1
|
Hong JD, Palczewski K. A short story on how chromophore is hydrolyzed from rhodopsin for recycling. Bioessays 2023; 45:e2300068. [PMID: 37454357 PMCID: PMC10614701 DOI: 10.1002/bies.202300068] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/24/2023] [Accepted: 05/30/2023] [Indexed: 07/18/2023]
Abstract
The photocycle of visual opsins is essential to maintain the light sensitivity of the retina. The early physical observations of the rhodopsin photocycle by Böll and Kühne in the 1870s inspired over a century's worth of investigations on rhodopsin biochemistry. A single photon isomerizes the Schiff-base linked 11-cis-retinylidene chromophore of rhodopsin, converting it to the all-trans agonist to elicit phototransduction through photoactivated rhodopsin (Rho*). Schiff base hydrolysis of the agonist is a key step in the photocycle, not only diminishing ongoing phototransduction but also allowing for entry and binding of fresh 11-cis chromophore to regenerate the rhodopsin pigment and maintain light sensitivity. Many challenges have been encountered in measuring the rate of this hydrolysis, but recent advancements have facilitated studies of the hydrolysis within the native membrane environment of rhodopsin. These techniques can now be applied to study hydrolysis of agonist in other opsin proteins that mediate phototransduction or chromophore turnover. In this review, we discuss the progress that has been made in characterizing the rhodopsin photocycle and the journey to characterize the hydrolysis of its all-trans-retinylidene agonist.
Collapse
Affiliation(s)
- John D. Hong
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California Irvine, Irvine, CA 92697, USA
- Department of Chemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California Irvine, Irvine, CA 92697, USA
- Department of Chemistry, University of California Irvine, Irvine, CA 92697, USA
- Department of Physiology and Biophysics, University of California Irvine, Irvine, CA 92697, USA
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA
| |
Collapse
|
2
|
Wang F, Fernandez-Gonzalez P, Ramon E, Gomez-Gutierrez P, Morillo M, Garriga P. Effect of Trace Metal Ions on the Conformational Stability of the Visual Photoreceptor Rhodopsin. Int J Mol Sci 2023; 24:11231. [PMID: 37446409 DOI: 10.3390/ijms241311231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 07/15/2023] Open
Abstract
Trace metals are essential elements that play key roles in a number of biochemical processes governing human visual physiology in health and disease. Several trace metals, such as zinc, have been shown to play important roles in the visual phototransduction process. In spite of this, there has been little research conducted on the direct effect of trace metal elements on the visual photoreceptor rhodopsin. In the current study, we have determined the effect of several metal ions, such as iron, copper, chromium, manganese, and nickel, on the conformational stability of rhodopsin. To this aim, we analyzed, by means of UV-visible and fluorescence spectroscopic methods, the effects of these trace elements on the thermal stability of dark rhodopsin, the stability of its active Metarhodopsin II conformation, and its chromophore regeneration. Our results show that copper prevented rhodopsin regeneration and slowed down the retinal release process after illumination. In turn, Fe3+, but not Fe2+, increased the thermal stability of the dark inactive conformation of rhodopsin, whereas copper ions markedly decreased it. These findings stress the important role of trace metals in retinal physiology at the photoreceptor level and may be useful for the development of novel therapeutic strategies to treat retinal disease.
Collapse
Affiliation(s)
- Feifei Wang
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya-Barcelona Tech, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| | - Pol Fernandez-Gonzalez
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya-Barcelona Tech, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| | - Eva Ramon
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya-Barcelona Tech, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| | - Patricia Gomez-Gutierrez
- Departament d'Enginyeria Química, Universitat Politècnica de Catalunya-Barcelona Tech, Edifici ETSEIB, Av. Diagonal 647, 08028 Barcelona, Catalonia, Spain
| | - Margarita Morillo
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya-Barcelona Tech, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| | - Pere Garriga
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya-Barcelona Tech, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| |
Collapse
|
3
|
Hofmann KP, Lamb TD. Rhodopsin, light-sensor of vision. Prog Retin Eye Res 2023; 93:101116. [PMID: 36273969 DOI: 10.1016/j.preteyeres.2022.101116] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/06/2022]
Abstract
The light sensor of vertebrate scotopic (low-light) vision, rhodopsin, is a G-protein-coupled receptor comprising a polypeptide chain with bound chromophore, 11-cis-retinal, that exhibits remarkable physicochemical properties. This photopigment is extremely stable in the dark, yet its chromophore isomerises upon photon absorption with 70% efficiency, enabling the activation of its G-protein, transducin, with high efficiency. Rhodopsin's photochemical and biochemical activities occur over very different time-scales: the energy of retinaldehyde's excited state is stored in <1 ps in retinal-protein interactions, but it takes milliseconds for the catalytically active state to form, and many tens of minutes for the resting state to be restored. In this review, we describe the properties of rhodopsin and its role in rod phototransduction. We first introduce rhodopsin's gross structural features, its evolution, and the basic mechanisms of its activation. We then discuss light absorption and spectral sensitivity, photoreceptor electrical responses that result from the activity of individual rhodopsin molecules, and recovery of rhodopsin and the visual system from intense bleaching exposures. We then provide a detailed examination of rhodopsin's molecular structure and function, first in its dark state, and then in the active Meta states that govern its interactions with transducin, rhodopsin kinase and arrestin. While it is clear that rhodopsin's molecular properties are exquisitely honed for phototransduction, from starlight to dawn/dusk intensity levels, our understanding of how its molecular interactions determine the properties of scotopic vision remains incomplete. We describe potential future directions of research, and outline several major problems that remain to be solved.
Collapse
Affiliation(s)
- Klaus Peter Hofmann
- Institut für Medizinische Physik und Biophysik (CC2), Charité, and, Zentrum für Biophysik und Bioinformatik, Humboldt-Unversität zu Berlin, Berlin, 10117, Germany.
| | - Trevor D Lamb
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia.
| |
Collapse
|
4
|
Ancient whale rhodopsin reconstructs dim-light vision over a major evolutionary transition: Implications for ancestral diving behavior. Proc Natl Acad Sci U S A 2022; 119:e2118145119. [PMID: 35759662 PMCID: PMC9271160 DOI: 10.1073/pnas.2118145119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Cetaceans are fully aquatic mammals that descended from terrestrial ancestors, an iconic evolutionary transition characterized by adaptations for underwater foraging via breath-hold diving. Although the evolutionary history of this specialized behavior is challenging to reconstruct, coevolving sensory systems may offer valuable clues. The dim-light visual pigment, rhodopsin, which initiates phototransduction in the rod photoreceptors of the eye, has provided insight into the visual ecology of depth in several aquatic vertebrate lineages. Here, we use ancestral sequence reconstruction and protein resurrection experiments to quantify light-activation metrics in rhodopsin pigments from ancestors bracketing the cetacean terrestrial-to-aquatic transition. By comparing multiple reconstruction methods on a broadly sampled cetartiodactyl species tree, we generated highly robust ancestral sequence estimates. Our experimental results provide direct support for a blue-shift in spectral sensitivity along the branch separating cetaceans from terrestrial relatives. This blue-shift was 14 nm, resulting in a deep-sea signature (λmax = 486 nm) similar to many mesopelagic-dwelling fish. We also discovered that the decay rates of light-activated rhodopsin increased in ancestral cetaceans, which may indicate an accelerated dark adaptation response typical of deeper-diving mammals. Because slow decay rates are thought to help sequester cytotoxic photoproducts, this surprising result could reflect an ecological trade-off between rod photoprotection and dark adaptation. Taken together, these ancestral shifts in rhodopsin function suggest that some of the first fully aquatic cetaceans could dive into the mesopelagic zone (>200 m). Moreover, our reconstructions indicate that this behavior arose before the divergence of toothed and baleen whales.
Collapse
|
5
|
Tian H, Gunnison KM, Kazmi MA, Sakmar TP, Huber T. FRET sensors reveal the retinal entry pathway in the G protein-coupled receptor rhodopsin. iScience 2022; 25:104060. [PMID: 35355518 PMCID: PMC8958324 DOI: 10.1016/j.isci.2022.104060] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 01/11/2022] [Accepted: 03/04/2022] [Indexed: 11/26/2022] Open
|
6
|
Xia Y, Cui Y, Wang A, Liu F, Chi H, Potter JHT, Williamson J, Chen X, Rossiter SJ, Liu Y. Convergent Phenotypic Evolution of Rhodopsin for Dim-Light Sensing across Deep-Diving Vertebrates. Mol Biol Evol 2021; 38:5726-5734. [PMID: 34463769 PMCID: PMC8662592 DOI: 10.1093/molbev/msab262] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Rhodopsin comprises an opsin attached to a retinal chromophore and is the only visual pigment conferring dim-light vision in vertebrates. On activation by photons, the retinal group becomes detached from the opsin, which is then inactive until it is recharged. Of all vertebrate species, those that dive face unique visual challenges, experiencing rapid decreases in light level and hunting in near darkness. Here, we combine sequence analyses with functional assays to show that the rhodopsin pigments of four divergent lineages of deep-diving vertebrates have undergone convergent increases in their retinal release rate. We compare gene sequences and detect parallel amino acids between penguins and diving mammals and perform mutagenesis to show that a single critical residue fully explains the observed increases in retinal release rate in both the emperor penguin and beaked whale. At the same time, we find that other shared sites have no significant effect on retinal release, implying that convergence does not always signify adaptive significance. We propose that accelerated retinal release confers rapid rhodopsin recharging, enabling the visual systems of diving species to adjust quickly to changing light levels as they descend through the water column. This contrasts with nocturnal species, where adaptation to darkness has been attributed to slower retinal release rates.
Collapse
Affiliation(s)
- Yu Xia
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yimeng Cui
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | | | - Fangnan Liu
- College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Hai Chi
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Joshua H T Potter
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
| | - Joseph Williamson
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
| | | | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.,Key Laboratory of Zoonosis of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| |
Collapse
|
7
|
Sheng Y, Chen L, Ren X, Jiang Z, Yau KW. Molecular determinants of response kinetics of mouse M1 intrinsically-photosensitive retinal ganglion cells. Sci Rep 2021; 11:23424. [PMID: 34873237 PMCID: PMC8648817 DOI: 10.1038/s41598-021-02832-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 11/19/2021] [Indexed: 11/28/2022] Open
Abstract
Intrinsically-photosensitive retinal ganglion cells (ipRGCs) are non-rod/non-cone retinal photoreceptors expressing the visual pigment, melanopsin, to detect ambient irradiance for various non-image-forming visual functions. The M1-subtype, amongst the best studied, mediates primarily circadian photoentrainment and pupillary light reflex. Their intrinsic light responses are more prolonged than those of rods and cones even at the single-photon level, in accordance with the typically slower time course of non-image-forming vision. The short (OPN4S) and long (OPN4L) alternatively-spliced forms of melanopsin proteins are both present in M1-ipRGCs, but their functional difference is unclear. We have examined this point by genetically removing the Opn4 gene (Opn4-/-) in mouse and re-expressing either OPN4S or OPN4L singly in Opn4-/- mice by using adeno-associated virus, but found no obvious difference in their intrinsic dim-flash responses. Previous studies have indicated that two dominant slow steps in M1-ipRGC phototransduction dictate these cells' intrinsic dim-flash-response kinetics, with time constants (τ1 and τ2) at room temperature of ~ 2 s and ~ 20 s, respectively. Here we found that melanopsin inactivation by phosphorylation or by β-arrestins may not be one of these two steps, because their genetic disruptions did not prolong the two time constants or affect the response waveform. Disruption of GAP (GTPase-Activating-Protein) activity on the effector enzyme, PLCβ4, in M1-ipRGC phototransduction to slow down G-protein deactivation also did not prolong the response decay, but caused its rising phase to become slightly sigmoidal by giving rise to a third time constant, τ3, of ~ 2 s (room temperature). This last observation suggests that GAP-mediated G-protein deactivation does partake in the flash-response termination, although normally with a time constant too short to be visible in the response waveform.
Collapse
Affiliation(s)
- Yanghui Sheng
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, 725 North Wolfe St, Baltimore, MD, 21205, USA
- Graduate Neuroscience Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Lujing Chen
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, 725 North Wolfe St, Baltimore, MD, 21205, USA
- Graduate Neuroscience Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurobiology, Harvard Medical School, 220 Longwood Ave, Boston, MA, 02115, USA
| | - Xiaozhi Ren
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, 725 North Wolfe St, Baltimore, MD, 21205, USA
- Vedere Bio II, Inc., 700 Main St, Cambridge, MA, 02139, USA
| | - Zheng Jiang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, 725 North Wolfe St, Baltimore, MD, 21205, USA
- Department of Ophthalmology, Baylor College of Medicine, 6565 Fannin St, Houston, TX, 77030, USA
| | - King-Wai Yau
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, 725 North Wolfe St, Baltimore, MD, 21205, USA.
| |
Collapse
|
8
|
Abstract
Rhodopsins are photoreceptive membrane proteins consisting of a common heptahelical transmembrane architecture that contains a retinal chromophore. Rhodopsin was first discovered in the animal retina in 1876, but a different type of rhodopsin, bacteriorhodopsin, was reported to be present in the cell membrane of an extreme halophilic archaeon, Halobacterium salinarum, 95 years later. Although these findings were made by physiological observation of pigmented tissue and cell bodies, recent progress in genomic and metagenomic analyses has revealed that there are more than 10,000 microbial rhodopsins and 9000 animal rhodopsins with large diversity and tremendous new functionality. In this Cell Science at a Glance article and accompanying poster, we provide an overview of the diversity of functions, structures, color discrimination mechanisms and optogenetic applications of these two rhodopsin families, and will also highlight the third distinctive rhodopsin family, heliorhodopsin.
Collapse
Affiliation(s)
- Takashi Nagata
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan.,PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| |
Collapse
|
9
|
Identification of small molecule allosteric modulators that act as enhancers/disrupters of rhodopsin oligomerization. J Biol Chem 2021; 297:101401. [PMID: 34774799 PMCID: PMC8665362 DOI: 10.1016/j.jbc.2021.101401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/01/2021] [Accepted: 11/04/2021] [Indexed: 11/27/2022] Open
Abstract
The elongated cilia of the outer segment of rod and cone photoreceptor cells can contain concentrations of visual pigments of up to 5 mM. The rod visual pigments, G protein–coupled receptors called rhodopsins, have a propensity to self-aggregate, a property conserved among many G protein–coupled receptors. However, the effect of rhodopsin oligomerization on G protein signaling in native cells is less clear. Here, we address this gap in knowledge by studying rod phototransduction. As the rod outer segment is known to adjust its size proportionally to overexpression or reduction of rhodopsin expression, genetic perturbation of rhodopsin cannot be used to resolve this question. Therefore, we turned to high-throughput screening of a diverse library of 50,000 small molecules and used a novel assay for the detection of rhodopsin dimerization. This screen identified nine small molecules that either disrupted or enhanced rhodopsin dimer contacts in vitro. In a subsequent cell-free binding study, we found that all nine compounds decreased intrinsic fluorescence without affecting the overall UV-visible spectrum of rhodopsin, supporting their actions as allosteric modulators. Furthermore, ex vivo electrophysiological recordings revealed that a disruptive, hit compound #7 significantly slowed down the light response kinetics of intact rods, whereas compound #1, an enhancing hit candidate, did not substantially affect the photoresponse kinetics but did cause a significant reduction in light sensitivity. This study provides a monitoring tool for future investigation of the rhodopsin signaling cascade and reports the discovery of new allosteric modulators of rhodopsin dimerization that can also alter rod photoreceptor physiology.
Collapse
|
10
|
Colozo AT, Vasudevan S, Park PSH. Retinal degeneration in mice expressing the constitutively active G90D rhodopsin mutant. Hum Mol Genet 2021; 29:881-891. [PMID: 31960909 DOI: 10.1093/hmg/ddaa008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/11/2019] [Accepted: 01/15/2020] [Indexed: 11/13/2022] Open
Abstract
Rhodopsin is the G protein-coupled receptor in rod photoreceptor cells that initiates vision upon photon capture. The light receptor is normally locked in an inactive state in the dark by the covalently bound inverse agonist 11-cis retinal. Mutations can render the receptor active even in the absence of light. This constitutive activity can desensitize rod photoreceptor cells and lead to night blindness. A G90D mutation in rhodopsin causes the receptor to be constitutively active and leads to congenital stationary night blindness, which is generally thought to be devoid of retinal degeneration. The constitutively active species responsible for the night blindness phenotype is unclear. Moreover, the classification as a stationary disease devoid of retinal degeneration is also misleading. A transgenic mouse model for congenital stationary night blindness that expresses the G90D rhodopsin mutant was examined to better understand the origin of constitutive activity and the potential for retinal degeneration. Heterozygous mice for the G90D mutation did not exhibit retinal degeneration whereas homozygous mice exhibited progressive retinal degeneration. Only a modest reversal of retinal degeneration was observed when transducin signaling was eliminated genetically, indicating that some of the retinal degeneration occurred in a transducin-independent manner. Biochemical studies on purified rhodopsin from mice indicated that multiple species can potentially contribute to the constitutive activity causing night blindness.
Collapse
Affiliation(s)
- Alejandro T Colozo
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sreelakshmi Vasudevan
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Paul S-H Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| |
Collapse
|
11
|
Pitch SG, Yao W, Szundi I, Fay J, Chen E, Shumate A, Kliger DS, Farrens DL. Functional integrity of membrane protein rhodopsin solubilized by styrene-maleic acid copolymer. Biophys J 2021; 120:3508-3515. [PMID: 34022241 DOI: 10.1016/j.bpj.2021.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/18/2021] [Accepted: 05/13/2021] [Indexed: 11/25/2022] Open
Abstract
Membrane proteins often require solubilization to study their structure or define the mechanisms underlying their function. In this study, the functional properties of the membrane protein rhodopsin in its native lipid environment were investigated after being solubilized with styrene-maleic acid (SMA) copolymer. The static absorption spectra of rhodopsin before and after the addition of SMA were recorded at room temperature to quantify the amount of membrane protein solubilized. The samples were then photobleached to analyze the functionality of rhodopsin upon solubilization. Samples with low or high SMA/rhodopsin ratios were compared to find a threshold in which the maximal amount of active rhodopsin was solubilized from membrane suspensions. Interestingly, whereas the highest SMA/rhodopsin ratios yielded the most solubilized rhodopsin, the rhodopsin produced under these conditions could not reach the active (Meta II) state upon photoactivation. The results confirm that SMA is a useful tool for membrane protein research, but SMA added in excess can interfere with the dynamics of protein activation.
Collapse
Affiliation(s)
- Stephanie G Pitch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Weekie Yao
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon
| | - Istvan Szundi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Jonathan Fay
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon
| | - Eefei Chen
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Anthony Shumate
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon
| | - David S Kliger
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - David L Farrens
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon.
| |
Collapse
|
12
|
Fanelli F, Felline A, Marigo V. Structural aspects of rod opsin and their implication in genetic diseases. Pflugers Arch 2021; 473:1339-1359. [PMID: 33728518 DOI: 10.1007/s00424-021-02546-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 02/17/2021] [Accepted: 02/22/2021] [Indexed: 01/04/2023]
Abstract
Vision in dim-light conditions is triggered by photoactivation of rhodopsin, the visual pigment of rod photoreceptor cells. Rhodopsin is made of a protein, the G protein coupled receptor (GPCR) opsin, and the chromophore 11-cis-retinal. Vertebrate rod opsin is the GPCR best characterized at the atomic level of detail. Since the release of the first crystal structure 20 years ago, a huge number of structures have been released that, in combination with valuable spectroscopic determinations, unveiled most aspects of the photobleaching process. A number of spontaneous mutations of rod opsin have been found linked to vision-impairing diseases like autosomal dominant or autosomal recessive retinitis pigmentosa (adRP or arRP, respectively) and autosomal congenital stationary night blindness (adCSNB). While adCSNB is mainly caused by constitutive activation of rod opsin, RP shows more variegate determinants affecting different aspects of rod opsin function. The vast majority of missense rod opsin mutations affects folding and trafficking and is linked to adRP, an incurable disease that awaits light on its molecular structure determinants. This review article summarizes all major structural information available on vertebrate rod opsin conformational states and the insights gained so far into the structural determinants of adCSNB and adRP linked to rod opsin mutations. Strategies to design small chaperones with therapeutic potential for selected adRP rod opsin mutants will be discussed as well.
Collapse
Affiliation(s)
- Francesca Fanelli
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125, Modena, Italy. .,Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, via Campi 287, Modena, 41125, Italy.
| | - Angelo Felline
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125, Modena, Italy
| | - Valeria Marigo
- Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, via Campi 287, Modena, 41125, Italy.,Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 287, 41125, Modena, Italy
| |
Collapse
|
13
|
Schafer CT, Shumate A, Farrens DL. Novel fluorescent GPCR biosensor detects retinal equilibrium binding to opsin and active G protein and arrestin signaling conformations. J Biol Chem 2020; 295:17486-17496. [PMID: 33453993 DOI: 10.1074/jbc.ra120.014631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/25/2020] [Indexed: 01/14/2023] Open
Abstract
Rhodopsin is a canonical class A photosensitive G protein-coupled receptor (GPCR), yet relatively few pharmaceutical agents targeting this visual receptor have been identified, in part due to the unique characteristics of its light-sensitive, covalently bound retinal ligands. Rhodopsin becomes activated when light isomerizes 11-cis-retinal into an agonist, all-trans-retinal (ATR), which enables the receptor to activate its G protein. We have previously demonstrated that, despite being covalently bound, ATR can display properties of equilibrium binding, yet how this is accomplished is unknown. Here, we describe a new approach for both identifying compounds that can activate and attenuate rhodopsin and testing the hypothesis that opsin binds retinal in equilibrium. Our method uses opsin-based fluorescent sensors, which directly report the formation of active receptor conformations by detecting the binding of G protein or arrestin fragments that have been fused onto the receptor's C terminus. We show that these biosensors can be used to monitor equilibrium binding of the agonist, ATR, as well as the noncovalent binding of β-ionone, an antagonist for G protein activation. Finally, we use these novel biosensors to observe ATR release from an activated, unlabeled receptor and its subsequent transfer to the sensor in real time. Taken together, these data support the retinal equilibrium binding hypothesis. The approach we describe should prove directly translatable to other GPCRs, providing a new tool for ligand discovery and mutant characterization.
Collapse
Affiliation(s)
- Christopher T Schafer
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon, USA
| | - Anthony Shumate
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon, USA
| | - David L Farrens
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon, USA.
| |
Collapse
|
14
|
Bocchero U, Falleroni F, Mortal S, Li Y, Cojoc D, Lamb T, Torre V. Mechanosensitivity is an essential component of phototransduction in vertebrate rods. PLoS Biol 2020; 18:e3000750. [PMID: 32667916 PMCID: PMC7384764 DOI: 10.1371/journal.pbio.3000750] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/27/2020] [Accepted: 06/26/2020] [Indexed: 12/01/2022] Open
Abstract
Photoreceptors are specialized cells devoted to the transduction of the incoming visual signals. Rods are able also to shed from their tip old disks and to synthesize at the base of the outer segment (OS) new disks. By combining electrophysiology, optical tweezers (OTs), and biochemistry, we investigate mechanosensitivity in the rods of Xenopus laevis, and we show that 1) mechanosensitive channels (MSCs), transient receptor potential canonical 1 (TRPC1), and Piezo1 are present in rod inner segments (ISs); 2) mechanical stimulation—of the order of 10 pN—applied briefly to either the OS or IS evokes calcium transients; 3) inhibition of MSCs decreases the duration of photoresponses to bright flashes; 4) bright flashes of light induce a rapid shortening of the OS; and 5) the genes encoding the TRPC family have an ancient association with the genes encoding families of protein involved in phototransduction. These results suggest that MSCs play an integral role in rods’ phototransduction. It is widely thought that sensory neurons are specialized to transduce just a single sensory modality. A combination of electrophysiology, optical tweezers, and histochemistry reveals that rod photoreceptors not only express mechanosensitive channels but display mechanosensitivity, which is crucial for phototransduction.
Collapse
Affiliation(s)
- Ulisse Bocchero
- Neurobiology Department, International School for Advanced Studies, Trieste, Italy
| | - Fabio Falleroni
- Neurobiology Department, International School for Advanced Studies, Trieste, Italy
| | - Simone Mortal
- Neurobiology Department, International School for Advanced Studies, Trieste, Italy
| | - Yunzhen Li
- Neurobiology Department, International School for Advanced Studies, Trieste, Italy
| | - Dan Cojoc
- Institute of Materials, National Research Council of Italy (CNR), Trieste, Italy
| | - Trevor Lamb
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Vincent Torre
- Neurobiology Department, International School for Advanced Studies, Trieste, Italy
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Zhejiang, China
- Center of Systems Medicine, Chinese Academy of Medical Sciences, Suzhou Institute of Systems Medicine, Suzhou Industrial Park, Suzhou, China
- * E-mail:
| |
Collapse
|
15
|
Getter T, Gulati S, Zimmerman R, Chen Y, Vinberg F, Palczewski K. Stereospecific modulation of dimeric rhodopsin. FASEB J 2019; 33:9526-9539. [PMID: 31121099 PMCID: PMC6662988 DOI: 10.1096/fj.201900443rr] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/23/2019] [Indexed: 11/11/2022]
Abstract
The classic concept that GPCRs function as monomers has been challenged by the emerging evidence of GPCR dimerization and oligomerization. Rhodopsin (Rh) is the only GPCR whose native oligomeric arrangement was revealed by atomic force microscopy demonstrating that Rh exists as a dimer. However, the role of Rh dimerization in retinal physiology is currently unknown. In this study, we identified econazole and sulconazole, two small molecules that disrupt Rh dimer contacts, by implementing a cell-based high-throughput screening assay. Racemic mixtures of identified lead compounds were separated and tested for their stereospecific binding to Rh using UV-visible spectroscopy and intrinsic fluorescence of tryptophan (Trp) 265 after illumination. By following the changes in UV-visible spectra and Trp265 fluorescence in vitro, we found that binding of R-econazole modulates the formation of Meta III and quenches the intrinsic fluorescence of Trp265. In addition, electrophysiological ex vivo recording revealed that R-econazole slows photoresponse kinetics, whereas S-econazole decreased the sensitivity of rods without effecting the kinetics. Thus, this study contributes new methodology to identify compounds that disrupt the dimerization of GPCRs in general and validates the first active compounds that disrupt the Rh dimer specifically.-Getter, T., Gulati, S., Zimmerman, R., Chen, Y., Vinberg, F., Palczewski, K. Stereospecific modulation of dimeric rhodopsin.
Collapse
Affiliation(s)
- Tamar Getter
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California–Irvine, California, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Sahil Gulati
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California–Irvine, California, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Physiology and Biophysics, University of California–Irvine, Irvine, California, USA
| | - Remy Zimmerman
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California–Irvine, California, USA
| | - Yuanyuan Chen
- Department of Ophthalmology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- McGowan Institute of Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Frans Vinberg
- Department of Ophthalmology and Visual Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Krzysztof Palczewski
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California–Irvine, California, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Physiology and Biophysics, University of California–Irvine, Irvine, California, USA
| |
Collapse
|
16
|
Gutierrez EDA, Castiglione GM, Morrow JM, Schott RK, Loureiro LO, Lim BK, Chang BSW. Functional Shifts in Bat Dim-Light Visual Pigment Are Associated with Differing Echolocation Abilities and Reveal Molecular Adaptation to Photic-Limited Environments. Mol Biol Evol 2019; 35:2422-2434. [PMID: 30010964 DOI: 10.1093/molbev/msy140] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Bats are excellent models for studying the molecular basis of sensory adaptation. In Chiroptera, a sensory trade-off has been proposed between the visual and auditory systems, though the extent of this association has yet to be fully examined. To investigate whether variation in visual performance is associated with echolocation, we experimentally assayed the dim-light visual pigment rhodopsin from bat species with differing echolocation abilities. While spectral tuning properties were similar among bats, we found that the rate of decay of their light-activated state was significantly slower in a nonecholocating bat relative to species that use distinct echolocation strategies, consistent with a sensory trade-off hypothesis. We also found that these rates of decay were remarkably slower compared with those of other mammals, likely indicating an adaptation to dim light. To examine whether functional changes in rhodopsin are associated with shifts in selection intensity upon bat Rh1 sequences, we implemented selection analyses using codon-based likelihood clade models. While no shifts in selection were identified in response to diverse echolocation abilities of bats, we detected a significant increase in the intensity of evolutionary constraint accompanying the diversification of Chiroptera. Taken together, this suggests that substitutions that modulate the stability of the light-activated rhodopsin state were likely maintained through intensified constraint after bats diversified, being finely tuned in response to novel sensory specializations. Our study demonstrates the power of combining experimental and computational approaches for investigating functional mechanisms underlying the evolution of complex sensory adaptations.
Collapse
Affiliation(s)
- Eduardo de A Gutierrez
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Gianni M Castiglione
- Department of Cell and Systems Biology, University of Toronto, ON, Canada.,Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James M Morrow
- Department of Cell and Systems Biology, University of Toronto, ON, Canada.,Centre of Forensic Sciences, Toronto, ON, Canada
| | - Ryan K Schott
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Livia O Loureiro
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Belinda S W Chang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Department of Cell and Systems Biology, University of Toronto, ON, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
17
|
Scotopic rod vision in tetrapods arose from multiple early adaptive shifts in the rate of retinal release. Proc Natl Acad Sci U S A 2019; 116:12627-12628. [PMID: 31182589 PMCID: PMC6600910 DOI: 10.1073/pnas.1900481116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The ability of vertebrates to occupy diverse niches has been linked to the spectral properties of rhodopsin, conferring rod-based vision in low-light conditions. More recent insights have come from nonspectral kinetics, including the retinal release rate of the active state of rhodopsin, a key aspect of scotopic vision that shows strong associations with light environments in diverse taxa. We examined the retinal release rates in resurrected proteins across early vertebrates and show that the earliest forms were characterized by much faster rates of retinal release than more recent ancestors. We also show that scotopic vision at the origin of tetrapods is a derived state that arose via at least 4 major shifts in retinal release rate. Our results suggest that early rhodopsin had a function intermediate to that of modern rod and cone pigments and that its well-developed adaptation to low light is a relatively recent innovation since the origin of tetrapods.
Collapse
|
18
|
Mitchell J, Balem F, Tirupula K, Man D, Dhiman HK, Yanamala N, Ollesch J, Planas-Iglesias J, Jennings BJ, Gerwert K, Iannaccone A, Klein-Seetharaman J. Comparison of the molecular properties of retinitis pigmentosa P23H and N15S amino acid replacements in rhodopsin. PLoS One 2019; 14:e0214639. [PMID: 31100078 PMCID: PMC6524802 DOI: 10.1371/journal.pone.0214639] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 03/19/2019] [Indexed: 12/16/2022] Open
Abstract
Mutations in the RHO gene encoding for the visual pigment protein, rhodopsin, are among the most common cause of autosomal dominant retinitis pigmentosa (ADRP). Previous studies of ADRP mutations in different domains of rhodopsin have indicated that changes that lead to more instability in rhodopsin structure are responsible for more severe disease in patients. Here, we further test this hypothesis by comparing side-by-side and therefore quantitatively two RHO mutations, N15S and P23H, both located in the N-terminal intradiscal domain. The in vitro biochemical properties of these two rhodopsin proteins, expressed in stably transfected tetracycline-inducible HEK293S cells, their UV-visible absorption, their Fourier transform infrared, circular dichroism and Metarhodopsin II fluorescence spectroscopy properties were characterized. As compared to the severely impaired P23H molecular function, N15S is only slightly defective in structure and stability. We propose that the molecular basis for these structural differences lies in the greater distance of the N15 residue as compared to P23 with respect to the predicted rhodopsin folding core. As described previously for WT rhodopsin, addition of the cytoplasmic allosteric modulator chlorin e6 stabilizes especially the P23H protein, suggesting that chlorin e6 may be generally beneficial in the rescue of those ADRP rhodopsin proteins whose stability is affected by amino acid replacement.
Collapse
Affiliation(s)
- James Mitchell
- Division of Biomedical Sciences, Medical School, University of Warwick, Coventry, United Kingdom
| | - Fernanda Balem
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Kalyan Tirupula
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - David Man
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Harpreet Kaur Dhiman
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Naveena Yanamala
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Julian Ollesch
- Department of Biophysics, Ruhr-University Bochum, Bochum, Germany
| | - Joan Planas-Iglesias
- Division of Biomedical Sciences, Medical School, University of Warwick, Coventry, United Kingdom
| | - Barbara J Jennings
- Retinal Degeneration & Ophthalmic Genetics Service & Lions Visual Function Diagnostic Lab, Hamilton Eye Institute, Dept. Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Klaus Gerwert
- Department of Biophysics, Ruhr-University Bochum, Bochum, Germany
| | - Alessandro Iannaccone
- Retinal Degeneration & Ophthalmic Genetics Service & Lions Visual Function Diagnostic Lab, Hamilton Eye Institute, Dept. Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Judith Klein-Seetharaman
- Division of Biomedical Sciences, Medical School, University of Warwick, Coventry, United Kingdom
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| |
Collapse
|
19
|
Ortega JT, Parmar T, Jastrzebska B. Flavonoids enhance rod opsin stability, folding, and self-association by directly binding to ligand-free opsin and modulating its conformation. J Biol Chem 2019; 294:8101-8122. [PMID: 30944172 DOI: 10.1074/jbc.ra119.007808] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/27/2019] [Indexed: 12/29/2022] Open
Abstract
Rhodopsin (Rho) is a visual G protein-coupled receptor expressed in the rod photoreceptors of the eye, where it mediates transmission of a light signal into a cell and converts this signal into a nerve impulse. More than 100 mutations in Rho are linked to various ocular impairments, including retinitis pigmentosa (RP). Accordingly, much effort has been directed toward developing ligands that target Rho and improve its folding and stability. Natural compounds may provide another viable approach to such drug discovery efforts. The dietary polyphenol compounds, ubiquitously present in fruits and vegetables, have beneficial effects in several eye diseases. However, the underlying mechanism of their activity is not fully understood. In this study, we used a combination of computational methods, biochemical and biophysical approaches, including bioluminescence resonance energy transfer, and mammalian cell expression systems to clarify the effects of four common bioactive flavonoids (quercetin, myricetin, and their mono-glycosylated forms quercetin-3-rhamnoside and myricetrin) on rod opsin stability, function, and membrane organization. We observed that by directly interacting with ligand-free opsin, flavonoids modulate its conformation, thereby causing faster entry of the retinal chromophore into its binding pocket. Moreover, flavonoids significantly increased opsin stability, most likely by introducing structural rigidity and promoting receptor self-association within the biological membranes. Of note, the binding of flavonoids to an RP-linked P23H opsin variant partially restored its normal cellular trafficking. Together, our results suggest that flavonoids could be utilized as lead compounds in the development of effective nonretinoid therapeutics for managing RP-related retinopathies.
Collapse
Affiliation(s)
- Joseph T Ortega
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Tanu Parmar
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Beata Jastrzebska
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106.
| |
Collapse
|
20
|
Mitchell J, Yanamala N, Tan YL, Gardner EE, Tirupula KC, Balem F, Sheves M, Nietlispach D, Klein‐Seetharaman J. Structural and Functional Consequences of the Weak Binding of Chlorin e6 to Bovine Rhodopsin. Photochem Photobiol 2019; 95:787-802. [DOI: 10.1111/php.13074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 12/07/2018] [Indexed: 12/14/2022]
Affiliation(s)
- James Mitchell
- Biomedical Sciences Division Warwick Medical School University of Warwick Coventry UK
| | - Naveena Yanamala
- Department of Structural Biology School of Medicine University of Pittsburgh Pittsburgh PA
| | - Yi Lei Tan
- Department of Biochemistry University of Cambridge Cambridge UK
| | - Eric E. Gardner
- Department of Structural Biology School of Medicine University of Pittsburgh Pittsburgh PA
| | - Kalyan C. Tirupula
- Department of Structural Biology School of Medicine University of Pittsburgh Pittsburgh PA
| | - Fernanda Balem
- Department of Structural Biology School of Medicine University of Pittsburgh Pittsburgh PA
| | - Mordechai Sheves
- Organic Chemistry Department Weizmann Institute of Science Rehovot Israel
| | | | - Judith Klein‐Seetharaman
- Biomedical Sciences Division Warwick Medical School University of Warwick Coventry UK
- Department of Structural Biology School of Medicine University of Pittsburgh Pittsburgh PA
| |
Collapse
|
21
|
Roushar FJ, Gruenhagen TC, Penn WD, Li B, Meiler J, Jastrzebska B, Schlebach JP. Contribution of Cotranslational Folding Defects to Membrane Protein Homeostasis. J Am Chem Soc 2018; 141:204-215. [PMID: 30537820 DOI: 10.1021/jacs.8b08243] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Membrane proteins are prone to misfolding and degradation within the cell, yet the nature of the conformational defects involved in this process remain poorly understood. The earliest stages of membrane protein folding are mediated by the Sec61 translocon, a molecular machine that facilitates the lateral partitioning of the polypeptide into the membrane. Proper membrane integration is an essential prerequisite for folding of the nascent chain. However, the marginal energetic drivers of this reaction suggest the translocon may operate with modest fidelity. In this work, we employed biophysical modeling in conjunction with quantitative biochemical measurements in order to evaluate the extent to which cotranslational folding defects influence membrane protein homeostasis. Protein engineering was employed to selectively perturb the topological energetics of human rhodopsin, and the expression and cellular trafficking of engineered variants were quantitatively compared. Our results reveal clear relationships between topological energetics and the efficiency of rhodopsin biogenesis, which appears to be limited by the propensity of a polar transmembrane domain to achieve its correct topological orientation. Though the polarity of this segment is functionally constrained, we find that its topology can be stabilized in a manner that enhances biogenesis without compromising the functional properties of rhodopsin. Furthermore, sequence alignments reveal this topological instability has been conserved throughout the course of evolution. These results suggest that topological defects significantly contribute to the inefficiency of membrane protein folding in the cell. Additionally, our findings suggest that the marginal stability of rhodopsin may represent an evolved trait.
Collapse
Affiliation(s)
- Francis J Roushar
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Timothy C Gruenhagen
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Wesley D Penn
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Bian Li
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Jens Meiler
- Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Beata Jastrzebska
- Department of Pharmacology , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Jonathan P Schlebach
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| |
Collapse
|
22
|
Castiglione GM, Chang BS. Functional trade-offs and environmental variation shaped ancient trajectories in the evolution of dim-light vision. eLife 2018; 7:35957. [PMID: 30362942 PMCID: PMC6203435 DOI: 10.7554/elife.35957] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 09/09/2018] [Indexed: 12/11/2022] Open
Abstract
Trade-offs between protein stability and activity can restrict access to evolutionary trajectories, but widespread epistasis may facilitate indirect routes to adaptation. This may be enhanced by natural environmental variation, but in multicellular organisms this process is poorly understood. We investigated a paradoxical trajectory taken during the evolution of tetrapod dim-light vision, where in the rod visual pigment rhodopsin, E122 was fixed 350 million years ago, a residue associated with increased active-state (MII) stability but greatly diminished rod photosensitivity. Here, we demonstrate that high MII stability could have likely evolved without E122, but instead, selection appears to have entrenched E122 in tetrapods via epistatic interactions with nearby coevolving sites. In fishes by contrast, selection may have exploited these epistatic effects to explore alternative trajectories, but via indirect routes with low MII stability. Our results suggest that within tetrapods, E122 and high MII stability cannot be sacrificed-not even for improvements to rod photosensitivity.
Collapse
Affiliation(s)
- Gianni M Castiglione
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Belinda Sw Chang
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada
| |
Collapse
|
23
|
Mallory DP, Gutierrez E, Pinkevitch M, Klinginsmith C, Comar WD, Roushar FJ, Schlebach JP, Smith AW, Jastrzebska B. The Retinitis Pigmentosa-Linked Mutations in Transmembrane Helix 5 of Rhodopsin Disrupt Cellular Trafficking Regardless of Oligomerization State. Biochemistry 2018; 57:5188-5201. [PMID: 30085663 DOI: 10.1021/acs.biochem.8b00403] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
G protein-coupled receptors can exist as dimers and higher-order oligomers in biological membranes. The specific oligomeric assembly of these receptors is believed to play a major role in their function, and the disruption of native oligomers has been implicated in specific human pathologies. Computational predictions and biochemical analyses suggest that two molecules of rhodopsin (Rho) associate through the interactions involving its fifth transmembrane helix (TM5). Interestingly, there are several pathogenic loss-of-function mutations within TM5 that face the lipid bilayer in a manner that could potentially influence the dimerization of Rho. Though several of these mutations are known to induce misfolding, the pathogenic defects associated with V209M and F220C Rho remain unclear. In this work, we utilized a variety of biochemical and biophysical approaches to elucidate the effects of these mutations on the dimerization, folding, trafficking, and function of Rho in relation to other pathogenic TM5 variants. Chemical cross-linking, bioluminescence energy transfer, and pulsed-interleaved excitation fluorescence cross-correlation spectroscopy experiments revealed that each of these mutants exhibits a wild type-like propensity to self-associate within the plasma membrane. However, V209M and F220C each exhibit subtle defects in cellular trafficking. Together, our results suggest that the RP pathology associated with the expression of the V209M and F220C mutants could arise from defects in folding and cellular trafficking rather than the disruption of dimerization, as has been previously proposed.
Collapse
Affiliation(s)
- D Paul Mallory
- Department of Chemistry , University of Akron , 190 Buchtel Common , Akron , Ohio 44325 , United States
| | - Elizabeth Gutierrez
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine , Case Western Reserve University , 10900 Euclid Avenue , Cleveland , Ohio 44106 , United States
| | - Margaret Pinkevitch
- Department of Chemistry , University of Akron , 190 Buchtel Common , Akron , Ohio 44325 , United States
| | - Christie Klinginsmith
- Department of Chemistry , University of Akron , 190 Buchtel Common , Akron , Ohio 44325 , United States
| | - William D Comar
- Department of Chemistry , University of Akron , 190 Buchtel Common , Akron , Ohio 44325 , United States
| | - Francis J Roushar
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , Indiana 47405-7102 , United States
| | - Jonathan P Schlebach
- Department of Chemistry , Indiana University , 800 East Kirkwood Avenue , Bloomington , Indiana 47405-7102 , United States
| | - Adam W Smith
- Department of Chemistry , University of Akron , 190 Buchtel Common , Akron , Ohio 44325 , United States
| | - Beata Jastrzebska
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine , Case Western Reserve University , 10900 Euclid Avenue , Cleveland , Ohio 44106 , United States
| |
Collapse
|
24
|
Park B, Yang H, Ha TH, Park HS, Oh SJ, Ryu YS, Cho Y, Kim HS, Oh J, Lee DK, Kim C, Lee T, Seo M, Choi J, Jhon YM, Woo DH, Lee S, Kim SH, Lee HJ, Jun SC, Song HS, Park TH, Kim JH. Artificial Rod and Cone Photoreceptors with Human-Like Spectral Sensitivities. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1706764. [PMID: 29775503 DOI: 10.1002/adma.201706764] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 03/21/2018] [Indexed: 06/08/2023]
Abstract
Photosensitive materials contain biologically engineered elements and are constructed using delicate techniques, with special attention devoted to efficiency, stability, and biocompatibility. However, to date, no photosensitive material has been developed to replace damaged visual-systems to detect light and transmit the signal to a neuron in the human body. In the current study, artificial nanovesicle-based photosensitive materials are observed to possess the characteristics of photoreceptors similar to the human eye. The materials exhibit considerably effective spectral characteristics according to each pigment. Four photoreceptors originating from the human eye with color-distinguishability are produced in human embryonic kidney (HEK)-293 cells and partially purified in the form of nanovesicles. Under various wavelengths of visible light, electrochemical measurements are performed to analyze the physiological behavior and kinetics of the photoreceptors, with graphene, performing as an electrode, playing an important role in the lipid bilayer deposition and oxygen reduction processes. Four nanovesicles with different photoreceptors, namely, rhodopsin (Rho), short-, medium-, and longwave sensitive opsin 1 (1SW, 1MW, 1LW), show remarkable color-dependent characteristics, consistent with those of natural human retina. With four different light-emitting diodes for functional verification, the photoreceptors embedded in nanovesicles show remarkably specific color sensitivity. This study demonstrates the potential applications of light-activated platforms in biological optoelectronic industries.
Collapse
Affiliation(s)
- Byeongho Park
- Korean Institute of Science and Technology, Seoul, 02792, Republic of Korea
- Department of Mechanical Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Heehong Yang
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Protein Engineering Laboratory, Recombinants Unit, MOGAM Institute for Biomedical Research, Yongin, 16924, Republic of Korea
| | - Tai Hwan Ha
- Hazards Monitoring Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34134, Republic of Korea
| | - Hyun Seo Park
- Korean Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Seung Ja Oh
- Korean Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Yong-Sang Ryu
- Korean Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Youngho Cho
- Korean Institute of Science and Technology, Seoul, 02792, Republic of Korea
- College of Science and Technology, Kookmin University, Seoul, 02707, Republic of Korea
| | - Hyo-Suk Kim
- Korean Institute of Science and Technology, Seoul, 02792, Republic of Korea
- Department of Electronics and Communications Engineering, Kwang-woon University, Seoul, 01890, Republic of Korea
| | - Juyeong Oh
- Korean Institute of Science and Technology, Seoul, 02792, Republic of Korea
- Department of Mechanical Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Dong Kyu Lee
- Korean Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Chulki Kim
- Korean Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Taikjin Lee
- Korean Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Minah Seo
- Korean Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Jaebin Choi
- Korean Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Young Min Jhon
- Korean Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Deok Ha Woo
- Korean Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Seok Lee
- Korean Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Seok Hwan Kim
- Department of Ophthalmology, Seoul National University Boramae Hospital, Seoul, 07061, Republic of Korea
| | - Hyuk-Jae Lee
- College of Science and Technology, Kookmin University, Seoul, 02707, Republic of Korea
| | - Seong Chan Jun
- Department of Mechanical Engineering, Yonsei University, Seoul, 03722, Republic of Korea
| | - Hyun Seok Song
- Korea Basic Science Institute (KBSI), Republic of Korea
- Center for Convergent Research of Emerging Virus Infection, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
- Department of Bio-Analytical Science, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Tai Hyun Park
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae Hun Kim
- Korean Institute of Science and Technology, Seoul, 02792, Republic of Korea
| |
Collapse
|
25
|
Chen Y, Chen Y, Jastrzebska B, Golczak M, Gulati S, Tang H, Seibel W, Li X, Jin H, Han Y, Gao S, Zhang J, Liu X, Heidari-Torkabadi H, Stewart PL, Harte WE, Tochtrop GP, Palczewski K. A novel small molecule chaperone of rod opsin and its potential therapy for retinal degeneration. Nat Commun 2018; 9:1976. [PMID: 29773803 PMCID: PMC5958115 DOI: 10.1038/s41467-018-04261-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 04/13/2018] [Indexed: 12/21/2022] Open
Abstract
Rhodopsin homeostasis is tightly coupled to rod photoreceptor cell survival and vision. Mutations resulting in the misfolding of rhodopsin can lead to autosomal dominant retinitis pigmentosa (adRP), a progressive retinal degeneration that currently is untreatable. Using a cell-based high-throughput screen (HTS) to identify small molecules that can stabilize the P23H-opsin mutant, which causes most cases of adRP, we identified a novel pharmacological chaperone of rod photoreceptor opsin, YC-001. As a non-retinoid molecule, YC-001 demonstrates micromolar potency and efficacy greater than 9-cis-retinal with lower cytotoxicity. YC-001 binds to bovine rod opsin with an EC50 similar to 9-cis-retinal. The chaperone activity of YC-001 is evidenced by its ability to rescue the transport of multiple rod opsin mutants in mammalian cells. YC-001 is also an inverse agonist that non-competitively antagonizes rod opsin signaling. Significantly, a single dose of YC-001 protects Abca4 -/- Rdh8 -/- mice from bright light-induced retinal degeneration, suggesting its broad therapeutic potential.
Collapse
Affiliation(s)
- Yuanyuan Chen
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.
- The McGowan Institute for Regenerative Medicine, University of Pittsburgh, 450 Technology Drive Suite 300, Pittsburgh, PA, 15219, USA.
- Department of Ophthalmology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA, 15260, USA.
| | - Yu Chen
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
- Yueyang Hospital and Clinical Research Institute of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, 200437, Shanghai, China
| | - Beata Jastrzebska
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, 1819 E. 101st Street, Cleveland, OH, 44106, USA
| | - Marcin Golczak
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, 1819 E. 101st Street, Cleveland, OH, 44106, USA
| | - Sahil Gulati
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, 1819 E. 101st Street, Cleveland, OH, 44106, USA
| | - Hong Tang
- Drug Discovery Center, University of Cincinnati, 2180 E. Galbraith Road, Cincinnati, OH, 45237, USA
| | - William Seibel
- Drug Discovery Center, University of Cincinnati, 2180 E. Galbraith Road, Cincinnati, OH, 45237, USA
| | - Xiaoyu Li
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Hui Jin
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Yong Han
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Songqi Gao
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Jianye Zhang
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Xujie Liu
- Department of Ophthalmology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA, 15260, USA
| | - Hossein Heidari-Torkabadi
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Phoebe L Stewart
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, 1819 E. 101st Street, Cleveland, OH, 44106, USA
| | - William E Harte
- Office of Translation and Innovation, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Gregory P Tochtrop
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Krzysztof Palczewski
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, 1819 E. 101st Street, Cleveland, OH, 44106, USA.
| |
Collapse
|
26
|
Behnen P, Felline A, Comitato A, Di Salvo MT, Raimondi F, Gulati S, Kahremany S, Palczewski K, Marigo V, Fanelli F. A Small Chaperone Improves Folding and Routing of Rhodopsin Mutants Linked to Inherited Blindness. iScience 2018; 4:1-19. [PMID: 30240733 PMCID: PMC6147235 DOI: 10.1016/j.isci.2018.05.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 04/06/2018] [Accepted: 04/30/2018] [Indexed: 11/24/2022] Open
Abstract
The autosomal dominant form of retinitis pigmentosa (adRP) is a blindness-causing conformational disease largely linked to mutations of rhodopsin. Molecular simulations coupled to the graph-based protein structure network (PSN) analysis and in vitro experiments were conducted to determine the effects of 33 adRP rhodopsin mutations on the structure and routing of the opsin protein. The integration of atomic and subcellular levels of analysis was accomplished by the linear correlation between indices of mutational impairment in structure network and in routing. The graph-based index of structural perturbation served also to divide the mutants in four clusters, consistent with their differences in subcellular localization and responses to 9-cis retinal. The stability core of opsin inferred from PSN analysis was targeted by virtual screening of over 300,000 anionic compounds leading to the discovery of a reversible orthosteric inhibitor of retinal binding more effective than retinal in improving routing of three adRP mutants. In silico and in vitro analyses of adRP rhodopsin mutants bridged folding and routing Structure network analysis grouped mutants amenable to treatment with small chaperones Virtual compound screening against the stability core of opsin found a small chaperone The pharmacoperone is a reversible orthosteric inhibitor of retinal binding
Collapse
Affiliation(s)
- Petra Behnen
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 287, 41125 Modena, Italy
| | - Angelo Felline
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy
| | - Antonella Comitato
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 287, 41125 Modena, Italy
| | - Maria Teresa Di Salvo
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 287, 41125 Modena, Italy
| | - Francesco Raimondi
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy
| | - Sahil Gulati
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, 1819 East 101st Street, Cleveland, OH 44106, USA
| | - Shirin Kahremany
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Krzysztof Palczewski
- Department of Pharmacology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, 1819 East 101st Street, Cleveland, OH 44106, USA
| | - Valeria Marigo
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 287, 41125 Modena, Italy; Center for Neuroscience and Neurotechnology, via Campi 287, 41125 Modena, Italy.
| | - Francesca Fanelli
- Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 103, 41125 Modena, Italy; Center for Neuroscience and Neurotechnology, via Campi 287, 41125 Modena, Italy.
| |
Collapse
|
27
|
Srinivasan S, Fernández-Sampedro MA, Morillo M, Ramon E, Jiménez-Rosés M, Cordomí A, Garriga P. Human Blue Cone Opsin Regeneration Involves Secondary Retinal Binding with Analog Specificity. Biophys J 2018; 114:1285-1294. [PMID: 29590586 PMCID: PMC5883618 DOI: 10.1016/j.bpj.2018.01.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 01/22/2018] [Accepted: 01/29/2018] [Indexed: 12/16/2022] Open
Abstract
Human color vision is mediated by the red, green, and blue cone visual pigments. Cone opsins are G-protein-coupled receptors consisting of an opsin apoprotein covalently linked to the 11-cis-retinal chromophore. All visual pigments share a common evolutionary origin, and red and green cone opsins exhibit a higher homology, whereas blue cone opsin shows more resemblance to the dim light receptor rhodopsin. Here we show that chromophore regeneration in photoactivated blue cone opsin exhibits intermediate transient conformations and a secondary retinoid binding event with slower binding kinetics. We also detected a fine-tuning of the conformational change in the photoactivated blue cone opsin binding site that alters the retinal isomer binding specificity. Furthermore, the molecular models of active and inactive blue cone opsins show specific molecular interactions in the retinal binding site that are not present in other opsins. These findings highlight the differential conformational versatility of human cone opsin pigments in the chromophore regeneration process, particularly compared to rhodopsin, and point to relevant functional, unexpected roles other than spectral tuning for the cone visual pigments.
Collapse
Affiliation(s)
| | | | | | - Eva Ramon
- Universitat Politècnica de Catalunya, Terrassa, Spain
| | - Mireia Jiménez-Rosés
- Unitat de Bioestadística Bellaterra, Laboratori de Medicina Computacional, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Arnau Cordomí
- Unitat de Bioestadística Bellaterra, Laboratori de Medicina Computacional, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Pere Garriga
- Universitat Politècnica de Catalunya, Terrassa, Spain.
| |
Collapse
|
28
|
Dungan SZ, Chang BSW. Epistatic interactions influence terrestrial-marine functional shifts in cetacean rhodopsin. Proc Biol Sci 2018; 284:rspb.2016.2743. [PMID: 28250185 DOI: 10.1098/rspb.2016.2743] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 02/03/2017] [Indexed: 12/12/2022] Open
Abstract
Like many aquatic vertebrates, whales have blue-shifting spectral tuning substitutions in the dim-light visual pigment, rhodopsin, that are thought to increase photosensitivity in underwater environments. We have discovered that known spectral tuning substitutions also have surprising epistatic effects on another function of rhodopsin, the kinetic rates associated with light-activated intermediates. By using absorbance spectroscopy and fluorescence-based retinal release assays on heterologously expressed rhodopsin, we assessed both spectral and kinetic differences between cetaceans (killer whale) and terrestrial outgroups (hippo, bovine). Mutation experiments revealed that killer whale rhodopsin is unusually resilient to pleiotropic effects on retinal release from key blue-shifting substitutions (D83N and A292S), largely due to a surprisingly specific epistatic interaction between D83N and the background residue, S299. Ancestral sequence reconstruction indicated that S299 is an ancestral residue that predates the evolution of blue-shifting substitutions at the origins of Cetacea. Based on these results, we hypothesize that intramolecular epistasis helped to conserve rhodopsin's kinetic properties while enabling blue-shifting spectral tuning substitutions as cetaceans adapted to aquatic environments. Trade-offs between different aspects of molecular function are rarely considered in protein evolution, but in cetacean and other vertebrate rhodopsins, may underlie multiple evolutionary scenarios for the selection of specific amino acid substitutions.
Collapse
Affiliation(s)
- Sarah Z Dungan
- Department Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2
| | - Belinda S W Chang
- Department Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2 .,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada M5S 3B2.,Department Cell and Systems Biology, University of Toronto, Toronto, ON, Canada M5S 3G5
| |
Collapse
|
29
|
Woods KN, Pfeffer J, Klein-Seetharaman J. Chlorophyll-Derivative Modulation of Rhodopsin Signaling Properties through Evolutionarily Conserved Interaction Pathways. Front Mol Biosci 2017; 4:85. [PMID: 29312953 PMCID: PMC5733091 DOI: 10.3389/fmolb.2017.00085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 11/28/2017] [Indexed: 01/04/2023] Open
Abstract
Retinal is the light-absorbing chromophore that is responsible for the activation of visual pigments and light-driven ion pumps. Evolutionary changes in the intermolecular interactions of the retinal with specific amino acids allow for adaptation of the spectral characteristics, referred to as spectral tuning. However, it has been proposed that a specific species of dragon fish has bypassed the adaptive evolutionary process of spectral tuning and replaced it with a single evolutionary event: photosensitization of rhodopsin by chlorophyll derivatives. Here, by using a combination of experimental measurements and computational modeling to probe retinal-receptor interactions in rhodopsin, we show how the binding of the chlorophyll derivative, chlorin-e6 (Ce6) in the intracellular domain (ICD) of the receptor allosterically excites G-protein coupled receptor class A (GPCR-A) conserved long-range correlated fluctuations that connect distant parts of the receptor. These long-range correlated motions are associated with regulating the dynamics and intermolecular interactions of specific amino acids in the retinal ligand-binding pocket that have been associated with shifts in the absorbance peak maximum (λmax) and hence, spectral sensitivity of the visual system. Moreover, the binding of Ce6 affects the overall global properties of the receptor. Specifically, we find that Ce6-induced dynamics alter the thermal stability of rhodopsin by adjusting hydrogen-bonding interactions near the receptor active-site that consequently also influences the intrinsic conformational equilibrium of the receptor. Due to the conservation of the ICD residues amongst different receptors in this class and the fact that all GPCR-A receptors share a common mechanism of activation, it is possible that the allosteric associations excited in rhodopsin with Ce6 binding are a common feature in all class A GPCRs.
Collapse
Affiliation(s)
- Kristina N. Woods
- Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians-Universität, München, Germany
- *Correspondence: Kristina N. Woods
| | - Jürgen Pfeffer
- Bavarian School of Public Policy, Technical University of Munich, München, Germany
| | | |
Collapse
|
30
|
Hauser FE, Ilves KL, Schott RK, Castiglione GM, López-Fernández H, Chang BSW. Accelerated Evolution and Functional Divergence of the Dim Light Visual Pigment Accompanies Cichlid Colonization of Central America. Mol Biol Evol 2017; 34:2650-2664. [PMID: 28957507 DOI: 10.1093/molbev/msx192] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Cichlids encompass one of the most diverse groups of fishes in South and Central America, and show extensive variation in life history, morphology, and colouration. While studies of visual system evolution in cichlids have focussed largely on the African rift lake species flocks, Neotropical cichlids offer a unique opportunity to investigate visual system evolution at broader temporal and geographic scales. South American cichlid colonization of Central America has likely promoted accelerated rates of morphological evolution in Central American lineages as they encountered reduced competition, renewed ecological opportunity, and novel aquatic habitats. To investigate whether such transitions have influenced molecular evolution of vision in Central American cichlids, we sequenced the dim-light rhodopsin gene in 101 Neotropical cichlid species, spanning the diversity of the clade. We find strong evidence for increased rates of evolution in Central American cichlid rhodopsin relative to South American lineages, and identify several sites under positive selection in rhodopsin that likely contribute to adaptation to different photic environments. We expressed a Neotropical cichlid rhodopsin protein invitro for the first time, and found that while its spectral tuning properties were characteristic of typical vertebrate rhodopsin pigments, the rate of decay of its active signalling form was much slower, consistent with dim light adaptation in other vertebrate rhodopsins. Using site-directed mutagenesis combined with spectroscopic assays, we found that a key amino acid substitution present in some Central American cichlids accelerates the rate of decay of active rhodopsin, which may mediate adaptation to clear water habitats.
Collapse
Affiliation(s)
- Frances E Hauser
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Katriina L Ilves
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
- Department of Biology, Pace University, New York, NY
| | - Ryan K Schott
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Gianni M Castiglione
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Hernán López-Fernández
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
- Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Belinda S W Chang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
31
|
Flavonoid allosteric modulation of mutated visual rhodopsin associated with retinitis pigmentosa. Sci Rep 2017; 7:11167. [PMID: 28894166 PMCID: PMC5593859 DOI: 10.1038/s41598-017-11391-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/22/2017] [Indexed: 11/08/2022] Open
Abstract
Dietary flavonoids exhibit many biologically-relevant functions and can potentially have beneficial effects in the treatment of pathological conditions. In spite of its well known antioxidant properties, scarce structural information is available on the interaction of flavonoids with membrane receptors. Advances in the structural biology of a specific class of membrane receptors, the G protein-coupled receptors, have significantly increased our understanding of drug action and paved the way for developing improved therapeutic approaches. We have analyzed the effect of the flavonoid quercetin on the conformation, stability and function of the G protein-coupled receptor rhodopsin, and the G90V mutant associated with the retinal degenerative disease retinitis pigmentosa. By using a combination of experimental and computational methods, we suggest that quercetin can act as an allosteric modulator of opsin regenerated with 9-cis-retinal and more importantly, that this binding has a positive effect on the stability and conformational properties of the G90V mutant associated with retinitis pigmentosa. These results open new possibilities to use quercetin and other flavonoids, in combination with specific retinoids like 9-cis-retinal, for the treatment of retinal degeneration associated with retinitis pigmentosa. Moreover, the use of flavonoids as allosteric modulators may also be applicable to other members of the G protein-coupled receptors superfamily.
Collapse
|
32
|
Tian H, Sakmar TP, Huber T. The Energetics of Chromophore Binding in the Visual Photoreceptor Rhodopsin. Biophys J 2017; 113:60-72. [PMID: 28700926 DOI: 10.1016/j.bpj.2017.05.036] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 05/04/2017] [Accepted: 05/25/2017] [Indexed: 01/06/2023] Open
Abstract
The visual photoreceptor rhodopsin is a prototypical G-protein-coupled receptor (GPCR) that stabilizes its inverse agonist ligand, 11-cis-retinal (11CR), by a covalent, protonated Schiff base linkage. In the visual dark adaptation, the fundamental molecular event after photobleaching of rhodopsin is the recombination reaction between its apoprotein opsin and 11CR. Here we present a detailed analysis of the kinetics and thermodynamics of this reaction, also known as the "regeneration reaction". We compared the regeneration of purified rhodopsin reconstituted into phospholipid/detergent bicelles with rhodopsin reconstituted into detergent micelles. We found that the lipid bilayer of bicelles stabilized the chromophore-free opsin over the long timescale required for the regeneration experiments, and also facilitated the ligand reuptake binding reaction. We utilized genetic code expansion and site-specific bioorthogonal labeling of rhodopsin with Alexa488 to enable, to our knowledge, a novel fluorescence resonance energy transfer-based measurement of the binding kinetics between opsin and 11CR. Based on these results, we report a complete energy diagram for the regeneration reaction of rhodopsin. We show that the dissociation reaction of rhodopsin to 11CR and opsin has a 25-pM equilibrium dissociation constant, which corresponds to only 0.3 kcal/mol stabilization compared to the noncovalent, tightly bound antagonist-GPCR complex of iodopindolol and β-adrenergic receptor. However, 11CR dissociates four orders-of-magnitude slower than iodopindolol, which corresponds to a 6-kcal/mol higher dissociation free energy barrier. We further used isothermal titration calorimetry to show that ligand binding in rhodopsin is enthalpy driven with -22 kcal/mol, which is 12 kcal/mol more stable than the antagonist-GPCR complex. Our data provide insights into the ligand-receptor binding reaction for rhodopsin in particular, and for GPCRs more broadly.
Collapse
Affiliation(s)
- He Tian
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York; Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Huddinge, Sweden.
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York.
| |
Collapse
|
33
|
Tian H, Sakmar TP, Huber T. Measurement of Slow Spontaneous Release of 11-cis-Retinal from Rhodopsin. Biophys J 2017; 112:153-161. [PMID: 28076806 DOI: 10.1016/j.bpj.2016.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 11/08/2016] [Accepted: 12/05/2016] [Indexed: 01/05/2023] Open
Abstract
The vertebrate visual photoreceptor rhodopsin (Rho) is a unique G protein-coupled receptor as it utilizes a covalently tethered inverse agonist (11-cis-retinal) as the native ligand. Previously, electrophysiological studies showed that ligand binding of 11-cis-retinal in dark-adapted Rho was essentially irreversible with a half-life estimated to be 420 years, until after thermal isomerization to all-trans-retinal, which then slowly dissociates. This long lifetime of 11-cis-retinal binding was considered to be physiologically important for minimizing background signal (dark noise) of the visual system. However, in vitro biochemical studies on the thermal stability of Rho showed that Rho decays with a half-life on the order of days. In this study, we resolve the discrepancy by measuring the chromophore exchange rate of the bound 11-cis-retinal chromophore with free 9-cis-retinal from Rho in an in vitro phospholipid/detergent bicelle system. We conclude that the thermal decay of Rho primarily proceeds through spontaneous breaking of the covalent linkage between opsin and 11-cis-retinal, which was overlooked in the electrophysiological recording. We estimate that this slow spontaneous release of 11-cis-retinal from Rho should result in 104 to 105 free opsin molecules in a dark-adapted rod cell-a number that is three orders of magnitude higher than previously expected. We also discuss the physiological implications of these findings on the basal activity of opsins and the associated dark noise in the visual system.
Collapse
Affiliation(s)
- He Tian
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY; Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Huddinge, Sweden.
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY.
| |
Collapse
|
34
|
Morrow JM, Castiglione GM, Dungan SZ, Tang PL, Bhattacharyya N, Hauser FE, Chang BSW. An experimental comparison of human and bovine rhodopsin provides insight into the molecular basis of retinal disease. FEBS Lett 2017; 591:1720-1731. [PMID: 28369862 DOI: 10.1002/1873-3468.12637] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/22/2017] [Accepted: 03/25/2017] [Indexed: 11/05/2022]
Abstract
Rhodopsin is the visual pigment that mediates dim-light vision in vertebrates and is a model system for the study of retinal disease. The majority of rhodopsin experiments are performed using bovine rhodopsin; however, recent evidence suggests that significant functional differences exist among mammalian rhodopsins. In this study, we identify differences in both thermal decay and light-activated retinal release rates between bovine and human rhodopsin and perform mutagenesis studies to highlight two clusters of substitutions that contribute to these differences. We also demonstrate that the retinitis pigmentosa-associated mutation G51A behaves differently in human rhodopsin compared to bovine rhodopsin and determine that the thermal decay rate of an ancestrally reconstructed mammalian rhodopsin displays an intermediate phenotype compared to the two extant pigments.
Collapse
Affiliation(s)
- James M Morrow
- Department of Cell and Systems Biology, University of Toronto, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Canada
| | | | - Sarah Z Dungan
- Department of Ecology and Evolutionary Biology, University of Toronto, Canada
| | - Portia L Tang
- Department of Cell and Systems Biology, University of Toronto, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Canada
| | | | - Frances E Hauser
- Department of Ecology and Evolutionary Biology, University of Toronto, Canada
| | - Belinda S W Chang
- Department of Cell and Systems Biology, University of Toronto, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Canada
| |
Collapse
|
35
|
Alexander NS, Katayama K, Sun W, Salom D, Gulati S, Zhang J, Mogi M, Palczewski K, Jastrzebska B. Complex binding pathways determine the regeneration of mammalian green cone opsin with a locked retinal analogue. J Biol Chem 2017; 292:10983-10997. [PMID: 28487362 DOI: 10.1074/jbc.m117.780478] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 05/04/2017] [Indexed: 01/09/2023] Open
Abstract
Phototransduction is initiated when the absorption of light converts the 11-cis-retinal chromophore to its all-trans configuration in both rod and cone vertebrate photoreceptors. To sustain vision, 11-cis-retinal is continuously regenerated from its all-trans conformation through a series of enzymatic steps comprising the "visual or retinoid" cycle. Abnormalities in this cycle can compromise vision because of the diminished supply of 11-cis-retinal and the accumulation of toxic, constitutively active opsin. As shown previously for rod cells, attenuation of constitutively active opsin can be achieved with the unbleachable analogue, 11-cis-6-membered ring (11-cis-6mr)-retinal, which has therapeutic effects against certain degenerative retinal diseases. However, to discern the molecular mechanisms responsible for this action, pigment regeneration with this locked retinal analogue requires delineation also in cone cells. Here, we compared the regenerative properties of rod and green cone opsins with 11-cis-6mr-retinal and demonstrated that this retinal analogue could regenerate rod pigment but not green cone pigment. Based on structural modeling suggesting that Pro-205 in green cone opsin could prevent entry and binding of 11-cis-6mr-retinal, we initially mutated this residue to Ile, the corresponding residue in rhodopsin. However, this substitution did not enable green cone opsin to regenerate with 11-cis-6mr-retinal. Interestingly, deletion of 16 N-terminal amino acids in green cone opsin partially restored the binding of 11-cis-6mr-retinal. These results and our structural modeling indicate that a more complex binding pathway determines the regeneration of mammalian green cone opsin with chromophore analogues such as 11-cis-6mr-retinal.
Collapse
Affiliation(s)
| | - Kota Katayama
- From the Department of Pharmacology, School of Medicine and
| | - Wenyu Sun
- Polgenix Inc., Cleveland, Ohio 44106, and
| | - David Salom
- From the Department of Pharmacology, School of Medicine and
| | - Sahil Gulati
- From the Department of Pharmacology, School of Medicine and
| | - Jianye Zhang
- From the Department of Pharmacology, School of Medicine and
| | - Muneto Mogi
- the Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139
| | - Krzysztof Palczewski
- From the Department of Pharmacology, School of Medicine and .,Polgenix Inc., Cleveland, Ohio 44106, and.,the Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Beata Jastrzebska
- From the Department of Pharmacology, School of Medicine and .,the Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, Ohio 44106
| |
Collapse
|
36
|
Abstract
Conformational equilibria of G-protein-coupled receptors (GPCRs) are intimately involved in intracellular signaling. Here conformational substates of the GPCR rhodopsin are investigated in micelles of dodecyl maltoside (DDM) and in phospholipid nanodiscs by monitoring the spatial positions of transmembrane helices 6 and 7 at the cytoplasmic surface using site-directed spin labeling and double electron-electron resonance spectroscopy. The photoactivated receptor in DDM is dominated by one conformation with weak pH dependence. In nanodiscs, however, an ensemble of pH-dependent conformational substates is observed, even at pH 6.0 where the MIIbH+ form defined by proton uptake and optical spectroscopic methods is reported to be the sole species present in native disk membranes. In nanodiscs, the ensemble of substates in the photoactivated receptor spontaneously decays to that characteristic of the inactive state with a lifetime of ∼16 min at 20 °C. Importantly, transducin binding to the activated receptor selects a subset of the ensemble in which multiple substates are apparently retained. The results indicate that in a native-like lipid environment rhodopsin activation is not analogous to a simple binary switch between two defined conformations, but the activated receptor is in equilibrium between multiple conformers that in principle could recognize different binding partners.
Collapse
|
37
|
Morrow JM, Lazic S, Dixon Fox M, Kuo C, Schott RK, de A Gutierrez E, Santini F, Tropepe V, Chang BSW. A second visual rhodopsin gene, rh1-2, is expressed in zebrafish photoreceptors and found in other ray-finned fishes. ACTA ACUST UNITED AC 2016; 220:294-303. [PMID: 27811293 DOI: 10.1242/jeb.145953] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 10/25/2016] [Indexed: 12/19/2022]
Abstract
Rhodopsin (rh1) is the visual pigment expressed in rod photoreceptors of vertebrates that is responsible for initiating the critical first step of dim-light vision. Rhodopsin is usually a single copy gene; however, we previously discovered a novel rhodopsin-like gene expressed in the zebrafish retina, rh1-2, which we identified as a functional photosensitive pigment that binds 11-cis retinal and activates in response to light. Here, we localized expression of rh1-2 in the zebrafish retina to a subset of peripheral photoreceptor cells, which indicates a partially overlapping expression pattern with rh1 We also expressed, purified and characterized Rh1-2, including investigation of the stability of the biologically active intermediate. Using fluorescence spectroscopy, we found the half-life of the rate of retinal release of Rh1-2 following photoactivation to be more similar to that of the visual pigment rhodopsin than to the non-visual pigment exo-rhodopsin (exorh), which releases retinal around 5 times faster. Phylogenetic and molecular evolutionary analyses show that rh1-2 has ancient origins within teleost fishes, is under similar selective pressure to rh1, and likely experienced a burst of positive selection following its duplication and divergence from rh1 These findings indicate that rh1-2 is another functional visual rhodopsin gene, which contradicts the prevailing notion that visual rhodopsin is primarily found as a single copy gene within ray-finned fishes. The reasons for retention of this duplicate gene, as well as possible functional consequences for the visual system, are discussed.
Collapse
Affiliation(s)
- James M Morrow
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada, M5S 3B2
| | - Savo Lazic
- Department of Molecular Genetics, University of Toronto, Toronto, Canada, M5S 1A8
| | - Monica Dixon Fox
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5
| | - Claire Kuo
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5
| | - Ryan K Schott
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada, M5S 3B2
| | - Eduardo de A Gutierrez
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada, M5S 3B2
| | - Francesco Santini
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Vincent Tropepe
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5.,Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Canada, M5T 3A9.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada, M5S 3B2
| | - Belinda S W Chang
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada, M5S 3G5 .,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada, M5S 3B2.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada, M5S 3B2
| |
Collapse
|
38
|
Decay of an active GPCR: Conformational dynamics govern agonist rebinding and persistence of an active, yet empty, receptor state. Proc Natl Acad Sci U S A 2016; 113:11961-11966. [PMID: 27702898 DOI: 10.1073/pnas.1606347113] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Here, we describe two insights into the role of receptor conformational dynamics during agonist release (all-trans retinal, ATR) from the visual G protein-coupled receptor (GPCR) rhodopsin. First, we show that, after light activation, ATR can continually release and rebind to any receptor remaining in an active-like conformation. As with other GPCRs, we observe that this equilibrium can be shifted by either promoting the active-like population or increasing the agonist concentration. Second, we find that during decay of the signaling state an active-like, yet empty, receptor conformation can transiently persist after retinal release, before the receptor ultimately collapses into an inactive conformation. The latter conclusion is based on time-resolved, site-directed fluorescence labeling experiments that show a small, but reproducible, lag between the retinal leaving the protein and return of transmembrane helix 6 (TM6) to the inactive conformation, as determined from tryptophan-induced quenching studies. Accelerating Schiff base hydrolysis and subsequent ATR dissociation, either by addition of hydroxylamine or introduction of mutations, further increased the time lag between ATR release and TM6 movement. These observations show that rhodopsin can bind its agonist in equilibrium like a traditional GPCR, provide evidence that an active GPCR conformation can persist even after agonist release, and raise the possibility of targeting this key photoreceptor protein by traditional pharmaceutical-based treatments.
Collapse
|
39
|
Ploier B, Caro LN, Morizumi T, Pandey K, Pearring JN, Goren MA, Finnemann SC, Graumann J, Arshavsky VY, Dittman JS, Ernst OP, Menon AK. Dimerization deficiency of enigmatic retinitis pigmentosa-linked rhodopsin mutants. Nat Commun 2016; 7:12832. [PMID: 27694816 PMCID: PMC5059438 DOI: 10.1038/ncomms12832] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 08/03/2016] [Indexed: 02/05/2023] Open
Abstract
Retinitis pigmentosa (RP) is a blinding disease often associated with mutations in rhodopsin, a light-sensing G protein-coupled receptor and phospholipid scramblase. Most RP-associated mutations affect rhodopsin's activity or transport to disc membranes. Intriguingly, some mutations produce apparently normal rhodopsins that nevertheless cause disease. Here we show that three such enigmatic mutations—F45L, V209M and F220C—yield fully functional visual pigments that bind the 11-cis retinal chromophore, activate the G protein transducin, traffic to the light-sensitive photoreceptor compartment and scramble phospholipids. However, tests of scramblase activity show that unlike wild-type rhodopsin that functionally reconstitutes into liposomes as dimers or multimers, F45L, V209M and F220C rhodopsins behave as monomers. This result was confirmed in pull-down experiments. Our data suggest that the photoreceptor pathology associated with expression of these enigmatic RP-associated pigments arises from their unexpected inability to dimerize via transmembrane helices 1 and 5. Retinitis pigmentosa is often caused by mutations that affect the activity or transport of rhodopsin, but some mutations cause disease even though an apparently functional protein is produced. Here the authors show that three such enigmatic mutants retain scramblase activity but are unable to dimerize.
Collapse
Affiliation(s)
- Birgit Ploier
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, USA
| | - Lydia N Caro
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Kalpana Pandey
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, USA
| | - Jillian N Pearring
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Michael A Goren
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, USA
| | - Silvia C Finnemann
- Department of Biological Sciences, Center for Cancer, Genetic Diseases and Gene Regulation, Fordham University, Bronx, New York 10458, USA
| | - Johannes Graumann
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, USA.,Weill Cornell Medicine-Qatar, Qatar Foundation, Education City P.O.Box 24144, Doha, State of Qatar
| | - Vadim Y Arshavsky
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina 27710, USA.,Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | - Jeremy S Dittman
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, USA
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Anant K Menon
- Department of Biochemistry, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, USA
| |
Collapse
|
40
|
Kimata N, Pope A, Sanchez-Reyes OB, Eilers M, Opefi CA, Ziliox M, Reeves PJ, Smith SO. Free backbone carbonyls mediate rhodopsin activation. Nat Struct Mol Biol 2016; 23:738-43. [PMID: 27376589 PMCID: PMC4972713 DOI: 10.1038/nsmb.3257] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 06/09/2016] [Indexed: 11/22/2022]
Abstract
Conserved prolines in the transmembrane helices of G-protein-coupled receptors (GPCRs) are often considered to function as hinges that divide the helix into two segments capable of independent motion. Depending on their potential to hydrogen-bond, the free C=O groups associated with these prolines can facilitate conformational flexibility, conformational switching or stabilization of the receptor structure. To address the role of conserved prolines in family A GPCRs through solid-state NMR spectroscopy, we focus on bovine rhodopsin, a GPCR in the visual receptor subfamily. The free backbone C=O groups on helices H5 and H7 stabilize the inactive rhodopsin structure through hydrogen-bonds to residues on adjacent helices. In response to light-induced isomerization of the retinal chromophore, hydrogen-bonding interactions involving these C=O groups are released, thus facilitating repacking of H5 and H7 onto the transmembrane core of the receptor. These results provide insights into the multiple structural and functional roles of prolines in membrane proteins.
Collapse
Affiliation(s)
- Naoki Kimata
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Andreyah Pope
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Omar B Sanchez-Reyes
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Markus Eilers
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | | | - Martine Ziliox
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Philip J Reeves
- School of Biological Sciences, University of Essex, Essex, UK
| | - Steven O Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| |
Collapse
|
41
|
Tian H, Fürstenberg A, Huber T. Labeling and Single-Molecule Methods To Monitor G Protein-Coupled Receptor Dynamics. Chem Rev 2016; 117:186-245. [DOI: 10.1021/acs.chemrev.6b00084] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- He Tian
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Alexandre Fürstenberg
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Thomas Huber
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| |
Collapse
|
42
|
Jones Brunette AM, Sinha A, David L, Farrens DL. Evidence that the Rhodopsin Kinase (GRK1) N-Terminus and the Transducin Gα C-Terminus Interact with the Same "Hydrophobic Patch" on Rhodopsin TM5. Biochemistry 2016; 55:3123-35. [PMID: 27078130 DOI: 10.1021/acs.biochem.6b00328] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Phosphorylation of G protein-coupled receptors (GPCRs) terminates their ability to couple with and activate G proteins by increasing their affinity for arrestins. Unfortunately, detailed information regarding how GPCRs interact with the kinases responsible for their phosphorylation is still limited. Here, we purified fully functional GPCR kinase 1 (GRK1) using a rapid method and used it to gain insights into how this important kinase interacts with the GPCR rhodopsin. Specifically, we find that GRK1 uses the same site on rhodopsin as the transducin (Gt) Gtα C-terminal tail and the arrestin "finger loop", a cleft formed in the cytoplasmic face of the receptor upon activation. Our studies also show GRK1 requires two conserved residues located in this cleft (L226 and V230) that have been shown to be required for Gt activation due to their direct interactions with hydrophobic residues on the Gα C-terminal tail. Our data and modeling studies are consistent with the idea that all three proteins (Gt, GRK1, and visual arrestin) bind, at least in part, in the same site on rhodopsin and interact with the receptor through a similar hydrophobic contact-driven mechanism.
Collapse
Affiliation(s)
- Amber M Jones Brunette
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University , Portland, Oregon 97239-3098, United States
| | - Abhinav Sinha
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University , Portland, Oregon 97239-3098, United States
| | - Larry David
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University , Portland, Oregon 97239-3098, United States
| | - David L Farrens
- Department of Biochemistry and Molecular Biology, Oregon Health and Science University , Portland, Oregon 97239-3098, United States
| |
Collapse
|
43
|
van Hazel I, Dungan SZ, Hauser FE, Morrow JM, Endler JA, Chang BSW. A comparative study of rhodopsin function in the great bowerbird (Ptilonorhynchus nuchalis): Spectral tuning and light-activated kinetics. Protein Sci 2016; 25:1308-18. [PMID: 26889650 DOI: 10.1002/pro.2902] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/16/2016] [Accepted: 02/16/2016] [Indexed: 12/18/2022]
Abstract
Rhodopsin is the visual pigment responsible for initiating the phototransduction cascade in vertebrate rod photoreceptors. Although well-characterized in a few model systems, comparative studies of rhodopsin function, particularly for nonmammalian vertebrates are comparatively lacking. Bowerbirds are rare among passerines in possessing a key substitution, D83N, at a site that is otherwise highly conserved among G protein-coupled receptors. While this substitution is present in some dim-light adapted vertebrates, often accompanying another unusual substitution, A292S, its functional relevance in birds is uncertain. To investigate functional effects associated with these two substitutions, we use the rhodopsin gene from the great bowerbird (Ptilonorhynchus nuchalis) as a background for site-directed mutagenesis, in vitro expression and functional characterization. We also mutated these sites in two additional rhodopsins that do not naturally possess N83, chicken and bovine, for comparison. Both sites were found to contribute to spectral blue-shifts, but had opposing effects on kinetic rates. Substitutions at site 83 were found to primarily affect the kinetics of light-activated rhodopsin, while substitutions at site 292 had a larger impact on spectral tuning. The contribution of substitutions at site 83 to spectral tuning in particular depended on genetic background, but overall, the effects of substitutions were otherwise surprisingly additive, and the magnitudes of functional shifts were roughly similar across all three genetic backgrounds. By employing a comparative approach with multiple species, our study provides new insight into the joint impact of sites 83 and 292 on rhodopsin structure-function as well as their evolutionary significance for dim-light vision across vertebrates.
Collapse
Affiliation(s)
- Ilke van Hazel
- Department of Ecology and Evolutionary Biology, University of Toronto, Canada
| | - Sarah Z Dungan
- Department of Ecology and Evolutionary Biology, University of Toronto, Canada
| | - Frances E Hauser
- Department of Ecology and Evolutionary Biology, University of Toronto, Canada
| | - James M Morrow
- Department of Cell and Systems Biology, University of Toronto, Canada
| | - John A Endler
- Centre for Integrative Ecology, Deakin University, Australia
| | - Belinda S W Chang
- Department of Ecology and Evolutionary Biology, University of Toronto, Canada.,Department of Cell and Systems Biology, University of Toronto, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Canada
| |
Collapse
|
44
|
Srinivasan S, Cordomí A, Ramon E, Garriga P. Beyond spectral tuning: human cone visual pigments adopt different transient conformations for chromophore regeneration. Cell Mol Life Sci 2016; 73:1253-63. [PMID: 26387074 PMCID: PMC11108329 DOI: 10.1007/s00018-015-2043-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 09/09/2015] [Accepted: 09/10/2015] [Indexed: 01/01/2023]
Abstract
Human red and green visual pigments are seven transmembrane receptors of cone photoreceptor cells of the retina that mediate color vision. These pigments share a very high degree of homology and have been assumed to feature analogous structural and functional properties. We report on a different regeneration mechanism among red and green cone opsins with retinal analogs using UV-Vis/fluorescence spectroscopic analyses, molecular modeling and site-directed mutagenesis. We find that photoactivated green cone opsin adopts a transient conformation which regenerates via an unprotonated Schiff base linkage with its natural chromophore, whereas red cone opsin forms a typical protonated Schiff base. The chromophore regeneration kinetics is consistent with a secondary retinal uptake by the cone pigments. Overall, our findings reveal, for the first time, structural differences in the photoactivated conformation between red and green cone pigments that may be linked to their molecular evolution, and support the proposal of secondary retinal binding to visual pigments, in addition to binding to the canonical primary site, which may serve as a regulatory mechanism of dark adaptation in the phototransduction process.
Collapse
Affiliation(s)
- Sundaramoorthy Srinivasan
- Departament d'Enginyeria Química, Centre de Biotecnologia Molecular, Universitat Politècnica de Catalunya, Rambla de Sant Nebridi 22, 08222, Terrassa, Spain
| | - Arnau Cordomí
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193, Barcelona, Spain
| | - Eva Ramon
- Departament d'Enginyeria Química, Centre de Biotecnologia Molecular, Universitat Politècnica de Catalunya, Rambla de Sant Nebridi 22, 08222, Terrassa, Spain
| | - Pere Garriga
- Departament d'Enginyeria Química, Centre de Biotecnologia Molecular, Universitat Politècnica de Catalunya, Rambla de Sant Nebridi 22, 08222, Terrassa, Spain.
| |
Collapse
|
45
|
Fernández-Sampedro MA, Invergo BM, Ramon E, Bertranpetit J, Garriga P. Functional role of positively selected amino acid substitutions in mammalian rhodopsin evolution. Sci Rep 2016; 6:21570. [PMID: 26865329 PMCID: PMC4749998 DOI: 10.1038/srep21570] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 01/27/2016] [Indexed: 12/22/2022] Open
Abstract
Visual rhodopsins are membrane proteins that function as light photoreceptors in the vertebrate retina. Specific amino acids have been positively selected in visual pigments during mammal evolution, which, as products of adaptive selection, would be at the base of important functional innovations. We have analyzed the top candidates for positive selection at the specific amino acids and the corresponding reverse changes (F13M, Q225R and A346S) in order to unravel the structural and functional consequences of these important sites in rhodopsin evolution. We have constructed, expressed and immunopurified the corresponding mutated pigments and analyzed their molecular phenotypes. We find that position 13 is very important for the folding of the receptor and also for proper protein glycosylation. Position 225 appears to be important for the function of the protein affecting the G-protein activation process, and position 346 would also regulate functionality of the receptor by enhancing G-protein activation and presumably affecting protein phosphorylation by rhodopsin kinase. Our results represent a link between the evolutionary analysis, which pinpoints the specific amino acid positions in the adaptive process, and the structural and functional analysis, closer to the phenotype, making biochemical sense of specific selected genetic sequences in rhodopsin evolution.
Collapse
Affiliation(s)
- Miguel A Fernández-Sampedro
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| | - Brandon M Invergo
- IBE - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
| | - Eva Ramon
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| | - Jaume Bertranpetit
- IBE - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
| | - Pere Garriga
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| |
Collapse
|
46
|
Bickelmann C, Morrow JM, Du J, Schott RK, van Hazel I, Lim S, Müller J, Chang BSW. The molecular origin and evolution of dim-light vision in mammals. Evolution 2015; 69:2995-3003. [PMID: 26536060 DOI: 10.1111/evo.12794] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 09/23/2015] [Accepted: 09/27/2015] [Indexed: 01/19/2023]
Abstract
The nocturnal origin of mammals is a longstanding hypothesis that is considered instrumental for the evolution of endothermy, a potential key innovation in this successful clade. This hypothesis is primarily based on indirect anatomical inference from fossils. Here, we reconstruct the evolutionary history of rhodopsin--the vertebrate visual pigment mediating the first step in phototransduction at low-light levels--via codon-based model tests for selection, combined with gene resurrection methods that allow for the study of ancient proteins. Rhodopsin coding sequences were reconstructed for three key nodes: Amniota, Mammalia, and Theria. When expressed in vitro, all sequences generated stable visual pigments with λMAX values similar to the well-studied bovine rhodopsin. Retinal release rates of mammalian and therian ancestral rhodopsins, measured via fluorescence spectroscopy, were significantly slower than those of the amniote ancestor, indicating altered molecular function possibly related to nocturnality. Positive selection along the therian branch suggests adaptive evolution in rhodopsin concurrent with therian ecological diversification events during the Mesozoic that allowed for an exploration of the environment at varying light levels.
Collapse
Affiliation(s)
- Constanze Bickelmann
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, 10115, Berlin, Germany.
| | - James M Morrow
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Jing Du
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Ryan K Schott
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Ilke van Hazel
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Steve Lim
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Johannes Müller
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, 10115, Berlin, Germany
| | - Belinda S W Chang
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada. .,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada. .,Centre for the Analysis of Genome Evolution and Function, Toronto, ON, M5S 3B2, Canada.
| |
Collapse
|
47
|
Miller LM, Gragg M, Kim TG, Park PSH. Misfolded opsin mutants display elevated β-sheet structure. FEBS Lett 2015; 589:3119-25. [PMID: 26358292 DOI: 10.1016/j.febslet.2015.08.042] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 08/31/2015] [Indexed: 01/04/2023]
Abstract
Mutations in rhodopsin can cause misfolding and aggregation of the receptor, which leads to retinitis pigmentosa, a progressive retinal degenerative disease. The structure adopted by misfolded opsin mutants and the associated cell toxicity is poorly understood. Förster resonance energy transfer (FRET) and Fourier transform infrared (FTIR) microspectroscopy were utilized to probe within cells the structures formed by G188R and P23H opsins, which are misfolding mutants that cause autosomal dominant retinitis pigmentosa. Both mutants formed aggregates in the endoplasmic reticulum and exhibited altered secondary structure with elevated β-sheet and reduced α-helical content. The newly formed β-sheet structure may facilitate the aggregation of misfolded opsin mutants. The effects observed for the mutants were unrelated to retention of opsin molecules in the endoplasmic reticulum itself.
Collapse
Affiliation(s)
- Lisa M Miller
- National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, NY 11973, USA.
| | - Megan Gragg
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Tae Gyun Kim
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Paul S-H Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA.
| |
Collapse
|
48
|
Dong X, Ramon E, Herrera-Hernández MG, Garriga P. Phospholipid Bicelles Improve the Conformational Stability of Rhodopsin Mutants Associated with Retinitis Pigmentosa. Biochemistry 2015; 54:4795-804. [PMID: 26181234 DOI: 10.1021/acs.biochem.5b00435] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Mutations in the visual photoreceptor rhodopsin are the cause of the retinal degenerative disease retinitis pigmentosa. Some naturally occurring mutations can lead to protein conformational instability. Two such mutations, N55K and G90V, in the first and second transmembrane helices of the receptor, have been associated with sector and classical retinitis pigmentosa, respectively, and showed enhanced thermal sensitivity. We have carefully analyzed the effect of phospholipid bicelles on the stability and ligand binding properties of these two mutants and compared it with those of the detergent-solubilized samples. We have used a phospholipid bilayer consisting of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) and 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC). We find that DMPC/DHPC bicelles dramatically increase the thermal stability of the rhodopsin mutants G90V and N55K. The chromophore stability and regeneration of the mutants were also increased in bicelles when compared to their behavior in a dodecyl maltoside detergent solution. The retinal release process was slowed in bicelles, and chromophore entry, after illumination, was improved for the G90V mutant but not for N55K. Furthermore, fluorescence spectroscopy measurements showed that bicelles allowed more exogenous retinal binding to the photoactivated G90V mutant than in a detergent solution. In contrast, N55K could not reposition any chromophore either in the detergent or in bicelles. The results demonstrate that DMPC/DHPC bicelles can counteract the destabilizing effect of the disease-causing mutations and can modulate the structural changes in the ensuing receptor photoactivation in a distinct specific manner for different retinitis pigmentosa mutant phenotypes.
Collapse
Affiliation(s)
- Xiaoyun Dong
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| | - Eva Ramon
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| | - María Guadalupe Herrera-Hernández
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| | - Pere Garriga
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| |
Collapse
|
49
|
Morrow JM, Chang BSW. Comparative Mutagenesis Studies of Retinal Release in Light-Activated Zebrafish Rhodopsin Using Fluorescence Spectroscopy. Biochemistry 2015; 54:4507-18. [PMID: 26098991 DOI: 10.1021/bi501377b] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Rhodopsin is the visual pigment responsible for initiating scotopic (dim-light) vision in vetebrates. Once activated by light, release of all-trans-retinal from rhodopsin involves hydrolysis of the Schiff base linkage, followed by dissociation of retinal from the protein moiety. This kinetic process has been well studied in model systems such as bovine rhodopsin, but not in rhodopsins from cold-blooded animals, where physiological temperatures can vary considerably. Here, we characterize the rate of retinal release from light-activated rhodopsin in an ectotherm, zebrafish (Danio rerio), demonstrating in a fluorescence assay that this process occurs more than twice as fast as bovine rhodopsin at similar temperatures in 0.1% dodecyl maltoside. Using site-directed mutagenesis, we found that differences in retinal release rates can be attributed to a series of variable residues lining the retinal channel in three key structural motifs: an opening in metarhodopsin II between transmembrane helix 5 (TM5) and TM6, in TM3 near E122, and in the "retinal plug" formed by extracellular loop 2 (EL2). The majority of these sites are more proximal to the β-ionone ring of retinal than the Schiff base, indicating their influence on retinal release is more likely due to steric effects during retinal dissociation, rather than alterations to Schiff base stability. An Arrhenius plot of zebrafish rhodopsin was consistent with this model, inferring that the activation energy for Schiff base hydrolysis is similar to that of bovine rhodopsin. Functional variation at key sites identified in this study is consistent with the idea that retinal release might be an adaptive property of rhodopsin in vertebrates. Our study is one of the few investigating a nonmammalian rhodopsin, which will help establish a better understanding of the molecular mechanisms contributing to vision in cold-blooded vertebrates.
Collapse
|
50
|
Origin of the low thermal isomerization rate of rhodopsin chromophore. Sci Rep 2015; 5:11081. [PMID: 26061742 PMCID: PMC4462023 DOI: 10.1038/srep11081] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 05/14/2015] [Indexed: 02/07/2023] Open
Abstract
Low dark noise is a prerequisite for rod cells, which mediate our dim-light vision. The low dark noise is achieved by the extremely stable character of the rod visual pigment, rhodopsin, which evolved from less stable cone visual pigments. We have developed a biochemical method to quickly evaluate the thermal activation rate of visual pigments. Using an isomerization locked chromophore, we confirmed that thermal isomerization of the chromophore is the sole cause of thermal activation. Interestingly, we revealed an unexpected correlation between the thermal stability of the dark state and that of the active intermediate MetaII. Furthermore, we assessed key residues in rhodopsin and cone visual pigments by mutation analysis and identified two critical residues (E122 and I189) in the retinal binding pocket which account for the extremely low thermal activation rate of rhodopsin.
Collapse
|