1
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Haggerty KN, Eshelman SC, Sexton LA, Frimpong E, Rogers LM, Agosto MA, Robichaux MA. Super-resolution mapping in rod photoreceptors identifies rhodopsin trafficking through the inner segment plasma membrane as an essential subcellular pathway. PLoS Biol 2024; 22:e3002467. [PMID: 38190419 PMCID: PMC10773939 DOI: 10.1371/journal.pbio.3002467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 12/10/2023] [Indexed: 01/10/2024] Open
Abstract
Photoreceptor cells in the vertebrate retina have a highly compartmentalized morphology for efficient phototransduction and vision. Rhodopsin, the visual pigment in rod photoreceptors, is densely packaged into the rod outer segment sensory cilium and continuously renewed through essential synthesis and trafficking pathways housed in the rod inner segment. Despite the importance of this region for rod health and maintenance, the subcellular organization of rhodopsin and its trafficking regulators in the mammalian rod inner segment remain undefined. We used super-resolution fluorescence microscopy with optimized retinal immunolabeling techniques to perform a single molecule localization analysis of rhodopsin in the inner segments of mouse rods. We found that a significant fraction of rhodopsin molecules was localized at the plasma membrane, at the surface, in an even distribution along the entire length of the inner segment, where markers of transport vesicles also colocalized. Thus, our results collectively establish a model of rhodopsin trafficking through the inner segment plasma membrane as an essential subcellular pathway in mouse rod photoreceptors.
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Affiliation(s)
- Kristen N. Haggerty
- Department of Ophthalmology & Visual Sciences and Department of Biochemistry & Molecular Medicine, West Virginia University, Morgantown, West Virginia, United States of America
| | - Shannon C. Eshelman
- Department of Ophthalmology & Visual Sciences and Department of Biochemistry & Molecular Medicine, West Virginia University, Morgantown, West Virginia, United States of America
| | - Lauren A. Sexton
- Department of Ophthalmology & Visual Sciences and Department of Biochemistry & Molecular Medicine, West Virginia University, Morgantown, West Virginia, United States of America
| | - Emmanuel Frimpong
- Department of Ophthalmology & Visual Sciences and Department of Biochemistry & Molecular Medicine, West Virginia University, Morgantown, West Virginia, United States of America
| | - Leah M. Rogers
- Department of Ophthalmology & Visual Sciences and Department of Biochemistry & Molecular Medicine, West Virginia University, Morgantown, West Virginia, United States of America
| | - Melina A. Agosto
- Retina and Optic Nerve Research Laboratory, Department of Physiology and Biophysics, and Department of Ophthalmology and Visual Sciences, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Michael A. Robichaux
- Department of Ophthalmology & Visual Sciences and Department of Biochemistry & Molecular Medicine, West Virginia University, Morgantown, West Virginia, United States of America
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2
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Abdalla Elsayed MEA, Taylor LJ, Josan AS, Fischer MD, MacLaren RE. Choroideremia: The Endpoint Endgame. Int J Mol Sci 2023; 24:14354. [PMID: 37762657 PMCID: PMC10532430 DOI: 10.3390/ijms241814354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/25/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
Choroideremia is an X-linked retinal degeneration resulting from the progressive, centripetal loss of photoreceptors and choriocapillaris, secondary to the degeneration of the retinal pigment epithelium. Affected individuals present in late childhood or early teenage years with nyctalopia and progressive peripheral visual loss. Typically, by the fourth decade, the macula and fovea also degenerate, resulting in advanced sight loss. Currently, there are no approved treatments for this condition. Gene therapy offers the most promising therapeutic modality for halting or regressing functional loss. The aims of the current review are to highlight the lessons learnt from clinical trials in choroideremia, review endpoints, and propose a future strategy for clinical trials.
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Affiliation(s)
- Maram E. A. Abdalla Elsayed
- Oxford Eye Hospital, Oxford University Hospitals National Health Service Foundation Trust, Oxford OX3 9DU, UK
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Laura J. Taylor
- Oxford Eye Hospital, Oxford University Hospitals National Health Service Foundation Trust, Oxford OX3 9DU, UK
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Amandeep S. Josan
- Oxford Eye Hospital, Oxford University Hospitals National Health Service Foundation Trust, Oxford OX3 9DU, UK
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - M. Dominik Fischer
- Oxford Eye Hospital, Oxford University Hospitals National Health Service Foundation Trust, Oxford OX3 9DU, UK
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
| | - Robert E. MacLaren
- Oxford Eye Hospital, Oxford University Hospitals National Health Service Foundation Trust, Oxford OX3 9DU, UK
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK
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3
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Skiba NP, Lewis TR, Spencer WJ, Castillo CM, Shevchenko A, Arshavsky VY. Absolute Quantification of Photoreceptor Outer Segment Proteins. J Proteome Res 2023; 22:2703-2713. [PMID: 37493966 PMCID: PMC10513726 DOI: 10.1021/acs.jproteome.3c00267] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Photoreceptor cells generate neuronal signals in response to capturing light. This process, called phototransduction, takes place in a highly specialized outer segment organelle. There are significant discrepancies in the reported amounts of many proteins supporting this process, particularly those of low abundance, which limits our understanding of their molecular organization and function. In this study, we used quantitative mass spectrometry to simultaneously determine the abundances of 20 key structural and functional proteins residing in mouse rod outer segments. We computed the absolute number of molecules of each protein residing within an individual outer segment and the molar ratio among all 20 proteins. The molar ratios of proteins comprising three well-characterized constitutive complexes in outer segments differed from the established subunit stoichiometries of these complexes by less than 7%, highlighting the exceptional precision of our quantification. Overall, this study resolves multiple existing discrepancies regarding the outer segment abundances of these proteins, thereby advancing our understanding of how the phototransduction pathway functions as a single, well-coordinated molecular ensemble.
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Affiliation(s)
- Nikolai P. Skiba
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710
| | - Tylor R. Lewis
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710
| | - William J. Spencer
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710
| | - Carson M. Castillo
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany 01307
| | - Vadim Y. Arshavsky
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710
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4
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Haggerty KN, Eshelman SC, Sexton LA, Frimpong E, Rogers LM, Agosto MA, Robichaux MA. Mapping rhodopsin trafficking in rod photoreceptors with quantitative super-resolution microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.20.537413. [PMID: 37131638 PMCID: PMC10153271 DOI: 10.1101/2023.04.20.537413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Photoreceptor cells in the vertebrate retina have a highly compartmentalized morphology for efficient long-term phototransduction. Rhodopsin, the visual pigment in rod photoreceptors, is densely packaged into the rod outer segment sensory cilium and continuously renewed through essential synthesis and trafficking pathways housed in the rod inner segment. Despite the importance of this region for rod health and maintenance, the subcellular organization of rhodopsin and its trafficking regulators in the mammalian rod inner segment remain undefined. We used super-resolution fluorescence microscopy with optimized retinal immunolabeling techniques to perform a single molecule localization analysis of rhodopsin in the inner segments of mouse rods. We found that a significant fraction of rhodopsin molecules was localized at the plasma membrane in an even distribution along the entire length of the inner segment, where markers of transport vesicles also colocalized. Thus, our results collectively establish a model of rhodopsin trafficking through the inner segment plasma membrane as an essential subcellular pathway in mouse rod photoreceptors.
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Affiliation(s)
- Kristen N. Haggerty
- Department of Ophthalmology & Visual Sciences and Department of Biochemistry & Molecular Medicine, West Virginia University, Morgantown, WV, 26506
| | - Shannon C. Eshelman
- Department of Ophthalmology & Visual Sciences and Department of Biochemistry & Molecular Medicine, West Virginia University, Morgantown, WV, 26506
| | - Lauren A. Sexton
- Department of Ophthalmology & Visual Sciences and Department of Biochemistry & Molecular Medicine, West Virginia University, Morgantown, WV, 26506
| | - Emmanuel Frimpong
- Department of Ophthalmology & Visual Sciences and Department of Biochemistry & Molecular Medicine, West Virginia University, Morgantown, WV, 26506
| | - Leah M. Rogers
- Department of Ophthalmology & Visual Sciences and Department of Biochemistry & Molecular Medicine, West Virginia University, Morgantown, WV, 26506
| | - Melina A. Agosto
- Retina and Optic Nerve Research Laboratory, Department of Physiology and Biophysics, and Department of Ophthalmology and Visual Sciences, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Michael A. Robichaux
- Department of Ophthalmology & Visual Sciences and Department of Biochemistry & Molecular Medicine, West Virginia University, Morgantown, WV, 26506
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5
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Frederick CE, Zenisek D. Ribbon Synapses and Retinal Disease: Review. Int J Mol Sci 2023; 24:5090. [PMID: 36982165 PMCID: PMC10049380 DOI: 10.3390/ijms24065090] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/30/2023] Open
Abstract
Synaptic ribbons are presynaptic protein complexes that are believed to be important for the transmission of sensory information in the visual system. Ribbons are selectively associated with those synapses where graded changes in membrane potential drive continuous neurotransmitter release. Defective synaptic transmission can arise as a result of the mutagenesis of a single ribbon component. Visual diseases that stem from malfunctions in the presynaptic molecular machinery of ribbon synapses in the retina are rare. In this review, we provide an overview of synaptopathies that give rise to retinal malfunction and our present understanding of the mechanisms that underlie their pathogenesis and discuss muscular dystrophies that exhibit ribbon synapse involvement in the pathology.
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Affiliation(s)
| | - David Zenisek
- Department of Molecular and Cellular Physiology, Yale University School of Medicine, 333 Cedar Street, P.O. Box 208026, New Haven, CT 06510, USA
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6
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Gulati S, Palczewski K. Structural view of G protein-coupled receptor signaling in the retinal rod outer segment. Trends Biochem Sci 2023; 48:172-186. [PMID: 36163145 PMCID: PMC9868064 DOI: 10.1016/j.tibs.2022.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 01/26/2023]
Abstract
Visual phototransduction is the most extensively studied G protein-coupled receptor (GPCR) signaling pathway because of its quantifiable stimulus, non-redundancy of genes, and immense importance in vision. We summarize recent discoveries that have advanced our understanding of rod outer segment (ROS) morphology and the pathological basis of retinal diseases. We have combined recently published cryo-electron tomography (cryo-ET) data on the ROS with structural knowledge on individual proteins to define the precise spatial limitations under which phototransduction occurs. Although hypothetical, the reconstruction of the rod phototransduction system highlights the potential roles of phosphodiesterase 6 (PDE6) and guanylate cyclases (GCs) in maintaining the spacing between ROS discs, suggesting a plausible mechanism by which intrinsic optical signals are generated in the retina.
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Affiliation(s)
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute and the Department of Ophthalmology, Center for Translational Vision Research, Department of Physiology and Biophysics, Department of Chemistry, Molecular Biology, and Biochemistry, University of California Irvine, 850 Health Sciences Road, Irvine, CA 92697-4375, USA.
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7
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Skiba NP, Lewis TR, Spencer WJ, Castillo CM, Shevchenko A, Arshavsky VY. Absolute quantification of photoreceptor outer segment proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.19.524794. [PMID: 36711880 PMCID: PMC9882265 DOI: 10.1101/2023.01.19.524794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Photoreceptor cells generate neuronal signals in response to capturing light. This process, called phototransduction, takes place in a highly specialized outer segment organelle. There are significant discrepancies in the reported amounts of many proteins supporting this process, particularly those of low abundance, which limits our understanding of their molecular organization and function. In this study, we used quantitative mass spectrometry to simultaneously measure the outer segment content of twenty key structural and functional proteins. We determined the molar ratio amongst all twenty proteins as well as the number of molecules of each protein residing within an outer segment. To assess the precision of this quantification, we took advantage of the fact that seven of these proteins exist within three constitutive complexes of well-established subunit stoichiometries. Remarkably, our measurements differed from these stoichiometries by less than 7%, highlighting the exceptional precision of our quantification. This allowed us to resolve the existing discrepancies regarding the outer segment abundances of these proteins, thereby advancing our understanding of how the phototransduction pathway functions as a single, well-coordinated molecular ensemble.
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8
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Galvanetto N, Ye Z, Marchesi A, Mortal S, Maity S, Laio A, Torre VA. Unfolding and identification of membrane proteins in situ. eLife 2022; 11:77427. [PMID: 36094473 PMCID: PMC9531951 DOI: 10.7554/elife.77427] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Single-molecule force spectroscopy (SMFS) uses the cantilever tip of an AFM to apply a force able to unfold a single protein. The obtained force-distance curve encodes the unfolding pathway, and from its analysis it is possible to characterize the folded domains. SMFS has been mostly used to study the unfolding of purified proteins, in solution or reconstituted in a lipid bilayer. Here, we describe a pipeline for analyzing membrane proteins based on SMFS, that involves the isolation of the plasma membrane of single cells and the harvesting of force-distance curves directly from it. We characterized and identified the embedded membrane proteins combining, within a Bayesian framework, the information of the shape of the obtained curves, with the information from Mass Spectrometry and proteomic databases. The pipeline was tested with purified/reconstituted proteins and applied to five cell types where we classified the unfolding of their most abundant membrane proteins. We validated our pipeline by overexpressing 4 constructs, and this allowed us to gather structural insights of the identified proteins, revealing variable elements in the loop regions. Our results set the basis for the investigation of the unfolding of membrane proteins in situ, and for performing proteomics from a membrane fragment.
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Affiliation(s)
| | - Zhongjie Ye
- International School for Advanced Studies, Trieste, Italy
| | - Arin Marchesi
- Nano Life Science Institute, Kanazawa Medical University, Kanazawa, Japan
| | - Simone Mortal
- International School for Advanced Studies, Trieste, Italy
| | - Sourav Maity
- Moleculaire Biofysica, University of Groningen, Groningen, Netherlands
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9
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Verra DM, Spinnhirny P, Sandu C, Grégoire S, Acar N, Berdeaux O, Brétillon L, Sparrow JR, Hicks D. Intrinsic differences in rod and cone membrane composition: implications for cone degeneration. Graefes Arch Clin Exp Ophthalmol 2022; 260:3131-3148. [PMID: 35524799 DOI: 10.1007/s00417-022-05684-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 11/04/2022] Open
Abstract
PURPOSE In many retinal pathological conditions, rod and cone degeneration differs. For example, the early-onset maculopathy Stargardts disease type 1 (STGD1) is typified by loss of cones while rods are often less affected. We wanted to examine whether there exist intrinsic membrane differences between rods and cones that might explain such features. METHODS Abca4 mRNA and protein levels were quantified in rod- and cone-enriched samples from wild-type and Nrl-/- mice retinas; rod- and cone-enriched outer segments (ROS and COS respectively) were prepared from pig retinas, and total lipids were analyzed by flame ionization, chromatography, and tandem mass spectrometry. Immunohistochemical staining of cone-rich rodent Arvicanthis ansorgei retinas was conducted, and ultra-high performance liquid chromatography of lipid species in porcine ROS and COS was performed. RESULTS Abca4 mRNA and Abca4 protein content was significantly higher (50-300%) in cone compared to rod-enriched samples. ROS and COS displayed dramatic differences in several lipids, including very long chain poly-unsaturated fatty acids (VLC-PUFAs), especially docosahexaenoic acid (DHA, 22:6n-3): ROS 20.6% DHA, COS 3.3% (p < 0.001). VLC-PUFAs (> 50 total carbons) were virtually absent from COS. COS were impoverished (> 6× less) in phosphatidylethanolamine compared to ROS. ELOVL4 ("ELOngation of Very Long chain fatty acids 4") antibody labelled Arvicanthis cones only very weakly compared to rods. Finally, there were large amounts (905 a.u.) of the bisretinoid A2PE in ROS, whereas it was much lower (121 a.u., ~ 7.5-fold less) in COS fractions. In contrast, COS contained fivefold higher amounts of all-trans-retinal dimer (115 a.u. compared to 22 a.u. in rods). CONCLUSIONS Compared to rods, cones expressed higher levels of Abca4 mRNA and Abca4 protein, were highly impoverished in PUFA (especially DHA) and phosphatidylethanolamine, and contained significant amounts of all-trans-retinal dimer. Based on these and other data, we propose that in contrast to rods, cones are preferentially vulnerable to stress and may die through direct cellular toxicity in pathologies such as STGD1.
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Affiliation(s)
- Daniela M Verra
- Département de Neurobiologie des Rythmes, Institut des Neurosciences Cellulaires et Intégratives, CNRS UPR 3212, 8 Allée Général Rouvillois, 67000, Strasbourg Cedex, France
| | - Perrine Spinnhirny
- Département de Neurobiologie des Rythmes, Institut des Neurosciences Cellulaires et Intégratives, CNRS UPR 3212, 8 Allée Général Rouvillois, 67000, Strasbourg Cedex, France
| | - Cristina Sandu
- Département de Neurobiologie des Rythmes, Institut des Neurosciences Cellulaires et Intégratives, CNRS UPR 3212, 8 Allée Général Rouvillois, 67000, Strasbourg Cedex, France
| | - Stéphane Grégoire
- UMR 1324 Centre des Sciences du Goût et de l'Alimentation, Eye and Nutrition Research Group, INRA, Dijon, France.,UMR 6265 Centre des Sciences du Goût et de l'Alimentation, CNRS, Dijon, France.,Centre des Sciences du Goût et de l'Alimentation, Université de Bourgogne, Dijon, France
| | - Niyazi Acar
- UMR 1324 Centre des Sciences du Goût et de l'Alimentation, Eye and Nutrition Research Group, INRA, Dijon, France.,UMR 6265 Centre des Sciences du Goût et de l'Alimentation, CNRS, Dijon, France.,Centre des Sciences du Goût et de l'Alimentation, Université de Bourgogne, Dijon, France
| | - Olivier Berdeaux
- UMR 1324 Centre des Sciences du Goût et de l'Alimentation, Eye and Nutrition Research Group, INRA, Dijon, France.,UMR 6265 Centre des Sciences du Goût et de l'Alimentation, CNRS, Dijon, France.,Centre des Sciences du Goût et de l'Alimentation, Université de Bourgogne, Dijon, France
| | - Lionel Brétillon
- UMR 1324 Centre des Sciences du Goût et de l'Alimentation, Eye and Nutrition Research Group, INRA, Dijon, France.,UMR 6265 Centre des Sciences du Goût et de l'Alimentation, CNRS, Dijon, France.,Centre des Sciences du Goût et de l'Alimentation, Université de Bourgogne, Dijon, France
| | - Janet R Sparrow
- Departments of Ophthalmology, and Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - David Hicks
- Département de Neurobiologie des Rythmes, Institut des Neurosciences Cellulaires et Intégratives, CNRS UPR 3212, 8 Allée Général Rouvillois, 67000, Strasbourg Cedex, France.
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10
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Molday RS, Garces FA, Scortecci JF, Molday LL. Structure and function of ABCA4 and its role in the visual cycle and Stargardt macular degeneration. Prog Retin Eye Res 2021; 89:101036. [PMID: 34954332 DOI: 10.1016/j.preteyeres.2021.101036] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/07/2021] [Accepted: 12/13/2021] [Indexed: 12/17/2022]
Abstract
ABCA4 is a member of the superfamily of ATP-binding cassette (ABC) transporters that is preferentially localized along the rim region of rod and cone photoreceptor outer segment disc membranes. It uses the energy from ATP binding and hydrolysis to transport N-retinylidene-phosphatidylethanolamine (N-Ret-PE), the Schiff base adduct of retinal and phosphatidylethanolamine, from the lumen to the cytoplasmic leaflet of disc membranes. This ensures that all-trans-retinal and excess 11-cis-retinal are efficiently cleared from photoreceptor cells thereby preventing the accumulation of toxic retinoid compounds. Loss-of-function mutations in the gene encoding ABCA4 cause autosomal recessive Stargardt macular degeneration, also known as Stargardt disease (STGD1), and related autosomal recessive retinopathies characterized by impaired central vision and an accumulation of lipofuscin and bis-retinoid compounds. High resolution structures of ABCA4 in its substrate and nucleotide free state and containing bound N-Ret-PE or ATP have been determined by cryo-electron microscopy providing insight into the molecular architecture of ABCA4 and mechanisms underlying substrate recognition and conformational changes induced by ATP binding. The expression and functional characterization of a large number of disease-causing missense ABCA4 variants have been determined. These studies have shed light into the molecular mechanisms underlying Stargardt disease and a classification that reliably predicts the effect of a specific missense mutation on the severity of the disease. They also provide a framework for developing rational therapeutic treatments for ABCA4-associated diseases.
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Affiliation(s)
- Robert S Molday
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, B.C., Canada; Department of Ophthalmology & Visual Sciences, University of British Columbia, Vancouver, B.C., Canada.
| | - Fabian A Garces
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, B.C., Canada
| | | | - Laurie L Molday
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, B.C., Canada
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11
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Pöge M, Mahamid J, Imanishi SS, Plitzko JM, Palczewski K, Baumeister W. Determinants shaping the nanoscale architecture of the mouse rod outer segment. eLife 2021; 10:e72817. [PMID: 34931611 PMCID: PMC8758146 DOI: 10.7554/elife.72817] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/09/2021] [Indexed: 12/02/2022] Open
Abstract
The unique membrane organization of the rod outer segment (ROS), the specialized sensory cilium of rod photoreceptor cells, provides the foundation for phototransduction, the initial step in vision. ROS architecture is characterized by a stack of identically shaped and tightly packed membrane disks loaded with the visual receptor rhodopsin. A wide range of genetic aberrations have been reported to compromise ROS ultrastructure, impairing photoreceptor viability and function. Yet, the structural basis giving rise to the remarkably precise arrangement of ROS membrane stacks and the molecular mechanisms underlying genetically inherited diseases remain elusive. Here, cryo-electron tomography (cryo-ET) performed on native ROS at molecular resolution provides insights into key structural determinants of ROS membrane architecture. Our data confirm the existence of two previously observed molecular connectors/spacers which likely contribute to the nanometer-scale precise stacking of the ROS disks. We further provide evidence that the extreme radius of curvature at the disk rims is enforced by a continuous supramolecular assembly composed of peripherin-2 (PRPH2) and rod outer segment membrane protein 1 (ROM1) oligomers. We suggest that together these molecular assemblies constitute the structural basis of the highly specialized ROS functional architecture. Our Cryo-ET data provide novel quantitative and structural information on the molecular architecture in ROS and substantiate previous results on proposed mechanisms underlying pathologies of certain PRPH2 mutations leading to blindness.
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Affiliation(s)
- Matthias Pöge
- Max Planck Institute of Biochemistry, Department of Molecular Structural BiologyMartinsriedGermany
| | - Julia Mahamid
- Max Planck Institute of Biochemistry, Department of Molecular Structural BiologyMartinsriedGermany
| | - Sanae S Imanishi
- Eugene and Marilyn Glick Eye Institute and the Department of Ophthalmology, Indiana University School of MedicineyIndianapolisUnited States
| | - Jürgen M Plitzko
- Max Planck Institute of Biochemistry, Department of Molecular Structural BiologyMartinsriedGermany
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute and the Department of Ophthalmology, Center for Translational Vision Research, Department of Physiology & Biophysics, Department of Chemistry, Department of Molecular Biology and BiochemistryIrvineUnited States
| | - Wolfgang Baumeister
- Max Planck Institute of Biochemistry, Department of Molecular Structural BiologyMartinsriedGermany
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12
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Sander CL, Sears AE, Pinto AF, Choi EH, Kahremany S, Gao F, Salom D, Jin H, Pardon E, Suh S, Dong Z, Steyaert J, Saghatelian A, Skowronska-Krawczyk D, Kiser PD, Palczewski K. Nano-scale resolution of native retinal rod disk membranes reveals differences in lipid composition. J Cell Biol 2021; 220:e202101063. [PMID: 34132745 PMCID: PMC8240855 DOI: 10.1083/jcb.202101063] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/26/2021] [Accepted: 05/18/2021] [Indexed: 02/07/2023] Open
Abstract
Photoreceptors rely on distinct membrane compartments to support their specialized function. Unlike protein localization, identification of critical differences in membrane content has not yet been expanded to lipids, due to the difficulty of isolating domain-specific samples. We have overcome this by using SMA to coimmunopurify membrane proteins and their native lipids from two regions of photoreceptor ROS disks. Each sample's copurified lipids were subjected to untargeted lipidomic and fatty acid analysis. Extensive differences between center (rhodopsin) and rim (ABCA4 and PRPH2/ROM1) samples included a lower PC to PE ratio and increased LC- and VLC-PUFAs in the center relative to the rim region, which was enriched in shorter, saturated FAs. The comparatively few differences between the two rim samples likely reflect specific protein-lipid interactions. High-resolution profiling of the ROS disk lipid composition gives new insights into how intricate membrane structure and protein activity are balanced within the ROS, and provides a model for future studies of other complex cellular structures.
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Affiliation(s)
- Christopher L. Sander
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - Avery E. Sears
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - Antonio F.M. Pinto
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA
| | - Elliot H. Choi
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - Shirin Kahremany
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - Fangyuan Gao
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - David Salom
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - Hui Jin
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH
| | - Els Pardon
- Vlaams Instituut voor Biotechnologie–Vrije Universiteit Brussel Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Susie Suh
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - Zhiqian Dong
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
| | - Jan Steyaert
- Vlaams Instituut voor Biotechnologie–Vrije Universiteit Brussel Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA
| | - Dorota Skowronska-Krawczyk
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA
| | - Philip D. Kiser
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA
- Research Service, VA Long Beach Healthcare System, Long Beach, CA
| | - Krzysztof Palczewski
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California, Irvine, Irvine, CA
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA
- Department of Chemistry, University of California, Irvine, Irvine, CA
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13
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Skiba NP, Cady MA, Molday L, Han JYS, Lewis TR, Spencer WJ, Thompson WJ, Hiles S, Philp NJ, Molday RS, Arshavsky VY. TMEM67, TMEM237, and Embigin in Complex With Monocarboxylate Transporter MCT1 Are Unique Components of the Photoreceptor Outer Segment Plasma Membrane. Mol Cell Proteomics 2021; 20:100088. [PMID: 33933680 PMCID: PMC8167285 DOI: 10.1016/j.mcpro.2021.100088] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/25/2021] [Accepted: 04/26/2021] [Indexed: 01/18/2023] Open
Abstract
The outer segment (OS) organelle of vertebrate photoreceptors is a highly specialized cilium evolved to capture light and initiate light response. The plasma membrane which envelopes the OS plays vital and diverse roles in supporting photoreceptor function and health. However, little is known about the identity of its protein constituents, as this membrane cannot be purified to homogeneity. In this study, we used the technique of protein correlation profiling to identify unique OS plasma membrane proteins. To achieve this, we used label-free quantitative MS to compare relative protein abundances in an enriched preparation of the OS plasma membrane with a preparation of total OS membranes. We have found that only five proteins were enriched at the same level as previously validated OS plasma membrane markers. Two of these proteins, TMEM67 and TMEM237, had not been previously assigned to this membrane, and one, embigin, had not been identified in photoreceptors. We further showed that embigin associates with monocarboxylate transporter MCT1 in the OS plasma membrane, facilitating lactate transport through this cellular compartment.
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Affiliation(s)
- Nikolai P Skiba
- Albert Eye Research Institute, Duke University Medical Center, Durham, North Carolina, USA.
| | - Martha A Cady
- Albert Eye Research Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Laurie Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - John Y S Han
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Tylor R Lewis
- Albert Eye Research Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - William J Spencer
- Albert Eye Research Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Will J Thompson
- Duke Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina, USA
| | - Sarah Hiles
- Duke Proteomics and Metabolomics Shared Resource, Duke University, Durham, North Carolina, USA
| | - Nancy J Philp
- Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Robert S Molday
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Vadim Y Arshavsky
- Albert Eye Research Institute, Duke University Medical Center, Durham, North Carolina, USA.
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14
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Zeitz C, Nassisi M, Laurent-Coriat C, Andrieu C, Boyard F, Condroyer C, Démontant V, Antonio A, Lancelot ME, Frederiksen H, Kloeckener-Gruissem B, El-Shamieh S, Zanlonghi X, Meunier I, Roux AF, Mohand-Saïd S, Sahel JA, Audo I. CHM mutation spectrum and disease: An update at the time of human therapeutic trials. Hum Mutat 2021; 42:323-341. [PMID: 33538369 DOI: 10.1002/humu.24174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 12/21/2020] [Accepted: 01/20/2021] [Indexed: 12/15/2022]
Abstract
Choroideremia is an X-linked inherited retinal disorder (IRD) characterized by the degeneration of retinal pigment epithelium, photoreceptors, choriocapillaris and choroid affecting males with variable phenotypes in female carriers. Unlike other IRD, characterized by a large clinical and genetic heterogeneity, choroideremia shows a specific phenotype with causative mutations in only one gene, CHM. Ongoing gene replacement trials raise further interests in this disorder. We describe here the clinical and genetic data from a French cohort of 45 families, 25 of which carry novel variants, in the context of 822 previously reported choroideremia families. Most of the variants represent loss-of-function mutations with eleven families having large (i.e. ≥6 kb) genomic deletions, 18 small insertions, deletions or insertion deletions, six showing nonsense variants, eight splice site variants and two missense variants likely to affect splicing. Similarly, 822 previously published families carry mostly loss-of-function variants. Recurrent variants are observed worldwide, some of which linked to a common ancestor, others arisen independently in specific CHM regions prone to mutations. Since all exons of CHM may harbor variants, Sanger sequencing combined with quantitative polymerase chain reaction or multiplex ligation-dependent probe amplification experiments are efficient to achieve the molecular diagnosis in patients with typical choroideremia features.
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Affiliation(s)
- Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Marco Nassisi
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Camille Andrieu
- CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC1423, Paris, France
| | - Fiona Boyard
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Vanessa Démontant
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Aline Antonio
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Helen Frederiksen
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Barbara Kloeckener-Gruissem
- Institute of Medical Molecular Genetics, University of Zurich, Schlieren, Switzerland.,Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Said El-Shamieh
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
| | - Xavier Zanlonghi
- Clinique Pluridisciplinaire Jules Verne, Institut Ophtalmologique de l'Ouest, Nantes, France
| | - Isabelle Meunier
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, Montpellier University Hospital, Montpellier, France.,Institute for Neurosciences of Montpellier (INM), University of Montpellier, INSERM, Montpellier, France
| | - Anne-Françoise Roux
- Laboratoire de Génétique Moléculaire, CHU de Montpellier, Université de Montpellier, Montpellier, France
| | - Saddek Mohand-Saïd
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC1423, Paris, France
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC1423, Paris, France.,Fondation Ophtalmologique Adolphe de Rothschild, Paris, France.,Académie des Sciences-Institut de France, Paris, France.,Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, DHU Sight Restore, INSERM-DHOS CIC1423, Paris, France.,Department of Genetics, UCL-Institute of Ophthalmology, London, UK
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15
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Villar PS, Vergara C, Bacigalupo J. Energy sources that fuel metabolic processes in protruding finger-like organelles. FEBS J 2020; 288:3799-3812. [PMID: 33142020 DOI: 10.1111/febs.15620] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/16/2020] [Accepted: 11/02/2020] [Indexed: 12/19/2022]
Abstract
Cells possess a variety of organelles with characteristic structure and subcellular localization intimately linked to their specific function. While most are intracellular and found in virtually all eukaryotic cells, there is a small group of organelles of elongated cylindrical shapes in highly specialized cells that protrude into the extracellular space, such as cilia, flagella, and microvilli. The ATP required by intracellular organelles is amply available in the cytosol, largely generated by mitochondria. However, such is not the case for cilia and flagella, whose slender structures cannot accommodate mitochondria. These organelles consume massive amounts of ATP to carry out high energy-demanding functions, such as sensory transduction or motility. ATP from the nearest mitochondria or other reactions within the cell body is severely limited by diffusion and generally insufficient to fuel the entire length of cilia and flagella. These organelles overcome this fuel restriction by local generation of ATP, using mechanisms that vary depending on the nutrients that are available in their particular external environment. Here, we review, with emphasis in mammals, the remarkable adaptations that cilia and flagella use to fuel their metabolic needs. Additionally, we discuss how a decrease in nutrients surrounding olfactory cilia might impair olfaction in COVID-19 patients.
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Affiliation(s)
- Pablo S Villar
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Cecilia Vergara
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Juan Bacigalupo
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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16
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Song P, Fogerty J, Cianciolo LT, Stupay R, Perkins BD. Cone Photoreceptor Degeneration and Neuroinflammation in the Zebrafish Bardet-Biedl Syndrome 2 ( bbs2) Mutant Does Not Lead to Retinal Regeneration. Front Cell Dev Biol 2020; 8:578528. [PMID: 33324636 PMCID: PMC7726229 DOI: 10.3389/fcell.2020.578528] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/03/2020] [Indexed: 11/17/2022] Open
Abstract
Bardet-Biedl syndrome (BBS) is a heterogeneous and pleiotropic autosomal recessive disorder characterized by obesity, retinal degeneration, polydactyly, renal dysfunction, and mental retardation. BBS results from defects in primary and sensory cilia. Mutations in 21 genes have been linked to BBS and proteins encoded by 8 of these genes form a multiprotein complex termed the BBSome. Mutations in BBS2, a component of the BBSome, result in BBS as well as non-syndromic retinal degeneration in humans and rod degeneration in mice, but the role of BBS2 in cone photoreceptor survival is not clear. We used zebrafish bbs2–/– mutants to better understand how loss of bbs2 leads to photoreceptor degeneration. Zebrafish bbs2–/– mutants exhibited impaired visual function as larvae and adult zebrafish underwent progressive cone photoreceptor degeneration. Cone degeneration was accompanied by increased numbers of activated microglia, indicating an inflammatory response. Zebrafish exhibit a robust ability to regenerate lost photoreceptors following retinal damage, yet cone degeneration and inflammation was insufficient to trigger robust Müller cell proliferation. In contrast, high intensity light damage stimulated Müller cell proliferation and photoreceptor regeneration in both wild-type and bbs2–/– mutants, although the bbs2–/– mutants could only restore cones to pre-damaged densities. In summary, these findings suggest that cone degeneration leads to an inflammatory response in the retina and that BBS2 is necessary for cone survival. The zebrafish bbs2 mutant also represents an ideal model to identify mechanisms that will enhance retinal regeneration in degenerating diseases.
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Affiliation(s)
- Ping Song
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Joseph Fogerty
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Lauren T Cianciolo
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Rachel Stupay
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Brian D Perkins
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, United States.,Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, United States.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, United States
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17
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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.
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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:
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18
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Ropelewski P, Imanishi Y. RPE Cells Engulf Microvesicles Secreted by Degenerating Rod Photoreceptors. eNeuro 2020; 7:ENEURO.0507-19.2020. [PMID: 32376599 PMCID: PMC7242815 DOI: 10.1523/eneuro.0507-19.2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 04/10/2020] [Accepted: 04/24/2020] [Indexed: 01/11/2023] Open
Abstract
Rhodopsin is mislocalized to the inner segment plasma membrane (IS PM) in various blinding disorders including autosomal-dominant retinitis pigmentosa caused by class I rhodopsin mutations. In these disorders, rhodopsin-laden microvesicles are secreted into the extracellular milieu by afflicted photoreceptor cells. Using a Xenopus laevis model expressing class I mutant rhodopsin or Na+/K+-ATPase (NKA) fused to Dendra2, we fluorescently labeled the microvesicles and found retinal pigment epithelial (RPE) cells are capable of engulfing microvesicles containing rhodopsin. A unique sorting mechanism allows class I mutant rhodopsin, but not NKA, to be packaged into the microvesicles. Under normal physiological conditions, NKA is not shed as microvesicles to the extracellular space, but is degraded intracellularly. Those studies provide novel insights into protein homeostasis in the photoreceptor IS PM.
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Affiliation(s)
- Philip Ropelewski
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106
| | - Yoshikazu Imanishi
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106
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19
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Lewis TR, Makia MS, Kakakhel M, Al-Ubaidi MR, Arshavsky VY, Naash MI. Photoreceptor Disc Enclosure Occurs in the Absence of Normal Peripherin-2/rds Oligomerization. Front Cell Neurosci 2020; 14:92. [PMID: 32410962 PMCID: PMC7198881 DOI: 10.3389/fncel.2020.00092] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 03/30/2020] [Indexed: 12/11/2022] Open
Abstract
Mutations in the peripherin-2 gene (PRPH2, also known as rds) cause a heterogeneous range of autosomal dominant retinal diseases. PRPH2 encodes a photoreceptor-specific tetraspanin protein, PRPH2, that is a main structural component of the photoreceptor outer segment. PRPH2 distributes to the rims of outer segment disc membranes as they undergo the process of disc membrane enclosure. Within these rims, PRPH2 exists in homo-oligomeric form or as a hetero-oligomer with another tetraspanin protein, ROM1. While complete loss of PRPH2 prevents photoreceptor outer segment formation, mutations affecting the state of its oligomerization, including C150S, C213Y and Y141C, produce outer segment structural defects. In this study, we addressed whether any of these mutations also affect disc enclosure. We employed recently developed methodology for ultrastructural analysis of the retina, involving tissue processing with tannic acid, to assess the status of disc enclosure in knockin mouse models bearing either one or two alleles of the C150S, C213Y and Y141C PRPH2 mutations. While varying degrees of outer segment structural abnormalities were observed in each of these mouse models, they contained both newly forming “open” discs and mature “enclosed” discs. These data demonstrate that normal PRPH2 oligomerization is not essential for photoreceptor disc enclosure.
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Affiliation(s)
- Tylor R Lewis
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, United States
| | - Mustafa S Makia
- Department of Biomedical Engineering, University of Houston, Houston, TX, United States
| | - Mashal Kakakhel
- Department of Biomedical Engineering, University of Houston, Houston, TX, United States
| | - Muayyad R Al-Ubaidi
- Department of Biomedical Engineering, University of Houston, Houston, TX, United States.,College of Optometry, University of Houston, Houston, TX, United States
| | - Vadim Y Arshavsky
- Department of Ophthalmology, Duke University Medical Center, Durham, NC, United States.,Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, United States
| | - Muna I Naash
- Department of Biomedical Engineering, University of Houston, Houston, TX, United States.,College of Optometry, University of Houston, Houston, TX, United States
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20
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Datta P, Hendrickson B, Brendalen S, Ruffcorn A, Seo S. The myosin-tail homology domain of centrosomal protein 290 is essential for protein confinement between the inner and outer segments in photoreceptors. J Biol Chem 2019; 294:19119-19136. [PMID: 31694913 DOI: 10.1074/jbc.ra119.009712] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/30/2019] [Indexed: 12/13/2022] Open
Abstract
Mutations in the centrosomal protein 290 (CEP290) gene cause various ciliopathies involving retinal degeneration. CEP290 proteins localize to the ciliary transition zone and are thought to act as a gatekeeper that controls ciliary protein trafficking. However, precise roles of CEP290 in photoreceptors and pathomechanisms of retinal degeneration in CEP290-associated ciliopathies are not sufficiently understood. Using conditional Cep290 mutant mice, in which the C-terminal myosin-tail homology domain of CEP290 is disrupted after the connecting cilium is assembled, we show that this domain is essential for protein confinement between the inner and the outer segments. Upon disruption of the myosin-tail homology domain, inner segment plasma membrane proteins, including syntaxin 3 (STX3), synaptosome-associated protein 25 (SNAP25), and interphotoreceptor matrix proteoglycan 2 (IMPG2), rapidly accumulated in the outer segment. In contrast, localization of endomembrane proteins was not altered. Trafficking and confinement of most outer segment-resident proteins appeared to be unaffected or only minimally affected in Cep290 mutant mice. One notable exception was rhodopsin (RHO), which severely mislocalized to inner segments during the initial stage of degeneration. Similar mislocalization phenotypes were observed in Cep290rd16 mice. These results suggest that a failure of protein confinement at the connecting cilium and consequent accumulation of inner segment membrane proteins in the outer segment, along with insufficient RHO delivery, is part of the disease mechanisms that cause retinal degeneration in CEP290-associated ciliopathies. Our study provides insights into the pathomechanisms of retinal degenerations associated with compromised ciliary gates.
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Affiliation(s)
- Poppy Datta
- Department of Ophthalmology and Visual Sciences, University of Iowa College of Medicine, Iowa City, Iowa 52242.,Institute for Vision Research, University of Iowa, Iowa City, Iowa 52242
| | - Brandon Hendrickson
- Department of Ophthalmology and Visual Sciences, University of Iowa College of Medicine, Iowa City, Iowa 52242.,Institute for Vision Research, University of Iowa, Iowa City, Iowa 52242
| | - Sarah Brendalen
- Department of Ophthalmology and Visual Sciences, University of Iowa College of Medicine, Iowa City, Iowa 52242.,Institute for Vision Research, University of Iowa, Iowa City, Iowa 52242
| | - Avri Ruffcorn
- Department of Ophthalmology and Visual Sciences, University of Iowa College of Medicine, Iowa City, Iowa 52242.,Institute for Vision Research, University of Iowa, Iowa City, Iowa 52242
| | - Seongjin Seo
- Department of Ophthalmology and Visual Sciences, University of Iowa College of Medicine, Iowa City, Iowa 52242 .,Institute for Vision Research, University of Iowa, Iowa City, Iowa 52242
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21
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Blond F, Léveillard T. Functional Genomics of the Retina to Elucidate its Construction and Deconstruction. Int J Mol Sci 2019; 20:E4922. [PMID: 31590277 PMCID: PMC6801968 DOI: 10.3390/ijms20194922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/01/2019] [Indexed: 12/20/2022] Open
Abstract
The retina is the light sensitive part of the eye and nervous tissue that have been used extensively to characterize the function of the central nervous system. The retina has a central position both in fundamental biology and in the physiopathology of neurodegenerative diseases. We address the contribution of functional genomics to the understanding of retinal biology by reviewing key events in their historical perspective as an introduction to major findings that were obtained through the study of the retina using genomics, transcriptomics and proteomics. We illustrate our purpose by showing that most of the genes of interest for retinal development and those involved in inherited retinal degenerations have a restricted expression to the retina and most particularly to photoreceptors cells. We show that the exponential growth of data generated by functional genomics is a future challenge not only in terms of storage but also in terms of accessibility to the scientific community of retinal biologists in the future. Finally, we emphasize on novel perspectives that emerge from the development of redox-proteomics, the new frontier in retinal biology.
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Affiliation(s)
- Frédéric Blond
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France.
| | - Thierry Léveillard
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France.
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22
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Cehajic Kapetanovic J, Barnard AR, MacLaren RE. Molecular Therapies for Choroideremia. Genes (Basel) 2019; 10:genes10100738. [PMID: 31548516 PMCID: PMC6826983 DOI: 10.3390/genes10100738] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/14/2019] [Accepted: 09/20/2019] [Indexed: 01/03/2023] Open
Abstract
Advances in molecular research have culminated in the development of novel gene-based therapies for inherited retinal diseases. We have recently witnessed several groundbreaking clinical studies that ultimately led to approval of Luxturna, the first gene therapy for an inherited retinal disease. In parallel, international research community has been engaged in conducting gene therapy trials for another more common inherited retinal disease known as choroideremia and with phase III clinical trials now underway, approval of this therapy is poised to follow suit. This chapter discusses new insights into clinical phenotyping and molecular genetic testing in choroideremia with review of molecular mechanisms implicated in its pathogenesis. We provide an update on current gene therapy trials and discuss potential inclusion of female carries in future clinical studies. Alternative molecular therapies are discussed including suitability of CRISPR gene editing, small molecule nonsense suppression therapy and vision restoration strategies in late stage choroideremia.
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Affiliation(s)
- Jasmina Cehajic Kapetanovic
- Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford OX3 9DU, UK; (A.R.B.); (R.E.M.)
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
- Correspondence:
| | - Alun R. Barnard
- Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford OX3 9DU, UK; (A.R.B.); (R.E.M.)
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Robert E. MacLaren
- Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford OX3 9DU, UK; (A.R.B.); (R.E.M.)
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
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23
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Modes of Accessing Bicarbonate for the Regulation of Membrane Guanylate Cyclase (ROS-GC) in Retinal Rods and Cones. eNeuro 2019; 6:eN-NWR-0393-18. [PMID: 30783616 PMCID: PMC6378327 DOI: 10.1523/eneuro.0393-18.2019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/20/2018] [Accepted: 01/15/2019] [Indexed: 11/21/2022] Open
Abstract
The membrane guanylate cyclase, ROS-GC, that synthesizes cyclic GMP for use as a second messenger for visual transduction in retinal rods and cones, is stimulated by bicarbonate. Bicarbonate acts directly on ROS-GC1, because it enhanced the enzymatic activity of a purified, recombinant fragment of bovine ROS-GC1 consisting solely of the core catalytic domain. Moreover, recombinant ROS-GC1 proved to be a true sensor of bicarbonate, rather than a sensor for CO2. Access to bicarbonate differed in rods and cones of larval salamander, Ambystoma tigrinum, of unknown sex. In rods, bicarbonate entered at the synapse and diffused to the outer segment, where it was removed by Cl--dependent exchange. In contrast, cones generated bicarbonate internally from endogenous CO2 or from exogenous CO2 that was present in extracellular solutions of bicarbonate. Bicarbonate production from both sources of CO2 was blocked by the carbonic anhydrase inhibitor, acetazolamide. Carbonic anhydrase II expression was verified immunohistochemically in cones but not in rods. In addition, cones acquired bicarbonate at their outer segments as well as at their inner segments. The multiple pathways for access in cones may support greater uptake of bicarbonate than in rods and buffer changes in its intracellular concentration.
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Wang J, Molday LL, Hii T, Coleman JA, Wen T, Andersen JP, Molday RS. Proteomic Analysis and Functional Characterization of P4-ATPase Phospholipid Flippases from Murine Tissues. Sci Rep 2018; 8:10795. [PMID: 30018401 PMCID: PMC6050252 DOI: 10.1038/s41598-018-29108-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/05/2018] [Indexed: 01/31/2023] Open
Abstract
P4-ATPases are a subfamily of P-type ATPases that flip phospholipids across membranes to generate lipid asymmetry, a property vital to many cellular processes. Mutations in several P4-ATPases have been linked to severe neurodegenerative and metabolic disorders. Most P4-ATPases associate with one of three accessory subunit isoforms known as CDC50A (TMEM30A), CDC50B (TMEM30B), and CDC50C (TMEM30C). To identify P4-ATPases that associate with CDC50A, in vivo, and determine their tissue distribution, we isolated P4-ATPases-CDC50A complexes from retina, brain, liver, testes, and kidney on a CDC50A immunoaffinity column and identified and quantified P4-ATPases from their tryptic peptides by mass spectrometry. Of the 12 P4-ATPase that associate with CDC50 subunits, 10 P4-ATPases were detected. Four P4-ATPases (ATP8A1, ATP11A, ATP11B, ATP11C) were present in all five tissues. ATP10D was found in low amounts in liver, brain, testes, and kidney, and ATP8A2 was present in significant amounts in retina, brain, and testes. ATP8B1 was detected only in liver, ATP8B3 and ATP10A only in testes, and ATP8B2 primarily in brain. We also show that ATP11A, ATP11B and ATP11C, like ATP8A1 and ATP8A2, selectively flip phosphatidylserine and phosphatidylethanolamine across membranes. These studies provide new insight into the tissue distribution, relative abundance, subunit interactions and substrate specificity of P4-ATPase-CDC50A complexes.
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Affiliation(s)
- Jiao Wang
- Department of Biochemistry and Molecular Biology, Centre for Macular Research, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
- Laboratory of Molecular Neural Biology, Institute of Systems Biology, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Laurie L Molday
- Department of Biochemistry and Molecular Biology, Centre for Macular Research, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Theresa Hii
- Department of Biochemistry and Molecular Biology, Centre for Macular Research, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Jonathan A Coleman
- Department of Biochemistry and Molecular Biology, Centre for Macular Research, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Tieqiao Wen
- Laboratory of Molecular Neural Biology, Institute of Systems Biology, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Jens P Andersen
- Department of Biomedicine, Aarhus University, Ole Worms Allé 4, Bldg. 1160, DK-8000, Aarhus C, Denmark
| | - Robert S Molday
- Department of Biochemistry and Molecular Biology, Centre for Macular Research, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.
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Bruschi M, Petretto A, Caicci F, Bartolucci M, Calzia D, Santucci L, Manni L, Ramenghi LA, Ghiggeri G, Traverso CE, Candiano G, Panfoli I. Proteome of Bovine Mitochondria and Rod Outer Segment Disks: Commonalities and Differences. J Proteome Res 2018; 17:918-925. [PMID: 29299929 DOI: 10.1021/acs.jproteome.7b00741] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The retinal rod outer segment (OS) is a stack of disks surrounded by the plasma membrane, housing proteins related to phototransduction, as well as mitochondrial proteins involved in oxidative phosphorylation (OxPhos). This prompted us to compare the proteome of bovine OS disks and mitochondria to assess the significant top gene signatures of each sample. The two proteomes, obtained by LTQ-Orbitrap Velos mass spectrometry, were compared by statistical analyses. In total, 4139 proteins were identified, 2045 of which overlapping in the two sets. Nonhierarchical Spearman's correlogram revealed that the groups were clearly discriminated. Partial least square discriminant plus support vector machine analysis identified the major discriminative proteins, implied in phototransduction and lipid metabolism, respectively. Gene Ontology analysis identified top gene signatures of the disk proteome, enriched in vesiculation, glycolysis, and OxPhos proteins. The tricarboxylic acid cycle and the electron transport proteins were similarly enriched in the two samples, but the latter was up regulated in disks. Data suggest that the mitochondrial OxPhos proteins may represent a true OS proteome component, outside the mitochondrion. This knowledge may help the scientific community in the further studies of retinal physiology and pathology.
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Affiliation(s)
| | | | - Federico Caicci
- Department of Biology, Università di Padova , 35121 Padova, Italy
| | | | - Daniela Calzia
- Dipartimento di Farmacia-DIFAR, Università di Genova , 16132 Genoa, Italy
| | | | - Lucia Manni
- Department of Biology, Università di Padova , 35121 Padova, Italy
| | | | | | - Carlo E Traverso
- Clinica Oculistica, (Di.N.O.G.M.I.) Università Department of Intensive Care di Genova, IRCCS Azienda Ospedaliera Universitaria San Martino-IST , 16132 Genoa, Italy
| | | | - Isabella Panfoli
- Dipartimento di Farmacia-DIFAR, Università di Genova , 16132 Genoa, Italy
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Retinal Degeneration Protein 3 (RD3) in normal human tissues: Novel insights. Sci Rep 2017; 7:13154. [PMID: 29030614 PMCID: PMC5640666 DOI: 10.1038/s41598-017-13337-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 09/21/2017] [Indexed: 12/28/2022] Open
Abstract
The 195-amino-acid-long human Retinal Degeneration Protein 3 (RD3) is critical in the regulation of guanylate cyclase (GC) signaling and photoreceptor cell survival. Recently, we identified significant loss of RD3 in high-risk neuroblastoma and the influential role of RD3 in tumor progression. However, the functional characterization of RD3 in tumor systems has been hampered by the dearth of information on its localization in normal tissue and by the lack of antibodies suitable for staining FFPE tissue, primarily due to the inaccessibility of the epitopes. In this study, we validated a custom-synthesized RD3 antibody and investigated the expression/localization of RD3 in assorted human tissues. We observed stratified expression of RD3 in different cell types and subcellular location of retina. We demonstrated extensive positive RD3 immunoreactivity in various normal tissues and particularly strong dot-like perinuclear staining in the lining epithelial cells, suggesting that RD3 may play an important role in the normal functioning of epithelial cells. RD3 expression is limited in the CNS. While neuroblastoma is often RD3-positive, the adrenal medulla, where many neuroblastomas originate, is RD3-negative. Meta-analysis of RD3 transcriptional expression across normal tissues confirmed tissue-specific RD3 mRNA levels. Our results revealed the tissue-specific expression/localization profile of RD3 for the first time.
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Maity S, Ilieva N, Laio A, Torre V, Mazzolini M. New views on phototransduction from atomic force microscopy and single molecule force spectroscopy on native rods. Sci Rep 2017; 7:12000. [PMID: 28931892 PMCID: PMC5607320 DOI: 10.1038/s41598-017-11912-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/25/2017] [Indexed: 12/11/2022] Open
Abstract
By combining atomic force microscopy (AFM) imaging and single-molecule force spectroscopy (SMFS), we analyzed membrane proteins of the rod outer segments (OS). With this combined approach we were able to study the membrane proteins in their natural environment. In the plasma membrane we identified native cyclic nucleotide-gated (CNG) channels which are organized in single file strings. We also identified rhodopsin located both in the discs and in the plasma membrane. SMFS reveals strikingly different mechanical properties of rhodopsin unfolding in the two environments. Molecular dynamic simulations suggest that this difference is likely to be related to the higher hydrophobicity of the plasma membrane, due to the higher cholesterol concentration. This increases rhodopsin mechanical stability lowering the rate of transition towards its active form, hindering, in this manner, phototransduction.
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Affiliation(s)
- Sourav Maity
- International School for Advanced Studies (SISSA-ISAS) via Bonomea 265, 34136, Trieste, Italy
| | - Nina Ilieva
- International School for Advanced Studies (SISSA-ISAS) via Bonomea 265, 34136, Trieste, Italy
| | - Alessandro Laio
- International School for Advanced Studies (SISSA-ISAS) via Bonomea 265, 34136, Trieste, Italy
| | - Vincent Torre
- International School for Advanced Studies (SISSA-ISAS) via Bonomea 265, 34136, Trieste, Italy.
| | - Monica Mazzolini
- International School for Advanced Studies (SISSA-ISAS) via Bonomea 265, 34136, Trieste, Italy.
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Chinchore Y, Begaj T, Wu D, Drokhlyansky E, Cepko CL. Glycolytic reliance promotes anabolism in photoreceptors. eLife 2017; 6. [PMID: 28598329 PMCID: PMC5499945 DOI: 10.7554/elife.25946] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 06/01/2017] [Indexed: 12/18/2022] Open
Abstract
Vertebrate photoreceptors are among the most metabolically active cells, exhibiting a high rate of ATP consumption. This is coupled with a high anabolic demand, necessitated by the diurnal turnover of a specialized membrane-rich organelle, the outer segment, which is the primary site of phototransduction. How photoreceptors balance their catabolic and anabolic demands is poorly understood. Here, we show that rod photoreceptors in mice rely on glycolysis for their outer segment biogenesis. Genetic perturbations targeting allostery or key regulatory nodes in the glycolytic pathway impacted the size of the outer segments. Fibroblast growth factor signaling was found to regulate glycolysis, with antagonism of this pathway resulting in anabolic deficits. These data demonstrate the cell autonomous role of the glycolytic pathway in outer segment maintenance and provide evidence that aerobic glycolysis is part of a metabolic program that supports the biosynthetic needs of a normal neuronal cell type. DOI:http://dx.doi.org/10.7554/eLife.25946.001 Living cells need building materials and energy to grow and carry out their activities. Most cells in the body use sugars like glucose for these purposes. In a process known as glycolysis, cells break down glucose into molecules that are eventually converted to carbon dioxide and water to form the chemical ATP – the cellular currency for energy. Developing cells that have not yet fully specialized, and rapidly dividing cells, like cancer cells, consume large amounts of glucose via aerobic glycolysis (also known as the Warburg effect) as they require high levels of energy and building materials. As cells become more specialized and divide less often, they have a reduced need for building blocks, and adjust their consumption and breakdown of glucose accordingly. One exception is the photoreceptor cells, found in the light-sensitive part of our eyes. Although these specialized cells do not divide, they still need a lot of energy and building blocks to constantly renew their light-sensing and processing structures, and to capture and convert the information from the environment into signals. Previous research has shown that the eye also uses the Warburg effect. However, until now, it was not known whether the photoreceptors or other cells in the eye carry out this form of glycolysis. Using genetic tools, Chinchore et al. analysed how the photoreceptor cells in mice used glucose. The experiments demonstrated that the photoreceptors do indeed carry out the Warburg effect. Chinchore et al. further discovered that the Warburg effect is regulated by the same key enzymes and signalling molecules that cancer cells use. This indicates that specialized cells like photoreceptors might choose to retain certain metabolic features of their precursor cells, if they need to. These findings provide new insight into how photoreceptors use glucose. The next step will be to understand how aerobic glycolysis is regulated in healthy eyes as well as in eyes that are affected by degenerating diseases, which may ultimately lead to new ways of treating blindness. DOI:http://dx.doi.org/10.7554/eLife.25946.002
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Affiliation(s)
- Yashodhan Chinchore
- Departments of Genetics and Ophthalmology, Harvard Medical School, Boston, United States
| | - Tedi Begaj
- Departments of Genetics and Ophthalmology, Harvard Medical School, Boston, United States
| | - David Wu
- Departments of Genetics and Ophthalmology, Harvard Medical School, Boston, United States
| | - Eugene Drokhlyansky
- Departments of Genetics and Ophthalmology, Harvard Medical School, Boston, United States
| | - Constance L Cepko
- Departments of Genetics and Ophthalmology, Harvard Medical School, Boston, United States.,Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
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29
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May-Simera H, Nagel-Wolfrum K, Wolfrum U. Cilia - The sensory antennae in the eye. Prog Retin Eye Res 2017; 60:144-180. [PMID: 28504201 DOI: 10.1016/j.preteyeres.2017.05.001] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 05/04/2017] [Accepted: 05/08/2017] [Indexed: 12/21/2022]
Abstract
Cilia are hair-like projections found on almost all cells in the human body. Originally believed to function merely in motility, the function of solitary non-motile (primary) cilia was long overlooked. Recent research has demonstrated that primary cilia function as signalling hubs that sense environmental cues and are pivotal for organ development and function, tissue hoemoestasis, and maintenance of human health. Cilia share a common anatomy and their diverse functional features are achieved by evolutionarily conserved functional modules, organized into sub-compartments. Defects in these functional modules are responsible for a rapidly growing list of human diseases collectively termed ciliopathies. Ocular pathogenesis is common in virtually all classes of syndromic ciliopathies, and disruptions in cilia genes have been found to be causative in a growing number of non-syndromic retinal dystrophies. This review will address what is currently known about cilia contribution to visual function. We will focus on the molecular and cellular functions of ciliary proteins and their role in the photoreceptor sensory cilia and their visual phenotypes. We also highlight other ciliated cell types in tissues of the eye (e.g. lens, RPE and Müller glia cells) discussing their possible contribution to disease progression. Progress in basic research on the cilia function in the eye is paving the way for therapeutic options for retinal ciliopathies. In the final section we describe the latest advancements in gene therapy, read-through of non-sense mutations and stem cell therapy, all being adopted to treat cilia dysfunction in the retina.
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Affiliation(s)
- Helen May-Simera
- Institute of Molecular Physiology, Cilia Biology, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany
| | - Kerstin Nagel-Wolfrum
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany
| | - Uwe Wolfrum
- Institute of Molecular Physiology, Molecular Cell Biology, Johannes Gutenberg-Universität Mainz, 55099 Mainz, Germany.
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30
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Fukagawa T, Takafuji K, Tachibanaki S, Kawamura S. Purification of cone outer segment for proteomic analysis on its membrane proteins in carp retina. PLoS One 2017; 12:e0173908. [PMID: 28291804 PMCID: PMC5349680 DOI: 10.1371/journal.pone.0173908] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 02/28/2017] [Indexed: 11/18/2022] Open
Abstract
Rods and cones are both photoreceptors in the retina, but they are different in many aspects including the light response characteristics and, for example, cell morphology and metabolism. These differences would be caused by differences in proteins expressed in rods and cones. To understand the molecular bases of these differences between rods and cones, one of the ways is to compare proteins expressed in rods and cones, and to find those expressed specifically or dominantly. In the present study, we are interested in proteins in the outer segment (OS), the site responsible for generation of rod- or cone-characteristic light responses and also the site showing different morphology between rods and cones. For this, we established a method to purify the OS and the inner segment (IS) of rods and also of cones from purified carp rods and cones, respectively, using sucrose density gradient. In particular, we were interested in proteins tightly bound to the membranes of cone OS. To identify these proteins, we analyzed proteins in some selected regions of an SDS-gel of washed membranes of the OS and the IS obtained from both rods and cones, with Liquid Chromatography-tandem Mass Spectrometry (LC-MS/MS) using a protein database constructed from carp retina. By comparing the lists of the proteins found in the OS and the IS of both rods and cones, we found some proteins present in cone OS membranes specifically or dominantly, in addition to the proteins already known to be present specifically in cone OS.
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Affiliation(s)
- Takashi Fukagawa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Kazuaki Takafuji
- Center of Medical Innovation and Translational Research, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Shuji Tachibanaki
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Suita, Osaka, Japan
- * E-mail: (ST); (SK)
| | - Satoru Kawamura
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Suita, Osaka, Japan
- * E-mail: (ST); (SK)
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Schott RK, Panesar B, Card DC, Preston M, Castoe TA, Chang BS. Targeted Capture of Complete Coding Regions across Divergent Species. Genome Biol Evol 2017; 9:398-414. [PMID: 28137744 PMCID: PMC5381602 DOI: 10.1093/gbe/evx005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2017] [Indexed: 02/06/2023] Open
Abstract
Despite continued advances in sequencing technologies, there is a need for methods that can efficiently sequence large numbers of genes from diverse species. One approach to accomplish this is targeted capture (hybrid enrichment). While these methods are well established for genome resequencing projects, cross-species capture strategies are still being developed and generally focus on the capture of conserved regions, rather than complete coding regions from specific genes of interest. The resulting data is thus useful for phylogenetic studies, but the wealth of comparative data that could be used for evolutionary and functional studies is lost. Here, we design and implement a targeted capture method that enables recovery of complete coding regions across broad taxonomic scales. Capture probes were designed from multiple reference species and extensively tiled in order to facilitate cross-species capture. Using novel bioinformatics pipelines we were able to recover nearly all of the targeted genes with high completeness from species that were up to 200 myr divergent. Increased probe diversity and tiling for a subset of genes had a large positive effect on both recovery and completeness. The resulting data produced an accurate species tree, but importantly this same data can also be applied to studies of molecular evolution and function that will allow researchers to ask larger questions in broader phylogenetic contexts. Our method demonstrates the utility of cross-species approaches for the capture of full length coding sequences, and will substantially improve the ability for researchers to conduct large-scale comparative studies of molecular evolution and function.
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Affiliation(s)
- Ryan K. Schott
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
| | - Bhawandeep Panesar
- Department of Cell and Systems Biology, University of Toronto, Ontario, Canada
| | - Daren C. Card
- Department of Biology, University of Texas at Arlington, Arlington, TX
| | - Matthew Preston
- Department of Cell and Systems Biology, University of Toronto, Ontario, Canada
| | - Todd A. Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX
| | - Belinda S.W. Chang
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario, Canada
- Department of Cell and Systems Biology, University of Toronto, Ontario, Canada
- Centre for the Analysis of Genomes and Function, University of Toronto, Canada
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Abstract
Retinal photoreceptor cells contain a specialized outer segment (OS) compartment that functions in the capture of light and its conversion into electrical signals in a process known as phototransduction. In rods, photoisomerization of 11-cis to all-trans retinal within rhodopsin triggers a biochemical cascade culminating in the closure of cGMP-gated channels and hyperpolarization of the cell. Biochemical reactions return the cell to its 'dark state' and the visual cycle converts all-trans retinal back to 11-cis retinal for rhodopsin regeneration. OS are continuously renewed, with aged membrane removed at the distal end by phagocytosis and new membrane added at the proximal end through OS disk morphogenesis linked to protein trafficking. The molecular basis for disk morphogenesis remains to be defined in detail although several models have been proposed, and molecular mechanisms underlying protein trafficking are under active investigation. The aim of this Cell Science at a Glance article and the accompanying poster is to highlight our current understanding of photoreceptor structure, phototransduction, the visual cycle, OS renewal, protein trafficking and retinal degenerative diseases.
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Affiliation(s)
- Robert S Molday
- Department of Biochemistry and Molecular Biology, Centre for Macular Research, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3 Department of Ophthalmology and Visual Sciences, Centre for Macular Research, University of British Columbia, Vancouver, British Columbia, Canada V5Z 3N9
| | - Orson L Moritz
- Department of Ophthalmology and Visual Sciences, Centre for Macular Research, University of British Columbia, Vancouver, British Columbia, Canada V5Z 3N9
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Rueda EM, Johnson JE, Giddabasappa A, Swaroop A, Brooks MJ, Sigel I, Chaney SY, Fox DA. The cellular and compartmental profile of mouse retinal glycolysis, tricarboxylic acid cycle, oxidative phosphorylation, and ~P transferring kinases. Mol Vis 2016; 22:847-85. [PMID: 27499608 PMCID: PMC4961465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 07/21/2016] [Indexed: 10/26/2022] Open
Abstract
PURPOSE The homeostatic regulation of cellular ATP is achieved by the coordinated activity of ATP utilization, synthesis, and buffering. Glucose is the major substrate for ATP synthesis through glycolysis and oxidative phosphorylation (OXPHOS), whereas intermediary metabolism through the tricarboxylic acid (TCA) cycle utilizes non-glucose-derived monocarboxylates, amino acids, and alpha ketoacids to support mitochondrial ATP and GTP synthesis. Cellular ATP is buffered by specialized equilibrium-driven high-energy phosphate (~P) transferring kinases. Our goals were twofold: 1) to characterize the gene expression, protein expression, and activity of key synthesizing and regulating enzymes of energy metabolism in the whole mouse retina, retinal compartments, and/or cells and 2) to provide an integrative analysis of the results related to function. METHODS mRNA expression data of energy-related genes were extracted from our whole retinal Affymetrix microarray data. Fixed-frozen retinas from adult C57BL/6N mice were used for immunohistochemistry, laser scanning confocal microscopy, and enzymatic histochemistry. The immunoreactivity levels of well-characterized antibodies, for all major retinal cells and their compartments, were obtained using our established semiquantitative confocal and imaging techniques. Quantitative cytochrome oxidase (COX) and lactate dehydrogenase (LDH) activity was determined histochemically. RESULTS The Affymetrix data revealed varied gene expression patterns of the ATP synthesizing and regulating enzymes found in the muscle, liver, and brain. Confocal studies showed differential cellular and compartmental distribution of isozymes involved in glucose, glutamate, glutamine, lactate, and creatine metabolism. The pattern and intensity of the antibodies and of the COX and LDH activity showed the high capacity of photoreceptors for aerobic glycolysis and OXPHOS. Competition assays with pyruvate revealed that LDH-5 was localized in the photoreceptor inner segments. The combined results indicate that glycolysis is regulated by the compartmental expression of hexokinase 2, pyruvate kinase M1, and pyruvate kinase M2 in photoreceptors, whereas the inner retinal neurons exhibit a lower capacity for glycolysis and aerobic glycolysis. Expression of nucleoside diphosphate kinase, mitochondria-associated adenylate kinase, and several mitochondria-associated creatine kinase isozymes was highest in the outer retina, whereas expression of cytosolic adenylate kinase and brain creatine kinase was higher in the cones, horizontal cells, and amacrine cells indicating the diversity of ATP-buffering strategies among retinal neurons. Based on the antibody intensities and the COX and LDH activity, Müller glial cells (MGCs) had the lowest capacity for glycolysis, aerobic glycolysis, and OXPHOS. However, they showed high expression of glutamate dehydrogenase, alpha-ketoglutarate dehydrogenase, succinate thiokinase, GABA transaminase, and ~P transferring kinases. This suggests that MGCs utilize TCA cycle anaplerosis and cataplerosis to generate GTP and ~P transferring kinases to produce ATP that supports MGC energy requirements. CONCLUSIONS Our comprehensive and integrated results reveal that the adult mouse retina expresses numerous isoforms of ATP synthesizing, regulating, and buffering genes; expresses differential cellular and compartmental levels of glycolytic, OXPHOS, TCA cycle, and ~P transferring kinase proteins; and exhibits differential layer-by-layer LDH and COX activity. New insights into cell-specific and compartmental ATP and GTP production, as well as utilization and buffering strategies and their relationship with known retinal and cellular functions, are discussed. Developing therapeutic strategies for neuroprotection and treating retinal deficits and degeneration in a cell-specific manner will require such knowledge. This work provides a platform for future research directed at identifying the molecular targets and proteins that regulate these processes.
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Affiliation(s)
- Elda M. Rueda
- College of Optometry, University of Houston, Houston TX
| | - Jerry E. Johnson
- Department of Natural Sciences, University of Houston-Downtown, Houston TX
- Department of Biology and Biochemistry, University of Houston, Houston TX
| | - Anand Giddabasappa
- Department of Biology and Biochemistry, University of Houston, Houston TX
| | | | | | - Irena Sigel
- College of Optometry, University of Houston, Houston TX
| | - Shawnta Y. Chaney
- Department of Biology and Biochemistry, University of Houston, Houston TX
| | - Donald A. Fox
- College of Optometry, University of Houston, Houston TX
- Department of Biology and Biochemistry, University of Houston, Houston TX
- Department of Pharmacology and Pharmaceutical Sciences, University of Houston, Houston TX
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Chakraborty D, Conley SM, Pittler SJ, Naash MI. Role of RDS and Rhodopsin in Cngb1-Related Retinal Degeneration. Invest Ophthalmol Vis Sci 2016; 57:787-97. [PMID: 26934134 PMCID: PMC4777275 DOI: 10.1167/iovs.15-18516] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Rod photoreceptor outer segment (OS) morphogenesis, structural integrity, and proper signal transduction rely on critical proteins found in the different OS membrane domains (e.g., plasma, disc, and disc rim membrane). Among these key elements are retinal degeneration slow (RDS, also known as peripherin-2), rhodopsin, and the beta subunit of the cyclic nucleotide gated channel (CNGB1a), which have been found to interact in a complex. The purpose of this study was to evaluate the potential interplay between these three proteins by examining retinal disease phenotypes in animal models expressing varying amounts of CNGB1a, rhodopsin, and RDS. Methods Outer segment trafficking, retinal function, and photoreceptor structure were evaluated using knockout mouse lines. Results Eliminating Cngb1 and reducing RDS leads to additive defects in RDS expression levels and rod electroretinogram (ERG) function, (e.g., Cngb1−/−/rds+/− versus rds+/− or Cngb1−/−) but not to additive defects in rod ultrastructure. These additive effects also manifested in cone function: Photopic ERG responses were significantly lower in the Cngb1−/−/rds+/− versus rds+/− or Cngb1−/−, suggesting that eliminating Cngb1 can accelerate the cone degeneration that usually presents later in the rds+/−. This was not the case with rhodopsin; reducing rhodopsin levels in concert with eliminating CNGB1a did not lead to phenotypes more severe than those observed in the Cngb1 knockout alone. Conclusions These data support a role for RDS as the core component of a multiprotein plasma membrane-rim-disc complex that has both a structural role in photoreceptor OS formation and maintenance and a functional role in orienting proteins for optimal signal transduction.
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Affiliation(s)
- Dibyendu Chakraborty
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States
| | - Shannon M Conley
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States
| | - Steven J Pittler
- Department of Vision Sciences, School of Optometry, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Muna I Naash
- Department of Biomedical Engineering, University of Houston, Houston, Texas, United States
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Goldberg AFX, Moritz OL, Williams DS. Molecular basis for photoreceptor outer segment architecture. Prog Retin Eye Res 2016; 55:52-81. [PMID: 27260426 DOI: 10.1016/j.preteyeres.2016.05.003] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 05/27/2016] [Accepted: 05/29/2016] [Indexed: 01/11/2023]
Abstract
To serve vision, vertebrate rod and cone photoreceptors must detect photons, convert the light stimuli into cellular signals, and then convey the encoded information to downstream neurons. Rods and cones are sensory neurons that each rely on specialized ciliary organelles to detect light. These organelles, called outer segments, possess elaborate architectures that include many hundreds of light-sensitive membranous disks arrayed one atop another in precise register. These stacked disks capture light and initiate the chain of molecular and cellular events that underlie normal vision. Outer segment organization is challenged by an inherently dynamic nature; these organelles are subject to a renewal process that replaces a significant fraction of their disks (up to ∼10%) on a daily basis. In addition, a broad range of environmental and genetic insults can disrupt outer segment morphology to impair photoreceptor function and viability. In this chapter, we survey the major progress that has been made for understanding the molecular basis of outer segment architecture. We also discuss key aspects of organelle lipid and protein composition, and highlight distributions, interactions, and potential structural functions of key OS-resident molecules, including: kinesin-2, actin, RP1, prominin-1, protocadherin 21, peripherin-2/rds, rom-1, glutamic acid-rich proteins, and rhodopsin. Finally, we identify key knowledge gaps and challenges that remain for understanding how normal outer segment architecture is established and maintained.
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Affiliation(s)
- Andrew F X Goldberg
- Eye Research Institute, Oakland University, 417 Dodge Hall, Rochester, MI, 48309, USA.
| | - Orson L Moritz
- Department of Ophthalmology & Visual Sciences, University of British Columbia, Vancouver, BC, Canada
| | - David S Williams
- Department of Ophthalmology and Jules Stein Eye Institute, Department of Neurobiology, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
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36
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Zhao L, Chen Y, Bajaj AO, Eblimit A, Xu M, Soens ZT, Wang F, Ge Z, Jung SY, He F, Li Y, Wensel TG, Qin J, Chen R. Integrative subcellular proteomic analysis allows accurate prediction of human disease-causing genes. Genome Res 2016; 26:660-9. [PMID: 26912414 PMCID: PMC4864458 DOI: 10.1101/gr.198911.115] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 02/19/2016] [Indexed: 12/04/2022]
Abstract
Proteomic profiling on subcellular fractions provides invaluable information regarding both protein abundance and subcellular localization. When integrated with other data sets, it can greatly enhance our ability to predict gene function genome-wide. In this study, we performed a comprehensive proteomic analysis on the light-sensing compartment of photoreceptors called the outer segment (OS). By comparing with the protein profile obtained from the retina tissue depleted of OS, an enrichment score for each protein is calculated to quantify protein subcellular localization, and 84% accuracy is achieved compared with experimental data. By integrating the protein OS enrichment score, the protein abundance, and the retina transcriptome, the probability of a gene playing an essential function in photoreceptor cells is derived with high specificity and sensitivity. As a result, a list of genes that will likely result in human retinal disease when mutated was identified and validated by previous literature and/or animal model studies. Therefore, this new methodology demonstrates the synergy of combining subcellular fractionation proteomics with other omics data sets and is generally applicable to other tissues and diseases.
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Affiliation(s)
- Li Zhao
- Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, Texas 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yiyun Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Amol Onkar Bajaj
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Aiden Eblimit
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mingchu Xu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Zachry T Soens
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Feng Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Zhongqi Ge
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sung Yun Jung
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Feng He
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Theodore G Wensel
- Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jun Qin
- Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Rui Chen
- Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, Texas 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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Burgoyne T, Meschede IP, Burden JJ, Bailly M, Seabra MC, Futter CE. Rod disc renewal occurs by evagination of the ciliary plasma membrane that makes cadherin-based contacts with the inner segment. Proc Natl Acad Sci U S A 2015; 112:15922-7. [PMID: 26668363 PMCID: PMC4702997 DOI: 10.1073/pnas.1509285113] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The outer segments of vertebrate rod photoreceptors are renewed every 10 d. Outer segment components are transported from the site of synthesis in the inner segment through the connecting cilium, followed by assembly of the highly ordered discs. Two models of assembly of discrete discs involving either successive fusion events between intracellular rhodopsin-bearing vesicles or the evagination of the plasma membrane followed by fusion of adjacent evaginations have been proposed. Here we use immuno-electron microscopy and electron tomography to show that rhodopsin is transported from the inner to the outer segment via the ciliary plasma membrane, subsequently forming successive evaginations that "zipper" up proximally, but at their leading edges are free to make junctions containing the protocadherin, PCDH21, with the inner segment plasma membrane. Given the physical dimensions of the evaginations, coupled with likely instability of the membrane cortex at the distal end of the connecting cilium, we propose that the evagination occurs via a process akin to blebbing and is not driven by actin polymerization. Disassembly of these junctions is accompanied by fusion of the leading edges of successive evaginations to form discrete discs. This fusion is topologically different to that mediated by the membrane fusion proteins, SNAREs, as initial fusion is between exoplasmic leaflets, and is accompanied by gain of the tetraspanin rim protein, peripherin.
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Affiliation(s)
- Thomas Burgoyne
- Institute of Ophthalmology, University College London, London, EC1V9EL, United Kingdom
| | - Ingrid P Meschede
- Institute of Ophthalmology, University College London, London, EC1V9EL, United Kingdom
| | - Jemima J Burden
- Laboratory for Molecular and Cell Biology, University College London, London, WC1E6BT, United Kingdom
| | - Maryse Bailly
- Institute of Ophthalmology, University College London, London, EC1V9EL, United Kingdom
| | - Miguel C Seabra
- National Heart and Lung Institute, Imperial College, London, SW72AZ, United Kingdom; Centro de Estudos de Doenças Crónicas, NOVA Medical School/Faculdade de Ciências Médicas, Universidade Nova de Lisboa, 1169-056, Lisboa, Portugal
| | - Clare E Futter
- Institute of Ophthalmology, University College London, London, EC1V9EL, United Kingdom;
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Zulliger R, Conley SM, Mwoyosvi ML, Stuck MW, Azadi S, Naash MI. SNAREs Interact with Retinal Degeneration Slow and Rod Outer Segment Membrane Protein-1 during Conventional and Unconventional Outer Segment Targeting. PLoS One 2015; 10:e0138508. [PMID: 26406599 PMCID: PMC4583372 DOI: 10.1371/journal.pone.0138508] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 08/31/2015] [Indexed: 12/31/2022] Open
Abstract
Mutations in the photoreceptor protein peripherin-2 (also known as RDS) cause severe retinal degeneration. RDS and its homolog ROM-1 (rod outer segment protein 1) are synthesized in the inner segment and then trafficked into the outer segment where they function in tetramers and covalently linked larger complexes. Our goal is to identify binding partners of RDS and ROM-1 that may be involved in their biosynthetic pathway or in their function in the photoreceptor outer segment (OS). Here we utilize several methods including mass spectrometry after affinity purification, in vitro co-expression followed by pull-down, in vivo pull-down from mouse retinas, and proximity ligation assay to identify and confirm the SNARE proteins Syntaxin 3B and SNAP-25 as novel binding partners of RDS and ROM-1. We show that both covalently linked and non-covalently linked RDS complexes interact with Syntaxin 3B. RDS in the mouse is trafficked from the inner segment to the outer segment by both conventional (i.e., Golgi dependent) and unconventional secretory pathways, and RDS from both pathways interacts with Syntaxin3B. Syntaxin 3B and SNAP-25 are enriched in the inner segment (compared to the outer segment) suggesting that the interaction with RDS/ROM-1 occurs in the inner segment. Syntaxin 3B and SNAP-25 are involved in mediating fusion of vesicles carrying other outer segment proteins during outer segment targeting, so could be involved in the trafficking of RDS/ROM-1.
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Affiliation(s)
- Rahel Zulliger
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, United States of America
| | - Shannon M. Conley
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, United States of America
| | - Maggie L. Mwoyosvi
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, United States of America
| | - Michael W. Stuck
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, United States of America
| | - Seifollah Azadi
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, United States of America
| | - Muna I. Naash
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, United States of America
- * E-mail:
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Yang HJ, Ratnapriya R, Cogliati T, Kim JW, Swaroop A. Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease. Prog Retin Eye Res 2015; 46:1-30. [PMID: 25668385 PMCID: PMC4402139 DOI: 10.1016/j.preteyeres.2015.01.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 01/18/2015] [Accepted: 01/21/2015] [Indexed: 01/10/2023]
Abstract
Genomics and genetics have invaded all aspects of biology and medicine, opening uncharted territory for scientific exploration. The definition of "gene" itself has become ambiguous, and the central dogma is continuously being revised and expanded. Computational biology and computational medicine are no longer intellectual domains of the chosen few. Next generation sequencing (NGS) technology, together with novel methods of pattern recognition and network analyses, has revolutionized the way we think about fundamental biological mechanisms and cellular pathways. In this review, we discuss NGS-based genome-wide approaches that can provide deeper insights into retinal development, aging and disease pathogenesis. We first focus on gene regulatory networks (GRNs) that govern the differentiation of retinal photoreceptors and modulate adaptive response during aging. Then, we discuss NGS technology in the context of retinal disease and develop a vision for therapies based on network biology. We should emphasize that basic strategies for network construction and analyses can be transported to any tissue or cell type. We believe that specific and uniform guidelines are required for generation of genome, transcriptome and epigenome data to facilitate comparative analysis and integration of multi-dimensional data sets, and for constructing networks underlying complex biological processes. As cellular homeostasis and organismal survival are dependent on gene-gene and gene-environment interactions, we believe that network-based biology will provide the foundation for deciphering disease mechanisms and discovering novel drug targets for retinal neurodegenerative diseases.
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Affiliation(s)
- Hyun-Jin Yang
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Rinki Ratnapriya
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Tiziana Cogliati
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Jung-Woong Kim
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA.
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Rhodopsin Trafficking and Mistrafficking: Signals, Molecular Components, and Mechanisms. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2015; 132:39-71. [PMID: 26055054 DOI: 10.1016/bs.pmbts.2015.02.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Rhodopsin is a seven-transmembrane G protein-coupled receptor (GPCR) and is the main component of the photoreceptor outer segment (OS), a ciliary compartment essential for vision. Because the OSs are incapable of protein synthesis, rhodopsin must first be synthesized in the inner segments (ISs) and subsequently trafficked across the connecting cilia to the OSs where it participates in the phototransduction cascade. Rapid turnover of the OS necessitates a high rate of synthesis and efficient trafficking of rhodopsin to the cilia. This cilia-targeting mechanism is shared among other ciliary-localized GPCRs. In this review, we will discuss the process of rhodopsin trafficking from the IS to the OS beginning with the trafficking signals present on the protein. Starting from the endoplasmic reticulum and the Golgi apparatus within the IS, we will cover the molecular components assisting the biogenesis and the proper sorting. We will also review the confirmed binding and interacting partners that help target rhodopsin toward the connecting cilium as well as the cilia-localized components which direct proteins into the proper compartments of the OS. While rhodopsin is the most critical and abundant component of the photoreceptor OS, mutations in the rhodopsin gene commonly lead to its mislocalization within the photoreceptors. In addition to covering the trafficking patterns of rhodopsin, we will also review some of the most common rhodopsin mutants which cause mistrafficking and subsequent death of photoreceptors. Toward the goal of understanding the pathogenesis, three major mechanisms of aberrant trafficking as well as putative mechanisms of photoreceptor degeneration will be discussed.
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41
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Baker BY, Gulati S, Shi W, Wang B, Stewart PL, Palczewski K. Crystallization of proteins from crude bovine rod outer segments. Methods Enzymol 2015; 557:439-58. [PMID: 25950977 DOI: 10.1016/bs.mie.2014.11.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Obtaining protein crystals suitable for X-ray diffraction studies comprises the greatest challenge in the determination of protein crystal structures, especially for membrane proteins and protein complexes. Although high purity has been broadly accepted as one of the most significant requirements for protein crystallization, a recent study of the Escherichia coli proteome showed that many proteins have an inherent propensity to crystallize and do not require a highly homogeneous sample (Totir et al., 2012). As exemplified by RPE65 (Kiser, Golczak, Lodowski, Chance, & Palczewski, 2009), there also are cases of mammalian proteins crystallized from less purified samples. To test whether this phenomenon can be applied more broadly to the study of proteins from higher organisms, we investigated the protein crystallization profile of bovine rod outer segment (ROS) crude extracts. Interestingly, multiple protein crystals readily formed from such extracts, some of them diffracting to high resolution that allowed structural determination. A total of seven proteins were crystallized, one of which was a membrane protein. Successful crystallization of proteins from heterogeneous ROS extracts demonstrates that many mammalian proteins also have an intrinsic propensity to crystallize from complex biological mixtures. By providing an alternative approach to heterologous expression to achieve crystallization, this strategy could be useful for proteins and complexes that are difficult to purify or obtain by recombinant techniques.
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Affiliation(s)
- Bo Y Baker
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA; Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.
| | - Sahil Gulati
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA; Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Wuxian Shi
- Center for Proteomics and Bioinformatics, Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Benlian Wang
- Center for Proteomics and Bioinformatics, Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Phoebe L Stewart
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA; Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Krzysztof Palczewski
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA; Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA.
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Duda T, Wen XH, Isayama T, Sharma RK, Makino CL. Bicarbonate Modulates Photoreceptor Guanylate Cyclase (ROS-GC) Catalytic Activity. J Biol Chem 2015; 290:11052-60. [PMID: 25767116 DOI: 10.1074/jbc.m115.650408] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Indexed: 01/13/2023] Open
Abstract
By generating the second messenger cGMP in retinal rods and cones, ROS-GC plays a central role in visual transduction. Guanylate cyclase-activating proteins (GCAPs) link cGMP synthesis to the light-induced fall in [Ca(2+)]i to help set absolute sensitivity and assure prompt recovery of the response to light. The present report discloses a surprising feature of this system: ROS-GC is a sensor of bicarbonate. Recombinant ROS-GCs synthesized cGMP from GTP at faster rates in the presence of bicarbonate with an ED50 of 27 mM for ROS-GC1 and 39 mM for ROS-GC2. The effect required neither Ca(2+) nor use of the GCAPs domains; however, stimulation of ROS-GC1 was more powerful in the presence of GCAP1 or GCAP2 at low [Ca(2+)]. When applied to retinal photoreceptors, bicarbonate enhanced the circulating current, decreased sensitivity to flashes, and accelerated flash response kinetics. Bicarbonate was effective when applied either to the outer or inner segment of red-sensitive cones. In contrast, bicarbonate exerted an effect when applied to the inner segment of rods but had little efficacy when applied to the outer segment. The findings define a new regulatory mechanism of the ROS-GC system that affects visual transduction and is likely to affect the course of retinal diseases caused by cGMP toxicity.
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Affiliation(s)
- Teresa Duda
- From the Research Divisions of Biochemistry and Molecular Biology, Unit of Regulatory and Molecular Biology, Salus University, Elkins Park, Pennsylvania 19027 and
| | - Xiao-Hong Wen
- the Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, Massachusetts 02114
| | - Tomoki Isayama
- the Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, Massachusetts 02114
| | - Rameshwar K Sharma
- From the Research Divisions of Biochemistry and Molecular Biology, Unit of Regulatory and Molecular Biology, Salus University, Elkins Park, Pennsylvania 19027 and
| | - Clint L Makino
- the Department of Ophthalmology, Massachusetts Eye and Ear Infirmary and Harvard Medical School, Boston, Massachusetts 02114
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Zulliger R, Naash MI, Rajala RVS, Molday RS, Azadi S. Impaired association of retinal degeneration-3 with guanylate cyclase-1 and guanylate cyclase-activating protein-1 leads to leber congenital amaurosis-1. J Biol Chem 2014; 290:3488-99. [PMID: 25477517 DOI: 10.1074/jbc.m114.616656] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
One-fifth of all cases of Leber congenital amaurosis are type 1 (LCA1). LCA1 is a severe form of retinal dystrophy caused by loss-of-function mutations in guanylate cyclase 1 (GC1), a key member of the phototransduction cascade involved in modulating the photocurrents. Although GC1 has been studied for some time, the mechanisms responsible for its regulation and membrane targeting are not fully understood. We reported earlier that retinal degeneration 3 (RD3) protein interacts with GC1 and promotes its targeting to the photoreceptor outer segments (POS). Here, we extend our studies to show a direct association between RD3 and guanylate cyclase activating protein 1 (GCAP1). Furthermore, we demonstrate that this functional interaction is important for GC1 targeting to POS. We also show that most LCA1-causing mutations in GC1 result in lost GC1 interaction with RD3 or GC1 being targeted to the plasma membrane. Our data suggest that GC1, GCAP1, and RD3 form a complex in the endoplasmic reticulum that targets GC1 to POS. Interruption of this assembly is likely the underlying mechanism for a subset of LCA1. This study offers insights for the development of therapeutic strategies to treat this severe form of blindness.
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Affiliation(s)
| | | | - Raju V S Rajala
- From the Departments of Cell Biology, Ophthalmology, and Physiology, University of Oklahoma Health Sciences Center and the Dean McGee Eye Institute, Oklahoma City, Oklahoma 73104 and
| | - Robert S Molday
- the Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Seifollah Azadi
- From the Departments of Cell Biology, the Dean McGee Eye Institute, Oklahoma City, Oklahoma 73104 and
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Wang F, Wang Y, Zhang B, Zhao L, Lyubasyuk V, Wang K, Xu M, Li Y, Wu F, Wen C, Bernstein PS, Lin D, Zhu S, Wang H, Zhang K, Chen R. A missense mutation in HK1 leads to autosomal dominant retinitis pigmentosa. Invest Ophthalmol Vis Sci 2014; 55:7159-64. [PMID: 25316723 DOI: 10.1167/iovs.14-15520] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Retinitis pigmentosa (RP) is a genetically heterogeneous disease with over 60 causative genes known to date. Nevertheless, approximately 40% of RP cases remain genetically unsolved, suggesting that many novel disease-causing genes are yet to be identified. In this study, we aimed to identify the causative mutation for a large autosomal dominant RP (adRP) family with negative results from known retinal disease gene screening. METHODS Linkage analysis followed by whole-exome sequencing was performed. Stringent variant filtering and prioritization was carried out to identify the causative mutation. RESULTS Linkage analysis identified a minimal disease region of 8 Mb on chromosome 10 with a peak parametric logarithm (base 10) of odds (LOD) score of 3.500. Further whole-exome sequencing identified a heterozygous missense mutation (NM_000188.2:c.2539G>A, p.E847K) in hexokinase 1 (HK1) that segregated with the disease phenotype in the family. Biochemical assays showed that the E847K mutation does not affect hexokinase enzymatic activity or the protein stability, suggesting that the mutation may impact other uncharacterized function or result in a gain of function of HK1. CONCLUSIONS Here, we identified HK1 as a novel causative gene for adRP. This is the first report that associates the glucose metabolic pathway with human retinal degenerative disease, suggesting a potential new disease mechanism.
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Affiliation(s)
- Feng Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Yandong Wang
- Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Bin Zhang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Li Zhao
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, Texas, United States
| | - Vera Lyubasyuk
- Shiley Eye Center and Institute for Genomic Medicine, University of California-San Diego, La Jolla, California, United States
| | - Keqing Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Mingchu Xu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Frances Wu
- Shiley Eye Center and Institute for Genomic Medicine, University of California-San Diego, La Jolla, California, United States
| | - Cindy Wen
- Shiley Eye Center and Institute for Genomic Medicine, University of California-San Diego, La Jolla, California, United States
| | - Paul S Bernstein
- Department of Ophthalmology and Visual Sciences, Moran Eye Center, University of Utah School of Medicine, Salt Lake City, Utah, United States
| | - Danni Lin
- Shiley Eye Center and Institute for Genomic Medicine, University of California-San Diego, La Jolla, California, United States
| | - Susanna Zhu
- Shiley Eye Center and Institute for Genomic Medicine, University of California-San Diego, La Jolla, California, United States
| | - Hui Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Kang Zhang
- Shiley Eye Center and Institute for Genomic Medicine, University of California-San Diego, La Jolla, California, United States Veterans Administration Healthcare System, San Diego, California, United States
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, Texas, United States The Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States
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45
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Köster M, Dell'Orco D, Koch KW. The interaction network of rhodopsin involving the heterotrimeric G-protein transducin and the monomeric GTPase Rac1 is determined by distinct binding processes. FEBS J 2014; 281:5175-85. [PMID: 25243418 DOI: 10.1111/febs.13064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 09/12/2014] [Accepted: 09/18/2014] [Indexed: 12/01/2022]
Abstract
The monomeric G-protein Rac1, a member of the family of Rho/Rac/Cdc42 GTPases, is involved in light-induced photoreceptor degeneration, but its specific role remains elusive. In particular, reports on Rac1 interacting with the visual pigment rhodopsin are puzzling and need a more quantitative examination. We probed the presence of Rac1 in rod outer segments by immunohistochemical staining of bovine retinae and western blot analysis of isolated rod outer segments. Rac1 was present throughout the whole retina except in the outer and inner nuclear layers, but was strongly expressed in photoreceptor cells. Rac1 was distributed in three different fractions of rod outer segments: one fraction was soluble in detergents, a second fraction cosegregated with lipid rafts, and a third fraction was associated with lipid bilayer free axonemal/cytoskeletal structures. We also investigated the interaction between rhodopsin and Rac1 by using surface plasmon resonance spectroscopy under dark and light conditions. Biophysical interaction studies revealed that Rac1 could interact with rhodopsin, but in a light-independent manner, and kinetic analysis indicated that binding of Rac1 occurred with lower affinity and speed than the association of transducin and rhodopsin. Thus, in dark-adapted rod cells, Rac1 cannot compete with transducin for binding to rhodopsin, and signalling can proceed normally. Instead, the concentration of transducin has to drop significantly so that Rac1 can bind to rhodopsin; in the outer segment, this occurs only under intense illumination, when transducin is translocated to the inner segment.
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Affiliation(s)
- Maike Köster
- Department of Neurosciences, Biochemistry Group, University of Oldenburg, Germany
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46
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Baker BY, Shi W, Wang B, Palczewski K. High-resolution crystal structures of the photoreceptor glyceraldehyde 3-phosphate dehydrogenase (GAPDH) with three and four-bound NAD molecules. Protein Sci 2014; 23:1629-39. [PMID: 25176140 DOI: 10.1002/pro.2543] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 08/25/2014] [Accepted: 08/26/2014] [Indexed: 11/09/2022]
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) catalyzes the oxidative phosphorylation of d-glyceraldehyde 3-phosphate (G3P) into 1,3-diphosphoglycerate (BGP) in the presence of the NAD cofactor. GAPDH is an important drug target because of its central role in glycolysis, and nonglycolytic processes such as nuclear RNA transport, DNA replication/repair, membrane fusion and cellular apoptosis. Recent studies found that GAPDH participates in the development of diabetic retinopathy and its progression after the cessation of hyperglycemia. Here, we report two structures for native bovine photoreceptor GAPDH as a homotetramer with differing occupancy by NAD, bGAPDH(NAD)4 , and bGAPDH(NAD)3 . The bGAPDH(NAD)4 was solved at 1.52 Å, the highest resolution for GAPDH. Structural comparison of the bGAPDH(NAD)4 and bGAPDH(NAD)3 models revealed novel details of conformational changes induced by cofactor binding, including a loop region (residues 54-56). Structure analysis of bGAPDH confirmed the importance of Phe34 in NAD binding, and demonstrated that Phe34 was stabilized in the presence of NAD but displayed greater mobility in its absence. The oxidative state of the active site Cys149 residue is regulated by NAD binding, because this residue was found oxidized in the absence of dinucleotide. The distance between Cys149 and His176 decreased upon NAD binding and Cys149 remained in a reduced state when NAD was bound. These findings provide an important structural step for understanding the mechanism of GAPDH activity in vision and its pathological role in retinopathies.
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Affiliation(s)
- Bo Y Baker
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio, 44106
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47
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Pearring JN, Lieu EC, Winter JR, Baker SA, Arshavsky VY. R9AP targeting to rod outer segments is independent of rhodopsin and is guided by the SNARE homology domain. Mol Biol Cell 2014; 25:2644-9. [PMID: 25009288 PMCID: PMC4148253 DOI: 10.1091/mbc.e14-02-0747] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
R9AP, the membrane anchor for transducin's GTPase-activating complex, contains targeting information within its SNARE homology domain that is both necessary and sufficient for R9AP delivery to photoreceptor outer segments. R9AP's targeting is independent of rhodopsin, the most abundant protein residing in the outer segment organelle. In vertebrate photoreceptor cells, rapid recovery from light excitation is dependent on the RGS9⋅Gβ5 GTPase-activating complex located in the light-sensitive outer segment organelle. RGS9⋅Gβ5 is tethered to the outer segment membranes by its membrane anchor, R9AP. Recent studies indicated that RGS9⋅Gβ5 possesses targeting information that excludes it from the outer segment and that this information is overridden by association with R9AP, which allows outer segment targeting of the entire complex. It was also proposed that R9AP itself does not contain specific targeting information and instead is delivered to the outer segment in the same post-Golgi vesicles as rhodopsin, because they are the most abundant transport vesicles in photoreceptor cells. In this study, we revisited this concept by analyzing R9AP targeting in rods of wild-type and rhodopsin-knockout mice. We found that the R9AP targeting mechanism does not require the presence of rhodopsin and further demonstrated that R9AP is actively targeted in rods by its SNARE homology domain.
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Affiliation(s)
- Jillian N Pearring
- Albert Eye Research Institute, Duke Eye Center, Duke University, Durham, NC 27710
| | - Eric C Lieu
- Albert Eye Research Institute, Duke Eye Center, Duke University, Durham, NC 27710
| | - Joan R Winter
- Albert Eye Research Institute, Duke Eye Center, Duke University, Durham, NC 27710
| | - Sheila A Baker
- Department of Biochemistry and Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Vadim Y Arshavsky
- Albert Eye Research Institute, Duke Eye Center, Duke University, Durham, NC 27710
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48
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Busskamp V, Krol J, Nelidova D, Daum J, Szikra T, Tsuda B, Jüttner J, Farrow K, Scherf BG, Alvarez CPP, Genoud C, Sothilingam V, Tanimoto N, Stadler M, Seeliger M, Stoffel M, Filipowicz W, Roska B. miRNAs 182 and 183 are necessary to maintain adult cone photoreceptor outer segments and visual function. Neuron 2014; 83:586-600. [PMID: 25002228 DOI: 10.1016/j.neuron.2014.06.020] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2014] [Indexed: 12/31/2022]
Abstract
The outer segments of cones serve as light detectors for daylight color vision, and their dysfunction leads to human blindness conditions. We show that the cone-specific disruption of DGCR8 in adult mice led to the loss of miRNAs and the loss of outer segments, resulting in photoreceptors with significantly reduced light responses. However, the number of cones remained unchanged. The loss of the outer segments occurred gradually over 1 month, and during this time the genetic signature of cones decreased. Reexpression of the sensory-cell-specific miR-182 and miR-183 prevented outer segment loss. These miRNAs were also necessary and sufficient for the formation of inner segments, connecting cilia and short outer segments, as well as light responses in stem-cell-derived retinal cultures. Our results show that miR-182- and miR-183-regulated pathways are necessary for cone outer segment maintenance in vivo and functional outer segment formation in vitro.
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Affiliation(s)
- Volker Busskamp
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Jacek Krol
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Dasha Nelidova
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4058 Basel, Switzerland
| | - Janine Daum
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4058 Basel, Switzerland
| | - Tamas Szikra
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Ben Tsuda
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Josephine Jüttner
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Karl Farrow
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Brigitte Gross Scherf
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | | | - Christel Genoud
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Vithiyanjali Sothilingam
- Division of Ocular Neurodegeneration, Institute for Ophthalmic Research, Department of Ophthalmology, Eberhard-Karls University, 72076 Tübingen, Germany
| | - Naoyuki Tanimoto
- Division of Ocular Neurodegeneration, Institute for Ophthalmic Research, Department of Ophthalmology, Eberhard-Karls University, 72076 Tübingen, Germany
| | - Michael Stadler
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Mathias Seeliger
- Division of Ocular Neurodegeneration, Institute for Ophthalmic Research, Department of Ophthalmology, Eberhard-Karls University, 72076 Tübingen, Germany
| | - Markus Stoffel
- Institute for Molecular Health Sciences, ETH, 8093 Zürich
| | - Witold Filipowicz
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4058 Basel, Switzerland.
| | - Botond Roska
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
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49
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Molday LL, Jefferies T, Molday RS. Insights into the role of RD3 in guanylate cyclase trafficking, photoreceptor degeneration, and Leber congenital amaurosis. Front Mol Neurosci 2014; 7:44. [PMID: 24904271 PMCID: PMC4033307 DOI: 10.3389/fnmol.2014.00044] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 04/29/2014] [Indexed: 11/13/2022] Open
Abstract
Retinal degeneration 3 (RD3) is an evolutionarily conserved 23 kDa protein expressed in rod and cone photoreceptor cells. Mutations in the gene encoding RD3 resulting in unstable non-functional C-terminal truncated proteins are responsible for early onset photoreceptor degeneration in Leber Congenital Amaurosis 12 patients, the rd3 mice, and the rcd2 collies. Recent studies have shown that RD3 interacts with guanylate cyclases GC1 and GC2 in retinal cell extracts and HEK293 cells co-expressing GC and RD3. This interaction inhibits GC catalytic activity and promotes the exit of GC1 and GC2 from the endoplasmic reticulum and their trafficking to photoreceptor outer segments. Adeno-associated viral vector delivery of the normal RD3 gene to photoreceptors of the rd3 mouse restores GC1 and GC2 expression and outer segment localization and leads to the long-term recovery of visual function and photoreceptor cell survival. This review focuses on the genetic and biochemical studies that have provided insight into the role of RD3 in photoreceptor function and survival.
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Affiliation(s)
- Laurie L Molday
- Department of Biochemistry and Molecular Biology, Center for Macular Research, University of British Columbia Vancouver, BC, USA
| | - Thomas Jefferies
- Department of Biochemistry and Molecular Biology, Center for Macular Research, University of British Columbia Vancouver, BC, USA
| | - Robert S Molday
- Department of Biochemistry and Molecular Biology, Center for Macular Research, University of British Columbia Vancouver, BC, USA
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50
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Coleman JA, Zhu X, Djajadi HR, Molday LL, Smith RS, Libby RT, John SWM, Molday RS. Phospholipid flippase ATP8A2 is required for normal visual and auditory function and photoreceptor and spiral ganglion cell survival. J Cell Sci 2014; 127:1138-49. [PMID: 24413176 DOI: 10.1242/jcs.145052] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
ATP8A2 is a P4-ATPase that is highly expressed in the retina, brain, spinal cord and testes. In the retina, ATP8A2 is localized in photoreceptors where it uses ATP to transport phosphatidylserine (PS) and phosphatidylethanolamine (PE) from the exoplasmic to the cytoplasmic leaflet of membranes. Although mutations in ATP8A2 have been reported to cause mental retardation in humans and degeneration of spinal motor neurons in mice, the role of ATP8A2 in sensory systems has not been investigated. We have analyzed the retina and cochlea of ATP8A2-deficient mice to determine the role of ATP8A2 in visual and auditory systems. ATP8A2-deficient mice have shortened photoreceptor outer segments, a reduction in photoresponses and decreased photoreceptor viability. The ultrastructure and phagocytosis of the photoreceptor outer segment appeared normal, but the PS and PE compositions were altered and the rhodopsin content was decreased. The auditory brainstem response threshold was significantly higher and degeneration of spiral ganglion cells was apparent. Our studies indicate that ATP8A2 plays a crucial role in photoreceptor and spiral ganglion cell function and survival by maintaining phospholipid composition and contributing to vesicle trafficking.
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Affiliation(s)
- Jonathan A Coleman
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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