" through Evolutionary Time and Taxonomic Space

In 1986, Vladimir Skulachev and his colleagues coined the term "Sodium World" for the group of diverse organisms with sodium (Na)-based bioenergetics. Albeit only few such organisms had been discovered by that time, the authors insightfully noted that "the great taxonomic variety of organisms employing the Na-cycle points to the ubiquitous distribution of this novel type of membrane-linked energy transductions". Here we used tools of bioinformatics to follow expansion of the Sodium World through the evolutionary time and taxonomic space. We searched for those membrane protein families in prokaryotic genomes that correlate with the use of the Na-potential for ATP synthesis by different organisms. In addition to the known Na-translocators, we found a plethora of uncharacterized protein families; most of them show no homology with studied proteins. In addition, we traced the presence of Na-based energetics in many novel archaeal and bacterial clades, which were recently identified by metagenomic techniques. The data obtained support the view that the Na-based energetics preceded the proton-dependent energetics in evolution and prevailed during the first two billion years of the Earth history before the oxygenation of atmosphere. Hence, the full capacity of Na-based energetics in prokaryotes remains largely unexplored. The Sodium World expanded owing to the acquisition of new functions by Na-translocating systems. Specifically, most classes of G-protein-coupled receptors (GPCRs), which are targeted by almost half of the known drugs, appear to evolve from the Na-translocating microbial rhodopsins. Thereby the GPCRs of class A, with 700 representatives in human genome, retained the Na-binding site in the center of the transmembrane heptahelical bundle together with the capacity of Na-translocation. Mathematical modeling showed that the class A GPCRs could use the energy of transmembrane Na-potential for increasing both their sensitivity and selectivity. Thus, GPCRs, the largest protein family coded by human genome, stem from the Sodium World, which encourages exploration of other Na-dependent enzymes of eukaryotes.

Genome-wide identification of nonvisual opsin family reveals amplification of RPE-retinal G protein receptor gene (RGR) and offers novel insights into functions of RGR(s) in Paralichthys olivaceus (Paralichthyidae, Teleostei)

Opsins play important roles in the image-forming visual pathways and numerous biological systems such as the biological clock and circadian rhythm. However, the nonvisual opsins involved in nonimage forming process are not clear to date. The aim of this study was to characterize nonvisual opsins in Paralichthys olivaceus. A total of 24 nonvisual opsin genes were identified. Expressions of these genes in eye, brain, heart, testis, and fin were investigated by quantitative real-time polymerase chain reaction (qRT-PCR). Testis contained a surprisingly large number of nonvisual opsins including Opn4m2, Tmt2a, Tmt3b, Opn3, RRH, Opn7a, and Opn7b. Syntenic and phylogenetic analyses confirmed that the RGRa and RGRb originated from the teleost-specific genome duplication (TSGD). qRT-PCR results demonstrated high RGRa and RGRb expression in the eye, while the expression levels in the brain, heart, testis, and fin were relatively weak. In situ hybridization results presented here revealed the presence of both RGRa and RGRb mRNA-positive signals in the ganglion cell layer but absence in the intracellular compartment of retinal pigment epithelium (RPE) and Müller glial cells. Therefore, we hypothesized that RGRa and RGRb had undergone subfunctionalization in P. olivaceus after TSGD. In conclusion, this study provides novel insights into the evolutionary fates of the RGR genes, still, further studies need to be done to explore the mechanism about the lack of RGR genes' expression in RPE.

NYD-OP7/PLC regulatory signaling pathway regulates deltamethrin resistance in Culex pipiens pallens (Diptera: Culicidae)

BACKGROUND

Investigation of insecticide resistance mechanisms is considered a vital first step towards the creation of effective strategies to control resistant mosquitoes and manage mosquito-borne diseases. Our previous study revealed that NYD-OP7 may be associated with deltamethrin resistance in Culex pipiens pallen. However, the precise function of NYD-OP7 in deltamethrin resistance is still unclear. In this study, we investigated the role of NYD-OP7 in the molecular mechanisms underlying pyrethroid resistance.

RESULTS

Knockdown of NYD-OP7 not only increased the susceptibility of the mosquitoes to deltamethrin in vivo but also simultaneously repressed both expression and enzyme activity of its downstream effector molecule, phospholipase C (PLC) and expression of several insecticide resistance-related P450 genes. Knockdown of PLC also sensitized the mosquitoes to deltamethrin and reduced the expression of the P450 genes.

CONCLUSIONS

Our results revealed that NYD-OP7 and its downstream effector PLC contribute to deltamethrin resistance by regulating the expression of P450s in Cx. pipiens pallens.

Phosphorylation-induced conformational changes of photoactivated rhodopsin probed by fluorescent labeling at Cys140 and Cys316

In order to monitor conformational changes following photoactivation and phosphorylation of bovine rhodopsin, the two reactive sulfhydryl groups at Cys¹⁴⁰ and Cys³¹⁶ were specifically labeled with the monobromobimane (mBBr) fluorophore. Although alterations in conformation after light exposure of rhodopsin were not detected by fluorescence excitation scans (300-450 nm) of the mBBr-labeled protein, the fluorescence signal was reduced ∼ 90% in samples containing photoactivated phosphorhodopsin. Predominant labeling at either Cys¹⁴⁰ or Cys³¹⁶ in light-activated and phosphorylated rhodopsin merely generated a decrease of ∼38% and 28%, respectively, in the fluorescence excitation intensity. Thus, neither mBBr-modified Cys¹⁴⁰ nor mBBr-modified Cys³¹⁶ were involved single-handedly in the remarkable fall seen on the signal following phosphorylation of the protein; rather, the incorporation of phosphate groups on the mBBr-labeled light-activated rhodopsin appeared to affect its fluorescence signal in a cooperative or synergistic manner. These findings demonstrated that the phosphorylation of specific hydroxyl groups at the carboxyl terminal tail of rhodopsin causes definite conformational changes in the three-dimensional fold of the protein. Apparently, amino acid residues that are buried in the interior of the inactive protein become accessible following illumination and phosphorylation of rhodopsin, quenching in turn the fluorescence excitation signal of mBBr-modified rhodopsin.

A Review on Bacteriorhodopsin-Based Bioelectronic Devices

Bacteriorhodopsin protein extracted from Halobacterium salinarum is widely used in many biohybrid electronic devices and forms a research subject known as bioelectronics, which merges biology with electronic technique. The specific molecule structure and components of bR lead to its unique photocycle characteristic, which consists of several intermediates (bR, K, L, M, N, and O) and results in proton pump function. In this review, working principles and properties of bacteriorhodopsin are briefly introduced, as well as bR layer preparation method. After that, different bR-based devices divided into photochemical and photoelectric applications are shown. Finally, outlook and conclusions are drawn to inspire new design of high-performance bR-based biohybrid electronic devices.

Molecular Mechanisms of GPCR Signaling: A Structural Perspective

G protein-coupled receptors (GPCRs) are cell surface receptors that respond to a wide variety of stimuli, from light, odorants, hormones, and neurotransmitters to proteins and extracellular calcium. GPCRs represent the largest family of signaling proteins targeted by many clinically used drugs. Recent studies shed light on the conformational changes that accompany GPCR activation and the structural state of the receptor necessary for the interactions with the three classes of proteins that preferentially bind active GPCRs, G proteins, G protein-coupled receptor kinases (GRKs), and arrestins. Importantly, structural and biophysical studies also revealed activation-related conformational changes in these three types of signal transducers. Here, we summarize what is already known and point out questions that still need to be answered. Clear understanding of the structural basis of signaling by GPCRs and their interaction partners would pave the way to designing signaling-biased proteins with scientific and therapeutic potential.

Membrane protein trafficking in Drosophila photoreceptor cells

Membrane protein trafficking occurs throughout the lifetime of neurons and includes the initial protein synthesis and anterograde transport to the plasma membrane as well as internalization, degradation, and recycling of plasma membrane proteins. Defects in protein trafficking can result in neuronal degeneration and underlie blinding diseases such as retinitis pigmentosa as well as other neuronal disorders. Drosophila photoreceptor cells have emerged as a model system for identifying the components and mechanisms involved in membrane protein trafficking in neurons. Here we summarize the current knowledge about trafficking of three Drosophila phototransduction proteins, the visual pigment rhodopsin and the two light-activated ion channels TRP (transient receptor potential) and TRPL (TRP-like). Despite some common requirements shared by rhodopsin and TRP, details in the trafficking of these proteins differ considerably, suggesting the existence of several trafficking pathways for these photoreceptor proteins.

Light-Activated Reversible Imine Isomerization: Towards a Photochromic Protein Switch

Mutants of cellular retinoic acid-binding protein II (CRABPII), engineered to bind all-trans-retinal as an iminium species, demonstrate photochromism upon irradiation with light at different wavelengths. UV light irradiation populates the cis-imine geometry, which has a high pKa , leading to protonation of the imine and subsequent "turn-on" of color. Yellow light irradiation yields the trans-imine isomer, which has a depressed pKa , leading to loss of color because the imine is not protonated. The protein-bound retinylidene chromophore undergoes photoinduced reversible interconversion between the colored and uncolored species, with excellent fatigue resistance.

Eukaryotic G protein-coupled receptors as descendants of prokaryotic sodium-translocating rhodopsins

Abstract

Microbial rhodopsins and G-protein coupled receptors (GPCRs, which include animal rhodopsins) are two distinct (super) families of heptahelical (7TM) membrane proteins that share obvious structural similarities but no significant sequence similarity. Comparison of the recently solved high-resolution structures of the sodium-translocating bacterial rhodopsin and various Na⁺-binding GPCRs revealed striking similarity of their sodium-binding sites. This similarity allowed us to construct a structure-guided sequence alignment for the two (super)families, which highlighted their evolutionary relatedness. Our analysis supports a common underlying molecular mechanism for both families that involves a highly conserved aromatic residue playing a pivotal role in rotation of the 6th transmembrane helix.

Reviewers

This article was reviewed by Oded Beja, G. P. S. Raghava and L. Aravind.

Electronic supplementary material

The online version of this article (doi:10.1186/s13062-015-0091-4) contains supplementary material, which is available to authorized users.

The ins and outs of adrenergic signaling

Adrenergic signaling, in particular signaling in the sympathetic nervous system, is a prime example of the control of an essential physiological system. It has served as a model system both for the control of mediator release and for receptor signaling and regulation. This review covers the historical development of the field and then addresses issues that represent key fields of ongoing research: the mechanisms and kinetics of receptor activation, temporal patterns of downstream signaling and signal bias, receptor mobility and aggregation, and signal compartmentation and specificity. The available evidence suggests that adrenergic signaling may involve complex spatiotemporal patterns, which give texture to the signaling process and may contain additional biological information.

Intracellular transport of fat-soluble vitamins A and E

Vitamins are compounds that are essential for the normal growth, reproduction and functioning of the human body. Of the 13 known vitamins, vitamins A, D, E and K are lipophilic compounds and are therefore called fat-soluble vitamins. Because of their lipophilicity, fat-soluble vitamins are solubilized and transported by intracellular carrier proteins to exert their actions and to be metabolized properly. Vitamin A and its derivatives, collectively called retinoids, are solubilized by intracellular retinoid-binding proteins such as cellular retinol-binding protein (CRBP), cellular retinoic acid-binding protein (CRABP) and cellular retinal-binding protein (CRALBP). These proteins act as chaperones that regulate the metabolism, signaling and transport of retinoids. CRALBP-mediated intracellular retinoid transport is essential for vision in human. α-Tocopherol, the main form of vitamin E found in the body, is transported by α-tocopherol transfer protein (α-TTP) in hepatic cells. Defects of α-TTP cause vitamin E deficiency and neurological disorders in humans. Recently, it has been shown that the interaction of α-TTP with phosphoinositides plays a critical role in the intracellular transport of α-tocopherol and is associated with familial vitamin E deficiency. In this review, we summarize the mechanisms and biological significance of the intracellular transport of vitamins A and E.

Chemistry and biology of the initial steps in vision: the Friedenwald lecture

Visual transduction is the process in the eye whereby absorption of light in the retina is translated into electrical signals that ultimately reach the brain. The first challenge presented by visual transduction is to understand its molecular basis. We know that maintenance of vision is a continuous process requiring the activation and subsequent restoration of a vitamin A-derived chromophore through a series of chemical reactions catalyzed by enzymes in the retina and retinal pigment epithelium (RPE). Diverse biochemical approaches that identified key proteins and reactions were essential to achieve a mechanistic understanding of these visual processes. The three-dimensional arrangements of these enzymes' polypeptide chains provide invaluable insights into their mechanisms of action. A wealth of information has already been obtained by solving high-resolution crystal structures of both rhodopsin and the retinoid isomerase from pigment RPE (RPE65). Rhodopsin, which is activated by photoisomerization of its 11-cis-retinylidene chromophore, is a prototypical member of a large family of membrane-bound proteins called G protein-coupled receptors (GPCRs). RPE65 is a retinoid isomerase critical for regeneration of the chromophore. Electron microscopy (EM) and atomic force microscopy have provided insights into how certain proteins are assembled to form much larger structures such as rod photoreceptor cell outer segment membranes. A second challenge of visual transduction is to use this knowledge to devise therapeutic approaches that can prevent or reverse conditions leading to blindness. Imaging modalities like optical coherence tomography (OCT) and scanning laser ophthalmoscopy (SLO) applied to appropriate animal models as well as human retinal imaging have been employed to characterize blinding diseases, monitor their progression, and evaluate the success of therapeutic agents. Lately two-photon (2-PO) imaging, together with biochemical assays, are revealing functional aspects of vision at a new molecular level. These multidisciplinary approaches combined with suitable animal models and inbred mutant species can be especially helpful in translating provocative cell and tissue culture findings into therapeutic options for further development in animals and eventually in humans. A host of different approaches and techniques is required for substantial progress in understanding fundamental properties of the visual system.

Binding of rhodopsin and rhodopsin analogues to transducin, rhodopsin kinase and arrestin-1

AIM: To investigate the interaction of reconstituted rhodopsin, 9-cis-retinal-rhodopsin and 13-cis-retinal-rhodopsin with transducin, rhodopsin kinase and arrestin-1.

METHODS: Rod outer segments (ROS) were isolated from bovine retinas. Following bleaching of ROS membranes with hydroxylamine, rhodopsin and rhodopsin analogues were generated with the different retinal isomers and the concentration of the reconstituted pigments was calculated from their UV/visible absorption spectra. Transducin and arrestin-1 were purified to homogeneity by column chromatography, and an enriched-fraction of rhodopsin kinase was obtained by extracting freshly prepared ROS in the dark. The guanine nucleotide binding activity of transducin was determined by Millipore filtration using β,γ-imido-(³H)-guanosine 5’-triphosphate. Recognition of the reconstituted pigments by rhodopsin kinase was determined by autoradiography following incubation of ROS membranes containing the various regenerated pigments with partially purified rhodopsin kinase in the presence of (γ-³²P) ATP. Binding of arrestin-1 to the various pigments in ROS membranes was determined by a sedimentation assay analyzed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis.

RESULTS: Reconstituted rhodopsin and rhodopsin analogues containing 9-cis-retinal and 13-cis-retinal rendered an absorption spectrum showing a maximum peak at 498 nm, 486 nm and about 467 nm, respectively, in the dark; which was shifted to 380 nm, 404 nm and about 425 nm, respectively, after illumination. The percentage of reconstitution of rhodopsin and the rhodopsin analogues containing 9-cis-retinal and 13-cis-retinal was estimated to be 88%, 81% and 24%, respectively. Although only residual activation of transducin was observed in the dark when reconstituted rhodopsin and 9-cis-retinal-rhodopsin was used, the rhodopsin analogue containing the 13-cis isomer of retinal was capable of activating transducin independently of light. Moreover, only a basal amount of the reconstituted rhodopsin and 9-cis-retinal-rhodopsin was phosphorylated by rhodopsin kinase in the dark, whereas the pigment containing the 13-cis-retinal was highly phosphorylated by rhodopsin kinase even in the dark. In addition, arrestin-1 was incubated with rhodopsin, 9-cis-retinal-rhodopsin or 13-cis-retinal-rhodopsin. Experiments were performed using both phosphorylated and non-phosphorylated regenerated pigments. Basal amounts of arrestin-1 interacted with rhodopsin, 9-cis-retinal-rhodopsin and 13-cis-retinal-rhodopsin under dark and light conditions. Residual arrestin-1 was also recognized by the phosphorylated rhodopsin and phosphorylated 9-cis-retinal-rhodopsin in the dark. However, arrestin-1 was recognized by phosphorylated 13-cis-retinal-rhodopsin in the dark. As expected, all reformed pigments were capable of activating transducin and being phosphorylated by rhodopsin kinase in a light-dependent manner. Additionally, all reconstituted photolyzed and phosphorylated pigments were capable of interacting with arrestin-1.

CONCLUSION: In the dark, the rhodopsin analogue containing the 13-cis isomer of retinal appears to fold in a pseudo-active conformation that mimics the active photointermediate of rhodopsin.

Arrestin interactions with G protein-coupled receptors

G-protein-coupled receptors (GPCRs) are the primary interaction partners for arrestins. The visual arrestins, arrestin1 and arrestin4, physiologically bind to only very few receptors, i.e., rhodopsin and the color opsins, respectively. In contrast, the ubiquitously expressed nonvisual variants β-arrestin1 and 2 bind to a large number of receptors in a fairly nonspecific manner. This binding requires two triggers, agonist activation and receptor phosphorylation by a G-protein-coupled receptor kinase (GRK). These two triggers are mediated by two different regions of the arrestins, the "phosphorylation sensor" in the core of the protein and a less well-defined "activation sensor." Binding appears to occur mostly in a 1:1 stoichiometry, involving the N-terminal domain of GPCRs, but in addition a second GPCR may loosely bind to the C-terminal domain when active receptors are abundant.Arrestin binding initially uncouples GPCRs from their G-proteins. It stabilizes receptors in an active conformation and also induces a conformational change in the arrestins that involves a rotation of the two domains relative to each other plus changes in the polar core. This conformational change appears to permit the interaction with further downstream proteins. The latter interaction, demonstrated mostly for β-arrestins, triggers receptor internalization as well as a number of nonclassical signaling pathways.Open questions concern the exact stoichiometry of the interaction, possible specificity with regard to the type of agonist and of GRK involved, selective regulation of downstream signaling (=biased signaling), and the options to use these mechanisms as therapeutic targets.

Constitutively active rhodopsin and retinal disease

Rhodopsin is the light receptor in rod photoreceptor cells of the retina that initiates scotopic vision. In the dark, rhodopsin is bound to the chromophore 11-cis retinal, which locks the receptor in an inactive state. The maintenance of an inactive rhodopsin in the dark is critical for rod photoreceptor cells to remain highly sensitive. Perturbations by mutation or the absence of 11-cis retinal can cause rhodopsin to become constitutively active, which leads to the desensitization of photoreceptor cells and, in some instances, retinal degeneration. Constitutive activity can arise in rhodopsin by various mechanisms and can cause a variety of inherited retinal diseases including Leber congenital amaurosis, congenital night blindness, and retinitis pigmentosa. In this review, the molecular and structural properties of different constitutively active forms of rhodopsin are overviewed, and the possibility that constitutive activity can arise from different active-state conformations is discussed.

The Camerino symposium series (1978-2013): a privileged observatory of receptorology development

The organizers of the Camerino Receptor Symposia survey the development of receptorology. They trace the course from the first Symposium in 1978, which laid the foundation for Pirenzepine, the first selective muscarinic antagonist, to the 2010 Symposium, which highlighted the utility of functional simple domain antibodies (nanobodies) as novel G Protein-Coupled Receptor (GPCR) modulators. This 30-year period sees the acceptance of terms such as G-protein, auto- and heteroreceptors, site-directed mutagenesis, chimeric receptors, constitutive activity, inverse agonism, and orphan receptors. GPCRs are finally a reality and Langley and Ehrlich, if they returned to their laboratories, would be proud of how their intuitions have been realized.

A molecular piston mechanism of pumping protons by bacteriorhodopsin

In this review the proton-pumping mechanism proposed recently for bacteriorhodopsin [Chou, K. C. (1993) Journal of Protein Chemistry, 12: 337-350] is illustrated in terms of a phenomenological model. According to the model, theβ-ionone of the retinal chromophore in bacteriorhodopsin can be phenomenologically imagined as a molecular "piston". The photon capture by bacteriorhodopsin would "pull" it up while the spontaneous decrease in potential energy would "push" it down so that it would be up and down alternately during the photocycle process. When it is pulled up, the gate of pore is open and the water channel for the proton translocation is through; when it is pushed down, the gate of pore is closed and the water channel is shut up. Such a model not only is quite consistent with experimental observations, but also provides useful insights and a different view to elucidate the protonpumping mechanism of bacteriorhodopsin. The essence of the model might be useful in investigating the mechanism of ion-channels of other membrane proteins.

Characterisation and localisation of the opsin protein repertoire in the brain and retinas of a spider and an onychophoran

BACKGROUND

Opsins have been found in the majority of animals and their most apparent functions are related to vision and light-guided behaviour. As an increasing number of sequences have become available it has become clear that many opsin-like transcripts are expressed in tissues other than the eyes. Opsins can be divided into three main groups: rhabdomeric opsins (r-opsins), ciliary opsins (c-opsins) and group 4 opsins. In arthropods, the main focus has been on the r-opsins involved in vision. However, with increased sequencing it is becoming clear that arthropods also possess opsins of the c-type, group 4 opsins and the newly discovered arthropsins but the functions of these opsins are unknown in arthropods and data on their localisation is limited or absent.

RESULTS

We identified opsins from the spider Cupiennius salei and the onychophoran Euperipatoides kanangrensis and characterised the phylogeny and localisation of these transcripts. We recovered all known visual opsins in C. salei, and in addition found a peropsin, a c-opsin and an opsin resembling Daphnia pulex arthropsin. The peropsin was expressed in all eye types except the anterior median eyes. The arthropsin and the c-opsin were expressed in the central nervous system but not the eyes. In E. kanangrensis we found: a c-opsin; an opsin resembling D. pulex arthropsins; and an r-opsin with high sequence similarity to previously published onychophoran onychopsins. The E. kanangrensis c-opsin and onychopsin were expressed in both the eyes and the brain but the arthropsin only in the brain.

CONCLUSION

Our novel finding that opsins of both the ciliary and rhabdomeric type are present in the onychophoran and a spider suggests that these two types of opsins were present in the last common ancestor of the Onychophora and Euarthropoda. The expression of the c-opsin in the eye of an onychophoran indicates that c-opsins may originally have been involved in vision in the arthropod clade. The lack of c-opsin expression in the spider retina suggests that the role for c-opsin in vision was lost in the euarthropods. Our discovery of arthropsin in onychophorans and spiders dates the emergence of arthropsin to the common ancestor of Onychophora and Euarthropoda and their expression in the brain suggests a non-visual function.

Molecular properties of muscarinic acetylcholine receptors

Muscarinic acetylcholine receptors, which comprise five subtypes (M1-M5 receptors), are expressed in both the CNS and PNS (particularly the target organs of parasympathetic neurons). M1-M5 receptors are integral membrane proteins with seven transmembrane segments, bind with acetylcholine (ACh) in the extracellular phase, and thereafter interact with and activate GTP-binding regulatory proteins (G proteins) in the intracellular phase: M1, M3, and M5 receptors interact with Gq-type G proteins, and M2 and M4 receptors with Gi/Go-type G proteins. Activated G proteins initiate a number of intracellular signal transduction systems. Agonist-bound muscarinic receptors are phosphorylated by G protein-coupled receptor kinases, which initiate their desensitization through uncoupling from G proteins, receptor internalization, and receptor breakdown (down regulation). Recently the crystal structures of M2 and M3 receptors were determined and are expected to contribute to the development of drugs targeted to muscarinic receptors. This paper summarizes the molecular properties of muscarinic receptors with reference to the historical background and bias to studies performed in our laboratories.

Docking studies of novel pyrazinopyridoindoles class of antihistamines with the homology modelled H(1)-receptor

Histamine is an important neurotransmitter as it controls a multitude of physiological functions by activating specific receptors on target cells. It exerts its effects by binding to four different histamine receptors (H(1)-H(4)), which all belong to the large family of G protein-coupled receptors (GPCRs). Research and development of H(1) ligand has largely focused on antagonists which are used for their anti-allergy effects in the periphery. Recent understanding of the clinical importance of H(1) receptors in brain, however, suggests the pharmacotherapeutic potential of H(1) agonists in neurodegenerative and neuropsychiatric disorders. Despite the therapeutic importance of the H(1) receptor, for many years the molecular features of the H(1) receptor protein had been unknown. In view of the recently reported crystal structure of human H(1) receptor and in continuation of our work on 3D-pharmacophore on antihistamine H(1) and homology model of histamine H(1) receptor, docking studies have been carried out on some promising pyrazinopyridoindole class of antihistamine H(1), including two outliers, to validate our earlier reported models/hypotheses on H(1)-receptor, where a good explanation between estimated and observed activities has been obtained. In addition, the docking study also provided insights about the optimal activity of the outliers, for which no explanation was reported previously.

Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist

The parasympathetic limb of the autonomic nervous system regulates the activity of multiple organ systems. Muscarinic receptors are G protein coupled receptors (GPCRs) that mediate the response to acetylcholine released from parasympathetic nerves.^1–5 Their role in the unconscious regulation of organ and central nervous system function makes them potential therapeutic targets for a broad spectrum of diseases. The M₂ muscarinic acetylcholine receptor (M₂ receptor) is essential for the physiologic control of cardiovascular function through activation of G protein-coupled inwardly-rectifying potassium channels, and is of particular interest because of its extensive pharmacological characterization with both orthosteric and allosteric ligands. Here we report the structure of antagonist-bound M₂ receptor, the first human acetylcholine receptor to be characterized structurally. The antagonist QNB binds in the middle of a long aqueous channel extending approximately two-thirds through the membrane. The orthosteric binding pocket is formed by amino acids that are identical in all 5 muscarinic receptor subtypes, and shares structural homology with other functionally unrelated acetylcholine binding proteins from different species. A layer of tyrosine residues forms an aromatic cap restricting dissociation of the bound ligand. A binding site for allosteric ligands has been mapped to residues at the entrance to the binding pocket near this aromatic cap. The M₂ receptor structure provides insights into the challenges of developing subtype-selective ligands for muscarinic receptors and their propensity for allosteric regulation.

Crystallizing thinking about the beta2-adrenergic receptor

Two recently determined crystal structures of the human beta2-adrenergic receptor (beta2AR) provide a long-awaited advance in the field of G protein-coupled receptor research. The beta2AR is only the second member of this, the largest family of receptors encoded in the human genome, whose structure has been solved. It follows structures of rhodopsin that were determined previously. Here we set these developments in historical context, discuss the daunting challenges that have been overcome, and appraise what has and has not been learned.

Seven transmembrane receptors: something old, something new

Receptors for hormones, neurotransmitters, drugs, sensory stimuli and many other agents represent the gateway to cellular metabolism and activity. They regulate virtually all physiological processes in mammals. Yet as recently as 40 years ago their very existence was still in question. One class of receptors, those coupled to G proteins (also known as GPCRs or seven transmembrane receptors) comprise by far the largest group (approx. 1000), and are the most important target of clinically used drugs. Here I provide a very personal retrospective of research over the past 35 years which ultimately led to the identification, purification, reconstitution and cloning of the adrenergic receptors; the discovery of their homology with the seven transmembrane spanning visual light receptor rhodopsin and the realization that there was a large gene family of G protein coupled receptors; the elucidation of the molecular mechanisms of receptor desensitization and signalling through G protein-coupled receptor kinases and beta-arrestins; and the appreciation that the structure, signalling, and regulatory mechanisms of the receptors are all highly conserved across the large receptor superfamily.

Expansion of signal transduction by G proteins. The second 15 years or so: from 3 to 16 alpha subunits plus betagamma dimers

The first 15 years, or so, brought the realization that there existed a G protein coupled signal transduction mechanism by which hormone receptors regulate adenylyl cyclases and the light receptor rhodopsin activates visual phosphodiesterase. Three G proteins, Gs, Gi and transducin (T) had been characterized as alphabetagamma heterotrimers, and Gsalpha-GTP and Talpha-GTP had been identified as the sigaling arms of Gs and T. These discoveries were made using classical biochemical approaches, and culminated in the purification of these G proteins. The second 15 years, or so, are the subject of the present review. This time coincided with the advent of powerful recombinant DNA techniques. Combined with the classical approaches, the field expanded the repertoire of G proteins from 3 to 16, discovered the superfamily of seven transmembrane G protein coupled receptors (GPCRs) -- which is not addressed in this article -- and uncovered an amazing repertoire of effector functions regulated not only by alphaGTP complexes but also by betagamma dimers. Emphasis is placed in presenting how the field developed with the hope of conveying why many of the new findings were made.

Seven transmembrane receptors—A brief personal retrospective

Receptors have fascinated biologists for more than a century and they have fascinated me for the entirety of my own research career. The seven transmembrane receptors, also known as G protein coupled receptors, represent the largest of the several families of plasma membrane receptors, comprising more than a thousand genes and regulating virtually all known physiological processes in mammals. Moreover, they represent one of the commonest targets of currently used drugs. I have spent the entirety of my research career working on these receptors. Here I set down some personal reflections on the evolution of the field during the past 35 years, hanging the thread of the story on some of the work from my own laboratory.

Role of the Cys18–Cys274 disulfide bond and of the third extracellular loop in the constitutive activation and internalization of angiotensin II type 1 receptor

An insertion of residues in the third extracellular loop and a disulfide bond linking this loop to the N-terminal domain were identified in a structural model of a G-protein coupled receptor specific to angiotensin II (AT1 receptor), built in homology to the seven-transmembrane-helix bundle of rhodopsin. Both the insertion and the disulfide bond were located close to an extracellular locus, flanked by the second extracellular loop (EC-2), the third extracellular loop (EC-3) and the N-terminal domain of the receptor; they contained residues identified by mutagenesis studies to bind the angiotensin II N-terminal segment (residues D1 and R2). It was postulated that the insertion and the disulfide bond, also found in other receptors such as those for bradykinin, endothelin, purine and other ligands, might play a role in regulating the function of the AT1 receptor. This possibility was investigated by assaying AT1 forms devoid of the insertion and with mutations to Ser on both positions of Cys residues forming the disulfide bond. Binding and activation experiments showed that abolition of this bond led to constitutive activation, decay of agonist binding and receptor activation levels. Furthermore, the receptors thus mutated were translocated to cytosolic environments including those in the nucleus. The receptor form with full deletion of the EC-3 loop residue insertion, displayed a wild type receptor behavior.

Functionally Relevant Coupled Dynamic Profile of Bacteriorhodopsin and Lipids in Purple Membranes

The dynamics of bacteriorhodopsin (bR) and the lipid headgroups in oriented purple membranes (PMs) was determined at various temperatures and relative humidity (rh) using solid-state NMR spectroscopy. The 31P NMR spectra of the alpha- and gamma-phosphate groups in methyl phosphatidylglycerophosphate (PGP-Me), which is the major phospholipid in the PM, changed sensitively with hydration levels. Between 253 and 233 K, the signals from a fully hydrated sample became broadened similarly to those of a dry sample at 293 K. The 15N cross polarization (CP) NMR spectral intensities from [15N]Gly bR incorporated into fully hydrated PMs were suppressed in 15N CP NMR spectra at 293 K compared with those of dry membranes but gradually recovered at low temperatures or at lower hydration (75%) levels. The suppression of the NMR signals, which is due to interference with proton decoupling frequency (approximately 45 kHz), coupled with short spin-spin relaxation times (T2) indicates that the loops of bR, in particular, have motional components around this frequency. The motion of the transmembrane alpha-helices in bR was largely affected by the freezing of excess water at low temperatures. While between 253 and 233 K, where a dynamic phase transition-like change was observed in the 31P NMR spectra for the phosphate lipid headgroups, the molecular motion of the loops and the C- and N-termini slowed, suggesting lipid-loop interactions, although protein-protein interactions between stacks cannot be excluded. The results of T2 measurements of dry samples, which do not have proton pumping activity, were similar to those for fully hydrated samples below 213 K where the M-intermediates can be trapped. These results suggest that motions in the 10s micros correlation regime may be functionally important for the photocycle of bR, and protein-lipid interactions are motionally coupled in this dynamic regime.