1
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Minoshima M, Reja SI, Hashimoto R, Iijima K, Kikuchi K. Hybrid Small-Molecule/Protein Fluorescent Probes. Chem Rev 2024; 124:6198-6270. [PMID: 38717865 DOI: 10.1021/acs.chemrev.3c00549] [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: 05/23/2024]
Abstract
Hybrid small-molecule/protein fluorescent probes are powerful tools for visualizing protein localization and function in living cells. These hybrid probes are constructed by diverse site-specific chemical protein labeling approaches through chemical reactions to exogenous peptide/small protein tags, enzymatic post-translational modifications, bioorthogonal reactions for genetically incorporated unnatural amino acids, and ligand-directed chemical reactions. The hybrid small-molecule/protein fluorescent probes are employed for imaging protein trafficking, conformational changes, and bioanalytes surrounding proteins. In addition, fluorescent hybrid probes facilitate visualization of protein dynamics at the single-molecule level and the defined structure with super-resolution imaging. In this review, we discuss development and the bioimaging applications of fluorescent probes based on small-molecule/protein hybrids.
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Affiliation(s)
- Masafumi Minoshima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Shahi Imam Reja
- Immunology Frontier Research Center, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Ryu Hashimoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kohei Iijima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kazuya Kikuchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
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2
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Motorina DM, Galimova YA, Battulina NV, Omelina ES. Systems for Targeted Silencing of Gene Expression and Their Application in Plants and Animals. Int J Mol Sci 2024; 25:5231. [PMID: 38791270 PMCID: PMC11121118 DOI: 10.3390/ijms25105231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
At present, there are a variety of different approaches to the targeted regulation of gene expression. However, most approaches are devoted to the activation of gene transcription, and the methods for gene silencing are much fewer in number. In this review, we describe the main systems used for the targeted suppression of gene expression (including RNA interference (RNAi), chimeric transcription factors, chimeric zinc finger proteins, transcription activator-like effectors (TALEs)-based repressors, optogenetic tools, and CRISPR/Cas-based repressors) and their application in eukaryotes-plants and animals. We consider the advantages and disadvantages of each approach, compare their effectiveness, and discuss the peculiarities of their usage in plant and animal organisms. This review will be useful for researchers in the field of gene transcription suppression and will allow them to choose the optimal method for suppressing the expression of the gene of interest depending on the research object.
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Affiliation(s)
| | | | | | - Evgeniya S. Omelina
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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3
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Zhan ML, Zhao X, Li XD, Tan ZZ, Xu QZ, Zhou M, Zhao KH. Photoreversible Aggregation of the Biliprotein Containing the First and Second GAF Domains of a Cyanobacteriochrome All2699 in Nostoc sp. PCC7120. Biochemistry 2024; 63:1225-1233. [PMID: 38682295 DOI: 10.1021/acs.biochem.4c00058] [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: 05/01/2024]
Abstract
As plant photoreceptors, phytochromes are capable of detecting red light and far-red light, thereby governing plant growth. All2699 is a photoreceptor found in Nostoc sp. PCC7120 that specifically responds to red light and far-red light. All2699g1g2 is a truncated protein carrying the first and second GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA) domains of All2699. In this study, we found that, upon exposure to red light, the protein underwent aggregation, resulting in the formation of protein aggregates. Conversely, under far-red light irradiation, these protein aggregates dissociated. We delved into the factors that impact the aggregation of All2699g1g2, focusing on the protein structure. Our findings showed that the GAF2 domain contains a low-complexity (LC) loop region, which plays a crucial role in mediating protein aggregation. Specifically, phenylalanine at position 239 within the LC loop region was identified as a key site for the aggregation process. Furthermore, our research revealed that various factors, including irradiation time, temperature, concentration, NaCl concentration, and pH value, can impact the aggregation of All2699g1g2. The aggregation led to variations in Pfr concentration depending on temperature, NaCl concentration, and pH value. In contrast, ΔLC did not aggregate and therefore lacked responses to these factors. Consequently, the LC loop region of All2699g1g2 extended and enhanced sensory properties.
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Affiliation(s)
- Min-Li Zhan
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Xi Zhao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Xiao-Dan Li
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Zi-Zhu Tan
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Qian-Zhao Xu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Ming Zhou
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Kai-Hong Zhao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, P. R. China
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4
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Baloban M, Kasatkina LA, Verkhusha VV. iLight2: A near-infrared optogenetic tool for gene transcription with low background activation. Protein Sci 2024; 33:e4993. [PMID: 38647395 PMCID: PMC11034490 DOI: 10.1002/pro.4993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
Optogenetic tools (OTs) operating in the far-red and near-infrared (NIR) region offer advantages for light-controlling biological processes in deep tissues and spectral multiplexing with fluorescent probes and OTs acting in the visible range. However, many NIR OTs suffer from background activation in darkness. Through shortening linkers, we engineered a novel NIR OT, iLight2, which exhibits a significantly reduced background activity in darkness, thereby increasing the light-to-dark activation contrast. The resultant optimal configuration of iLight2 components suggests a molecular mechanism of iLight2 action. Using a biliverdin reductase knock-out mouse model, we show that iLight2 exhibits advanced performance in mouse primary cells and deep tissues in vivo. Efficient light-controlled cell migration in wound healing cellular model demonstrates the possibility of using iLight2 in therapy and, overall, positions it as a valuable addition to the NIR OT toolkit for gene transcription applications.
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Affiliation(s)
- Mikhail Baloban
- Department of Genetics and Gruss‐Lipper Biophotonics CenterAlbert Einstein College of MedicineBronxNew YorkUSA
| | - Ludmila A. Kasatkina
- Department of Genetics and Gruss‐Lipper Biophotonics CenterAlbert Einstein College of MedicineBronxNew YorkUSA
| | - Vladislav V. Verkhusha
- Department of Genetics and Gruss‐Lipper Biophotonics CenterAlbert Einstein College of MedicineBronxNew YorkUSA
- Medicum, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
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5
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Hu X, Xu Y, Yi J, Wang C, Zhu Z, Yue T, Zhang H, Wang X, Wu F, Xue L, Bai L, Liu H, Chen Q. Using Protein Design and Directed Evolution to Monomerize a Bright Near-Infrared Fluorescent Protein. ACS Synth Biol 2024; 13:1177-1190. [PMID: 38552148 DOI: 10.1021/acssynbio.3c00643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
The small ultrared fluorescent protein (smURFP) is a bright near-infrared (NIR) fluorescent protein (FP) that forms a dimer and binds its fluorescence chromophore, biliverdin, at its dimer interface. To engineer a monomeric NIR FP based on smURFP potentially more suitable for bioimaging, we employed protein design to extend the protein backbone with a new segment of two helices that shield the original dimer interface while covering the biliverdin binding pocket in place of the second chain in the original dimer. We experimentally characterized 13 designs and obtained a monomeric protein with a weak fluorescence. We enhanced the fluorescence of this designed protein through two rounds of directed evolution and obtained designed monomeric smURFP (DMsmURFP), a bright, stable, and monomeric NIR FP with a molecular weight of 19.6 kDa. We determined the crystal structures of DMsmURFP both in the apo state and in complex with biliverdin, which confirmed the designed structure. The use of DMsmURFP in in vivo imaging of mammalian systems was demonstrated. The backbone design-based strategy used here can also be applied to monomerize other naturally multimeric proteins with intersubunit functional sites.
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Affiliation(s)
- Xiuhong Hu
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Yang Xu
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Junxi Yi
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Chenchen Wang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Zhongliang Zhu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Ting Yue
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Haiyan Zhang
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Xinyu Wang
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Fan Wu
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Lin Xue
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Li Bai
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Haiyan Liu
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China
- School of Data Science, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Quan Chen
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Hefei National Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230027, China
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230027, China
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6
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Jiang XX, Hou YN, Lu LW, Zhao KH. Monomeric Far-red and Near-infrared Fluorescent Biliproteins of Ultrahigh Brightness. Chembiochem 2024:e202400068. [PMID: 38623786 DOI: 10.1002/cbic.202400068] [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: 01/24/2024] [Revised: 04/01/2024] [Accepted: 04/15/2024] [Indexed: 04/17/2024]
Abstract
Far-red and near-infrared fluorescent proteins have regions of maximum transmission in most tissues and can be widely used as fluorescent biomarkers. We report that fluorescent phycobiliproteins originating from the phycobilisome core subunit ApcF2 can covalently bind biliverdin, named BDFPs. To further improve BDFPs, we conducted a series of studies. Firstly, we mutated K53Q and T144A of BDFPs to increase their effective brightness up to 190 % in vivo. Secondly, by homochromatic tandem fusion of high-brightness BDFPs to achieve monomerization, which increases the effective brightness by up to 180 % in vivo, and can effectively improve the labeling effect. By combining the above two approaches, the brightness of the tandem BDFPs was much improved compared with that of the previously reported fluorescent proteins in a similar spectral range. The tandem BDFPs were expressed stably while maintaining fluorescence in mammalian cells and Caenorhabditis elegans. They were also photostable and resistant to high temperature, low pH, and chemical denaturation. The tandem BDFPs advantages were proved in applications as biomarkers for imaging in super-resolution microscopy.
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Affiliation(s)
- Xiang-Xiang Jiang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Ya-Nan Hou
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Li-Wen Lu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Kai-Hong Zhao
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
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7
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Pennacchietti F, Alvelid J, Morales RA, Damenti M, Ollech D, Oliinyk OS, Shcherbakova DM, Villablanca EJ, Verkhusha VV, Testa I. Blue-shift photoconversion of near-infrared fluorescent proteins for labeling and tracking in living cells and organisms. Nat Commun 2023; 14:8402. [PMID: 38114484 PMCID: PMC10730883 DOI: 10.1038/s41467-023-44054-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/24/2023] [Indexed: 12/21/2023] Open
Abstract
Photolabeling of intracellular molecules is an invaluable approach to studying various dynamic processes in living cells with high spatiotemporal precision. Among fluorescent proteins, photoconvertible mechanisms and their products are in the visible spectrum (400-650 nm), limiting their in vivo and multiplexed applications. Here we report the phenomenon of near-infrared to far-red photoconversion in the miRFP family of near infrared fluorescent proteins engineered from bacterial phytochromes. This photoconversion is induced by near-infrared light through a non-linear process, further allowing optical sectioning. Photoconverted miRFP species emit fluorescence at 650 nm enabling photolabeling entirely performed in the near-infrared range. We use miRFPs as photoconvertible fluorescent probes to track organelles in live cells and in vivo, both with conventional and super-resolution microscopy. The spectral properties of miRFPs complement those of GFP-like photoconvertible proteins, allowing strategies for photoconversion and spectral multiplexed applications.
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Affiliation(s)
- Francesca Pennacchietti
- Department of Applied Physics and SciLifeLab, KTH Royal Institute of Technology, Stockholm, 17165, Sweden.
| | - Jonatan Alvelid
- Department of Applied Physics and SciLifeLab, KTH Royal Institute of Technology, Stockholm, 17165, Sweden
| | - Rodrigo A Morales
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, 17176, Sweden
- Center for Molecular Medicine (CMM), Stockholm, 17176, Sweden
| | - Martina Damenti
- Department of Applied Physics and SciLifeLab, KTH Royal Institute of Technology, Stockholm, 17165, Sweden
| | - Dirk Ollech
- Department of Applied Physics and SciLifeLab, KTH Royal Institute of Technology, Stockholm, 17165, Sweden
| | | | - Daria M Shcherbakova
- Department of Genetics, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Eduardo J Villablanca
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, 17176, Sweden
- Center for Molecular Medicine (CMM), Stockholm, 17176, Sweden
| | - Vladislav V Verkhusha
- Medicum, University of Helsinki, Helsinki, 00290, Finland
- Department of Genetics, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ilaria Testa
- Department of Applied Physics and SciLifeLab, KTH Royal Institute of Technology, Stockholm, 17165, Sweden.
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8
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Singh A, Hassen WM, St-Onge R, Dubowski JJ. Galvanic Displacement Reaction Enabled Specific and Sensitive Detection of Bacteria with a Digital Photocorrosion GaAs/AlGaAs Biosensor. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2023; 127:21768-21776. [PMID: 37969924 PMCID: PMC10641864 DOI: 10.1021/acs.jpcc.3c05200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 11/17/2023]
Abstract
The conjugation of ionic gold with bacterial antibodies makes it possible to induce a specific interaction between targeted bacteria and the surface of a GaAs/AlGaAs biochip. The process of immobilization is based on a galvanic displacement reaction (GDR) involving electron transfer between GaAs and Au3+ ions that leads to the formation of a Au-Ga alloy anchoring bacteria to the biochip surface. The GDR-based immobilization of Escherichia coli on biochips comprising a stack of GaAs/AlGaAs nanolayers (dGaAs = 12 nm, dAlGaAs = 10 nm) was confirmed by X-ray photoelectron spectroscopy and atomic force microscopy-based infrared experiments. We report the successful application of this approach for highly sensitive detection of E. coli with a digital photocorrosion (DIP) biosensor. The photoluminescence (PL) monitored DIP of GaAs/AlGaAs nanolayers results in the formation of a PL intensity maximum whose temporal appearance depends on the electric charge transfer between bacteria and the biochip. The formation of a robust bacteria-biochip interface achieved with the GDR process allowed us to observe the role of bacteria on the temporal position of a PL intensity maximum related to the etching of two pairs of GaAs/AlGaAs nanolayers extending up to 24 nm below the biochip surface. We demonstrate the attractive detection of E. coli at 250 CFU/mL, and we discuss the potential of this approach for designing a family of biosensors addressing the quasi-continuous monitoring of a water environment for the presence of pathogenic bacteria.
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Affiliation(s)
- Amanpreet Singh
- Laboratory for Quantum Semiconductors
and Photon-Based BioNanotechnology, Interdisciplinary Institute for
Technological Innovation (3IT), CNRS IRL-3463, Department of Electrical
and Computer Engineering, Université
de Sherbrooke, 3000 boul. de l’Université, Sherbrooke, Québec J1K 0A5, Canada
| | - Walid M. Hassen
- Laboratory for Quantum Semiconductors
and Photon-Based BioNanotechnology, Interdisciplinary Institute for
Technological Innovation (3IT), CNRS IRL-3463, Department of Electrical
and Computer Engineering, Université
de Sherbrooke, 3000 boul. de l’Université, Sherbrooke, Québec J1K 0A5, Canada
| | - René St-Onge
- Laboratory for Quantum Semiconductors
and Photon-Based BioNanotechnology, Interdisciplinary Institute for
Technological Innovation (3IT), CNRS IRL-3463, Department of Electrical
and Computer Engineering, Université
de Sherbrooke, 3000 boul. de l’Université, Sherbrooke, Québec J1K 0A5, Canada
| | - Jan J. Dubowski
- Laboratory for Quantum Semiconductors
and Photon-Based BioNanotechnology, Interdisciplinary Institute for
Technological Innovation (3IT), CNRS IRL-3463, Department of Electrical
and Computer Engineering, Université
de Sherbrooke, 3000 boul. de l’Université, Sherbrooke, Québec J1K 0A5, Canada
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9
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Kaltbeitzel J, Wich PR. Protein-based Nanoparticles: From Drug Delivery to Imaging, Nanocatalysis and Protein Therapy. Angew Chem Int Ed Engl 2023; 62:e202216097. [PMID: 36917017 DOI: 10.1002/anie.202216097] [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] [Received: 11/01/2022] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 03/16/2023]
Abstract
Proteins and enzymes are versatile biomaterials for a wide range of medical applications due to their high specificity for receptors and substrates, high degradability, low toxicity, and overall good biocompatibility. Protein nanoparticles are formed by the arrangement of several native or modified proteins into nanometer-sized assemblies. In this review, we will focus on artificial nanoparticle systems, where proteins are the main structural element and not just an encapsulated payload. While under natural conditions, only certain proteins form defined aggregates and nanoparticles, chemical modifications or a change in the physical environment can further extend the pool of available building blocks. This allows the assembly of many globular proteins and even enzymes. These advances in preparation methods led to the emergence of new generations of nanosystems that extend beyond transport vehicles to diverse applications, from multifunctional drug delivery to imaging, nanocatalysis and protein therapy.
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Affiliation(s)
- Jonas Kaltbeitzel
- School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
- Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Peter R Wich
- School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
- Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW 2052, Australia
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10
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Pounot K, Schirò G, Levantino M. Tracking the structural dynamics of proteins with time-resolved X-ray solution scattering. Curr Opin Struct Biol 2023; 82:102661. [PMID: 37536065 DOI: 10.1016/j.sbi.2023.102661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/03/2023] [Accepted: 06/29/2023] [Indexed: 08/05/2023]
Abstract
Relevant events during protein function such as ligand binding/release and interaction with substrates or with light are often accompanied by out-of-equilibrium structural dynamics. Time-resolved experimental techniques have been developed to follow protein structural changes as they happen in real time after a given reaction-triggering event. Time-resolved X-ray solution scattering is a promising approach that bears structural sensitivity with temporal resolution in the femto-to-millisecond time range, depending on the X-ray source characteristics and the triggering method. Here we present the basic principles of the technique together with a description of the most relevant results recently published and a discussion on the computational methods currently developed to achieve a structural interpretation of the time-resolved X-ray solution scattering experimental data.
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Affiliation(s)
- Kevin Pounot
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, CS40220, 38043 Grenoble Cedex 9, France
| | - Giorgio Schirò
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France.
| | - Matteo Levantino
- ESRF - The European Synchrotron, 71 Avenue des Martyrs, CS40220, 38043 Grenoble Cedex 9, France.
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11
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Mim MS, Knight C, Zartman JJ. Quantitative insights in tissue growth and morphogenesis with optogenetics. Phys Biol 2023; 20:061001. [PMID: 37678266 PMCID: PMC10594237 DOI: 10.1088/1478-3975/acf7a1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 08/15/2023] [Accepted: 09/07/2023] [Indexed: 09/09/2023]
Abstract
Cells communicate with each other to jointly regulate cellular processes during cellular differentiation and tissue morphogenesis. This multiscale coordination arises through the spatiotemporal activity of morphogens to pattern cell signaling and transcriptional factor activity. This coded information controls cell mechanics, proliferation, and differentiation to shape the growth and morphogenesis of organs. While many of the molecular components and physical interactions have been identified in key model developmental systems, there are still many unresolved questions related to the dynamics involved due to challenges in precisely perturbing and quantitatively measuring signaling dynamics. Recently, a broad range of synthetic optogenetic tools have been developed and employed to quantitatively define relationships between signal transduction and downstream cellular responses. These optogenetic tools can control intracellular activities at the single cell or whole tissue scale to direct subsequent biological processes. In this brief review, we highlight a selected set of studies that develop and implement optogenetic tools to unravel quantitative biophysical mechanisms for tissue growth and morphogenesis across a broad range of biological systems through the manipulation of morphogens, signal transduction cascades, and cell mechanics. More generally, we discuss how optogenetic tools have emerged as a powerful platform for probing and controlling multicellular development.
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Affiliation(s)
- Mayesha Sahir Mim
- Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, United States of America
| | - Caroline Knight
- Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, United States of America
| | - Jeremiah J Zartman
- Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, United States of America
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12
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Yan X, Liu X, Zhao C, Chen GQ. Applications of synthetic biology in medical and pharmaceutical fields. Signal Transduct Target Ther 2023; 8:199. [PMID: 37169742 PMCID: PMC10173249 DOI: 10.1038/s41392-023-01440-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 05/13/2023] Open
Abstract
Synthetic biology aims to design or assemble existing bioparts or bio-components for useful bioproperties. During the past decades, progresses have been made to build delicate biocircuits, standardized biological building blocks and to develop various genomic/metabolic engineering tools and approaches. Medical and pharmaceutical demands have also pushed the development of synthetic biology, including integration of heterologous pathways into designer cells to efficiently produce medical agents, enhanced yields of natural products in cell growth media to equal or higher than that of the extracts from plants or fungi, constructions of novel genetic circuits for tumor targeting, controllable releases of therapeutic agents in response to specific biomarkers to fight diseases such as diabetes and cancers. Besides, new strategies are developed to treat complex immune diseases, infectious diseases and metabolic disorders that are hard to cure via traditional approaches. In general, synthetic biology brings new capabilities to medical and pharmaceutical researches. This review summarizes the timeline of synthetic biology developments, the past and present of synthetic biology for microbial productions of pharmaceutics, engineered cells equipped with synthetic DNA circuits for diagnosis and therapies, live and auto-assemblied biomaterials for medical treatments, cell-free synthetic biology in medical and pharmaceutical fields, and DNA engineering approaches with potentials for biomedical applications.
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Affiliation(s)
- Xu Yan
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Xu Liu
- PhaBuilder Biotech Co. Ltd., Shunyi District, Zhaoquan Ying, 101309, Beijing, China
| | - Cuihuan Zhao
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, 100084, Beijing, China.
- Center for Synthetic and Systems Biology, Tsinghua University, 100084, Beijing, China.
- MOE Key Lab for Industrial Biocatalysis, Dept Chemical Engineering, Tsinghua University, 100084, Beijing, China.
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13
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Jiang D, Tan Q, Shen Y, Ye M, Li J, Zhou Y. NIR-excited imaging and in vivo visualization of β-galactosidase activity using a pyranonitrile-modified upconversion nanoprobe. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 292:122411. [PMID: 36731306 DOI: 10.1016/j.saa.2023.122411] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
β-galactosidase (β-gal) is a diagnostic biomarker of primary ovarian cancers. The development of effective fluorescent probes for investigating the activity of β-gal will be beneficial to cancer diagnosis. Herein, a near-infrared (NIR) excited ratiometric nanoprobe (DCM-β-gal-UCNPs) by assembling pyranonitrile dye (DCM-β-gal) on the surface of upconversion nanophosphors (UCNPs) was designed for the evaluation of β-gal activity in vivo. Upon the interaction with β-gal, a marked decrease of upconversion luminescence (UCL) signal in the green channel was observed owing to the luminescence resonance energy transfer from the UCNPs to pyranonitrile chromophore, whereas the NIR UCL emission at 800 nm was almost no influence. Thus, the β-gal activity could be quantitatively detected by the UCL intensity ratio of UCL543 nm/UCL800 nm with the limit of detection of 3.1 × 10-4 U/mL. Moreover, DCM-β-gal-UCNPs was effectively applied for monitoring β-gal fluctuation in living cells and zebrafish by a ratiometric UCL signal excited by 980 nm laser. We envision that nanoprobe DCM-β-gal-UCNPs might be used as a potential bioimaging tool to disclose more biological information of β-gal in β-gal-associated diseases in the future.
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Affiliation(s)
- Detao Jiang
- College of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Qi Tan
- College of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Yuhan Shen
- College of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Minan Ye
- College of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Jingyun Li
- Department of Plastic&Cosmetic Surgery, Maternal and Child Health Medical Institute, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing 210004, PR China
| | - Yi Zhou
- College of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, PR China.
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14
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Sineshchekov VA. Two Distinct Molecular Types of Phytochrome A in Plants: Evidence of Existence and Implications for Functioning. Int J Mol Sci 2023; 24:ijms24098139. [PMID: 37175844 PMCID: PMC10179679 DOI: 10.3390/ijms24098139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Phytochrome (phy) system in plants comprising a small number of phytochromes with phyA and phyB as major ones is responsible for acquiring light information in the red-far-red region of the solar spectrum. It provides optimal strategy for plant development under changing light conditions throughout all its life cycle beginning from seed germination and seedling establishment to fruiting and plant senescence. The phyA was shown to participate in the regulation of this cycle which is especially evident at its early stages. It mediates three modes of reactions-the very low and low fluence responses (VLFR and LFR) and the high irradiance responses (HIR). The phyA is the sole light receptor in the far-red spectral region responsible for plant's survival under a dense plant canopy where light is enriched with the far-red component. Its appearance is believed to be one of the main factors of plants' successful evolution. So far, it is widely accepted that one molecular phyA species is responsible for its complex functional manifestations. In this review, the evidence of the existence of two distinct phyA types-major, light-labile and soluble phyA' and minor, relatively light-stable and amphiphilic phyA″-is presented as what may account for the diverse modes of phyA action.
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15
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Sineshchekov VA. Two Distinct Molecular Types of Phytochrome A in Plants: Evidence of Existence and Implications for Functioning. Int J Mol Sci 2023; 24:8139. [DOI: https:/doi.org/10.3390/ijms24098139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
Phytochrome (phy) system in plants comprising a small number of phytochromes with phyA and phyB as major ones is responsible for acquiring light information in the red—far-red region of the solar spectrum. It provides optimal strategy for plant development under changing light conditions throughout all its life cycle beginning from seed germination and seedling establishment to fruiting and plant senescence. The phyA was shown to participate in the regulation of this cycle which is especially evident at its early stages. It mediates three modes of reactions—the very low and low fluence responses (VLFR and LFR) and the high irradiance responses (HIR). The phyA is the sole light receptor in the far-red spectral region responsible for plant’s survival under a dense plant canopy where light is enriched with the far-red component. Its appearance is believed to be one of the main factors of plants′ successful evolution. So far, it is widely accepted that one molecular phyA species is responsible for its complex functional manifestations. In this review, the evidence of the existence of two distinct phyA types—major, light-labile and soluble phyA′ and minor, relatively light-stable and amphiphilic phyA″—is presented as what may account for the diverse modes of phyA action.
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16
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Chernov KG, Manoilov KY, Oliinyk OS, Shcherbakova DM, Verkhusha VV. Photodegradable by Yellow-Orange Light degFusionRed Optogenetic Module with Autocatalytically Formed Chromophore. Int J Mol Sci 2023; 24:6526. [PMID: 37047499 PMCID: PMC10095432 DOI: 10.3390/ijms24076526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/26/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Optogenetic systems driven by yellow-orange light are required for the simultaneous regulation of several cellular processes. We have engineered the red fluorescent protein FusionRed into a 26 kDa monomeric optogenetic module, called degFusionRed. Unlike other fluorescent protein-based optogenetic domains, which exhibit light-induced self-inactivation by generating reactive oxygen species, degFusionRed undergoes proteasomal degradation upon illumination with 567 nm light. Similarly to the parent protein, degFusionRed has minimal absorbance at 450 nm and above 650 nm, making it spectrally compatible with blue and near-infrared-light-controlled optogenetic tools. The autocatalytically formed chromophore provides degFusionRed with an additional advantage over most optogenetic tools that require the binding of the exogenous chromophores, the amount of which varies in different cells. The degFusionRed efficiently performed in the engineered light-controlled transcription factor and in the targeted photodegradation of the protein of interest, demonstrating its versatility as the optogenetic module of choice for spectral multiplexed interrogation of various cellular processes.
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Affiliation(s)
| | - Kyrylo Yu. Manoilov
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Olena S. Oliinyk
- Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | - Daria M. Shcherbakova
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Vladislav V. Verkhusha
- Medicum, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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17
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Zhu YH, Liu XX, Fang Q, Liu XY, Fang WH, Cui G. Multiple Photoisomerization Pathways of the Green Fluorescent Protein Chromophore in a Reversibly Photoswitchable Fluorescent Protein: Insights from Quantum Mechanics/Molecular Mechanics Simulations. J Phys Chem Lett 2023; 14:2588-2598. [PMID: 36881005 DOI: 10.1021/acs.jpclett.3c00165] [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: 06/18/2023]
Abstract
Herein, we have employed a combined CASPT2//CASSCF approach within the quantum mechanics/molecular mechanics (QM/MM) framework to explore the early time photoisomerization of rsEGFP2 starting from its two OFF trans states, i.e., Trans1 and Trans2. The results show similar vertical excitation energies to the S1 state in their Franck-Condon regions. Considering the clockwise and counterclockwise rotations of the C11-C9 bond, four pairs of the S1 excited-state minima and low-lying S1/S0 conical intersections were optimized, based on which we determined four S1 photoisomerization paths that are essentially barrierless to the relevant S1/S0 conical intersections leading to efficient excited-state deactivation to the S0 state. Most importantly, our work first identified multiple photoisomerization and excited-state decay paths, which must be seriously considered in the future. This work not only sheds significant light on the primary trans-cis photoisomerization of rsEGFP2 but also aids in the understanding of the microscopic mechanism of GFP-like RSFPs and the design of novel GFP-like fluorescent proteins.
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Affiliation(s)
- Yun-Hua Zhu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xin-Xin Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Qiu Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xiang-Yang Liu
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu 610068, China
| | - Wei-Hai Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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18
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Mukherjee S, Manna P, Douglas N, Chapagain PP, Jimenez R. Conformational Dynamics of mCherry Variants: A Link between Side-Chain Motions and Fluorescence Brightness. J Phys Chem B 2023; 127:52-61. [PMID: 36574626 DOI: 10.1021/acs.jpcb.2c05584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The 3-fold higher brightness of the recently developed mCherry-XL red fluorescent protein (FP) compared to its progenitor, mCherry, is due to a significant decrease in the nonradiative decay rate underlying its increased fluorescence quantum yield. To examine the structural and dynamic role of the four mutations that distinguish the two FPs and closely related variants, we employed microsecond time scale, all-atom molecular dynamics simulations. The simulations revealed that the I197R mutation leads to the formation of multiple hydrogen-bonded contacts and increased rigidity of the β-barrel. In particular, mCherryXL showed reduced nanosecond time scale breathing of the gap between the β7 and β10-strands, which was previously shown to be the most flexible region of mCherry. Together with experimental results, the simulations also reveal steric interactions of residue 161 and a network of hydrogen-bonding interactions of the chromophore with residues at positions 59, 143, and 163 that are critical in perturbing the chromophore electronic structure. Finally, we shed light on the conformational dynamics of the conserved residues R95 and S146, which are hydrogen-bonded to the chromophore, and provide physical insights into the observed photophysics. To the best of our knowledge, this is the first study that evaluates the conformational space for a set of closely related FPs generated by directed evolution.
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Affiliation(s)
- Srijit Mukherjee
- JILA, University of Colorado, Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, 215 UCB, Boulder, Colorado 80309, United States
| | - Premashis Manna
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nancy Douglas
- Department of Chemistry, University of Colorado, Boulder, 215 UCB, Boulder, Colorado 80309, United States
| | - Prem P Chapagain
- Department of Physics, Florida International University, 11200 SW Eighth Street, CP204, Miami, Florida 33199, United States
| | - Ralph Jimenez
- JILA, University of Colorado, Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, 215 UCB, Boulder, Colorado 80309, United States
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19
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Cai Y, Pan Y, Liu L, Zhang T, Liang C, Mou X, Ye X, Wang W, Dong X. Succinct croconic acid-based near-infrared functional materials for biomedical applications. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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20
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Yang Y, Liu S, Deng DD, Chen Z, Pu S. D-A-D type cyclohexyl and cycloheptyl-modified benzo[d]imidazole derivatives with different aggregation-induced emission enhancement (AIEE) and mechanofluorochromic properties. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2022.134027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Lukyanov KA. Fluorescent proteins for a brighter science. Biochem Biophys Res Commun 2022; 633:29-32. [DOI: 10.1016/j.bbrc.2022.08.089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 11/06/2022]
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22
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Protein control of photochemistry and transient intermediates in phytochromes. Nat Commun 2022; 13:6838. [PMID: 36369284 PMCID: PMC9652276 DOI: 10.1038/s41467-022-34640-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
Phytochromes are ubiquitous photoreceptors responsible for sensing light in plants, fungi and bacteria. Their photoactivation is initiated by the photoisomerization of the embedded chromophore, triggering large conformational changes in the protein. Despite numerous experimental and computational studies, the role of chromophore-protein interactions in controlling the mechanism and timescale of the process remains elusive. Here, we combine nonadiabatic surface hopping trajectories and adiabatic molecular dynamics simulations to reveal the molecular details of such control for the Deinococcus radiodurans bacteriophytochrome. Our simulations reveal that chromophore photoisomerization proceeds through a hula-twist mechanism whose kinetics is mainly determined by the hydrogen bond of the chromophore with a close-by histidine. The resulting photoproduct relaxes to an early intermediate stabilized by a tyrosine, and finally evolves into a late intermediate, featuring a more disordered binding pocket and a weakening of the aspartate-to-arginine salt-bridge interaction, whose cleavage is essential to interconvert the phytochrome to the active state.
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23
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Fang Y, Huang H, Lin K, Xu C, Gu FL, Lan Z. The impact of different geometrical restrictions on the nonadiabatic photoisomerization of biliverdin chromophores. Phys Chem Chem Phys 2022; 24:26190-26199. [PMID: 36278817 DOI: 10.1039/d2cp02941c] [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: 06/16/2023]
Abstract
The photoisomerization mechanism of the chromophore of bacterial biliverdin (BV) phytochromes is explored via nonadiabatic dynamics simulation by using the on-the-fly trajectory surface-hopping method at the semi-empirical OM2/MRCI level. Particularly, the current study focuses on the influence of geometrical constrains on the nonadiabatic photoisomerization dynamics of the BV chromophore. Here a rather simplified approach is employed in the nonadiabatic dynamics to capture the features of geometrical constrains, which adds mechanical restrictions to the specific moieties of the BV chromophore. This simplified method provides a rather quick approach to examine the influence of geometrical restrictions on photoisomerization. As expected, different constrains bring distinctive influences on the photoisomerization mechanism of the BV chromophore, giving either strong or minor modification of both involved reaction channels and excited-state lifetimes after the constrains are added in different ring moieties. These observations not only contribute to the primary understanding of the role of the spatial restriction caused by biological environments in photoinduced dynamics of the BV chromophore, but also provide useful ideas for the artificial regulation of the photoisomerization reaction channels of phytochrome proteins.
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Affiliation(s)
- Yuan Fang
- School of Chemistry, South China Normal University, Guangzhou 510006, China
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, P. R. China.
| | - Haiyi Huang
- School of Chemistry, South China Normal University, Guangzhou 510006, China
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, P. R. China.
| | - Kunni Lin
- School of Chemistry, South China Normal University, Guangzhou 510006, China
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, P. R. China.
| | - Chao Xu
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, P. R. China.
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
| | - Feng Long Gu
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, P. R. China.
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
| | - Zhenggang Lan
- MOE Key Laboratory of Environmental Theoretical Chemistry, South China Normal University, Guangzhou 510006, P. R. China.
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, School of Environment, South China Normal University, Guangzhou 510006, P. R. China
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24
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Hu Y, Zhang RQ, Wang ZG, Liu SL. In Situ Quantification of Lipids in Live Cells by Using Lipid-Binding Domain-Based Biosensors. Bioconjug Chem 2022; 33:2076-2087. [DOI: 10.1021/acs.bioconjchem.2c00469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yusi Hu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Centre for New Organic Matter, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry and School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Rui-Qiao Zhang
- Qingdao Academy of Agricultural Sciences, Qingdao 266100, P. R. China
| | - Zhi-Gang Wang
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Centre for New Organic Matter, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry and School of Medicine, Nankai University, Tianjin 300071, P. R. China
| | - Shu-Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Frontiers Science Centre for New Organic Matter, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Research Centre for Analytical Sciences, College of Chemistry and School of Medicine, Nankai University, Tianjin 300071, P. R. China
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25
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Ohlendorf R, Möglich A. Light-regulated gene expression in Bacteria: Fundamentals, advances, and perspectives. Front Bioeng Biotechnol 2022; 10:1029403. [PMID: 36312534 PMCID: PMC9614035 DOI: 10.3389/fbioe.2022.1029403] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
Numerous photoreceptors and genetic circuits emerged over the past two decades and now enable the light-dependent i.e., optogenetic, regulation of gene expression in bacteria. Prompted by light cues in the near-ultraviolet to near-infrared region of the electromagnetic spectrum, gene expression can be up- or downregulated stringently, reversibly, non-invasively, and with precision in space and time. Here, we survey the underlying principles, available options, and prominent examples of optogenetically regulated gene expression in bacteria. While transcription initiation and elongation remain most important for optogenetic intervention, other processes e.g., translation and downstream events, were also rendered light-dependent. The optogenetic control of bacterial expression predominantly employs but three fundamental strategies: light-sensitive two-component systems, oligomerization reactions, and second-messenger signaling. Certain optogenetic circuits moved beyond the proof-of-principle and stood the test of practice. They enable unprecedented applications in three major areas. First, light-dependent expression underpins novel concepts and strategies for enhanced yields in microbial production processes. Second, light-responsive bacteria can be optogenetically stimulated while residing within the bodies of animals, thus prompting the secretion of compounds that grant health benefits to the animal host. Third, optogenetics allows the generation of precisely structured, novel biomaterials. These applications jointly testify to the maturity of the optogenetic approach and serve as blueprints bound to inspire and template innovative use cases of light-regulated gene expression in bacteria. Researchers pursuing these lines can choose from an ever-growing, versatile, and efficient toolkit of optogenetic circuits.
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Affiliation(s)
- Robert Ohlendorf
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Andreas Möglich
- Department of Biochemistry, University of Bayreuth, Bayreuth, Germany
- Bayreuth Center for Biochemistry and Molecular Biology, Universität Bayreuth, Bayreuth, Germany
- North-Bavarian NMR Center, Universität Bayreuth, Bayreuth, Germany
- *Correspondence: Andreas Möglich,
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26
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Abstract
Micro-/nanorobots (MNRs) can be autonomously propelled on demand in complex biological environments and thus may bring revolutionary changes to biomedicines. Fluorescence has been widely used in real-time imaging, chemo-/biosensing, and photo-(chemo-) therapy. The integration of MNRs with fluorescence generates fluorescent MNRs with unique advantages of optical trackability, on-the-fly environmental sensitivity, and targeting chemo-/photon-induced cytotoxicity. This review provides an up-to-date overview of fluorescent MNRs. After the highlighted elucidation about MNRs of various propulsion mechanisms and the introductory information on fluorescence with emphasis on the fluorescent mechanisms and materials, we systematically illustrate the design and preparation strategies to integrate MNRs with fluorescent substances and their biomedical applications in imaging-guided drug delivery, intelligent on-the-fly sensing and photo-(chemo-) therapy. In the end, we summarize the main challenges and provide an outlook on the future directions of fluorescent MNRs. This work is expected to attract and inspire researchers from different communities to advance the creation and practical application of fluorescent MNRs on a broad horizon.
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Affiliation(s)
- Manyi Yang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, P. R. China
| | - Xia Guo
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, P. R. China
| | - Fangzhi Mou
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, P. R. China
| | - Jianguo Guan
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, International School of Materials Science and Engineering, Wuhan University of Technology, Wuhan 430070, P. R. China
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27
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Significant impact of deprotonated status on the photoisomerization dynamics of bacteriophytochrome chromophore. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.107850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Hou Y, Höppner A, Rao AG, Lahav Y, Kumar Das P, Ding W, Jiang X, Hu J, Schapiro I, Noy D, Zhao K. Control of a far‐red/near‐infrared spectral switch in an artificial fluorescent biliprotein derived from allophycocyanin. Protein Sci 2022. [DOI: 10.1002/pro.4412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ya‐Nan Hou
- State Key Laboratory of Agricultural Microbiology Huazhong Agricultural University Wuhan China
| | - Astrid Höppner
- Center for Structural Studies Heinrich‐Heine‐Universität Düsseldorf Germany
| | - Aditya G. Rao
- Fritz Haber Center for Molecular Dynamics Research, Institute for Chemistry The Hebrew University of Jerusalem Jerusalem Israel
| | - Yigal Lahav
- Fritz Haber Center for Molecular Dynamics Research, Institute for Chemistry The Hebrew University of Jerusalem Jerusalem Israel
- MIGAL‐Galilee Research Institute S. Industrial Zone Kiryat Shmona Israel
| | - Prabir Kumar Das
- MIGAL‐Galilee Research Institute S. Industrial Zone Kiryat Shmona Israel
| | - Wen‐Long Ding
- State Key Laboratory of Agricultural Microbiology Huazhong Agricultural University Wuhan China
| | - Xiang‐Xiang Jiang
- State Key Laboratory of Agricultural Microbiology Huazhong Agricultural University Wuhan China
| | - Ji‐Ling Hu
- State Key Laboratory of Agricultural Microbiology Huazhong Agricultural University Wuhan China
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute for Chemistry The Hebrew University of Jerusalem Jerusalem Israel
| | - Dror Noy
- MIGAL‐Galilee Research Institute S. Industrial Zone Kiryat Shmona Israel
- Faculty of Sciences and Technology Tel‐Hai Academic College Upper Galilee Israel
| | - Kai‐Hong Zhao
- State Key Laboratory of Agricultural Microbiology Huazhong Agricultural University Wuhan China
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29
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Rémond E, Fehrentz J, Liénart L, Clément S, Banères J, Cavelier F. Fluorescent P‐Hydroxyphosphole for Peptide Labeling through P‐N Bond Formation. Chemistry 2022; 28:e202201526. [DOI: 10.1002/chem.202201526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Emmanuelle Rémond
- Institut des Biomolécules Max Mousseronm IBMM, UMR 5247 Pôle Chimie Balard 1919, route de Mende 34093 Montpellier cedex 5 France
| | - Jean‐Alain Fehrentz
- Institut des Biomolécules Max Mousseronm IBMM, UMR 5247 Pôle Chimie Balard 1919, route de Mende 34093 Montpellier cedex 5 France
| | - Laure Liénart
- Institut des Biomolécules Max Mousseronm IBMM, UMR 5247 Pôle Chimie Balard 1919, route de Mende 34093 Montpellier cedex 5 France
| | - Sébastien Clément
- Institut Charles Gerhardt Montpellier, ICGM, UMR 5253 Pôle Chimie Balard 1919, route de Mende 34093 Montpellier cedex 5 France
| | - Jean‐Louis Banères
- Institut des Biomolécules Max Mousseronm IBMM, UMR 5247 Pôle Chimie Balard 1919, route de Mende 34093 Montpellier cedex 5 France
| | - Florine Cavelier
- Institut des Biomolécules Max Mousseronm IBMM, UMR 5247 Pôle Chimie Balard 1919, route de Mende 34093 Montpellier cedex 5 France
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30
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Kurttila M, Etzl S, Rumfeldt J, Takala H, Galler N, Winkler A, Ihalainen JA. The structural effect between the output module and chromophore-binding domain is a two-way street via the hairpin extension. PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES : OFFICIAL JOURNAL OF THE EUROPEAN PHOTOCHEMISTRY ASSOCIATION AND THE EUROPEAN SOCIETY FOR PHOTOBIOLOGY 2022; 21:1881-1894. [PMID: 35984631 PMCID: PMC9630206 DOI: 10.1007/s43630-022-00265-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/30/2022] [Indexed: 11/23/2022]
Abstract
Signal transduction typically starts with either ligand binding or cofactor activation, eventually affecting biological activities in the cell. In red light-sensing phytochromes, isomerization of the bilin chromophore results in regulation of the activity of diverse output modules. During this process, several structural elements and chemical events influence signal propagation. In our study, we have studied the full-length bacteriophytochrome from Deinococcus radiodurans as well as a previously generated optogenetic tool where the native histidine kinase output module has been replaced with an adenylate cyclase. We show that the composition of the output module influences the stability of the hairpin extension. The hairpin, often referred as the PHY tongue, is one of the central structural elements for signal transduction. It extends from a distinct domain establishing close contacts with the chromophore binding site. If the coupling between these interactions is disrupted, the dynamic range of the enzymatic regulation is reduced. Our study highlights the complex conformational properties of the hairpin extension as a bidirectional link between the chromophore-binding site and the output module, as well as functional properties of diverse output modules.
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Affiliation(s)
- Moona Kurttila
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Stefan Etzl
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria
| | - Jessica Rumfeldt
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Heikki Takala
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland
| | - Nadine Galler
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010, Graz, Austria.
| | - Janne A Ihalainen
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014, Jyväskylä, Finland.
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31
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Yoo K, Chen RT. Dual-Polarization Bandwidth-Bridged Bandpass Sampling Fourier Transform Spectrometer from Visible to Near-Infrared on a Silicon Nitride Platform. ACS PHOTONICS 2022; 9:2691-2701. [PMID: 35996368 PMCID: PMC9390785 DOI: 10.1021/acsphotonics.2c00451] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Indexed: 06/15/2023]
Abstract
On-chip broadband optical spectrometers that cover the entire tissue transparency window (λ = 650-1050 nm) with high resolution are highly demanded for miniaturized biosensing and bioimaging applications. The standard spatial heterodyne Fourier transform spectrometer (SHFTS) requires a large number of Mach-Zehnder interferometer (MZI) arrays to obtain a broad spectral bandwidth while maintaining high resolution. Here, we propose a novel type of SHFTS integrated with a subwavelength grating coupler (SWGC) for the dual-polarization bandpass sampling on the Si3N4 platform to solve the intrinsic trade-off limitation between the bandwidth and resolution of the SHFTS without having an outrageous number of MZI arrays or adding additional active photonic components. By applying the bandpass sampling theorem, the continuous broadband input spectrum is divided into multiple narrow-band channels through tuning the phase-matching condition of the SWGC with different polarization and coupling angles. Thereby, it is able to reconstruct each band separately far beyond the Nyquist criterion without aliasing error or degrading the resolution. We experimentally demonstrated the broadband spectrum retrieval results with the overall bandwidth coverage of 400 nm, bridging the wavelengths from 650 to 1050 nm, with a resolution of 2-5 nm. The bandpass sampling SHFTS is designed to have 32 linearly unbalanced MZIs with the maximum optical path length difference of 93 μm within an overall footprint size of 4.7 mm × 0.65 mm, and the coupling angles of SWGC are varied from 0° to 32° to cover the entire tissue transparency window.
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Affiliation(s)
- Kyoung
Min Yoo
- Department
of Electrical and Computer Engineering, The University of Texas at Austin, 10100 Burnet Road, Austin, Texas 78758, United States
| | - Ray T. Chen
- Department
of Electrical and Computer Engineering, The University of Texas at Austin, 10100 Burnet Road, Austin, Texas 78758, United States
- Omega
Optics Inc., 8500 Shoal
Creek Boulevard, Building 4, Suite 200, Austin, Texas 78757, United States
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32
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Hou YN, Ding WL, Jiang XX, Hu JL, Tan ZZ, Zhao KH. New Far-Red and Near-Infrared Fluorescent Phycobiliproteins with Excellent Brightness and Photostability. Chembiochem 2022; 23:e202200267. [PMID: 35811374 DOI: 10.1002/cbic.202200267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/10/2022] [Indexed: 11/11/2022]
Abstract
Far-red and near-infrared fluorescent proteins can be used as fluorescence biomarkers in the region of maximal transmission of most tissues and facilitate multiplexing. Recently, we reported the generation and properties of far-red and near-infrared fluorescent phycobiliproteins, termed BeiDou Fluorescent Proteins (BDFPs), which can covalently bind the more readily accessible biliverdin. Far-red BDFPs maximally fluoresce at ∼670 nm, while near-infrared BDFPs fluoresce at ∼710 nm. In this work, we molecularly evolved BDFPs as follows: (a) mutations L58Q, S68R and M81K of BDFPs, which can maximally enhance the effective brightness in vivo by 350 %; (b) minimization and monomerization of far-red BDFPs 2.1, 2.2, 2.3, and near-infrared BDFPs 2.4, 2.5 and 2.6. These newly developed BDFPs are remarkably brighter than the formerly reported far-red and near-infrared fluorescent proteins. Their advantages are demonstrated by biolabeling in mammalian cells using super-resolution microscopy.
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Affiliation(s)
- Ya-Nan Hou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Wen-Long Ding
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Xiang-Xiang Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Ji-Ling Hu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Zi-Zhu Tan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Kai-Hong Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, P. R. China
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33
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Stepanenko OV, Kuznetsova IM, Turoverov KK, Stepanenko OV. Impact of Double Covalent Binding of BV in NIR FPs on Their Spectral and Physicochemical Properties. Int J Mol Sci 2022; 23:ijms23137347. [PMID: 35806351 PMCID: PMC9267011 DOI: 10.3390/ijms23137347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 02/01/2023] Open
Abstract
Understanding the photophysical properties and stability of near-infrared fluorescent proteins (NIR FPs) based on bacterial phytochromes is of great importance for the design of efficient fluorescent probes for use in cells and in vivo. Previously, the natural ligand of NIR FPs biliverdin (BV) has been revealed to be capable of covalent binding to the inherent cysteine residue in the PAS domain (Cys15), and to the cysteine residue introduced into the GAF domain (Cys256), as well as simultaneously with these two residues. Here, based on the spectroscopic analysis of several NIR FPs with both cysteine residues in PAS and GAF domains, we show that the covalent binding of BV simultaneously with two domains is the reason for the higher quantum yield of BV fluorescence in these proteins as a result of rigid fixation of the chromophore in their chromophore-binding pocket. We demonstrate that since the attachment sites are located in different regions of the polypeptide chain forming a figure-of-eight knot, their binding to BV leads to shielding of many sites of proteolytic degradation due to additional stabilization of the entire protein structure. This makes NIR FPs with both cysteine residues in PAS and GAF domains less susceptible to cleavage by intracellular proteases.
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34
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Fang J, Huang S, Liu F, He G, Li X, Huang X, Chen HJ, Xie X. Semi-Implantable Bioelectronics. NANO-MICRO LETTERS 2022; 14:125. [PMID: 35633391 PMCID: PMC9148344 DOI: 10.1007/s40820-022-00818-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/09/2022] [Indexed: 06/15/2023]
Abstract
Developing techniques to effectively and real-time monitor and regulate the interior environment of biological objects is significantly important for many biomedical engineering and scientific applications, including drug delivery, electrophysiological recording and regulation of intracellular activities. Semi-implantable bioelectronics is currently a hot spot in biomedical engineering research area, because it not only meets the increasing technical demands for precise detection or regulation of biological activities, but also provides a desirable platform for externally incorporating complex functionalities and electronic integration. Although there is less definition and summary to distinguish it from the well-reviewed non-invasive bioelectronics and fully implantable bioelectronics, semi-implantable bioelectronics have emerged as highly unique technology to boost the development of biochips and smart wearable device. Here, we reviewed the recent progress in this field and raised the concept of "Semi-implantable bioelectronics", summarizing the principle and strategies of semi-implantable device for cell applications and in vivo applications, discussing the typical methodologies to access to intracellular environment or in vivo environment, biosafety aspects and typical applications. This review is meaningful for understanding in-depth the design principles, materials fabrication techniques, device integration processes, cell/tissue penetration methodologies, biosafety aspects, and applications strategies that are essential to the development of future minimally invasive bioelectronics.
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Affiliation(s)
- Jiaru Fang
- State Key Laboratory of Optoelectronic Materials and Technologies, Guangdong Province Key Laboratory of Display Material and Technology, School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou, 510006, People's Republic of China
| | - Shuang Huang
- State Key Laboratory of Optoelectronic Materials and Technologies, Guangdong Province Key Laboratory of Display Material and Technology, School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou, 510006, People's Republic of China
| | - Fanmao Liu
- State Key Laboratory of Optoelectronic Materials and Technologies, Guangdong Province Key Laboratory of Display Material and Technology, School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou, 510006, People's Republic of China
| | - Gen He
- State Key Laboratory of Optoelectronic Materials and Technologies, Guangdong Province Key Laboratory of Display Material and Technology, School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou, 510006, People's Republic of China
| | - Xiangling Li
- State Key Laboratory of Optoelectronic Materials and Technologies, Guangdong Province Key Laboratory of Display Material and Technology, School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou, 510006, People's Republic of China
| | - Xinshuo Huang
- State Key Laboratory of Optoelectronic Materials and Technologies, Guangdong Province Key Laboratory of Display Material and Technology, School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou, 510006, People's Republic of China
| | - Hui-Jiuan Chen
- State Key Laboratory of Optoelectronic Materials and Technologies, Guangdong Province Key Laboratory of Display Material and Technology, School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou, 510006, People's Republic of China
| | - Xi Xie
- State Key Laboratory of Optoelectronic Materials and Technologies, Guangdong Province Key Laboratory of Display Material and Technology, School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou, 510006, People's Republic of China.
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35
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Pócsi I, Szigeti ZM, Emri T, Boczonádi I, Vereb G, Szöllősi J. Use of red, far-red, and near-infrared light in imaging of yeasts and filamentous fungi. Appl Microbiol Biotechnol 2022; 106:3895-3912. [PMID: 35599256 PMCID: PMC9200671 DOI: 10.1007/s00253-022-11967-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/02/2022] [Accepted: 05/07/2022] [Indexed: 11/30/2022]
Abstract
Abstract While phototoxicity can be a useful therapeutic modality not only for eliminating malignant cells but also in treating fungal infections, mycologists aiming to observe morphological changes or molecular events in fungi, especially when long observation periods or high light fluxes are warranted, encounter problems owed to altered regulatory pathways or even cell death caused by various photosensing mechanisms. Consequently, the ever expanding repertoire of visible fluorescent protein toolboxes and high-resolution microscopy methods designed to investigate fungi in vitro and in vivo need to comply with an additional requirement: to decrease the unwanted side effects of illumination. In addition to optimizing exposure, an obvious solution is red-shifted illumination, which, however, does not come without compromises. This review summarizes the interactions of fungi with light and the various molecular biology and technology approaches developed for exploring their functions on the molecular, cellular, and in vivo microscopic levels, and outlines the progress towards reducing phototoxicity through applying far-red and near-infrared light. Key points • Fungal biological processes alter upon illumination, also under the microscope • Red shifted fluorescent protein toolboxes decrease interference by illumination • Innovations like two-photon, lightsheet, and near IR microscopy reduce phototoxicity
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Affiliation(s)
- István Pócsi
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.
| | - Zsuzsa M Szigeti
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - Tamás Emri
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - Imre Boczonádi
- Department of Molecular Biotechnology and Microbiology, Institute of Biotechnology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - György Vereb
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.,MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.,Faculty of Pharmacy, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - János Szöllősi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary.,MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
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36
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Oliinyk OS, Baloban M, Clark CL, Carey E, Pletnev S, Nimmerjahn A, Verkhusha VV. Single-domain near-infrared protein provides a scaffold for antigen-dependent fluorescent nanobodies. Nat Methods 2022; 19:740-750. [PMID: 35606446 DOI: 10.1038/s41592-022-01467-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 03/24/2022] [Indexed: 12/16/2022]
Abstract
Small near-infrared (NIR) fluorescent proteins (FPs) are much needed as protein tags for imaging applications. We developed a 17 kDa NIR FP, called miRFP670nano3, which brightly fluoresces in mammalian cells and enables deep-brain imaging. By exploring miRFP670nano3 as an internal tag, we engineered 32 kDa NIR fluorescent nanobodies, termed NIR-Fbs, whose stability and fluorescence strongly depend on the presence of specific intracellular antigens. NIR-Fbs allowed background-free visualization of endogenous proteins, detection of viral antigens, labeling of cells expressing target molecules and identification of double-positive cell populations with bispecific NIR-Fbs against two antigens. Applying NIR-Fbs as destabilizing fusion partners, we developed molecular tools for directed degradation of targeted proteins, controllable protein expression and modulation of enzymatic activities. Altogether, NIR-Fbs enable the detection and manipulation of a variety of cellular processes based on the intracellular protein profile.
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Affiliation(s)
- Olena S Oliinyk
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mikhail Baloban
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Charles L Clark
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Erin Carey
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Sergei Pletnev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Axel Nimmerjahn
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Vladislav V Verkhusha
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland. .,Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA.
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37
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Kasatkina LA, Ma C, Matlashov ME, Vu T, Li M, Kaberniuk AA, Yao J, Verkhusha VV. Optogenetic manipulation and photoacoustic imaging using a near-infrared transgenic mouse model. Nat Commun 2022; 13:2813. [PMID: 35589810 PMCID: PMC9120076 DOI: 10.1038/s41467-022-30547-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 05/06/2022] [Indexed: 12/21/2022] Open
Abstract
Optogenetic manipulation and optical imaging in the near-infrared range allow non-invasive light-control and readout of cellular and organismal processes in deep tissues in vivo. Here, we exploit the advantages of Rhodopseudomonas palustris BphP1 bacterial phytochrome, which incorporates biliverdin chromophore and reversibly photoswitches between the ground (740-800 nm) and activated (620-680 nm) states, to generate a loxP-BphP1 transgenic mouse model. The mouse enables Cre-dependent temporal and spatial targeting of BphP1 expression in vivo. We validate the optogenetic performance of endogenous BphP1, which in the activated state binds its engineered protein partner QPAS1, to trigger gene transcription in primary cells and living mice. We demonstrate photoacoustic tomography of BphP1 expression in different organs, developing embryos, virus-infected tissues and regenerating livers, with the centimeter penetration depth. The transgenic mouse model provides opportunities for both near-infrared optogenetics and photoacoustic imaging in vivo and serves as a source of primary cells and tissues with genomically encoded BphP1.
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Affiliation(s)
- Ludmila A Kasatkina
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Chenshuo Ma
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Mikhail E Matlashov
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Tri Vu
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Mucong Li
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Andrii A Kaberniuk
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Junjie Yao
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA.
| | - Vladislav V Verkhusha
- Department of Genetics and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, 10461, USA. .,Medicum, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland.
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Baumschlager A. Engineering Light-Control in Biology. Front Bioeng Biotechnol 2022; 10:901300. [PMID: 35573251 PMCID: PMC9096073 DOI: 10.3389/fbioe.2022.901300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
Unraveling the transformative power of optogenetics in biology requires sophisticated engineering for the creation and optimization of light-regulatable proteins. In addition, diverse strategies have been used for the tuning of these light-sensitive regulators. This review highlights different protein engineering and synthetic biology approaches, which might aid in the development and optimization of novel optogenetic proteins (Opto-proteins). Focusing on non-neuronal optogenetics, chromophore availability, general strategies for creating light-controllable functions, modification of the photosensitive domains and their fusion to effector domains, as well as tuning concepts for Opto-proteins are discussed. Thus, this review shall not serve as an encyclopedic summary of light-sensitive regulators but aims at discussing important aspects for the engineering of light-controllable proteins through selected examples.
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Affiliation(s)
- Armin Baumschlager
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Basel, Switzerland
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39
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Li H, Burgie ES, Gannam ZTK, Li H, Vierstra RD. Plant phytochrome B is an asymmetric dimer with unique signalling potential. Nature 2022; 604:127-133. [PMID: 35355010 PMCID: PMC9930725 DOI: 10.1038/s41586-022-04529-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/07/2022] [Indexed: 12/24/2022]
Abstract
Many aspects of plant photoperception are mediated by the phytochrome (Phy) family of bilin-containing photoreceptors that reversibly interconvert between inactive Pr and active Pfr conformers1,2. Despite extensive biochemical studies, full understanding of plant Phy signalling has remained unclear due to the absence of relevant 3D models. Here we report a cryo-electron microscopy structure of Arabidopsis PhyB in the Pr state that reveals a topologically complex dimeric organization that is substantially distinct from its prokaryotic relatives. Instead of an anticipated parallel architecture, the C-terminal histidine-kinase-related domains (HKRDs) associate head-to-head, whereas the N-terminal photosensory regions associate head-to-tail to form a parallelogram-shaped platform with near two-fold symmetry. The platform is internally linked by the second of two internal Per/Arnt/Sim domains that binds to the photosensory module of the opposing protomer and a preceding 'modulator' loop that assembles tightly with the photosensory module of its own protomer. Both connections accelerate the thermal reversion of Pfr back to Pr, consistent with an inverse relationship between dimer assembly and Pfr stability. Lopsided contacts between the HKRDs and the platform create profound asymmetry to PhyB that might imbue distinct signalling potentials to the protomers. We propose that this unique structural dynamism creates an extensive photostate-sensitive surface for conformation-dependent interactions between plant Phy photoreceptors and their signalling partners.
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Affiliation(s)
- Hua Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - E Sethe Burgie
- Department of Biology, Washington University in St Louis, St Louis, MO, USA
| | - Zira T K Gannam
- Department of Biology, Washington University in St Louis, St Louis, MO, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
| | - Richard D Vierstra
- Department of Biology, Washington University in St Louis, St Louis, MO, USA.
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40
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Optogenetic tools for microbial synthetic biology. Biotechnol Adv 2022; 59:107953. [DOI: 10.1016/j.biotechadv.2022.107953] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/09/2022] [Accepted: 04/04/2022] [Indexed: 12/22/2022]
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41
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Rydzewski J, Walczewska-Szewc K, Czach S, Nowak W, Kuczera K. Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome. J Phys Chem B 2022; 126:2647-2657. [PMID: 35357137 PMCID: PMC9014414 DOI: 10.1021/acs.jpcb.2c00131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The ability of phytochromes
to act as photoswitches in plants and
microorganisms depends on interactions between a bilin-like chromophore
and a host protein. The interconversion occurs between the spectrally
distinct red (Pr) and far-red (Pfr) conformers. This conformational
change is triggered by the photoisomerization of the chromophore D-ring
pyrrole. In this study, as a representative example of a phytochrome-bilin
system, we consider biliverdin IXα (BV) bound to bacteriophytochrome
(BphP) from Deinococcus radiodurans. In the absence
of light, we use an enhanced sampling molecular dynamics (MD) method
to overcome the photoisomerization energy barrier. We find that the
calculated free energy (FE) barriers between essential metastable
states agree with spectroscopic results. We show that the enhanced
dynamics of the BV chromophore in BphP contributes to triggering nanometer-scale
conformational movements that propagate by two experimentally determined
signal transduction pathways. Most importantly, we describe how the
metastable states enable a thermal transition known as the dark reversion
between Pfr and Pr, through a previously unknown intermediate state
of Pfr. We present the heterogeneity of temperature-dependent Pfr
states at the atomistic level. This work paves a way toward understanding
the complete mechanism of the photoisomerization of a bilin-like chromophore
in phytochromes.
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Affiliation(s)
- Jakub Rydzewski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Katarzyna Walczewska-Szewc
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Sylwia Czach
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Wieslaw Nowak
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Krzysztof Kuczera
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66047, United States.,Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
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42
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Zheng P, Kasani S, Tan W, Boryczka J, Gao X, Yang F, Wu N. Plasmon-enhanced near-infrared fluorescence detection of traumatic brain injury biomarker glial fibrillary acidic protein in blood plasma. Anal Chim Acta 2022; 1203:339721. [DOI: 10.1016/j.aca.2022.339721] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/20/2022] [Accepted: 03/09/2022] [Indexed: 12/11/2022]
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Woźniak M, Płoska A, Siekierzycka A, Dobrucki LW, Kalinowski L, Dobrucki IT. Molecular Imaging and Nanotechnology-Emerging Tools in Diagnostics and Therapy. Int J Mol Sci 2022; 23:ijms23052658. [PMID: 35269797 PMCID: PMC8910312 DOI: 10.3390/ijms23052658] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/24/2022] [Accepted: 02/24/2022] [Indexed: 12/12/2022] Open
Abstract
Personalized medicine is emerging as a new goal in the diagnosis and treatment of diseases. This approach aims to establish differences between patients suffering from the same disease, which allows to choose the most effective treatment. Molecular imaging (MI) enables advanced insight into molecule interactions and disease pathology, improving the process of diagnosis and therapy and, for that reason, plays a crucial role in personalized medicine. Nanoparticles are widely used in MI techniques due to their size, high surface area to volume ratio, and multifunctional properties. After conjugation to specific ligands and drugs, nanoparticles can transport therapeutic compounds directly to their area of action and therefore may be used in theranostics—the simultaneous implementation of treatment and diagnostics. This review summarizes different MI techniques, including optical imaging, ultrasound imaging, magnetic resonance imaging, nuclear imaging, and computed tomography imaging with theranostics nanoparticles. Furthermore, it explores the potential use of constructs that enables multimodal imaging and track diseases in real time.
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Affiliation(s)
- Marcin Woźniak
- Department of Medical Laboratory Diagnostics-Fahrenheit Biobank BBMRI.pl, Medical University of Gdansk, 80-210 Gdansk, Poland; (M.W.); (A.P.); (A.S.); (L.W.D.)
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Mathews Ave, MC-251, Urbana, IL 61801, USA
| | - Agata Płoska
- Department of Medical Laboratory Diagnostics-Fahrenheit Biobank BBMRI.pl, Medical University of Gdansk, 80-210 Gdansk, Poland; (M.W.); (A.P.); (A.S.); (L.W.D.)
| | - Anna Siekierzycka
- Department of Medical Laboratory Diagnostics-Fahrenheit Biobank BBMRI.pl, Medical University of Gdansk, 80-210 Gdansk, Poland; (M.W.); (A.P.); (A.S.); (L.W.D.)
- Department of Neurobiology, Maj Institute of Pharmacology, Polish Academy of Sciences, 31-343 Krakow, Poland
| | - Lawrence W. Dobrucki
- Department of Medical Laboratory Diagnostics-Fahrenheit Biobank BBMRI.pl, Medical University of Gdansk, 80-210 Gdansk, Poland; (M.W.); (A.P.); (A.S.); (L.W.D.)
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Mathews Ave, MC-251, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Leszek Kalinowski
- Department of Medical Laboratory Diagnostics-Fahrenheit Biobank BBMRI.pl, Medical University of Gdansk, 80-210 Gdansk, Poland; (M.W.); (A.P.); (A.S.); (L.W.D.)
- BioTechMed Centre, Department of Mechanics of Materials and Structures, University of Technology, 80-210 Gdansk, Poland
- Correspondence: (L.K.); (I.T.D.); Tel.: +48-58-349-27-91 or +48-58-349-27-92 (L.K.)
| | - Iwona T. Dobrucki
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 N Mathews Ave, MC-251, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Correspondence: (L.K.); (I.T.D.); Tel.: +48-58-349-27-91 or +48-58-349-27-92 (L.K.)
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Zhang X, Pan Y, Kang S, Gu L. Combinatorial Approaches for Efficient Design of Photoswitchable Protein-Protein Interactions as In Vivo Actuators. Front Bioeng Biotechnol 2022; 10:844405. [PMID: 35211467 PMCID: PMC8863173 DOI: 10.3389/fbioe.2022.844405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Light switchable two-component protein dimerization systems offer versatile manipulation and dissection of cellular events in living systems. Over the past 20 years, the field has been driven by the discovery of photoreceptor-based interaction systems, the engineering of light-actuatable binder proteins, and the development of photoactivatable compounds as dimerization inducers. This perspective is to categorize mechanisms and design approaches of these dimerization systems, compare their advantages and limitations, and bridge them to emerging applications. Our goal is to identify new opportunities in combinatorial protein design that can address current engineering challenges and expand in vivo applications.
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Affiliation(s)
- Xiao Zhang
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, United States
| | - Yuxin Pan
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, United States
| | - Shoukai Kang
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, United States
| | - Liangcai Gu
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, United States
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45
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Alifu N, Ma R, Zhu L, Du Z, Chen S, Yan T, Alimu G, Zhang L, Zhang X. A novel TMTP1-modified theranostic nanoplatform for targeted in vivo NIR-II fluorescence imaging-guided chemotherapy for cervical cancer. J Mater Chem B 2022; 10:506-517. [PMID: 34988561 DOI: 10.1039/d1tb02481g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Near-infrared II (NIR-II, 900-1700 nm) fluorescence bioimaging with advantages of good biosafety, excellent spatial resolution, high sensitivity, and contrast has attracted great attention in biomedical research fields. However, most of the nanoprobes used for NIR-II fluorescence imaging have poor tumor-targeting ability and therapeutic efficiency. To overcome these limitations, a novel NIR-II-emissive theranostic nanoplatform for fluorescence imaging and treatment of cervical cancer was designed and prepared. The NIR-II-emissive dye IR-783 and chemotherapy drug doxorubicin (DOX) were encapsulated into liposomes, and the tumor-targeting peptide TMTP1 (a polypeptide with a sequence of cyclic ASN Val Val Arg Gln Cys) was conjugated to the surface of the liposomes to form IR-783-DOX-TMTP1 nanoparticles (NPs) via self-assembly methods. The IR-783-DOX-TMTP1 NPs showed strong NIR-II emission, excellent biocompatibility and a long lifetime in vivo. Furthermore, high-definition NIR-II fluorescence microscopy images of ear blood vessels and intratumoral blood vessels were obtained from IR-783-DOX-TMTP1 NP-stained mice with high spatial resolution under 808 nm laser excitation. Moreover, IR-783-DOX-TMTP1 NPs showed strong tumor-targeting ability and highly efficient chemotherapeutic characteristics towards cervical tumors. The novel targeting and NIR-II-emissive IR-783-DOX-TMTP1 NPs have great potential in diagnosis and therapy for cervical cancer.
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Affiliation(s)
- Nuernisha Alifu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia School of Medical Engineering and Technology, Xinjiang Medical University, Urumqi, 830011, China.
| | - Rong Ma
- State Key Laboratory of Pathogenesis, Prevention, and Treatment of High Incidence Diseases in Central Asia, Department of Gynecology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830054, China
| | - Lijun Zhu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia School of Medical Engineering and Technology, Xinjiang Medical University, Urumqi, 830011, China.
| | - Zhong Du
- State Key Laboratory of Pathogenesis, Prevention, and Treatment of High Incidence Diseases in Central Asia, Department of Gynecology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830054, China
| | - Shuang Chen
- State Key Laboratory of Pathogenesis, Prevention, and Treatment of High Incidence Diseases in Central Asia, Department of Gynecology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830054, China
| | - Ting Yan
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia School of Medical Engineering and Technology, Xinjiang Medical University, Urumqi, 830011, China.
| | - Gulinigaer Alimu
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia School of Medical Engineering and Technology, Xinjiang Medical University, Urumqi, 830011, China.
| | - Linxue Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia School of Medical Engineering and Technology, Xinjiang Medical University, Urumqi, 830011, China.
| | - Xueliang Zhang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia School of Medical Engineering and Technology, Xinjiang Medical University, Urumqi, 830011, China.
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Dwijayanti A, Zhang C, Poh CL, Lautier T. Toward Multiplexed Optogenetic Circuits. Front Bioeng Biotechnol 2022; 9:804563. [PMID: 35071213 PMCID: PMC8766309 DOI: 10.3389/fbioe.2021.804563] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/06/2021] [Indexed: 11/25/2022] Open
Abstract
Owing to its ubiquity and easy availability in nature, light has been widely employed to control complex cellular behaviors. Light-sensitive proteins are the foundation to such diverse and multilevel adaptive regulations in a large range of organisms. Due to their remarkable properties and potential applications in engineered systems, exploration and engineering of natural light-sensitive proteins have significantly contributed to expand optogenetic toolboxes with tailor-made performances in synthetic genetic circuits. Progressively, more complex systems have been designed in which multiple photoreceptors, each sensing its dedicated wavelength, are combined to simultaneously coordinate cellular responses in a single cell. In this review, we highlight recent works and challenges on multiplexed optogenetic circuits in natural and engineered systems for a dynamic regulation breakthrough in biotechnological applications.
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Affiliation(s)
| | - Congqiang Zhang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chueh Loo Poh
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Thomas Lautier
- CNRS@CREATE, Singapore, Singapore
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
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Lehtinen K, Nokia MS, Takala H. Red Light Optogenetics in Neuroscience. Front Cell Neurosci 2022; 15:778900. [PMID: 35046775 PMCID: PMC8761848 DOI: 10.3389/fncel.2021.778900] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/02/2021] [Indexed: 12/25/2022] Open
Abstract
Optogenetics, a field concentrating on controlling cellular functions by means of light-activated proteins, has shown tremendous potential in neuroscience. It possesses superior spatiotemporal resolution compared to the surgical, electrical, and pharmacological methods traditionally used in studying brain function. A multitude of optogenetic tools for neuroscience have been created that, for example, enable the control of action potential generation via light-activated ion channels. Other optogenetic proteins have been used in the brain, for example, to control long-term potentiation or to ablate specific subtypes of neurons. In in vivo applications, however, the majority of optogenetic tools are operated with blue, green, or yellow light, which all have limited penetration in biological tissues compared to red light and especially infrared light. This difference is significant, especially considering the size of the rodent brain, a major research model in neuroscience. Our review will focus on the utilization of red light-operated optogenetic tools in neuroscience. We first outline the advantages of red light for in vivo studies. Then we provide a brief overview of the red light-activated optogenetic proteins and systems with a focus on new developments in the field. Finally, we will highlight different tools and applications, which further facilitate the use of red light optogenetics in neuroscience.
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Affiliation(s)
- Kimmo Lehtinen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - Miriam S. Nokia
- Department of Psychology, University of Jyväskylä, Jyväskylä, Finland
- Centre for Interdisciplinary Brain Research, University of Jyväskylä, Jyväskylä, Finland
| | - Heikki Takala
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
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48
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Lewis KJ. Musculoskeletal mechanobiology. Connect Tissue Res 2022; 63:1-2. [PMID: 34781792 DOI: 10.1080/03008207.2021.2005172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Karl J Lewis
- Meinig School of Biomedical Engineering, Cornell University Weill Hall, 237 Tower Road Ithaca NY 14853
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49
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Huang P, Zhao Z, Duan L. Optogenetic activation of intracellular signaling based on light-inducible protein-protein homo-interactions. Neural Regen Res 2022; 17:25-30. [PMID: 34100422 PMCID: PMC8451544 DOI: 10.4103/1673-5374.314293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Dynamic protein-protein interactions are essential for proper cell functioning. Homo-interaction events—physical interactions between the same type of proteins—represent a pivotal subset of protein-protein interactions that are widely exploited in activating intracellular signaling pathways. Capacities of modulating protein-protein interactions with spatial and temporal resolution are greatly desired to decipher the dynamic nature of signal transduction mechanisms. The emerging optogenetic technology, based on genetically encoded light-sensitive proteins, provides promising opportunities to dissect the highly complex signaling networks with unmatched specificity and spatiotemporal precision. Here we review recent achievements in the development of optogenetic tools enabling light-inducible protein-protein homo-interactions and their applications in optical activation of signaling pathways.
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Affiliation(s)
- Peiyuan Huang
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Sha Tin, Hong Kong Special Administrative Region, China
| | - Zhihao Zhao
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Sha Tin, Hong Kong Special Administrative Region, China
| | - Liting Duan
- Department of Biomedical Engineering; Shun Hing Institute of Advanced Engineering (SHIAE), The Chinese University of Hong Kong, Sha Tin, Hong Kong Special Administrative Region, China
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50
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Tang K, Beyer HM, Zurbriggen MD, Gärtner W. The Red Edge: Bilin-Binding Photoreceptors as Optogenetic Tools and Fluorescence Reporters. Chem Rev 2021; 121:14906-14956. [PMID: 34669383 PMCID: PMC8707292 DOI: 10.1021/acs.chemrev.1c00194] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Indexed: 12/15/2022]
Abstract
This review adds the bilin-binding phytochromes to the Chemical Reviews thematic issue "Optogenetics and Photopharmacology". The work is structured into two parts. We first outline the photochemistry of the covalently bound tetrapyrrole chromophore and summarize relevant spectroscopic, kinetic, biochemical, and physiological properties of the different families of phytochromes. Based on this knowledge, we then describe the engineering of phytochromes to further improve these chromoproteins as photoswitches and review their employment in an ever-growing number of different optogenetic applications. Most applications rely on the light-controlled complex formation between the plant photoreceptor PhyB and phytochrome-interacting factors (PIFs) or C-terminal light-regulated domains with enzymatic functions present in many bacterial and algal phytochromes. Phytochrome-based optogenetic tools are currently implemented in bacteria, yeast, plants, and animals to achieve light control of a wide range of biological activities. These cover the regulation of gene expression, protein transport into cell organelles, and the recruitment of phytochrome- or PIF-tagged proteins to membranes and other cellular compartments. This compilation illustrates the intrinsic advantages of phytochromes compared to other photoreceptor classes, e.g., their bidirectional dual-wavelength control enabling instant ON and OFF regulation. In particular, the long wavelength range of absorption and fluorescence within the "transparent window" makes phytochromes attractive for complex applications requiring deep tissue penetration or dual-wavelength control in combination with blue and UV light-sensing photoreceptors. In addition to the wide variability of applications employing natural and engineered phytochromes, we also discuss recent progress in the development of bilin-based fluorescent proteins.
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Affiliation(s)
- Kun Tang
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Hannes M. Beyer
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Matias D. Zurbriggen
- Institute
of Synthetic Biology and CEPLAS, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse
1, D-40225 Düsseldorf, Germany
| | - Wolfgang Gärtner
- Retired: Max Planck Institute
for Chemical Energy Conversion. At present: Institute for Analytical Chemistry, University
Leipzig, Linnéstrasse
3, 04103 Leipzig, Germany
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