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Vlasova AD, Bukhalovich SM, Bagaeva DF, Polyakova AP, Ilyinsky NS, Nesterov SV, Tsybrov FM, Bogorodskiy AO, Zinovev EV, Mikhailov AE, Vlasov AV, Kuklin AI, Borshchevskiy VI, Bamberg E, Uversky VN, Gordeliy VI. Intracellular microbial rhodopsin-based optogenetics to control metabolism and cell signaling. Chem Soc Rev 2024; 53:3327-3349. [PMID: 38391026 DOI: 10.1039/d3cs00699a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Microbial rhodopsin (MRs) ion channels and pumps have become invaluable optogenetic tools for neuroscience as well as biomedical applications. Recently, MR-optogenetics expanded towards subcellular organelles opening principally new opportunities in optogenetic control of intracellular metabolism and signaling via precise manipulations of organelle ion gradients using light. This new optogenetic field expands the opportunities for basic and medical studies of cancer, cardiovascular, and metabolic disorders, providing more detailed and accurate control of cell physiology. This review summarizes recent advances in studies of the cellular metabolic processes and signaling mediated by optogenetic tools targeting mitochondria, endoplasmic reticulum (ER), lysosomes, and synaptic vesicles. Finally, we discuss perspectives of such an optogenetic approach in both fundamental and applied research.
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Affiliation(s)
- Anastasiia D Vlasova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Siarhei M Bukhalovich
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Diana F Bagaeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Aleksandra P Polyakova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Nikolay S Ilyinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Semen V Nesterov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Fedor M Tsybrov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Andrey O Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Egor V Zinovev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anatolii E Mikhailov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexey V Vlasov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Alexander I Kuklin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Valentin I Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Valentin I Gordeliy
- Institut de Biologie Structurale Jean-Pierre Ebel, Université Grenoble Alpes-Commissariat à l'Energie Atomique et aux Energies Alternatives-CNRS, 38027 Grenoble, France.
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2
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Peterson A, Baskett C, Ratcliff WC, Burnetti A. Transforming yeast into a facultative photoheterotroph via expression of vacuolar rhodopsin. Curr Biol 2024; 34:648-654.e3. [PMID: 38218181 DOI: 10.1016/j.cub.2023.12.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 11/03/2023] [Accepted: 12/13/2023] [Indexed: 01/15/2024]
Abstract
Phototrophic metabolism, the capture of light for energy, was a pivotal biological innovation that greatly increased the total energy available to the biosphere. Chlorophyll-based photosynthesis is the most familiar phototrophic metabolism, but retinal-based microbial rhodopsins transduce nearly as much light energy as chlorophyll does,1 via a simpler mechanism, and are found in far more taxonomic groups. Although this system has apparently spread widely via horizontal gene transfer,2,3,4 little is known about how rhodopsin genes (with phylogenetic origins within prokaryotes5,6) are horizontally acquired by eukaryotic cells with complex internal membrane architectures or the conditions under which they provide a fitness advantage. To address this knowledge gap, we sought to determine whether Saccharomyces cerevisiae, a heterotrophic yeast with no known evolutionary history of phototrophy, can function as a facultative photoheterotroph after acquiring a single rhodopsin gene. We inserted a rhodopsin gene from Ustilago maydis,7 which encodes a proton pump localized to the vacuole, an organelle normally acidified via a V-type rotary ATPase, allowing the rhodopsin to supplement heterotrophic metabolism. Probes of the physiology of modified cells show that they can deacidify the cytoplasm using light energy, demonstrating the ability of rhodopsins to ameliorate the effects of starvation and quiescence. Further, we show that yeast-bearing rhodopsins gain a selective advantage when illuminated, proliferating more rapidly than their non-phototrophic ancestor or rhodopsin-bearing yeast cultured in the dark. These results underscore the ease with which rhodopsins may be horizontally transferred even in eukaryotes, providing novel biological function without first requiring evolutionary optimization.
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Affiliation(s)
- Autumn Peterson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA
| | - Carina Baskett
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA.
| | - Anthony Burnetti
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30309, USA; Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30309, USA.
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3
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Nieto-Panqueva F, Rubalcava-Gracia D, Hamel PP, González-Halphen D. The constraints of allotopic expression. Mitochondrion 2023; 73:30-50. [PMID: 37739243 DOI: 10.1016/j.mito.2023.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/28/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
Allotopic expression is the functional transfer of an organellar gene to the nucleus, followed by synthesis of the gene product in the cytosol and import into the appropriate organellar sub compartment. Here, we focus on mitochondrial genes encoding OXPHOS subunits that were naturally transferred to the nucleus, and critically review experimental evidence that claim their allotopic expression. We emphasize aspects that may have been overlooked before, i.e., when modifying a mitochondrial gene for allotopic expression━besides adapting the codon usage and including sequences encoding mitochondrial targeting signals━three additional constraints should be considered: (i) the average apparent free energy of membrane insertion (μΔGapp) of the transmembrane stretches (TMS) in proteins earmarked for the inner mitochondrial membrane, (ii) the final, functional topology attained by each membrane-bound OXPHOS subunit; and (iii) the defined mechanism by which the protein translocator TIM23 sorts cytosol-synthesized precursors. The mechanistic constraints imposed by TIM23 dictate the operation of two pathways through which alpha-helices in TMS are sorted, that eventually determine the final topology of membrane proteins. We used the biological hydrophobicity scale to assign an average apparent free energy of membrane insertion (μΔGapp) and a "traffic light" color code to all TMS of OXPHOS membrane proteins, thereby predicting which are more likely to be internalized into mitochondria if allotopically produced. We propose that the design of proteins for allotopic expression must make allowance for μΔGapp maximization of highly hydrophobic TMS in polypeptides whose corresponding genes have not been transferred to the nucleus in some organisms.
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Affiliation(s)
- Felipe Nieto-Panqueva
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Diana Rubalcava-Gracia
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico; Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Patrice P Hamel
- Department of Molecular Genetics and Department of Biological Chemistry and Pharmacology, Ohio State University, Columbus, OH, USA; Vellore Institute of Technology (VIT), School of BioScience and Technology, Vellore, Tamil Nadu, India
| | - Diego González-Halphen
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico.
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Tiwary V, Galow AM, Wojtovich AP, Peleg S. Using light to drive energy transduction in metazoan aging. Trends Biochem Sci 2023; 48:920-922. [PMID: 37704489 PMCID: PMC10592090 DOI: 10.1016/j.tibs.2023.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/11/2023] [Accepted: 08/22/2023] [Indexed: 09/15/2023]
Abstract
Mitochondrial dysfunction is a central hallmark of aging and energy transduction is a promising target for longevity interventions. New research suggests that interventions in how energy is transduced could benefit healthy longevity. Here, we propose using light as an alternative energy source to fuel mitochondria and increase metazoan lifespan.
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Affiliation(s)
- Vaibhav Tiwary
- Research Group Epigenetics, Metabolism, and Longevity, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
| | - Anne-Marie Galow
- Institute for Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
| | - Andrew P Wojtovich
- University of Rochester Medical Center, Department of Anesthesiology and Perioperative Medicine, 575 Elmwood Avenue, Rochester, NY 14642, USA.
| | - Shahaf Peleg
- Research Group Epigenetics, Metabolism, and Longevity, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany.
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Piatkevich KD, Boyden ES. Optogenetic control of neural activity: The biophysics of microbial rhodopsins in neuroscience. Q Rev Biophys 2023; 57:e1. [PMID: 37831008 DOI: 10.1017/s0033583523000033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
Optogenetics, the use of microbial rhodopsins to make the electrical activity of targeted neurons controllable by light, has swept through neuroscience, enabling thousands of scientists to study how specific neuron types contribute to behaviors and pathologies, and how they might serve as novel therapeutic targets. By activating a set of neurons, one can probe what functions they can initiate or sustain, and by silencing a set of neurons, one can probe the functions they are necessary for. We here review the biophysics of these molecules, asking why they became so useful in neuroscience for the study of brain circuitry. We review the history of the field, including early thinking, early experiments, applications of optogenetics, pre-optogenetics targeted neural control tools, and the history of discovering and characterizing microbial rhodopsins. We then review the biophysical attributes of rhodopsins that make them so useful to neuroscience - their classes and structure, their photocycles, their photocurrent magnitudes and kinetics, their action spectra, and their ion selectivity. Our hope is to convey to the reader how specific biophysical properties of these molecules made them especially useful to neuroscientists for a difficult problem - the control of high-speed electrical activity, with great precision and ease, in the brain.
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Affiliation(s)
- Kiryl D Piatkevich
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Edward S Boyden
- McGovern Institute and Koch Institute, Departments of Brain and Cognitive Sciences, Media Arts and Sciences, and Biological Engineering, K. Lisa Yang Center for Bionics and Center for Neurobiological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
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6
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Sushmita K, Sharma S, Singh Kaushik M, Kateriya S. Algal rhodopsins encoding diverse signal sequence holds potential for expansion of organelle optogenetics. Biophys Physicobiol 2023; 20:e201008. [PMID: 38362319 PMCID: PMC10865886 DOI: 10.2142/biophysico.bppb-v20.s008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
Rhodopsins have been extensively employed for optogenetic regulation of bioelectrical activity of excitable cells and other cellular processes across biological systems. Various strategies have been adopted to attune the cellular processes at the desired subcellular compartment (plasma membrane, endoplasmic reticulum, Golgi, mitochondria, lysosome) within the cell. These strategies include-adding signal sequences, tethering peptides, specific interaction sites, or mRNA elements at different sites in the optogenetic proteins for plasma membrane integration and subcellular targeting. However, a single approach for organelle optogenetics was not suitable for the relevant optogenetic proteins and often led to the poor expression, mislocalization, or altered physical and functional properties. Therefore, the current study is focused on the native subcellular targeting machinery of algal rhodopsins. The N- and C-terminus signal prediction led to the identification of rhodopsins with diverse organelle targeting signal sequences for the nucleus, mitochondria, lysosome, endosome, vacuole, and cilia. Several identified channelrhodopsins and ion-pumping rhodopsins possess effector domains associated with DNA metabolism (repair, replication, and recombination) and gene regulation. The identified algal rhodopsins with diverse effector domains and encoded native subcellular targeting sequences hold immense potential to establish expanded organelle optogenetic regulation and associated cellular signaling.
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Affiliation(s)
- Kumari Sushmita
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sunita Sharma
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Manish Singh Kaushik
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Suneel Kateriya
- Laboratory of Optobiotechnology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
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de Grip WJ, Ganapathy S. Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering. Front Chem 2022; 10:879609. [PMID: 35815212 PMCID: PMC9257189 DOI: 10.3389/fchem.2022.879609] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/16/2022] [Indexed: 01/17/2023] Open
Abstract
The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.
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Affiliation(s)
- Willem J. de Grip
- Leiden Institute of Chemistry, Department of Biophysical Organic Chemistry, Leiden University, Leiden, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Srividya Ganapathy
- Department of Imaging Physics, Delft University of Technology, Netherlands
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True-atomic-resolution insights into the structure and functional role of linear chains and low-barrier hydrogen bonds in proteins. Nat Struct Mol Biol 2022; 29:440-450. [PMID: 35484235 DOI: 10.1038/s41594-022-00762-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/14/2022] [Indexed: 12/21/2022]
Abstract
Hydrogen bonds are fundamental to the structure and function of biological macromolecules and have been explored in detail. The chains of hydrogen bonds (CHBs) and low-barrier hydrogen bonds (LBHBs) were proposed to play essential roles in enzyme catalysis and proton transport. However, high-resolution structural data from CHBs and LBHBs is limited. The challenge is that their 'visualization' requires ultrahigh-resolution structures of the ground and functionally important intermediate states to identify proton translocation events and perform their structural assignment. Our true-atomic-resolution structures of the light-driven proton pump bacteriorhodopsin, a model in studies of proton transport, show that CHBs and LBHBs not only serve as proton pathways, but also are indispensable for long-range communications, signaling and proton storage in proteins. The complete picture of CHBs and LBHBs discloses their multifunctional roles in providing protein functions and presents a consistent picture of proton transport and storage resolving long-standing debates and controversies.
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Abstract
Research on type 1 rhodopsins spans now a history of 50 years. Originally, just archaeal ion pumps and sensors have been discovered. However, with modern genetic techniques and gene sequencing tools, more and more proteins were identified in all kingdoms of life. Spectroscopic and other biophysical studies revealed quite diverse functions. Ion pumps, sensors, and channels are imprinted in the same seven-helix transmembrane protein scaffold carrying a retinal prosthetic group. In this review, molecular biology methods are described, which enabled the elucidation of their function and structure leading to optogenetic applications.
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Affiliation(s)
- Martin Engelhard
- Department Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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10
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Abstract
Optogenetics has revolutionized not only neuroscience but also had an impact on muscle physiology and cell biology. Rhodopsin-based optogenetics started with the discovery of the light-gated cation channels, called channelrhodopsins. Together with the light-driven ion pumps, these channels allow light-mediated control of electrically excitable cells in culture tissue and living animals. They can be activated (depolarized) or silenced (hyperpolarized) by light with incomparably high spatiotemporal resolution. Optogenetics allows the light manipulation of cells under electrode-free conditions in a minimally invasive manner. Through modern genetic techniques, virus-induced transduction can be performed with extremely high cell specificity in tissue and living animals, allowing completely new approaches for analyzing neural networks, behavior studies, and investigations of neurodegenerative diseases. First clinical trials for the optogenetic recovery of vision are underway.This chapter provides a comprehensive description of the structure and function of the different light-gated channels and some new light-activated ion pumps. Some of them already play an essential role in optogenetics while others are supposed to become important tools for more specialized applications in the future.At the moment, a large number of publications are available concerning intrinsic mechanisms of microbial rhodopsins. Mostly they describe CrChR2 and its variants, as CrChR2 is still the most prominent optogenetic tool. Therefore, many biophysically and biochemically oriented groups contributed to the overwhelming mass of information on this unique ion channel's molecular mechanism. In this context, the function of new optogenetic tools is discussed, which is essential for rational optimization of the optogenetic approach for an eventual biomedical application. The comparison of the effectivity of ion pumps versus ion channels is discussed as well.Applications of rhodopsins-based optogenetic tools are also discussed in the chapter. Because of the enormous number of these applications in neuroscience, only exemplary studies on cell culture neural tissue, muscle physiology, and remote control of animal behavior are presented.
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Affiliation(s)
- Alexey Alekseev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Valentin Gordeliy
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
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Adam S, Wiebeler C, Schapiro I. Structural Factors Determining the Absorption Spectrum of Channelrhodopsins: A Case Study of the Chimera C1C2. J Chem Theory Comput 2021; 17:6302-6313. [PMID: 34255519 DOI: 10.1021/acs.jctc.1c00160] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Channelrhodopsins are photosensitive proteins that trigger flagella motion in single-cell algae and have been successfully utilized in optogenetic applications. In optogenetics, light is used to activate neural cells in living organisms, which can be achieved by exploiting the ion channel signaling of channelrhodopsins. Tailoring channelrhodopsins for such applications includes the tuning of the absorption maximum. In order to establish rational design and to obtain a desired spectral shift, a basic understanding of the absorption spectrum is required. We have studied the chimera C1C2 as a representative of this protein family and the first member with an available crystal structure. For this purpose, we sampled the conformations of C1C2 using quantum mechanical/molecular mechanical molecular dynamics and subjected the resulting snapshots of the trajectory to excitation energy calculations using ADC(2) and simplified time-dependent density functional theory. In contrast to previous reports, we found that different hydrogen-bonding networks-involving the retinal protonated Schiff base, the putative counterions E162 and D292, and water molecules-had only a small impact on the absorption spectrum. However, in the case of deprotonated E162, increasing the distance to the Schiff base hydrogen-bonding partner led to a systematic blue shift. The β-ionone ring rotation was identified as another important contributor. Yet the most important factors were found to be the bond length alternation and bond order alternation that were linearly correlated to the absorption maximum by up to 62 and 82%, respectively. We ascribe this novel insight into the structural basis of the absorption spectrum to our enhanced protein setup that includes membrane embedding as well as long and extensive sampling.
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Affiliation(s)
- Suliman Adam
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Christian Wiebeler
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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Bogorodskiy A, Okhrimenko I, Maslov I, Maliar N, Burkatovskii D, von Ameln F, Schulga A, Jakobs P, Altschmied J, Haendeler J, Katranidis A, Sorokin I, Mishin A, Gordeliy V, Büldt G, Voos W, Gensch T, Borshchevskiy V. Accessing Mitochondrial Protein Import in Living Cells by Protein Microinjection. Front Cell Dev Biol 2021; 9:698658. [PMID: 34307376 PMCID: PMC8292824 DOI: 10.3389/fcell.2021.698658] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/15/2021] [Indexed: 01/06/2023] Open
Abstract
Mitochondrial protein biogenesis relies almost exclusively on the expression of nuclear-encoded polypeptides. The current model postulates that most of these proteins have to be delivered to their final mitochondrial destination after their synthesis in the cytoplasm. However, the knowledge of this process remains limited due to the absence of proper experimental real-time approaches to study mitochondria in their native cellular environment. We developed a gentle microinjection procedure for fluorescent reporter proteins allowing a direct non-invasive study of protein transport in living cells. As a proof of principle, we visualized potential-dependent protein import into mitochondria inside intact cells in real-time. We validated that our approach does not distort mitochondrial morphology and preserves the endogenous expression system as well as mitochondrial protein translocation machinery. We observed that a release of nascent polypeptides chains from actively translating cellular ribosomes by puromycin strongly increased the import rate of the microinjected pre-protein. This suggests that a substantial amount of mitochondrial translocase complexes was involved in co-translational protein import of endogenously expressed pre-proteins. Our protein microinjection method opens new possibilities to study the role of mitochondrial protein import in cell models of various pathological conditions as well as aging processes.
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Affiliation(s)
- Andrey Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan Okhrimenko
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan Maslov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Nina Maliar
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Dmitrii Burkatovskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Florian von Ameln
- Environmentally-Induced Cardiovascular Degeneration, Central Institute of Clinical Chemistry and Laboratory Medicine, Medical Faculty, University Hospital and Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- IUF–Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Alexey Schulga
- Molecular Immunology Laboratory, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Philipp Jakobs
- Environmentally-Induced Cardiovascular Degeneration, Central Institute of Clinical Chemistry and Laboratory Medicine, Medical Faculty, University Hospital and Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Joachim Altschmied
- Environmentally-Induced Cardiovascular Degeneration, Central Institute of Clinical Chemistry and Laboratory Medicine, Medical Faculty, University Hospital and Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
- IUF–Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Judith Haendeler
- Environmentally-Induced Cardiovascular Degeneration, Central Institute of Clinical Chemistry and Laboratory Medicine, Medical Faculty, University Hospital and Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Alexandros Katranidis
- Institute of Biological Information Processing (IBI-6: Cellular Structural Biology), Forschungszentrum Jülich, Jülich, Germany
| | - Ivan Sorokin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Georg Büldt
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Wolfgang Voos
- Institute of Biochemistry and Molecular Biology (IBMB), Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Thomas Gensch
- Institute of Biological Information Processing (IBI-1: Molecular and Cellular Physiology), Forschungszentrum Jülich, Jülich, Germany
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
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13
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Abstract
Rhodopsins, most of which are proton pumps generating transmembrane electrochemical proton gradients, span all three domains of life, are abundant in the biosphere, and could play a crucial role in the early evolution of life on earth. Whereas archaeal and bacterial proton pumps are among the best structurally characterized proteins, rhodopsins from unicellular eukaryotes have not been well characterized. To fill this gap in the current understanding of the proton pumps and to gain insight into the evolution of rhodopsins using a structure-based approach, we performed a structural and functional analysis of the light-driven proton pump LR (Mac) from the pathogenic fungus Leptosphaeria maculans. The first high-resolution structure of fungi rhodopsin and its functional properties reveal the striking similarity of its membrane part to archaeal but not to bacterial rhodopsins. We show that an unusually long N-terminal region stabilizes the protein through direct interaction with its extracellular loop (ECL2). We compare to our knowledge all available structures and sequences of outward light-driven proton pumps and show that eukaryotic and archaeal proton pumps, most likely, share a common ancestor. Zabelskii et al. present a structural and functional analysis of the lightdriven proton pump LR (Mac) from the fungus Leptosphaeria maculans. Their findings indicate that the archaeal ancestry of eukaryotic type 1 rhodopsins, and that the archaeal host of the proto-mitochondrial endosymbiont was capable of light-driven proton pumping.
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14
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Walter M, Schlesinger R. Nanodisc Reconstitution of Channelrhodopsins Heterologously Expressed in Pichia pastoris for Biophysical Investigations. Methods Mol Biol 2021; 2191:29-48. [PMID: 32865737 DOI: 10.1007/978-1-0716-0830-2_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
For a successful characterization of channelrhodopsins with biophysical methods like FTIR, Raman, EPR and NMR spectroscopy and X-ray crystallography, large amounts of purified protein are requested. For proteins of eukaryotic origin, which are poorly expressing in bacterial systems or not at all, the yeast Pichia pastoris represents a promising alternative for overexpression. Here we describe the methods for cloning, overexpression and mutagenesis as well as the purification procedures for channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2), channelrhodopsin-1 from Chlamydomonas augustae (CaChR1) and the scaffold protein MSP1D1 for reconstitution of the membrane proteins into nanodiscs. Finally, protocols are provided to study CaChR1 by FTIR difference spectroscopy and by time-resolved UV/Vis spectroscopy.
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Affiliation(s)
- Maria Walter
- Experimental Physics: Genetic Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Ramona Schlesinger
- Experimental Physics: Genetic Biophysics, Freie Universität Berlin, Berlin, Germany.
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15
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Kojima K, Shibukawa A, Sudo Y. The Unlimited Potential of Microbial Rhodopsins as Optical Tools. Biochemistry 2019; 59:218-229. [PMID: 31815443 DOI: 10.1021/acs.biochem.9b00768] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Microbial rhodopsins, a photoactive membrane protein family, serve as fundamental tools for optogenetics, an innovative technology for controlling biological activities with light. Microbial rhodopsins are widely distributed in nature and have a wide variety of biological functions. Regardless of the many different known types of microbial rhodopsins, only a few of them have been used in optogenetics to control neural activity to understand neural networks. The efforts of our group have been aimed at identifying and characterizing novel rhodopsins from nature and also at engineering novel variant rhodopsins by rational design. On the basis of the molecular and functional characteristics of those novel rhodopsins, we have proposed new rhodopsin-based optogenetics tools to control not only neural activities but also "non-neural" activities. In this Perspective, we introduce the achievements and summarize future challenges in creating optogenetics tools using rhodopsins. The implementation of optogenetics deep inside an in vivo brain is the well-known challenge for existing rhodopsins. As a perspective to address this challenge, we introduce innovative optical illumination techniques using wavefront shaping that can reinforce the low light sensitivity of the rhodopsins and realize deep-brain optogenetics. The applications of our optogenetics tools could be extended to manipulate non-neural biological activities such as gene expression, apoptosis, energy production, and muscle contraction. We also discuss the potentially unlimited biotechnological applications of microbial rhodopsins in the future such as in photovoltaic devices and in drug delivery systems. We believe that advances in the field will greatly expand the potential uses of microbial rhodopsins as optical tools.
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Affiliation(s)
- Keiichi Kojima
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences , Okayama University , Okayama 700-8530 , Japan
| | - Atsushi Shibukawa
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences , Okayama University , Okayama 700-8530 , Japan
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences , Okayama University , Okayama 700-8530 , Japan
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16
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Gleason FH, Larkum AW, Raven JA, Manohar CS, Lilje O. Ecological implications of recently discovered and poorly studied sources of energy for the growth of true fungi especially in extreme environments. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2018.12.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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17
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Abstract
The utilization of light energy to power organic-chemical transformations is a fundamental strategy of the terrestrial energy cycle. Inspired by the elegance of natural photosynthesis, much interdisciplinary research effort has been devoted to the construction of simplified cell mimics based on artificial vesicles to provide a novel tool for biocatalytic cascade reactions with energy-demanding steps. By inserting natural or even artificial photosynthetic systems into liposomes or polymersomes, the light-driven proton translocation and the resulting formation of electrochemical gradients have become possible. This is the basis for the conversion of photonic into chemical energy in form of energy-rich molecules such as adenosine triphosphate (ATP), which can be further utilized by energy-dependent biocatalytic reactions, e.g. carbon fixation. This review compares liposomes and polymersomes as artificial compartments and summarizes the types of light-driven proton pumps that have been employed in artificial photosynthesis so far. We give an overview over the methods affecting the orientation of the photosystems within the membranes to ensure a unidirectional transport of molecules and highlight recent examples of light-driven biocatalysis in artificial vesicles. Finally, we summarize the current achievements and discuss the next steps needed for the transition of this technology from the proof-of-concept status to preparative applications.
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18
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Engelhard C, Chizhov I, Siebert F, Engelhard M. Microbial Halorhodopsins: Light-Driven Chloride Pumps. Chem Rev 2018; 118:10629-10645. [DOI: 10.1021/acs.chemrev.7b00715] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - Igor Chizhov
- Institute for Biophysical Chemistry, Hannover Medical School, OE8830 Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Friedrich Siebert
- Institut für Molekulare Medizin und Zellforschung, Sektion Biophysik, Albert-Ludwigs-Universität Freiburg, Hermann-Herderstr. 9, 79104 Freiburg, Germany
| | - Martin Engelhard
- Max Planck Institute for Molecular Physiology, Otto Hahn Str. 11, 44227 Dortmund, Germany
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19
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Optogenetic Tools for Subcellular Applications in Neuroscience. Neuron 2017; 96:572-603. [PMID: 29096074 DOI: 10.1016/j.neuron.2017.09.047] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 03/30/2017] [Accepted: 09/26/2017] [Indexed: 12/21/2022]
Abstract
The ability to study cellular physiology using photosensitive, genetically encoded molecules has profoundly transformed neuroscience. The modern optogenetic toolbox includes fluorescent sensors to visualize signaling events in living cells and optogenetic actuators enabling manipulation of numerous cellular activities. Most optogenetic tools are not targeted to specific subcellular compartments but are localized with limited discrimination throughout the cell. Therefore, optogenetic activation often does not reflect context-dependent effects of highly localized intracellular signaling events. Subcellular targeting is required to achieve more specific optogenetic readouts and photomanipulation. Here we first provide a detailed overview of the available optogenetic tools with a focus on optogenetic actuators. Second, we review established strategies for targeting these tools to specific subcellular compartments. Finally, we discuss useful tools and targeting strategies that are currently missing from the optogenetics repertoire and provide suggestions for novel subcellular optogenetic applications.
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20
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A simple optogenetic MAPK inhibitor design reveals resonance between transcription-regulating circuitry and temporally-encoded inputs. Nat Commun 2017; 8:15017. [PMID: 28497795 PMCID: PMC5437309 DOI: 10.1038/ncomms15017] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 02/20/2017] [Indexed: 12/31/2022] Open
Abstract
Engineering light-sensitive protein regulators has been a tremendous multidisciplinary challenge. Optogenetic regulators of MAPKs, central nodes of cellular regulation, have not previously been described. Here we present OptoJNKi, a light-regulated JNK inhibitor based on the AsLOV2 light-sensor domain using the ubiquitous FMN chromophore. OptoJNKi gene-transfer allows optogenetic applications, whereas protein delivery allows optopharmacology. Development of OptoJNKi suggests a design principle for other optically regulated inhibitors. From this, we generate Optop38i, which inhibits p38MAPK in intact illuminated cells. Neurons are known for interpreting temporally-encoded inputs via interplay between ion channels, membrane potential and intracellular calcium. However, the consequences of temporal variation of JNK-regulating trophic inputs, potentially resulting from synaptic activity and reversible cellular protrusions, on downstream targets are unknown. Using OptoJNKi, we reveal maximal regulation of c-Jun transactivation can occur at unexpectedly slow periodicities of inhibition depending on the inhibitor's subcellular location. This provides evidence for resonance in metazoan JNK-signalling circuits. Light-sensitive regulators of protein kinases could offer valuable insights into intracellular signalling. Here the authors design an optogenetic inhibitor of c-Jun N-terminal kinase (JNK) and show evidence for resonance in JNK signalling circuits in neurons, and use the same design principle to develop an inhibitor for p38MAPK.
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21
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Optogenetic acidification of synaptic vesicles and lysosomes. Nat Neurosci 2015; 18:1845-1852. [PMID: 26551543 PMCID: PMC4869830 DOI: 10.1038/nn.4161] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/08/2015] [Indexed: 12/12/2022]
Abstract
Acidification is required for the function of many intracellular organelles, but methods
to acutely manipulate their intraluminal pH have not been available. Here we
present a targeting strategy to selectively express the light-driven proton pump
Arch3 on synaptic vesicles. Our new tool, pHoenix, can functionally replace
endogenous proton pumps, enabling optogenetic control of vesicular acidification
and neurotransmitter accumulation. Under physiological conditions, glutamatergic
vesicles are nearly full, as additional vesicle acidification with pHoenix only
slightly increased the quantal size. By contrast, we found that incompletely
filled vesicles exhibited a lower release probability than full vesicles,
suggesting preferential exocytosis of vesicles with high transmitter content.
Our subcellular targeting approach can be transferred to other organelles, as
demonstrated for a pHoenix variant that allows light-activated acidification of
lysosomes.
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22
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Abstract
Over the past 10 years, the development and convergence of microbial opsin engineering, modular genetic methods for cell-type targeting and optical strategies for guiding light through tissue have enabled versatile optical control of defined cells in living systems, defining modern optogenetics. Despite widespread recognition of the importance of spatiotemporally precise causal control over cellular signaling, for nearly the first half (2005-2009) of this 10-year period, as optogenetics was being created, there were difficulties in implementation, few publications and limited biological findings. In contrast, the ensuing years have witnessed a substantial acceleration in the application domain, with the publication of thousands of discoveries and insights into the function of nervous systems and beyond. This Historical Commentary reflects on the scientific landscape of this decade-long transition.
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Affiliation(s)
- Karl Deisseroth
- Departments of Bioengineering and of Psychiatry and Behavioral Sciences and the Howard Hughes Medical Institute, Stanford University, Stanford, California, USA
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23
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Allen BD, Singer AC, Boyden ES. Principles of designing interpretable optogenetic behavior experiments. ACTA ACUST UNITED AC 2015; 22:232-8. [PMID: 25787711 PMCID: PMC4371169 DOI: 10.1101/lm.038026.114] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Over the last decade, there has been much excitement about the use of optogenetic tools to test whether specific cells, regions, and projection pathways are necessary or sufficient for initiating, sustaining, or altering behavior. However, the use of such tools can result in side effects that can complicate experimental design or interpretation. The presence of optogenetic proteins in cells, the effects of heat and light, and the activity of specific ions conducted by optogenetic proteins can result in cellular side effects. At the network level, activation or silencing of defined neural populations can alter the physiology of local or distant circuits, sometimes in undesired ways. We discuss how, in order to design interpretable behavioral experiments using optogenetics, one can understand, and control for, these potential confounds.
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Affiliation(s)
- Brian D Allen
- Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA Departments of Biological Engineering and Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Annabelle C Singer
- Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA Departments of Biological Engineering and Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Edward S Boyden
- Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA Departments of Biological Engineering and Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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24
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Abstract
Can we develop technologies to systematically map classical mechanisms throughout the brain, while retaining the flexibility to investigate new mechanisms as they are discovered? We discuss principles of scalable, flexible technologies that could yield comprehensive maps of brain function.
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Affiliation(s)
- Adam H Marblestone
- Synthetic Neurobiology Group, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Edward S Boyden
- Synthetic Neurobiology Group, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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25
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Claassens NJ, Volpers M, dos Santos VAPM, van der Oost J, de Vos WM. Potential of proton-pumping rhodopsins: engineering photosystems into microorganisms. Trends Biotechnol 2013; 31:633-42. [PMID: 24120288 DOI: 10.1016/j.tibtech.2013.08.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 08/19/2013] [Accepted: 08/27/2013] [Indexed: 01/04/2023]
Abstract
A wide range of proton-pumping rhodopsins (PPRs) have been discovered in recent years. Using a synthetic biology approach, PPR photosystems with different features can be easily introduced in nonphotosynthetic microbial hosts. PPRs can provide hosts with the ability to harvest light and drive the sustainable production of biochemicals or biofuels. PPRs use light energy to generate an outward proton flux, and the resulting proton motive force can subsequently power cellular processes. Recently, the introduction of PPRs in microbial production hosts has successfully led to light-driven biotechnological conversions. In this review, we discuss relevant features of natural PPRs, evaluate reported biotechnological applications of microbial production hosts equipped with PPRs, and provide an outlook on future developments.
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Affiliation(s)
- Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
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26
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Walter JM, Greenfield D, Liphardt J. Potential of light-harvesting proton pumps for bioenergy applications. Curr Opin Biotechnol 2010; 21:265-70. [DOI: 10.1016/j.copbio.2010.03.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 03/09/2010] [Accepted: 03/09/2010] [Indexed: 10/19/2022]
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27
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Abstract
This article highlights areas of research at the interface of nanotechnology, the physical sciences, and biology that are related to energy conversion: specifically, those related to photovoltaic applications. Although much ongoing work is seeking to understand basic processes of photosynthesis and chemical conversion, such as light harvesting, electron transfer, and ion transport, application of this knowledge to the development of fully synthetic and/or hybrid devices is still in its infancy. To develop systems that produce energy in an efficient manner, it is important both to understand the biological mechanisms of energy flow for optimization of primary structure and to appreciate the roles of architecture and assembly. Whether devices are completely synthetic and mimic biological processes or devices use natural biomolecules, much of the research for future power systems will happen at the intersection of disciplines.
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Affiliation(s)
- David A. LaVan
- *Department of Mechanical Engineering, Yale University, New Haven, CT 06511; and
- To whom correspondence may be addressed at:
Department of Mechanical Engineering, Yale University, 9 Hillhouse Avenue, Mason Lab Building, Room M3, New Haven, CT 06511. E-mail:
| | - Jennifer N. Cha
- IBM Almaden Research, 650 Harry Road, San Jose, CA 95120
- To whom correspondence may be addressed. E-mail:
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28
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Abstract
Much of the research on integral membrane proteins mirrors that on soluble proteins; however, membrane protein engineering also has its own ends and means, many of which take advantage of the peculiar situation of membrane proteins, whose chains are distributed between one lipidic and two aqueous phases. Extramembrane loops have been shortened, cut, or elongated with segments forming proteolytic cleavage sites, foreign epitopes, extra transmembrane segments, or even whole proteins, with the aim of facilitating purification, biochemical/biophysical studies, or crystallogenesis. Transmembrane alpha-helices have been deleted, duplicated, exchanged, transported into a foreign context or replaced with synthetic peptides, in order to both understand their integration into, and assembly in, the membrane and unravel their functional role. Insertion of cysteine residues has been the basis for a great diversity of experiments, ranging from the exploration of secondary, tertiary and quaternary structures of the transmembrane region to the creation of anchoring points for reporter molecules. Chemical engineering--the synthesis of protein fragments or even of whole proteins--offers particularly exciting new prospects, given the small size of folding domains in alpha-helical membrane proteins. Membrane protein engineering is rapidly developing its own agenda of questions and tool chest of techniques.
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Affiliation(s)
- J L Popot
- Institut de Biologie Physico-Chimique, Paris, France
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29
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Claros MG, Perea J, Shu Y, Samatey FA, Popot JL, Jacq C. Limitations to in vivo Import of Hydrophobic Proteins into Yeast Mitochondria. The Case of a Cytoplasmically Synthesized Apocytochrome b. ACTA ACUST UNITED AC 1995. [DOI: 10.1111/j.1432-1033.1995.0762m.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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30
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Mittler R, Shulaev V, Lam E. Coordinated Activation of Programmed Cell Death and Defense Mechanisms in Transgenic Tobacco Plants Expressing a Bacterial Proton Pump. THE PLANT CELL 1995; 7:29-42. [PMID: 12242350 PMCID: PMC160762 DOI: 10.1105/tpc.7.1.29] [Citation(s) in RCA: 111] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In plants, programmed cell death is thought to be activated during the hypersensitive response to certain avirulent pathogens and in the course of several differentiation processes. We describe a transgenic model system that mimics the activation of programmed cell death in higher plants. In this system, expression of a bacterial proton pump in transgenic tobacco plants activates a cell death pathway that may be similar to that triggered by recognition of an incompatible pathogen. Thus, spontaneous lesions that resemble hypersensitive response lesions are formed, multiple defense mechanisms are apparently activated, and systemic resistance is induced in the absence of a pathogen. Interestingly, mutation of a single amino acid in the putative channel of this proton pump renders it inactive with respect to lesion formation and induction of resistance to pathogen challenge. This transgenic model system may provide insights into the mechanisms involved in mediating cell death in higher plants. In addition, it may also be used as a general agronomic tool to enhance disease protection.
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Affiliation(s)
- R. Mittler
- AgBiotech Center and Department of Plant Science, P.O. Box 759, Waksman Institute, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
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