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Guan N, Gao X, Ye H. Engineering of optogenetic devices for biomedical applications in mammalian synthetic biology. ENGINEERING BIOLOGY 2022; 6:35-49. [PMID: 36969102 PMCID: PMC9996731 DOI: 10.1049/enb2.12022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 06/20/2022] [Accepted: 06/29/2022] [Indexed: 11/19/2022] Open
Abstract
Gene- and cell-based therapies are the next frontiers in the field of medicine. Both are transformative and innovative therapies; however, a lack of safety data limits the translation of such promising technologies to the clinic. Improving the safety and promoting the clinical translation of these therapies can be achieved by tightly regulating the release and delivery of therapeutic outputs. In recent years, the rapid development of optogenetic technology has provided opportunities to develop precision-controlled gene- and cell-based therapies, in which light is introduced to precisely and spatiotemporally manipulate the behaviour of genes and cells. This review focuses on the development of optogenetic tools and their applications in biomedicine, including photoactivated genome engineering and phototherapy for diabetes and tumours. The prospects and challenges of optogenetic tools for future clinical applications are also discussed.
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Affiliation(s)
- Ningzi Guan
- Synthetic Biology and Biomedical Engineering LaboratoryBiomedical Synthetic Biology Research CenterShanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Xianyun Gao
- Synthetic Biology and Biomedical Engineering LaboratoryBiomedical Synthetic Biology Research CenterShanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghaiChina
| | - Haifeng Ye
- Synthetic Biology and Biomedical Engineering LaboratoryBiomedical Synthetic Biology Research CenterShanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghaiChina
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Gordeliy V, Kovalev K, Bamberg E, Rodriguez-Valera F, Zinovev E, Zabelskii D, Alekseev A, Rosselli R, Gushchin I, Okhrimenko I. Microbial Rhodopsins. Methods Mol Biol 2022; 2501:1-52. [PMID: 35857221 DOI: 10.1007/978-1-0716-2329-9_1] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The first microbial rhodopsin, a light-driven proton pump bacteriorhodopsin from Halobacterium salinarum (HsBR), was discovered in 1971. Since then, this seven-α-helical protein, comprising a retinal molecule as a cofactor, became a major driver of groundbreaking developments in membrane protein research. However, until 1999 only a few archaeal rhodopsins, acting as light-driven proton and chloride pumps and also photosensors, were known. A new microbial rhodopsin era started in 2000 when the first bacterial rhodopsin, a proton pump, was discovered. Later it became clear that there are unexpectedly many rhodopsins, and they are present in all the domains of life and even in viruses. It turned out that they execute such a diversity of functions while being "nearly the same." The incredible evolution of the research area of rhodopsins and the scientific and technological potential of the proteins is described in the review with a focus on their function-structure relationships.
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Affiliation(s)
- Valentin Gordeliy
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France.
| | - Kirill Kovalev
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Francisco Rodriguez-Valera
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Alicante, Spain
| | - Egor Zinovev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Dmitrii Zabelskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Alexey Alekseev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Riccardo Rosselli
- Departamento de Fisiología, Genetica y Microbiología. Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Ivan Okhrimenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
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Nakamizo Y, Fujisawa T, Kikukawa T, Okamura A, Baba H, Unno M. Low-temperature Raman spectroscopy of sodium-pump rhodopsin from Indibacter alkaliphilus: insight of Na + binding for active Na + transport. Phys Chem Chem Phys 2021; 23:2072-2079. [PMID: 33433533 DOI: 10.1039/d0cp05652a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We carried out the low-temperature Raman measurement of a sodium pump rhodopsin from Indibacter alkaliphilus (IaNaR) and examined the primary structural change for the light-driven Na+ pump. We observed that photoexcitation of IaNaR produced the distorted 13-cis retinal chromophore in the presence of Na+, while the structural distortion was significantly relaxed in the absence of Na+. This structural difference of the chromophore with/without Na+ was attributed to the Na+ binding to the protein, which alters the active site. Using the spectral sensitivity to the ion binding, we found that IaNaR had a second Na+ binding site in addition to the one already specified on the extracellular surface. To date, the Na+ binding has not been considered as a prerequisite for Na+ transport. However, this study provides insight that the protein structural change induced by the ion binding involved the formation of an R108-D250 salt bridge, which has critical importance in the active transport of Na+.
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Affiliation(s)
- Yushi Nakamizo
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan.
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Zhao H, Ma B, Ji L, Li L, Wang H, Chen D. Coexistence of light-driven Na + and H + transport in a microbial rhodopsin from Nonlabens dokdonensis. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 172:70-76. [PMID: 28527429 DOI: 10.1016/j.jphotobiol.2017.05.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 04/06/2017] [Accepted: 05/04/2017] [Indexed: 02/04/2023]
Abstract
Ion pumping microbial rhodopsins are photochemically active membrane proteins, converting light energy into ion-motive-force for ATP synthesis. Nonlabens dokdonensis rhodopsin 2 (NdR2), was recently identified as a light-driven Na+ pump. However, few functional studies on NdR2 have been conducted to elucidate its mechanism of ion transport. By reconstituting NdR2 into liposomes, we proved that NdR2 functions as a light-driven Na+/H+ pump. As Na+ concentration increased, the dominant H+ pump activity switched to the Na+ pump activity at neutral pH. The inversion of pH change by the addition of CCCP at low Na+ further suggested that the transport of Na+ and H+ should coexist in NdR2. By increasing H+ concentration, the affinity for Na+ lowered, which was indicated by an increase in KM from ~31mM at pH ~7.5, to ~74mM at pH ~6.5. These results demonstrated that Na+ transport competed with H+ transport in NdR2, which was confirmed by the dominant H+ pump activity at pH ~5.7. Kinetic experiments using pyranine uncovered a transient H+ uptake, followed by an H+ release at the millisecond time scale in both Na+ and K+ solutions. Therefore, these NdR2 results may provide functional and kinetic insights into the ion transport mechanism in light-driven Na+ pumps.
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Affiliation(s)
- Hongshen Zhao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baofu Ma
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liangliang Ji
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Longjie Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huanhuan Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Deliang Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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