151
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Nguyen MTT, Vemaraju S, Nayak G, Odaka Y, Buhr ED, Alonzo N, Tran U, Batie M, Upton BA, Darvas M, Kozmik Z, Rao S, Hegde RS, Iuvone PM, Van Gelder RN, Lang RA. An opsin 5-dopamine pathway mediates light-dependent vascular development in the eye. Nat Cell Biol 2019; 21:420-429. [PMID: 30936473 PMCID: PMC6573021 DOI: 10.1038/s41556-019-0301-x] [Citation(s) in RCA: 34] [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: 03/27/2018] [Accepted: 02/19/2019] [Indexed: 02/07/2023]
Abstract
During mouse postnatal eye development, the embryonic hyaloid vascular network regresses from the vitreous as an adaption for high-acuity vision. This process occurs with precisely controlled timing. Here, we show that opsin 5 (OPN5; also known as neuropsin)-dependent retinal light responses regulate vascular development in the postnatal eye. In Opn5-null mice, hyaloid vessels regress precociously. We demonstrate that 380-nm light stimulation via OPN5 and VGAT (the vesicular GABA/glycine transporter) in retinal ganglion cells enhances the activity of inner retinal DAT (also known as SLC6A3; a dopamine reuptake transporter) and thus suppresses vitreal dopamine. In turn, dopamine acts directly on hyaloid vascular endothelial cells to suppress the activity of vascular endothelial growth factor receptor 2 (VEGFR2) and promote hyaloid vessel regression. With OPN5 loss of function, the vitreous dopamine level is elevated and results in premature hyaloid regression. These investigations identify violet light as a developmental timing cue that, via an OPN5-dopamine pathway, regulates optic axis clearance in preparation for visual function.
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Affiliation(s)
- Minh-Thanh T Nguyen
- The Visual Systems Group, Abrahamson Pediatric Eye Institute, Division of Pediatric Ophthalmology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Chronobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Shruti Vemaraju
- The Visual Systems Group, Abrahamson Pediatric Eye Institute, Division of Pediatric Ophthalmology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Chronobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Gowri Nayak
- The Visual Systems Group, Abrahamson Pediatric Eye Institute, Division of Pediatric Ophthalmology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Chronobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Yoshinobu Odaka
- The Visual Systems Group, Abrahamson Pediatric Eye Institute, Division of Pediatric Ophthalmology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Chronobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ethan D Buhr
- Department of Ophthalmology, University of Washington Medical School, Seattle, WA, USA
| | - Nuria Alonzo
- The Visual Systems Group, Abrahamson Pediatric Eye Institute, Division of Pediatric Ophthalmology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Uyen Tran
- The Visual Systems Group, Abrahamson Pediatric Eye Institute, Division of Pediatric Ophthalmology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Matthew Batie
- Clinical Engineering, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Brian A Upton
- The Visual Systems Group, Abrahamson Pediatric Eye Institute, Division of Pediatric Ophthalmology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Chronobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Martin Darvas
- Pathology, University of Washington Medical School, Seattle, WA, USA
| | - Zbynek Kozmik
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Sujata Rao
- Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Rashmi S Hegde
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - P Michael Iuvone
- Department of Ophthalmology, Emory University School of Medicine, Atlanta, GA, USA
- Pharmacology, Emory University School of Medicine, Atlanta, GA, USA
| | - Russell N Van Gelder
- Department of Ophthalmology, University of Washington Medical School, Seattle, WA, USA
- Pathology, University of Washington Medical School, Seattle, WA, USA
- Biological Structure, University of Washington Medical School, Seattle, WA, USA
| | - Richard A Lang
- The Visual Systems Group, Abrahamson Pediatric Eye Institute, Division of Pediatric Ophthalmology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Center for Chronobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Ophthalmology, University of Cincinnati, College of Medicine, Cincinnati, OH, USA.
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152
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Antognazza MR, Abdel Aziz I, Lodola F. Use of Exogenous and Endogenous Photomediators as Efficient ROS Modulation Tools: Results and Perspectives for Therapeutic Purposes. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2019; 2019:2867516. [PMID: 31049131 PMCID: PMC6462332 DOI: 10.1155/2019/2867516] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 01/15/2019] [Indexed: 01/09/2023]
Abstract
Reactive Oxygen Species (ROS) play an essential dual role in living systems. Healthy levels of ROS modulate several signaling pathways, but at the same time, when they exceed normal physiological amounts, they work in the opposite direction, playing pivotal functions in the pathophysiology of multiple severe medical conditions (i.e., cancer, diabetes, neurodegenerative and cardiovascular diseases, and aging). Therefore, the research for methods to detect their levels via light-sensitive fluorescent probes has been extensively studied over the years. However, this is not the only link between light and ROS. In fact, the modulation of ROS mediated by light has been exploited already for a long time. In this review, we report the state of the art, as well as recent developments, in the field of photostimulation of oxidative stress, from photobiomodulation (PBM) mediated by naturally expressed light-sensitive proteins to the most recent optogenetic approaches, and finally, we describe the main methods of exogenous stimulation, in particular highlighting the new insights based on optically driven ROS modulation mediated by polymeric materials.
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Affiliation(s)
- Maria Rosa Antognazza
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Pascoli 70/3, 20133 Milano, Italy
| | - Ilaria Abdel Aziz
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Pascoli 70/3, 20133 Milano, Italy
- Politecnico di Milano, Dipartimento di Fisica, Piazza L. Da Vinci 32, 20133 Milano, Italy
| | - Francesco Lodola
- Center for Nano Science and Technology, Istituto Italiano di Tecnologia, Via Pascoli 70/3, 20133 Milano, Italy
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153
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Srinivasan S, Guixà-González R, Cordomí A, Garriga P. Ligand Binding Mechanisms in Human Cone Visual Pigments. Trends Biochem Sci 2019; 44:629-639. [PMID: 30853245 DOI: 10.1016/j.tibs.2019.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/04/2019] [Accepted: 02/07/2019] [Indexed: 12/13/2022]
Abstract
Vertebrate vision starts with light absorption by visual pigments in rod and cone photoreceptor cells of the retina. Rhodopsin, in rod cells, responds to dim light, whereas three types of cone opsins (red, green, and blue) function under bright light and mediate color vision. Cone opsins regenerate with retinal much faster than rhodopsin, but the molecular mechanism of regeneration is still unclear. Recent advances in the area pinpoint transient intermediate opsin conformations, and a possible secondary retinal-binding site, as determinant factors for regeneration. In this Review, we compile previous and recent findings to discuss possible mechanisms of ligand entry in cone opsins, involving a secondary binding site, which may have relevant functional and evolutionary implications.
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Affiliation(s)
- Sundaramoorthy Srinivasan
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya-Barcelona Tech, Rambla de Sant Nebridi 22, 08222 Terrassa, Spain
| | - Ramon Guixà-González
- Laboratori de Medicina Computational, Universitat Autonòma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Arnau Cordomí
- Laboratori de Medicina Computational, Universitat Autonòma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Pere Garriga
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya-Barcelona Tech, Rambla de Sant Nebridi 22, 08222 Terrassa, Spain.
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154
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Green light irradiation during sex differentiation induces female-to-male sex reversal in the medaka Oryzias latipes. Sci Rep 2019; 9:2383. [PMID: 30787482 PMCID: PMC6382872 DOI: 10.1038/s41598-019-38908-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/11/2019] [Indexed: 01/05/2023] Open
Abstract
This study investigated whether irradiation of a specific light wavelength could affect the sex differentiation of fish. We first found that the photoreceptor genes responsible for receiving red, green, and ultraviolet light were expressed in the eyes of medaka during the sex differentiation period. Second, we revealed that testes developed in 15.9% of genotypic females reared under green light irradiation. These female-to-male sex-reversed fish (i.e. neo-males) showed male-specific secondary sexual characteristics and produced motile sperm. Finally, progeny tests using the sperm of neo-males (XX) and eggs of normal females (XX) revealed that all F1 offspring were female, indicating for the first time in animals that irradiation with light of a specific wavelength can trigger sex reversal.
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155
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Miyahara T, Nakatsuji H. Light-Driven Proton, Sodium Ion, and Chloride Ion Transfer Mechanisms in Rhodopsins: SAC-CI Study. J Phys Chem A 2019; 123:1766-1784. [DOI: 10.1021/acs.jpca.8b10203] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Tomoo Miyahara
- Quantum Chemistry Research Institute, Kyoto Technoscience Center 16, 14 Yoshida Kawara-machi, Sakyou-ku, Kyoto 606-8305, Japan
| | - Hiroshi Nakatsuji
- Quantum Chemistry Research Institute, Kyoto Technoscience Center 16, 14 Yoshida Kawara-machi, Sakyou-ku, Kyoto 606-8305, Japan
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156
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Singh M, Katayama K, Béjà O, Kandori H. Anion binding to mutants of the Schiff base counterion in heliorhodopsin 48C12. Phys Chem Chem Phys 2019; 21:23663-23671. [DOI: 10.1039/c9cp04102h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The anion binds as the direct H-bonding acceptor of the Schiff base in E107A, while E107Q indirectly accommodates an anion.
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Affiliation(s)
- Manish Singh
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
- OptoBioTechnology Research Center
| | - Oded Béjà
- Faculty of Biology
- Technion – Israel Institute of Technology
- Haifa
- Israel
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
- OptoBioTechnology Research Center
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157
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Dalesio NM, Barreto Ortiz SF, Pluznick JL, Berkowitz DE. Olfactory, Taste, and Photo Sensory Receptors in Non-sensory Organs: It Just Makes Sense. Front Physiol 2018; 9:1673. [PMID: 30542293 PMCID: PMC6278613 DOI: 10.3389/fphys.2018.01673] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/07/2018] [Indexed: 01/28/2023] Open
Abstract
Sensory receptors that detect and respond to light, taste, and smell primarily belong to the G-protein-coupled receptor (GPCR) superfamily. In addition to their established roles in the nose, tongue, and eyes, these sensory GPCRs have been found in many ‘non-sensory' organs where they respond to different physicochemical stimuli, initiating signaling cascades in these extrasensory systems. For example, taste receptors in the airway, and photoreceptors in vascular smooth muscle cells, both cause smooth muscle relaxation when activated. In addition, olfactory receptors are present within the vascular system, where they play roles in angiogenesis as well as in modulating vascular tone. By better understanding the physiological and pathophysiological roles of sensory receptors in non-sensory organs, novel therapeutic agents can be developed targeting these receptors, ultimately leading to treatments for pathological conditions and potential cures for various disease states.
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Affiliation(s)
- Nicholas M Dalesio
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, Baltimore, MD, United States.,Department of Otolaryngology/Head & Neck Surgery, Johns Hopkins University, Baltimore, MD, United States
| | - Sebastian F Barreto Ortiz
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Jennifer L Pluznick
- Department of Physiology, Johns Hopkins University, Baltimore, MD, United States
| | - Dan E Berkowitz
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, Baltimore, MD, United States
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158
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Jiang Z, Yue WWS, Chen L, Sheng Y, Yau KW. Cyclic-Nucleotide- and HCN-Channel-Mediated Phototransduction in Intrinsically Photosensitive Retinal Ganglion Cells. Cell 2018; 175:652-664.e12. [PMID: 30270038 PMCID: PMC6203304 DOI: 10.1016/j.cell.2018.08.055] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 03/19/2018] [Accepted: 08/21/2018] [Indexed: 02/06/2023]
Abstract
Non-image-forming vision in mammals is mediated primarily by melanopsin-expressing, intrinsically photosensitive retinal ganglion cells (ipRGCs). In mouse M1-ipRGCs, by far the best-studied subtype, melanopsin activates PLCβ4 (phospholipase C-β4) to open TRPC6,7 channels, mechanistically similar to phototransduction in fly rhabdomeric (microvillous) photoreceptors. We report here that, surprisingly, mouse M4-ipRGCs rely on a different and hitherto undescribed melanopsin-driven, ciliary phototransduction mechanism involving cyclic nucleotide as the second messenger and HCN channels rather than CNG channels as the ion channel for phototransduction. Even more surprisingly, within an individual mouse M2-ipRGC, this HCN-channel-dependent, ciliary phototransduction pathway operates in parallel with the TRPC6,7-dependent rhabdomeric pathway. These findings reveal a complex heterogeneity in phototransduction among ipRGCs and, more importantly, break a general dogma about segregation of the two phototransduction motifs, likely with strong evolutionary implications.
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Affiliation(s)
- Zheng Jiang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Sensory Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Wendy W S Yue
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Sensory Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lujing Chen
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Sensory Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Neuroscience Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yanghui Sheng
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Sensory Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Neuroscience Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - King-Wai Yau
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Center for Sensory Biology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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159
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Rodgers J, Peirson SN, Hughes S, Hankins MW. Functional characterisation of naturally occurring mutations in human melanopsin. Cell Mol Life Sci 2018; 75:3609-3624. [PMID: 29700553 PMCID: PMC6133154 DOI: 10.1007/s00018-018-2813-0] [Citation(s) in RCA: 9] [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: 12/01/2017] [Revised: 03/06/2018] [Accepted: 04/05/2018] [Indexed: 12/12/2022]
Abstract
Melanopsin is a blue light-sensitive opsin photopigment involved in a range of non-image forming behaviours, including circadian photoentrainment and the pupil light response. Many naturally occurring genetic variants exist within the human melanopsin gene (OPN4), yet it remains unclear how these variants affect melanopsin protein function and downstream physiological responses to light. Here, we have used bioinformatic analysis and in vitro expression systems to determine the functional phenotypes of missense human OPN4 variants. From 1242 human OPN4 variants collated in the NCBI Short Genetic Variation database (dbSNP), we identified 96 that lead to non-synonymous amino acid substitutions. These 96 missense mutations were screened using sequence alignment and comparative approaches to select 16 potentially deleterious variants for functional characterisation using calcium imaging of melanopsin-driven light responses in HEK293T cells. We identify several previously uncharacterised OPN4 mutations with altered functional properties, including attenuated or abolished light responses, as well as variants demonstrating abnormal response kinetics. These data provide valuable insight into the structure-function relationships of human melanopsin, including several key functional residues of the melanopsin protein. The identification of melanopsin variants with significantly altered function may serve to detect individuals with disrupted melanopsin-based light perception, and potentially highlight those at increased risk of sleep disturbance, circadian dysfunction, and visual abnormalities.
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Affiliation(s)
- Jessica Rodgers
- Nuffield Laboratory of Ophthalmology, Sleep and Circadian Neuroscience Institute, Nuffield Department of Clinical Neurosciences, Sir William Dunn School of Pathology, University of Oxford, OMPI G, South Parks Road, Oxford, OX1 3RE, UK
| | - Stuart N Peirson
- Nuffield Laboratory of Ophthalmology, Sleep and Circadian Neuroscience Institute, Nuffield Department of Clinical Neurosciences, Sir William Dunn School of Pathology, University of Oxford, OMPI G, South Parks Road, Oxford, OX1 3RE, UK
| | - Steven Hughes
- Nuffield Laboratory of Ophthalmology, Sleep and Circadian Neuroscience Institute, Nuffield Department of Clinical Neurosciences, Sir William Dunn School of Pathology, University of Oxford, OMPI G, South Parks Road, Oxford, OX1 3RE, UK.
| | - Mark W Hankins
- Nuffield Laboratory of Ophthalmology, Sleep and Circadian Neuroscience Institute, Nuffield Department of Clinical Neurosciences, Sir William Dunn School of Pathology, University of Oxford, OMPI G, South Parks Road, Oxford, OX1 3RE, UK.
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160
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Sato K, Yamashita T, Kojima K, Sakai K, Matsutani Y, Yanagawa M, Yamano Y, Wada A, Iwabe N, Ohuchi H, Shichida Y. Pinopsin evolved as the ancestral dim-light visual opsin in vertebrates. Commun Biol 2018; 1:156. [PMID: 30302400 PMCID: PMC6167363 DOI: 10.1038/s42003-018-0164-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 09/06/2018] [Indexed: 11/13/2022] Open
Abstract
Pinopsin is the opsin most closely related to vertebrate visual pigments on the phylogenetic tree. This opsin has been discovered among many vertebrates, except mammals and teleosts, and was thought to exclusively function in their brain for extraocular photoreception. Here, we show the possibility that pinopsin also contributes to scotopic vision in some vertebrate species. Pinopsin is distributed in the retina of non-teleost fishes and frogs, especially in their rod photoreceptor cells, in addition to their brain. Moreover, the retinal chromophore of pinopsin exhibits a thermal isomerization rate considerably lower than those of cone visual pigments, but comparable to that of rhodopsin. Therefore, pinopsin can function as a rhodopsin-like visual pigment in the retinas of these lower vertebrates. Since pinopsin diversified before the branching of rhodopsin on the phylogenetic tree, two-step adaptation to scotopic vision would have occurred through the independent acquisition of pinopsin and rhodopsin by the vertebrate lineage.
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Affiliation(s)
- Keita Sato
- Department of Cytology and Histology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8558, Japan
| | - Takahiro Yamashita
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan.
| | - Keiichi Kojima
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Kazumi Sakai
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Yuki Matsutani
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | | | - Yumiko Yamano
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University, Kobe, 658-8558, Japan
| | - Akimori Wada
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University, Kobe, 658-8558, Japan
| | - Naoyuki Iwabe
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Hideyo Ohuchi
- Department of Cytology and Histology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8558, Japan
| | - Yoshinori Shichida
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan.
- Research Organization for Science and Technology, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan.
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161
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Salamanca DA, Brown F. Sub-functionalization of dorsal and ventral eyes in a whirligig beetle (Coleoptera: Gyrinidae). NEOTROPICAL BIODIVERSITY 2018. [DOI: 10.1080/23766808.2018.1510567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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162
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Kojima K, Watanabe HC, Doi S, Miyoshi N, Kato M, Ishikita H, Sudo Y. Mutational analysis of the conserved carboxylates of anion channelrhodopsin-2 (ACR2) expressed in Escherichia coli and their roles in anion transport. Biophys Physicobiol 2018; 15:179-188. [PMID: 30349802 PMCID: PMC6194965 DOI: 10.2142/biophysico.15.0_179] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/18/2018] [Indexed: 12/01/2022] Open
Abstract
Anion channelrhodopsin-2 (ACR2), a light-gated channel recently identified from the cryptophyte alga Guillardia theta, exhibits anion channel activity with exclusive selectivity. In addition to its novel function, ACR2 has become a focus of interest as a powerful tool for optogenetics. Here we combined experimental and computational approaches to investigate the roles of conserved carboxylates on the anion transport activity of ACR2 in Escherichia coli membrane. First, we replaced six conserved carboxylates with a neutral residue (i.e. E9Q, E56Q, E64Q, E159Q, E219Q and D230N), and measured anion transport activity using E. coli expression system. E159Q and D230N exhibited significantly lower anion transport activity compared with wild-type ACR2 (1/12~1/3.4), which suggests that E159 and D230 play important roles in the anion transport. Second, to explain its molecular aspects, we constructed a homology model of ACR2 based on the crystal structure of a cation channelrhodopsin (ChR). The model structure showed a cavity formed by four transmembrane helices (TM1, TM2, TM3 and TM7) similar to ChRs, as a putative anion conducting pathway. Although E159 is not located in the putative pathway, the model structure showed hydrogen bonds between E159 and R129 with a water molecule. D230 is located in the pathway near the protonated Schiff base (PSB) of the chromophore retinal, which suggests that there is an interaction between D230 and the PSB. Thus, we demonstrated the functional importance and the hypothetical roles of two conserved carboxylates, E159 and D230, in the anion transport activity of ACR2 in E. coli membrane.
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Affiliation(s)
- Keiichi Kojima
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Hiroshi C Watanabe
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8654, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan.,Japan Science and Technology Agency, PRESTO, Kawaguchi, Saitama 332-0012, Japan
| | - Satoko Doi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Natsuki Miyoshi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Misaki Kato
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8654, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8654, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo 153-8904, Japan
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
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163
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Pérez-Moreno JL, Balázs G, Bracken-Grissom HD. Transcriptomic Insights into the Loss of Vision in Molnár János Cave’s Crustaceans. Integr Comp Biol 2018; 58:452-464. [DOI: 10.1093/icb/icy071] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Jorge L Pérez-Moreno
- Department of Biological Sciences, Florida International University—Biscayne Bay Campus, North Miami, FL 33181, USA
| | - Gergely Balázs
- Department of Systematic Zoology and Ecology, Eötvös Loránd University, Budapest, 1117, Hungary
| | - Heather D Bracken-Grissom
- Department of Biological Sciences, Florida International University—Biscayne Bay Campus, North Miami, FL 33181, USA
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164
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Hypothesis on monochromatic vision in scorpionflies questioned by new transcriptomic data. Sci Rep 2018; 8:9872. [PMID: 29959337 PMCID: PMC6026179 DOI: 10.1038/s41598-018-28098-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 06/12/2018] [Indexed: 11/08/2022] Open
Abstract
In the scorpionfly Panorpa, a recent study suggested monochromatic vision due to evidence of only a single opsin found in transcriptome data. To reconsider this hypothesis, the present study investigates opsin expression using transcriptome data of 21 species including representatives of all major lineages of scorpionflies (Mecoptera) and of three families of their closest relatives, the fleas (Siphonaptera). In most mecopteran species investigated, transcripts encode two opsins with predicted peak absorbances in the green, two in the blue, and one in the ultraviolet spectral region. Only in groups with reduced or absent ocelli, like Caurinus and Apteropanorpa, less than four visual opsin messenger RNAs have been identified. In addition, we found a Rh7-like opsin in transcriptome data derived from larvae of the mecopteran Nannochorista, and in two flea species. Peropsin expression was observed in two mecopterans. In light of these new data, we question the hypothesis on monochromatic vision in the genus Panorpa. In a broader phylogenetic perspective, it is suggested that the common ancestor of the monophyletic taxon Antliophora (Diptera, Mecoptera and Siphonaptera) possessed the full set of visual opsins, a Rh7-like opsin, and in addition a pteropsin as well as a peropsin. In the course of evolution individual opsins were likely lost in several lineages of this clade.
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165
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El-Tahawy MMT, Nenov A, Weingart O, Olivucci M, Garavelli M. Relationship between Excited State Lifetime and Isomerization Quantum Yield in Animal Rhodopsins: Beyond the One-Dimensional Landau-Zener Model. J Phys Chem Lett 2018; 9:3315-3322. [PMID: 29791163 PMCID: PMC6650607 DOI: 10.1021/acs.jpclett.8b01062] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
We show that the speed of the chromophore photoisomerization of animal rhodopsins is not a relevant control knob for their light sensitivity. This result is at odds with the momentum-driven tunnelling rationale (i.e., assuming a one-dimensional Landau-Zener model for the decay: Zener, C. Non-Adiabatic Crossing of Energy Levels. Proc. R. Soc. London, Ser. A 1932, 137 (833), 696-702) holding that a faster nuclear motion through the conical intersection translates into a higher quantum yield and, thus, light sensitivity. Instead, a model based on the phase-matching of specific excited state vibrational modes should be considered. Using extensive semiclassical hybrid quantum mechanics/molecular mechanics trajectory computations to simulate the photoisomerization of three animal rhodopsin models (visual rhodopsin, squid rhodopsin and human melanopsin), we also demonstrate that phase-matching between three different modes (the reactive carbon and hydrogen twisting coordinates and the bond length alternation mode) is required to achieve high quantum yields. In fact, such "phase-matching" mechanism explains the computational results and provides a tool for the prediction of the photoisomerization outcome in retinal proteins.
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Affiliation(s)
- Mohsen M. T. El-Tahawy
- Dipartimento di Chimica Industriale “Toso Montanari″, Università degli Studi di Bologna, Viale del Risorgimento, 4I -40136 Bologna, Italy
- Chemistry Department, Faculty of Science, Damanhour University, Damanhour 22511, Egypt
| | - Artur Nenov
- Dipartimento di Chimica Industriale “Toso Montanari″, Università degli Studi di Bologna, Viale del Risorgimento, 4I -40136 Bologna, Italy
| | - Oliver Weingart
- Institut für Theoretische Chemie und Computerchemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Massimo Olivucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, I-53100 Siena, Italy
- Chemistry Department, Bowling Green State University, Bowling Green, OH 43403
- Corresponding Author; (M.O.): ; Phone: +39 051 20 9 9476. Fax: +39 051 20 9 9456 (M.G.)
| | - Marco Garavelli
- Dipartimento di Chimica Industriale “Toso Montanari″, Università degli Studi di Bologna, Viale del Risorgimento, 4I -40136 Bologna, Italy
- Corresponding Author; (M.O.): ; Phone: +39 051 20 9 9476. Fax: +39 051 20 9 9456 (M.G.)
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166
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Takayama R, Kaneko A, Okitsu T, Tsunoda SP, Shimono K, Mizuno M, Kojima K, Tsukamoto T, Kandori H, Mizutani Y, Wada A, Sudo Y. Production of a Light-Gated Proton Channel by Replacing the Retinal Chromophore with Its Synthetic Vinylene Derivative. J Phys Chem Lett 2018; 9:2857-2862. [PMID: 29750864 DOI: 10.1021/acs.jpclett.8b00879] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Rhodopsin is widely distributed in organisms as a membrane-embedded photoreceptor protein, consisting of the apoprotein opsin and vitamin-A aldehyde retinal, A1-retinal and A2-retinal being the natural chromophores. Modifications of opsin (e.g., by mutations) have provided insight into the molecular mechanism of the light-induced functions of rhodopsins as well as providing tools in chemical biology to control cellular activity by light. Instead of the apoprotein opsin, in this study, we focused on the retinal chromophore and synthesized three vinylene derivatives of A2-retinal. One of them, C(14)-vinylene A2-retinal (14V-A2), was successfully incorporated into the opsin of a light-driven proton pump archaerhodopsin-3 (AR3). Electrophysiological experiments revealed that the opsin of AR3 (archaeopsin3, AO3) with 14V-A2 functions as a light-gated proton channel. The engineered proton channel showed characteristic photochemical properties, which are significantly different from those of AR3. Thus, we successfully produced a proton channel by replacing the chromophore of AR3.
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Affiliation(s)
- Riho Takayama
- Faculty of Pharmaceutical Sciences , Okayama University , Okayama 700-8530 , Japan
| | - Akimasa Kaneko
- Faculty of Pharmaceutical Sciences , Okayama University , Okayama 700-8530 , Japan
| | - Takashi Okitsu
- Laboratory of Organic Chemistry for Life Science , Kobe Pharmaceutical University , Kobe 658-8558 , Japan
| | - Satoshi P Tsunoda
- Department of Frontier Materials , Nagoya Institute of Technology , Nagoya 466-8555 , Japan
- PRESTO, Japan Science and Technology Agency , 4-1-8 Honcho , Kawaguchi , Saitama 332-0012 , Japan
| | - Kazumi Shimono
- Faculty of Pharmaceutical Sciences , Toho University , Funabashi 274-8510 , Japan
| | - Misao Mizuno
- Department of Chemistry , Graduate School of Science, Osaka University , Toyonaka 560-0043 , Japan
| | - Keiichi Kojima
- Faculty of Pharmaceutical Sciences , Okayama University , Okayama 700-8530 , Japan
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences , Okayama University , Okayama 700-8530 , Japan
| | - Takashi Tsukamoto
- Faculty of Pharmaceutical Sciences , Okayama University , Okayama 700-8530 , Japan
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences , Okayama University , Okayama 700-8530 , Japan
| | - Hideki Kandori
- Department of Frontier Materials , Nagoya Institute of Technology , Nagoya 466-8555 , Japan
| | - Yasuhisa Mizutani
- Department of Chemistry , Graduate School of Science, Osaka University , Toyonaka 560-0043 , Japan
| | - Akimori Wada
- Laboratory of Organic Chemistry for Life Science , Kobe Pharmaceutical University , Kobe 658-8558 , Japan
| | - Yuki Sudo
- Faculty of Pharmaceutical Sciences , Okayama University , Okayama 700-8530 , Japan
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences , Okayama University , Okayama 700-8530 , Japan
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167
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Zanini D, Giraldo D, Warren B, Katana R, Andrés M, Reddy S, Pauls S, Schwedhelm-Domeyer N, Geurten BR, Göpfert MC. Proprioceptive Opsin Functions in Drosophila Larval Locomotion. Neuron 2018; 98:67-74.e4. [DOI: 10.1016/j.neuron.2018.02.028] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 01/15/2018] [Accepted: 02/26/2018] [Indexed: 01/13/2023]
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168
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Opn5L1 is a retinal receptor that behaves as a reverse and self-regenerating photoreceptor. Nat Commun 2018; 9:1255. [PMID: 29593298 PMCID: PMC5871776 DOI: 10.1038/s41467-018-03603-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 02/25/2018] [Indexed: 11/09/2022] Open
Abstract
Most opsins are G protein-coupled receptors that utilize retinal both as a ligand and as a chromophore. Opsins' main established mechanism is light-triggered activation through retinal 11-cis-to-all-trans photoisomerization. Here we report a vertebrate non-visual opsin that functions as a Gi-coupled retinal receptor that is deactivated by light and can thermally self-regenerate. This opsin, Opn5L1, binds exclusively to all-trans-retinal. More interestingly, the light-induced deactivation through retinal trans-to-cis isomerization is followed by formation of a covalent adduct between retinal and a nearby cysteine, which breaks the retinal-conjugated double bond system, probably at the C11 position, resulting in thermal re-isomerization to all-trans-retinal. Thus, Opn5L1 acts as a reverse photoreceptor. We conclude that, like vertebrate rhodopsin, Opn5L1 is a unidirectional optical switch optimized from an ancestral bidirectional optical switch, such as invertebrate rhodopsin, to increase the S/N ratio of the signal transduction, although the direction of optimization is opposite to that of vertebrate rhodopsin.
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169
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Wu C, Jiang Q, Wei L, Cai Z, Chen J, Yu W, He C, Wang J, Guo W, Wang X. A Rhodopsin-Like Gene May Be Associated With the Light-Sensitivity of Adult Pacific Oyster Crassostrea gigas. Front Physiol 2018; 9:221. [PMID: 29615921 PMCID: PMC5868073 DOI: 10.3389/fphys.2018.00221] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 02/27/2018] [Indexed: 12/27/2022] Open
Abstract
Light-sensitivity is important for mollusc survival, as it plays a vital role in reproduction and predator avoidance. Light-sensitivity has been demonstrated in the adult Pacific oyster Crassostrea gigas, but the genes associated with light-sensitivity remain unclear. In the present study, we designed experiments to identify the genes associated with light-sensitivity in adult oysters. First, we assessed the Pacific oyster genome and identified 368 genes annotated with the terms associated with light-sensitivity. Second, the function of the four rhodopsin-like superfamily member genes was tested by using RNAi. The results showed that the highest level of mRNA expression of the vision-related genes was in the mantle; however, this finding is not true for all oyster genes. Interestingly, we also found four rhodopsin-like superfamily member genes expressed at an very high level in the mantle tissue. In the RNAi experiment, when one of rhodopsin-like superfamily member genes (CGI_1001253) was inhibited, the light-sensitivity capacity of the injected oysters was significantly reduced, suggesting that CGI_10012534 may be associated with light-sensitivity in the adult Pacific oyster.
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Affiliation(s)
- Changlu Wu
- School of Agriculture, Ludong University, Yantai, China
| | - Qiuyun Jiang
- School of Agriculture, Ludong University, Yantai, China
| | - Lei Wei
- School of Agriculture, Ludong University, Yantai, China
| | - Zhongqiang Cai
- Changdao Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Changdao, China
| | - Jun Chen
- School of Agriculture, Ludong University, Yantai, China
| | - Wenchao Yu
- School of Agriculture, Ludong University, Yantai, China
| | - Cheng He
- School of Agriculture, Ludong University, Yantai, China
| | - Jiao Wang
- School of Agriculture, Ludong University, Yantai, China
| | - Wen Guo
- Center for Mollusc Study and Development, Marine Biology Institute of Shandong Province, Qingdao, China
| | - Xiaotong Wang
- School of Agriculture, Ludong University, Yantai, China
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170
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Removal of the blue component of light significantly decreases retinal damage after high intensity exposure. PLoS One 2018; 13:e0194218. [PMID: 29543853 PMCID: PMC5854379 DOI: 10.1371/journal.pone.0194218] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 02/27/2018] [Indexed: 12/14/2022] Open
Abstract
Light causes damage to the retina (phototoxicity) and decreases photoreceptor responses to light. The most harmful component of visible light is the blue wavelength (400–500 nm). Different filters have been tested, but so far all of them allow passing a lot of this wavelength (70%). The aim of this work has been to prove that a filter that removes 94% of the blue component may protect the function and morphology of the retina significantly. Three experimental groups were designed. The first group was unexposed to light, the second one was exposed and the third one was exposed and protected by a blue-blocking filter. Light damage was induced in young albino mice (p30) by exposing them to white light of high intensity (5,000 lux) continuously for 7 days. Short wavelength light filters were used for light protection. The blue component was removed (94%) from the light source by our filter. Electroretinographical recordings were performed before and after light damage. Changes in retinal structure were studied using immunohistochemistry, and TUNEL labeling. Also, cells in the outer nuclear layer were counted and compared among the three different groups. Functional visual responses were significantly more conserved in protected animals (with the blue-blocking filter) than in unprotected animals. Also, retinal structure was better kept and photoreceptor survival was greater in protected animals, these differences were significant in central areas of the retina. Still, functional and morphological responses were significantly lower in protected than in unexposed groups. In conclusion, this blue-blocking filter decreases significantly photoreceptor damage after exposure to high intensity light. Actually, our eyes are exposed for a very long time to high levels of blue light (screens, artificial light LED, neons…). The potential damage caused by blue light can be palliated.
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171
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Suzuki DG, Grillner S. The stepwise development of the lamprey visual system and its evolutionary implications. Biol Rev Camb Philos Soc 2018; 93:1461-1477. [PMID: 29488315 DOI: 10.1111/brv.12403] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/29/2018] [Accepted: 02/05/2018] [Indexed: 01/11/2023]
Abstract
Lampreys, which represent the oldest group of living vertebrates (cyclostomes), show unique eye development. The lamprey larva has only eyespot-like immature eyes beneath a non-transparent skin, whereas after metamorphosis, the adult has well-developed image-forming camera eyes. To establish a functional visual system, well-organised visual centres as well as motor components (e.g. trunk muscles for locomotion) and interactions between them are needed. Here we review the available knowledge concerning the structure, function and development of the different parts of the lamprey visual system. The lamprey exhibits stepwise development of the visual system during its life cycle. In prolarvae and early larvae, the 'primary' retina does not have horizontal and amacrine cells, but does have photoreceptors, bipolar cells and ganglion cells. At this stage, the optic nerve projects mostly to the pretectum, where the dendrites of neurons in the nucleus of the medial longitudinal fasciculus (nMLF) appear to receive direct visual information and send motor outputs to the neck and trunk muscles. This simple neural circuit may generate negative phototaxis. Through the larval period, the lateral region of the retina grows again to form the 'secondary' retina and the topographic retinotectal projection of the optic nerve is formed, and at the same time, the extra-ocular muscles progressively develop. During metamorphosis, horizontal and amacrine cells differentiate for the first time, and the optic tectum expands and becomes laminated. The adult lamprey then has a sophisticated visual system for image-forming and visual decision-making. In the adult lamprey, the thalamic pathway (retina-thalamus-cortex/pallium) also transmits visual stimuli. Because the primary, simple light-detecting circuit in larval lamprey shares functional and developmental similarities with that of protochordates (amphioxus and tunicates), the visual development of the lamprey provides information regarding the evolutionary transition of the vertebrate visual system from the protochordate-type to the vertebrate-type.
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Affiliation(s)
- Daichi G Suzuki
- Department of Neuroscience, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Sten Grillner
- Department of Neuroscience, Karolinska Institutet, SE-171 77, Stockholm, Sweden
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172
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Samanta D, Galaktionova D, Gemen J, Shimon LJW, Diskin-Posner Y, Avram L, Král P, Klajn R. Reversible chromism of spiropyran in the cavity of a flexible coordination cage. Nat Commun 2018; 9:641. [PMID: 29440687 PMCID: PMC5811438 DOI: 10.1038/s41467-017-02715-6] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 12/20/2017] [Indexed: 11/08/2022] Open
Abstract
Confining molecules to volumes only slightly larger than the molecules themselves can profoundly alter their properties. Molecular switches-entities that can be toggled between two or more forms upon exposure to an external stimulus-often require conformational freedom to isomerize. Therefore, placing these switches in confined spaces can render them non-operational. To preserve the switchability of these species under confinement, we work with a water-soluble coordination cage that is flexible enough to adapt its shape to the conformation of the encapsulated guest. We show that owing to its flexibility, the cage is not only capable of accommodating-and solubilizing in water-several light-responsive spiropyran-based molecular switches, but, more importantly, it also provides an environment suitable for the efficient, reversible photoisomerization of the bound guests. Our findings pave the way towards studying various molecular switching processes in confined environments.
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Affiliation(s)
- Dipak Samanta
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Daria Galaktionova
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Julius Gemen
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Linda J W Shimon
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yael Diskin-Posner
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Liat Avram
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Petr Král
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, 60607, USA
- Department of Physics, University of Illinois at Chicago, Chicago, IL, 60607, USA
- Department of Biopharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Rafal Klajn
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel.
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173
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Pantzartzi CN, Pergner J, Kozmik Z. The role of transposable elements in functional evolution of amphioxus genome: the case of opsin gene family. Sci Rep 2018; 8:2506. [PMID: 29410521 PMCID: PMC5802833 DOI: 10.1038/s41598-018-20683-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/22/2018] [Indexed: 11/30/2022] Open
Abstract
Transposable elements (TEs) are able to jump to new locations (transposition) in the genome, usually after replication. They constitute the so-called selfish or junk DNA and take over large proportions of some genomes. Due to their ability to move around they can change the DNA landscape of genomes and are therefore a rich source of innovation in genes and gene regulation. Surge of sequence data in the past years has significantly facilitated large scale comparative studies. Cephalochordates have been regarded as a useful proxy to ancestral chordate condition partially due to the comparatively slow evolutionary rate at morphological and genomic level. In this study, we used opsin gene family from three Branchiostoma species as a window into cephalochordate genome evolution. We compared opsin complements in terms of family size, gene structure and sequence allowing us to identify gene duplication and gene loss events. Furthermore, analysis of the opsin containing genomic loci showed that they are populated by TEs. In summary, we provide evidence of the way transposable elements may have contributed to the evolution of opsin gene family and to the shaping of cephalochordate genomes in general.
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Affiliation(s)
- Chrysoula N Pantzartzi
- Laboratory of Eye Biology, Institute of Molecular Genetics of the ASCR, v.v.i., Division BIOCEV, Prumyslová 595, 252 50, Vestec, Czech Republic
| | - Jiri Pergner
- Department of Transcriptional Regulation, Institute of Molecular Genetics of the ASCR, v.v.i., Videnska 1083, 14220, Prague 4, Czech Republic
| | - Zbynek Kozmik
- Laboratory of Eye Biology, Institute of Molecular Genetics of the ASCR, v.v.i., Division BIOCEV, Prumyslová 595, 252 50, Vestec, Czech Republic. .,Department of Transcriptional Regulation, Institute of Molecular Genetics of the ASCR, v.v.i., Videnska 1083, 14220, Prague 4, Czech Republic.
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174
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Schwab IR. The evolution of eyes: major steps. The Keeler lecture 2017: centenary of Keeler Ltd. Eye (Lond) 2018; 32:302-313. [PMID: 29052606 PMCID: PMC5811732 DOI: 10.1038/eye.2017.226] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 07/31/2017] [Indexed: 01/10/2023] Open
Abstract
Ocular evolution is an immense topic, and I do not expect to cover all the details of this process in this manuscript. I will present some concepts about some of the major steps in the evolutionary process to stimulate your thinking about this interesting and complex topic. In the prebiotic soup, vision was not inevitable. Eyes were not preordained. Nor were their shapes, sizes, or current physiology. Sight is an evolutionary gift but it was not ineluctable. The existence of eyes is so basic to our profession that we often do not consider how and why vision appeared or evolved on earth at all. Although vision is a principal sensory modality for at least three major phyla and is present in three or four more phyla, there are other sensory mechanisms that could have been and were occasionally selected instead. Some animals rely on other sensory mechanisms such as audition, echolocation, or olfaction that are much more effective in their particular niche than would be vision. We may not believe those sensory mechanisms to be as robust as vision, but the creatures using those skills would argue otherwise. Why does vision exist at all? And why is it so dominant at least in the number of species that rely upon it for their principal sensory mechanism? How did vision begin? What were the important steps in the evolution of eyes? How did eyes differentiate along their various paths, and why?
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Affiliation(s)
- I R Schwab
- Department of Ophthalmology & Vision Science, University of California, Davis, Sacramento, CA, USA
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175
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Eickelbeck D, Karapinar R, Herlitze S, Spoida K. Optogenetic Approaches for Controlling Neuronal Activity and Plasticity. HANDBOOK OF BEHAVIORAL NEUROSCIENCE 2018. [DOI: 10.1016/b978-0-12-812028-6.00016-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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176
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Yoshida K, Yamashita T, Sasaki K, Inoue K, Shichida Y, Kandori H. Chimeric microbial rhodopsins for optical activation of Gs-proteins. Biophys Physicobiol 2017; 14:183-190. [PMID: 29362703 PMCID: PMC5774426 DOI: 10.2142/biophysico.14.0_183] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 11/10/2017] [Indexed: 12/01/2022] Open
Abstract
We previously showed that the chimeric proteins of microbial rhodopsins, such as light-driven proton pump bacteriorhodopsin (BR) and Gloeobacter rhodopsin (GR) that contain cytoplasmic loops of bovine rhodopsin, are able to activate Gt protein upon light absorption. These facts suggest similar protein structural changes in both the light-driven proton pump and animal rhodopsin. Here we report two trials to engineer chimeric rhodopsins, one for the inserted loop, and another for the microbial rhodopsin template. For the former, we successfully activated Gs protein by light through the incorporation of the cytoplasmic loop of β2-adrenergic receptor (β2AR). For the latter, we did not observe any G-protein activation for the light-driven sodium pump from Indibacter alkaliphilus (IndiR2) or a light-driven chloride pump halorhodopsin from Natronomonas pharaonis (NpHR), whereas the light-driven proton pump GR showed light-dependent G-protein activation. This fact suggests that a helix opening motion is common to G protein coupled receptor (GPCR) and GR, but not to IndiR2 and NpHR. Light-induced difference FTIR spectroscopy revealed similar structural changes between WT and the third loop chimera for each light-driven pump. A helical structural perturbation, which was largest for GR, was further enhanced in the chimera. We conclude that similar structural dynamics that occur on the cytoplasmic side of GPCR are needed to design chimeric microbial rhodopsins.
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Affiliation(s)
- Kazuho Yoshida
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
| | - Takahiro Yamashita
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Kengo Sasaki
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
| | - Keiichi Inoue
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Yoshinori Shichida
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
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177
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Jacobs GH. Photopigments and the dimensionality of animal color vision. Neurosci Biobehav Rev 2017; 86:108-130. [PMID: 29224775 DOI: 10.1016/j.neubiorev.2017.12.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/04/2017] [Accepted: 12/05/2017] [Indexed: 12/31/2022]
Abstract
Early color-matching studies established that normal human color vision is trichromatic. Subsequent research revealed a causal link between trichromacy and the presence in the retina of three classes of cone photopigments. Over the years, measurements of the photopigment complements of other species have expanded greatly and these are frequently used to predict the dimensionality of an animal's color vision. This review provides an account of how the linkage between the number of active photopigments and the dimensions of human color vision developed, summarizes the various mechanisms that can impact photopigment spectra and number, and provides an across-species survey to examine cases where the photopigment link to the dimensionality of color vision has been claimed. The literature reveals numerous instances where the human model fails to account for the ways in which the visual systems of other animals exploit information obtained from the presence of multiple photopigments in support of their behavior.
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Affiliation(s)
- Gerald H Jacobs
- Department of Psychological and Brain Science, University of California, Santa Barbara, CA 93106, USA.
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178
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Morshedian A, Fain GL. The evolution of rod photoreceptors. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0074. [PMID: 28193819 DOI: 10.1098/rstb.2016.0074] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2016] [Indexed: 12/29/2022] Open
Abstract
Photoreceptors in animals are generally of two kinds: the ciliary or c-type and the rhabdomeric or r-type. Although ciliary photoreceptors are found in many phyla, vertebrates seem to be unique in having two distinct kinds which together span the entire range of vision, from single photons to bright light. We ask why the principal photoreceptors of vertebrates are ciliary and not rhabdomeric, and how rods evolved from less sensitive cone-like photoreceptors to produce our duplex retina. We suggest that the principal advantage of vertebrate ciliary receptors is that they use less ATP than rhabdomeric photoreceptors. This difference may have provided sufficient selection pressure for the development of a completely ciliary eye. Although many of the details of rod evolution are still uncertain, present evidence indicates that (i) rods evolved very early before the split between the jawed and jawless vertebrates, (ii) outer-segment discs make no contribution to rod sensitivity but may have evolved to increase the efficiency of protein renewal, and (iii) evolution of the rod was incremental and multifaceted, produced by the formation of several novel protein isoforms and by changes in protein expression, with no one alteration having more than a few-fold effect on transduction activation or inactivation.This article is part of the themed issue 'Vision in dim light'.
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Affiliation(s)
- Ala Morshedian
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA 90095-7239, USA
| | - Gordon L Fain
- Department of Integrative Biology and Physiology, University of California Los Angeles, Los Angeles, CA 90095-7239, USA .,Department of Ophthalmology and Jules Stein Eye Institute, University of California Los Angeles, Los Angeles, CA 90095-7000, USA
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179
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Salari V, Scholkmann F, Vimal RLP, Császár N, Aslani M, Bókkon I. Phosphenes, retinal discrete dark noise, negative afterimages and retinogeniculate projections: A new explanatory framework based on endogenous ocular luminescence. Prog Retin Eye Res 2017; 60:101-119. [DOI: 10.1016/j.preteyeres.2017.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/13/2017] [Accepted: 07/15/2017] [Indexed: 02/07/2023]
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180
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Sakai K, Tsutsui K, Yamashita T, Iwabe N, Takahashi K, Wada A, Shichida Y. Drosophila melanogaster rhodopsin Rh7 is a UV-to-visible light sensor with an extraordinarily broad absorption spectrum. Sci Rep 2017; 7:7349. [PMID: 28779161 PMCID: PMC5544684 DOI: 10.1038/s41598-017-07461-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/28/2017] [Indexed: 01/15/2023] Open
Abstract
The genome of Drosophila melanogaster contains seven rhodopsin genes. Rh1-6 proteins are known to have respective absorption spectra and function as visual pigments in ocelli and compound eyes. In contrast, Rh7 protein was recently revealed to function as a circadian photoreceptor in the brain. However, its molecular properties have not been characterized yet. Here we successfully prepared a recombinant protein of Drosophila Rh7 in mammalian cultured cells. Drosophila Rh7 bound both 11-cis-retinal and 11-cis-3-hydroxyretinal to form photo-pigments which can absorb UV light. Irradiation with UV light caused formation of a visible-light absorbing metarhodopsin that activated Gq-type of G protein. This state could be photoconverted back to the original state and, thus Rh7 is a Gq-coupled bistable pigment. Interestingly, Rh7 (lambda max = 350 nm) exhibited an unusual broad spectrum with a longer wavelength tail reaching 500 nm, whose shape is like a composite of spectra of two pigments. In contrast, replacement of lysine at position 90 with glutamic acid caused the formation of a normal-shaped absorption spectrum with maximum at 450 nm. Therefore, Rh7 is a unique photo-sensor that can cover a wide wavelength region by a single pigment to contribute to non-visual photoreception.
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Affiliation(s)
- Kazumi Sakai
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Kei Tsutsui
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Takahiro Yamashita
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Naoyuki Iwabe
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Keisuke Takahashi
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Akimori Wada
- Department of Organic Chemistry for Life Science, Kobe Pharmaceutical University, Kobe, 658-8558, Japan
| | - Yoshinori Shichida
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan. .,Research Organization for Science and Technology, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan.
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181
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Structural and functional alterations associated with deutan N94K and R330Q mutations of green cone opsin. Biochim Biophys Acta Mol Basis Dis 2017; 1863:1840-1847. [DOI: 10.1016/j.bbadis.2017.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 04/04/2017] [Accepted: 05/05/2017] [Indexed: 01/28/2023]
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182
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Martin C, Gross V, Hering L, Tepper B, Jahn H, de Sena Oliveira I, Stevenson PA, Mayer G. The nervous and visual systems of onychophorans and tardigrades: learning about arthropod evolution from their closest relatives. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2017; 203:565-590. [DOI: 10.1007/s00359-017-1186-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/02/2017] [Accepted: 05/29/2017] [Indexed: 12/19/2022]
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183
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Evolutionary steps involving counterion displacement in a tunicate opsin. Proc Natl Acad Sci U S A 2017; 114:6028-6033. [PMID: 28533401 DOI: 10.1073/pnas.1701088114] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Ci-opsin1 is a visible light-sensitive opsin present in the larval ocellus of an ascidian, Ciona intestinalis This invertebrate opsin belongs to the vertebrate visual and nonvisual opsin groups in the opsin phylogenetic tree. Ci-opsin1 contains candidate counterions (glutamic acid residues) at positions 113 and 181; the former is a newly acquired position in the vertebrate visual opsin lineage, whereas the latter is an ancestral position widely conserved among invertebrate opsins. Here, we show that Glu113 and Glu181 in Ci-opsin1 act synergistically as counterions, which imparts molecular properties to Ci-opsin1 intermediate between those of vertebrate- and invertebrate-type opsins. Synergy between the counterions in Ci-opsin1 was demonstrated by E113Q and E181Q mutants that exhibit a pH-dependent spectral shift, whereas only the E113Q mutation in vertebrate rhodopsin yields this spectral shift. On absorbing light, Ci-opsin1 forms an equilibrium between two intermediates with protonated and deprotonated Schiff bases, namely the MI-like and MII-like intermediates, respectively. Adding G protein caused the equilibrium to shift toward the MI-like intermediate, indicating that Ci-opsin1 has a protonated Schiff base in its active state, like invertebrate-type opsins. Ci-opsin1's G protein activation efficiency is between the efficiencies of vertebrate- and invertebrate-type opsins. Interestingly, the E113Y and E181S mutations change the molecular properties of Ci-opsin1 into those resembling invertebrate-type or bistable opsins and vertebrate ancient/vertebrate ancient-long or monostable opsins, respectively. These results strongly suggest that acquisition of counterion Glu113 changed the molecular properties of visual opsin in a vertebrate/tunicate common ancestor as a crucial step in the evolution of vertebrate visual opsins.
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184
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Narayan DS, Chidlow G, Wood JP, Casson RJ. Glucose metabolism in mammalian photoreceptor inner and outer segments. Clin Exp Ophthalmol 2017; 45:730-741. [PMID: 28334493 DOI: 10.1111/ceo.12952] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 02/25/2017] [Accepted: 03/20/2017] [Indexed: 12/22/2022]
Abstract
Photoreceptors are the first-order neurons of the visual pathway, converting light into electrical signals. Rods and cones are the two main types of photoreceptors in the mammalian retina. Rods are specialized for sensitivity at the expense of resolution and are responsible for vision in dimly lit conditions. Cones are responsible for high acuity central vision and colour vision. Many human retinal diseases are characterized by a progressive loss of photoreceptors. Photoreceptors consist of four primary regions: outer segments, inner segments, cell bodies and synaptic terminals. Photoreceptors consume large amounts of energy, and therefore, energy metabolism may be a critical juncture that links photoreceptor function and survival. Cones require more energy than rods, and cone degeneration is the main cause of clinically significant vision loss in retinal diseases. Photoreceptor segments are capable of utilizing various energy substrates, including glucose, to meet their large energy demands. The pathways by which photoreceptor segments meet their energy demands remain incompletely understood. Improvements in the understanding of glucose metabolism in photoreceptor segments may provide insight into the reasons why photoreceptors degenerate due to energy failure. This may, in turn, assist in developing bio-energetic therapies aimed at protecting photoreceptors.
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Affiliation(s)
- Daniel S Narayan
- Ophthalmic Research Laboratories, Hanson Institute Centre for Neurological Diseases, Adelaide, South Austalia, Australia.,South Australian Institute of Ophthalmology, University of Adelaide, Adelaide, South Austalia, Australia
| | - Glyn Chidlow
- Ophthalmic Research Laboratories, Hanson Institute Centre for Neurological Diseases, Adelaide, South Austalia, Australia.,South Australian Institute of Ophthalmology, University of Adelaide, Adelaide, South Austalia, Australia
| | - John Pm Wood
- Ophthalmic Research Laboratories, Hanson Institute Centre for Neurological Diseases, Adelaide, South Austalia, Australia.,South Australian Institute of Ophthalmology, University of Adelaide, Adelaide, South Austalia, Australia
| | - Robert J Casson
- Ophthalmic Research Laboratories, Hanson Institute Centre for Neurological Diseases, Adelaide, South Austalia, Australia.,South Australian Institute of Ophthalmology, University of Adelaide, Adelaide, South Austalia, Australia
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185
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Hofrnann L, Alexander NS, Sun W, Zhang J, Orban T, Palczewski K. Hydrogen/Deuterium Exchange Mass Spectrometry of Human Green Opsin Reveals a Conserved Pro-Pro Motif in Extracellular Loop 2 of Monostable Visual G Protein-Coupled Receptors. Biochemistry 2017; 56:2338-2348. [PMID: 28402104 PMCID: PMC5501310 DOI: 10.1021/acs.biochem.7b00165] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Opsins comprise the protein component of light sensitive G protein-coupled receptors (GPCRs) in the retina of the eye that are responsible for the transduction of light into a biochemical signal. Here, we used hydrogen/deuterium (H/D) exchange coupled with mass spectrometry to map conformational changes in green cone opsin upon light activation. We then compared these findings with those reported for rhodopsin. The extent of H/D exchange in green cone opsin was greater than in rhodopsin in the dark and bleached states, suggesting a higher structural heterogeneity for green cone opsin. Further analysis revealed that green cone opsin exists as a dimer in both dark (inactive) and bleached (active) states, and that the predicted glycosylation sites at N32 and N34 are indeed glycosylated. Comparison of deuterium uptake between inactive and active states of green cone opsin also disclosed a reduced solvent accessibility of the extracellular N-terminal region and an increased accessibility of the chromophore binding site. Increased H/D exchange at the extracellular side of transmembrane helix four (TM4) combined with an analysis of sequence alignments revealed a conserved Pro-Pro motif in extracellular loop 2 (EL2) of monostable visual GPCRs. These data present new insights into the locus of chromophore release at the extracellular side of TM4 and TM5 and provide a foundation for future functional evaluation.
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Affiliation(s)
- Lukas Hofrnann
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Nathan S. Alexander
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Wenyu Sun
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Jianye Zhang
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Tivadar Orban
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Krzysztof Palczewski
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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186
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Ahrendt SR, Medina EM, Chang CEA, Stajich JE. Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling. PeerJ 2017; 5:e3206. [PMID: 28462022 PMCID: PMC5410147 DOI: 10.7717/peerj.3206] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 03/20/2017] [Indexed: 01/16/2023] Open
Abstract
Background Opsin proteins are seven transmembrane receptor proteins which detect light. Opsins can be classified into two types and share little sequence identity: type 1, typically found in bacteria, and type 2, primarily characterized in metazoa. The type 2 opsins (Rhodopsins) are a subfamily of G-protein coupled receptors (GPCRs), a large and diverse class of seven transmembrane proteins and are generally restricted to metazoan lineages. Fungi use light receptors including opsins to sense the environment and transduce signals for developmental or metabolic changes. Opsins characterized in the Dikarya (Ascomycetes and Basidiomycetes) are of the type 1 bacteriorhodopsin family but the early diverging fungal lineages have not been as well surveyed. We identified by sequence similarity a rhodopsin-like GPCR in genomes of early diverging chytrids and examined the structural characteristics of this protein to assess its likelihood to be homologous to animal rhodopsins and bind similar chromophores. Methods We used template-based structure modeling, automated ligand docking, and molecular modeling to assess the structural and binding properties of an identified opsin-like protein found in Spizellomyces punctatus, a unicellular, flagellated species belonging to Chytridiomycota, one of the earliest diverging fungal lineages. We tested if the sequence and inferred structure were consistent with a solved crystal structure of a type 2 rhodopsin from the squid Todarodes pacificus. Results Our results indicate that the Spizellomyces opsin has structural characteristics consistent with functional animal type 2 rhodopsins and is capable of maintaining a stable structure when associated with the retinaldehyde chromophore, specifically the 9-cis-retinal isomer. Together, these results support further the homology of Spizellomyces opsins to animal type 2 rhodopsins. Discussion This represents the first test of structure/function relationship of a type 2 rhodopsin identified in early branching fungal lineages, and provides a foundation for future work exploring pathways and components of photoreception in early fungi.
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Affiliation(s)
- Steven R Ahrendt
- Department of Plant Pathology & Microbiology, University of California, Riverside, CA, USA.,Institute for Integrative Genome Biology, University of California, Riverside, CA, USA.,Genetics, Genomics, and Bioinformatics Program, University of California, Riverside, CA, USA
| | - Edgar Mauricio Medina
- Department of Biology, Duke University, Durham, NC, USA.,Center for Genomic and Computational Biology, Duke University, Durham, NC, USA
| | - Chia-En A Chang
- Institute for Integrative Genome Biology, University of California, Riverside, CA, USA.,Department of Chemistry, University of California, Riverside, CA, USA
| | - Jason E Stajich
- Department of Plant Pathology & Microbiology, University of California, Riverside, CA, USA.,Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
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187
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Kamiya M, Hayashi S. Photoactivation Intermediates of a G-Protein Coupled Receptor Rhodopsin Investigated by a Hybrid Molecular Simulation. J Phys Chem B 2017; 121:3842-3852. [PMID: 28240904 DOI: 10.1021/acs.jpcb.6b13050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhodopsin is a G-protein coupled receptor functioning as a photoreceptor for vision through photoactivation of a covalently bound ligand of a retinal protonated Schiff base chromophore. Despite the availability of structural information on the inactivated and activated forms of the receptor, the transition processes initiated by the photoabsorption have not been well understood. Here we theoretically examined the photoactivation processes by means of molecular dynamics (MD) simulations and ab initio quantum mechanical/molecular mechanical (QM/MM) free energy geometry optimizations which enabled accurate geometry determination of the ligand molecule in ample statistical conformational samples of the protein. Structures of the intermediate states of the activation process, blue-shifted intermediate and Lumi, as well as the dark state first generated by MD simulations and then refined by the QM/MM free energy geometry optimizations were characterized by large displacement of the β-ionone ring of retinal along with change in the hydrogen bond of the protonated Schiff base. The ab initio calculations of vibrational and electronic spectroscopic properties of those states well reproduced the experimental observations and successfully identified the molecular origins underlying the spectroscopic features. The structural evolution in the formation of the intermediates provides a molecular insight into the efficient activation processes of the receptor.
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Affiliation(s)
- Motoshi Kamiya
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University , Kyoto 606-8502, Japan
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188
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Arany PR. Special Issue on Stem Cells and Photobiomodulation Therapy. Photomed Laser Surg 2017; 34:495-496. [PMID: 27841967 DOI: 10.1089/pho.2016.4216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Praveen R Arany
- Department of Oral Biology, School of Dental Medicine, University at Buffalo , Buffalo, New York
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189
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Marques DA, Taylor JS, Jones FC, Di Palma F, Kingsley DM, Reimchen TE. Convergent evolution of SWS2 opsin facilitates adaptive radiation of threespine stickleback into different light environments. PLoS Biol 2017; 15:e2001627. [PMID: 28399148 PMCID: PMC5388470 DOI: 10.1371/journal.pbio.2001627] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/06/2017] [Indexed: 11/18/2022] Open
Abstract
Repeated adaptation to a new environment often leads to convergent phenotypic changes whose underlying genetic mechanisms are rarely known. Here, we study adaptation of color vision in threespine stickleback during the repeated postglacial colonization of clearwater and blackwater lakes in the Haida Gwaii archipelago. We use whole genomes from 16 clearwater and 12 blackwater populations, and a selection experiment, in which stickleback were transplanted from a blackwater lake into an uninhabited clearwater pond and resampled after 19 y to test for selection on cone opsin genes. Patterns of haplotype homozygosity, genetic diversity, site frequency spectra, and allele-frequency change support a selective sweep centered on the adjacent blue- and red-light sensitive opsins SWS2 and LWS. The haplotype under selection carries seven amino acid changes in SWS2, including two changes known to cause a red-shift in light absorption, and is favored in blackwater lakes but disfavored in the clearwater habitat of the transplant population. Remarkably, the same red-shifting amino acid changes occurred after the duplication of SWS2 198 million years ago, in the ancestor of most spiny-rayed fish. Two distantly related fish species, bluefin killifish and black bream, express these old paralogs divergently in black- and clearwater habitats, while sticklebacks lost one paralog. Our study thus shows that convergent adaptation to the same environment can involve the same genetic changes on very different evolutionary time scales by reevolving lost mutations and reusing them repeatedly from standing genetic variation.
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Affiliation(s)
- David A. Marques
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
- * E-mail:
| | - John S. Taylor
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Felicity C. Jones
- Stanford University School of Medicine, Department of Developmental Biology, Stanford, California, United States of America
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Federica Di Palma
- Earlham Institute and University of East Anglia, Department of Biological Sciences, Norwich, United Kingdom
| | - David M. Kingsley
- Stanford University School of Medicine, Department of Developmental Biology, Stanford, California, United States of America
| | - Thomas E. Reimchen
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
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190
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Salesse C. Physiologie du signal visuel rétinien : de la phototransduction jusqu’au cycle visuel. J Fr Ophtalmol 2017; 40:239-250. [DOI: 10.1016/j.jfo.2016.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 12/16/2016] [Indexed: 11/28/2022]
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191
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DONG Z, YUWEN Y, SIMA Y, DONG Y, ZHAN H, CHEN G, LIU D. Photokinesis andDjopsingene expression analysis during the regeneration of planarian eyes. Integr Zool 2017; 12:157-164. [DOI: 10.1111/1749-4877.12234] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Zimei DONG
- College of Life Science; Henan Normal University; Xinxiang Henan China
| | - Yanqing YUWEN
- College of Life Science; Henan Normal University; Xinxiang Henan China
| | - Yingxu SIMA
- College of Life Science; Henan Normal University; Xinxiang Henan China
| | - Yanping DONG
- College of Life Science; Henan Normal University; Xinxiang Henan China
| | - Huina ZHAN
- College of Life Science; Henan Normal University; Xinxiang Henan China
| | - Guangwen CHEN
- College of Life Science; Henan Normal University; Xinxiang Henan China
| | - Dezeng LIU
- College of Life Science; Henan Normal University; Xinxiang Henan China
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192
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Gokuladhas K, Sivapriya N, Barath M, NewComer CH. Ocular progenitor cells and current applications in regenerative medicines - Review. Genes Dis 2017; 4:88-99. [PMID: 30258910 PMCID: PMC6136601 DOI: 10.1016/j.gendis.2017.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/31/2017] [Indexed: 12/31/2022] Open
Abstract
The recent emerging field of regenerative medicine is to present solutions for chronic diseases which cannot be sufficiently repaired by the body's own mechanisms. Stem cells are undifferentiated biological cells and have the potential to develop into many different cell types in the body during early life and growth. Self renewal and totipotency are the characteristic features of stem cells and it holds a promising result for treating various diseases like diabetic foot ulcer, heart diseases, lung diseases, Autism, Skin diseases, arthritis including eye disease. Failure of complete recovery of eye diseases and complications that follow conventional treatments have shifted search to a new form of regenerative medicine using Stem cells. The ocular progenitor cells are remarkable in stem cell biology and replenishing degenerated cells despite being present in low quantity and quiescence in our body has a high therapeutic value. In this paper we have review the applications on ocular progenitor stem cells in treatment of human eye diseases and address the strategies that have been exploited in an effort to regain visual function in the advance treatment of stem cells without any side effects and also present the significance in advance stem cell research.
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Affiliation(s)
- K Gokuladhas
- World Stem Cell Clinic India LLP (ISO 9001:2015 Certified Clinic), #6, 9th Cross Street, Kapaleeshwar Nagar, Neelankarai, Chennai 600115, India
| | - N Sivapriya
- World Stem Cell Clinic India LLP (ISO 9001:2015 Certified Clinic), #6, 9th Cross Street, Kapaleeshwar Nagar, Neelankarai, Chennai 600115, India
| | - M Barath
- World Stem Cell Clinic India LLP (ISO 9001:2015 Certified Clinic), #6, 9th Cross Street, Kapaleeshwar Nagar, Neelankarai, Chennai 600115, India
| | - Charles H NewComer
- World Stem Cell Clinic India LLP (ISO 9001:2015 Certified Clinic), #6, 9th Cross Street, Kapaleeshwar Nagar, Neelankarai, Chennai 600115, India
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193
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Mühlhäuser WW, Fischer A, Weber W, Radziwill G. Optogenetics - Bringing light into the darkness of mammalian signal transduction. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:280-292. [DOI: 10.1016/j.bbamcr.2016.11.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/04/2016] [Accepted: 11/10/2016] [Indexed: 01/01/2023]
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194
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Brandon CS, Greenwold MJ, Dudycha JL. Ancient and Recent Duplications Support Functional Diversity of Daphnia Opsins. J Mol Evol 2016; 84:12-28. [PMID: 28004131 DOI: 10.1007/s00239-016-9777-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/04/2016] [Indexed: 11/26/2022]
Abstract
Daphnia pulex has the largest known family of opsins, genes critical for photoreception and vision in animals. This diversity may be functionally redundant, arising from recent processes, or ancient duplications may have been preserved due to distinct functions and independent contributions to fitness. We analyzed opsins in D. pulex and its distant congener Daphnia magna. We identified 48 opsins in the D. pulex genome and 32 in D. magna. We inferred the complement of opsins in the last common ancestor of all Daphnia and evaluated the history of opsin duplication and loss. We further analyzed sequence variation to assess possible functional diversification among Daphnia opsins. Much of the opsin expansion occurred before the D. pulex-D. magna split more than 145 Mya, and both Daphnia lineages preserved most ancient opsins. More recent expansion occurred in pteropsins and long-wavelength visual opsins in both species, particularly D. pulex. Recent duplications were not random: the same ancestral genes duplicated independently in each modern species. Most ancient and some recent duplications involved differentiation at residues known to influence spectral tuning of visual opsins. Arthropsins show evidence of gene conversion between tandemly arrayed paralogs in functionally important domains. Intron-exon gene structure was generally conserved within clades inferred from sequences, although pteropsins showed substantial intron size variation. Overall, our analyses support the hypotheses that diverse opsins are maintained due to diverse functional roles in photoreception and vision, that functional diversification is both ancient and recent, and that multiple evolutionary processes have influenced different types of opsins.
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Affiliation(s)
- Christopher S Brandon
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Matthew J Greenwold
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Jeffry L Dudycha
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA.
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Liang D, Zhao M, Wang T, McManus DP, Cummins SF. GPCR and IR genes in Schistosoma mansoni miracidia. Parasit Vectors 2016; 9:563. [PMID: 27784323 PMCID: PMC5080760 DOI: 10.1186/s13071-016-1837-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/05/2016] [Indexed: 11/25/2022] Open
Abstract
Background Schistosoma species are responsible for the disease schistosomiasis, a highly prevalent helminthic disease that requires a freshwater snail as intermediate host. The S. mansoni free-living miracidium must utilize olfaction to find a suitable snail host, and certain types of rhodopsin G protein-coupled receptors (GPCRs) and ionotropic receptors (IRs) have been identified as olfactory receptors in other animal phyla. The Schistosoma genome project, together with the recent availability of proteomic databases, allowed for studies to explore receptors within S. mansoni, some of which may contribute to host finding. Results We have identified 17 rhodopsin-type GPCR sequences in S. mansoni belonging to four subclasses, including ligand-specific GPCRs (i.e. neuropeptide and opsin). RT-PCR demonstrated the expression of nine out of the 17 GPCRs in the free-living miracidia, each of which have been characterized for homology to S. haematobium. Among the nine GPCRs, two are predicted as Gq-opsins. We also describe the characterization of a Schistosoma-encoded IR based on similarity with other species IR and conservation of IR-like domains. Schistosoma mansoni IR is expressed in miracidia at 3 and 6 h post-hatch. Conclusions The identification of receptors in S. mansoni miracidia, presented here, contributes not only to further understanding of Schistosoma biology and signal transduction but also provides a basis for approaches that may modify parasite behaviour. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1837-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Di Liang
- Faculty of Science, Health and Education, University of the Sunshine Coast, Maroochydore, QLD, 4558, Australia
| | - Min Zhao
- Faculty of Science, Health and Education, University of the Sunshine Coast, Maroochydore, QLD, 4558, Australia
| | - Tianfang Wang
- Faculty of Science, Health and Education, University of the Sunshine Coast, Maroochydore, QLD, 4558, Australia
| | - Donald P McManus
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Q4006, Australia
| | - Scott F Cummins
- Faculty of Science, Health and Education, University of the Sunshine Coast, Maroochydore, QLD, 4558, Australia.
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Nissilä JS, Mänttäri SK, Särkioja TT, Tuominen HJ, Takala TE, Kiviniemi VJ, Sormunen RT, Saarela SYO, Timonen MJ. The distribution of melanopsin (OPN4) protein in the human brain. Chronobiol Int 2016; 34:37-44. [PMID: 27690288 DOI: 10.1080/07420528.2016.1232269] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Until now, melanopsin (OPN4) - a specialized photopigment being responsive especially to blue light wavelengths - has not been found in the human brain at protein level outside the retina. More specifically, OPN4 has only been found in about 2% of retinal ganglion cells (i.e. in intrinsically photosensitive retinal ganglion cells), and in a subtype of retinal cone-cells. Given that Allen Institute for Brain Science has described a wide distribution of OPN4 mRNA in two human brains, we aimed to investigate whether OPN4 is present in the human brain also at protein level. Western blotting and immunohistochemistry, as well as immunoelectron microscopy, were used to analyse the existence and distribution of OPN4 protein in 18 investigated areas of the human brain in samples obtained in forensic autopsies from 10 male subjects (54 ± 3.5 years). OPN4 protein expression was found in all subjects, and, furthermore, in 5 out of 10 subjects in all investigated brain areas localized in membranous compartments and cytoplasmic vesicles of neurons. To our opinion, the wide distribution of OPN4 in central areas of the human brain evokes a question whether ambient light has important straight targets in the human brain outside the retinohypothalamic tract (RHT). Further studies are, however, needed to investigate the putative physiological phototransductive actions of inborn OPN4 protein outside the RHT in the human brain.
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Affiliation(s)
- Juuso S Nissilä
- a University of Oulu, Center for Life Course Health Research , Oulu , Finland.,b Department of Biology, University of Oulu , Oulu , Finland
| | - Satu K Mänttäri
- b Department of Biology, University of Oulu , Oulu , Finland
| | - Terttu T Särkioja
- c University of Oulu , Institute of Diagnostics, Forensic Medicine , Oulu , Finland
| | - Hannu J Tuominen
- d University of Oulu , Institute of Diagnostics, Pathology , Oulu , Finland.,e Department of Pathology , Oulu University Hospital , Oulu , Finland
| | | | - Vesa J Kiviniemi
- g Department of Diagnostic Radiology , Oulu University Hospital , Oulu , Finland
| | - Raija T Sormunen
- d University of Oulu , Institute of Diagnostics, Pathology , Oulu , Finland.,e Department of Pathology , Oulu University Hospital , Oulu , Finland.,h Biocenter Oulu , University of Oulu , Oulu , Finland
| | | | - Markku J Timonen
- a University of Oulu, Center for Life Course Health Research , Oulu , Finland
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197
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Gagnon YL, Wilby D, Temple SE. Losing focus: how lens position and viewing angle affect the function of multifocal lenses in fishes. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2016; 33:1901-1909. [PMID: 27607515 DOI: 10.1364/josaa.33.001901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Light rays of different wavelengths are focused at different distances when they pass through a lens (longitudinal chromatic aberration [LCA]). For animals with color vision this can pose a serious problem, because in order to perceive a sharp image the rays must be focused at the shallow plane of the photoreceptor's outer segments in the retina. A variety of fish and tetrapods have been found to possess multifocal lenses, which correct for LCA by assigning concentric zones to correctly focus specific wavelengths. Each zone receives light from a specific beam entrance position (BEP) (the lateral distance between incoming light and the center of the lens). Any occlusion of incoming light at specific BEPs changes the composition of the wavelengths that are correctly focused on the retina. Here, we calculated the effect of lens position relative to the plane of the iris and light entering the eye at oblique angles on how much of the lens was involved in focusing the image on the retina (measured as the availability of BEPs). We used rotational photography of fish eyes and mathematical modeling to quantify the degree of lens occlusion. We found that, at most lens positions and viewing angles, there was a decrease of BEP availability and in some cases complete absence of some BEPs. Given the implications of these effects on image quality, we postulate that three morphological features (aphakic spaces, curvature of the iris, and intraretinal variability in spectral sensitivity) may, in part, be adaptations to mitigate the loss of spectral image quality in the periphery of the eyes of fishes.
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198
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Abstract
Understanding the evolution of early nervous systems is hazardous because we lack good criteria for determining homology between the systems of distant taxa; the timing of the evolutionary events is contested, and thus the relevant ecological and geological settings for them are also unclear. Here I argue that no simple approach will resolve the first issue, but that it remains likely that animals evolved relatively late, and that their nervous systems thus arose during the late Ediacaran, in a context provided by the changing planktonic and benthic environments of the time. The early trace fossil provides the most concrete evidence for early behavioural diversification, but it cannot simply be translated into increasing nervous system complexity: behavioural complexity does not map on a one-to-one basis onto nervous system complexity, both because of possible limitations to behaviour caused by the environment and because we know that even organisms without nervous systems are capable of relatively complex behaviour.
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Affiliation(s)
- Graham E Budd
- Department of Earth Sciences, Palaeobiology Programme, Uppsala University, Villavägen 16, Uppsala 752 36, Sweden
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199
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A new transcriptome and transcriptome profiling of adult and larval tissue in the box jellyfish Alatina alata: an emerging model for studying venom, vision and sex. BMC Genomics 2016; 17:650. [PMID: 27535656 PMCID: PMC4989536 DOI: 10.1186/s12864-016-2944-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/18/2016] [Indexed: 12/28/2022] Open
Abstract
Background Cubozoans (box jellyfish) are cnidarians that have evolved a number of distinguishing features. Many cubozoans have a particularly potent sting, effected by stinging structures called nematocysts; cubozoans have well-developed light sensation, possessing both image-forming lens eyes and light-sensitive eye spots; and some cubozoans have complex mating behaviors, including aggregations, copulation and internal fertilization. The cubozoan Alatina alata is emerging as a cnidarian model because it forms predictable monthly nearshore breeding aggregations in tropical to subtropical waters worldwide, making both adult and larval material reliably accessible. To develop resources for A. alata, this study generated a functionally annotated transcriptome of adult and larval tissue, applying preliminary differential expression analyses to identify candidate genes involved in nematogenesis and venom production, vision and extraocular sensory perception, and sexual reproduction, which for brevity we refer to as “venom”, “vision” and “sex”. Results We assembled a transcriptome de novo from RNA-Seq data pooled from multiple body parts (gastric cirri, ovaries, tentacle (with pedalium base) and rhopalium) of an adult female A. alata medusa and larval planulae. Our transcriptome comprises ~32 K transcripts, after filtering, and provides a basis for analyzing patterns of gene expression in adult and larval box jellyfish tissues. Furthermore, we annotated a large set of candidate genes putatively involved in venom, vision and sex, providing an initial molecular characterization of these complex features in cubozoans. Expression profiles and gene tree reconstruction provided a number of preliminary insights into the putative sites of nematogenesis and venom production, regions of phototransduction activity and fertilization dynamics in A. alata. Conclusions Our Alatina alata transcriptome significantly adds to the genomic resources for this emerging cubozoan model. This study provides the first annotated transcriptome from multiple tissues of a cubozoan focusing on both the adult and larvae. Our approach of using multiple body parts and life stages to generate this transcriptome effectively identified a broad range of candidate genes for the further study of coordinated processes associated with venom, vision and sex. This new genomic resource and the candidate gene dataset are valuable for further investigating the evolution of distinctive features of cubozoans, and of cnidarians more broadly. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2944-3) contains supplementary material, which is available to authorized users.
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200
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Ingram NT, Sampath AP, Fain GL. Why are rods more sensitive than cones? J Physiol 2016; 594:5415-26. [PMID: 27218707 DOI: 10.1113/jp272556] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/16/2016] [Indexed: 12/11/2022] Open
Abstract
One hundred and fifty years ago Max Schultze first proposed the duplex theory of vision, that vertebrate eyes have two types of photoreceptor cells with differing sensitivity: rods for dim light and cones for bright light and colour detection. We now know that this division is fundamental not only to the photoreceptors themselves but to the whole of retinal and visual processing. But why are rods more sensitive, and how did the duplex retina first evolve? Cells resembling cones are very old, first appearing among cnidarians; the emergence of rods was a key step in the evolution of the vertebrate eye. Many transduction proteins have different isoforms in rods and cones, and others are expressed at different levels. Moreover rods and cones have a different anatomy, with only rods containing membranous discs enclosed by the plasma membrane. These differences must be responsible for the difference in absolute sensitivity, but which are essential? Recent research particularly expressing cone proteins in rods or changing the level of expression seem to show that many of the molecular differences in the activation and decay of the response may have each made a small contribution as evolution proceeded stepwise with incremental increases in sensitivity. Rod outer-segment discs were not essential and developed after single-photon detection. These experiments collectively provide a new understanding of the two kinds of photoreceptors and help to explain how gene duplication and the formation of rod-specific proteins produced the duplex retina, which has remained remarkably constant in physiology from amphibians to man.
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Affiliation(s)
- Norianne T Ingram
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, 90095-7239, USA
| | - Alapakkam P Sampath
- Department of Ophthalmology and Jules Stein Eye Institute, University of California, Los Angeles, CA, 90095-7000, USA
| | - Gordon L Fain
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA, 90095-7239, USA. .,Department of Ophthalmology and Jules Stein Eye Institute, University of California, Los Angeles, CA, 90095-7000, USA.
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